{"messages":[{"status":"ok","category":"all","interval":"2024-08-01:2024-08-31","funder":"all","cursor":"201","count":100,"count_new_papers":"3469","total":"4881"}], "collection":[{"title":"Severe fire regimes decrease resilience of ectothermic populations","authors":"Sousa, H. C.; Malvasio, A.; Colli, G. R.; Salguero-Gomez, R. C.","author_corresponding":"Heitor C Sousa","author_corresponding_institution":"Universidade Federal do Tocantins","doi":"10.1101\/2023.06.25.546448","date":"2024-08-16","version":"4","type":"new results","license":"cc_by_nc_nd","category":"ecology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/16\/2023.06.25.546448.source.xml","abstract":"O_LIUnderstanding populations responses to environmental change is crucial for mitigating human-induced disturbances.\nC_LIO_LIHere, we test hypotheses regarding how three essential components of demographic resilience (resistance, compensation, and recovery) co-vary along the distinct life histories of three lizard species exposed to variable, prescribed fire regimes.\nC_LIO_LIUsing a Bayesian hierarchical framework, we estimate vital rates (survival, growth, and reproduction) with 14 years of monthly individual-level data and mark-recapture models to parameterize stochastic Integral Projection Models from five sites in Brazilian savannas, each historically subjected to different fire regimes. With these models, we investigate how weather, microclimate, and ecophysiological traits of each species influence their vital rates, emergent life history traits, and demographic resilience components in varying fire regimes.\nC_LIO_LIOverall, weather and microclimate are better predictors of the species vital rates, rather than their ecophysiological traits. Our findings reveal that severe fire regimes increase populations resistance, but decrease compensation or recovery abilities. Instead, populations have higher compensatory and recovery abilities at intermediate degrees of fire severity. Additionally, we identify generation time and reproductive output as predictors of resilience trends across fire regimes and climate. Our analyses demonstrate that the probability and quantity of monthly reproduction are the proximal drivers of demographic resilience across the three species.\nC_LIO_LIOur findings suggest that populations surpass a tipping point in severe fire regimes and achieve an alternative stable state to persist. Thus, higher heterogeneity in fire regimes can increase the reproductive aspects and resilience of different populations and avoid high-severity regimes that homogenize the environment. Despite being more resistant, species with long generation times and low reproductive output take longer to recover and cannot compensate as much as species with faster paces of life. We emphasize how reproductive constraints, such as viviparity and fixed clutch sizes, impact the ability of ectothermic populations to benefit and recover from disturbances, underscoring their relevance in conservation assessments.\nC_LI","funder":"NA","published":"10.1111\/1365-2656.14188","server":"bioRxiv"},{"title":"Hundreds of myosin 10s are pushed to the tips of filopodia and could cause traffic jams on actin","authors":"Shangguan, J.; Rock, R. S.","author_corresponding":"Ronald S Rock","author_corresponding_institution":"The University of Chicago","doi":"10.1101\/2023.06.26.546598","date":"2024-08-15","version":"3","type":"new results","license":"cc_by_nc_nd","category":"cell biology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/15\/2023.06.26.546598.source.xml","abstract":"Impact StatementImproved technology for counting proteins captures myosin-10 dynamics throughout the filopodial lifecycle, defines requirements for initiating filopodia, and reveals a crowded filopodial tip where motors frequently exceed available actin.\n\nMyosin 10 (Myo10) is a motor protein known for its role in filopodia formation. Although Myo10-driven filopodial dynamics have been characterized, there is no information about the absolute number of Myo10 molecules during the filopodial lifecycle. To better understand molecular stoichiometries and packing restraints in filopodia, we measured Myo10 abundance in these structures. We combined SDS-PAGE densitometry with epifluorescence microscopy to quantitate HaloTag-labeled Myo10 in U2OS cells. About 6% of total intracellular Myo10 localizes to filopodia, where it enriches at opposite cellular ends. Hundreds of Myo10s are in a typical filopodium, and their distribution across filopodia is log-normal. Some filopodial tips even contain more Myo10 than accessible binding sites on the actin filament bundle. Live-cell movies reveal a dense cluster of over a hundred Myo10 molecules that initiates filopodial elongation. Hundreds of Myo10 molecules continue to accumulate during filopodial growth, but accumulation ceases when retraction begins. Rates of filopodial elongation, second-phase elongation, and retraction are inversely related to Myo10 quantities. Our estimates of Myo10 molecules in filopodia provide insight into the physics of packing Myo10, its cargo, and other filopodia-associated proteins in narrow membrane compartments. Our protocol provides a framework for future work analyzing Myo10 abundance and distribution upon perturbation.","funder":"NA","published":"10.7554\/elife.90603.4","server":"bioRxiv"},{"title":"A whole-organism landscape of X-inactivation in humans","authors":"Gylemo, B.; Bensberg, M.; Nestor, C. E.","author_corresponding":"Colm E. Nestor","author_corresponding_institution":"Linkoping University, Department of Biomedical and Clinical Sciences (BKV)","doi":"10.1101\/2023.06.26.546519","date":"2024-08-22","version":"2","type":"new results","license":"cc_no","category":"genetics","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/22\/2023.06.26.546519.source.xml","abstract":"As females are mosaic for X-inactivation, direct determination of X-linked allelic expression in bulk tissues is typically unfeasible. Using females that are non-mosaic (completely skewed) for X-inactivation (nmXCI) has proven a powerful and natural genetic system for profiling X-inactivation in humans. By combining allele-resolution data for one previously reported and two newly identified nmXCI females, we directly determined X-inactivation status of 380 X-linked genes across 30 normal tissues, including 198 genes for which XCI status is directly determined for the first time. Our findings represent a substantial advance in our understanding of human X-inactivation and will serve as a reference for dissecting the genetic origin of sex-bias in human traits. In addition, our study reveals nmXCI as a common feature of the human female population, with profound consequences for the penetrance and expressivity of X-linked traits in humans.","funder":"NA","published":"10.7554\/eLife.102701","server":"bioRxiv"},{"title":"Prediction tendency, eye movements, and attention in a unified framework of neural speech tracking","authors":"Schubert, J.; Gehmacher, Q.; Schmidt, F.; Hartmann, T.; Weisz, N.","author_corresponding":"Juliane Schubert","author_corresponding_institution":"University of Salzburg","doi":"10.1101\/2023.06.27.546746","date":"2024-08-27","version":"3","type":"new results","license":"cc_by_nc_nd","category":"neuroscience","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/27\/2023.06.27.546746.source.xml","abstract":"Auditory speech comprehension is a multi-faceted process in which attention, prediction, and sensorimotor integration (via active sensing) interact with or complement each other. Although different conceptual models that focus on one of these aspects exist, we still lack a unified understanding of their role in speech processing. Here, we first replicated two recently published studies from our lab, confirming 1) a positive relationship between individual prediction tendencies and neural speech tracking, and 2) the phenomenon of ocular speech tracking - the tracking of attended speech by eye movements - and its shared contribution with neural activity to speech processing. In addition, we extended these findings with complementary analyses and investigated these phenomena in relation to each other in a multi-speaker paradigm with continuous, narrative speech. Importantly, prediction tendency and ocular speech tracking seem to be unrelated. In contrast to the shared contributions of oculomotor and neural activity to speech processing over a distributed set of brain regions that are critical for attention, individual prediction tendency and its relation to neural speech tracking seem to be largely independent of attention. Based on these findings, we propose a framework that aims to bridge the gaps between attention, prediction, and active (ocular) sensing in order to contribute to a holistic understanding of neural speech processing. In this speculative framework for listening, auditory inflow is, on a basic level, temporally modulated via active ocular sensing, and incoming information is interpreted based on probabilistic assumptions.","funder":"NA","published":"NA","server":"bioRxiv"},{"title":"Tuberculosis susceptibility in genetically diverse mice reveals functional diversity of neutrophils","authors":"Ravesloot-Chavez, M. M.; Van Dis, E.; Fox, D.; Anaya-Sanchez, A.; Espich, S.; Nguyenla, X. H.; Rawal, S. L.; Samani, H.; Ballinger, M. A.; Thomas, H.; Kotov, D. I.; Vance, R.; Nachman, M.; Stanley, S.","author_corresponding":"Sarah Stanley","author_corresponding_institution":"University of California, Berkeley","doi":"10.1101\/2023.06.29.547125","date":"2024-08-06","version":"2","type":"new results","license":"cc_no","category":"immunology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/06\/2023.06.29.547125.source.xml","abstract":"Tuberculosis (TB) is a heterogenous disease in humans with individuals exhibiting a wide range of susceptibility. This heterogeneity is not captured by standard laboratory mouse lines. We used a new collection of 19 wild-derived inbred mouse lines collected from diverse geographic sites to identify novel phenotypes during Mycobacterium tuberculosis (Mtb) infection. Wild derived mice have heterogenous immune responses to infection that result in differential ability to control disease at early timepoints. Correlation analysis with multiple parameters including sex, weight, and cellular immune responses in the lungs revealed that enhanced control of infection is associated with increased numbers of CD4 T cells, CD8 T cells and B cells. Surprisingly, we did not observe strong correlations between IFN-{gamma} production and control of infection. Although in most lines high neutrophils were associated with susceptibility, we identified a mouse line that harbors high neutrophils numbers yet controls infection. Using single-cell RNA sequencing, we identified a novel neutrophil signature associated with failure to control infection.","funder":"NA","published":"10.7554\/eLife.102441.2","server":"bioRxiv"},{"title":"Laminin gamma1-dependent basement membranes are instrumental to ensure proper olfactory placode shape, position and boundary with the brain, as well as olfactory axon development","authors":"Tignard, P.; Pottin, K.; Geeverding, A.; Doulazmi, M.; Cabrera, M.; Fouquet, C.; Liffran, M.; Fouchard, J.; Rosello, M.; Albadri, S.; Del Bene, F.; Trembleau, A.; Breau, M. A.","author_corresponding":"Marie Anne Breau","author_corresponding_institution":"Sorbonne University, Centre National de la Recherche Scientifique (CNRS UMR7622), Institut de Biologie Paris-Seine (IBPS), Paris, France, and Institut National ","doi":"10.1101\/2023.06.29.547040","date":"2024-08-29","version":"2","type":"new results","license":"cc_no","category":"developmental biology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/29\/2023.06.29.547040.source.xml","abstract":"Despite recent progress, the complex roles played by the extracellular matrix in development and disease are still far from being fully understood. Here, we took advantage of the zebrafish sly mutation which affects Laminin {gamma}1, a major component of basement membranes, to explore its role in the development of the olfactory system. Following a detailed characterisation of Laminin distribution in the developing olfactory circuit, we analysed basement membrane integrity, olfactory placode and brain morphogenesis, and olfactory axon development in sly mutants, using a combination of immunochemistry, electron microscopy and quantitative live imaging of cell movements and axon behaviours. Our results point to an original and dual contribution of Laminin {gamma}1-dependent basement membranes in organising the border between the olfactory placode and the adjacent brain: they maintain placode shape and position in the face of major brain morphogenetic movements, they establish a robust physical barrier between the two tissues while at the same time allowing the local entry of the sensory axons into the brain and their navigation towards the olfactory bulb. This work thus identifies key roles of Laminin {gamma}1-dependent basement membranes in neuronal tissue morphogenesis and axon development in vivo.","funder":"NA","published":"10.7554\/elife.92004","server":"bioRxiv"},{"title":"Postsynaptic frequency filters shaped by the interplay of synaptic short-term plasticity and cellular time scales","authors":"Mondal, Y.; Villanueva Benito, G.; Pena, R. F.; Rotstein, H. G.","author_corresponding":"Horacio G. Rotstein","author_corresponding_institution":"New Jersey Institute of Technology and Rutgers University","doi":"10.1101\/2023.07.02.547439","date":"2024-08-15","version":"2","type":"new results","license":"cc_by_nc_nd","category":"neuroscience","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/15\/2023.07.02.547439.source.xml","abstract":"Neuronal frequency filters can be thought of as constituent building blocks underlying the ability of neuronal systems to process information, generate rhythms and perform computations. How neuronal filters are generated by the concerted activity of a multiplicity of processes (e.g., electric circuit, history-dependent) and interacting time scales within and across levels of neuronal network organization is poorly understood. In this paper, we use mathematical modeling, numerical simulations and analytical calculations of the postsynaptic response to presynaptic spike trains to address this issue in a basic feedforward network motif in the presence of synaptic short-term plasticity (STP, depression and facilitation). The network motif consists of a presynaptic spike-train, a postsynaptic passive cell, and an excitatory (AMPA) chemical synapse. The dynamics of each network component are controlled by one or more time scales. We explain the mechanisms by which the participating time scales shape the neuronal filters at the (i) synaptic update level (the target of the synaptic variable in response to presynaptic spikes), which is shaped by STP, (ii) the synaptic level, and (iii) the postsynaptic membrane potential (PSP) level. We focus on three metrics that gives rise to three types of profiles (curves of the corresponding metrics as a function of the spike-train input frequency or firing rate): (i) peak profiles, (ii) peak-to-trough amplitude profiles, and (iii) phase profiles. The effects of STP are present at the synaptic update level and are communicated to the synaptic level where they interact with the synaptic time scales. The PSP filters result from the interaction between these variables and time scales and the biophysical properties and time scales of the postsynaptic cell. Band-pass filters (BPFs) result from a combination of low-pass filters (LPFs) and high-pass filters (HPFs) operating at the same or different levels of organization. PSP BPFs can be inherited from the synaptic level (STP-mediated BPFs) or they can be generated across levels of organization due to the interaction between (i) a synaptic LPF and the PSP summation-mediated HPF (PSP peaks), and (ii) a synaptic HPF and the PSP summation-mediated LPF (PSP amplitude). These types of BPFs persist in response to more realistic presynaptic spike trains: jittered (randomly perturbed) periodic spike trains and Poisson-distributed spike trains. The response variability is frequency-dependent and is controlled by STP in a non-monotonic frequency manner. The results and and lessons learned from the investigation of this basic network motif are a necessary step for the construction of a framework to analyze the mechanisms of generation of neuronal filters in networks with more complex architectures and a variety of interacting cellular, synaptic and plasticity time scales.","funder":"NA","published":"10.1007\/s10827-025-00908-3","server":"bioRxiv"},{"title":"Fractal cycles of sleep: a new aperiodic activity-based definition of sleep cycles","authors":"Rosenblum, Y.; Jafarzadeh Esfahani, M.; Adelho\u0308fer, N.; Zerr, P.; Furrer, M.; Huber, R.; Roest, F. F.; Steiger, A.; Zeising, M.; Horvath, C. G.; Schneider, B.; Bodizs, R.; Dresler, M.","author_corresponding":"Yevgenia Rosenblum","author_corresponding_institution":"Radboudumc","doi":"10.1101\/2023.07.04.547323","date":"2024-08-05","version":"4","type":"new results","license":"cc_by_nc_nd","category":"neuroscience","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/05\/2023.07.04.547323.source.xml","abstract":"Nocturnal human sleep consists of 4 - 6 ninety-minute cycles defined as episodes of non-rapid eye movement (non-REM) sleep followed by an episode of REM sleep. While sleep cycles are considered fundamental components of sleep, their functional significance largely remains unclear. One of the reasons for a lack of research progress in this field is the absence of a data-driven definition of sleep cycles. Here, we proposed to base such a definition on fractal (aperiodic) neural activity, a well-established marker of arousal and sleep stages.\n\nWe explored temporal dynamics of fractal activity during nocturnal sleep using electroencephalography. Based on the observed pattern of fractal fluctuations, we introduced a new concept of fractal activity-based cycles of sleep or \"fractal cycles\" for short, defined as a time interval during which fractal activity descends from its local maximum to its local minimum and then leads back to the next local maximum. Next, we assessed correlations between fractal and classical (i.e., non-REM - REM) sleep cycle durations. We also studied cycles with skipped REM sleep, i.e., the cycles where the REM phase is expected to appear except that it does not, being replaced by lightening of sleep.\n\nRegarding the sample, we examined fractal cycles in healthy adults (age range: 18 - 75 years, n = 205) as well as in children and adolescents (range: 8 - 17 years, n = 21), the group characterized by deeper sleep and a higher frequency of cycles with skipped REM sleep. Further, we studied fractal cycles in major depressive disorder (n = 111), the condition characterized by altered REM sleep (in addition to its clinical symptoms).\n\nWe found that fractal and classical cycle durations (89 {+\/-} 34 min vs 90 {+\/-} 25 min) correlated positively (r = 0.5, p < 0.001). Cycle-to-cycle overnight dynamics showed an inverted U-shape of both fractal and classical cycle durations and a gradual decrease in absolute amplitudes of the fractal descents and ascents from early to late cycles. In adults, the fractal cycle duration and participants age correlated negatively (r = -0.2, p = 0.006). Children and adolescents had shorter fractal cycles compared to young adults (76 {+\/-} 34 vs 94 {+\/-} 32 min, p < 0.001). The fractal cycle algorithm detected cycles with skipped REM sleep in 91 - 98% of cases. Medicated patients with depression showed longer fractal cycles compared to their own unmedicated state (107 {+\/-} 51 min vs 92 {+\/-} 38 min, p < 0.001) and age-matched controls (104 {+\/-} 49 vs 88 {+\/-} 31 min, p < 0.001).\n\nIn conclusion, fractal cycles are an objective, quantifiable, continuous and biologically plausible way to display sleep neural activity and its cycles. They are useful in healthy adult and pediatric populations as well as in patients with major depressive disorder. Fractal cycles should be extensively studied to advance theoretical research on sleep structure.\n\nHighlights- Fractal activity-based cycles of sleep or \"fractal cycles\" for short is a new concept based on cyclic changes in fractal (aperiodic) neural activity during sleep.\n- Durations of fractal and classical cycles correlate, and both show an inverted U-shape when seen from early to late cycles.\n- The fractal cycle algorithm is effective in detecting cycles with skipped REM sleep.\n- Older healthy adults shower shorter fractal - but not classical - cycle durations.\n- Fractal cycle duration is shorter in children and adolescents compared to young adults.\n- In major depressive disorder, antidepressant medication is associated with longer fractal cycles.","funder":"NA","published":"10.7554\/elife.96784","server":"bioRxiv"},{"title":"A Highly-Efficient, Scalable Pipeline for Fixed Feature Extraction from Large-Scale High-Content Imaging Screens","authors":"Comolet, G.; Bose, N.; Winchell, J. M.; Duren-Lubancki, a.; Rusielewicz, T.; Horn, g.; Goldberg, j.; Paull, D.; Migliori, B.","author_corresponding":"Bianca Migliori","author_corresponding_institution":"New York Stem Cells foundation","doi":"10.1101\/2023.07.06.547985","date":"2024-08-20","version":"2","type":"new results","license":"cc_by_nc","category":"cell biology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/20\/2023.07.06.547985.source.xml","abstract":"Leveraging artificial intelligence (AI) in image-based morphological profiling of cell populations is proving increasingly valuable for identifying diseased states and drug responses in high-content imaging (HCI) screens. When the differences between populations (such as a healthy and diseased) are completely unknown and undistinguishable by the human eye, it is crucial that HCI screens are large in scale, allowing numerous replicates for developing reliable models, as well as accounting for confounding factors such as individual (donor) and intra-experimental variation. However, as screen sizes increase, challenges arise including the lack of scalable solutions for analyzing high-dimensional datasets and processing the results in a timely manner. For this purpose, many tools have been developed to reduce images into a set of features using unbiased methods, such as embedding vectors extracted from pre-trained neural networks or autoencoders. While these methods preserve most of the predictive power contained in each image despite reducing the dimensionality significantly, they do not provide easily interpretable information. Alternatively, techniques to extract specific cellular features from data are typically slow, difficult to scale, and often produce redundant outputs, which can lead to the model learning from irrelevant data, which might distort future predictions. Here we present ScaleFExSM, a memory efficient and scalable open-source Python pipeline that extracts biologically meaningful features from large high-content imaging datasets. It requires only modest computational resources but can also be deployed on high-powered cloud computing infrastructure. ScaleFExSM can be used in conjunction with AI models to cluster data and subsequently explore, identify, and rank features to provide insights into the morphological hallmarks of the phenotypic categories. We demonstrate the performance of this tool on a dataset consisting of control and drug-treated cells from a cohort of 20 donors, benchmarking it against the state-of-the-art tool, CellProfiler, and analyze the features underlying the phenotypic shift induced by chemical compounds. In addition, the tools generalizability and utility is shown in the analysis of publicly available datasets. Overall, ScaleFExSM constitutes a robust and compact pipeline for identifying the effects of drugs on morphological phenotypes and defining interpretable features that can be leveraged in disease profiling and drug discovery.","funder":"NA","published":"10.1016\/j.isci.2024.111434","server":"bioRxiv"},{"title":"Enrichment of Cysteine S-palmitoylation using Sodium Deoxycholate Acid Precipitation - SDC-ACE","authors":"Larsen, M. R.; Jensen, P. T.; Palmisano, G.; Rhodes, C. J.","author_corresponding":"Martin R Larsen","author_corresponding_institution":"Department of Biochemistry and Molecular Biology, University of Southern Denmark","doi":"10.1101\/2023.07.09.548252","date":"2024-08-13","version":"2","type":"new results","license":"cc_no","category":"biochemistry","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/13\/2023.07.09.548252.source.xml","abstract":"S-palmitoylation is a poorly understood post-translational modification that is gaining more attention as an essential regulator of cellular processes. The reversible nature of S-palmitoylation allows for fine-tuned control of cellular events and adaptation to stimuli. The enrichment of S-palmitoylated proteins and peptides includes the Acyl-Biotin Exchange (ABE) method, Acyl resin-assisted Capture (Acyl-RAC), metabolic labelling, and derivatives thereof. We present a novel method of enrichment of S-palmitoylated peptides termed SDC Acid Precipitation Enrichment (SDC-ACE). Here, S-palmitoylated peptides are enriched by taking advantage of their co-precipitation with Sodium-Deoxycholate (SDC) under acidic conditions, allowing easy and fast separation of lipidated peptides from the sample suspension. We applied our novel method for the characterization of the mouse brain, providing an in-depth analysis of S-palmitoylation events within the brain and comprehensive profile of the mouse brain S-palmitoylome. Furthermore, we applied our method for mapping mouse tissue-specific S-palmitoylation, highlighting the extensive role of S-palmitoylation throughout various organs in the body. Finally, we applied our methods for studying the brain palmitoylome of diabetic db\/db mouse, uncovering alterations in the palmitoylation related to obesity and type 2 diabetes. The SDC-ACE method allows fast and easy enrichment of S-palmitoylated peptides, providing a valuable tool for exploring the dynamics and function of S-palmitoylation in diverse biological systems.","funder":"NA","published":"NA","server":"bioRxiv"},{"title":"Meta-analysis of gonadal transcriptome provides novel insights into sex change mechanism across protogynous fishes","authors":"Nozu, R.; Kadota, M.; Nakamura, M.; Kuraku, S.; Bono, H.","author_corresponding":"Hidemasa Bono","author_corresponding_institution":"Hiroshima University","doi":"10.1101\/2023.07.09.545663","date":"2024-08-25","version":"5","type":"new results","license":"cc_by","category":"zoology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/25\/2023.07.09.545663.source.xml","abstract":"Protogyny, being capable of changing from female to male during their lifetime, is prevalent in 20 families of teleosts but is believed to have evolved within specific evolutionary lineages. Therefore, shared regulatory factors governing the sex change process are expected to be conserved across protogynous fishes. However, a comprehensive understanding of this mechanism remains elusive. To identify these factors, we conducted a meta-analysis using gonadal transcriptome data from seven species. We curated data pairs of ovarian tissue and transitional gonad, and employed ratios of expression level as a unified criterion for differential expression, enabling a meta-analysis across species. Our approach revealed that classical sex change-related genes exhibited differential expression levels between the ovary and transitional gonads, consistent with previous reports. These results validate our methodologys robustness. Additionally, we identified novel genes not previously linked to gonadal sex change in fish. Notably, changes in the expression levels of acetoacetyl-CoA synthetase and apolipoprotein Eb, which are involved in cholesterol synthesis and transport, respectively, suggest that the levels of cholesterol, a precursor of steroid hormones crucial for sex change, are decreased upon sex change onset in the gonads. This implies a potential universal influence of cholesterol dynamics on gonadal transformation in protogyny.","funder":"NA","published":"10.1111\/gtc.13166","server":"bioRxiv"},{"title":"Spatial predictive context speeds up visual search by biasing local attentional competition","authors":"Bouwkamp, F. G.; de Lange, F.; Spaak, E.","author_corresponding":"Floortje G Bouwkamp","author_corresponding_institution":"Donders Institute for Brain, Cognition and Behaviour","doi":"10.1101\/2023.07.14.548976","date":"2024-08-30","version":"4","type":"new results","license":"cc_by","category":"neuroscience","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/30\/2023.07.14.548976.source.xml","abstract":"The human visual system is equipped to rapidly and implicitly learn and exploit the statistical regularities in our environment. Within visual search, contextual cueing demonstrates how implicit knowledge of scenes can improve search performance. This is commonly interpreted as spatial context in the scenes becoming predictive of the target location, which leads to a more efficient guidance of attention during search. However, what drives this enhanced guidance is unknown. First, it is under debate whether the entire scene (global context) or more local context drives this phenomenon. Second, it is unclear how exactly improved attentional guidance is enabled by target enhancement and distractor suppression. In the present MEG experiment, we leveraged Rapid Invisible Frequency Tagging (RIFT) to answer these two outstanding questions. We found that the improved performance when searching implicitly familiar scenes was accompanied by a stronger neural representation of the target stimulus, at the cost specifically of those distractors directly surrounding the target. Crucially, this biasing of local attentional competition was behaviorally relevant when searching familiar scenes. Taken together, we conclude that implicitly learned spatial predictive context improves how we search our environment by sharpening the attentional field.","funder":"NA","published":"10.1162\/jocn_a_02254","server":"bioRxiv"},{"title":"Crystal Structure of the 4-Hydroxybutyryl-CoA Synthetase (ADP-forming) from Nitrosopumilus maritimus","authors":"Johnson, J. A.; Tolar, B. B.; Tosun, B.; Yoshikuni, Y.; Francis, C. A.; Wakatsuki, S.; Demirci, H.","author_corresponding":"Hasan Demirci","author_corresponding_institution":"MBGE Department","doi":"10.1101\/2023.07.14.549078","date":"2024-08-08","version":"3","type":"new results","license":"cc_no","category":"biophysics","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/08\/2023.07.14.549078.source.xml","abstract":"The 3-hydroxypropionate\/4-hydroxybutyrate (3HP\/4HB) cycle from ammonia-oxidizing Thaumarchaeota is currently considered the most energy-efficient aerobic carbon fixation pathway. The Nitrosopumilus maritimus 4-hydroxybutyryl-CoA synthetase (ADP-forming; Nmar_0206) represents one of several enzymes from this cycle that exhibit increased efficiency over crenarchaeal counterparts. This enzyme reduces energy requirements on the cell, reflecting thaumarchaeal success in adapting to low-nutrient environments. Here we show the structure of Nmar_0206 from Nitrosopumilus maritimus SCM1, which reveals a highly conserved interdomain linker loop between the CoA-binding and ATP-grasp domains. Phylogenetic analysis suggests the widespread prevalence of this loop and highlights both its underrepresentation within the PDB and structural importance within the (ATP-forming) acyl- CoA synthetase (ACD) superfamily. This linker is shown to have a possible influence on conserved interface interactions between domains, thereby influencing homodimer stability. These results provide a structural basis for the energy efficiency of this key enzyme in the modified 3HP\/4HB cycle of Thaumarchaeota.","funder":"NA","published":"10.1038\/s42003-024-06432-x","server":"bioRxiv"},{"title":"Intestinal LKB1 loss drives a pre-malignant program along the serrated cancer pathway","authors":"Plugge, S. F.; Ma, H.; van der Vaart, J. Y.; Sprangers, J.; Morsink, F. H. M.; Xanthakis, D.; Jamieson, C.; Keijzer, A. R.; Margaritis, T.; Candelli, T.; Straver, R.; de Ridder, J.; Holstege, F. C. P.; de Leng, W. W. J.; Offerhaus, G. J. A.; Merenda, A.; Maurice, M. M.","author_corresponding":"Madelon M. Maurice","author_corresponding_institution":"Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands","doi":"10.1101\/2023.07.17.548873","date":"2024-08-15","version":"3","type":"new results","license":"cc_by_nc_nd","category":"cancer biology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/15\/2023.07.17.548873.source.xml","abstract":"Background & AimsHeterozygous inactivating mutations of Serine Threonine Kinase 11 (STK11)\/Liver Kinase B1 (LKB1) are causative to the Peutz-Jeghers syndrome (PJS), a hereditary disease characterized by gastrointestinal hamartomatous polyposis and increased cancer susceptibility. While LKB1 loss-induced polyp formation has been ascribed to non-epithelial tissues, how LKB1 deficiency increases cancer risk of patients by altering the phenotypical landscape and hierarchical organization of epithelial tissues remains poorly understood.\n\nMethodsUsing CRISPR\/Cas9, we generated heterozygous and homozygous Lkb1-deficient mouse small intestinal and human colon organoids. These organoids were characterized by an integrated approach that combines imaging, bulk and single-cell RNA sequencing and growth factor dependency assays. Our findings were validated in human PJS-derived tissues using immunohistochemistry and linked to colorectal cancer profiles using the TCGA cancer database.\n\nResultsOur results reveal that heterozygous Lkb1 loss is sufficient to push intestinal cells into a premalignant transcriptional program associated with serrated colorectal cancer, which is further amplified by loss-of-heterozygosity. This altered epithelial growth state associates with persistent features of regeneration and enhanced EGFR ligand and receptor expression, conferring niche-independent growth properties to Lkb1-deficient organoids. Moreover, our newly generated LKB1-mutant signature is enriched in sporadic serrated colorectal cancer, and synergistic cooperation of Lkb1-deficiency with mutant Kras was experimentally confirmed by assessing organoid growth properties and transcriptomes.\n\nConclusionsHeterozygous loss of LKB1 pushes intestinal cells into a chronic regenerative state which is amplified upon loss-of-heterozygosity. Lkb1-deficiency thereby generates fertile ground for serrated colorectal cancer formation in the intestine, potentially explaining the increased cancer risk observed in PJS.","funder":"NA","published":"NA","server":"bioRxiv"},{"title":"What if...? Computational anatomy in the cerebellar granular layer","authors":"Gilbert, M.; Rasmussen, A.","author_corresponding":"Mike Gilbert","author_corresponding_institution":"University of Birmingham","doi":"10.1101\/2023.07.14.548987","date":"2024-08-22","version":"5","type":"new results","license":"cc_no","category":"neuroscience","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/22\/2023.07.14.548987.source.xml","abstract":"We present a theory of the inner layer of the cerebellar cortex, the granular layer, where the main excitatory input to the cerebellum is received. We ask how input signals are converted into an internal code and what form that has. While there is a computational element, and the ideas are quantified with a computer simulation, the approach is primarily evidence-led and aimed at experimenters rather than the computational community. Network models are often simplified to provide a noiseless medium for sophisticated computations. We propose, with evidence, the reverse: physiology is highly adapted to provide a noiseless medium for straightforward computations. We find that input data are converted to a hyper low-resolution internal code. Information is coded in the joint activity of large cell groups and therefore has minimum spatial dimensions - the dimensions of a code group. The conversion exploits statistical effects of random sampling. Code group dimensions are an effect of topography, cell morphologies and granular layer architecture. The activity of a code group is the smallest unit of information but not the smallest unit of code - the same information is coded in any random sample of signals. Code in this form is unexpectedly wasteful - there is a huge sacrifice of resolution - but may be a solution to fundamental problems involved in the biological representation of information.","funder":"NA","published":"10.1098\/rsos.241665","server":"bioRxiv"},{"title":"A gene-regulatory network model for density-dependent and sex-biased dispersal evolution during range expansions.","authors":"Deshpande, J. N.; Fronhofer, E. A.","author_corresponding":"Jhelam N. Deshpande","author_corresponding_institution":"ISEM, Universite de Montpellier, CNRS, IRD, EPHE, Montpellier, France","doi":"10.1101\/2023.07.18.549508","date":"2024-08-14","version":"3","type":"new results","license":"cc_by_nc","category":"evolutionary biology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/14\/2023.07.18.549508.source.xml","abstract":"Dispersal is key to understanding ecological and evolutionary dynamics. Dispersal may itself evolve and exhibit phenotypic plasticity. Specifically, organisms may modulate their dispersal rates in response to the density of their conspecifics (density-dependent dispersal) and their own sex (sex-biased dispersal). While optimal dispersal plastic responses have been derived from first principles, the genetic and molecular basis of dispersal plasticity has not been modelled. An understanding of the genetic architecture of dispersal plasticity is especially relevant for understanding dispersal evolution during rapidly changing spatial ecological conditions such as range expansions. In this context, we develop an individual-based metapopulation model of the evolution of density-dependent and sex-biased dispersal during range expansions. We represent the dispersal trait as a gene-regulatory network (GRN), which can take population density and an individuals sex as an input and analyse emergent context- and condition-dependent dispersal responses. We compare dispersal evolution and ecological dynamics in this GRN model to a standard reaction norm (RN) approach under equilibrium metapopulation conditions and during range expansions. We find that under equilibrium metapopulation conditions, the GRN model produces emergent densitydependent and sex-biased dispersal plastic response shapes that match the theoretical expectation of the RN model. However, during range expansion, when mutation effects are large enough, the GRN model leads to faster range expansion because GRNs can maintain higher adaptive potential. Our results imply that, in order to understand eco-evolutionary dynamics in contemporary time, the genetic architecture of traits must be taken into account.","funder":[{"name":"Agence Nationale de la Recherche","id":"https:\/\/ror.org\/00rbzpz17","id-type":"ROR","award":"ANR-19-CE02-0015;"}],"published":"10.24072\/pcjournal.626","server":"bioRxiv"},{"title":"A spatial threshold for astrocyte calcium surge","authors":"Lines, J.; Baraibar, A. M.; Nanclares, C.; Martin, E.; Aguilar, J. d. l. R.; Kofuji, P.; Navarrete, M.; Araque, A.","author_corresponding":"Justin Lines","author_corresponding_institution":"University of Minnesota","doi":"10.1101\/2023.07.18.549563","date":"2024-08-08","version":"2","type":"new results","license":"cc_no","category":"neuroscience","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/08\/2023.07.18.549563.source.xml","abstract":"Astrocytes are active cells involved in brain function through the bidirectional communication with neurons, in which the astrocyte calcium signal plays a crucial role. Synaptically-evoked calcium increases can be localized to independent subcellular domains or expand to the entire cell, i.e., calcium surge. In turn, astrocytes may regulate individual synapses by calcium-dependent release of gliotransmitters. Because a single astrocyte may contact [~]100,000 synapses, the control of the intracellular calcium signal propagation may have relevant consequences on brain function by regulating the spatial range of astrocyte neuromodulation of synapses. Yet, the properties governing the spatial dynamics of the astrocyte calcium signal remains poorly defined. Imaging subcellular responses of cortical astrocytes to sensory stimulation in mice, we show that sensory-evoked astrocyte calcium responses originated and remained localized in domains of the astrocytic arborization, but eventually propagated to the entire cell if a spatial threshold of >23% of the arborization being activated was surpassed. Using transgenic IP3R2-\/- mice, we found that type-2 IP3 receptors were necessary for the generation of the astrocyte calcium surge. We finally show using in situ electrophysiological recordings that the spatial threshold of the astrocyte calcium signal consequently determined the gliotransmitter release. Present results reveal a fundamental property of astrocyte calcium physiology, i.e., a spatial threshold for the astrocyte intracellular calcium signal propagation, which depends on astrocyte intrinsic properties and governs the astrocyte integration of local synaptic activity and the subsequent neuromodulation.\n\nOne-Sentence SummaryThere is a spatial threshold for the astrocyte intracellular calcium signal propagation that is determined by astrocyte intrinsic properties and controls gliotransmission.","funder":"NA","published":"10.7554\/elife.90046","server":"bioRxiv"},{"title":"Migration and standing genetic variation in vaginal and rectal yeast populations in recurrent vulvovaginal candidiasis","authors":"Adamu Bukari, A.-R.; Kukurudz-Gorowski, R.; de Graaf, A.; Habon, D.; Manyaz, B.; Syvolos, Y.; Sumanarathnea, A.; Poliquin, V.; Gerstein, A. C.","author_corresponding":"Aleeza C Gerstein","author_corresponding_institution":"University of Manitoba","doi":"10.1101\/2023.07.19.549743","date":"2024-08-07","version":"2","type":"new results","license":"cc_by_nc_nd","category":"microbiology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/07\/2023.07.19.549743.source.xml","abstract":"Vulvovaginal candidiasis is one of the most common fungal infections. Most are successfully treated with antifungal drugs, yet [~]8% lead to recurrent vulvovaginal candidiasis (\"RVVC\"). Previous research found closely-related isolates within vaginal and rectal populations. However, their methods preclude assessing fine-scale relationships among closely related isolates and measuring genetic variation, a fundamental property with evolutionary potential implications. To address this gap, we isolated 12 vaginal and 12 rectal yeast isolates during symptomatic relapse from four individuals with a history of RVVC. Three had Candida albicans infections, while the fourth had Nakaseomyces glabratus. All isolates were whole-genome sequenced and phenotyped. The isolates were placed into global phylogenies built from short-read WGS data, including an updated N. glabratus tree with over 500 isolates. Genotypic and phenotypic analyses were consistent with migration between sites. There was little phenotypic diversity for drug response and no consistent difference between isolates from different sites for invasive growth. Although there are few comparables, C. albicans nucleotide diversity was similar to most commensal oral and rectal populations, while N. glabratus was similar to some bloodstream infections (though higher than others). Single nucleotide changes drove diversity; no aneuploidies were found, and only a single loss-of-heterozygosity tract on chr1L varied among isolates from one participant. This study provides baseline measurements and describes techniques to quantify within-population diversity in fungal microbes. We highlight a need for comparable studies that use the same sampling effort and analysis methods to understand the interplay in shaping fungal microbial communities in important contexts.\n\nAuthor SummaryRecurrent vaginal yeast infections are relatively common, and we do not understand why some people experience these chronic infections when many others have a single infection that is successfully treated and cleared. Many open questions remain about the basic biology of the yeast populations involved. We quantified diversity using modern sequencing technology within vaginal and rectal yeast populations from four individuals with a history of recurrent yeast infections experiencing symptoms. Three participants had a Candida albicans infection (the most common causative species), while the fourth had a Nakaseomyces glabratus infection (the second most common and increasingly implicated). We found that vaginal and rectal isolates were closely related, indicating the same population is present at the two sites. Surprisingly, we found that diversity was similar to the yeast populations found at other body sites in healthy people. Our study highlights a critical need for additional studies following the same methods in different contexts to better understand the fungal microbial populations in our bodies.","funder":"NA","published":"10.1128\/msystems.00157-25","server":"bioRxiv"},{"title":"SYS-1\/beta-catenin inheritance and regulation by Wnt-signaling during asymmetric cell division.","authors":"Valdes Michel, M. F.; Phillips, B. T.","author_corresponding":"Bryan T Phillips","author_corresponding_institution":"Department of Biology, Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA","doi":"10.1101\/2023.07.21.550069","date":"2024-08-19","version":"3","type":"new results","license":"cc_no","category":"developmental biology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/19\/2023.07.21.550069.source.xml","abstract":"Asymmetric cell division (ACD) allows daughter cells of a polarized mother to acquire different developmental fates. In C. elegans, the Wnt\/{beta}-catenin Asymmetry (W{beta}A) pathway oversees many embryonic and larval ACDs; here, a Wnt gradient induces an asymmetric distribution of Wnt signaling components within the dividing mother cell. One terminal nuclear effector of the W{beta}A pathway is the transcriptional activator SYS-1\/{beta}-catenin. SYS-1 is sequentially negatively regulated during ACD; first by centrosomal regulation and subsequent proteasomal degradation and second by asymmetric activity of the {beta}-catenin \"destruction complex\" in one of the two daughter cells, which decreases SYS-1 levels in the absence of W{beta}A signaling. However, the extent to which mother cell SYS-1 influences cell fate decisions of the daughters is unknown. Here, we quantify inherited SYS-1 in the differentiating daughter cells and the role of SYS-1 inheritance in Wnt-directed ACD. Photobleaching experiments demonstrate the GFP::SYS-1 present in daughter cell nuclei is comprised of inherited and de novo translated SYS-1 pools. We used a photoconvertible DENDRA2::SYS-1, to directly observe the dynamics of inherited SYS-1. Photoconversion during mitosis reveals that SYS-1 clearance at the centrosome preferentially degrades older SYS-1, and this accumulation is regulated via dynein trafficking. Photoconversion of the EMS cell during Wnt-driven ACD shows daughter cell inheritance of mother cell SYS-1. Additionally, loss of centrosomal SYS-1 increased inherited SYS-1 and, surprisingly, loss of centrosomal SYS-1 also resulted in increased levels of de novo SYS-1 in both EMS daughter cells. Lastly, we show that daughter cell negative regulation of SYS-1 via the destruction complex member APR-1\/APC is key to limit both the de novo and the inherited SYS-1 pools in both the E and the MS cells. We conclude that regulation of both inherited and newly translated SYS-1 via centrosomal processing in the mother cell and daughter cell regulation via Wnt signaling are critical to maintain sister SYS-1 asymmetry during ACD.","funder":"NA","published":"NA","server":"bioRxiv"},{"title":"Cross-transmission of resistant gastrointestinal nematodes between wildlife and transhumant sheep","authors":"Beaumelle, C.; Toigo, C.; Papet, R.; Benabed, S.; Beurier, M.; Bordes, L.; Brignone, A.; Curt-Grand-Gaudin, N.; Garel, M.; Ginot, J.; Jacquiet, P.; Miquel, C.; Poirel, M.-T.; Serafino, A.; Vannard, E.; Bourgoin, G.; Yannic, G.","author_corresponding":"Camille Beaumelle","author_corresponding_institution":"Universite Savoie Mont Blanc","doi":"10.1101\/2023.07.21.550073","date":"2024-08-10","version":"6","type":"new results","license":"cc_by_nc_nd","category":"ecology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/10\/2023.07.21.550073.source.xml","abstract":"Wild and domestic ungulates can be infected with the same species of gastrointestinal parasitic nematodes. These parasites have free-living stages in the environment that contribute to the ease of transmission among different host species. In addition, gastrointestinal nematodes have developed resistance to anthelmintics which is now considered a major problem for the livestock sector. In a context where wild and domestic ungulates share the same pastures, the maintenance and circulation of resistant gastrointestinal nematodes between species have rarely been explored.\n\nIn the European Alps, domestic sheep are driven to high-altitude summer pastures and live in sympatry with wild ungulates for several months each year. In this study, we investigated the nemabiome of domestic sheep and Alpine ibex, Capra ibex, in three different areas of the French Alps to evaluate parasite circulation between the two host species. The Alpine ibex is a protected mountain ungulate that is phylogenetically related to sheep and hosts nematode species common to sheep.\n\nUsing internal transcribed spacer 2 (ITS-2) nemabiome metabarcoding, we found sheep and ibex share similar gastrointestinal nematodes, except for a few species such as Marshallagia marshalli and Trichostrongylus axei. This suggests that the long-term co-occurrence of sheep and ibex on mountain pastures has promoted the exchange of gastrointestinal nematodes between the two hosts. Based on the sequencing of the isotype 1 of the beta tubulin gene, associated with benzimidazole resistance, we found resistant nematodes in all sheep flocks and in all ibex populations. Our results demonstrated that ibex can host and shed resistant strains before transhumant sheep arrive on pastures, and thus could act as a refuge or even contribute to maintaining resistant gastrointestinal nematodes. The relative role of ibex in the maintenance and circulation of resistant strains in sheep remain to be determined.","funder":"NA","published":"10.24072\/pcjournal.477","server":"bioRxiv"},{"title":"Visuomotor prediction during action planning in the human frontoparietal cortex and cerebellum","authors":"Quirmbach, F.; Limanowski, J.","author_corresponding":"Jakub Limanowski","author_corresponding_institution":"Universitaet Greifswald","doi":"10.1101\/2023.07.20.549926","date":"2024-08-28","version":"3","type":"new results","license":"cc_by_nc","category":"neuroscience","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/28\/2023.07.20.549926.source.xml","abstract":"The concept of forward models in the brain, classically applied to describing on-line motor control, can in principle be extended to action planning; i.e., assuming forward sensory predictions are issued during the mere preparation of movements. To test this idea, we combined a delayed movement task with a virtual reality based manipulation of visuomotor congruence during functional magnetic resonance imaging (fMRI). Participants executed simple hand movements after a delay. During the delay, two aspects of the upcoming movement could be cued: the movement type and the visuomotor mapping (i.e., (in)congruence of executed hand movements and visual movement feedback by a glove- controlled virtual hand). Frontoparietal areas showed increased delay period activity when preparing pre-specified movements (cued > uncued). The cerebellum showed increased activity during the preparation for incongruent > congruent visuomotor mappings. The left anterior intraparietal sulcus (aIPS) showed an interaction effect, responding most strongly when a pre-specified (cued) movement was prepared under expected visuomotor incongruence. These results suggest that motor planning entails a forward prediction of visual body movement feedback, which can be adjusted in anticipation of nonstandard visuomotor mappings, and which is likely computed by the cerebellum and integrated with state estimates for (planned) control in the aIPS.","funder":"NA","published":"10.1093\/cercor\/bhae382","server":"bioRxiv"},{"title":"Internal Neural Representations in Task-Switching Guided by Context Biases","authors":"Galella, S.; Ardid, S.","author_corresponding":"Salva Ardid","author_corresponding_institution":"Universitat Politecnica de Valencia","doi":"10.1101\/2023.07.24.550365","date":"2024-08-17","version":"2","type":"new results","license":"cc_by","category":"neuroscience","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/17\/2023.07.24.550365.source.xml","abstract":"AO_SCPLOWBSTRACTC_SCPLOWOur brain can filter and integrate external information with internal representations to accomplish goal-directed behavior. The ability to switch between tasks effectively in response to context and external stimuli is a hallmark of cognitive control. Task switching occurs rapidly and efficiently, allowing us to perform multiple tasks with ease. Similarly, artificial intelligence can be tailored to exhibit multitask capabilities and achieve high performance across domains. In this study, we delve into neural representations learned by task-switching feedforward networks, which use task-specific biases for multitasking mediated by context inputs. Task-specific biases are learned by alternating the tasks the neural network learns during training. By using two-alternative choice tasks, we find that task-switching networks produce representations that resemble other multitasking paradigms, namely parallel networks in the early stages of processing and independent subnetworks in later stages. This transition in information processing is akin to that in the cortex. We then analyze the impact of inserting task contexts in different stages of processing, and the role of its location in the alignment between the task and the stimulus features. To confirm the generality of results, we display neural representations during task switching for different task and data sets. In summary, the use of context inputs improves the interpretability of feedforward neural networks for multitasking, setting the basis for studying architectures and tasks of higher complexity, including biological microcircuits in the brain carrying out context-dependent decision making.","funder":"NA","published":"NA","server":"bioRxiv"},{"title":"A step in the deep evolution of Alvinellidae (Annelida: Polychaeta): a phylogenomic comparative approach based on transcriptomes","authors":"Brun, P.-G.; Hourdez, S.; Ballenghien, M.; Zhou, Y.; Mary, J.; Jollivet, D.","author_corresponding":"Didier Jollivet","author_corresponding_institution":"CNRS","doi":"10.1101\/2023.07.24.550320","date":"2024-08-21","version":"3","type":"new results","license":"cc_by_nc","category":"evolutionary biology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/21\/2023.07.24.550320.source.xml","abstract":"The Alvinellidae are a family of worms that are endemic to deep-sea hydrothermal vents in the Pacific and Indian Oceans. These annelid worms, a sister group to the Ampharetidae, occupy a wide range of thermal habitats. The family includes the most thermotolerant marine animals described to date such as the Pompeii worm Alvinella pompejana, and other species living at much lower temperatures such as Paralvinella grasslei or Paralvinella pandorae. The phylogeny of this family has not been studied extensively. It is, however, a complex case where molecular phylogenies have given conflicting results, especially concerning the monophyletic or polyphyletic nature of the genus Paralvinella.\n\nWe carried out a comprehensive study of the phylogeny of this family using the best molecular data currently available from RNAseq datasets, leading to several hundred orthologous transcripts for 11 of the 14 species currently described or in description. The results obtained by the two most popular phylogenetic inference models (using either gene concatenation with maximum likelihood, or a coalescent-based model from gene trees) were compared using a series of ampharetid and terebellid outgroups.\n\nOur study shows that the global phylogenetic signal favors the hypothesis of paraphyly for the Paralvinella genus, with P. pandorae being sister species of the other Alvinellidae. However, a high number of gene trees also supports the hypothesis of alternative trees in which the monophyly of the Paralvinella genus, as initially proposed by Desbruyeres and Laubier, is valid with the species P. pandorae and Paralvinella unidentata being sister species. According to molecular dating, the radiation of the Alvinellidae was rapid and took place in a short period of time between 80 and 110 million years ago. This is reflected at the genomic scale by gene trees equally separated between different phylogenetic hypothesis, showing high rates of incomplete lineage sorting between the first lineages of the Alvinellidae and probable gene transfers. Although different genomic regions seem to have different phylogenetic stories in the early step of the alvinellid radiation, our study supports the view that the two P. pandorae species can be grouped into a separate genus (possibly Nautalvinella) and that the Miralvinella subgenus, defined by Desbruyeres and Laubier, is not valid anymore.","funder":"NA","published":"10.1016\/j.ympev.2024.108207","server":"bioRxiv"},{"title":"Individual patterns of functional connectivity in neonates as revealed by surface-based Bayesian modeling","authors":"Derman, D.; Pham, D. D.; Mejia, A. F.; Ferradal, S. L.","author_corresponding":"Diego Derman","author_corresponding_institution":"Indiana University","doi":"10.1101\/2023.07.24.550218","date":"2024-08-08","version":"2","type":"confirmatory results","license":"cc_by","category":"neuroscience","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/08\/2023.07.24.550218.source.xml","abstract":"Resting-state functional connectivity is a widely used approach to study the functional brain network organization during early brain development. However, the estimation of functional connectivity networks in individual infants has been rather elusive due to the unique challenges involved with functional magnetic resonance imaging (fMRI) data from young populations. Here, we use fMRI data from the developing Human Connectome Project (dHCP) database to characterize individual variability in a large cohort of term-born infants (N = 289) using a novel data-driven Bayesian framework. To enhance alignment across individuals, the analysis was conducted exclusively on the cortical surface, employing surface-based registration guided by age-matched neonatal atlases. Using 10 minutes of resting-state fMRI data, we successfully estimated subject-level maps for fourteen brain networks\/subnetworks along with individual functional parcellation maps that revealed differences between subjects. We also found a significant relationship between age and mean connectivity strength in all brain regions, including previously unreported findings in higher-order networks. These results illustrate the advantages of surface-based methods and Bayesian statistical approaches in uncovering individual variability within very young populations.","funder":"NA","published":"10.1162\/imag_a_00504","server":"bioRxiv"},{"title":"DNA methylation insulates genic regions from CTCF loops near nuclear speckles","authors":"Roseman, S. A.; Siegenfeld, A. P.; Lee, C.; Lue, N. Z.; Waterbury, A. L.; Liau, B. B.","author_corresponding":"Brian B Liau","author_corresponding_institution":"Harvard University","doi":"10.1101\/2023.07.26.550645","date":"2024-08-31","version":"2","type":"new results","license":"cc_no","category":"genomics","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/31\/2023.07.26.550645.source.xml","abstract":"The insulator protein CTCF is essential for mediating chromatin loops and regulating gene expression. While it is established that DNA methylation hinders CTCF binding, the impacts of this methylation-sensitive CTCF binding on chromatin architecture and transcription are poorly defined. Here, we used a selective DNMT1 inhibitor (DNMT1i) to investigate the characteristics and functions of  DNMT1i-specific CTCF peaks resulting from global DNA demethylation. We found that DNMT1i-specific peaks preferentially form chromatin loops on gene bodies and interact with highly-looping partner peaks located in regions of active chromatin. Notably, both DNMT1i-specific CTCF peaks and their highly-looping partners are enriched near nuclear speckles, condensate bodies implicated in transcription and splicing. Utilizing targeted protein degradation, we specifically depleted CTCF and nuclear speckles to elucidate their functional interplay. By degrading CTCF upon DNMT1 inhibition, we revealed that CTCF is important for DNMT1i-dependent interactions between chromatin and speckle proteins. Moreover, we found that CTCF promotes the activation of genes near speckles upon DNMT1 inhibition. Conversely, acute depletion of nuclear speckles revealed that they influence RNA abundance but do not maintain CTCF binding or looping. Collectively, our study suggests a model wherein DNA methylation prevents spurious CTCF occupancy and interactions with regulatory elements near nuclear speckles, yet CTCF looping is robust towards the loss of speckles.","funder":"NA","published":"10.7554\/eLife.102930","server":"bioRxiv"},{"title":"Chromatin enhancer activity of I\u03baB\u03b1 mediates the exit from nai\u0308ve pluripotency","authors":"Palma, L. G.; Alvarez-Villanueva, D.; Maqueda, M.; Barrero, M.; IGLESIAS, A.; Bertran, j.; ALVAREZ, D.; GARCIA-PRIETO, C.; BALLARE, C.; RODRIGUEZ-CORTEZ, V.; BUENO, C.; VIDAL, A.; Villanueva, A.; Menendez, P.; Stik, G.; Di Croce, L.; Payer, B.; Esteller, M.; Espinosa, L.; Bigas, A.","author_corresponding":"Anna Bigas","author_corresponding_institution":"Institut Hospital del Mar d'Investigacions Mediques Barcelona","doi":"10.1101\/2023.07.28.550934","date":"2024-08-22","version":"5","type":"new results","license":"cc_no","category":"cell biology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/22\/2023.07.28.550934.source.xml","abstract":"Maintenance of pluripotency is a multifactorial process in which NF-{kappa}B is a negative regulator. Our previous work identified a chromatin role for I{kappa}B, the master regulator of NF-{kappa}B signaling, that is critical for the proper regulation of various tissue stem cells. Here, we found that I{kappa}B accumulates specifically in the chromatin fraction of pluripotent embryonic stem cells. I{kappa}B depletion does not affect NF-kB-dependent transcription, but causes a profound epigenetic rewiring in pluripotent stem cells, including alterations in H3K27me3, a histone mark catalyzed by Polycomb repression complex 2. Chromatin changes induced by I{kappa}B depletion affect a subset of pluripotency genes and are associated with altered gene transcription. At the cellular level, I{kappa}B-deficient embryonic stem cells are arrested in a naive pluripotency state when cultured in serum\/LIF conditions and fail to exit pluripotency under differentiation conditions. By constructing separation-of-function mutants, we show that the effects of I{kappa}B in regulating stem cell pluripotency are NF-{kappa}B-independent, but mainly rely on its chromatin-related function. Taken together, our results reveal a novel mechanism by which I{kappa}B participates in the regulation of the pluripotent state of embryonic stem cells and shed light on the interplay between inflammatory signals and the regulation of pluripotency.","funder":[{"name":"Spanish Ministry of Science and Innovation","id":"","id-type":"ROR","award":"PID2019-104695RB-I00;PID2022-137945OB-I00;PLEC2021-007518;PDC2021-120817-I00;PID2019-108322GB-100;PID2022-142679NB-I00;"},{"name":"Generalitat de Catalunya","id":"https:\/\/ror.org\/01bg62x04","id-type":"ROR","award":"2021SGR 39;SLT002\/16\/00299;2021 SGR 01222;"}],"published":"NA","server":"bioRxiv"},{"title":"Interdependence of plasma membrane nanoscale dynamics of a kinase and its cognate substrate underlies Arabidopsis response to viral infection","authors":"Jolivet, M.-D.; Deroubaix, A.-F.; Boudsocq, M.; Abel, N. B.; Rocher, M.; Robbe, T.; Wattelet, V.; Huard, J.; Lefebvre, D.; Lu, Y.-J.; Day, B.; Saias, G.; Ahmed, J.; Cotelle, V.; Giovinazzo, N.; Gallois, J.-L.; Yamaji, Y.; German-Retana, S.; Gronnier, J.; Ott, T.; Mongrand, S.; Germain, V.","author_corresponding":"Veronique Germain","author_corresponding_institution":"UMR5200: Laboratoire de Biogenese Membranaire","doi":"10.1101\/2023.07.31.551174","date":"2024-08-19","version":"4","type":"new results","license":"cc_no","category":"plant biology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/19\/2023.07.31.551174.source.xml","abstract":"Plant viruses represent a risk to agricultural production and as only a few treatments exist, it is urgent to identify resistance mechanisms and factors. In plant immunity, plasma membrane (PM)-localized proteins play an essential role in sensing the extracellular threat presented by bacteria, fungi or herbivores. Viruses are intracellular pathogens and as such the role of the plant PM in detection and resistance against viruses is often overlooked. We investigated the role of the partially PM-bound Calcium-dependent protein kinase 3 (CPK3) in viral infection and we discovered that it displayed a specific ability to hamper viral propagation over CPK isoforms that are involved in immune response to extracellular pathogens. More and more evidence support that the lateral organization of PM proteins and lipids underlies signal transduction in plants. We showed here that CPK3 diffusion in the PM is reduced upon activation as well as upon viral infection and that such immobilization depended on its substrate, Remorin (REM1.2), a scaffold protein. Furthermore, we discovered that the viral infection induced a CPK3-dependent increase of REM1.2 PM diffusion. Such interdependence was also observable regarding viral propagation. This study unveils a complex relationship between a kinase and its substrate that contrasts with the commonly described co-stabilisation upon activation while it proposes a PM-based mechanism involved in decreased sensitivity to viral infection in plants.","funder":"NA","published":"10.7554\/elife.90309.3","server":"bioRxiv"},{"title":"Selective inhibition of hsp90 paralogs: Uncovering the role of helix 1 in Grp94-selective ligand binding","authors":"Que, N. L. S.; Seidler, P. M.; Aw, W. J.; Chiosis, G.; Gewirth, D. T.","author_corresponding":"Daniel T. Gewirth","author_corresponding_institution":"Hauptman Woodward Institute","doi":"10.1101\/2023.07.31.551342","date":"2024-08-19","version":"2","type":"new results","license":"cc_by_nc_nd","category":"biochemistry","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/19\/2023.07.31.551342.source.xml","abstract":"Grp94 is the endoplasmic reticulum paralog of the hsp90 family of chaperones, which have been targeted for therapeutic intervention via their highly conserved ATP binding sites. The design of paralog-selective inhibitors relies on understanding the protein structural elements that drive higher affinity in selective inhibitors. Here, we determined the structures of Grp94 and Hsp90 in complex with the Grp94-selective inhibitor PU-H36, and of Grp94 with the non-selective inhibitor PU-H71. In Grp94, PU-H36 derives its higher affinity by utilizing Site 2, a Grp94-specific side pocket adjoining the ATP binding cavity, but in Hsp90 PU-H36 occupies Site 1, a side pocket that is accessible in all paralogs with which it makes lower affinity interactions. The structure of Grp94 in complex with PU-H71 shows only Site 1 binding. While changes in the conformation of helices 4 and 5 in the N-terminal domain occur when ligands bind to Site 1 of both Hsp90 and Grp94, large conformational shifts that also involve helix 1 are associated with the engagement of the Site 2 pocket in Grp94 only. Site 2 in Hsp90 is blocked and its helix 1 conformation is insensitive to ligand binding. To understand the role of helix 1 in ligand selectivity, we tested the binding of PU-H36 and other Grp94-selective ligands to chimeric Grp94\/Hsp90 constructs. These studies show that helix 1 is the major determinant of selectivity for Site 2 targeted ligands, and also influences the rate of ATPase activity in Hsp90 paralogs.","funder":"NA","published":"10.1002\/prot.26756","server":"bioRxiv"},{"title":"Chaperone-assisted cryo-EM structure of P. aeruginosa PhuR reveals molecular basis for heme binding","authors":"Knejski, P. P.; Erramilli, S. K.; Kossiakoff, A. A.","author_corresponding":"Anthony A. Kossiakoff","author_corresponding_institution":"The University of Chicago","doi":"10.1101\/2023.08.01.551527","date":"2024-08-05","version":"2","type":"new results","license":"cc_by_nc_nd","category":"biochemistry","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/05\/2023.08.01.551527.source.xml","abstract":"Pathogenic bacteria, such as Pseudomonas aeruginosa, depend on scavenging heme for the acquisition of iron, an essential nutrient. The TonB-dependent transporter (TBDT) PhuR is the major heme uptake protein in P. aeruginosa clinical isolates. However, a comprehensive understanding of heme recognition and TBDT transport mechanisms, especially PhuR, remains limited. In this study, we employed single-particle cryogenic electron microscopy (cryo-EM) and a phage display-generated synthetic antibody (sAB) as a fiducial marker to enable the determination of a high-resolution (2.5 [A]) structure of PhuR with a bound heme. Notably, the structure reveals iron coordination by Y529 on a conserved extracellular loop, shedding light on the role of tyrosine in heme binding. Biochemical assays and negative-stain EM demonstrated that the sAB specifically targets the heme-bound state of PhuR. These findings provide insights into PhuRs heme binding and offer a template for developing conformation-specific sABs against outer membrane proteins (OMPs) for structure-function investigations.","funder":"NA","published":"NA","server":"bioRxiv"},{"title":"High-intensity physiological activation disrupts the neural signatures of conflict processing","authors":"Avancini, C.; Ciria, L. F.; Alameda, C.; Palenciano, A. F.; Canales-Johnson, A.; Bekinschtein, T. A.; Sanabria, D.","author_corresponding":"Chiara Avancini","author_corresponding_institution":"University of Granada","doi":"10.1101\/2023.07.31.550835","date":"2024-08-06","version":"2","type":"new results","license":"cc_by_nc_nd","category":"neuroscience","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/06\/2023.07.31.550835.source.xml","abstract":"Physical activation fluctuates throughout the day. Previous studies have shown that during periods of reduced activation, cognitive control remains resilient due to neural compensatory mechanisms. In this study, we in-vestigated the effects of high physical activation on both behavioural and neural markers of cognitive control. We hypothesized that while behavioural measures of cognitive control would remain intact during periods of high activation, there would be observable changes in neural correlates. In our electroencephalography study, we manipulated levels of physical activation through physical exercise. Although we observed no significant impact on behavioural measures of cognitive conflict, both univariate and multivariate time-frequency markers proved unreliable under conditions of high activation. Moreover, there was no modulation of whole-brain connectivity measures by physical activation. We suggest that this dissociation between behavioural and neural measures indicates that the human cognitive control system remains resilient even at high activation, possibly due to underlying neural compensatory mechanisms.","funder":"NA","published":"10.1038\/s42003-024-06851-w","server":"bioRxiv"},{"title":"Effect of diffusivity of amyloid beta monomers on the formation of senile plaques","authors":"Kuznetsov, A. V.","author_corresponding":"Andrey V Kuznetsov","author_corresponding_institution":"North Carolina State University","doi":"10.1101\/2023.07.31.551367","date":"2024-08-11","version":"7","type":"new results","license":"cc_by_nc_nd","category":"biophysics","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/11\/2023.07.31.551367.source.xml","abstract":"Alzheimers disease (AD) presents a perplexing question: why does its development span decades, even though individual amyloid beta (A{beta}) deposits (senile plaques) can form rapidly in as little as 24 hours, as recent publications suggest? This study investigated whether the formation of senile plaques can be limited by factors other than polymerization kinetics alone. Instead, their formation may be limited by the diffusion-driven supply of A{beta} monomers, along with the rate at which the monomers are produced from amyloid precursor protein (APP) and the rate at which A{beta} monomers undergo degradation. A mathematical model incorporating the nucleation and autocatalytic process (via the Finke-Watzky model), as well as A{beta} monomer diffusion, was proposed. The obtained system of partial differential equations was solved numerically, and a simplified version was investigated analytically. The computational results predicted that it takes approximately 7 years for A{beta} aggregates to reach a neurotoxic concentration of 50 M. Additionally, a sensitivity analysis was performed to examine how the diffusivity of A{beta} monomers and their production rate impact the concentration of A{beta} aggregates.","funder":"NA","published":"10.1093\/imammb\/dqae019","server":"bioRxiv"},{"title":"Strategic acyl carrier protein engineering enables functional type II polyketide synthase reconstitution in vitro","authors":"Li, K. K.; Cho, Y. I.; Tran, M. A.; Wiedemann, C.; Zhang, S.; Koweek, R. S.; Hoang, N. K.; Hamrick, G.; Bowen, M.; Kokona, B.; Stallforth, P.; Beld, J.; Hellmich, U.; Charkoudian, L. K.","author_corresponding":"Louise K. Charkoudian","author_corresponding_institution":"Haverford College","doi":"10.1101\/2023.08.02.551649","date":"2024-08-12","version":"2","type":"new results","license":"cc_no","category":"biochemistry","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/12\/2023.08.02.551649.source.xml","abstract":"Microbial polyketides represent a structurally diverse class of secondary metabolites with medicinally relevant properties and are synthesized by polyketide synthases (PKS). While Type I PKSs are large biosynthetic machineries composed of a single polypeptide chain, type II PKSs are minimally composed of a ketosynthase-chain length factor (KS-CLF) and a phosphopantetheinylated acyl carrier protein (holo-ACP) expressed separately. Although type II PKSs are found throughout the bacterial kingdom, and despite their importance to strategic bioengineering, type II PKSs have not been well-studied in vitro: In cases where the KS-CLF can be accessed via E. coli heterologous expression, the cognate ACPs are not activatable by the broad specificity Bacillus subtilis surfactin-producing phosphopantetheinyl transferase (PPTase) Sfp and, conversely, in systems where the ACP can be activated by Sfp, the corresponding KS-CLF is typically not readily obtained. Here, we report the high-yield heterologous expression of both cyanobacterial Gloeocapsa sp. PCC 7428 minimal type II PKS (gloPKS) components in E. coli, which allowed us to functionally reconstitute this minimal type II PKS in vitro. Initially, neither the cognate PPTase nor Sfp converted gloACP to its active holo state. However, by examining sequence differences between Sfp-compatible and -incompatible ACPs, we identified two conserved residues in gloACP that, when mutated, enabled high-yield phosphopantetheinylation of gloACP by Sfp. Using analogous mutations, other previously Sfp-incompatible type II PKS ACPs from different bacterial phyla were also rendered activatable by Sfp. This demonstrates the generalizability of our approach and breaks down a longstanding barrier to type II PKS studies and the exploration of complex biosynthetic pathways.","funder":"NA","published":"10.1021\/acschembio.4c00678","server":"bioRxiv"},{"title":"Modeling corticotroph deficiency with pituitary organoids supports the functional role of NFKB2 in human pituitary differentiation","authors":"Mac, T. T.; Fauquier, T.; Jullien, N.; Romanet, P.; Etchevers, H. C.; Barlier, A.; Castinetti, F.; Brue, T.","author_corresponding":"Thierry Brue","author_corresponding_institution":"Aix Marseille Univ, APHM, INSERM, MMG, Department of Endocrinology, La Conception Hospital, Institut MarMaRa, Marseille, France","doi":"10.1101\/2023.08.03.551772","date":"2024-08-01","version":"2","type":"new results","license":"cc_by","category":"developmental biology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/01\/2023.08.03.551772.source.xml","abstract":"BackgroundDeficient Anterior pituitary with common Variable Immune Deficiency (DAVID) syndrome, combining adrenocorticotropic hormone deficiency (ACTHD) and primary hypogammaglobulinemia, is caused by NFKB2 heterozygous mutations. Nuclear factor kappa B (NFKB) signaling is a key regulator of the immune system; however, the underlying mechanism of its association with endocrine symptoms remains unknown. The role of NFKB2 in the development of the human pituitary was called into question by Nfkb2-deficient Lym1 mice, which have normal pituitary functions.\n\nPurposeThe aim of this study was to create a human disease model to define the role of NFKB2 in human pituitary development.\n\nMethodsWe established pituitary organoids in three-dimensional (3D) culture after directed differentiation from CRISPR\/Cas9-edited human induced pluripotent stem cells (hiPSC). First, we conducted a proof-of-concept study, introducing a homozygous TBX19K146R\/K146R missense pathogenic variant in hiPSC, an allele found in patients with congenital isolated ACTHD. We then used the same method to produce NFKB2D865G\/D865G mutant organoids, harboring the pathogenic missense variant previously identified in DAVID patients. This mutation causes a failure of NFKB2 p100 phosphorylation that blocks processing to form active NFKB2 p52. We further characterized pituitary organoid development with bulk RNA sequencing and validated findings with quantitative RT-PCR and by immunofluorescence in section and whole organoids.\n\nResultsAnalysis of wild-type (WT) organoids demonstrated that this in vitro model recapitulates corticotroph cell differentiation. TBX19K146R\/K146R organoids conserved early expression of HESX1, but had significantly decreased PITX1, TBX19, LHX3, and POMC transcription. NFKB2D865G\/D865G organoids also had dramatically reduced corticotrophs. Furthermore, NFKB2D865G\/D865G significantly perturbs the expression of 67 genes known to contribute to pituitary development, among which 39 transcription factors. Differential expression was found for several growth factor genes or genes associated with the epithelial-to-mesenchymal transition and terminal endocrine differentiation.\n\nConclusionWe used a combination of CRISPR\/Cas9 editing and refinement of a 3D organoid culture protocol to model human ACTHD due to TBX19 or NFKB2 mutations. The NFKB2 variant studied induced a significant decrease in corticotroph differentiation, confirming the causative role of NFKB2 in isolated or syndromic ACTHD and demonstrating for the first time a direct functional role of NFKB2 in human pituitary development.","funder":"NA","published":"10.7554\/elife.90875.3","server":"bioRxiv"},{"title":"Interpreting SNP heritability in admixed populations","authors":"Huang, J.; Kleman, N.; Basu, S.; Shriver, M. D.; Zaidi, A. A.","author_corresponding":"Arslan A Zaidi","author_corresponding_institution":"University of Minnesota","doi":"10.1101\/2023.08.04.551959","date":"2024-08-06","version":"3","type":"new results","license":"cc_by","category":"genetics","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/06\/2023.08.04.551959.source.xml","abstract":"SNP heritability [Formula] is defined as the proportion of phenotypic variance explained by genotyped SNPs and is believed to be a lower bound of heritability (h2), being equal to it if all causal variants are genotyped. Despite the simple intuition behind [Formula], its interpretation and equivalence to h2 is unclear, particularly in the presence of admixture and assortative mating. Here we use analytical theory and simulations to describe the behavior of h2 and three widely used random-effect estimators of [Formula] Genome-wide restricted maximum likelihood (GREML), Haseman-Elston (HE) regression, and LD score regression (LDSC) - in admixed populations. We show that [Formula] estimates can be biased in admixed populations, even if all causal variants are genotyped and in the absence of confounding due to shared environment. This is largely because admixture generates directional LD, which contributes to the genetic variance, and therefore to heritability. Random-effect estimators of [Formula], because they assume that SNP effects are independent, do not capture the contribution, which can be positive or negative depending on the genetic architecture, leading to under- or over-estimates of [Formula] relative to h2. For the same reason, estimates of local ancestry heritability [Formula] are also biased in the presence of directional LD. We describe this bias in [Formula] and [Formula] as a function of admixture history and the genetic architecture of the trait, clarifying their interpretation and implication for genome-wide association studies and polygenic prediction in admixed populations.","funder":"NA","published":"10.1093\/genetics\/iyaf100","server":"bioRxiv"},{"title":"Resistance and resilience of soil microbiomes under climate change","authors":"Boyle, J. A.; Murphy, B. K.; Ensminger, I.; Stinchcombe, J. R.; Frederickson, M. E.","author_corresponding":"Julia Anne Boyle","author_corresponding_institution":"University of Toronto","doi":"10.1101\/2023.08.04.551981","date":"2024-08-29","version":"3","type":"new results","license":"cc_by_nc_nd","category":"ecology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/29\/2023.08.04.551981.source.xml","abstract":"Soil microbiomes play key roles in plant productivity and nutrient cycling, and we need to understand whether and how they will withstand the effects of global climate change. We exposed in situ soil microbial communities to multiple rounds of heat, drought, or both treatments, and profiled microbial communities with 16S rRNA and ITS amplicon sequencing during and after these climatic changes, and then tested how domain and symbiotic lifestyle affected responses. Fungal community composition strongly shifted due to drought and its legacy. In contrast, bacterial community composition resisted change during the experiment, but still was affected by the legacy of drought. We identified fungal and bacterial taxa with differential abundance due to heat and drought and found that taxa affected during climate events are not necessarily the taxa affected in recovery periods, showing the complexity and importance of legacy effects. Additionally, we found evidence that symbiotic groups of microbes important to plant performance respond in diverse ways to climate treatments and their legacy, suggesting plants may be impacted by past climatic events like drought and warming even if they do not experience the event themselves.","funder":"NA","published":"10.1002\/ecs2.70077","server":"bioRxiv"},{"title":"Oligomerization and positive feedback on membrane recruitment encode dynamically stable PAR-3 asymmetries in the C. elegans zygote.","authors":"Lang, C. F.; Maxian, O.; Anneken, A.; Munro, E.","author_corresponding":"Edwin Munro","author_corresponding_institution":"University of Chicago","doi":"10.1101\/2023.08.04.552031","date":"2024-08-28","version":"2","type":"new results","license":"cc_by","category":"cell biology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/28\/2023.08.04.552031.source.xml","abstract":"Studies of PAR polarity have emphasized a paradigm in which mutually antagonistic PAR proteins form complementary polar domains in response to transient cues. A growing body of work suggests that the oligomeric scaffold PAR-3 can form unipolar asymmetries without mutual antagonism, but how it does so is largely unknown. Here we combine single molecule analysis and modeling to show how the interplay of two positive feedback loops promotes dynamically stable unipolar PAR-3 asymmetries in early C. elegans embryos. First, the intrinsic dynamics of PAR-3 membrane binding and oligomerization encode negative feedback on PAR-3 dissociation. Second, membrane-bound PAR-3 promotes its own recruitment through a mechanism that requires the anterior polarity proteins PAR-6 and PKC-3. Using a kinetic model tightly constrained by our experimental measurements, we show that these two feedback loops are individually required and jointly sufficient to encode dynamically stable and locally inducible unipolar PAR-3 asymmetries in the absence of posterior inhibition. Given the central role of PAR-3, and the conservation of PAR-3 membrane-binding, oligomerization, and core interactions with PAR-6\/PKC-3, these results have widespread implications for PAR-mediated polarity in metazoa.","funder":[{"name":"National Institute of General Medical Sciences","id":"https:\/\/ror.org\/04q48ey07","id-type":"ROR","award":"T32 GM007197;1R01GM098441;"}],"published":"NA","server":"bioRxiv"},{"title":"Targeting the dependence on PIK3C3-mTORC1 signaling in dormancy-prone breast cancer cells blunts metastasis initiation","authors":"Elkholi, I. E.; Robert, A.; Malouf, C.; Kuasne, H.; Drapela, S.; Macleod, G.; Hebert, S.; Pacis, A.; Calderon, V.; Kleinman, C. L.; Gomes, A. P.; Aguirre-Ghiso, J. A.; Park, M.; Angers, S.; Cote, J.-F.","author_corresponding":"Jean-Francois Cote","author_corresponding_institution":"IRCM","doi":"10.1101\/2023.08.02.551681","date":"2024-08-08","version":"3","type":"new results","license":"cc_no","category":"cancer biology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/08\/2023.08.02.551681.source.xml","abstract":"Halting breast cancer metastatic relapses following primary tumor removal and the clinical dormant phase, remains challenging, due to a lack of specific vulnerabilities to target during dormancy. To address this, we conducted genome-wide CRISPR screens on two breast cancer cell lines with distinct dormancy properties: 4T1 (short-term dormancy) and 4T07 (prolonged dormancy). We discovered that loss of class-III PI3K, Pik3c3, revealed a unique vulnerability in 4T07 cells. Surprisingly, dormancy-prone 4T07 cells exhibited higher mTORC1 activity than 4T1 cells, due to lysosome-dependent signaling occurring at the cell periphery. Pharmacological inhibition of Pik3c3 counteracted this phenotype in 4T07 cells, and selectively reduced metastasis burden only in the 4T07 dormancy-prone model. This mechanism was also detected in human breast cancer cell lines in addition to a breast cancer patient-derived xenograft supporting that it may be relevant in humans. Our findings suggest dormant cancer cell-initiated metastasis may be prevented in patients carrying tumor cells that display PIK3C3-peripheral lysosomal signaling to mTORC1.\n\nStatement of SignificanceWe reveal that dormancy-prone breast cancer cells depend on the class III PI3K to mediate a constant peripheral lysosomal positioning and mTORC1 hyperactivity. Targeting this pathway might blunt breast cancer metastasis.","funder":"NA","published":"10.1158\/0008-5472.CAN-23-2654","server":"bioRxiv"},{"title":"Topological stress triggers persistent DNA lesions in ribosomal DNA with ensuing formation of PML-nucleolar compartment","authors":"Urbancokova, A.; Hornofova, T.; Novak, J.; Salajkova, S. A.; Stemberkova Hubackova, S.; Uvizl, A.; Buchtova, T.; Mistrik, M.; Mac Stay, B.; Hodny, Z.; Bartek, J.; Vasicova, P.","author_corresponding":"Pavla Vasicova","author_corresponding_institution":"Institute of Molecular Genetics","doi":"10.1101\/2023.08.05.552131","date":"2024-08-19","version":"3","type":"confirmatory results","license":"cc_by_nc_nd","category":"cell biology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/19\/2023.08.05.552131.source.xml","abstract":"PML, a multifunctional protein, is crucial for forming PML-nuclear bodies involved in stress responses. Under specific conditions, PML associates with nucleolar caps formed after RNA polymerase I (RNAPI) inhibition, leading to PML-nucleolar associations (PNAs). This study investigates PNAs-inducing stimuli by exposing cells to various genotoxic stresses. We found that the most potent inducers of PNAs introduced topological stress and inhibited RNAPI. Doxorubicin, the most effective compound, induced double-strand breaks (DSBs) in the rDNA locus. PNAs co-localized with damaged rDNA, segregating it from active nucleoli. Cleaving the rDNA locus with I-PpoI confirmed rDNA damage as a genuine stimulus for PNAs. Inhibition of ATM, ATR kinases, and RAD51 reduced I-PpoI-induced PNAs, highlighting the importance of ATM\/ATR-dependent nucleolar cap formation and homologous recombination (HR) in their triggering. I-PpoI-induced PNAs co-localized with rDNA DSBs positive for RPA32-pS33 but deficient in RAD51, indicating resected DNA unable to complete HR repair. Our findings suggest that PNAs form in response to persistent rDNA damage within the nucleolar cap, highlighting the interplay between PML\/PNAs and rDNA alterations due to topological stress, RNAPI inhibition, and rDNA DSBs destined for HR. Cells with persistent PNAs undergo senescence, suggesting PNAs help avoid rDNA instability, with implications for tumorigenesis and aging.","funder":"NA","published":"10.7554\/elife.91304","server":"bioRxiv"},{"title":"Deficiency of Orexin Receptor Type 1 in Dopaminergic Neurons Increases Novelty-Induced Locomotion and Exploration","authors":"Xiao, X.; Yeghiazaryan, G.; Eggersmann, F.; Cremer, A. L.; Backes, H.; Kloppenburg, P.; Hausen, A. C.","author_corresponding":"Anne Christine Hausen","author_corresponding_institution":"Max Planck Institute for Metabolism Research, Department of Neuronal Control of Metabolism","doi":"10.1101\/2023.08.06.552140","date":"2024-08-16","version":"2","type":"new results","license":"cc_by","category":"neuroscience","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/16\/2023.08.06.552140.source.xml","abstract":"Orexin signaling in the ventral tegmental area and substantia nigra promotes locomotion and reward processing, but it is not clear whether dopaminergic neurons directly mediate these effects. We show that dopaminergic neurons in these areas mainly express orexin receptor subtype 1 (Ox1R). In contrast, only a minor population in the medial ventral tegmental area express orexin receptor subtype 2 (Ox2R). To analyze the functional role of Ox1R signaling in dopaminergic neurons, we deleted Ox1R specifically in dopamine transporter-expressing neurons of mice and investigated the functional consequences. Deletion of Ox1R increased locomotor activity and exploration during exposure to novel environments or when intracerebroventricularely injected with orexin A. Spontaneous activity in home cages, anxiety, reward processing, and energy metabolism did not change. Positron emission tomography imaging revealed that Ox1R signaling in dopaminergic neurons affected distinct neural circuits depending on the stimulation mode. In line with an increase of neural activity in the lateral paragigantocellular nucleus (LPGi) of Ox1R{Delta}DAT mice, we found that dopaminergic projections innervate the LPGi in regions where the inhibitory dopamine receptor subtype D2 but not the excitatory D1 subtype resides. These data suggest a crucial regulatory role of Ox1R signaling in dopaminergic neurons in novelty-induced locomotion and exploration.","funder":"NA","published":"10.7554\/elife.91716","server":"bioRxiv"},{"title":"Contrastive learning explains the emergence and function of visual category-selective regions","authors":"Prince, J. S.; Alvarez, G. A.; Konkle, T.","author_corresponding":"Jacob S. Prince","author_corresponding_institution":"Harvard University","doi":"10.1101\/2023.08.04.551888","date":"2024-08-19","version":"2","type":"new results","license":"cc_by","category":"neuroscience","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/19\/2023.08.04.551888.source.xml","abstract":"Modular and distributed coding theories of category selectivity along the human ventral visual stream have long existed in tension. Here, we present a reconciling framework - contrastive coding - based on a series of analyses relating category selectivity within biological and artificial neural networks. We discover that, in models trained with contrastive self-supervised objectives over a rich natural image diet, category-selective tuning naturally emerges for faces, bodies, scenes, and words. Further, lesions of these model units lead to selective, dissociable recognition deficits, highlighting their distinct functional roles in information processing. Finally, these pre-identified units can predict neural responses in all corresponding face-, scene-, body-, and word-selective regions of human visual cortex, under a highly constrained sparse-positive encoding procedure. The success of this single model indicates that brain-like functional specialization can emerge without category-specific learning pressures, as the system learns to untangle rich image content. Contrastive coding, therefore, provides a unifying account of object category emergence and representation in the human brain.","funder":"NA","published":"10.1126\/sciadv.adl1776","server":"bioRxiv"},{"title":"Cell-free chromatin particles from dying cells promote the induction of an immune response in human lymphocytes","authors":"Shabrish, S.; Raghuram, G. V.; Raphael, N.; Narayanan, R.; Lopes, R.; Kondhalkar, D.; Khare, N. K.; Mittra, I.","author_corresponding":"Indraneel Mittra","author_corresponding_institution":"Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre; Homi Bhabha National Institute","doi":"10.1101\/2023.08.07.551233","date":"2024-08-08","version":"2","type":"new results","license":"cc_no","category":"immunology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/08\/2023.08.07.551233.source.xml","abstract":"It is long established that cell death and immune response are closely related, although the nature of this relationship has remained unclear. We earlier reported that cell-free chromatin particles (cfChPs) released from the billions of cells that die in the body every day to enter into the blood circulation, or those that are released locally from dying cells, can readily enter into healthy cells to induce DNA damage and activate inflammatory cytokines. In this study we investigated whether cfChPs from dying cells might be the missing link between cell death and immune response. We treated human lymphocytes with cfChPs isolated from sera of healthy individuals or with cfChPs released from hypoxia-induced dying lymphocytes. We observed that cfChPs from both sources readily entered into lymphocytes to accumulate in their nuclei within 2 h. This was associated with marked activation of CD69 and release of inflammatory cytokines, as well as of p-STING and cGAS expression. The addition of the STING protein inhibitor H151 to the cfChPs treated cells abolished the release of inflammatory cytokines. These findings lead us to suggest that cfChPs from dying cells are the critical triggers of immune response which act via cGAS-STING pathway.","funder":"NA","published":"NA","server":"bioRxiv"},{"title":"Shared and distinct molecular effects of regulatory genetic variants provide insight into mechanisms of distal enhancer-promoter communication","authors":"Ray-Jones, H.; Song, Z.; Chan, L. T.; Haglund, A.; Artemov, P.; Della Rosa, M.; Ruje, L.; Burden, F.; Kreuzhuber, R.; Litovskikh, A.; Weyenbergh, E.; Brusselaers, Z.; Tan, V. X. H.; Frontini, M.; Wallace, C.; Malysheva, V.; Bottolo, L.; Vigorito, E.; Spivakov, M.","author_corresponding":"Mikhail Spivakov","author_corresponding_institution":"MRC London Institute of Medical Sciences","doi":"10.1101\/2023.08.04.551251","date":"2024-08-27","version":"3","type":"new results","license":"cc_no","category":"genetics","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/27\/2023.08.04.551251.source.xml","abstract":"Gene enhancers often form long-range contacts with promoters, but it remains unclear if enhancer activity and their chromosomal contacts are mediated by the same DNA sequences and recruited factors. We studied the effects of expression quantitative trait loci (eQTLs) on enhancer activity and promoter contacts in primary monocytes isolated from 34 individuals. Using eQTL-Capture Hi-C and a Bayesian approach considering both intra- and inter-individual variation, we initially detected 19 eQTLs associated with enhancer-eGene promoter contacts, most of which also associated with enhancer accessibility and activity. Capitalising on these shared effects, we devised a multi-modality Bayesian strategy, which identified 629 \"trimodal QTLs\" jointly associated with enhancer accessibility, eGene promoter contact, and gene expression. Causal mediation analysis and CRISPR interference revealed causal relationships between these three modalities. Many detected QTLs overlapped disease susceptibility loci and influenced the predicted binding of myeloid transcription factors, including SPI1, GABPB and STAT3. Additionally, a variant associated with PCK2 promoter contact directly disrupted a CTCF binding motif and impacted promoter insulation from downstream enhancers. Jointly, our findings suggest an inherent genetic link between the activity and connectivity of enhancers with relevance for human disease, and highlight the role of genetically-determined chromatin boundaries in gene control.","funder":"NA","published":"10.1038\/s41467-025-55900-3","server":"bioRxiv"},{"title":"Disease modification upon brief exposure to tofacitinib during chronic epilepsy.","authors":"Hoffman, O. R.; Koehler, J. L.; Espina, J. E. C.; Patterson, A.; Gohar, E.; Coleman, E.; Schoenike, B.; Espinosa-Garcia, C.; Paredes, F.; Dingledine, R.; Maguire, J.; Roopra, A.","author_corresponding":"Avtar Roopra","author_corresponding_institution":"University of Wisconsin-Madison School of Medicine and Public Health","doi":"10.1101\/2023.08.07.552299","date":"2024-08-15","version":"11","type":"new results","license":"cc_no","category":"neuroscience","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/15\/2023.08.07.552299.source.xml","abstract":"All current drug treatments for epilepsy, a neurological disorder affecting over 50 million people(1, 2) merely treat symptoms, and a third of patients do not respond to medication. There are no disease modifying treatments that may be administered briefly to patients to enduringly eliminate spontaneous seizures and reverse cognitive deficits(3, 4). Applying network approaches to rodent models and human temporal lobectomy samples at both whole tissue and single-nuclei resolutions, we observe the well-characterized pattern of rapid induction and subsequent quenching exhibited of the JAK\/STAT pathway within days of epileptogenic insult. This is followed by a resurgent activation weeks to months later with the onset of spontaneous seizures. Targeting the first wave of activation after epileptic insult does not prevent disease. However, brief inhibition of the second wave with CP690550 (Tofacitinib) (5, 6) enduringly suppresses seizures, rescues deficits in spatial memory, and alleviates epilepsy-associated histopathological alterations. Seizure suppression lasts for at least 2 months after the final dose. Using discovery-based transcriptomic analysis across models of epilepsy and validation of putative mechanisms with human data, we demonstrate a powerful approach to identifying disease modifying targets; this may be useful for other neurological disorders. With this approach, we find that reignition of inflammatory JAK\/STAT3 signaling in chronic epilepsy opens a window for disease modification with the FDA-approved, orally available drug CP690550.","funder":"NA","published":"NA","server":"bioRxiv"},{"title":"Modelling human neuronal catecholaminergic pigmentation in rodents recapitulates age-related multisystem neurodegenerative deficits","authors":"Laguna, A.; Penuelas, N.; Gonzalez-Sepulveda, M.; Nicolau, A.; Arthaud, S.; Guilliard-Sirieix, C.; Lorente-Picon, M.; Compte, J.; Miquel-Rio, L.; Xicoy, H.; Liu, J.; Parent, A.; Cuadros, T.; Romero-Gimenez, J.; Pujol, G.; Gimenez-Llort, L.; Fort, P.; Bortolozzi, A.; Carballo-Carbajal, I.; Vila, M.","author_corresponding":"Miquel Vila","author_corresponding_institution":"Vall d'Hebron Research Institute","doi":"10.1101\/2023.08.08.552400","date":"2024-08-14","version":"3","type":"new results","license":"cc_by_nc_nd","category":"neuroscience","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/14\/2023.08.08.552400.source.xml","abstract":"One key limitation in developing effective treatments for neurodegenerative diseases is the lack of models accurately mimicking the complex physiopathology of the human disease. Humans accumulate with age the pigment neuromelanin inside neurons that synthesize catecholamines. Neurons reaching the highest neuromelanin levels preferentially degenerate in Parkinsons, Alzheimers and apparently healthy aging individuals. However, this brain pigment is not taken into consideration in current animal models because common laboratory species, such as rodents, do not produce neuromelanin. Here we generate a tissue-specific transgenic mouse, termed tgNM, that mimics the human age-dependent brain-wide distribution of neuromelanin within catecholaminergic regions, based on the constitutive catecholamine-specific expression of human melanin-producing enzyme tyrosinase. We show that, in parallel to progressive human-like neuromelanin pigmentation, these animals display age-related neuronal dysfunction and degeneration affecting numerous brain circuits and body tissues, linked to motor and non-motor deficits, reminiscent of early neurodegenerative stages. This model may open new research avenues in brain aging and neurodegeneration.","funder":"NA","published":"10.1038\/s41467-024-53168-7","server":"bioRxiv"},{"title":"Dynamic organization of visual cortical networks inferred from massive spiking datasets.","authors":"Graber, C.; Vlasov, Y.; Schwing, A. G.","author_corresponding":"Yurii Vlasov","author_corresponding_institution":"University of Illinois Urbana Champaign","doi":"10.1101\/2023.08.08.552512","date":"2024-08-07","version":"4","type":"new results","license":"cc_by_nd","category":"neuroscience","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/07\/2023.08.08.552512.source.xml","abstract":"Complex cognitive functions in a mammalian brain are distributed across many anatomically and functionally distinct areas and rely on highly dynamic routing of neural activity across the network. While modern electrophysiology methods enable recording of spiking activity from increasingly large neuronal populations at a cellular level, development of probabilistic methods to extract these dynamic inter-area interactions is lagging. Here, we introduce an unsupervised machine learning model that infers dynamic connectivity across the recorded neuronal population from a synchrony of their spiking activity. As opposed to traditional population decoding models that reveal dynamics of the whole population, the model produces cellular-level cell-type specific dynamic functional interactions that are otherwise omitted from analysis. The model is evaluated on ground truth synthetic data and compared to alternative methods to ensure quality and quantification of model predictions. Our strategy incorporates two sequential stages - extraction of static connectivity structure of the network followed by inference of temporal changes of the connection strength. This two-stage architecture enables detailed statistical criteria to be developed to evaluate confidence of the model predictions in comparison with traditional descriptive statistical methods. We applied the model to analyze large-scale in-vivo recordings of spiking activity across mammalian visual cortices. The model enables the discovery of cellular-level dynamic connectivity patterns in local and long-range circuits across the whole visual cortex with temporally varying strength of feedforward and feedback drives during sensory stimulation. Our approach provides a conceptual link between slow brain-wide network dynamics studied with neuroimaging and fast cellular-level dynamics enabled by modern electrophysiology that may help to uncover often overlooked dimensions of the brain code.","funder":"NA","published":"NA","server":"bioRxiv"},{"title":"A conditional protein diffusion model generates artificial programmable endonuclease sequences with enhanced activity","authors":"Zhou, B.; Zheng, L.; Wu, B.; Yi, K.; Zhong, B.; Tan, Y.; Liu, Q.; Lio, P.; Hong, L.","author_corresponding":"Bingxin Zhou","author_corresponding_institution":"Shanghai Jiao Tong University","doi":"10.1101\/2023.08.10.552783","date":"2024-08-13","version":"2","type":"new results","license":"cc_no","category":"bioengineering","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/13\/2023.08.10.552783.source.xml","abstract":"Deep learning-based methods for generating functional proteins address the growing need for novel biocatalysts, allowing for precise tailoring of functionalities to meet specific requirements. This emergence leads to the creation of highly efficient and specialized proteins with wide-ranging applications in scientific, technological, and biomedical domains. This study establishes a pipeline for protein sequence generation with a conditional protein diffusion model, namely CPDiffusion, to deliver diverse sequences of proteins with enhanced functions. CPDiffusion accommodates protein-specific conditions, such as secondary structure and highly conserved amino acids (AAs). Without relying on extensive training data, CPDiffusion effectively captures highly conserved residues and sequence features for a specific protein family. We applied CPDiffusion to generate artificial sequences of Argonaute (Ago) proteins based on the backbone structures of wild-type (WT) Kurthia massiliensis Ago (KmAgo) and Pyrococcus furiosus Ago (PfAgo), which are complex multi-domain programmable endonucleases. The generated sequences deviate by up to nearly 400 AAs from their WT templates. Experimental tests demonstrated that the majority of generated proteins show unambiguous activity in DNA cleavage for both KmAgo and PfAgo, with many of them exhibiting superior activity as compared to the WT. These findings underscore CPDiffusions remarkable success rate to generate novel sequences for proteins of complex structures and functions in a single step with enhanced activity. This approach facilitates the design of enzymes with multi-domain molecular structures and intricate functions through in silico generation and screening, all accomplished without any supervision from labeled data.","funder":"NA","published":"10.1038\/s41421-024-00728-2","server":"bioRxiv"},{"title":"An automated convergence diagnostic for phylogenetic MCMC analyses","authors":"Berling, L.; Bouckaert, R.; Gavryushkin, A.","author_corresponding":"Alex Gavryushkin","author_corresponding_institution":"University of Canterbury","doi":"10.1101\/2023.08.10.552869","date":"2024-08-30","version":"3","type":"new results","license":"cc_by_nc_nd","category":"bioinformatics","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/30\/2023.08.10.552869.source.xml","abstract":"Assessing convergence of Markov chain Monte Carlo (MCMC) based analyses is crucial but challenging, especially so in high dimensional and complex spaces such as the space of phylogenetic trees (treespace). In practice, it is assumed that the target distribution is the unique stationary distribution of the MCMC and convergence is achieved when samples appear to be stationary. Here we leverage recent advances in computational geometry of the treespace and introduce a method that combines classical statistical techniques and algorithms with geometric properties of the treespace to automatically evaluate and assess practical convergence of phylogenetic MCMC analyses. Our method monitors convergence across multiple MCMC chains and achieves high accuracy in detecting both practical convergence and convergence issues within treespace. Furthermore, our approach is developed to allow for real-time evaluation during the MCMC algorithm run, eliminating any of the chain post-processing steps that are currently required. Our tool therefore improves reliability and efficiency of MCMC based phylogenetic inference methods and makes analyses easier to reproduce and compare. We demonstrate the efficacy of our diagnostic via a well-calibrated simulation study and provide examples of its performance on real data sets. Although our method performs well in practice, a significant part of the underlying treespace probability theory is still missing, which creates an excellent opportunity for future mathematical research in this area.\n\nThe open source package for the phylogenetic inference framework BEAST2, called ASM, that implements these methods, making them accessible through a user-friendly GUI, is available from https:\/\/github.com\/rbouckaert\/asm\/. The open source Python package, called tetres, that provides an interface for these methods enabling their applications beyond BEAST2 can be accessed at https:\/\/github.com\/bioDS\/tetres\/.","funder":"NA","published":"10.1109\/TCBB.2024.3457875","server":"bioRxiv"},{"title":"Fixational Eye Movements Enhance the Precision of Visual Information Transmitted by the Primate Retina","authors":"Wu, E. G.; Brackbill, N.; Rhoades, C. E.; Kling, A.; Gogliettino, A. R.; Shah, N. P.; Sher, A.; Litke, A. M.; Simoncelli, E. P.; Chichilnisky, E. J.","author_corresponding":"Eric Gene Wu","author_corresponding_institution":"Stanford University","doi":"10.1101\/2023.08.12.552902","date":"2024-08-26","version":"4","type":"new results","license":"cc_by","category":"neuroscience","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/26\/2023.08.12.552902.source.xml","abstract":"Fixational eye movements alter the number and timing of spikes transmitted from the retina to the brain, but whether these changes enhance or degrade the retinal signal is unclear. To quantify this, we developed a Bayesian method for reconstructing natural images from the recorded spikes of hundreds of retinal ganglion cells (RGCs) in the macaque retina (male), combining a likelihood model for RGC light responses with the natural image prior implicitly embedded in an artificial neural network optimized for denoising. The method matched or surpassed the performance of previous reconstruction algorithms, and provides an interpretable framework for characterizing the retinal signal. Reconstructions were improved with artificial stimulus jitter that emulated fixational eye movements, even when the eye movement trajectory was assumed to be unknown and had to be inferred from retinal spikes. Reconstructions were degraded by small artificial perturbations of spike times, revealing more precise temporal encoding than suggested by previous studies. Finally, reconstructions were substantially degraded when derived from a model that ignored cell-to-cell interactions, indicating the importance of stimulusevoked correlations. Thus, fixational eye movements enhance the precision of the retinal representation.","funder":"NA","published":"10.1038\/s41467-024-52304-7","server":"bioRxiv"},{"title":"A molecular proximity sensor based on an engineered, dual-component guide RNA","authors":"Choi, J.; Chen, W.; Liao, H.; Li, X.; Shendure, J.","author_corresponding":"Jay Shendure","author_corresponding_institution":"University of Washington \/ HHMI","doi":"10.1101\/2023.08.14.553235","date":"2024-08-28","version":"3","type":"new results","license":"cc_by","category":"synthetic biology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/28\/2023.08.14.553235.source.xml","abstract":"One of the goals of synthetic biology is to enable the design of arbitrary molecular circuits with programmable inputs and outputs. Such circuits bridge the properties of electronic and natural circuits, processing information in a predictable manner within living cells. Genome editing is a potentially powerful component of synthetic molecular circuits, whether for modulating the expression of a target gene or for stably recording information to genomic DNA. However, programming molecular events such as protein-protein interactions or induced proximity as triggers for genome editing remains challenging. Here we demonstrate a strategy termed \"P3 editing\", which links protein-protein proximity to the formation of a functional CRISPR-Cas9 dual-component guide RNA. By engineering the crRNA:tracrRNA interaction, we demonstrate that various known protein-protein interactions, as well as the chemically-induced dimerization of protein domains, can be used to activate prime editing or base editing in human cells. Additionally, we explore how P3 editing can incorporate outputs from ADAR-based RNA sensors, potentially allowing specific RNAs to induce specific genome edits within a larger circuit. Our strategy enhances the controllability of CRISPR-based genome editing, facilitating its use in synthetic molecular circuits deployed in living cells.","funder":"NA","published":"10.7554\/elife.98110.3","server":"bioRxiv"},{"title":"Degeneracy in negative feedback (NFBL) and incoherent feedforward (IFFL) loops: Adaptation and resonance","authors":"Ventura, A. C.; Rotstein, H. G.","author_corresponding":"Horacio G. Rotstein","author_corresponding_institution":"New Jersey Institute of Technology","doi":"10.1101\/2023.08.13.553122","date":"2024-08-31","version":"2","type":"new results","license":"cc_by_nc_nd","category":"systems biology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/31\/2023.08.13.553122.source.xml","abstract":"Degeneracy in dynamic models refers to these situations where multiple combinations of parameter values produce identical patterns for the observable variable. We investigate this phenomenon in two qualitatively different adaptive circuit mechanisms: nonlinear feedback loop (NFBL) and incoherent feedback loop (IFFL). We use minimal models of these circuit types together with analytical calculations, regular perturbation analysis, dynamical systems tools and numerical simulations. In response to constant (or step-constant) inputs, NFBLs and IFFLs produce and overshoot allowing the observable variable to return to a value closer to baseline than the peak (adaptation). We identify the dynamic principles underlying the emergence of degeneracy in adaptive patterns both within and across circuit types in representative NFBL and IFFL models in terms of biologically plausible parameters. We identify the conditions under which degeneracy persists in response to oscillatory inputs with arbitrary frequencies, giving rise to resonance and phasonance degeneracy. This naturally extends to the response of adaptive systems to time-dependent inputs within a relatively large class. By using phase-plane analysis, we provide a mechanistic, dynamical systems-based interpretation of degeneracy. Our results have implication for the understanding of adaptive systems, for the relationship between adaptive and resonant\/phasonant systems, for the understanding of complex biochemical circuits, for neuronal computation, and for the development of methods for circuit and dynamical systems reconstruction based on experimental or observational data.","funder":"NA","published":"10.1137\/23M1593814","server":"bioRxiv"},{"title":"An atypical basement membrane forms a midline barrier during left-right asymmetric gut development in the chicken embryo","authors":"Demler, C. A.; Lawlor, J. C.; Yelin, R.; Llivichuzcha-Loja, D.; Shaulov, L.; Kim, D. S.; Stewart, M. A.; Lee, F.; Shylo, N. A.; Trainor, P.; Schultheiss, T. M.; Kurpios, N. A.","author_corresponding":"Natasza A Kurpios","author_corresponding_institution":"Cornell University","doi":"10.1101\/2023.08.15.553395","date":"2024-08-08","version":"2","type":"new results","license":"cc_by_nc_nd","category":"developmental biology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/08\/2023.08.15.553395.source.xml","abstract":"Correct intestinal morphogenesis depends on the early embryonic process of gut rotation, an evolutionarily conserved program in which a straight gut tube elongates and forms into its first loops. However, the gut tube requires guidance to loop in a reproducible manner. The dorsal mesentery (DM) connects the gut tube to the body and directs the lengthening gut into stereotypical loops via left-right (LR) asymmetric cellular and extracellular behavior. The LR asymmetry of the DM also governs blood and lymphatic vessel formation for the digestive tract, which is essential for prenatal organ development and postnatal vital functions including nutrient absorption. Although the genetic LR asymmetry of the DM has been extensively studied, a divider between the left and right DM has yet to be identified. Setting up LR asymmetry for the entire body requires a Lefty1+ midline barrier to separate the two sides of the embryo, without it, embryos have lethal or congenital LR patterning defects. Individual organs including the brain, heart, and gut also have LR asymmetry, and while the consequences of left and right signals mixing are severe or even lethal, organ-specific mechanisms for separating these signals are poorly understood. Here, we uncover a midline structure composed of a transient double basement membrane, which separates the left and right halves of the embryonic chick DM during the establishment of intestinal and vascular asymmetries. Unlike other basement membranes of the DM, the midline is resistant to disruption by intercalation of Netrin4 (Ntn4). We propose that this atypical midline forms the boundary between left and right sides and functions as a barrier necessary to establish and protect organ asymmetry.","funder":"NA","published":"10.7554\/eLife.89494","server":"bioRxiv"},{"title":"Projection neurons are necessary for the maintenance of the mouse olfactory circuit.","authors":"Sanchez-Guardado, L.; Razavi, P.; Wang, B.; Callejas-Marin, A.; Lois, C.","author_corresponding":"Carlos Lois","author_corresponding_institution":"California Institute of Technology","doi":"10.1101\/2023.08.14.553299","date":"2024-08-07","version":"2","type":"confirmatory results","license":"cc_by_nc_nd","category":"neuroscience","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/07\/2023.08.14.553299.source.xml","abstract":"The assembly and maintenance of neural circuits is crucial for proper brain function. Although the assembly of brain circuits has been extensively studied, much less is understood about the mechanisms controlling their maintenance as animals mature. In the olfactory system, the axons of olfactory sensory neurons (OSNs) expressing the same odor receptor converge into discrete synaptic structures of the olfactory bulb (OB) called glomeruli, forming a stereotypic odor map. The OB projection neurons, called mitral and tufted cells (M\/Ts), have a single dendrite that branches into a single glomerulus, where they make synapses with OSNs. We used a genetic method to progressively eliminate the vast majority of M\/T cells in early postnatal mice, and observed that the assembly of the OB bulb circuits proceeded normally. However, as the animals became adults the apical dendrite of remaining M\/Ts grew multiple branches that innervated several glomeruli, and OSNs expressing single odor receptors projected their axons into multiple glomeruli, disrupting the olfactory sensory map. Moreover, ablating the M\/Ts in adult animals also resulted in similar structural changes in the projections of remaining M\/Ts and axons from OSNs. Interestingly, the ability of these mice to detect odors was relatively preserved despite only having 1-5% of projection neurons transmitting odorant information to the brain, and having highly disrupted circuits in the OB. These results indicate that a reduced number of projection neurons does not affect the normal assembly of the olfactory circuit, but induces structural instability of the olfactory circuitry of adult animals.","funder":"NA","published":"10.7554\/elife.90296.3","server":"bioRxiv"},{"title":"A novel visual analysis interface enables integrative analyses of cancer transcriptomics data and iden-tifies potential markers of immunotherapy response via machine learning.","authors":"Kus, M. E.; Sahin, C.; Kilic, E.; Askin, A.; Ozgur, M. M.; Karahanogullari, G.; Aksit, A.; O'Connell, R. M.; Ekiz, H. A.","author_corresponding":"H. Atakan Ekiz","author_corresponding_institution":"Izmir Institute of Technology","doi":"10.1101\/2023.08.14.553075","date":"2024-08-11","version":"2","type":"new results","license":"cc_no","category":"bioinformatics","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/11\/2023.08.14.553075.source.xml","abstract":"The Cancer Genome Atlas (TCGA) initiative has been essential for revealing key mechanisms in human cancer leading to the development of novel therapeutics. Analysis of the cancer transcriptomics data in the TCGA and other public repositories require coding skills that are associated with a steep learning curve for most non-specialists. To enable a wider utilization of these data, we introduce The Cancer Genome Explorer (TCGEx), a web-based visual data analysis interface that can perform a number of sophisticated analyses ranging from survival modeling and gene set enrichment analysis to unsupervised clustering and linear regression-based machine learning. In addition to providing access to preprocessed data from TCGA and immune checkpoint inhibition studies on cBioportal and CRI-iAtlas, the TCGEx platform allows users to upload and investigate their own data. Using this tool, we investigated the molecular subsets of human melanoma and identified microRNAs associated with intratumoral interferon signaling. We validated these findings using independent data from clinical trials involving immune check-point inhibitors for melanoma and other cancers. Moreover, our analyses unveiled a subset of cytokines predictive of positive responses to diverse immune checkpoint inhibitors prior to treatment initiation. Built on the R\/Shiny framework, TCGEx modules offer customizable features to tailor the analysis to different study contexts and help generate publication-ready plots. TCGEx is freely available at https:\/\/tcgex.iyte.edu.tr, and it provides an interactive solution to extract meaningful insights from cancer transcriptomics data and guide scientific inquiry.","funder":"NA","published":"10.1038\/s44319-025-00407-7","server":"bioRxiv"},{"title":"Decoding reveals the neural representation of perceived and imagined musical sounds","authors":"Quiroga-Martinez, D. R.; Fernandez-Rubio, G.; Bonetti, L.; Achyutuni, K. G.; Tzovara, A.; Knight, R. T.; Vuust, P.","author_corresponding":"David Ricardo Quiroga-Martinez","author_corresponding_institution":"University of California at Berkeley","doi":"10.1101\/2023.08.15.553456","date":"2024-08-20","version":"3","type":"new results","license":"cc_by_nc","category":"neuroscience","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/20\/2023.08.15.553456.source.xml","abstract":"Vividly imagining a song or a melody is a skill that many people accomplish with relatively little effort. However, we are only beginning to understand how the brain represents, holds, and manipulates these musical \"thoughts\". Here, we decoded perceived and imagined melodies from magnetoencephalography (MEG) brain data (N = 71) to characterize their neural representation. We found that, during perception, auditory regions represent the sensory properties of individual sounds. In contrast, a widespread network including fronto-parietal cortex, hippocampus, basal nuclei, and sensorimotor regions hold the melody as an abstract unit during both perception and imagination. Furthermore, the mental manipulation of a melody systematically changes its neural representation, reflecting volitional control of auditory images. Our work sheds light on the nature and dynamics of auditory representations, informing future research on neural decoding of auditory imagination.","funder":"NA","published":"10.1371\/journal.pbio.3002858","server":"bioRxiv"},{"title":"Tertiary lymphoid structures are associated with enhanced macrophage activation, immune checkpoint expression and predict outcome in cervical cancer.","authors":"Gorvel, L.; Panouillot, M.; Rouviere, M.-S.; Billon, E.; Fattori, S.; Sonongbua, J.; Boucherit, N.; Ben Amara, A.; Quilichini, O.; GRANJEAUD, S.; Degos, C.; Carcopino, X.; Lambaudie, E.; Chretien, A.-S.; Sabatier, R.; Dieu-Nosjean, M.-C.; Olive, D.","author_corresponding":"Laurent Gorvel","author_corresponding_institution":"Immunity and Cancer Team, Cancer Research Center of Marseille, CRCM, INSERM U1068, CNRS UMR7258, Aix-Marseille University U105, Marseille, France","doi":"10.1101\/2023.08.17.552583","date":"2024-08-13","version":"2","type":"new results","license":"cc_by_nc_nd","category":"immunology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/13\/2023.08.17.552583.source.xml","abstract":"BackgroundCervical tumors are usually treated using surgery, chemotherapy, and radiotherapy, and would benefit from immunotherapies. However, the immune microenvironment in cervical cancer remains poorly described. Tertiary lymphoid structures (TLS) were recently described as markers for better immunotherapy response and overall better prognosis in cancer patients.\n\nMethodsWe integratedly evaluated the cervical tumor immune microenvironment, and specifically TLS importance, using combined high-throughput phenotyping, soluble factor dosage, spatial interaction analyses, and statistical analyses.\n\nResultsWe demonstrate that TLS presence is associated with a more inflammatory soluble microenvironment, with the presence of B cells as well as more activated macrophages and dendritic cells (DCs). Furthermore, this myeloid cell activation is associated with expression of immune checkpoints, such as PD-L1 and CD40, and close proximity of activated conventional DC2 to CD8+ T cells, therefore indicating better immune interactions and tumor control. Finally, we associate TLS presence, greater B cell density, and activated DC density to improved progression-free survival, and present it as an additional prognostic marker.\n\nConclusionTo conclude, our results provide an exhaustive depiction of the cervical tumor immune microenvironment where TLS presence marks cell activation and immunotherapy target expression. These findings provide predictive clues for patient response to targeted immunotherapies.\n\nSignificanceTLS maturation stratifies cervical cancer patients and associates with improved prognosis. TLS associate with the expression of immune checkpoints, notably in the macrophage compartment, which may represent a new therapeutic strategy.","funder":"NA","published":"10.1158\/2326-6066.CIR-24-0979","server":"bioRxiv"},{"title":"Neural signatures of attentional prioritization and facilitation in accessing repeated items inVisual Working memory","authors":"Narvaria, A. S.; Banerjee, A.; Roy, D.","author_corresponding":"Dipanjan Roy","author_corresponding_institution":"Indian Institute of Technology Jodhpur","doi":"10.1101\/2023.08.18.553911","date":"2024-08-07","version":"2","type":"new results","license":"cc_by","category":"neuroscience","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/07\/2023.08.18.553911.source.xml","abstract":"Visual Working memory (VWM) is a limited-capacity system where working memory items compete for retrieval. Some items are maintained in the working memory in the \"region of direct access,\" which holds information readily available for processing, while other items are in a passive or activated long-term memory state and require cognitive control. Moreover, their recognition requires moving from the most active template in VWM to another one with the shift of attention. Stimulus properties based on similarity can link items together, which can facilitate their retrieval due to prioritization. To investigate the neural dynamics of differential processing of repeated versus not-repeated items in working memory, we designed a modified Sternberg task for testing recognition in a VWM-based EEG study where human participants respond to a probe for an items presence or absence in the representation of an encoded memory array containing repeated and not repeated items. Significantly slower response times and comparatively poor accuracy for recognising not-repeated items suggest that they are not prioritized. We identified specific differences in spectral perturbations for sensor clusters in the power of different frequency bands as the neural correlate of probe matching for not-repeated vs. repeated conditions, reflecting biased access to VWM items. For not-repeated item probe matching, delay in beta desynchronization suggests poor memory-guided action selection behaviour. An increase in frontal theta and parietal alpha power demonstrated a demand for stronger cognitive control for retrieving items for not-repeated probe matching by shielding them from distracting repeated items. In summary, our study provides crucial empirical evidence of facilitation and prioritization of repeated items over non-repeated items and explains the probable role of different EEG rhythms in facilitated recognition of repeated items over goal-relevant, not-repeated items in VWM.","funder":[{"name":"Science and Engineering Research Board","id":"https:\/\/ror.org\/03ffdsr55","id-type":"ROR","award":"Core Research Grant (CRG) S\/SERB\/DPR\/20230033;"}],"published":"10.3389\/fnhum.2025.1642615","server":"bioRxiv"},{"title":"Shared and distinct neural signatures of feature and spatial attention","authors":"Yang, A.; Tian, J.; Wang, W.; Liu, J.; Zhou, L.; Zhou, K.","author_corresponding":"Ke Zhou","author_corresponding_institution":"Beijing Normal University","doi":"10.1101\/2023.08.20.554014","date":"2024-08-25","version":"2","type":"new results","license":"cc_no","category":"neuroscience","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/25\/2023.08.20.554014.source.xml","abstract":"The debate on whether feature attention (FA) and spatial attention (SA) share a common neural mechanism remains unresolved. Previous neuroimaging studies have identified fronto-parietal-temporal attention-related regions that exhibited consistent activation during various visual attention tasks. However, these studies have been limited by small sample sizes and methodological constraints inherent in univariate analysis. Here, we utilized a between-subject whole-brain machine learning approach with a large sample size (N = 235) to investigate the neural signatures of FA (FAS) and SA (SAS). Both FAS and SAS showed cross-task predictive capabilities, though inter-task prediction was weaker than intra-task prediction, suggesting both shared and distinct mechanisms. Specifically, the frontoparietal network exhibited the highest predictive performance for FA, while the visual network excelled in predicting SA, highlighting their respective prominence in the two attention processes. Moreover, both signatures demonstrated distributed representations across large-scale brain networks, as each cluster within the signatures was sufficient for predicting FA and SA, but none of them were deemed necessary for either FA or SA. Our study challenges traditional network-centric models of attention, emphasizing distributed brain functioning in attention, and provides comprehensive evidence for shared and distinct neural mechanisms underlying FA and SA.","funder":"NA","published":"10.1016\/j.neuroimage.2025.121296","server":"bioRxiv"},{"title":"Slow but flexible or fast but rigid? Discrete and continuous processes compared","authors":"Priorelli, M.; Stoianov, I. P.","author_corresponding":"Ivilin Peev Stoianov","author_corresponding_institution":"National Research Council","doi":"10.1101\/2023.08.20.554008","date":"2024-08-10","version":"3","type":"new results","license":"cc_by_nc_nd","category":"neuroscience","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/10\/2023.08.20.554008.source.xml","abstract":"AO_SCPLOWBSTRACTC_SCPLOWA tradeoff exists when dealing with complex tasks composed of multiple steps. High-level cognitive processes can find the best sequence of actions to achieve a goal in uncertain environments, but they are slow and require significant computational demand. In contrast, lower-level processing allows reacting to environmental stimuli rapidly, but with limited capacity to determine optimal actions or to replan when expectations are not met. Through reiteration of the same task, biological organisms find the optimal tradeoff: from action primitives, composite trajectories gradually emerge by creating task-specific neural structures. The two frameworks of active inference - a recent brain paradigm that views action and perception as subject to the same free energy minimization imperative - well capture high-level and low-level processes of human behavior, but how task specialization occurs in these terms is still unclear. In this study, we compare two strategies on a dynamic pick-and-place task: a hybrid (discrete-continuous) model with planning capabilities and a continuous-only model with fixed transitions. Both models rely on a hierarchical (intrinsic and extrinsic) structure, well suited for defining reaching and grasping movements, respectively. Our results show that continuous-only models perform better and with minimal resource expenditure but at the cost of less flexibility. Finally, we propose how discrete actions might lead to continuous attractors and compare the two frameworks with different motor learning phases, laying the foundations for further studies on bio-inspired task adaptation.","funder":"NA","published":"10.1016\/j.heliyon.2024.e39129","server":"bioRxiv"},{"title":"Plasticity, geographic variation and trait coordination in blue oak drought physiology","authors":"Anderegg, L. D. L.; Skelton, R. P.; Diaz, J.; Papper, P.; Ackerly, D. D.; Dawson, T. D. L.","author_corresponding":"Leander D.L. Anderegg","author_corresponding_institution":"University of California, Berkeley","doi":"10.1101\/2023.08.20.553748","date":"2024-08-29","version":"2","type":"new results","license":"cc_by_nc","category":"ecology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/29\/2023.08.20.553748.source.xml","abstract":"Our ability to predict drought stress across the landscape remains limited. This uncertainty stems in part from an incomplete understanding of within-species variation in hydraulic physiology, particularly coordinated variation across multiple traits. This variation reflects genetic differentiation among populations (ecotypic variation) and phenotypic plasticity. We examined among-population differentiation in morphological and hydraulic traits in California blue oak (Quercus douglasii) using a 30 year-old common garden. We compared trait differentiation and trait-trait coordination in the garden to wild phenotypes from the original source populations. We found remarkably limited among-population differentiation in all traits in the common garden but considerable site-to-site variation in the field that could rarely be explained with site climate variables. Trait-trait relationships were also stronger in the field than in the garden, particularly links between leaf morphology, leaf hydraulic efficiency and stem hydraulic efficiency. Only four trait-trait relationship were present in both the wild and garden, but 12 of 45 relationships showed significant wild phenotypic correlations, with strong coordination among leaf and stem hydraulic efficiency apparently mediated by leaf size. Ultimately, we found limited evidence for ecotypic variation but considerable geographic in phenotypic integration in the wild, suggesting considerable acclimation potential in the face of climate change.","funder":"NA","published":"NA","server":"bioRxiv"},{"title":"Evolution of resistance and disease tolerance mechanisms to oral bacterial infection in D. melanogaster","authors":"Paulo, T. F.; Akyaw, P. A.; Paixao, T.; Sucena, E.","author_corresponding":"Elio Sucena","author_corresponding_institution":"Faculdade de Ciencias da Universidade de Lisboa","doi":"10.1101\/2023.08.23.554397","date":"2024-08-21","version":"2","type":"new results","license":"cc_by_nc","category":"evolutionary biology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/21\/2023.08.23.554397.source.xml","abstract":"Pathogens exert strong selection on hosts, that evolve and deploy different defensive strategies, namely minimizing pathogen exposure (avoidance), directly promoting pathogen elimination (resistance), and\/or managing the deleterious effects of illness (disease tolerance). However, how the response to pathogens partitions across these processes has never been directly assessed in a single system, let alone in the context of known adaptive trajectories under controlled selection regimes. Here, an experimental evolution system composed of D. melanogaster and its natural pathogen P. entomophila is used to independently assess the role of behavioural traits, and of resistance and disease tolerance mechanisms on host evolution. We compare one replicate of a population adapted to oral infection with P. entomophila (BactOral) to a replicate of its control population to find no evidence for behavioural change but measurable differences in both resistance and disease tolerance. In BactOral, we identify a relative decrease in bacterial loads correlated with an increase in gut production of specific AMPs, but no differences in bacterial intake, in gut cell renewal rate, or in the rate of bacterial defecation, pointing to a strengthening in resistance. Additionally, we posit that disease tolerance also contributes to the adaptive response of the BactOral population through a tighter control of its immune response and of the deleterious effects of exposure. This study reveals a genetically complex and mechanistically multi-layered response, possibly reflecting the structure of adaptation to infection in natural populations.","funder":"NA","published":"NA","server":"bioRxiv"},{"title":"Rapid turnover of centromeric DNA reveals signatures of genetic conflict in Drosophila","authors":"Courret, C.; Hemmer, L.; Wei, X.; Patel, P. D.; Santinello, B.; Fuda, N. J.; Geng, X.; Chang, C.-H.; Mellone, B.; Larracuente, A. M.","author_corresponding":"Cecile Courret","author_corresponding_institution":"University of rochester","doi":"10.1101\/2023.08.22.554357","date":"2024-08-10","version":"2","type":"new results","license":"cc_by_nc_nd","category":"evolutionary biology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/10\/2023.08.22.554357.source.xml","abstract":"Centromeres reside in rapidly evolving, repeat-rich genomic regions, despite their essential function in chromosome segregation. Across organisms, centromeres are rich in selfish genetic elements such as transposable elements and satellite DNAs that can bias their transmission through meiosis. However, these elements still need to cooperate at some level and contribute to, or avoid interfering with, centromere function. To gain insight into the balance between conflict and cooperation at centromeric DNA, we take advantage of the close evolutionary relationships within the Drosophila simulans clade - D. simulans, D. sechellia, and D. mauritiana - and their relative, D. melanogaster. Using chromatin profiling combined with high resolution fluorescence in situ hybridization on stretched DNA, we characterize all centromeres across these species. We discovered dramatic centromere reorganization involving recurrent shifts between retroelements and satellite DNAs over short evolutionary timescales. We also reveal the recent origin (<240 Kya) of telocentric chromosomes in D. sechellia, where the X and 4th centromeres now sit on telomere-specific retroelements. Finally, the Y chromosome centromeres, which are the only chromosomes that do not experience female meiosis, do not show dynamic cycling between satDNA and TEs. The patterns of rapid centromere turnover in these species are consistent with genetic conflicts in the female germline and have implications for centromeric DNA function and karyotype evolution. Regardless of the evolutionary forces driving this turnover, the rapid reorganization of centromeric sequences over short evolutionary timescales highlights their potential as hotspots for evolutionary innovation.","funder":"NA","published":"10.1371\/journal.pbio.3002911","server":"bioRxiv"},{"title":"hnRNPA1 RGG-box acts a \"catalyst\" in UP1-induced destabilization of RNA and DNA telomeric G-Quadruplexes","authors":"Balasubramanian, S.; Roy, I.; Appadurai, R.; Srivastava, A.","author_corresponding":"Anand Srivastava","author_corresponding_institution":"Indian Institute of Science","doi":"10.1101\/2023.08.21.554222","date":"2024-08-17","version":"2","type":"new results","license":"cc_by","category":"biophysics","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/17\/2023.08.21.554222.source.xml","abstract":"hnRNPA1, a protein from the heterogeneous-nuclear ribonucleoprotein fam-ily, mediates cellular processes such as RNA metabolism and DNA telomere maintenance. Besides the folded RNA recognition motifs, hnRNPA1 has a [~] 135 amino-acids long low-complexity domain (LCD) consisting of an RGG-rich region and a prion-like domain (PrLD). Biochemical data suggest that RGG-rich region modulates recognition of G-quadruplexes (GQs) in the telomeric repeats. Here, we utilize an in-house developed replica exchange technique (REHT) to generate the heterogeneous conformation ensemble of hnRNPA1-RGG and explore its functional significance in telomere maintenance. Single chain statistics and abundance of structural motifs, as well as consistency with experimentally reported struc-tural data, suggest faithful recapitulation of local interactions. We also introduce a protocol to generate functionally significant IDP-nucleic acid complex structures that corroborate well with the experimental knowledge of their binding. We find that RGG-box preferentially binds to the grooves and loops of GQs providing specificity towards certain GQ structures with its Phe, Tyr, and Asn residues forming essential hydrogen bonds and electrostatic interactions. Several of these residues were also identified as important by the reported HSQC chemical shift data. Our binding and simulations studies also revealed that a minor population of the RGG-box can destabilize telomeric GQs, thereby expediting the unfolding activities of hnRNPA1-UP1 at the telomeric end.","funder":"NA","published":"NA","server":"bioRxiv"},{"title":"eGADA: enhanced Genomic Alteration Detection Algorithm, a fast genomic segmentation algorithm based on Sparse Bayesian Learning","authors":"Huang, Y. S.","author_corresponding":"Yu S. Huang","author_corresponding_institution":"WuXi Genecast Biotechnology Inc.","doi":"10.1101\/2023.08.20.553622","date":"2024-08-26","version":"3","type":"new results","license":"cc_by_nc","category":"bioinformatics","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/26\/2023.08.20.553622.source.xml","abstract":"eGADA is an enhanced version of GADA, which is a fast segmentation algorithm utilizing the Sparse Bayesian Learning (or Relevance Vector Machine) technique from Tipping 2001. It can be applied to array intensity data, NGS sequencing coverage data, or any sequential data that displays characteristics of stepwise functions. Improvements by eGADA over GADA include: a) a customized Red-Black tree to expedite the final backward elimination step of GADA; b) code in C++, which is safer and better structured than C; c) use Boost libraries extensively to provide user-friendly help and commandline argument processing; d) user-friendly input and output formats; e) export a dynamic library eGADA.so (packaged via Boost.Python) that offers API to Python; f) other bug fixes\/optimization. The code is published at https:\/\/github.com\/polyactis\/eGADA.","funder":"NA","published":"NA","server":"bioRxiv"},{"title":"Examining dynamics of three-dimensional genome organization with multi-task matrix factorization","authors":"Lee, D.-I.; Roy, S.","author_corresponding":"Sushmita Roy","author_corresponding_institution":"University of Wisconsin - Madison, Wisconsin Institute for Discovery","doi":"10.1101\/2023.08.25.554883","date":"2024-08-17","version":"2","type":"new results","license":"cc_by_nc_nd","category":"bioinformatics","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/17\/2023.08.25.554883.source.xml","abstract":"Three-dimensional (3D) genome organization, which determines how the DNA is packaged inside the nucleus, has emerged as a key component of the gene regulation machinery. High-throughput chromosome conformation datasets, such as Hi-C, have become available across multiple conditions and timepoints, offering a unique opportunity to examine changes in 3D genome organization and link them to phenotypic changes in normal and diseases processes. However, systematic detection of higher-order structural changes across multiple Hi-C datasets remains a major challenge. Existing computational methods either do not model higher-order structural units or cannot model dynamics across more than two conditions of interest. We address these limitations with Tree-Guided Integrated Factorization (TGIF), a generalizable multi-task Non-negative Matrix Factorization (NMF) approach that can be applied to time series or hierarchically related biological conditions. TGIF can identify large-scale changes at compartment or subcompartment levels, as well as local changes at boundaries of topologically associated domains (TADs). Compared to existing methods, TGIF boundaries are more enriched in CTCF and reproducible across biological replicates, normalization methods, depths, and resolutions. Application to three multi-sample mammalian datasets shows TGIF can detect differential regions at compartment, subcompartment, and boundary levels that are associated with significant changes in regulatory signals and gene expression enriched in tissue-specific processes. Finally, we leverage TGIF boundaries to prioritize sequence variants for multiple phenotypes from the NHGRI GWAS catalog. Taken together, TGIF is a flexible tool to examine 3D genome organization dynamics across disease and developmental processes.","funder":"NA","published":"NA","server":"bioRxiv"},{"title":"Local organization of spatial and shape information in the primate prefrontal cortex","authors":"Sun, Y.; Dang, W.; Jaffe, R. G.; Constantinidis, C.","author_corresponding":"Christos Constantinidis","author_corresponding_institution":"Vanderbilt University","doi":"10.1101\/2023.08.26.554962","date":"2024-08-31","version":"2","type":"new results","license":"cc_no","category":"neuroscience","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/31\/2023.08.26.554962.source.xml","abstract":"The current understanding of sensory and motor cortical areas has been defined by the existence of topographical maps across the brain surface, however, higher cortical areas, such as the prefrontal cortex, seem to lack an equivalent organization, and only limited evidence of functional clustering of neurons with similar stimulus properties is evident in them. We thus sought to examine whether neurons that represent similar spatial and object information are clustered in the monkey prefrontal cortex and whether such an organization only emerges as a result of training. To this end, we analyzed neurophysiological recordings from male macaque monkeys before and after training in spatial and shape working memory tasks. Neurons with similar spatial or shape selectivity were more likely than chance to be encountered at short distances from each other. Some aspects of organization were present even in naive animals, however other changes appeared after cognitive training. Our results reveal that prefrontal microstructure automatically supports orderly representations of spatial and object information.","funder":"NA","published":"10.1093\/cercor\/bhae384","server":"bioRxiv"},{"title":"Molecular Mechanism of PP2A\/B55\u03b1 Phosphatase Inhibition by IER5","authors":"Cao, R.; Jones, D. T.; Pan, L.; Wang, S.; Padi, S. K. R.; Rawson, S.; Aster, J. C.; Blacklow, S. C.","author_corresponding":"Stephen C Blacklow","author_corresponding_institution":"Harvard Medical School","doi":"10.1101\/2023.08.29.555174","date":"2024-08-26","version":"2","type":"new results","license":"cc_by_nc_nd","category":"biochemistry","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/26\/2023.08.29.555174.source.xml","abstract":"PP2A serine\/threonine phosphatases are heterotrimeric complexes that execute many essential physiologic functions. These activities are modulated by additional regulatory proteins, such as ARPP19, FAM122A, and IER5. Here, we report the cryoelectron microscopy structure of a complex of PP2A\/B55 with the N-terminal structured region of IER5 (IER5-N50), which occludes a surface on B55 used for substrate recruitment, and show that IER5-N50 inhibits PP2A\/B55 catalyzed dephosphorylation of pTau in biochemical assays. Mutations of full-length IER5 that disrupt its PP2A\/B55 interface interfere with co-immunoprecipitation of PP2A\/B55. These mutations and deletions that remove the nuclear localization sequence of IER5 suppress cellular events such as KRT1 expression that depend on association of IER5 with PP2A\/B55. Querying the Alphafold2 predicted structure database identified SERTA domain proteins as high-confidence PP2A\/B55-binding structural homologs of IER5-N50. These studies define the molecular basis of PP2A\/B55 inhibition by IER5-family proteins and suggest a roadmap for selective pharmacologic modulation of PP2A\/B55 complexes.","funder":"NA","published":"10.1016\/j.chembiol.2025.03.004","server":"bioRxiv"},{"title":"Water and chloride as allosteric inhibitors in WNK kinase osmosensing","authors":"Goldsmith, E. J.; Teixeira, L. R.; Radha, A.; Humphreys, J. M.; He, H.","author_corresponding":"Elizabeth J Goldsmith","author_corresponding_institution":"University of Texas Southwestern Medical Center","doi":"10.1101\/2023.08.29.555411","date":"2024-08-26","version":"2","type":"new results","license":"cc_no","category":"biophysics","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/26\/2023.08.29.555411.source.xml","abstract":"Osmotic stress and chloride regulate the autophosphorylation and activity of the WNK1 and WNK3 kinase domains. The kinase domain of unphosphorylated WNK1 (uWNK1) is an asymmetric dimer possessing water molecules conserved in multiple uWNK1 crystal structures. Conserved waters are present in two networks, referred to here as conserved water networks 1 and 2 (CWN1and CWN2). Here we show that PEG400 applied to crystals of dimeric uWNK1 induces de-dimerization. Both the WNK1 the water networks and the chloride binding site and are disrupted by PEG400. CWN1 is surrounded by a cluster of pan-WNK-conserved charged residues. Here we mutagenized these charges in WNK3, a highly active WNK isoform kinase domain, and WNK1, the isoform best studied crystallographically. Mutation of E314 in the Activation Loop of WNK3 (WNK3\/E314Q and WNK3\/E314A, and the homologous WNK1\/E388A) enhanced the rate of autophosphorylation, and reduced chloride sensitivity. Other WNK3 Cluster mutants reduced the rate of autophosphorylation activity coupled with greater chloride sensitivity than wild-type. The water and chloride regulation thus appear linked. The lower activity of some mutants may reflect effects on catalysis. Crystallography showed that activating mutants introduced conformational changes in similar parts of the structure to those induced by PEG400. WNK activating mutations and crystallography support a role for CWN1 in WNK inhibition consistent with water functioning as an allosteric ligand.","funder":"NA","published":"10.7554\/eLife.88224.3","server":"bioRxiv"},{"title":"Mitochondrial calcium modulates odor-mediated behavioral plasticity in C. elegans","authors":"Lee, H. K.; Joo, D.-K.; Park, K.-S.; Yoon, K.-h.","author_corresponding":"Kyoung-hye Yoon","author_corresponding_institution":"Yonsei University Wonju College of Medicine","doi":"10.1101\/2023.08.29.555059","date":"2024-08-20","version":"2","type":"new results","license":"cc_by_nc_nd","category":"neuroscience","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/20\/2023.08.29.555059.source.xml","abstract":"Despite growing understanding of the various roles mitochondria play in neurons, how they contribute to higher brain functions such as learning and memory remains underexplored. Here, using the nematode Caenorhabditis elegans, we found that the mitochondrial calcium uniporter (MCU) pore forming unit MCU-1 is required for aversive learning to specific odors sensed by a single sensory neuron, AWCON. MCU-1 expression was required in the sensory neuron at the time of odor conditioning for proper behavioral response to 60 min of prolonged odor exposure. Through genetic and pharmacological manipulation, we show evidence that MCU is activated in response to prolonged odor conditioning, causing mtROS production, leading to NLP-1 secretion. Finally, we show that the timing of MCU activation and neuropeptide release correspond with the OFF-neuron properties of the AWC neuron, suggesting that mitochondrial calcium entry and neuropeptide secretion coincide with AWC activation upon odor removal. Overall, our results demonstrate that, by regulating mitochondrial calcium influx, mitochondria can modulate the synaptic response to incoming stimuli in the sensory neuron, resulting in learning and modified behavior.","funder":"NA","published":"NA","server":"bioRxiv"},{"title":"The exocyst complex controls multiple events in the pathway of regulated exocytosis.","authors":"Freire, S. S.; Perez-Pandolfo, S.; Fresco, S. M.; Valinoti, J.; Sorianello, E.; Wappner, P.; Melani, M.","author_corresponding":"Mariana Melani","author_corresponding_institution":"Fundaci\u00f3n Instituto Leloir","doi":"10.1101\/2023.08.31.555734","date":"2024-08-19","version":"2","type":"new results","license":"cc_no","category":"cell biology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/19\/2023.08.31.555734.source.xml","abstract":"Eukaryotic cells depend on exocytosis to direct intracellularly synthesized material towards the extracellular space or the plasma membrane, so exocytosis constitutes a basic function for cellular homeostasis and communication between cells. The secretory pathway includes biogenesis of secretory granules (SGs), their maturation and fusion with the plasma membrane (exocytosis), resulting in release of SG content to the extracellular space. The larval salivary gland of Drosophila melanogaster is an excellent model for studying exocytosis. This gland synthesizes mucins that are packaged in SGs that sprout from the trans-Golgi network and then undergo a maturation process that involves homotypic fusion, condensation and acidification. Finally, mature SGs are directed to the apical domain of the plasma membrane with which they fuse, releasing their content into the gland lumen. The exocyst is a hetero-octameric complex that participates in tethering of vesicles to the plasma membrane during constitutive exocytosis. By precise temperature-dependent gradual activation of the Gal4-UAS expression system, we have induced different levels of silencing of exocyst complex subunits, and identified three temporarily distinctive steps of the regulated exocytic pathway where the exocyst is critically required: SG biogenesis, SG maturation and SG exocytosis. Our results shed light on previously unidentified functions of the exocyst along the exocytic pathway. We propose that the exocyst acts as a general tethering factor in various steps of this cellular process.\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=124 HEIGHT=200 SRC=\"FIGDIR\/small\/555734v2_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (33K):\norg.highwire.dtl.DTLVardef@4057f5org.highwire.dtl.DTLVardef@4ed694org.highwire.dtl.DTLVardef@1e9a859org.highwire.dtl.DTLVardef@12b971f_HPS_FORMAT_FIGEXP  M_FIG O_FLOATNOGraphical abstract.C_FLOATNO Proposed model of the action of the exocyst in maintenance of normal Golgi complex structure, maturation and exocytosis of secretory granules in Drosophila larval salivary gland cells.\n\n1-Before secretory granule (SG) biogenesis (<96 hours AEL), the exocyst (pink dots) localizes at the Golgi complex, where it is required to maintain the normal Golgi structure. The mucine Sgs3 (brown dots) moves through the secretory pathway from the endoplasmic reticulum (ER) to the Golgi complex, from where immature SGs containing the mucine sprout out. 2-After sprouting, SGs undergo maturation (96-116 hours AEL). During maturation, the exocyst localizes in between immature SGs, where it is required for homotypic fusion. The exocyst is also required for incorporation of maturation factors to the membrane of SGs. These maturation factors include Syt-1 (purple line), DC63 (orange line), Rab11 (green oval) and Rab1 (light blue oval). At this stage, the exocyst no longer localizes at the Golgi complex. 3-When maturation has been completed SGs fuse with the apical plasma membrane and exocytosis takes place. During exocytosis (116-120 hours AEL), the exocyst localizes at mature SGs, in contact with the apical plasma membrane, where it is required for tethering and subsequent fusion, prior to release of the SG content to the salivary gland lumen.\n\nC_FIG","funder":"NA","published":"10.7554\/elife.92404.3","server":"bioRxiv"},{"title":"Full-length direct RNA sequencing uncovers stress-granule dependent RNA decay upon cellular stress","authors":"Dar, S. A.; Malla, S.; Martinek, V.; Payea, M. J.; Lee, C. T.-Y.; Martin, J.; Khandeshi, A. J.; Martindale, J. L.; Belair, C.; Maragkakis, M.","author_corresponding":"Manolis Maragkakis","author_corresponding_institution":"National Institute on Aging, NIH","doi":"10.1101\/2023.08.31.555629","date":"2024-08-27","version":"3","type":"new results","license":"cc0","category":"cell biology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/27\/2023.08.31.555629.source.xml","abstract":"Cells react to stress by triggering response pathways, leading to extensive alterations in the transcriptome to restore cellular homeostasis. The role of RNA metabolism in shaping the cellular response to stress is vital, yet the global changes in RNA stability under these conditions remain unclear. In this work, we employ direct RNA sequencing with nanopores, enhanced by 5 end adaptor ligation, to comprehensively interrogate the human transcriptome at single-molecule and nucleotide resolution. By developing a statistical framework to identify robust RNA length variations in nanopore data, we find that cellular stress induces prevalent 5 end RNA decay that is coupled to translation and ribosome occupancy. Unlike typical RNA decay models in normal conditions, we show that stress-induced RNA decay is dependent on XRN1 but does not depend on deadenylation or decapping. We observed that RNAs undergoing decay are predominantly enriched in the stress granule transcriptome while inhibition of stress granule formation via genetic ablation of G3BP1 and G3BP2 rescues RNA length. Our findings reveal RNA decay as a key determinant of RNA metabolism upon cellular stress and dependent on stress-granule formation.","funder":"NA","published":"10.7554\/elife.96284.3","server":"bioRxiv"},{"title":"Homeostasis of cytoplasmic crowding by cell wall fluidization and ribosomal counterions","authors":"Mukherjee, A.; Huang, Y.; Oh, S.; Sanchez, C.; Chang, Y.-F.; Liu, X.; Bradshaw, G. A.; Benites, N. C.; Paulsson, J.; Kirschner, M. W.; Sung, Y.; Elgeti, J.; Basan, M.","author_corresponding":"Markus Basan","author_corresponding_institution":"HARVARD MEDICAL SCHOOL","doi":"10.1101\/2023.08.31.555748","date":"2024-08-07","version":"6","type":"new results","license":"cc_by_nc_nd","category":"microbiology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/07\/2023.08.31.555748.source.xml","abstract":"The cell wall is an essential cellular component of bacteria and the target of many antibiotics. However, how bacteria regulate the rate of cell wall biosynthesis as growth rates change remains unresolved. In E. coli, cell wall growth was thought to proceed independently from turgor pressure1, the osmotic pressure that the cytoplasm exerts on the cell wall. Here, we uncover a striking increase of turgor pressure with growth rate. Modulating turgor pressure and measuring cell wall biosynthesis, we find that turgor pressure is directly controls the rate of cell wall biosynthesis. The picture that emerges is that turgor pressure is largely generated by counterions of negatively charged cellular biomass. The increase in turgor pressure with growth rates results from more ribosomes and therefore higher concentrations of negatively charged ribosomal RNA. Elegantly, the coupling between biomass composition, turgor pressure and cell wall biosynthesis simultaneously explains how bacteria achieve homeostasis of cytoplasmic crowding and how they regulate the rate of cell wall biosynthesis across growth rates.","funder":"NA","published":"NA","server":"bioRxiv"},{"title":"Transcriptomic profiling of Schlemm's canal cells reveals a lymphatic-biased identity and three major cell states","authors":"Balasubramanian, R.; Kizhatil, K.; Li, T.; Tolman, N.; Bhandari, A.; Clark, G.; Bupp-Chickering, V.; Kelly, R. A.; Zhou, S.; Peregrin, J.; Simon, M.; Montgomery, C.; Stamer, W. D.; Qian, J.; John, S.","author_corresponding":"Simon John","author_corresponding_institution":"Columbia University Irving Medical Center","doi":"10.1101\/2023.08.31.555823","date":"2024-08-06","version":"3","type":"new results","license":"cc_by_nc_nd","category":"genomics","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/06\/2023.08.31.555823.source.xml","abstract":"Schlemms canal (SC) is central in intraocular pressure regulation but requires much characterization. It has distinct inner and outer walls, each composed of Schlemms canal endothelial cells (SECs) with different morphologies and functions. Recent transcriptomic studies of the anterior segment added important knowledge, but were limited in power by SEC numbers or did not focus on SC. To gain a more comprehensive understanding of SC biology, we performed bulk RNA sequencing on C57BL\/6J SC, blood vessel, and lymphatic endothelial cells from limbal tissue ([~]4500 SECs). We also analyzed mouse limbal tissues by single-cell and single-nucleus RNA sequencing (C57BL\/6J and 129\/Sj strains), successfully sequencing 903 individual SECs. Together, these datasets confirm that SC has molecular characteristics of both blood and lymphatic endothelia with a lymphatic phenotype predominating. SECs are enriched in pathways that regulate cell-cell junction formation pointing to the importance of junctions in determining SC fluid permeability. Importantly, and for the first time, our analyses characterize 3 molecular classes of SECs, molecularly distinguishing inner wall from outer wall SECs and discovering two inner wall cell states that likely result from local environmental differences. Further, and based on ligand and receptor expression patterns, we document key interactions between SECs and cells of the adjacent trabecular meshwork (TM) drainage tissue. Also, we present cell type expression for a collection of human glaucoma genes. These data provide a new molecular foundation that will enable the functional dissection of key homeostatic processes mediated by SECs as well as the development of new glaucoma therapeutics.\n\nSignificance statementSchlemms canal is a critical ocular drainage structure that maintains intraocular pressure with important consequences for glaucoma. Despite this, Schlemms canal has been relatively understudied with the molecular process that mediate its function, maintain its health, or that are compromised in glaucoma needing much deeper characterization. This study is important as it provides the most comprehensive molecular characterization of Schlemms canal cells to date providing a wealth of molecular details. In addition to highlighting important biological pathways, this information will guide studies to develop new treatments against glaucoma.","funder":"NA","published":"10.7554\/elife.96459.3","server":"bioRxiv"},{"title":"Environmental factors and cultural drift influence song evolution in New World Sparrows","authors":"Provost, K. L.; Yang, J.; Carstens, B. C.","author_corresponding":"Kaiya L Provost","author_corresponding_institution":"The Ohio State University","doi":"10.1101\/2023.09.01.555954","date":"2024-08-10","version":"2","type":"new results","license":"cc_by_nc","category":"evolutionary biology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/10\/2023.09.01.555954.source.xml","abstract":"Variation in bird song is often assumed to be determined by sexual selection, rather than natural selection. However, most investigations to date have drawn their conclusions from a handful of species due to the challenges with manually processing sound data. Here, we use deep machine learning to investigate nearly all species of New World Sparrows. We leverage existing data to identify the processes that structure variation in bird song and to determine how this variation corresponds to patterns in genes and traits. Song variation in ~40% of species can be explained by environment, geography, and time. Across a community and global scale, the action of natural selection on the evolution of song is at least as impactful as it is on other genetically-determined traits.","funder":"NA","published":"NA","server":"bioRxiv"},{"title":"Meisoindigo: An Effective Inhibitor of SARS-CoV-2 Main Protease Revealed by Yeast System","authors":"Grabinski, W.; Kicinska, A.; Kosicka, E.; Baranek-Grabinska, M.; Hejenkowska, E. D.; Budzik, J.; Sliska, P.; Sliwinska, W.; Karachitos, A.","author_corresponding":"Andonis Karachitos","author_corresponding_institution":"Department of Bioenergetics, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Pozna\u0144, Poland.","doi":"10.1101\/2023.09.03.555867","date":"2024-08-26","version":"2","type":"new results","license":"cc_by","category":"pharmacology and toxicology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/26\/2023.09.03.555867.source.xml","abstract":"The COVID-19 pandemic caused by SARS-CoV-2 has had a significant impact on global health and the global economy. Despite the availability of vaccines, limited accessibility and vaccine hesitancy pose challenges in controlling the spread of the disease. Effective therapeutic strategies, including antiviral drugs, are needed to combat the future spread of new SARS-CoV-2 virus variants. The main protease (Mpro) is a critical therapeutic target for COVID-19 medicines, as its inhibition impairs viral replication. However, the use of substances that inhibit Mpro may induce selection pressure. Thus, it is vital to monitor viral resistance to known drugs and to develop new drugs. Here, we have developed a yeast system for the identification of Mpro inhibitors as an alternative to costly and demanding high-biosecurity procedures. The system is based on stable expression of Mpro and does not require selection media. Yeast can be cultured on a rich carbon source, providing rapid growth and screening results. The designed tool was subsequently used to screen the FDA-Approved Drug Library. Several chemicals with Mpro inhibitory properties were identified. We found that meisoindigo, which was not previously known to have the potential to inhibit Mpro, was highly effective. Our results may promote the development of new derivatives with therapeutic properties against SARS-CoV-2 and other beta-coronaviruses.","funder":"NA","published":"NA","server":"bioRxiv"},{"title":"Post-replicative lesion processing limits DNA damage-induced mutagenesis","authors":"Maslowska, K. H.; Wong, R. P.; Ulrich, H. D.; Pages, V.","author_corresponding":"Vincent Pages","author_corresponding_institution":"CNRS","doi":"10.1101\/2023.09.04.556208","date":"2024-08-06","version":"3","type":"new results","license":"cc_no","category":"molecular biology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/06\/2023.09.04.556208.source.xml","abstract":"DNA lesions are a threat to genome stability. To cope with them during DNA replication, cells have evolved lesion bypass mechanisms: Translesion Synthesis (TLS), which allows the cell to insert a nucleotide directly opposite the lesion, with the risk of introducing a mutation, and error-free Damage Avoidance (DA), which uses homologous recombination to retrieve the genetic information from the sister chromatid.\n\nIn this study, we investigate the timing of lesion bypass and its implications for the accuracy of the process. Our findings reveal that DNA polymerase {eta} can bypass common, UV-induced TT-cyclobutane pyrimidine dimers at the fork, immediately after encountering the blocking lesion. In contrast, TLS at TT(6-4) photoproducts and bulky G-AAF adducts, mediated by Rev1 and Pol {zeta}, takes place behind the fork, at post-replicative gaps that are generated downstream of the lesion after repriming. We show that in this latter situation, TLS competes with the DA pathway, thus reducing overall mutagenicity of damage bypass. Additionally, our study demonstrates that Exo1 nuclease influences the balance between TLS and DA by modulating the size of the post-replicative gaps.","funder":"NA","published":"10.1093\/nar\/gkaf198","server":"bioRxiv"},{"title":"Human DCP1 is crucial for mRNA decapping and possesses paralog-specific gene regulating functions","authors":"Chen, T.-W.; Liao, H.-W.; Noble, M.; Siao, J.-Y.; Cheng, Y.-H.; Chiang, W.-C.; Lo, Y.-T.; Chang, C.-T.","author_corresponding":"Chung-Te Chang","author_corresponding_institution":"National Yang Ming Chiao Tung University","doi":"10.1101\/2023.09.04.556219","date":"2024-08-13","version":"3","type":"new results","license":"cc_by_nc_nd","category":"molecular biology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/13\/2023.09.04.556219.source.xml","abstract":"The mRNA 5-cap structure removal by the decapping enzyme DCP2 is a critical step in gene regulation. While DCP2 is the catalytic subunit in the decapping complex, its activity is strongly enhanced by multiple factors, particularly DCP1, which is the major activator in yeast. However, the precise role of DCP1 in metazoans has yet to be fully elucidated. Moreover, in humans, the specific biological functions of the two DCP1 paralogs, DCP1a and DCP1b, remain largely unknown. To investigate the role of human DCP1, we generated cell-lines that were deficient in DCP1a, DCP1b or both to evaluate the importance of DCP1 in the decapping machinery. Our results highlight the importance of human DCP1 in decapping process and show that the EVH1 domain of DCP1 enhances the mRNA-binding affinity of DCP2. Transcriptome and metabolome analyses outline the distinct functions of DCP1a and DCP1b in human cells, regulating specific endogenous mRNA targets and biological processes. Overall, our findings provide insights into the molecular mechanism of human DCP1 in mRNA decapping and shed light on the distinct functions of its paralogs.","funder":"NA","published":"10.7554\/eLife.94811","server":"bioRxiv"},{"title":"Combinatorial Wnt signaling landscape during brachiopod anteroposterior patterning","authors":"Vellutini, B. C.; Martin-Duran, J. M.; Borve, A.; Hejnol, A.","author_corresponding":"Bruno Cossermelli Vellutini","author_corresponding_institution":"Max Planck Institute of Molecular Cell Biology and Genetics","doi":"10.1101\/2023.09.03.556047","date":"2024-08-18","version":"3","type":"new results","license":"cc_by","category":"developmental biology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/18\/2023.09.03.556047.source.xml","abstract":"BackgroundWnt signaling pathways play crucial roles in animal development. They establish embryonic axes, specify cell fates, and regulate tissue morphogenesis from the early embryo to organogenesis. It is becoming increasingly recognized that these distinct developmental outcomes depend upon dynamic interactions between multiple ligands, receptors, antagonists, and other pathway modulators, consolidating the view that a combinatorial \"code\" controls the output of Wnt signaling. However, due to the lack of comprehensive analyses of Wnt components in several animal groups, it remains unclear if specific combinations always give rise to specific outcomes, and if these combinatorial patterns are conserved throughout evolution.\n\nResultsIn this work, we investigate the combinatorial expression of Wnt signaling components during the axial patterning of the brachiopod Terebratalia transversa. We find that T. transversa has a conserved repertoire of ligands, receptors, and antagonists. These genes are expressed throughout embryogenesis but undergo significant upregulation during axial elongation. At this stage, Frizzled domains occupy broad regions across the body while Wnt domains are narrower and distributed in partially overlapping patches; antagonists are mostly restricted to the anterior end. Based on their combinatorial expression, we identify a series of unique transcriptional subregions along the anteroposterior axis that coincide with the different morphological subdivisions of the brachiopod larval body. When comparing these data across the animal phylogeny, we find that the expression of Frizzled genes is relatively conserved, whereas the expression of Wnt genes is more variable.\n\nConclusionsOur results suggest that the differential activation of Wnt signaling pathways may play a role in regionalizing the anteroposterior axis of brachiopod larvae. More generally, our analyses suggest that changes in the receptor context of Wnt ligands may act as a mechanism for the evolution and diversification of the metazoan body axis.","funder":"NA","published":"10.1186\/s12915-024-01988-w","server":"bioRxiv"},{"title":"CBGTPy: An extensible cortico-basal ganglia-thalamic framework for modeling biological decision making","authors":"Clapp, M.; Bahuguna, J.; Giossi, C.; Rubin, J.; Verstynen, T. V.; Vich, C.","author_corresponding":"Jonathan Rubin","author_corresponding_institution":"University of Pittsburgh","doi":"10.1101\/2023.09.05.556301","date":"2024-08-04","version":"3","type":"new results","license":"cc_by_nc_nd","category":"neuroscience","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/04\/2023.09.05.556301.source.xml","abstract":"Here we introduce CBGTPy, a virtual environment for designing and testing goal-directed agents with internal dynamics that are modeled on the cortico-basal-ganglia-thalamic (CBGT) pathways in the mammalian brain. CBGTPy enables researchers to investigate the internal dynamics of the CBGT system during a variety of tasks, allowing for the formation of testable predictions about animal behavior and neural activity. The framework has been designed around the principle of flexibility, such that many experimental parameters in a decision making paradigm can be easily defined and modified. Here we demonstrate the capabilities of CBGTPy across a range of single and multi-choice tasks, highlighting the ease of set up and the biologically realistic behavior that it produces. We show that CBGTPy is extensible enough to apply to a range of experimental protocols and to allow for the implementation of model extensions with minimal developmental effort.\n\nAuthor summaryWe introduce a toolbox for producing biologically realistic simulations of the cortico-basal ganglia-thalamic dynamics during a variety of experimental tasks. The purpose is to foster the theory-experiment cycle, offering a tool for generating testable predictions of behavioral and neural responses that can be validated experimentally, in a framework that allows for simple updating as new experimental evidence emerges. We outline how our toolbox works and demonstrate its performance on a set of normative cognitive tasks.","funder":"NA","published":"10.1371\/journal.pone.0310367","server":"bioRxiv"},{"title":"Focal control of non-invasive deep brain stimulation using multipolar temporal interference","authors":"Botzanowski, B.; ACERBO, E.; lehmann, s.; Kearsley, S. L.; Steiner, M.; Neufeld, E.; MISSEY, F.; Muller, L.; Jirsa, V.; Corneil, B. D.; Williamson, A.","author_corresponding":"Adam Williamson","author_corresponding_institution":"Aix-Marseille Universite","doi":"10.1101\/2023.09.05.556444","date":"2024-08-26","version":"2","type":"new results","license":"cc_no","category":"neuroscience","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/26\/2023.09.05.556444.source.xml","abstract":"Temporal interference (TI) is a method of non-invasive brain stimulation using transcutaneous electrodes that allows the targeting and modulation of deeper brain structures, not normally associated with non-invasive simulation, while avoiding unwanted stimulation of shallower cortical structures. The properties of TI have been previously demonstrated, however, the problem of decoupling stimulation focality from stimulation intensity has not been addressed. In this paper, we provide a possible novel solution, multipolar TI (mTI), which allows increased independent control over both the size of the stimulated region and the stimulation intensity. The mTI method uses multiple carrier frequencies to create multiple overlapping amplitude-modulated envelopes, rather than using one envelope as in standard TI. The study presents an explanation of the concept of mTI along with experimental data gathered from Rhesus macaques and mice. We improved the focality at depth in anesthetized mice and monkeys, and using the new focality in awake monkeys, evoked targeted activity at depth in the superior colliculus. The mTI method could be an interesting and potentially useful new tool alongside other forms of non-invasive brain stimulation.\n\nTeaser: Multipolar Temporal Interference Stimulation can produce a more focal brain stimulation at depth compared to Temporal Interference.","funder":"NA","published":"10.1186\/s42234-025-00169-6","server":"bioRxiv"},{"title":"Unveiling Wolbachia pipientis transcriptomic signature in Aedes aegypti: a comprehensive meta-analysis","authors":"Mejias, S.; Jimenez, N. E.; Conca, C.; Salgado, J. C.; Gerdtzen, Z. P.","author_corresponding":"Natalia Jimenez","author_corresponding_institution":"Universidad de Chile Facultad de Ciencias Fisicas y Matematicas","doi":"10.1101\/2023.09.03.556149","date":"2024-08-01","version":"2","type":"new results","license":"cc_by_nc","category":"bioinformatics","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/01\/2023.09.03.556149.source.xml","abstract":"BackgroundAn effective strategy for arboviral control consists in transfecting Aedes aegypti mosquitoes with the intracellular bacteria Wolbachia pipientis, which reduces host viral susceptibility and spreads itself into wild populations via reproductive manipulations. However, the prospect of losing the efficacy of this strategy underscores the need for deepening the mechanistic knowledge of Diptera-Wolbachia systems and identifying relevant Wolbachia effects that could decline upon adaptation of A. aegypti transfections. A systematic comparison of publicly available Diptera-Wolbachia transcriptomic datasets could yield progress in this matter.\n\nMethodology\/Principal findingsWe derived differentially expressed gene (DEG) sets from previously published Diptera-Wolbachia transcriptomic datasets, subjected them to enrichment analysis of Gene Ontology terms, and intersected the results to identify patterns of host gene\/function regulation by Wolbachia. A putative farnesoic acid methyl transferase (AAEL004667) and a flavin-containing monooxygenase (AAEL000834) were consistently upregulated in transfected A. aegypti and linked to cytoplasmic incompatibility and viral susceptibility, being proposed as novel targets of study. Genes implicated in viral blocking --GNBPA1, PGRPS1, DEFC, Tf1, serine-type endopeptidases and endopeptidase inhibitors-- were consistently upregulated in transfected A. aegypti but not in native infections, indicating that they could lose responsiveness to Wolbachia over time and should be considered to keep the efficacy of arboviral control. The commonality of chitinase regulation by Wolbachia was identified and proposed as an explanation for the loss of desiccation resistance in transfected A. aegyptis eggs, which is a main obstacle for the introgression of Wolbachia in mosquito populations.\n\nConclusions\/SignificanceThe present work points out relevant gene targets to consider for arboviral control sustainability and provides new hypotheses for deepening the understanding of Diptera-Wolbachia systems.\n\nAuthor SummaryArboviral diseases (e.g. dengue), which are mainly transmitted by the mosquito Aedes aegypti, impose a global public health crisis. An effective strategy for controlling the spread of these diseases is to artificially infect A. aegypti populations with the bacteria Wolbachia pipientis, which reduces its capacity to transmit arboviruses. However, future adaptive changes in the novel A. aegypti-Wolbachia association could diminish the efficacy of this approach. To prevent this, it is crucial to have a solid biological understanding of Wolbachia infections and predictions about specific changes that artificial infections could undergo. By analyzing publicly available biological data from Wolbachia-infected mosquitoes and flies we were able to propose new hypotheses regarding general aspects of Wolbachia infection and to identify antiviral effects of Wolbachia in A. aegypti that could decline over time, thus providing relevant information for keeping sustainability of a key arboviral control strategy.","funder":"NA","published":"NA","server":"bioRxiv"},{"title":"A hierarchy of metabolite exchanges in metabolic models of microbial species and communities","authors":"Wedmark, Y. K.; Vik, J. O.; Oyas, O.","author_corresponding":"Ove \u00d8y\u00e5s","author_corresponding_institution":"Norwegian University of Life Sciences (NMBU)","doi":"10.1101\/2023.09.05.556413","date":"2024-08-11","version":"3","type":"new results","license":"cc_by_nc","category":"systems biology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/11\/2023.09.05.556413.source.xml","abstract":"The metabolic network of an organism can be analyzed as a constraint-based model. This analysis can be biased, optimizing an objective such as growth rate, or unbiased, aiming to describe the full feasible space of metabolic fluxes through pathway analysis or random flux sampling. In particular, pathway analysis can decompose the flux space into fundamental and formally defined metabolic pathways. Unbiased methods scale poorly with network size due to combinatorial explosion, but a promising approach to improve scalability is to focus on metabolic subnetworks, e.g., cells metabolite exchanges with each other and the environment, rather than the full metabolic networks. Here, we applied pathway enumeration and flux sampling to metabolite exchanges in microbial species and a microbial community, using models ranging from central carbon metabolism to genome-scale and focusing on pathway definitions that allow direct targeting of subnetworks such as metabolite exchanges (elementary conversion modes, elementary flux patterns, and minimal pathways). Enumerating growth-supporting metabolite exchanges, we found that metabolite exchanges from different pathway definitions were related through a hierarchy, and we show that this hierarchical relationship between pathways holds for metabolic networks and subnetworks more generally. Metabolite exchange frequencies, defined as the fraction of pathways in which each metabolite was exchanged, were similar across pathway definitions, with a few specific exchanges explaining large differences in pathway counts. This indicates that biological interpretation of predicted metabolite exchanges is robust to the choice of pathway definition, and it suggests strategies for more scalable pathway analysis. Our results also signal wider biological implications, facilitating detailed and interpretable analysis of metabolite exchanges and other subnetworks in fields such as metabolic engineering and synthetic biology.\n\nAuthor summaryPathway analysis of constraint-based metabolic models makes it possible to disentangle metabolism into formally defined metabolic pathways. A promising but underexplored application of pathway analysis is to analyze exchanges of metabolites between cells and their environment, which could also help overcome computational challenges and allow scaling to larger systems. Here, we used four different pathway definitions to enumerate combinations of metabolite exchanges that support growth in models of microbial species and a microbial community. We found that metabolite exchanges from different pathway definitions were related to each other through a previously unknown hierarchy, and we show that this hierarchical relationship between pathways holds more generally. Moreover, the fraction of pathways in which each metabolite was exchanged turned out to be remarkably consistent across pathway definitions despite large differences in pathway counts. In summary, our work shows how pathway definitions and their metabolite exchange predictions are related to each other, and it facilitates scalable and interpretable pathway analysis with applications in fields such as metabolic engineering.","funder":"NA","published":"10.1371\/journal.pcbi.1012472","server":"bioRxiv"},{"title":"PKA regulation of neuronal function requires the dissociation of catalytic subunits from regulatory subunits","authors":"Xiong, W.; Qin, M.; Zhong, H.","author_corresponding":"Haining Zhong","author_corresponding_institution":"Oregon Health & Science University","doi":"10.1101\/2023.09.05.556437","date":"2024-08-20","version":"3","type":"new results","license":"cc_by_nc_nd","category":"cell biology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/20\/2023.09.05.556437.source.xml","abstract":"Protein kinase A (PKA) plays essential roles in diverse cellular functions. However, the spatiotemporal dynamics of endogenous PKA upon activation remain debated. The classical model predicts that PKA catalytic subunits dissociate from regulatory subunits in the presence of cAMP, whereas a second model proposes that catalytic subunits remain associated with regulatory subunits following physiological activation. Here we report that different PKA subtypes, as defined by the regulatory subunit, exhibit distinct subcellular localization at rest in CA1 neurons of cultured hippocampal slices. Nevertheless, when all tested PKA subtypes are activated by norepinephrine, presumably via the {beta}-adrenergic receptor, catalytic subunits translocate to dendritic spines but regulatory subunits remain unmoved. These differential spatial dynamics between the subunits indicate that at least a significant fraction of PKA dissociates. Furthermore, PKA-dependent regulation of synaptic plasticity and transmission can be supported only by wildtype, dissociable PKA, but not by inseparable PKA. These results indicate that endogenous PKA regulatory and catalytic subunits dissociate to achieve PKA function in neurons.","funder":"NA","published":"10.7554\/elife.93766.3","server":"bioRxiv"},{"title":"Evaluating the Utilities of Foundation Models in Single-cell Data Analysis","authors":"Liu, T.; Li, K.; Wang, Y.; Li, H.; Zhao, H.","author_corresponding":"Hongyu Zhao","author_corresponding_institution":"Yale University","doi":"10.1101\/2023.09.08.555192","date":"2024-08-26","version":"6","type":"new results","license":"cc_no","category":"bioinformatics","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/26\/2023.09.08.555192.source.xml","abstract":"Foundation Models (FMs) have made significant strides in both industrial and scientific domains. In this paper, we evaluate the performance of FMs for single-cell sequencing data analysis through comprehensive experiments across eight downstream tasks pertinent to single-cell data. Overall, the top FMs include scGPT, Geneformer, and CellPLM by considering model performances and user accessibility among ten single-cell FMs. However, by comparing these FMs with task-specific methods, we found that single-cell FMs may not consistently excel than task-specific methods in all tasks, which challenges the necessity of developing foundation models for single-cell analysis. In addition, we evaluated the effects of hyper-parameters, initial settings, and stability for training single-cell FMs based on a proposed scEval framework, and provide guidelines for pre-training and fine-tuning, to enhance the performances of single-cell FMs. Our work summarizes the current state of single-cell FMs, points to their constraints and avenues for future development, and offers a freely available evaluation pipeline to benchmark new models and improve method development.","funder":"NA","published":"NA","server":"bioRxiv"},{"title":"Developmental stage determines the realized energy landscape for a flight specialist","authors":"Nourani, E.; Faure, L.; Bronnvik, H.; Scacco, M.; Bassi, E.; Fiedler, W.; Gruebler, M. U.; Hatzl, J. S.; Jenny, D.; Roverselli, A.; Sumasgutner, P.; Tschumi, M.; Wikelski, M.; Safi, K.","author_corresponding":"Elham Nourani","author_corresponding_institution":"Max Planck Institute of Animal Behavior","doi":"10.1101\/2023.09.07.556633","date":"2024-08-16","version":"5","type":"confirmatory results","license":"cc_by_nc","category":"animal behavior and cognition","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/16\/2023.09.07.556633.source.xml","abstract":"The heterogeneity of the physical environment determines the cost of transport for animals, shaping their energy landscape. Animals respond to this energy landscape by adjusting their distribution and movement to maximize gains and reduce costs. Much of our knowledge about energy landscape dynamics focuses on factors external to the animal, particularly the spatio-temporal variations of the environment. However, an animals internal state can significantly impact its ability to perceive and utilize available energy, creating a distinction between the \"fundamental\" and the \"realized\" energy landscapes. Here we show that the realized energy landscape varies along the ontogenetic axis. Locomotor and cognitive capabilities of individuals change over time, especially during the early life stages. We investigate the development of the realized energy landscape in the Central European Alpine population of the golden eagle Aquila chrysaetos, a large predator that requires negotiating the atmospheric environment to achieve energy-efficient soaring flight. We quantified weekly energy landscapes using environmental features for 55 juvenile golden eagles, demonstrating that energetic costs of traversing the landscape decreased with age. Consequently, the potentially flyable area within the Alpine region increased 2,170-fold during their first three years of independence. Our work contributes to a predictive understanding of animal movement by presenting ontogeny as a mechanism shaping the realized energy landscape.","funder":"NA","published":"10.7554\/elife.98818.3","server":"bioRxiv"},{"title":"Temporally resolved single cell transcriptomics in a human model of amniogenesis","authors":"Sekulovski, N.; Carleton, A. E.; Rengarajan, A. A.; Lin, C.-W.; Juga, L. L.; Whorton, A. E.; Kropp Schmidt, J.; Golos, T.; Taniguchi, K.","author_corresponding":"Kenichiro Taniguchi","author_corresponding_institution":"Medical College of Wisconsin","doi":"10.1101\/2023.09.07.556553","date":"2024-08-22","version":"3","type":"new results","license":"cc_by_nc","category":"developmental biology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/22\/2023.09.07.556553.source.xml","abstract":"Amniogenesis is triggered in a collection of pluripotent epiblast cells as the human embryo implants. To gain insights into the critical but poorly understood transcriptional machinery governing amnion fate determination, we examined the evolving transcriptome of a developing human pluripotent stem cell-derived amnion model at the single cell level. This analysis revealed several continuous amniotic fate progressing states with state-specific markers, which include a previously unrecognized CLDN10+ amnion progenitor state. Strikingly, we found that expression of CLDN10 is restricted to the amnion-epiblast boundary region in the human post-implantation amniotic sac model as well as in a peri-gastrula cynomolgus macaque embryo, bolstering the growing notion that, at this stage, the amnion-epiblast boundary is a site of active amniogenesis. Bioinformatic analysis of published primate peri-gastrula single cell sequencing data further confirmed that CLDN10 is expressed in cells progressing to amnion. Additionally, our loss of function analysis shows that CLDN10 promotes amniotic but suppresses primordial germ cell-like fate. Overall, this study presents a comprehensive amniogenic single cell transcriptomic resource and identifies a previously unrecognized CLDN10+ amnion progenitor population at the amnion-epiblast boundary of the primate peri-gastrula.","funder":"NA","published":"NA","server":"bioRxiv"},{"title":"Non-feature-specific elevated responses and feature-specific backward replay in human brain induced by visual sequence exposure","authors":"He, T.; Gong, X.; Wang, Q.; Zhu, X.; Liu, Y.; Fang, F.","author_corresponding":"Fang Fang","author_corresponding_institution":"Peking University","doi":"10.1101\/2023.09.07.556631","date":"2024-08-08","version":"3","type":"new results","license":"cc_by_nc","category":"neuroscience","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/08\/2023.09.07.556631.source.xml","abstract":"The ability of cortical circuits to adapt in response to experience is a fundamental property of the brain. After exposure to a moving dot sequence, flashing a dot as a cue at the starting point of the sequence can elicit successive elevated responses even in the absence of the sequence. These cue-triggered elevated responses have been shown to play a crucial role in predicting future events in dynamic environments. However, temporal sequences we are exposed typically contain rich feature information. It remains unknown whether the elevated responses are feature specific and, more crucially, how the brain organizes sequence information after exposure. To address these questions, participants were exposed to a predefined sequence of four motion directions for about 30 min, followed by the presentation of the start or end motion direction of the sequence as a cue. Surprisingly, we found that cue-triggered elevated responses were not specific to any motion direction. Interestingly, motion direction information was spontaneously reactivated, and the motion sequence was backward replayed in a time-compressed manner. These effects were observed even after brief exposure. Notably, no replay events were observed when the second or third motion direction of the sequence served as a cue. Further analyses revealed that activity in the medial temporal lobe (MTL) preceded the ripple power increase in visual cortex at the onset of replay, implying a coordinated relationship between the activities in the MTL and visual cortex. Together, these findings demonstrate that visual sequence exposure induces two-fold brain plasticity that may simultaneously serve for different functional purposes. The non-feature-specific elevated responses may facilitate general processing of upcoming stimuli, whereas the feature-specific backward replay may underpin passive learning of visual sequence.","funder":"NA","published":"10.7554\/eLife.101511","server":"bioRxiv"},{"title":"An actomyosin network organizes niche morphology and responds to feedback from recruited stem cells","authors":"Warder, B. N.; Nelson, K. A.; Sui, J.; Anllo, L.; DiNardo, S.","author_corresponding":"Stephen DiNardo","author_corresponding_institution":"Perelman School of Medicine, Univ. of Pennsylvania","doi":"10.1101\/2023.09.08.556877","date":"2024-08-07","version":"3","type":"new results","license":"cc_by_nc_nd","category":"developmental biology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/07\/2023.09.08.556877.source.xml","abstract":"SummaryStem cells often rely on signals from a niche, which in many tissues adopts a precise morphology. What remains elusive is how niches are formed, and how morphology impacts function. To address this, we leverage the Drosophila gonadal niche, which affords genetic tractability and live-imaging. We have previously shown mechanisms dictating niche cell migration to their appropriate position within the gonad, and the resultant consequences on niche function. Here, we show that once positioned, niche cells robustly polarize filamentous actin (F-actin) and Non-muscle Myosin II (MyoII) towards neighboring germ cells. Actomyosin tension along the niche periphery generates a highly reproducible smoothened contour. Without contractility, niches are misshapen and exhibit defects in their ability to regulate germline stem cell behavior. We additionally show that germ cells aid in polarizing MyoII within niche cells, and that extrinsic input is required for niche morphogenesis and function. Our work reveals a feedback mechanism where stem cells shape the niche that guides their behavior.","funder":"NA","published":"10.1016\/j.cub.2024.07.041","server":"bioRxiv"},{"title":"No single PCR test is sufficient to determine parvovirus IHHNV presence in or impact on farmed shrimp production","authors":"Sritunyalucksana, K.; Sanguanrut, P.; Srisala, J.; Thawonsuwan, J.; Saleetid, N.; Vanichviriyakit, R.; Chotwiwatthanakun, C.; FLEGEL, T. W.; Taengchaiyaphum, S.","author_corresponding":"Suparat Taengchaiyaphum","author_corresponding_institution":"National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Yothi office, Rama VI Rd., Bangk","doi":"10.1101\/2023.09.08.556791","date":"2024-08-08","version":"2","type":"new results","license":"cc_by_nc_nd","category":"zoology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/08\/2023.09.08.556791.source.xml","abstract":"The main purpose of this report is to provide hard evidence that the shrimp parvovirus IHHNV has not resulted \"in significant consequences e.g. production losses, morbidity or mortality at a zone or country level\" in Thailand since at least 2010. It also reveals that no single PCR test is sufficient to identify IHHNV-infected shrimp. It presents historical evidence and new evidence from 11 commercial ponds cultivating the giant tiger shrimp Penaeus monodon in Thailand. These ponds were selected because they were the ponds that gave positive PCR test results for IHHNV using 2 methods recommended for IHHNV diagnosis by WOAH. However, an additional in-house \"IHHNV Long-Amp method\" (IHHNV-LA) was also used to amplify 90% of the 4 kb IHHNV genome sequence, and it also gave false-positive test results with 2 of the 11 ponds. Further tests using normal histopathological analysis for the presence of pathognomonic Cowdry A type inclusions (CAI), in situ hybridization (ISH) and immunohistochemistry (IHC) could confirm IHHNV infections in only 2 of the 4 ponds PCR-positive using all 3 PCR methods. In addition, positive detection of CAI alone was equivalent to ISH or IHC in confirming IHHNV infection after a positive test with any of the PCR methods used. In summary, the recommended WOAH PCR methods gave false positive test results for IHHNV infection with 9\/11 ponds (82%). All 11 ponds gave profitable harvests despite the confirmation of IHHNV in 2 ponds, where it was accompanied by various additional pathogens. Unfortunately, according to current practice, positive PCR test results with the WOAH methods alone sometimes leads to rejection of traded shrimp products without assurance that the test results are not false positive results that may arise from endogenous viral elements (EVE).","funder":"NA","published":"10.1111\/jwas.70046","server":"bioRxiv"},{"title":"PfMORC protein regulates chromatin accessibility and transcriptional repression in the human malaria parasite, Plasmodium falciparum","authors":"Chahine, Z. M.; Gupta, M.; Lenz, T.; Hollin, T.; Abel, S.; Banks, C.; Saraf, A.; Prudhomme, J.; Bhanvadia, S.; Florens, L.; Le Roch, K. G.","author_corresponding":"Karine G Le Roch","author_corresponding_institution":"University of California Riverside","doi":"10.1101\/2023.09.11.557253","date":"2024-08-28","version":"2","type":"new results","license":"cc_by_nc_nd","category":"microbiology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/28\/2023.09.11.557253.source.xml","abstract":"The environmental challenges the human malaria parasite, Plasmodium falciparum, faces during its progression into its various lifecycle stages warrant the use of effective and highly regulated access to chromatin for transcriptional regulation. Microrchidia (MORC) proteins have been implicated in DNA compaction and gene silencing across plant and animal kingdoms. Accumulating evidence has shed light into the role MORC protein plays as a transcriptional switch in apicomplexan parasites. In this study, using CRISPR\/Cas9 genome editing tool along with complementary molecular and genomics approaches, we demonstrate that PfMORC not only modulates chromatin structure and heterochromatin formation throughout the parasite erythrocytic cycle, but is also essential to the parasite survival. Chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) experiments suggest that PfMORC binds to not only sub-telomeric regions and genes involved in antigenic variation but may also play a role in modulating stage transition. Protein knockdown experiments followed by chromatin conformation capture (Hi-C) studies indicate that downregulation of PfMORC impairs key histone marks and induces the collapse of the parasite heterochromatin structure leading to its death. All together these findings confirm that PfMORC plays a crucial role in chromatin structure and gene regulation, validating this factor as a strong candidate for novel antimalarial strategies.","funder":"NA","published":"10.7554\/elife.92499","server":"bioRxiv"},{"title":"The transcription factor Sfp1 imprints specific classes of mRNAs and links their synthesis to cytoplasmic decay","authors":"Kelbert,, M.; Jordan-Pla, A.; de-Miguel-Jimenez, L.; Garcia-Martinez, J.; Selitrennik, M.; Guterman,, A.; Henig,, N.; Granneman,, S.; Perez-Ortin, J. E.; Chavez, S.; Choder, M.","author_corresponding":"Mordechai Choder","author_corresponding_institution":"Technion - Israel Institute of Technology","doi":"10.1101\/2023.09.13.557510","date":"2024-08-30","version":"3","type":"new results","license":"cc_by_nc_nd","category":"molecular biology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/30\/2023.09.13.557510.source.xml","abstract":"To function effectively as an integrated system, the transcriptional and post-transcriptional machineries must communicate through mechanisms that are still poorly understood. Here we focus on Sfp1, known to regulate transcription of proliferation-related genes. We show that Sfp1 can regulate transcription either by binding to promoters, like most known transcription activators, or by binding to the transcribed regions (gene bodies), probably via RNA polymerase II (Pol II). We further studied the first mode of Sfp1 activity and found that, following promoter binding, Sfp1 binds to gene bodies and affects Pol II configuration, manifested by dissociation or conformational change of its Rpb4 subunit and increased backtracking. Surprisingly, Sfp1 binds to a subset of mRNAs co-transcriptionally and stabilizes them. The interaction between Sfp1 and its client mRNAs is controlled by their respective promoters and coincides with Sfp1s dissociation from chromatin. . Intriguingly, Sfp1 dissociation from the chromatin correlates with the extent of the backtracked Pol II. We propose that, following promoter recruitment, Sfp1 accompanies Pol II and regulates backtracking. The backtracked Pol II is more compatible with Sfp1s relocation to the nascent transcripts, whereupon Sfp1 accompanies these mRNAs to the cytoplasm and regulates their stability. Thus, Sfp1s co-transcriptional binding imprints the mRNA fate, serving as a paradigm for the cross-talk between the synthesis and decay of specific mRNAs. The interplay between Sfp1s two modes of transcription regulation remains to be examined.","funder":"NA","published":"10.7554\/elife.90766","server":"bioRxiv"},{"title":"Altered hepatic metabolism mediates sepsis preventive effects of reduced glucose supply in infected preterm newborns","authors":"Baek, O.; Muk, T.; Wu, Z.; Ye, Y.; Khakimov, B.; Casano, A. M.; Gangadharan, B.; Bilic, I.; Brunse, A.; Sangild, P. T.; Nguyen, D. N.","author_corresponding":"Duc Ninh Nguyen","author_corresponding_institution":"University of Copenhagen","doi":"10.1101\/2023.09.11.557116","date":"2024-08-28","version":"3","type":"new results","license":"cc_by_nd","category":"immunology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/28\/2023.09.11.557116.source.xml","abstract":"Preterm infants are susceptible to neonatal sepsis, a syndrome of pro-inflammatory activity, organ damage and altered metabolism following infection. Given the unique metabolic challenges and poor glucose regulatory capacity of preterm infants, their glucose intake during infection may have a high impact on the degree metabolism dysregulation and organ damage. Using a preterm pig model of neonatal sepsis, we previously showed that a drastic restriction in glucose supply during infection protects against sepsis via suppression of glycolysis-induced inflammation, but results in severe hypoglycemia. Now we explored clinically relevant options of reducing glucose intake to decrease sepsis risk, without causing hypoglycemia and further explore the involvement of the liver in these protective effects. We found that a reduced glucose regime during infection increased survival via reduced pro-inflammatory response, while maintaining normoglycemia. Mechanistically, this intervention enhanced hepatic oxidative phosphorylation and possibly gluconeogenesis, and dampened both circulating and hepatic inflammation. However, switching from a high to a reduced glucose supply after debut of clinical symptoms did not prevent sepsis, suggesting metabolic conditions at the start of infection are key in driving the outcome. Finally, an early therapy with purified human inter-alpha inhibitor protein, a liver derived anti-inflammatory protein, partially reversed the effects of low parenteral glucose provision, likely by inhibiting neutrophil functions that mediate pathogen clearance.\n\nOur findings suggest a clinically relevant regime of reduced glucose supply for infected preterm infants could prevent or delay the development of sepsis in vulnerable neonates.","funder":"NA","published":"10.7554\/elife.97830.3","server":"bioRxiv"},{"title":"Unpacking Unstructured Data: A Pilot Study on Extracting Insights from Neuropathological Reports of Parkinson's Disease Patients using Large Language Models","authors":"Stroganov, O.; Schedlbauer, A.; Lorenzen, E.; Kadhim, A.; Lobanova, A.; Lewis, D. A.; Glausier, J. R.","author_corresponding":"Oleg Stroganov","author_corresponding_institution":"Rancho BioSciences, LLC","doi":"10.1101\/2023.09.12.557252","date":"2024-08-06","version":"2","type":"new results","license":"cc_by_nc_nd","category":"pathology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/06\/2023.09.12.557252.source.xml","abstract":"ObjectiveThe aim of this study was to make unstructured neuropathological data, located in the NeuroBioBank (NBB), follow FAIR principles, and investigate the potential of Large Language Models (LLMs) in wrangling unstructured neuropathological reports. By making the currently inconsistent and disparate data findable, our overarching goal was to enhance research output and speed.\n\nMaterials and MethodsThe NBB catalog currently includes information from medical records, interview results, and neuropathological reports. These reports contain crucial information necessary for conducting in-depth analysis of NBB data but have multiple formats that vary across different NBB biorepositories and change over time. In this study we focused on a subset of 822 donors with Parkinsons disease (PD) from 7 NBB biorepositories. We developed a data model with combined Brain Region and Pathological Findings data at its core. This approach made it easier to build an extraction pipeline and was flexible enough to convert resulting data to Common Data Elements (CDEs), a standardized data collection tools used by the neuroscience community to improve consistency and facilitate data sharing across studies.\n\nResultsThis pilot study demonstrated the potential of LLMs in structuring unstructured neuropathological reports of PD patients available in the NBB. The pipeline enabled successful extraction of detailed tissue-level (microscopic) and gross anatomical (macroscopic) observations, along with staging information from pathology reports, with extraction quality comparable to manual curation results. To our knowledge, this is the first attempt to automatically standardize neuropathological information at this scale. The collected data has the potential to serve as a valuable resource for PD researchers, facilitating integration with clinical information and genetic data (such as genome-wide genotyping and whole genome sequencing) available through the NBB, hereby enabling a more comprehensive understanding of the disease.","funder":"NA","published":"10.1093\/biomethods\/bpae072","server":"bioRxiv"},{"title":"Evolution of sex differences in cooperation: the role of trade-offs with dispersal","authors":"Capilla-Lasheras, P.; Bircher, N.; Brown, A.; Harrison, X.; Reed, T. E.; York, J.; Cram, D.; Rutz, C.; Walker, L.; Naguib, M.; Young, A.","author_corresponding":"Pablo Capilla-Lasheras","author_corresponding_institution":"University of Glasgow","doi":"10.1101\/2023.09.13.557370","date":"2024-08-31","version":"4","type":"new results","license":"cc_by_nc_nd","category":"evolutionary biology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/31\/2023.09.13.557370.source.xml","abstract":"AbstractExplaining the evolution of sex differences in cooperation remains a major challenge. Comparative studies highlight that offspring of the more philopatric sex tend to be more cooperative within their family groups than those of the more dispersive sex but we do not understand why. The leading  Philopatry hypothesis proposes that the more philopatric sex cooperates more because their higher likelihood of natal breeding increases the direct fitness benefits of natal cooperation. However, the  Dispersal trade-off hypothesis proposes that the more dispersive sex cooperates less because preparations for dispersal, such as extra-territorial prospecting, trade-off against natal cooperation. Here, we test both hypotheses in cooperatively breeding white-browed sparrow weavers (Plocepasser mahali), using a novel high-resolution automated radio-tracking method. First, we show that males are the more dispersive sex (a rare reversal of the typical avian sex-difference in dispersal) and that, consistent with the predictions of both hypotheses, females contribute substantially more than males to cooperative care while within the natal group. However, the Philopatry hypothesis cannot readily explain this female-biased cooperation, as females are not more likely than males to breed within their natal group. Instead, our radio-tracking findings support the Dispersal trade-off hypothesis: males conduct pre-dispersal extra-territorial prospecting forays at higher rates than females and prospecting appears to trade-off against natal cooperation. Our findings thus highlight that the evolution of sex differences in cooperation could be widely attributable to trade-offs between cooperation and dispersal; a potentially general explanation that does not demand that cooperation yields direct fitness benefits.","funder":"NA","published":"NA","server":"bioRxiv"},{"title":"Amyloids at the border: deep mutagenesis and random sequence extension reveal an incomplete amyloid-forming motif in Bri2 that turns amyloidogenic upon C-terminal extension","authors":"Martin, M.; Bolognesi, B.","author_corresponding":"Benedetta Bolognesi","author_corresponding_institution":"Institute for Bioengineering of Catalunya IBEC","doi":"10.1101\/2023.09.15.557952","date":"2024-08-01","version":"3","type":"new results","license":"cc_by_nc","category":"genomics","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/01\/2023.09.15.557952.source.xml","abstract":"Stop-loss mutations cause over twenty different diseases. The effects of stop-loss mutations can have multiple consequences that are, however, hard to predict. Stop-loss in ITM2B\/BRI2 results in C-terminal extension of the encoded protein and, upon furin cleavage, in the production of two 34 amino acid long peptides, ADan and ABri, that accumulate as amyloids in the brains of patients affected by familial Danish and British Dementia. To systematically explore the consequences of Bri2 C-terminal extension, here, we measure amyloid formation for 676 ADan substitutions and identify the region that forms the putative amyloid core of ADan fibrils, located between positions 20 and 26, where stop-loss occurs. Moreover, we measure amyloid formation for [~]18,000 random C-terminal extensions of Bri2 and find that [~]32% of these sequences can nucleate amyloids. We find that the amino acid composition of these nucleating sequences varies with peptide length and that short extensions of 2 specific amino acids (Aliphatics, Aromatics and Cysteines) are sufficient to generate novel amyloid cores. Overall, our results show that the C-terminus of Bri2 contains an incomplete amyloid motif that can turn amyloidogenic upon extension. C-terminal extension with de novo formation of amyloid motifs may thus be a widespread pathogenic mechanism resulting from stop-loss, highlighting the importance of determining the impact of these mutations for other sequences across the genome.","funder":"NA","published":"NA","server":"bioRxiv"},{"title":"The interferon\/STAT1 signaling axis is a common feature of tumor-initiating cells in breast cancer","authors":"Souto, E. P.; Gong, P.; Landua, J. D.; Srinivasan, R. R.; Ganesan, A.; Dobrolecki, L. E.; Purdy, S. C.; Pan, X.; Zeosky, M.; Chung, A.; Yi, S. S.; Ford, H. L.; Lewis, M. T.","author_corresponding":"Michael T. Lewis","author_corresponding_institution":"Baylor College of Medicine","doi":"10.1101\/2023.09.15.557958","date":"2024-08-05","version":"2","type":"new results","license":"cc_no","category":"cancer biology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/05\/2023.09.15.557958.source.xml","abstract":"A tumor cell subpopulation of tumor-initiating cells (TIC), or \"cancer stem cells\", are associated with therapeutic resistance, as well as both local and distant recurrence. Enriched populations of TIC are identified by markers including aldehyde dehydrogenase (ALDH1) activity, the cell surface marker combination CD44+\/CD24-, or fluorescent reporters for signaling pathways that regulate TIC function. We showed previously that Signal Transducer and Activator of Transcription (STAT)-mediated transcription allows enrichment for TIC in claudin-low models of human triple-negative breast cancer using a STAT-responsive reporter. However, the molecular phenotypes of STAT TIC are not well understood, and there is no existing method to lineage-trace TIC as they undergo cell state changes. Using a new STAT-responsive lineage-tracing (LT) system in conjunction with our original reporter, we enriched for cells with enhanced mammosphere-forming potential in some, but not all, basal-like triple-negative breast cancer (TNBC) xenograft models (TNBC) indicating TIC-related and TIC-independent functions for STAT signaling. Single-cell RNA sequencing (scRNAseq) of reporter-tagged xenografts and clinical samples identified a common interferon (IFN)\/STAT1-associated transcriptional state, previously linked to inflammation and macrophage differentiation, in TIC. Surprisingly, most of the genes we identified are not present in previously published TIC signatures derived using bulk RNA sequencing. Finally, we demonstrated that bone marrow stromal cell antigen 2 (BST2), is a cell surface marker of this state, and that it functionally regulates TIC frequency. These results suggest TIC may exploit the IFN\/STAT1 signaling axis to promote their activity, and that targeting this pathway may help eliminate TIC.\n\nSignificanceTIC differentially express interferon response genes, which were not previously reported in bulk RNA sequencing-derived TIC signatures, highlighting the importance of coupling single-cell transcriptomics with enrichment to derive TIC signatures.","funder":"NA","published":"NA","server":"bioRxiv"},{"title":"The interferon\/STAT1 signaling axis is a common feature of tumor-initiating cells in breast cancer","authors":"Souto, E. P.; Gong, P.; Landua, J. D.; Srinivasan, R. R.; Ganesan, A.; Dobrolecki, L. E.; Purdy, S. C.; Pan, X.; Zeosky, M.; Chung, A.; Yi, S. S.; Ford, H. L.; Lewis, M. T.","author_corresponding":"Michael T. Lewis","author_corresponding_institution":"Baylor College of Medicine","doi":"10.1101\/2023.09.15.557958","date":"2024-08-17","version":"3","type":"new results","license":"cc_no","category":"cancer biology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/17\/2023.09.15.557958.source.xml","abstract":"A tumor cell subpopulation of tumor-initiating cells (TIC), or \"cancer stem cells\", are associated with therapeutic resistance, as well as both local and distant recurrence. Enriched populations of TIC are identified by markers including aldehyde dehydrogenase (ALDH1) activity, the cell surface marker combination CD44+\/CD24-, or fluorescent reporters for signaling pathways that regulate TIC function. We showed previously that Signal Transducer and Activator of Transcription (STAT)-mediated transcription allows enrichment for TIC in claudin-low models of human triple-negative breast cancer using a STAT-responsive reporter. However, the molecular phenotypes of STAT TIC are not well understood, and there is no existing method to lineage-trace TIC as they undergo cell state changes. Using a new STAT-responsive lineage-tracing (LT) system in conjunction with our original reporter, we enriched for cells with enhanced mammosphere-forming potential in some, but not all, basal-like triple-negative breast cancer (TNBC) xenograft models (TNBC) indicating TIC-related and TIC-independent functions for STAT signaling. Single-cell RNA sequencing (scRNAseq) of reporter-tagged xenografts and clinical samples identified a common interferon (IFN)\/STAT1-associated transcriptional state, previously linked to inflammation and macrophage differentiation, in TIC. Surprisingly, most of the genes we identified are not present in previously published TIC signatures derived using bulk RNA sequencing. Finally, we demonstrated that bone marrow stromal cell antigen 2 (BST2), is a cell surface marker of this state, and that it functionally regulates TIC frequency. These results suggest TIC may exploit the IFN\/STAT1 signaling axis to promote their activity, and that targeting this pathway may help eliminate TIC.\n\nSignificanceTIC differentially express interferon response genes, which were not previously reported in bulk RNA sequencing-derived TIC signatures, highlighting the importance of coupling single-cell transcriptomics with enrichment to derive TIC signatures.","funder":"NA","published":"NA","server":"bioRxiv"},{"title":"Synaptic interactions between stellate cells and parvalbumin interneurons in layer 2 of the medial entorhinal cortex are organized at the scale of grid cell clusters","authors":"Huang, L.-W.; Garden, D. L.; McCLure, C.; Nolan, M. F.","author_corresponding":"Matthew F Nolan","author_corresponding_institution":"University of Edinburgh","doi":"10.1101\/2023.09.18.558206","date":"2024-08-22","version":"4","type":"new results","license":"cc_by_nc","category":"neuroscience","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/22\/2023.09.18.558206.source.xml","abstract":"Interactions between excitatory and inhibitory neurons are critical to computations in cortical circuits but their organization is difficult to assess with standard electrophysiological approaches. Within the medial entorhinal cortex, representation of location by grid and other spatial cells involves circuits in layer 2 in which excitatory stellate cells interact with each other via inhibitory parvalbumin expressing interneurons. Whether this connectivity is structured to support local circuit computations is unclear. Here, we introduce strategies to address the functional organization of excitatory-inhibitory interactions using crossed Cre- and Flp-driver lines to direct targeted presynaptic optogenetic activation and postsynaptic cell identification. We then use simultaneous patch-clamp recordings from postsynaptic neurons to assess their shared input from optically activated presynaptic populations. We find that extensive axonal projections support spatially organized connectivity between stellate cells and parvalbumin interneurons, such that direct connections are often, but not always, shared by nearby neurons, whereas multisynaptic interactions coordinate inputs to neurons with greater spatial separation. We suggest that direct excitatory-inhibitory synaptic interactions may operate at the scale of grid cell clusters, with local modules defined by excitatory-inhibitory connectivity, while indirect interactions may coordinate activity at the scale of grid cell modules.","funder":"NA","published":"10.7554\/elife.92854.4","server":"bioRxiv"},{"title":"Engineered transcription-associated Cas9 targeting in eukaryotic cells","authors":"Goldberg, G. W.; Kogenaru, M.; Keegan, S.; Haase, M. A. B.; Kagermazova, L.; Arias, M. A.; Onyebeke, K.; Adams, S.; Beyer, D. K.; Fenyo, D.; Noyes, M. B.; Boeke, J. D.","author_corresponding":"Jef D Boeke","author_corresponding_institution":"Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA","doi":"10.1101\/2023.09.18.558319","date":"2024-08-18","version":"2","type":"new results","license":"cc_by_nc_nd","category":"molecular biology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/18\/2023.09.18.558319.source.xml","abstract":"DNA targeting Class 2 CRISPR-Cas effector nucleases, including the well-studied Cas9 proteins, evolved protospacer-adjacent motif (PAM) and guide RNA interactions that sequentially license their binding and cleavage activities at protospacer target sites. Both interactions are nucleic acid sequence specific but function constitutively; thus, they provide intrinsic spatial control over DNA targeting activities but naturally lack temporal control. Here we show that engineered Cas9 fusion proteins which bind to nascent RNAs near a protospacer can facilitate spatiotemporal coupling between transcription and DNA targeting at that protospacer: Transcription-associated Cas9 Targeting (TraCT). Engineered TraCT is enabled in eukaryotic yeast or human cells when suboptimal PAM interactions limit basal activity and when one or more nascent RNA substrates are still tethered to the actively transcribed target DNA in cis. Using yeast, we further show that this phenomenon can be applied for selective editing at one of two identical targets in distinct gene loci, or, in diploid allelic loci that are differentially transcribed. Our work demonstrates that temporal control over Cas9s targeting activity at specific DNA sites may be engineered without modifying Cas9s core domains and guide RNA components or their expression levels. More broadly, it establishes co-transcriptional RNA binding as a cis-acting mechanism that can conditionally stimulate CRISPR-Cas DNA targeting in eukaryotic cells.","funder":"NA","published":"10.1038\/s41467-024-54629-9","server":"bioRxiv"},{"title":"Dissociable roles of thalamic nuclei in the refinement of reaches to spatial targets","authors":"Sibener, L. J.; Mosberger, A. C.; Chen, T. X.; Athalye, V. R.; Murray, J. M.; Costa, R. M.","author_corresponding":"Leslie J Sibener","author_corresponding_institution":"Columbia University","doi":"10.1101\/2023.09.20.558560","date":"2024-08-01","version":"2","type":"new results","license":"cc_no","category":"neuroscience","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/01\/2023.09.20.558560.source.xml","abstract":"Reaches are complex movements that are critical for survival, and encompass the control of different aspects such as direction, speed, and endpoint precision. Complex movements have been postulated to be learned and controlled through distributed motor networks, of which the thalamus is a highly connected node. Still, the role of different thalamic circuits in learning and controlling specific aspects of reaches has not been investigated. We report dissociable roles of two distinct thalamic nuclei - the parafascicular (Pf) and ventroanterior\/ventrolateral (VAL) nuclei - in the refinement of spatial target reaches in mice. Using 2-photon calcium imaging in a head-fixed joystick task where mice learned to reach to a target in space, we found that glutamatergic neurons in both areas were most active during reaches early in learning. Reach-related activity in both areas decreased late in learning, as movement direction was refined and reaches increased in accuracy. Furthermore, the population dynamics of Pf, but not VAL, covaried in different subspaces in early and late learning, but eventually stabilized in late learning. The neural activity in Pf, but not VAL, encoded the direction of reaches in early but not late learning. Accordingly, bilateral lesions of Pf before, but not after learning, strongly and specifically impaired the refinement of reach direction. VAL lesions did not impact direction refinement, but instead resulted in increased speed and target overshoot. Our findings provide new evidence that the thalamus is a critical motor node in the learning and control of reaching movements, with specific subnuclei controlling distinct aspects of the reach early in learning.","funder":"NA","published":"NA","server":"bioRxiv"},{"title":"Multiple Intermediates in the Detergent-Induced Fusion of Lipid Vesicles","authors":"Dresser, L. G.; Kunstmann-Olsen, C.; Conteduca, D.; Hofmair, C. M.; Smith, N.; Clark, L.; Johnson, S.; Penedo, C.; Leake, M. C.; Quinn, S. D.","author_corresponding":"Steven D Quinn","author_corresponding_institution":"University of York","doi":"10.1101\/2023.09.21.558601","date":"2024-08-15","version":"2","type":"new results","license":"cc_by","category":"biophysics","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/08\/15\/2023.09.21.558601.source.xml","abstract":"Detergent-induced vesicle interactions, critical for applications including virus inactivation, varies according to the detergent type and membrane composition, but the underlying mechanistic details remain underexplored. Here, we use a lipid mixing assay based on Forster resonance energy transfer (FRET), and single-vesicle characterization approaches to identify that sub-micron sized vesicles are induced to fuse by the non-ionic detergent Triton-X 100. We demonstrate that the process is a multi-step mechanism, characterized by discrete values of FRET efficiency between membrane-embedded fluorophores, and involves permeabilization, vesicle docking, hemi-fusion and full lipid mixing at sub-solubilizing detergent concentrations. We also dissect the kinetics of vesicle fusion to surface-tethered vesicles using a label-free quartz-crystal microbalance with dissipation monitoring approach, opening a platform for biotechnology applications. The presented strategies provide mechanistic insight into the dynamics of vesicle fusion and have implications for applications including drug delivery and sensor development where transport and manipulation of encapsulated cargo is essential.","funder":"NA","published":"10.1038\/s43246-024-00628-8","server":"bioRxiv"}]}