bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clathrin Senses Membrane Curvature
Authors: Zeno Wade F. , Hochfelder Jacob B. , Thatte Ajay S. , Wang Liping , Gadok Avinash K. , Hayden Carl C. , Lafer Eileen M. , Stachowiak Jeanne C. 
Published: June 2020

ABSTRACTThe ability of proteins to sense membrane curvature is essential to diverse membrane remodeling processes including clathrin-mediated endocytosis. Multiple adaptor proteins within the clathrin pathway have been shown to assemble together at curved membrane sites, leading to local recruitment of the clathrin coat. Because clathrin does not bind to the membrane directly, it has remained unclear whether clathrin plays an active role in sensing curvature or is passively recruited by its adaptor proteins. Using a synthetic tag to assemble clathrin directly on membrane surfaces, here we show that clathrin is a strong sensor of membrane curvature, comparable to previously studied adaptor proteins. Interestingly, this sensitivity arises from clathrin assembly, rather than from the properties of unassembled triskelia, suggesting that triskelia have preferred angles of interaction, as predicted by earlier structural data. Further, when clathrin is recruited by adaptors, its curvature sensitivity is amplified by two to ten-fold, such that the resulting protein complex is up to 100 times more likely to assemble on a highly curved surface, compared to a flatter one. This exquisite sensitivity points to a synergistic relationship between the coat and its adaptor proteins, which enables clathrin to pinpoint sites of high membrane curvature, an essential step in ensuring robust membrane traffic. More broadly, these findings suggest that protein networks, rather than individual protein domains, are likely the critical drivers of membrane curvature sensing.
Distribution of droplets and immune responses after aerosol and intra-nasal delivery of influenza virus to the respiratory tract of pigs
Authors: Martini Veronica , Hinchcliffe Michael , Blackshaw Elaine , Joyce Mary , McNee Adam , Beverley Peter , Townsend Alain , MacLoughlin Ronan , Tchilian Elma 
Published: June 2020

AbstractRecent evidence indicates that local immune responses and tissue resident memory T cells (TRM) are critical for protection against respiratory infections but there is little information on the contributions of upper and lower respiratory tract (URT and LRT) immunity. To provide a rational basis for designing methods for optimal delivery of vaccines to the respiratory tract in a large animal model, we investigated the distribution of droplets generated by a mucosal atomization device (MAD) and two vibrating mesh nebulizers (VMNs) and the immune responses induced by delivery of influenza virus by MAD in pigs. We showed that droplets containing the drug albuterol, a radiolabel (99mTc-DTPA) or a model influenza virus vaccine (S-FLU) have similar aerosol characteristics.99mTc-DTPA scintigraphy showed that VMNs deliver droplets with uniform distribution throughout the lungs as well as the URT. Surprisingly MAD administration (1ml/nostril) also delivered a high proportion of the dose to the lungs, albeit concentrated in a small area. After MAD administration of influenza virus, antigen specific T cells were found at high frequency in nasal turbinates, trachea, broncho-alveolar lavage, lungs, tracheobronchial nodes and blood. We conclude that the pig is useful for investigating optimal targeting of vaccines to the respiratory tract.
Neural divergence and convergence for attention to and detection of interoceptive and somatosensory stimuli
Authors: Herman Aleksandra M. , Palmer Clare E. , Azevedo Ruben T. , Tsakiris Manos 
Published: June 2020

AbstractBody awareness is constructed by signals originating from within and outside the body. How do these apparently divergent signals converge? We developed a signal detection task to study the neural convergence and divergence of interoceptive and somatosensory signals. Participants focused on either cardiac or tactile events and reported their presence or absence. Beyond some evidence of divergence, we observed a robust overlap in the pattern of activation evoked across both conditions in frontal areas including the insular cortex, as well as parietal and occipital areas, and for both attention and detection of these signals. Psycho-physiological interaction analysis revealed that right insular cortex connectivity was modulated by the conscious detection of cardiac compared to somatosensory sensations, with greater connectivity to occipito-parietal regions when attending to cardiac signals. Our findings speak in favour of the inherent convergence of bodily-related signals and move beyond the apparent antagonism between exteroception and interoception.
Regulatory plasticity within a complex cytokine-sensing mammary enhancer during lactation
Authors: Lee Hye Kyung , Liu Chengyu , Hennighausen Lothar 
Published: June 2020

AbstractEnhancers are transcription factor platforms that synergize with promoters to activate gene expression up to several-thousand-fold. While genome-wide structural studies are used to predict enhancers, thein vivosignificance is less clear. Specifically, the biological importance of individual transcription factors within enhancer complexes remains to be understood. Here we investigate the structural and biological importance of individual transcription factor binding sites and redundancy among transcription components within a complex enhancerin vivo. TheCsn1s2bgene is expressed exclusively in mammary tissue and activated several thousand-fold during pregnancy and lactation. Using ChIP-seq we identified a complex lactation-specific candidate enhancer that binds multiple transcription factors and coincides with activating histone marks. Using experimental mouse genetics, we determined that deletion of canonical binding motifs for the transcription factors NFIB and STAT5, individually and combined, had a limited biological impact. Loss of these sites led to a shift of transcription factor binding to juxtaposed sites, suggesting exceptional plasticity that does not require direct protein-DNA interactions. Additional deletions revealed the critical importance of a non-canonical STAT5 binding site for enhancer activity. Our data also suggest that enhancer RNAs are not required for the activity of this specific enhancer. While ChIP-seq experiments predicted an additional candidate intronic enhancer, its deletion did not adversely affect gene expression, emphasizing the limited biological information provided by structural data. Our study provides comprehensive insight into the anatomy and biology of a composite mammary enhancer that activates its target gene several hundred-fold during lactation.
Differentiation of ciliated human midbrain-derived LUHMES neurons
Authors: Lauter Gilbert , Coschiera Andrea , Yoshihara Masahito , Sugiaman-Trapman Debora , Ezer Sini , Sethurathinam Shalini , Katayama Shintaro , Kere Juha , Swoboda Peter 
Published: June 2020

AbstractMany human cell types are ciliated, including neural progenitors and differentiated neurons. Ciliopathies are characterized by defective cilia and comprise various disease states, including brain phenotypes, where the underlying biological pathways are largely unknown. Our understanding of neuronal cilia is rudimentary and an easy-to-maintain, ciliated human neuronal cell model is missing.LUHMES is a ciliated neuronal cell line derived from human fetal mesencephalon. LUHMES cells can easily be maintained and differentiated into mature, functional neurons within one week. They have a single primary cilium as proliferating progenitor cells and as post-mitotic, differentiating neurons. These developmental stages are completely separable within one day of culture condition change. The Sonic Hedgehog (SHH) signaling pathway is active in differentiating LUHMES neurons. RNA-seq time course analyses reveal molecular pathways and gene-regulatory networks critical for ciliogenesis and axon outgrowth at the interface between progenitor cell proliferation, polarization and neuronal differentiation. Gene expression dynamics of cultured LUHMES neurons faithfully mimic the corresponding in vivo dynamics of human fetal midbrain.In LUHMES, neuronal cilia biology can be investigated along a complete timeline: from proliferation through differentiation to mature neurons.Summary StatementWith LUHMES, a ciliated human neuronal cell model, the underlying “neurobiology” of cilia and ciliopathies can be investigated along a complete time line: from proliferation through differentiation to mature neurons.
Divergent behavioral consequences of manipulations enhancing pyramidal neuron excitability in the prelimbic cortex
Authors: Rose Timothy R. , de Velasco Ezequiel Marron Fernandez , Vo Baovi N. , Tipps Megan E. , Wickman Kevin 
Published: June 2020

ABSTRACTBackgroundDrug-induced neuroadaptations in the prefrontal cortex are thought to underlie impaired executive functions that reinforce addictive behaviors. Repeated cocaine exposure increased layer 5/6 pyramidal neuron excitability in the mouse prelimbic cortex (PL), an adaptation attributable to a suppression of G protein-gated inwardly rectifying K+(GIRK/Kir3) channel activity. GIRK channel suppression in the PL of drug-naïve mice enhanced the motor-stimulatory effect of cocaine. The impact of cocaine on PL GABA neurons, key pyramidal neuron regulators, and the behavioral relevance of increased PL pyramidal neuron excitability, remain unclear.MethodsThe effect of repeated cocaine on mouse layer 5/6 PL GABA neurons was assessed using slice electrophysiology. Adaptations enhancing PL pyramidal neuron excitability were modeled in drug-naïve mice using persistent viral Cre ablation and acute chemogenetic approaches. The impact of these manipulations on PL-dependent behavior was assessed in motor activity and trace fear conditioning tests.ResultsRepeated cocaine treatment did not impact GIRK channel activity in, or excitability of, layer 5/6 PL GABA neurons. GIRK channel ablation in PL pyramidal neurons enhanced the motor-stimulatory effect of cocaine but did not impact baseline activity or fear learning. In contrast, direct or indirect chemogenetic activation of PL pyramidal neurons increased baseline and cocaine-induced motor activity and disrupted fear learning. These effects were mirrored by chemogenetic activation of PL pyramidal neurons projecting to the ventral tegmental area.ConclusionsManipulations enhancing the excitability of PL pyramidal neurons, including those projecting to the VTA, recapitulate behavioral hallmarks of repeated cocaine exposure.
Influence of the large–Z effect during contact between butterfly sister species
Authors: Nelson Erik D. , Cong Qian , Grishin Nick V. 
Published: June 2020

AbstractComparisons of genomes from recently diverged butterfly populations along a suture zone in central Texas have revealed high levels of divergence on the Z chromosome relative to autosomes, as measured by fixation index,Fst. The pattern of divergence appears to result from accumulation of incompatible alleles, obstructing introgression on the Z chromosome in hybrids. However, it is unknown whether this mechanism is sufficient to explain the data. Here, we simulate the effects of hybrid incompatibility on interbreeding butterfly populations using a model in which populations accumulate cross–incompatible alleles in allopatry prior to contact. We compute statistics for introgression and population divergence during contact between model butterfly populations and compare them to statistics obtained for 15 pairs of butterfly species interbreeding along the Texas suture zone. For populations that have evolved sufficiently in allopatry, the model exhibits high levels of divergence on the Z chromosome relative to autosomes in populations inter-breeding on time scales comparable to periods of interglacial contact between butterfly populations in central Texas. Levels of divergence on the Z chromosome increase when interacting groups of genes are closely linked, consistent with interacting clusters of functionally related genes in butterfly genomes. Results for various periods in allopatry are in qualitative agreement with the pattern of data for butterflies, supporting a picture of speciation in which populations are subjected to cycles of divergence in glacial isolation, and partial fusion during interglacial contact.
Analysis of socioeconomic disadvantage and pace of aging measured in saliva DNA methylation of children and adolescents
Authors: Raffington Laurel , Belsky Daniel W. , Malanchini Margherita , Tucker-Drob Elliot M. , Harden K. Paige 
Published: June 2020

AbstractChildren who grow up in socioeconomically disadvantaged families face increased burden of disease and disability as they mature into adulthood. One hypothesized mechanism for this increased burden is that early-life disadvantage and its associated psychological stress accelerate biological processes of aging, increasing vulnerability to subsequent disease. In order to evaluate this hypothesis and the potential impact of preventive interventions, measures to quantify the early acceleration of biological aging in childhood are needed. Here, we evaluated a novel DNA-methylation measure of the pace of aging, DunedinPoAm, and compared DunedinPoAm results with results for several published epigenetic clocks. Data on saliva DNA-methylation and socioeconomic circumstances were collected fromN= 600 children and adolescents aged 8- to 18-years-old (48% female) participating in the Texas Twin Project. Participants living in more disadvantaged families and neighborhoods exhibited faster pace of aging (r= 0.18,p= 0.001 for both). Latinx-identifying children exhibited faster DunedinPoAm compared to both White- and Latinx-White-identifying children, consistent with higher levels of disadvantage in this group. Children with more advanced pubertal development and those with had higher body-mass index also exhibited faster DunedinPoAm, but these covariates did not account for the observed socioeconomic gradient in methylation pace of aging. In contrast to findings for DunedinPoAm, we did not detect associations of socioeconomic disadvantage with five published epigenetic clocks. Findings suggest that DNA-methylation pace-of-aging measures may prove more sensitive to health damaging effects of adversity, particularly when measurements are taken early in the life course, before substantial aging has occurred.
T cell receptor is required for differentiation but not maintenance of intestinal intraepithelial lymphocytes
Authors: Bilate Angelina M. , London Mariya , Castro Tiago B. R. , Mesin Luka , Kongthong Suppawat , Harnagel Audrey , Victora Gabriel D. , Mucida Daniel 
Published: June 2020

SummaryThe gut epithelium is populated by intraepithelial lymphocytes (IELs), a heterogeneous T cell population with cytotoxic and regulatory properties. Migrating peripheral CD4+T cells, including regulatory (Treg) and conventional T cells (Tconv), acquire an IEL (CD4-IEL) program upon arrival at the epithelium. However, the specific role of the T cell receptor (TCR) in this process remains unclear. Single-cell TCR repertoire and transcriptomic analysis of intraepithelial CD4+T cells revealed different extents of clonal expansion and TCR overlap between cell states; fully differentiated CD4-IELs from Tregs or Tconvs were the least diverse. Conditional deletion of TCR on differentiating CD4+T cells or of MHCII on intestinal epithelial cells prevented CD4-IEL differentiation. However, TCR ablation on developed CD4-IELs did not affect their accumulation. These results indicate that local recognition of a limited set of antigens is an essential signal for the differentiation and adaptation of T cells to the epithelium.
Linking T cell receptor sequence to transcriptional profiles with clonotype neighbor graph analysis (CoNGA)
Authors: Schattgen Stefan A. , Guion Kate , Crawford Jeremy Chase , Souquette Aisha , Barrio Alvaro Martinez , Stubbington Michael J.T. , Thomas Paul G. , Bradley Philip 
Published: June 2020

AbstractMulti-modal single-cell technologies capable of simultaneously assaying gene expression and surface phenotype across large numbers of immune cells have described extensive heterogeneity within these complex populations, in healthy and diseased states. In the case of T cells, these technologies have made it possible to profile clonotype, defined by T cell receptor (TCR) sequence, and phenotype, as reflected in gene expression (GEX) profile, surface protein expression, and peptide:MHC (pMHC) binding, across large and diverse cell populations. These rich, high-dimensional datasets have the potential to reveal new relationships between TCR sequence and T cell phenotype that go beyond identification of features shared by clonally related cells. In order to uncover these connections in an unbiased way, we developed a graph-theoretic approach---clonotype neighbor-graph analysis or “CoNGA”---that identifies correlations between GEX profile and TCR sequence through statistical analysis of a pair of T cell similarity graphs, one in which cells are linked based on gene expression similarity and another in which cells are linked by similarity of TCR sequence. Applying CoNGA across diverse human and mouse T cell datasets uncovered known and novel associations between TCR sequence features and cellular phenotype including the classical invariant T cell subsets; a novel defined population of human blood CD8+ T cells expressing the transcription factorsHOBITandHELIOS, NK-associated receptors, and a biased TCR repertoire, representing a potential previously undescribed lineage of “natural lymphocytes”; a striking association between usage of a specific V-beta gene segment and expression of theEPHB6gene that is conserved between mouse and human; and TCR sequence determinants of differentiation in developing thymocytes. As the size and scale of single-cell datasets continue to grow, we expect that CoNGA will prove to be a useful tool for deconvolving complex relationships between TCR sequence and cellular state in single-cell applications.
Molecular characterization ofFasciola giganticain Punjab, Pakistan to infer the dispersal route among the neighbouring countries of the Indian subcontinent
Authors: Ur Rehman Zia , Tashibu Atsushi , Tashiro Michiyo , Rashid Imran , Ali Qasim , Zahid Osama , Ashraf Kamran , Shehzad Wasim , Chaudhry Umer , Ichikawa-Seki Madoka 
Published: June 2020

AbstractFasciola giganticais considered to be a major pathogen causing fasciolosis in the Indian subcontinent, resulting in millions of dollars production losses to the livestock industry. To understand the dispersal origin and the spread patterns ofF. giganticais important for preventing the disease. A total of 53Fasciolaflukes collected from buffalo and goat in the Punjab province of Pakistan, were identified asF. giganticabased on the multiplex PCR for the phosphoenolpyruvate carboxykinase (pepck) and the PCR-restriction fragment length polymorphism (RFLP) for DNA polymerase delta (pold). A significant genetic difference betweenF. giganticafrom buffalo and goats in Pakistan was indicated by the genetic analysis of two distinct mitochondrial markers [NADH dehydrogenase subunit 1 (nad1) and cytochrome C oxidase subunit 1 (cox1)]. Phylogenetic analysis of the seventeennad1haplotypes ofF. giganticafrom Pakistan with those in neighbouring countries of the Indian subcontinent revealed that all the haplotypes were clustered in haplogroup A.Fasciola giganticawith the eight haplotypes might be expanded in Pakistan from Indian origin, along with the migration of the domestic animals, since they were related to Indian haplotypes. In contrast, the remaining nine haplotypes were not shared with any neighbouring countries, suggesting independent origin, or possibly come from neighbouring Middle East countries. Our study provides a proof of concept for a method that could be used to investigate the epidemiology ofF. giganticaregarding the development of sustainable parasite control strategies.
Metabolome shift associated with thermal stress in coral holobionts
Authors: Williams Amanda , Chiles Eric N. , Conetta Dennis , Pathmanathan Jananan S. , Cleves Phillip A. , Putnam Hollie M. , Su Xiaoyang , Bhattacharya Debashish 
Published: June 2020

SummaryCoral reef systems are under global threat due to warming and acidifying oceans1. Understanding the response of the coral holobiont to environmental change is crucial to aid conservation efforts. The most pressing problem is “coral bleaching”, usually precipitated by prolonged thermal stress that disrupts the algal symbiosis sustaining the holobiont2,3. We used metabolomics to understand how the coral holobiont metabolome responds to heat stress with the goal of identifying diagnostic markers prior to bleaching onset. We studied the heat tolerantMontipora capitataand heat sensitivePocillopora acutacoral species from the Hawaiian reef system in Kāne’ohe Bay, O’ahu. Untargeted LC-MS analysis uncovered both known and novel metabolites that accumulate during heat stress. Among those showing the highest differential accumulation were a variety of co-regulated dipeptides present in both species. The structures of four of these compounds were determined (Arginine-Glutamine, Lysine-Glutamine, Arginine-Valine, and Arginine-Alanine). These dipeptides also showed differential accumulation in symbiotic and aposymbiotic (alga free) individuals of the sea anemone modelAiptasia4, suggesting their animal provenance and algal symbiont related function. Our results identify a suite of metabolites associated with thermal stress that can be used to diagnose coral health in wild samples.
Stepwise chromatin and transcriptional acquisition of an intraepithelial lymphocyte program
Authors: London Mariya , Bilate Angelina M. , Castro Tiago B. R. , Mucida Daniel 
Published: June 2020

AbstractMesenteric lymph node (mLN) T cells undergo tissue adaptation upon migrating to intestinal lamina propria (LP) and intraepithelial (IE) compartments, ensuring appropriate balance between tolerance and resistance. By combining mouse genetics with single-cell and chromatin analyses, we addressed the molecular imprinting of gut epithelium on T cells. Transcriptionally, conventional and regulatory (Treg) CD4+T cells from mLN, LP and IE segregate based on the gut layer they occupy; trajectory analysis suggests a stepwise loss of CD4-programming and acquisition of an intraepithelial profile. Treg fate–mapping coupled with RNA– and ATAC–sequencing revealed that the Treg program shuts down before an intraepithelial program becomes fully accessible at the epithelium. Ablation of CD4 lineage–defining transcription factor ThPOK results in premature acquisition of an IEL profile by mLN Tregs, partially recapitulating epithelium imprinting. Thus, coordinated replacement of circulating lymphocyte program with site–specific transcriptional and chromatin changes is necessary for tissue imprinting.