{"messages":[{"status":"ok","category":"all","interval":"2024-01-01:2024-01-31","funder":"all","cursor":0,"count":30,"count_new_papers":"3221","total":"4569"}], "collection":[{"title":"KCNQ2\/3 regulates efferent mediated slow excitation of vestibular afferents in mammals","authors":"Sinha, A. K.; Lee, C.; Holt, J. C.","author_corresponding":"Joseph C Holt","author_corresponding_institution":"Dept. of Pharmacology and Physiology, Univ. of Rochester, Rochester, New York 14642","doi":"10.1101\/2023.12.30.573731","date":"2024-01-01","version":"1","type":"new results","license":"cc_no","category":"neuroscience","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/01\/01\/2023.12.30.573731.source.xml","abstract":"Primary vestibular afferents transmit information from hair cells about head position and movement to the CNS, which is critical for maintaining balance, gaze stability and spatial navigation. The CNS, in turn, modulates hair cells and afferents via the efferent vestibular system (EVS) and its activation of several cholinergic signaling mechanisms. Electrical stimulation of EVS neurons gives rise to three kinetically- and mechanistically-distinct afferent responses including a slow excitation, a fast excitation, and a fast inhibition. EVS-mediated slow excitation is attributed to odd-numbered muscarinic acetylcholine receptors (mAChRs) on the afferent whose activation leads to the closure of a potassium conductance and increased afferent discharge.\n\nLikely effector candidates include low-threshold, voltage-gated potassium channels belonging to the KCNQ (Kv7.X) family, which are involved in neuronal excitability across the nervous system and are subject to mAChR modulation. Specifically, KCNQ2\/3 heteromeric channels may be the molecular correlates for the M-current, a potassium current that is blocked following the activation of odd-numbered mAChRs. To this end, multiple members of the KCNQ channel family, including KCNQ2 and KCNQ3, are localized to several microdomains within vestibular afferent endings, where they influence afferent excitability and could be targeted by EVS neurons. Additionally, the relative expression of KCNQ subunits appears to vary across the sensory epithelia and among different afferent types. However, it is unclear which KCNQ channel subunits are targeted by mAChR activation and whether that also varies among different afferent classes. Here we show that EVS-mediated slow excitation is blocked and enhanced by the non-selective KCNQ channel blocker XE991 and opener retigabine, respectively. Using KCNQ subunit-selective drugs, we observed that a KCNQ2 blocker blocks the slow response in irregular afferents, while a KCNQ2\/3 opener enhances slow responses in regular afferents. The KCNQ2 blockers did not appear to affect resting afferent discharge rates, while KCNQ2\/3 or KCNQ2\/4 openers decreased afferent excitability. Here, we show pharmacological evidence that KCNQ2\/3 subunits are likely targeted by mAChR activation in mammalian vestibular afferents. Additionally, we show that KCNQ3 KO mice have altered resting discharge rate as well as EVS-mediated slow response. These data together suggest that KCNQ channels play a role in slow response and discharge rate of vestibular afferents, which can be modulated by EVS in mammals.","funder":"NA","published":"NA","server":"bioRxiv"},{"title":"Synaptic connectivity and electrophysiological properties of the nucleus of the lateral olfactory tract","authors":"Penker, S.; Lawabny, N.; Dhamshy, A.; Licht, T.; Rokni, D.","author_corresponding":"Dan Rokni","author_corresponding_institution":"Hebrew University","doi":"10.1101\/2023.12.31.573522","date":"2024-01-01","version":"1","type":"new results","license":"cc_by_nc","category":"neuroscience","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/01\/01\/2023.12.31.573522.source.xml","abstract":"The sense of smell is tightly linked to emotions, a link that is thought to rely on the direct synaptic connections between the olfactory bulb and nuclei of the amygdala. A small number of amygdaloid nuclei are the recipients of such direct input from the olfactory bulb and their unique functions are not known. Among them, the nucleus of the lateral olfactory tract (NLOT) is unique in its developmental history and gene expression. NLOT has been very little studied and consequentially its function is unknown. Furthermore, formulation of informed hypotheses about NLOT function is at this stage limited by the lack of knowledge about its connectivity and physiological properties. Here, we used pseudo-rabies tracing methods to systematically reveal monosynaptic inputs into NLOT, and adeno-associated viruses to reveal NLOT projection targets. We found that the NLOT is interconnected with several olfactory brain regions and with the basolateral amygdala. Some of these connections were reciprocal, and some showed unique interhemispheric patterns. We tested the excitable properties of NLOT neurons and the properties of each of the major synaptic inputs. We found that the NLOT receives powerful input from piriform cortex, tenia tecta, and the basolateral amygdala, but only very weak input from the olfactory bulb. When input crosses threshold, NLOT neurons respond with calcium-dependent bursts of action potentials. This integration of olfactory and amygdalar inputs suggests that NLOT plays a role in behaviors that combine smell and emotion, possibly assigning emotional value to odors.\n\nSignificance statementDespite the well-known functional links between olfaction and emotions, the physiological properties of these links remain largely understudied. One major pathway by which olfactory and emotional signals interact, is via the nucleus of the lateral olfactory tract (NLOT). NLOT has been little studied and its function is yet unclear. The lack of physiological information hinders informed hypotheses. Here, we characterize the synaptic and intrinsic properties of NLOT neurons. We show that the NLOT receives converging olfactory and amygdalar inputs, and that NLOT neurons respond to input with high-rate bursts of action potentials. This suggests that the NLOT, that harbors [~]2500 cells, encodes a low-dimensional signal that is of high importance. We hypothesize that the NLOT assigns emotional value to odors.","funder":"NA","published":"10.1523\/JNEUROSCI.2420-23.2024","server":"bioRxiv"},{"title":"Transcriptomic Analysis Identifies Candidate Genes for Differential Expression during Xenopus laevis Inner Ear Development","authors":"Virk, S. M.; Trujillo-Provencio, C.; Serrano, E. E.","author_corresponding":"Elba E. Serrano","author_corresponding_institution":"New Mexico State University","doi":"10.1101\/2023.12.29.573599","date":"2024-01-01","version":"1","type":"new results","license":"cc_by","category":"neuroscience","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/01\/01\/2023.12.29.573599.source.xml","abstract":"BackgroundThe genes involved in inner ear development and maintenance of the adult organ have yet to be fully characterized. Previous genetic analysis has emphasized the early development that gives rise to the otic vesicle. This study aimed to bridge the knowledge gap and identify candidate genes that are expressed as the auditory and vestibular sensory organs continue to grow and develop until the systems reach postmetamorphic maturity.\n\nMethodsAffymetrix microarrays were used to assess inner ear transcriptome profiles from three Xenopus laevis developmental ages where all eight endorgans comprise mechanosensory hair cells: larval stages 50 and 56, and the post-metamorphic juvenile. Pairwise comparisons were made between the three developmental stages and the resulting differentially expressed X. laevis Probe Set IDs (Xl-PSIDs) were assigned to four groups based on differential expression patterns. DAVID analysis was undertaken to impart functional annotation to the differentially regulated Xl-PSIDs.\n\nResultsAnalysis identified 1510 candidate genes for differential gene expression in one or more pairwise comparison. Annotated genes not previously associated with inner ear development emerged from this analysis, as well as annotated genes with established inner ear function, such as oncomodulin, neurod1, and sp7. Notably, 36% of differentially expressed Xl-PSIDs were unannotated.\n\nConclusionsResults draw attention to the complex gene regulatory patterns that characterize Xenopus inner ear development, and underscore the need for improved annotation of the X. laevis genome. Outcomes can be utilized to select candidate inner ear genes for functional analysis, and to promote Xenopus as a model organism for biomedical studies of hearing and balance.","funder":"NA","published":"NA","server":"bioRxiv"},{"title":"Mechanisms of alcohol influence on fear conditioning: a computational model","authors":"Lonnberg, A.; Logrip, M. L.; Kuznetsov, A.","author_corresponding":"Alexey Kuznetsov","author_corresponding_institution":"IUPUI","doi":"10.1101\/2023.12.30.573310","date":"2024-01-01","version":"1","type":"new results","license":"cc_by_nd","category":"neuroscience","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/01\/01\/2023.12.30.573310.source.xml","abstract":"A connection between stress-related illnesses and alcohol use disorders is extensively documented. Fear conditioning is a standard procedure used to study stress learning and links it to the activation of amygdala circuitry. However, the connection between the changes in amygdala circuit and function induced by alcohol and fear conditioning is not well established. We introduce a computational model to test the mechanistic relationship between amygdala functional and circuit adaptations during fear conditioning and the impact of acute vs. repeated alcohol exposure. In accordance with experiments, both acute and prior repeated alcohol decreases speed and robustness of fear extinction in our simulations. The model predicts that, first, the delay in fear extinction in alcohol is mostly induced by greater activation of the basolateral amygdala (BLA) after fear acquisition due to alcohol-induced modulation of synaptic weights. Second, both acute and prior repeated alcohol shifts the amygdala network away from the robust extinction regime by inhibiting the activity in the central amygdala (CeA). Third, our model predicts that fear memories formed in acute or after chronic alcohol are more connected to the context. Thus, the model suggests how circuit changes induced by alcohol may affect fear behaviors and provides a framework for investigating the involvement of multiple neuromodulators in this neuroadaptive process.","funder":"NA","published":"10.1111\/acer.70071","server":"bioRxiv"},{"title":"The brainstem's red nucleus was evolutionarily upgraded to support goal-directed action","authors":"Krimmel, S. R.; Laumann, T. O.; Chauvin, R.; Hershey, T.; Roland, J. L.; Shimony, J. S.; Willie, J. T.; Norris, S. A.; Marek, S.; Van, A. N.; Monk, J.; Scheidter, K. M.; Whiting, F.; Ramirez-Perez, N.; Metoki, A.; Wang, A.; Kay, B. P.; Nahman-Averbuch, H.; Fair, D. A.; Lynch, C. J.; Raichle, M. E.; Gordon, E. M.; Dosenbach, N. U. F.","author_corresponding":"Samuel R Krimmel","author_corresponding_institution":"Washington University in St. Louis","doi":"10.1101\/2023.12.30.573730","date":"2024-01-01","version":"1","type":"new results","license":"cc_by_nc","category":"neuroscience","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/01\/01\/2023.12.30.573730.source.xml","abstract":"The red nucleus is a large brainstem structure that coordinates limb movement for locomotion in quadrupedal animals (Basile et al., 2021). The humans red nucleus has a different pattern of anatomical connectivity compared to quadrupeds, suggesting a unique purpose (Hatschek, 1907). Previously the function of the human red nucleus remained unclear at least partly due to methodological limitations with brainstem functional neuroimaging (Sclocco et al., 2018). Here, we used our most advanced resting-state functional connectivity (RSFC) based precision functional mapping (PFM) in highly sampled individuals (n = 5) and large group-averaged datasets (combined N [~] 45,000), to precisely examine red nucleus functional connectivity.\n\nNotably, red nucleus functional connectivity to motor-effector networks (somatomotor hand, foot, and mouth) was minimal. Instead, red nucleus functional connectivity along the central sulcus was specific to regions of the recently discovered somato-cognitive action network (SCAN; (Gordon et al., 2023)). Outside of primary motor cortex, red nucleus connectivity was strongest to the cingulo-opercular (CON) and salience networks, involved in action\/cognitive control (Dosenbach et al., 2007; Newbold et al., 2021) and reward\/motivated behavior (Seeley, 2019), respectively. Functional connectivity to these two networks was organized into discrete dorsal-medial and ventral-lateral zones. Red nucleus functional connectivity to the thalamus recapitulated known structural connectivity of the dento-rubral thalamic tract (DRTT) and could prove clinically useful in functionally targeting the ventral intermediate (VIM) nucleus. In total, our results indicate that far from being a  motor structure, the red nucleus is better understood as a brainstem nucleus for implementing goal-directed behavior, integrating behavioral valence and action plans.","funder":"NA","published":"NA","server":"bioRxiv"},{"title":"Precision Genome Editing Unveils a Breakthrough in Reversing Antibiotic Resistance: CRISPR\/Cas9 Targeting of Multi-Drug Resistance Genes in Methicillin-Resistant Staphylococcus aureus","authors":"Ates, A.; Tastan, C.; Ermertcan, S.","author_corresponding":"Aysegul Ates","author_corresponding_institution":"Ege University","doi":"10.1101\/2023.12.31.573511","date":"2024-01-01","version":"1","type":"new results","license":"cc_by_nc_nd","category":"microbiology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/01\/01\/2023.12.31.573511.source.xml","abstract":"Antibiotic resistance poses a global health crisis, limiting the efficacy of available therapeutic agents and hindering the development of new antibiotics. The pharmaceutical industrys waning interest in antibiotic production further exacerbates this challenge. Addressing antibiotic resistance demands innovative solutions. Here, we explore the application of CRISPR-Cas-based antimicrobials as a pioneering approach to combat multidrug resistance. Our study focuses on the methicillin-resistant clinical Staphylococcus aureus (MRSA), a significant clinical threat. Utilizing CRISPR\/Cas9 technology, we aimed to concurrently target methicillin (mecA), gentamicin (aacA), and ciprofloxacin (grlA, grlB) resistance genes, thereby altering the resistance profile and enhancing sensitivity to antibiotics. We engineered CRISPR plasmids containing sgRNAs specific to the target regions, which were subsequently electroporated into MRSA strains. Real-time Polymerase Chain Reaction (RT-PCR) assessed changes in resistance gene expression, while disk diffusion and broth microdilution methods determined alterations in resistance status. Western blotting analyzed changes in PBP2a expression, and Sanger sequence analysis confirmed mutations in target regions. Results revealed a statistically significant 1.5-fold decrease in mecA gene expression, 5.5-fold decrease in grlA gene, 6-fold decrease in grlB gene, and 4-fold decrease in aacA gene compared to the wild type strain, as determined by RT-PCR. Antibiotic susceptibility tests demonstrated the suppression of mecA, grlA, grlB, and aacA genes, resulting in the reversal of resistance to beta-lactam, quinolone, and aminoglycoside antibiotics. Western blot analysis showed 70% decrease in PBP2a expression, indicating the breakdown of beta-lactam resistance. Sanger sequence analysis confirmed point mutations in grlB and aacA genes, along with three-base mutations in grlA and mecA genes. Our findings underscore the potential of CRISPR\/Cas9 technology to mitigate antibiotic resistance, offering a transformative strategy to restore the efficacy of existing antibiotics in the face of multidrug-resistant pathogens.","funder":"NA","published":"NA","server":"bioRxiv"},{"title":"Nucleoid-associated proteins shape the global protein occupancy and transcriptional landscape of a clinical isolate of Vibrio cholerae","authors":"Rakibova, Y.; Dunham, D. T.; Seed, K. D.; Freddolino, L.","author_corresponding":"Lydia Freddolino","author_corresponding_institution":"University of Michigan","doi":"10.1101\/2023.12.30.573743","date":"2024-01-01","version":"1","type":"new results","license":"cc_by_nc_nd","category":"microbiology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/01\/01\/2023.12.30.573743.source.xml","abstract":"Vibrio cholerae, the causative agent of the diarrheal disease cholera, poses an ongoing health threat due to its wide repertoire of horizontally acquired elements (HAEs) and virulence factors. New clinical isolates of the bacterium with improved fitness abilities, often associated with HAEs, frequently emerge. The appropriate control and expression of such genetic elements is critical for the bacteria to thrive in the different environmental niches it occupies. H-NS, the histone-like nucleoid structuring protein, is the best studied xenogeneic silencer of HAEs in gamma-proteobacteria. Although H-NS and other highly abundant nucleoid-associated proteins (NAPs) have been shown to play important roles in regulating HAEs and virulence in model bacteria, we still lack a comprehensive understanding of how different NAPs modulate transcription in V. cholerae. By obtaining genome-wide measurements of protein occupancy and active transcription in a clinical isolate of V. cholerae, harboring recently discovered HAEs encoding for phage defense systems, we show that a lack of H-NS causes a robust increase in the expression of genes found in many HAEs. We further found that TsrA, a protein with partial homology to H-NS, regulates virulence genes primarily through modulation of H-NS activity. We also identified a few sites that are affected by TsrA independently of H-NS, suggesting TsrA may act with diverse regulatory mechanisms. Our results demonstrate how the combinatorial activity of NAPs is employed by a clinical isolate of an important pathogen to regulate recently discovered HAEs.\n\nImportanceNew strains of the bacterial pathogen Vibrio cholerae, bearing novel horizontally acquired elements (HAEs), frequently emerge. HAEs provide beneficial traits to the bacterium, such as antibiotic resistance and defense against invading bacteriophages. Xenogeneic silencers are proteins that help bacteria harness new HAEs and silence those HAEs until they are needed. H-NS is the best-studied xenogeneic silencer; it is one of the nucleoid-associated proteins (NAPs) in gamma-proteobacteria and is responsible for the proper regulation of HAEs within the bacterial transcriptional network. We studied the effects of H-NS and other NAPs on the HAEs of a clinical isolate of V. cholerae. Importantly, we found that H-NS partners with a small and poorly characterized protein, TsrA, to help domesticate new HAEs involved in bacterial survival and in causing disease. Proper understanding of the regulatory state in emerging isolates of V. cholerae will provide improved therapies against new isolates of the pathogen.","funder":"NA","published":"NA","server":"bioRxiv"},{"title":"Beyond Basic Characterization and Omics: Immunomodulatory Roles of Platelet-Derived Extracellular Vesicles Unveiled by Functional Testing","authors":"Palviainen, M.; Puutio, J.; Ostergaard, R. H.; Eble, J. A.; Maaninka, K.; Ndika, J.; Kari, O. K.; Kamali-Moghaddam, M.; Kjaer-Sorensen, K.; Oxvig, C.; Aransay, A. M.; Falcon-Perez, J. M.; Federico, A.; Greco, D.; Laitinen, S.; Hayashi, Y.; Siljander, P. R.-M.","author_corresponding":"Pia R-M Siljander","author_corresponding_institution":"University of Helsinki","doi":"10.1101\/2023.12.31.570750","date":"2024-01-01","version":"1","type":"new results","license":"cc_no","category":"cell biology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/01\/01\/2023.12.31.570750.source.xml","abstract":"Renowned for their role in hemostasis and thrombosis, platelets are also increasingly recognized for their contribution in innate immunity, immunothrombosis and inflammatory diseases. Platelets express a wide range of receptors, which allows them to reach a variety of activation endpoints and grants them immunomodulatory functions. Activated platelets release extracellular vesicles (PEVs), whose formation and molecular cargo has been shown to depend on receptor-mediated activation and environmental cues.\n\nThis study compares the immunomodulatory profiles of PEVs generated via activation of platelets by different receptors, glycoprotein VI, C-type lectin-like receptor 2, and combining all thrombin-collagen receptors. Functional assays in vivo in zebrafish and in vitro in human macrophages respectively highlighted distinct homing and secretory responses triggered by the PEVs. In contrast, omics analyses of protein and miRNA cargo combined with physicochemical particle characterization found only subtle differences between the PEV types, which were insufficient to explain their different functional immunomodulatory profiles. Constitutively released PEVs, formed in the absence of an exogenous activator, displayed a disparate activation profile from the receptor induced PEVs.\n\nOur findings underscore that PEVs are tunable through receptor-mediated activation. To truly comprehend their role(s) in mediating platelet functions among immune cells, conducting functional assays is imperative.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=140 SRC=\"FIGDIR\/small\/570750v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (53K):\norg.highwire.dtl.DTLVardef@75a9dborg.highwire.dtl.DTLVardef@e2787corg.highwire.dtl.DTLVardef@543525org.highwire.dtl.DTLVardef@6d1362_HPS_FORMAT_FIGEXP  M_FIG C_FIG","funder":"NA","published":"10.1002\/jev2.12513","server":"bioRxiv"},{"title":"Rapid turnover of CTLA4 is associated with a complex architecture of reversible ubiquitylation.","authors":"Tey, P. Y.; Dufner, A.; Knobeloch, K.-P.; Pruneda, J. N.; Clague, M. J.; Urbe, S.","author_corresponding":"Sylvie Urbe","author_corresponding_institution":"University of Liverpool","doi":"10.1101\/2023.12.31.573735","date":"2024-01-01","version":"1","type":"new results","license":"cc_by_nc_nd","category":"cell biology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/01\/01\/2023.12.31.573735.source.xml","abstract":"The immune checkpoint regulator CTLA4 is an unusually short-lived membrane protein. Here we show that its lysosomal degradation is dependent on ubiquitylation at Lysine residues 203 and 213. Inhibition of the v-ATPase partially restores CTLA4 levels following cycloheximide treatment, but also reveals a fraction that is secreted in exosomes. The endosomal deubiquitylase, USP8, interacts with CTLA4 and its loss enhances CTLA4 ubiquitylation in cancer cells, mouse CD4+ T cells and in cancer cell-derived exosomes. Depletion of the USP8 adapter protein, HD-PTP, but not ESCRT-0 recapitulates this cellular phenotype, but shows distinct properties vis-a-vis exosome incorporation. Re-expression of wild-type USP8, but neither a catalytically inactive, nor a localisation-compromised {Delta}MIT domain mutant can rescue delayed degradation of CTLA4, or counteract its accumulation in clustered endosomes. UbiCRest analysis of CTLA4-associated ubiquitin chain linkages identifies a complex mixture of conventional Lys63- and more unusual Lys27- and Lys29-linked polyubiquitin chains that may underly the rapidity of protein turnover.","funder":"NA","published":"10.1083\/jcb.202312141","server":"bioRxiv"},{"title":"Development of a PROTAC Targeting Chk1","authors":"Chowdhury, S. R.; Chuong, P.; Mgbemena, V. E.; Statsyuk, A. V.","author_corresponding":"Alexander V Statsyuk","author_corresponding_institution":"University of Houston","doi":"10.1101\/2023.12.30.573733","date":"2024-01-01","version":"1","type":"new results","license":"cc_by_nc_nd","category":"cell biology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/01\/01\/2023.12.30.573733.source.xml","abstract":"A series of Chk1 degraders were designed and synthesized. The degraders were developed through the conjugation of a promiscuous kinase binder and thalidomide. One of the degraders PROTAC-2 was able to decrease Chk1 levels in a concentration-dependent manner in A375 cells. The developed probes can be useful for the development of selective and more potent Chk1 degraders.","funder":"NA","published":"NA","server":"bioRxiv"},{"title":"Cell density couples tissue mechanics to control the elongation speed of the body axis","authors":"Lu, C.; Vidigueira, J. M. N.; Jie, C. C. J.; Maksymiuk, A.; Xiong, F.","author_corresponding":"Fengzhu Xiong","author_corresponding_institution":"University of Cambridge","doi":"10.1101\/2023.12.31.573670","date":"2024-01-01","version":"1","type":"new results","license":"cc_by","category":"developmental biology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/01\/01\/2023.12.31.573670.source.xml","abstract":"The vertebrate body forms by addition of new tissues at the posterior end. This leads to body axis elongation which balances the anterior segmentation process to produce the stereotypic body plan. How elongation speed is constrained remains unknown. Here we utilised modeling and tissue force microscopy on chicken embryos to show that cell density of the posterior presomitic mesoderm (pPSM) dynamically modulates elongation speed in a negative feedback loop. Elongation alters the cell density in the pPSM, which in turn controls progenitor cell influx through the mechanical coupling of body axis tissues. This enables responsive cell dynamics in over- and under-elongated axes that consequently self-adjust speed to achieve long-term robustness in axial length. Our simulations and experiments further suggest that cell density and FGF activity act synergistically to drive elongation. Our work supports a simple mechanism of morphogenetic speed control where the cell density relates negatively to progress, and positively to force generation.","funder":"NA","published":"10.1016\/j.isci.2024.110968","server":"bioRxiv"},{"title":"Discovery of Waddington's developmental canals elucidates the embryogenesis stability in Caenorhabditis elegans","authors":"Wang, J.; xiao, l.; yao, z.; deng, s.; Yang, J.-R.; Wu, C.-I.; Du, Z.; He, X.","author_corresponding":"Xionglei He","author_corresponding_institution":"State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China","doi":"10.1101\/2023.12.30.573745","date":"2024-01-01","version":"1","type":"new results","license":"cc_by_nc_nd","category":"developmental biology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/01\/01\/2023.12.30.573745.source.xml","abstract":"During embryogenesis, the cells in an embryo need to make numerous spatiotemporal decisions. However, there is inherent noise in each decision due to genetic or environmental fluctuations. How to suppress the noise accumulation to achieve stable embryonic end-products, a process known as Waddingtons developmental canalization, has been a major puzzle in biology since the 1940s. Previous studies have focused on the molecular noise within a cell instead of the cell noise within an embryo, thus providing indirect understandings (e,g., the well-known genetic capacitor Hsp90). In this study, we applied time-lapse microscopic imaging to capturing the spatiotemporal features of single cells, including cell position and cell cycle length, during the embryogenesis of approximately 2,100 Caenorhabditis elegans embryos exposed to various genetic or environmental perturbations. By treating the deviation of a cells spatiotemporal feature from the expected value as noise, we modeled the transmission of noise from each mother cell to their daughters. We discovered pervasive mother-daughter negative feedbacks, which collectively constitute continuous and comprehensive  canals for suppressing noise accumulation along the developmental cell lineages, with the steepness (measuring noise suppression efficacy) and depth (measuring noise tolerance level) of the canals quantitatively defined. The learned quantitative rules enabled us to develop a cell-noise-based model that accurately predicts the nematode hatching phenotype, revealing how embryonic stochasticity could cause phenotypic disparity. With a high-dimensional mathematical tool we then proved the system stability of embryogenesis against the cell spatiotemporal noise. We also revealed several dozen canal-maintaining genes and proposed a novel association study framework that links embryonic cells rather than genetic variants with organismal traits. In sum, this study discovered and quantitatively characterized the developmental canals that directly stabilize embryogenesis in a metazoan, illuminating an 80-year-old puzzle and paving a way for studying the phenotypic plasticity and robustness of multicellular organisms from the perspective of embryogenesis.","funder":"NA","published":"NA","server":"bioRxiv"},{"title":"Indirect effects of habitat amount mediated by habitat configuration determine bat diversity at the landscape-scale in Peninsular Malaysia","authors":"Hazard, Q. C. K.; Yoh, N.; Moore, J.; Senawi, J.; Gibson, L.; Froidevaux, J. S. P.; Palmeirim, A. F.","author_corresponding":"Quentin C.K. Hazard","author_corresponding_institution":"CIBIO, Centro de Investigacao em Biodiversidade e Recursos Geneticos, InBIO Laboratorio Associado, Campus de Vairao","doi":"10.1101\/2023.12.30.573737","date":"2024-01-01","version":"1","type":"new results","license":"cc_no","category":"ecology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/01\/01\/2023.12.30.573737.source.xml","abstract":"The impacts of fragmentation are often overlooked in landscape studies investigating how habitat loss impacts biodiversity, despite the casual relationship linking both processes. As habitat loss is the primary cause of fragmentation, understanding the inter-related effects of these twin processes on biodiversity is key to minimise biodiversity loss. Here we assess how habitat amount and configuration influence insectivorous bat assemblages, considering both the direct effects of these processes, as well as the indirect effects of habitat amount mediated through configuration. Bats were acoustically surveyed along independent gradients of habitat amount (forest cover) and configuration (number of patches and edge density) across 28 insular landscapes embedded within a Malaysian hydroelectric reservoir. Using Structural Equation Modelling, the direct and indirect effects of habitat amount were examined on bat sonotype richness, total, and guild-specific activity (forest, edge and open-space foragers). Forest cover had a direct and positive effect on sonotype richness and forest forager activity. The quadratic relationship linking edge density and forest cover was strong and overall positive, but while below 30% of forest cover, increasingly forested landscapes had increasingly high edge densities, the opposite pattern was observed in more forested landscapes. On the other hand, increasingly forested landscapes consistently harboured less patches. Owing to the overall low habitat amount in our landscapes and negative edge effects, the indirect effects of forest cover (mediated through edge density) were therefore negative on sonotype richness, outweighing any positive direct effect. The number of patches had little effect on the bat assemblage, except on total activity which was higher in landscapes harbouring more forest patches. As a result, negative indirect effects of forest cover mediated through number of patches were only observed on total activity. Our results highlight that, in natural settings, habitat amount can hardly be altered without influencing habitat configuration, thereby preventing any independent management of these threats. Minimising habitat loss is therefore essential to balance the associated prevailing negative effects of fragmentation on insectivorous bats across tropical forests.","funder":"NA","published":"NA","server":"bioRxiv"},{"title":"Genomic signatures of the evolution of loss of egg yolk in parasitoid wasps","authors":"Zhao, X.; Liu, Y.; Yang, Y.; He, C.; Chan, K. C.; Lin, H.; Fang, Q.; Ye, G.; Ye, X.","author_corresponding":"Xinhai Ye","author_corresponding_institution":"College of Advanced Agriculture Science, Zhejiang A&F University, Hangzhou 311300, China","doi":"10.1101\/2023.12.30.573744","date":"2024-01-01","version":"1","type":"new results","license":"cc_no","category":"evolutionary biology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/01\/01\/2023.12.30.573744.source.xml","abstract":"Trait regression and loss have occurred repeatedly in numerous lineages throughout evolutionary history in response to changing environments. In parasitoid wasps, a mega-diverse group of hymenopteran insects, loss or reduction of yolk in the egg has been reported in many species. This phenotypic change likely evolved as a response to the shift from ectoparasitism to endoparasitism. However, the genetic basis of this trait and the impact of its loss on genome evolution remain poorly understood. Here, we performed a comparative genomic analysis of 64 hymenopteran insects. The conserved insect yolk protein gene vitellogenin (Vg) underwent five independent loss events in four families, involving 23 of the analyzed endoparasitoid species. Whole-genome alignment suggested that Vg loss occurred during genome rearrangement events. Analysis of Vg receptor gene (VgR) loss, selection, and structural variation in lineages lacking Vg demonstrated functional biases in the patterns of gene loss. The ectoparasitism to endoparasitism transition did not appear to be the primary driver of Vg loss or the subsequent VgR evolution. A number of parallel and convergent genomic changes were observed between Vg-loss lineages, including gene family evolution and selection of genes related to transport, development, and metabolism. These changes may have facilitated embryonic development without the yolk in these lineages. Together, these findings reveal the genomic basis underlying a unique trait loss in parasitoid wasps. More broadly, this study enhances our understanding of yolk loss evolution outside the class Mammalia, highlighting a potential evolutionary trend arising from the availability of an alternative nutrient source for embryonic development.","funder":"NA","published":"10.1073\/pnas.2422292122","server":"bioRxiv"},{"title":"Functional consequences of reductive protein evolution in a minimal eukaryotic genome","authors":"Jiang, J.; Qu, R.; Grigorescu, M.; Zhao, W.; Reinke, A. W.","author_corresponding":"Aaron W Reinke","author_corresponding_institution":"University of Toronto","doi":"10.1101\/2023.12.31.573788","date":"2024-01-01","version":"1","type":"new results","license":"cc_by","category":"evolutionary biology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/01\/01\/2023.12.31.573788.source.xml","abstract":"Microsporidia are parasites with the smallest known eukaryotic genomes. The extent of protein loss in these organisms has been well documented, but much less is known about how compaction of microsporidia proteins affects their function. Taking a comparative genomic approach, we identified microsporidia orthologs of budding yeast proteins and show that these orthologs are enriched for essential yeast genes. We show that the median microsporidia protein is 21% shorter than its yeast counterpart and although extensive protein loss occurred after the divergence of microsporidia, reduced protein sizes were already present in microsporidian relatives. Microsporidia proteins are shorter through reduced domain lengths, diminished linker lengths, and domain loss, with 21% of microsporidia orthologs having lost domains present in yeast. On average, 34% of microsporidia orthologs have lost C-terminal residues essential for function in yeast, including 13 essential domains lost per genome. We also found that microsporidia display distinct phylogenetic patterns of domain loss, with losses occurring in a clade-specific manner. To investigate conservation of function, we used yeast complementation assays to test orthologs from several microsporidia species and their relative Rozella allomycis. These experiments reveal that most microsporidia proteins cannot complement their yeast orthologs, the ability to complement is about three-fold less than observed for R. allomycis orthologs, and proteins that do not complement are more reduced in length than their yeast orthologs. Altogether, our results demonstrate the drastic reduction of microsporidia proteins and show that these reductions have resulted in functional divergence from their fungal ancestors.","funder":"NA","published":"10.1016\/j.celrep.2025.116333","server":"bioRxiv"},{"title":"Phylogenomics analyses of all species of Swordtails (Genus Xiphophorus) highlights hybridization precedes speciation","authors":"Du, K.; Lu, Y.; Garcia-Olazabal, M.; Walter, R. B.; Warren, W. C.; Dodge, T.; Schumer, M.; Park, H.; Meyer, A.; Schartl, M.","author_corresponding":"Manfred Schartl","author_corresponding_institution":"The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas, TX 78666, USA; Developmental Biochemi","doi":"10.1101\/2023.12.30.573732","date":"2024-01-01","version":"1","type":"new results","license":"cc_no","category":"genomics","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/01\/01\/2023.12.30.573732.source.xml","abstract":"Hybridization has been recognized as an important driving force for evolution, however studies of the genetic consequence and its cause are still lagging behind in vertebrates due to the lack of appropriate experimental systems. Fish of the central American genus Xiphophorus were proposed to have evolved with multiple ancient and ongoing hybridization events, and served as a valuable research model in evolutionary biology and in biomedical research on human disease for more than a century. Here, we provide the complete genome resource and its annotation of all 26 Xiphophorus species. On this dataset we resolved the so far conflicting phylogeny. Through comparative genomic analyses we investigated the molecular evolution of genes related to melanoma, for a main sexually selected trait and for the genetic control of puberty timing, which are predicted to be involved in pre-and postzygotic isolation and thus to influence the probability of interspecific hybridization in Xiphophorus. We demonstrate dramatic size-variation of some gene families across species, despite the reticulate evolution and short divergence time. Finally, we clarify the hybridization history in the genus Xiphophorus genus, settle the long dispute on the hybridization origin of two Southern swordtails, highlight hybridizations precedes speciation, and reveal the distribution of hybridization ancestry remaining in the fused genome.","funder":"NA","published":"NA","server":"bioRxiv"},{"title":"Piggybacking functionalized DNA nanostructures into live cell nuclei","authors":"Roozbahani, G. M.; Colosi, P.; Oravecz, A.; Sorokina, E. M.; Pfeifer, W.; Shokri, S.; Wei, Y.; Didier, P.; DeLuca, M.; Arya, G.; Tora, L.; Lakadamyali, M.; Poirier, M. G.; Castro, C.","author_corresponding":"Carlos Castro","author_corresponding_institution":"The Ohio State University","doi":"10.1101\/2023.12.30.573746","date":"2024-01-01","version":"1","type":"new results","license":"cc_by_nc","category":"bioengineering","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/01\/01\/2023.12.30.573746.source.xml","abstract":"DNA origami (DO) are promising tools for in vitro or in vivo applications including drug delivery; biosensing, detecting biomolecules; and probing chromatin sub-structures. Targeting these nanodevices to mammalian cell nuclei could provide impactful approaches for probing visualizing and controlling important biological processes in live cells. Here we present an approach to deliver DO strucures into live cell nuclei. We show that labelled DOs do not undergo detectable structural degradation in cell culture media or human cell extracts for 24 hr. To deliver DO platforms into the nuclei of human U2OS cells, we conjugated 30 nm long DO nanorods with an antibody raised against the largest subunit of RNA Polymerase II (Pol II), a key enzyme involved in gene transcription. We find that DOs remain structurally intact in cells for 24hr, including within the nucleus. Using fluorescence microscopy we demonstrate that the electroporated anti-Pol II antibody conjugated DOs are efficiently piggybacked into nuclei and exihibit sub-diffusive motion inside the nucleus. Our results reveal that functionalizing DOs with an antibody raised against a nuclear factor is a highly effective method for the delivery of nanodevices into live cell nuclei.","funder":"NA","published":"NA","server":"bioRxiv"},{"title":"Pharmacological inhibition of mTORC1 reduces neural death and damage volume after MCAO by modulating microglial reactivity","authors":"Villa-Gonzalez, M.; Rubio, M.; Martin-Lopez, G.; R. Mallavibarrena, P.; Valles-Saiz, L.; Vivien, D.; Wandosell Jurado, F.; Perez-Alvarez, M. J.","author_corresponding":"Maria Jose Perez-Alvarez","author_corresponding_institution":"Universidad Autonoma de Madrid, Madrid (Spain)","doi":"10.1101\/2023.12.31.571469","date":"2024-01-01","version":"1","type":"new results","license":"cc_no","category":"neuroscience","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/01\/01\/2023.12.31.571469.source.xml","abstract":"Ischemic stroke is a sudden and acute disease characterized by neuronal death, glia activation, and a severe inflammatory process. Neuroinflammation is an early event after cerebral ischemia, with microglia playing a leading role. Microglial activation involves functional and morphological changes that drive a wide variety of phenotypes. In this context, deciphering the molecular mechanisms underlying such microglial activation is essential to devise strategies to protect neurons and maintain certain brain functions affected by early neuroinflammation after ischemia.\n\nHere, we studied the role of mammalian target of rapamycin (mTOR) activity in the microglial response using a murine model of cerebral ischemia in the acute phase. We also determined the therapeutic relevance of the pharmacological administration of rapamycin, a mTOR inhibitor, before and after ischemic injury.\n\nOur data show that rapamycin, administered before or after brain ischemia induction, reduced the volume of brain damage and neuronal loss by attenuating the microglial response. Therefore, our findings indicate that the pharmacological inhibition of mTORC1 in the acute phase of ischemia may provide an alternative strategy to reduce neuronal damage through attenuation of the associated neuroinflammation.","funder":"NA","published":"10.1186\/s13062-024-00470-5","server":"bioRxiv"},{"title":"Transcranial direct current stimulation alters cerebrospinal fluid-interstitial fluid exchange in mouse brain","authors":"Wang, Y.; Monai, H.","author_corresponding":"Hiromu Monai","author_corresponding_institution":"Graduate School of Humanities and Sciences, Ochanomizu University","doi":"10.1101\/2023.12.30.573695","date":"2024-01-01","version":"1","type":"new results","license":"cc_no","category":"neuroscience","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/01\/01\/2023.12.30.573695.source.xml","abstract":"BackgroundTranscranial direct current stimulation (tDCS) is a non-invasive brain stimulation technique that has gained prominence recently. Clinical studies have explored tDCS as an adjunct to neurologic disease rehabilitation, with evidence suggesting its potential in modulating brain clearance mechanisms. The glymphatic system, a proposed brain waste clearance system, posits that cerebrospinal fluid-interstitial fluid (CSF-ISF) exchange aids in efficient metabolic waste removal. While some studies have linked tDCS to astrocytes inositol trisphosphate (IP3)\/Ca2+ signaling, the impact of tDCS on CSF-ISF exchange dynamics remains unclear.\n\nHypothesistDCS influences the dynamics of CSF-ISF exchange through astrocytic IP3\/Ca2+ signaling.\n\nMethodsIn this study, we administered tDCS (0.1mA for 10 minutes) to C57BL\/6 mice anesthetized with ketamine-xylazine (KX). The anode was positioned on the cranial bone above the cortex, and the cathode was inserted into the neck. Following tDCS, we directly assessed brain fluid dynamics by injecting biotinylated dextran amine (BDA) as a CSF tracer into the cisterna magna (CM). The brain was then extracted after either 30 or 60 minutes and fixed. After 24 hours, the sectioned brain slices were stained with Alexa 594-conjugated streptavidin (SA) to visualize BDA using immunohistochemistry. We conducted Electroencephalography (EEG) recordings and aquaporin 4 (AQP4)\/CD31 immunostaining to investigate the underlying mechanisms of tDCS. Additionally, we monitored the efflux of Evans blue, injected into the cisterna magna, using cervical lymph node imaging. The experiments were subsequently repeated with inositol trisphosphate receptor type 2 (IP3R2)-knockout mice.\n\nResultsPost-tDCS, we observed an increased CSF tracer influx, indicating a modulation of CSF-ISF exchange by tDCS. Additionally, tDCS appeared to enhance the brains metabolic waste efflux. EEG recordings showed an increase in delta wave post-tDCS. But no significant change in AQP4 expression was detected 30 minutes post-tDCS.\n\nConclusionOur findings suggest that tDCS augments the glymphatic systems influx and efflux. Through astrocyte IP3\/Ca2+ signaling, tDCS was found to modify the delta wave, which correlates positively with brain clearance. This study underscores the potential of tDCS in modulating brain metabolic waste clearance.","funder":"NA","published":"10.1016\/j.brs.2024.04.009","server":"bioRxiv"},{"title":"Extinction Training Suppresses Activity of Fear Memory Ensembles Across the Hippocampus and Alters Transcriptomes of Fear-Encoding Cells","authors":"Zuniga, A.; Han, J.; Miller-Crews, I.; Agee, L. A.; Hofmann, H. A.; Drew, M. R.","author_corresponding":"Michael R Drew","author_corresponding_institution":"University of Texas at Austin","doi":"10.1101\/2023.12.31.573787","date":"2024-01-01","version":"1","type":"new results","license":"cc_no","category":"neuroscience","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/01\/01\/2023.12.31.573787.source.xml","abstract":"Contextual fear conditioning has been shown to activate a set of \"fear ensemble\" cells in the hippocampal dentate gyrus (DG) whose reactivation is necessary and sufficient for expression of contextual fear. We previously demonstrated that extinction learning suppresses reactivation of these fear ensemble cells and activates a competing set of DG cells - the \"extinction ensemble.\" Here, we tested whether extinction was sufficient to suppress reactivation in other regions and used single nucleus RNA sequencing (snRNA-seq) of cells in the dorsal dentate gyrus to examine how extinction affects the transcriptomic activity of fear ensemble and fear recall-activated cells. Our results confirm the suppressive effects of extinction in the dorsal and ventral dentate gyrus and demonstrate that this same effect extends to fear ensemble cells located in the dorsal CA1. Interestingly, the extinction-induced suppression of fear ensemble activity was not detected in ventral CA1. Our snRNA-seq analysis demonstrates that extinction training markedly changes transcription patterns in fear ensemble cells and that cells activated during recall of fear and recall of extinction have distinct transcriptomic profiles. Together, our results indicate that extinction training suppresses a broad portion of the fear ensemble in the hippocampus, and this suppression is accompanied by changes in the transcriptomes of fear ensemble cells and the emergence of a transcriptionally unique extinction ensemble.","funder":"NA","published":"10.1038\/s41386-024-01897-0","server":"bioRxiv"},{"title":"Neurotransmitter Genes in the Nucleus Accumbens that Are Involved in the Development of Behavioral Pathology After Positive Fighting Experiences and Their Deprivation. A Conceptual Paradigm for Neurogenomic Data Analysis","authors":"Kudryavtseva, N. N.; Smagin, D. A.; Redina, O. E.; Kovalenko, I. L.; Galyamina, A. G.; Babenko, V. N.","author_corresponding":"Natalia N Kudryavtseva","author_corresponding_institution":"FRC Institute of Cytology and Genetics, SB RAS","doi":"10.1101\/2023.12.30.573683","date":"2024-01-01","version":"1","type":"new results","license":"cc_no","category":"neuroscience","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/01\/01\/2023.12.30.573683.source.xml","abstract":"It has been shown earlier that repeated positive fighting experience in daily agonistic interactions is accompanied by the development of psychosis-like behavior with signs of an addiction-like state associated with changes in the expression of genes encoding the proteins involved in the main neurotransmitter events in some brain regions of aggressive male mice. Fighting deprivation (a no-fight period of 2 weeks) causes a significant increase in their aggressiveness. This paper is aimed at studying--after a period of fighting deprivation--the involvement of genes (associated with neurotransmitter systems within the nucleus accumbens) in the above phenomena. The nucleus accumbens is known to participate in reward-related mechanisms of aggression. We found the following differentially expressed genes (DEGs), whose expression significantly differed from that in controls and\/or mice with positive fighting experience in daily agonistic interactions followed by fighting deprivation: catecholaminergic genes Th, Drd1, Drd2, Adra2c, Ppp1r1b, and Maoa; serotonergic genes Maoa, Htr1a, Htr1f, and Htr3a; opioidergic genes Oprk1, Pdyn, and Penk; and glutamatergic genes Grid1, Grik4, Grik5, Grin3a, Grm2, Grm5, Grm7, and Gad1. The expression of DEGs encoding proteins of the GABAergic system in experienced aggressive male mice mostly returned to control levels after fighting deprivation except for Gabra5. In light of the conceptual paradigm for analyzing data that was chosen in our study, the aforementioned DEGs associated with the behavioral pathology can be considered responsible for consequences of aggression followed by fighting deprivation, including mechanisms of an aggression relapse.","funder":"NA","published":"10.3390\/ijms26178580","server":"bioRxiv"},{"title":"Decoding of resting-state using task-based multivariate pattern analysis supports the Incentive-Sensitization Theory in nicotine use disorder","authors":"Lor, C. S.; Steyrl, D.; Zhang, M.; Zhou, F.; Becker, B.; Herdener, M.; Quednow, B. B.; Haugg, A.; Scharnowski, F.","author_corresponding":"Cindy Sumaly Lor","author_corresponding_institution":"University of Vienna","doi":"10.1101\/2023.12.31.573585","date":"2024-01-01","version":"1","type":"new results","license":"cc_by_nc","category":"neuroscience","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/01\/01\/2023.12.31.573585.source.xml","abstract":"BackgroundThe Incentive-Sensitization Theory postulates that addiction is primarily driven by the sensitization of the brains reward system to addictive substances, such as nicotine. According to this theory, exposure to such substances leads to an increase in  wanting, while  liking the experience remains relatively unchanged. Although this candidate mechanism has been well substantiated through animal brain research, its translational validity for humans has only been partially demonstrated so far, with evidence from human neuroscience data being very limited.\n\nMethodsFrom fMRI data of N=31 individuals with Nicotine Use Disorder, we created multivoxel patterns capable of capturing wanting and liking-related dimensions from a smoking cue-reactivity task. Using these patterns, we then designed a novel resting-state  reading method to evaluate how much wanting or liking still persist as a neural trace after watching the cues.\n\nResultsWe found that the persistence of wanting-related brain patterns at rest increases with longer smoking history but this was not the case for liking-related patterns. Interestingly, such behavior has not been observed for non-temporal measures of smoking intensity.\n\nConclusionThis study provides basic human neuroscience evidence that the dissociation between liking and wanting escalates over time, further substantiating the Incentive-Sensitization Theory, at least for Nicotine Use Disorder. These results suggest that treatment approaches could be personalized to account for the variability in individuals neural adaptation to addiction by considering how individuals differ in the extent to which their incentive salience system is sensitized.","funder":"NA","published":"NA","server":"bioRxiv"},{"title":"Spatially Resolved Transcriptomic Signatures of Hippocampal Subregions and Arc-Expressing Ensembles in Active Place Avoidance Memory","authors":"Vingan, I. P.; Tung, V. S. K.; Phatarpekar, S.; Hernandez, A. I.; Evgrafov, O. V.; Alarcon, J. M.","author_corresponding":"Juan Marcos Alarcon","author_corresponding_institution":"SUNY Downstate Health Sciences University, Department of Pathology","doi":"10.1101\/2023.12.30.573225","date":"2024-01-01","version":"1","type":"new results","license":"cc_by","category":"neuroscience","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/01\/01\/2023.12.30.573225.source.xml","abstract":"The rodent hippocampus is a spatially organized neuronal network that supports the formation of spatial and episodic memories. We conducted bulk RNA sequencing and spatial transcriptomics experiments to measure gene expression changes in the dorsal hippocampus following the recall of active place avoidance (APA) memory. Through bulk RNA sequencing, we examined the gene expression changes following memory recall across the functionally distinct subregions of the dorsal hippocampus. We found that recall induced differentially expressed genes (DEGs) in the CA1 and CA3 hippocampal subregions were enriched with genes involved in synaptic transmission and synaptic plasticity, while DEGs in the dentate gyrus (DG) were enriched with genes involved in energy balance and ribosomal function. Through spatial transcriptomics, we examined gene expression changes following memory recall across an array of spots encompassing putative memory-associated neuronal ensembles marked by the expression of the IEGs Arc, Egr1, and c-Jun. Within samples from both trained and untrained mice, the subpopulations of spatial transcriptomic spots marked by these IEGs were transcriptomically and spatially distinct from one another. DEGs detected between Arc+ and Arc-spots exclusively in the trained mouse were enriched in several memory-related gene ontology terms, including \"regulation of synaptic plasticity\" and \"memory.\" Our results suggest that APA memory recall is supported by regionalized transcriptomic profiles separating the CA1 and CA3 from the DG, transcriptionally and spatially distinct IEG expressing spatial transcriptomic spots, and biological processes related to synaptic plasticity as a defining the difference between Arc+ and Arc-spatial transcriptomic spots.","funder":"NA","published":"NA","server":"bioRxiv"},{"title":"Genomic Transfer via Membrane Vesicle: A Strategy of Giant Phage phiKZ for Early Infection","authors":"Antonova, D.; Nichiporenko, A.; Sobinina, M.; Vishnyakov, I. E.; Moiseenko, A.; Kurdyumova, I.; Khodorkovskii, M.; Sokolova, O. S.; Yakunina, M. V.","author_corresponding":"Maria V. Yakunina","author_corresponding_institution":"Peter the Great St. Petersburg Polytechnical University","doi":"10.1101\/2023.12.31.573766","date":"2024-01-01","version":"1","type":"new results","license":"cc_by_nc_nd","category":"molecular biology","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/01\/01\/2023.12.31.573766.source.xml","abstract":"During infection, the giant phiKZ phage forms a specialized structure at the center of the host cell called the phage nucleus. This structure is crucial for safeguarding viral DNA against bacterial nucleases and for segregating the transcriptional activities of late genes. Here, we describe a morphological entity, the early phage infection vesicle (EPI vesicle), which appears to be responsible for earlier gene segregation at the beginning of the infection process. Using cryo-electron microscopy, electron tomography, and fluorescence microscopy with membrane-specific dyes, we found that the EPI vesicle is enclosed in a lipid bilayer originating, apparently, from the inner membrane of the bacterial cell. Our investigations further disclose that the phiKZ EPI vesicle contains both viral DNA and viral RNA polymerase (vRNAP). We have observed that the EPI vesicle migrates from the cell pole to the center, displaying co-localization with ChmA, the primary protein of the phage nucleus. While phage DNA is transported into the phage nucleus after phage maturation, the EPI vesicle remains outside. We hypothesized that the EPI vesicle acts as a membrane transport agent, efficiently delivering phage DNA to the phage nucleus while protecting it from the nucleases of the bacterium.","funder":"NA","published":"10.1128\/jvi.00205-24","server":"bioRxiv"},{"title":"DNA-PKcs Suppresses Illegitimate Chromosome Rearrangements","authors":"Wang, J.; Sadeghi, C.; Frock, R. L.","author_corresponding":"Richard L Frock","author_corresponding_institution":"Stanford University","doi":"10.1101\/2023.12.30.573736","date":"2024-01-01","version":"1","type":"new results","license":"cc_by_nc_nd","category":"genetics","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/01\/01\/2023.12.30.573736.source.xml","abstract":"Two DNA repair pathways, non-homologous end joining (NHEJ) and alternative end joining (A-EJ), are involved in V(D)J recombination and chromosome translocation. Previous studies reported distinct repair mechanisms for chromosome translocation, with NHEJ involved in human and A-EJ in mice predominantly. NHEJ depends on DNA-PKcs, a critical partner in synapsis formation and downstream component activation. While DNA-PKcs inhibition promotes chromosome translocations harboring microhomologies in mice, its synonymous effect in humans is not known. We find partial DNA-PKcs inhibition in human cells leads to increased translocations and the continued involvement of a dampened NHEJ. In contrast, complete DNA-PKcs inhibition substantially increased microhomology-mediated end joining (MMEJ), thus bridging the two different translocation mechanisms between human and mice. Similar to a previous study on Ku70 deletion, DNA-PKcs deletion in G1\/G0-phase mouse progenitor B cell lines, significantly impairs V(D)J recombination and generated higher rates of translocations as a consequence of dysregulated coding and signal end joining. Genetic DNA-PKcs inhibition suppresses NHEJ involvement entirely, with repair phenotypically resembling Ku70-deficient A-EJ. In contrast, we find DNA-PKcs necessary in generating the near-excusive MMEJ associated with Lig4 deficiency. Our study underscores DNA-PKcs in suppressing illegitimate chromosome rearrangement while also contributing to MMEJ in both species.","funder":"NA","published":"10.1093\/nar\/gkae140","server":"bioRxiv"},{"title":"Detection of Antibodies Against the African Parasite Trypanosoma brucei Using Synthetic glycosylphosphatidylinositol oligosaccharide fragments","authors":"Michel, M.; Stijlemans, B.; Michel, D.; Garg, M.; Geissner, A.; Seeberger, P.; Varon Silva, D.","author_corresponding":"Maurice Michel","author_corresponding_institution":"Karolinska Institutet","doi":"10.1101\/2023.12.31.573764","date":"2024-01-01","version":"1","type":"new results","license":"cc_by","category":"biochemistry","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/01\/01\/2023.12.31.573764.source.xml","abstract":"Trypanosoma brucei (T. brucei) parasites cause two major infectious diseases in Africa: African trypanosomiasis in humans (HAT) and Nagana in animals. Despite the enormous economic and social impact, vaccines and reliable diagnostic measures are still lacking for these diseases. The main obstacle to developing accurate diagnostic methods and an active vaccine is the parasites ability for antigenic variation and impairment of B cell maturation, which prevents the development of a long-lasting, effective immune response. The antigenic variation is sustained by random gene switching, segmental gene conversion, and altered glycosylation states of solvent-exposed regions of the corresponding variant surface glycoproteins (VSG). These glycoproteins use a glycosylphosphatidylinositol (GPI) anchor for attachment to the membrane. GPIs of T. brucei have specific branched structures that are further heterogeneously galactosylated. We synthesized a glycan fragment library containing T. brucei GPIs most prominent structural features and performed an epitope mapping using mice and human sera of infected specimens using glycan microarrays. The studies indicate that in contrast to VSG, T. brucei GPIs are recognized by both short-lived IgM and long-lasting IgG, indicating a specific immune response against GPI structures. These findings enable the development of diagnostic tests based on synthetic antigens for reliable diagnosis of human African trypanosomiasis and Nagana.","funder":"NA","published":"NA","server":"bioRxiv"},{"title":"Straightforward semi-quantitative MALDI-TOF MS based screening approach for selection of recombinant protein producing E. Coli","authors":"Kravtsov, I. N.; Solovyev, A. I.; Potemkina, E. A.; Kartashova, A. V.; Dmitrieva, M. A.; Danilova, K. V.; Tutykhina, I. L.; Polyakov, N. B.; Egorova, D. A.","author_corresponding":"Ivan N. Kravtsov","author_corresponding_institution":"National Research Center of Epidemiology and Microbiology n. a. N.F. Gamaleya","doi":"10.1101\/2023.12.31.573754","date":"2024-01-01","version":"1","type":"new results","license":"cc_by_nd","category":"bioengineering","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/01\/01\/2023.12.31.573754.source.xml","abstract":"MALDI-TOF MS represents a rapid and cost-effective method for identifying proteins and microorganisms. When obtaining recombinant protein producers, differences in expression levels among transformants necessitate the conduction of a small-scale screening of expression levels. This study proposes a fast and easy method for screening clones producing recombinant proteins using MALDI-TOF MS. Various recombinant proteins were utilized to test the proposed method","funder":"NA","published":"NA","server":"bioRxiv"},{"title":"Genomic background sequences systematically outperform synthetic ones in de novo motif discovery for ChIP-seq data","authors":"Raditsa, V. V.; Tsukanov, A. V.; Bogomolov, A. G.; Levitsky, V. G.","author_corresponding":"Victor G. Levitsky","author_corresponding_institution":"Institute of Cytology and Genetics, Novosibirsk, Russia","doi":"10.1101\/2023.12.30.573742","date":"2024-01-01","version":"1","type":"new results","license":"cc_by_nc_nd","category":"bioinformatics","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/01\/01\/2023.12.30.573742.source.xml","abstract":"Efficient de novo motif discovery from the results of wide-genome mapping of transcription factor binding sites (ChIP-seq) is dependent on the choice of background nucleotide sequences. The foreground sequences (peaks) represent not only specific motifs of target transcription factors, but also the motifs overrepresented throughout the genome, such as simple sequence repeats. We performed a massive comparison of the  synthetic and  genomic approaches to generate background sequences for de novo motif discovery. The  synthetic approach shuffled nucleotides in peaks, while in the  genomic approach randomly selected sequences from the reference genome or only from gene promoters according to the fraction of A\/T nucleotides in each sequence. We compiled the benchmark collections of ChIP-seq datasets for mammalian and Arabidopsis, and performed de novo motif discovery. We showed that the genomic approach has both more robust detection of the known motifs of target transcription factors and more stringent exclusion of the simple sequence repeats as possible non-specific motifs. The advantage of the genomic approach over the synthetic one was greater in plants compared to mammals. We developed the AntiNoise web service (https:\/\/denovosea.icgbio.ru\/antinoise\/) which implements a genomic approach to extract genomic background sequences for twelve eukaryotic genomes.","funder":"NA","published":"10.1093\/nargab\/lqae090","server":"bioRxiv"},{"title":"Multiparameter-based photosynthetic state transitions of single phytoplankton cells","authors":"Harris, P. D.; Ben Eliezer, N.; Keren, N.; Lerner, E.","author_corresponding":"Eitan Lerner","author_corresponding_institution":"Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem; Jerusalem, Israel, 9190401.","doi":"10.1101\/2023.12.31.573751","date":"2024-01-01","version":"1","type":"new results","license":"cc_by_nc_nd","category":"biophysics","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/01\/01\/2023.12.31.573751.source.xml","abstract":"Phytoplankton are a major source of primary production. Their photosynthetic fluorescence uniquely reports on their type, physiological state and response to environmental conditions. Changes in phytoplankton photophysiology are commonly monitored by bulk fluorescence spectroscopy, where gradual changes are reported in response to different perturbations such as light intensity changes. What is the meaning of such trends in bulk parameters if their values report ensemble averages of multiple unsynchronized cells? To answer this, we developed an experimental scheme that enables acquiring multiple fluorescence parameters, from multiple excitation sources and spectral bands. This enables tracking fluorescence intensities, brightnesses and their ratios, as well as mean photon nanotimes equivalent to mean fluorescence lifetimes, one cell at a time. We monitored three different phytoplankton species during diurnal cycles and in response to an abrupt increase in light intensity. Our results show that we can define specific subpopulations of fluorescence parameters for each of the phytoplankton species and in response to varying light conditions. Importantly, we identify the cells undergo well-defined transitions between these subpopulations that characterize the different light behaviors. The approach shown in this work will be useful in the exact characterization of phytoplankton cell states and parameter signatures in response to different changes these cells experience in marine environments, which will be useful in monitoring marine-related effects of global warming.\n\nSignificance StatementUsing three representatives of red-linage phytoplankton we demonstrate distinct photophysiological behaviors at the single cell level. The results indicate cell wide coordination into discrete cell states. We test cell state transitions as a function of light acclimation during diurnal cycle and in response to large intensity increases, which stimulate distinct photoprotective response mechanisms. The analysis was made possible through the development of flow-based confocal detection at multiple excitation and emission wavelengths monitoring both pigment composition and photosynthetic performance. Our findings show that with enough simultaneously recorded parameters per each cell, the detection of multiple phytoplankton species at their distinct cell states is possible. This approach will be useful in examining the response of complex natural marine populations to environmental perturbations.","funder":"NA","published":"NA","server":"bioRxiv"},{"title":"Cryo-EM structure and biochemical analysis of human chemokine receptor CCR8","authors":"Peng, Q.; Jiang, H.; Cheng, X.; Wang, N.; Zhou, S.; Zhang, Y.; Yang, T.; Chen, Y.; Zhang, W.; Lv, S.; Nan, W.; Wang, J.; Fan, G.-H.; Li, J.; Zhang, J.","author_corresponding":"Jin Zhang","author_corresponding_institution":"School of Basic Medical Sciences, Jiangxi Medical College, Nanchang University","doi":"10.1101\/2023.12.30.573520","date":"2024-01-01","version":"1","type":"new results","license":"cc_by_nc_nd","category":"biophysics","jatsxml":"https:\/\/www.biorxiv.org\/content\/early\/2024\/01\/01\/2023.12.30.573520.source.xml","abstract":"The C-C motif chemokine receptor 8 (CCR8) is a class A G-protein coupled receptor that has emerged as a promising therapeutic target in cancer and autoimmune diseases. Although the structures of human CCR8 in complex an antagonist antibody Fab1 and an endogenous agonist ligand CCL1 have been solved, the structure of ligand-free CCR8 remains to be determined. Here, we solved the cryo-electron microscopy (cryo-EM) structure of the human CCR8-Gi complex in the absence of a ligand. Structural analysis and comparison revealed that CCR8 in our apo structure undergoes some conformational change and is similar to that in the CCL1-CCR8 complex structure, indicating an active state. In addition, the key residues of CCR8 involved in the recognition of LMD-009, a potent nonpeptidic agonist, were investigated by mutating CCR8 and testing the calcium flux induced by LMD-009-CCR8 interaction. Two mutants of CCR8, Y1133.32A, and E2867.39A, showed a dramatically decreased ability in mediating calcium mobilization, indicating their key interaction with LMD-009. These structural and biochemical analyses provided molecular insights into the agonism and activation of CCR8 and will also facilitate CCR8-targeted therapy.","funder":"NA","published":"NA","server":"bioRxiv"}]}