bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mapping and targeting ofC1ql1-expressing cells in the mouse
Authors: Moghimyfiroozabad Shayan , Paul Maëla A. , Sigoillot Séverine M. , Selimi Fekrije 
Published: July 2023

AbstractThe C1Q complement protein C1QL1 is highly conserved in mammals where it is expressed in various tissues including the brain. This secreted protein interacts with Brain-specific Angiogenesis Inhibitor 3, BAI3/ADGRB3, and controls synapse formation and maintenance.C1ql1is expressed in the inferior olivary neurons that send projections to cerebellar Purkinje cells, but its expression in the rest of the brain is less documented. To mapC1ql1expression and enable the specific targeting ofC1ql1-expressing cells, we characterized a knockin mouse model expressing the Cre recombinase under the control ofC1ql1regulatory sequences. We characterized the capacity for Cre-driven recombination in the brain and mapped Cre expression in various neuron types using reporter mouse lines. Using an intersectional strategy with viral particle injections, we show that this mouse line can be used to target specific afferents of Purkinje cells. AsC1ql1is also expressed in other regions of the brain, as well as in other tissues such as adrenal glands, placenta, colon and testis, our mouse model is a useful tool to targetC1ql1-expressing cells in a broad variety of tissues.
Annual dynamics and distribution ofXylella fastidiosain infected almond trees
Authors: Zecharia Noa , Miri Vanunu , Dror Orit , Hatib Kamel , Holland Doron , Dani Shtienberg , Bahar Ofir 
Published: July 2023

ABSTRACTThis research focused on studying the dynamics of the bacterial pathogenXylella fastidiosain almond trees at different developmental stages and in various tree parts. The objective was to understand the annual distribution and concentration ofX. fastidiosawithin almond trees. Different tree parts, including leaf petioles, annual and perennial shoots, fruit parts, flowers, and roots, from tenX. fastidiosa-infected almond trees were sampled over two years. The distribution and concentration ofX. fastidiosawere determined using qPCR and serial dilution plating. Throughout the study,X. fastidiosawas never found in the fruit, flowers, and roots of almond trees, but it was present in leaves and annual and perennial shoots. We show that the inability ofX. fastidiosato colonize roots is likely due to incompatibility with the GF677 rootstock. The presence ofX. fastidiosain shoots remained consistent throughout the year, while in leaf petioles it varied across developmental stages, with lower detection during early and late stages of the season. Similarly, viableX. fastidiosacells could be isolated from shoots at all developmental stages, while in leaf petioles no successful isolations were achieved during the vegetative and nut growth stage. Examining the development of almond leaf scorch symptoms over time in trees with preliminary infections revealed that once symptoms have appeared on a single branch, other asymptomatic limbs were likely already colonized by the bacterium, hence, selective pruning of symptomatic branches is unlikely to cure the tree. Overall, this study enhances our understanding ofX. fastidiosadynamics in almonds and may have practical applications for its detection and control in almond orchards.
A natural disaster exacerbates and redistributes disease risk across free-ranging macaques by altering social structure
Authors: Motes-Rodrigo Alba , Albery Gregory F. , Negron-Del Valle Josue E. , Philips Daniel ,   Cayo Biobank Research Unit, Platt Michael L. , Brent Lauren J.N. , Testard Camille 
Published: July 2023

ABSTRACTClimate change is intensifying extreme weather events, with severe implications for ecosystem dynamics. A key behavioural mechanism whereby animals may cope with such events is by increasing social cohesion to improve access to scarce resources like refuges, which in turn could exacerbate epidemic risk due to increased close contact. However, how and to what extent natural disasters affect disease risk via changes in sociality remains unexplored in animal populations. By modelling disease spread in free-living rhesus macaque groups (Macaca mulatta) before and after a hurricane, we demonstrate doubled pathogen transmission rates up to five years following the disaster, equivalent to an increase in pathogen infectivity from 10% to 20%. Moreover, the hurricane redistributed the risk of infection across the population, decreasing status-related differences found in pre-hurricane years. These findings demonstrate that natural disasters can exacerbate and homogenise epidemic risk in an animal population via changes in sociality. These observations provide unexpected further mechanisms by which extreme weather events can threaten wildlife health, population viability, and spillover to humans.
Reanalysis of single-cell RNA sequencing data does not support herpes simplex virus 1 latency in non-neuronal ganglionic cells in mice
Authors: Ouwendijk Werner J.D. , Roychoudhury Pavitra , Cunningham Anthony L. , Jerome Keith R. , Koelle David M. , Kinchington Paul R. , Mohr Ian , Wilson Angus C. , Verjans Georges M.G.M. , Depledge Daniel P. 
Published: July 2023

AbstractMost individuals are latently infected with herpes simplex virus type 1 (HSV-1) and it is well-established that HSV-1 establishes latency in sensory neurons of peripheral ganglia. However, it was recently proposed that latent virus is also present in immune cells recovered from ganglia in a mouse model used for studying latency. Here, we reanalyzed the single-cell RNA sequencing (scRNA-Seq) data that formed the basis for this conclusion. Unexpectedly, off-target priming in 3’ scRNA-Seq experiments enabled the detection of non-polyadenylated HSV-1latency-associated transcript(LAT) intronic RNAs. However,LATreads were near-exclusively detected in a mixed population of cells undergoing cell death. Specific loss of HSV-1LATand neuronal transcripts during quality control filtering indicated widespread destruction of neurons, supporting the presence of contaminating cell-free RNA in other cells following tissue processing. In conclusion, the reported detection of latent HSV-1 in non-neuronal cells is best explained by inaccuracies in the data analyses.
Inflammasomes primarily restrict cytosolicSalmonellareplication within human macrophages
Authors: Egan Marisa S. , O’Rourke Emily A. , Mageswaran Shrawan Kumar , Zuo Biao , Martynyuk Inna , Demissie Tabitha , Hunter Emma N. , Bass Antonia R. , Chang Yi-Wei , Brodsky Igor E. , Shin Sunny 
Published: July 2023

AbstractSalmonella entericaserovar Typhimurium is a facultative intracellular pathogen that utilizes its type III secretion systems (T3SSs) to inject virulence factors into host cells and colonize the host. In turn, a subset of cytosolic immune receptors respond to T3SS ligands by forming multimeric signaling complexes called inflammasomes, which activate caspases that induce interleukin-1 (IL-1) family cytokine release and an inflammatory form of cell death called pyroptosis. Human macrophages mount a multifaceted inflammasome response toSalmonellainfection that ultimately restricts intracellular bacterial replication. However, how inflammasomes restrictSalmonellareplication remains unknown. We find that caspase-1 is essential for mediating inflammasome responses toSalmonellaand restricting bacterial replication within human macrophages, with caspase-4 contributing as well. We also demonstrate that the downstream pore-forming protein gasdermin D (GSDMD) and Ninjurin-1 (NINJ1), a mediator of terminal cell lysis, play a role in controllingSalmonellareplication in human macrophages. Notably, in the absence of inflammasome responses, we observed hyperreplication ofSalmonellawithin the cytosol of infected cells as well as increased bacterial replication within vacuoles, suggesting that inflammasomes controlSalmonellareplication primarily within the cytosol and also within vacuoles. These findings reveal that inflammatory caspases and pyroptotic factors mediate inflammasome responses that restrict the subcellular localization of intracellularSalmonellareplication within human macrophages.
Benchmarking and optimization of cell-free DNA deconvolution
Authors: Hill Tom , Redekar Neelam , Andargie Temesgen E. , Jang Moon K. , Agbor-Enoh Sean 
Published: July 2023

AbstractReference methylomes, used in deconvolution algorithms to determine cell-free DNA tissue sources, were based on driver CpGs from either microarray or sequencing platforms. Cross-validation of these algorithms is important to allow interpretation of data across studies, select optimal sequencing depth, and thus reduce costs of cf-DNA deconvolution assays. Towards this end, we assessed the performance of two reference-based deconvolution algorithms: ‘cfDNAme’, sequencing-based methylome signatures, and ‘Meth-Atlas’, a microarray-based methylome signatures using a cfDNA bisulfite sequencing. While both algorithms use NNLS model, cfDNAme uses CpG windows, while Meth-Atlas uses individual CpGs as cell or tissue signatures. We determined the optimal the number of informative CpGs signatures, and the best sequencing depths for precise deconvolution. We found that above 5-fold coverage, much lower coverage than what is frequently used, there is little difference between our two chosen algorithms, both identifying the correct tissue make-up with a high accuracy, suggesting that whole genome bisulfite sequencing for tissue of origin identification can be completed in a much more cost-effective manner than previously thought.
Fitness Tradeoffs of Multidrug Efflux Pumps inEscherichia coliK-12 in Acid or Base, and with Aromatic Phytochemicals
Authors: Liu Yangyang , Van Horn Andrew M. , Pham Minh T. N. , Dinh Bao Ngoc N. , Chen Rachel , Raphael Slaybrina D. R. , Paulino Alejandro , Thaker Kavya , Somadder Aaryan , Menke Chelsea C. , Slimak Zachary C. , Slonczewski Joan L. 
Published: July 2023

ABSTRACTMultidrug efflux pumps are the frontline defense mechanisms of Gram-negative bacteria, yet little is known of their relative fitness tradeoffs under gut conditions such as low pH and the presence of antimicrobial food molecules. Low pH is important as it contributes to the proton-motive force (PMF) that drives most efflux pumps. We show how the PMF-dependent pumps AcrAB-TolC, MdtEF-TolC, and EmrAB-TolC undergo selection at low pH and in the presence of membrane-permeant phytochemicals. Competition assays were performed by flow cytometry of co-culturedEscherichia coliK-12 strains possessing or lacking a given pump complex. All three pumps showed negative selection under conditions that deplete PMF (pH 5.5 with CCCP, or at pH 8.0). At pH 5.5, selection against AcrAB-TolC was increased by aromatic acids, alcohols, and related phytochemicals such as methyl salicylate. The degree of fitness cost for AcrA was correlated with the phytochemical’s lipophilicity (logP). MdtEF-TolC and EmrAB-TolC each conferred a fitness cost at pH 5.5, but salicylate and benzoate conferred a net positive fitness contribution for the pump. Expression of pump genes was measured by digital PCR. Between pH 5.5 – 8.0,acrAandemrAwere upregulated in log phase, whereasmdtEexpression was upregulated in transition-to-stationary phase and at pH 5.5 in log phase. Methyl salicylate did not affect pump gene expression, despite selecting against AcrAB-TolC. Our results suggest that lipophilic non-acidic molecules select against a major efflux pump without positive section for others.IMPORTANCEFor drugs that are administered orally, we need to understand how ingested phytochemicals modulate intrinsic drug resistance in our gut microbiome. Intrinsic drug resistance of bacteria is mediated by PMF-driven pumps that efflux many different antibiotics and cell waste products. These pumps play a key role in bacterial defense by conferring low-level resistance to antimicrobial agents at first exposure, while providing time for a pathogen to evolve resistance to higher levels of the antibiotic exposed. Nevertheless, efflux pumps confer energetic costs due to gene expression and pump energy expense. The bacterial PMF includes the transmembrane pH difference (ΔpH) which may be depleted by permeant acids and membrane disruptors. Understanding the fitness costs of efflux pumps may enable us to develop resistance breakers, that is, molecules that work together with antibiotics to potentiate their effect. We show that different pumps have distinct selection criteria, and we identified non-acidic aromatic molecules as promising candidates for drug resistance breakers.
EGFR-to-Src family tyrosine kinase switching in proliferating-DTP TNBC cells creates a hyperphosphorylation-dependent vulnerability to EGFR TKI
Authors: Chaudhary Nazia , Choudhary Bhagya Shree , Shivashankar Anusha , Manna Subhakankha , Ved Khyati , Shaikh Shagufa , Khanna Sonal , Barr Jeetnet , Dani Jagruti , Verma Nandini 
Published: July 2023

ABSTRACTTriple-Negative Breast Cancer (TNBC) is the most aggressive type of breast malignancy, with chemotherapy as the only mainstay treatment. TNBC patients have the worst prognoses as a large fraction of them do not achieve complete pathological response post-treatment and develop drug-resistant residual disease. Molecular mechanisms that trigger proliferation in drug-resistant chemo-residual TNBC cells are poorly understood due to the lack of investigations using clinically relevant cellular models. In this study, we have established TNBC subtype-specific cellular models of proliferating drug-tolerant persister (PDTP) cells using different classes of chemotherapeutic agents that recapitulate clinical residual disease with molecular heterogeneity. Analysis of total phospho-tyrosine signals in TNBC PDTPs showed an enhanced phospho-tyrosine content compared to the parental cells (PC). Interestingly, using mass-spectrometry analysis, we identified a dramatic decrease in epidermal growth factor receptor (EGFR) expression in the PDTPs, while the presence of hyper-activated tyrosine phosphorylation of EGFR compared to PC. Further, we show that EGFR has enhanced lysosomal trafficking in PDTPs with a concomitant increase in N-Myc Downstream Regulated-1 expression that co-localizes with EGFR to mediate receptor degradation. More surprisingly, we found that reduced protein levels of EGFR are coupled with a robust increase in Src family kinases, including Lyn and Fyn kinases, that creates a hyper-phosphorylation state of EGFR-Src tyrosine kinases axis in PDTPs and mediates downstream over-activation of STAT3, AKT and MAP kinases. Moreover, paclitaxel-derived PDTPs show increased sensitivity to EGFR TKI Gefitinib and its combination with paclitaxel selectively induced cell death in PDTP-P TNBC cells and 3D spheroids by strongly downregulating phosphorylation of EGFR-Src with concomitant downregulation of Lyn and Fyn tyrosine kinases. Collectively, this study identifies a unique hyper-phosphorylation cellular state of TNBC PDTPs established by switching of EGFR–Src family tyrosine kinases creating a vulnerability to EGFR TKI.
The SWI/SNF nucleosome remodeler constrains enhancer activity duringDrosophilawing development
Authors: Niederhuber Matthew J. , Leatham-Jensen Mary , McKay Daniel J. 
Published: July 2023

ABSTRACTChromatin remodeling is central to the dynamic changes in gene expression that drive cell fate determination. During development, the sets of enhancers that are accessible for use change globally as cells transition between stages. While transcription factors and nucleosome remodeling complexes are known to work together to control access to enhancers, it is unclear how the short stretches of DNA that they individually unmask yield the kilobase-sized accessible regions that are characteristic of active enhancers. Here, we performed a genetic screen to investigate the role of ATP-dependent nucleosome remodeling complexes in the control of dynamic enhancer activity. We find that theDrosophilaBAP complex, a member of the SWI/SNF family of nucleosome remodelers, is required for repression of a temporally dynamic enhancer,brdisc. Contrary to expectations, we find that the BAP-specific subunit, Osa, is dispensable for mediating changes in chromatin accessibility between early and late stages of wing development. Instead, we find that Osa is required to constrain the levels ofbrdiscactivity in imaginal wing discs when the enhancer is normally active. Genome-wide profiling reveals that Osa binds directly to thebrdiscenhancer as well as thousands of other developmentally dynamic regulatory sites, including multiple genes encoding components and targets of the Notch signaling pathway. We find that Osa loss of function results in development of ectopic sensory structures that are normally patterned by Notch signaling early in wing development. Moreover, we find that Osa loss of function results in hyperactivation of theDeltagene, which encodes the Notch ligand. Together, these findings indicate that proper constraint of enhancer activity is necessary for regulation of dose-dependent developmental events.
Methods for making and observing model lipid droplets
Authors: Gandhi Sonali A. , Parveen Shahnaz , Alduhailan Munirah , Tripathi Ramesh , Junedi Nasser , Saqallah Mohammad , Sanders Matthew A. , Hoffmann Peter M. , Truex Katherine , Granneman James G. , Kelly Christopher V 
Published: July 2023

SummaryThe mechanisms by which the lipid droplet (LD) membrane is remodeled in concert with the activation of lipolysis incorporate a complex interplay of proteins, phospholipids, and neutral lipids. Model LDs (mLDs) provide an isolated, purified system for testing the mechanisms by which the droplet composition, size, shape, and tension affects triglyceride metabolism. Described here are methods of making and testing mLDs ranging from 0.1 to 40 µm diameter with known composition. Methods are described for imaging mLDs with high-resolution microscopy during buffer exchanges for the measurement of membrane binding, diffusion, and tension via fluorescence correlation spectroscopy (FCS), fluorescence recovery after photobleaching (FRAP), fluorescence lifetime imaging microscopy (FLIM), atomic force microscopy (AFM), pendant droplet tensiometry, and imaging flow cytometry. These complementary, cross-validating methods of measuring LD membrane behavior reveal the interplay of biophysical processes in triglyceride metabolism.
Partitioning variance in cortical morphometry into genetic, environmental, and subject-specific components
Authors: Smith Diana M. , Parekh Pravesh , Kennedy Joseph , Loughnan Robert , Frei Oleksandr , Nichols Thomas E. , Andreassen Ole A. , Jernigan Terry L. , Dale Anders M. 
Published: July 2023

AbstractThe relative contributions of genetic variation and experience in shaping the morphology of the adolescent brain are not fully understood. Using longitudinal data from 11,665 subjects in the ABCD Study®, we fit vertex-wise variance components including family effects, genetic effects, and subject-level effects using a computationally efficient framework. Variance in cortical thickness and surface area is largely attributable to genetic influence, whereas sulcal depth is primarily explained by subject-level effects. Our results identify areas with heterogeneous distributions of heritability estimates that have not been seen in previous work using data from cortical regions. We discuss the biological importance of subject-specific variance and its implications for environmental influences on cortical development and maturation.
Can food and temperature influence regional connectivity patterns of Bivalvia in fragmented archipelagos? Evidence from biophysical modeling applied to French Polynesia
Authors: Raapoto H. , Monaco C.J. , Van Wynsberge S. , Le Gendre R. , Le Luyer J. 
Published: July 2023

ABSTRACTLarval dispersal and connectivity are key processes that drive marine metapopulation dynamics, and therefore should be well characterized when designing effective management strategies. While temperature and food availability can structure marine species connectivity patterns, their relative contribution has not been thoroughly investigated in highly fragmented archipelagos. We used biophysical modeling of larval dispersal to explore the connectivity patterns of species with complex life-cycles across French Polynesia (FP), a territory formed by more than a hundred small, geographically isolated islands covering an area as large as Europe. We first simulated ten years of larval dispersal to investigate the spatial and temporal (seasonal and interannual) variability in larval dispersal pathways for different hypothetical species exhibiting a range of Larval Precompetency Period (LPP) values. Then, using the black-lip pearl oyster (Pinctada margaritifera) as a model species, we accounted for variability in the LPP induced by temperature and food availability, as derived from a Dynamic Energy Budget (DEB) model. The model showed that food availability and meso-scale turbulence (eddies) in the Marquesas jointly constrained larval dispersal, reducing its potential connectivity with other archipelagos in FP. However, accounting for food and temperature effects on larval development, barely changed the connectivity pattern at regional scale due to the remoteness of this archipelago. The DEB simulations further revealed seasonal and interannual variability in connectivity driven by environmental conditions. Our results highlight the importance of considering temperature and food in biophysical models to adequately capture dispersal, connectivity and to identify appropriate management units at the regional scale.
Single-cell long-read targeted sequencing reveals transcriptional variation in ovarian cancer
Authors: Byrne Ashley , Le Daniel , Sereti Kostianna , Menon Hari , Patel Neha , Lund Jessica , Xavier-Magalhaes Ana , Shi Minyi , Sterne-Weiler Timothy , Modrusan Zora , Stephenson William 
Published: July 2023

AbstractSingle-cell RNA sequencing predominantly employs short-read sequencing to characterize cell types, states and dynamics; however, it is inadequate for comprehensive characterization of RNA isoforms. Long-read sequencing technologies enable single-cell RNA isoform detection but are hampered by lower throughput and unintended sequencing of artifacts. Here we developed Single-cell Targeted Isoform Long-Read Sequencing (scTaILoR-seq), a hybridization capture method which targets over a thousand genes of interest, improving the median number of unique transcripts per cell by 29-fold. We used scTaILoR-seq to identify and quantify RNA isoforms from ovarian cancer cell lines and primary tumors, yielding 10,796 single-cell transcriptomes. Using long-read variant calling we revealed associations of expressed single nucleotide variants (SNVs) with alternative transcript structures. In addition, phasing of SNVs across transcripts facilitated measurement of allelic imbalance within distinct cell populations. Overall, scTaILoR-seq is a long-read targeted RNA sequencing method and analytical framework for exploring transcriptional variation at single-cell resolution.