bluuebunny/crossref_metadata_2025_split huggingface dataset:
Focal adhesion protein vinculin inhibits Mef2c-driven sclerostin expression in osteocytes to promote bone formation in mice
Authors: Wang Yishu , Huang Jianmei , Lin Sixiong , Qin Lei , Hao Dingyu , Zhang Peijun , Huo Shaochuan , Zou Xuenong , Chen Di , Xiao Guozhi 
Published: November 2022

AbstractThe focal adhesion (FA) is the structural basis of the cell-extracellular matrix crosstalk and plays important roles in control of organ formation and function. Here we show that expression of FA protein vinculin is dramatically reduced in osteocytes in patients with aging-related osteoporosis. Deleting vinculin using the mouse 10-kbDmp1-Cretransgenic mice causes a severe osteopenia in both young and aged mice by impairing osteoblast function without affecting bone resorption. Vinculin loss impairs the anabolic response of skeleton to mechanical loading in mice. At the molecular level, vinculin knockdown increases, while vinculin overexpression decreases, sclerostin expression in osteocytes without impacting expression of Mef2c, a major transcriptional regulator of theSostgene, which encodes sclerostin. Vinculin interacts with Mef2c and vinculin loss enhances Mef2c nuclear translocation and binding to theSostenhancerECR5to promote sclerostin production in osteocytes. DeletingSostexpression reverses the osteopenic phenotypes caused by vinculin loss in mice. We demonstrate that estrogen is a major regulator of vinculin expression in osteocytes and that more importantly vinculin loss mediates estrogen deficiency induction of bone loss in mice. Thus, we demonstrate a novel mechanism through which vinculin inhibits the Mef2c-driven sclerostin expression in osteocytes to promote bone formation.
Automated segmentation and quantitative analysis of organelle morphology, localization and content using CellProfiler
Authors: Laan Sebastiaan N.J. , Dirven Richard J. , Eikenboom Jeroen , Bierings Ruben ,   for the SYMPHONY consortium
Published: November 2022

AbstractOne of the most used and versatile methods to study number, dimensions, content and localization of secretory organelles is confocal microscopy analysis. However, considerable heterogeneity exists in the number, size and shape of secretory organelles that can be present in the cell. One thus needs to analyze large numbers of organelles for valid quantification. Properly evaluating these parameters requires an automated, unbiased method to process and quantitatively analyze microscopy data. Here, we describe two pipelines, run by CellProfiler software, called OrganelleProfiler and OrganelleContentProfiler. These pipelines were used on confocal images of endothelial colony forming cells (ECFC) which contain unique secretory organelles called Weibel-Palade bodies. Results show that the pipelines can quantify the cell count and size, and the organelle count, size, shape, relation to cells and nuclei, and distance to these objects. Furthermore, the pipeline is able to quantify secondary signals located in or on the organelle or in the cytoplasm. Cell profiler measurements were checked for validity using Fiji. To conclude, these pipelines provide a powerful, high-processing quantitative tool for analysis of cell and organelle characteristics. These pipelines are freely available and easily editable for use on different cell types or organelles.
Helminth exposure protects against murine SARS-CoV-2 infection through macrophage dependent T cell activation
Authors: Hilligan Kerry L. , Oyesola Oyebola O. , Namasivayam Sivaranjani , Howard Nina , Clancy Chad S. , Oland Sandra D. , Garza Nicole L. , Lafont Bernard A. P. , Johnson Reed F. , Mayer-Barber Katrin D. , Sher Alan , Loke P’ng 
Published: November 2022

SummaryHelminth endemic regions report lower COVID-19 morbidity and mortality. Here, we show that lung remodeling from a prior infection with a lung migrating helminth,Nippostrongylus brasiliensis, enhances viral clearance and survival of human-ACE2 transgenic mice challenged with SARS-CoV-2 (SCV2). This protection is associated with a lymphocytic infiltrate including an increased accumulation of pulmonary SCV2-specific CD8+ T cells and anti-CD8 antibody depletion abrogated theN. brasiliensis-mediated reduction in viral loads. Pulmonary macrophages with a type-2 transcriptional signature persist in the lungs ofN. brasiliensisexposed mice after clearance of the parasite and establish a primed environment for increased antigen presentation. Accordingly, depletion of macrophages ablated the augmented viral clearance and accumulation of CD8+ T cells driven by priorN. brasiliensisinfection. Together, these findings support the concept that lung migrating helminths can limit disease severity during SCV2 infection through macrophage-dependent enhancement of anti-viral CD8+ T cell responses.Abstract Figure
A comparative atlas of single-cell chromatin accessibility in the human brain
Authors: Li Yang Eric , Preissl Sebastian , Miller Michael , Johnson Nicholas D. , Wang Zihan , Jiao Henry , Zhu Chenxu , Wang Zhaoning , Xie Yang , Poirion Olivier , Kern Colin , Pinto-Duarte Antonio , Tian Wei , Siletti Kimberly , Emerson Nora , Osteen Julia , Lucero Jacinta , Lin Lin , Yang Qian , Zhu Quan , Espinoza Sarah , Yanny Anna Marie , Nyhus Julie , Dee Nick , Casper Tamara , Shapovalova Nadiya , Hirschstein Daniel , Hodge Rebecca D. , Linnarsson Sten , Bakken Trygve , Levi Boaz , Keene C. Dirk , Shang Jingbo , Lein Ed S. , Wang Allen , Behrens M. Margarita , Ecker Joseph R. , Ren Bing 
Published: November 2022

AbstractThe human brain contains an extraordinarily diverse set of neuronal and glial cell types. Recent advances in single cell transcriptomics have begun to delineate the cellular heterogeneity in different brain regions, but the transcriptional regulatory programs responsible for the identity and function of each brain cell type remain to be defined. Here, we carried out single nucleus ATAC-seq analysis to probe the open chromatin landscape from over 1.1 million cells in 42 brain regions of three neurotypical adult donors. Integrative analysis of the resulting data identified 107 distinct cell types and revealed the cell-type-specific usage of 544,735 candidate cis-regulatory DNA elements (cCREs) in the human genome. Nearly 1/3 of them displayed sequence conservation as well as chromatin accessibility in the mouse brain. On the other hand, nearly 40% cCREs were human specific, with chromatin accessibility associated with species-restricted gene expression. Interestingly, these human specific cCREs were enriched for distinct families of retrotransposable elements, which displayed cell-type-specific chromatin accessibility. We uncovered strong associations between specific brain cell types and neuropsychiatric disorders. We futher developed deep learning models to predict regulatory function of non-coding disease risk variants.
A Biologically Plausible Spiking Neural Network for Decoding Kinematics in the Hippocampus and Premotor Cortex
Authors: Taeckens Elijah , Dong Ryan , Shah Sahil 
Published: November 2022

AbstractThis work presents a spiking neural network for predicting kinematics from neural data towards accurate and energy-efficient brain machine interface. A brain machine interface is a technological system that interprets neural signals to allow motor impaired patients to control prosthetic devices. Spiking neural networks have the potential to improve brain machine interface technology due to their low power cost and close similarity to biological neural structures. The SNN in this study uses the leaky integrate-and-fire model to simulate the behavior of neurons, and learns using a local learning method that uses surrogate gradient to learn the parameters of the network. The network implements a novel continuous time output encoding scheme that allows for regression-based learning. The SNN is trained and tested offline on neural and kinematic data recorded from the premotor cortex of a primate and the hippocampus of a rat. The model is evaluated by finding the correlation between the predicted kinematic data and true kinematic data, and achieves peak Pearson Correlation Coefficients of 0.77 for the premotor cortex recordings and 0.80 for the hippocampus recordings. The accuracy of the model is benchmarked against a Kalman filter decoder and a LSTM network, as well as a spiking neural network trained with backpropagation to compare the effects of local learning.
Adjuvant effects of multifunctional transcription factor and BCG target YB-1: exogenous YB-1 enhances specific antibody productionin vivoand protects mice against lethalE. colichallenge
Authors: Shepelyakovskaya Anna O. , Alekseeva Ludmila , Meshcheryakova Elena A. , Boziev Khanafiy , Tsitrina Alexandra , Ivanov Vadim T. , Brovko Fedor , Kotelevtsev Yuri , Lathe Richard , Laman Alexander G. 
Published: November 2022

ABSTRACTThere is growing interest in the beneficial effects of immune system boosting through the administration of adjuvants, not only in acute infections such as COVID but also in chronic degenerative disorders that are potentially associated with infection. The best-known immunopotentiators are Freund’s complete adjuvant (FCA) and its relative Bacille Calmete–Guérin (BCG), both based onMycobacteriumspecies. The key pathogen-associated molecular patterns (PAMPs) in both FCA and BCG are muramyl dipeptides (MDPs and glucosaminyl-MDP, GMDP). We previously identified the evolutionarily conserved protein Y-box factor YB-1/YBX1 as a primary target for MDP/GMDP. Unlike other host receptors for PAMPs, YB-1 is a diffusible molecule, and we therefore explored whetherin vivoadministration of YB-1, rather than its PAMP ligands, might enhance the immune response to a bacterial antigen and/or influence survival in the face of bacterial infection. We report that mice receiving YB-1 plus GMDPin vivomount a significantly increased B cell response versus GMDP alone against a test antigen (Yersinia pestisV antigen), and that YB-1 administration alone significantly promotes survival in the face of lethal bacterial (Escherichia coli) challengein vivo. Independent confirmation is warranted because recombinant YB-1 and its ligands could hold great promise both as adjuvants and as therapeutics.
Longitudinal map of transcriptome changes in the Lyme pathogenBorrelia burgdorferiduring tick-borne transmission
Authors: Sapiro Anne L. , Hayes Beth M. , Volk Regan F. , Zhang Jenny Y. , Brooks Diane M. , Martyn Calla , Radkov Atanas , Zhao Ziyi , Kinnersley Margie , Secor Patrick R. , Zaro Balyn W. , Chou Seemay 
Published: November 2022

ABSTRACTBorrelia burgdorferi(Bb), the causative agent of Lyme disease, adapts to vastly different environments as it cycles between tick vector and vertebrate host. During a tick bloodmeal,Bbalters its gene expression to prepare for vertebrate infection; however, the full range of transcriptional changes that occur over several days inside of the tick are technically challenging to capture. We developed an experimental approach to enrichBbcells to longitudinally define their global transcriptomic landscape inside nymphalIxodes scapularisticks during a transmitting bloodmeal. We identified 192Bbgenes that substantially change expression over the course of the bloodmeal from one to four days after host attachment. The majority of upregulated genes encode proteins found at the cell envelope or proteins of unknown function, including 45 outer surface lipoproteins embedded in the unusual protein-rich coat ofBb. As these proteins may facilitateBbinteractions with the host, we utilized mass spectrometry to identify candidate tick proteins that physically associate withBb. TheBbenrichment methodology along with theex vivo Bbtranscriptomes and candidate tick interacting proteins presented here provide a resource to facilitate investigations into key determinants ofBbpriming and transmission during the tick stage of its unique transmission cycle.
Modular, cement-free, customized headpost and connector-chamber implants for macaques
Authors: Psarou Eleni , Vezoli Julien , Schölvinck Marieke L. , Ferracci Pierre-Antoine , Zhang Yufeng , Grothe Iris , Roese Rasmus , Fries Pascal 
Published: November 2022

AbstractBackgroundNeurophysiological studies with awake macaques typically require chronic cranial implants. Headpost and connector-chamber implants are used to allow head stabilization and to house connectors of chronically implanted electrodes, respectively.New MethodWe present long- lasting, modular, cement-free headpost implants made of titanium that consist of two pieces: a baseplate and a top part. The baseplate is implanted first, covered by muscle and skin and allowed to heal and osseointegrate for several weeks to months. The percutaneous part is added in a second, brief surgery. Using a punch tool, a perfectly round skin cut is achieved providing a tight fit around the implant without any sutures. We describe the design, planning and production of manually bent and CNC-milled baseplates. We also developed a remote headposting technique that increases handling safety. Finally, we present a modular, footless connector chamber that is implanted in a similar two- step approach and achieves a minimized footprint on the skull.ResultsTwelve adult male macaques were successfully implanted with a headpost and one with the connector chamber. To date, we report no implant failure, great headpost stability and implant condition, in four cases even more than 9 years post-implantation.Comparison with Existing MethodsThe methods presented here build on several related previous methods and provide additional refinements to further increase implant longevity and handling safety.ConclusionsOptimized implants can remain stable and healthy for at least 9 years and thereby exceed the typical experiment durations. This minimizes implant-related complications and corrective surgeries and thereby significantly improves animal welfare.HighlightsLong-lasting titanium implants for non-human primatesRefined implantation techniques that reduce post-operative complicationsMinimized, footless connector chamber to house connectors of chronic arraysTwelve adult male macaques were implanted with long-lasting headpost implantsHeadpost implants so far without failure and with longevity up to > 9 years
Unsupervised Voxel-based Segmentation reveals a Landscape of Bacterial Ribosome Large Subunit Early Assembly
Authors: Sheng Kai , Li Ning , Rabuck-Gibbons Jessica N. , Dong Xiyu , Lyumkis Dmitry , Williamson James R. 
Published: November 2022

AbstractRibosome biogenesis is a complex but efficient process in rapidly growing bacteria, where assemble a functional 70S ribosome takes ~ 2 min, involving participation of 3 rRNAs, 50 r-proteins and dozens of assembly factors. In vitro reconstitution using different subsets of large subunit (50S, LSU) proteins with rRNAs, pioneered by Nierhaus lab, resulted in the Nierhaus assembly map, embodying the cooperativity and dependency for binding of LSU r-proteins to 23S rRNA. Critically absent from the Nierhaus map is the underlying folding of the rRNA that creates the binding sites for the r-proteins. In addition, the relationship of the observed cooperativity in vitro to the co-transcriptional assembly in cells remains to be determined.Pre-50S intermediates accumulate at low temperature in ΔdeaD, a DEAD-box helicase implicated in 50S assembly. We solved 21 pre-50S density maps from intermediate-containing fractions using cryo-EM. In the newly solved maps, we discovered the earliest intermediate ever reported, consisting of domain I at the 5’-end of 23S rRNA. To probe the mechanism behind the maps during assembly, we developed a novel density map segmentation and dependency analysis method. Ten cooperative assembly blocks were identified from segmentation of the maps, and these were organized into a block dependency map. This is the first time the dependencies on folding of rRNA helices and ribosomal protein binding could be integrated into a complete assembly map. In addition, we showed how the exit tunnel is folded on the solvent side, serving as a scaffold for 50S maturation. Using this new segmentation analysis method, we revisited previously reported bL17-depletion and ΔsrmB datasets. Most remarkably, the other two datasets are also consistent with the block dependency, implying a unified early assembly pathway and flexible maturation landscape in early 50S biogenesis.
Heterozygous Inversion Breakpoints Suppress Meiotic Crossovers by Altering Recombination Repair Outcomes
Authors: Li Haosheng , Berent Erica , Hadjipanteli Savannah , Galey Miranda , Miller Danny E. , Crown Nicole 
Published: November 2022

AbstractHeterozygous chromosome inversions suppress meiotic crossover (CO) formation within an inversion, potentially because they lead to gross chromosome rearrangements that produce inviable gametes. Interestingly, COs are also severely reduced in regions nearby but outside of inversion breakpoints even though COs in these regions do not result in rearrangements. Our mechanistic understanding of why COs are suppressed outside of inversion breakpoints is limited by a lack of data on the frequency of noncrossover gene conversions (NCOGCs) in these regions. To address this critical gap, we mapped the location and frequency of rare CO and NCOGC events that occurred outside of thedl-49 chrXinversion inD. melanogaster. We created full-sibling wildtype and inversion stocks and recovered COs and NCOGCs in the syntenic regions of both stocks, allowing us to directly compare rates and distributions of recombination events. We show that COs are completely suppressed within 500 kb of inversion breakpoints, are severely reduced within 2 Mb of an inversion breakpoint, and increase above wildtype levels 2-4 Mb from the breakpoint. We find that NCOGCs occur evenly throughout the chromosome and, importantly, occur at wildtype levels near inversion breakpoints. We propose a model in which COs are suppressed by inversion breakpoints in a distance-dependent manner through mechanisms that influence DNA double-strand break repair outcome but not double-strand break location or frequency. We suggest that subtle changes in the synaptonemal complex and chromosome pairing might lead to unstable interhomolog interactions during recombination that permits NCOGC formation but not CO formation.
Reduced cholecystokinin-expressing interneuron input contributes to disinhibition of the hippocampal CA2 region in a mouse model of temporal lobe epilepsy
Authors: Whitebirch Alexander C. , Barnett Anastasia , Santoro Bina , Scharfman Helen E. , Siegelbaum Steven A. 
Published: November 2022

ABSTRACTA significant proportion of temporal lobe epilepsy (TLE) patients experience drug-resistant seizures associated with mesial temporal sclerosis, in which there is extensive cell loss in the hippocampal CA1 and CA3 subfields, with a relative sparing of dentate gyrus granule cells and the CA2 pyramidal neurons. A role for CA2 in seizure generation was suggested based on findings of a reduction in synaptic inhibition (Williamson & Spencer, 1994) and the presence of interictal- like spike activity in resected hippocampal tissue from TLE patients (Wittner et al., 2009). We recently found that in the pilocarpine-inducedstatus epilepticusmouse model of TLE there was an increase in CA2 intrinsic excitability associated with a loss of CA2 synaptic inhibition. Furthermore, chemogenetic silencing of CA2 significantly reduced seizure frequency, consistent with a role of CA2 in promoting seizure generation and/or propagation (Whitebirch et al., 2022). In the present study we explored the basis of this inhibitory deficit using immunohistochemical and electrophysiological approaches. We report a widespread decrease in the density of pro- cholecystokinin-immunopositive interneurons and a functional impairment of cholecystokinin- expressing interneuron-mediated inhibition of CA2 pyramidal neurons. We also found a decrease in the density of CA2 parvalbumin-immunopositive interneurons and disruption to the pyramidal neuron-associated perisomatic perineuronal net in the CA2 subfield. These data reveal a set of pathological alterations that may disrupt inhibition of CA2 pyramidal neurons and their downstream targets in epileptic mice.
Rickettsia parkeriHijacks Tick Hemocytes to Manipulate Cellular and Humoral Transcriptional Responses
Authors: Adegoke Abdulsalam , Ribeiro Jose M.C. , Brown Sidney , Smith Ryan C. , Karim Shahid 
Published: November 2022

AbstractBlood-feeding arthropods rely on robust cellular and humoral immunity to control pathogen invasion and replication. Tick hemocytes produce factors that can facilitate or suppress microbial infection and pathogenesis. Despite the importance of hemocytes in regulating microbial infection, understanding of their basic biology and molecular mechanisms remains limited. Here we combined histomorphology and functional analysis to identify five distinct phagocytic and non-phagocytic hemocyte populations circulating within the Gulf Coast tickAmblyomma maculatum. Depletion of phagocytic hemocytes using clodronate liposomes revealed their function in eliminating bacterial infection. We provide the first direct evidence that an intracellular tick-borne pathogen,Rickettsia parkeri, infects phagocytic hemocytes inAm. maculatumto modify tick cellular immune responses. A massive RNA-seq dataset generated from hemocytes isolated from uninfected andR. parkeri-infected partially blood-fed ticks generated ∼40,000 differentially regulated transcripts, >11,000 of which were immune genes. Silencing two differentially regulated phagocytic immune marker genes (nimrod B2andeater) significantly reduced hemocyte phagocytosis. Together, these findings represent a significant step forward in understanding how hemocytes regulate microbial homeostasis and vector competence.
High-resolution small RNAs landscape provides insights into alkane adaptation in the marine alkane-degraderAlcanivorax dieseloleiB-5
Authors: Wei Guangshan , Li Sujie , Ye Sida , Wang Zining , Zarringhalam Kourosh , He Jianguo , Wang Wanpeng , Shao Zongze 
Published: November 2022

AbstractAlkanes are widespread in the ocean, andAlcanivoraxis one of the most ubiquitous alkane-degrading bacteria in the marine ecosystem. Small RNAs (sRNAs) are usually at the heart of regulatory pathways, but sRNA-mediated alkane metabolic adaptability still remains largely unknown due to the difficulties of identification. Here, differential RNA sequencing (dRNA-seq) modified with a size selection (∼50-nt to 500-nt) strategy was used to generate high-resolution sRNAs profiling in the model speciesAlcanivorax dieseloleiB-5 under alkane (n-hexadecane) and non-alkane (acetate) conditions. As a result, we identified 549 sRNA candidates at single-nucleotide resolution of 5’-ends, with 63.4% of transcription start sites (TSSs) and 36.6% of processing sites (PSSs). These sRNAs originated from almost any locations in the genome, regardless of intragenic (65.8%), antisense (20.6%) and intergenic (6.2%) regions, and RNase E may function in the maturation of sRNAs. Most sRNAs locally distribute across the 15 reference genomes ofAlcanivorax, and only 7.5% of sRNAs are broadly conserved in this genus. Expression responses to alkane of several core conserved sRNAs, including 6S RNA, M1 RNA and tmRNA, indicate that they may participate in alkane metabolisms and result in more actively global transcription, RNA processing and stresses mitigation. Two novel CsrA-related sRNAs are identified, which may be involved in the translational activation of alkane metabolism-related genes by sequestering the global repressor CsrA. The relationships of sRNAs with characterized genes of the alkane sensing (ompS), chemotaxis (mcp, cheR, cheW2), transporting (ompT1, ompT2, ompT3) and hydroxylation (alkB1, alkB2, almA) were created based on the genome-wide targets prediction. Overall, the sRNAs landscape lays the ground for uncovering cryptic regulations in the critical marine bacterium, among which both core and species-specific sRNAs are implicated in the alkane adaptive metabolisms.