bluuebunny/crossref_metadata_2025_split huggingface dataset:
Behavioral repeatability and foraging performance in wild free-flying nectarivorous bats (Glossophaga commissarisi)
Authors: Nachev Vladislav , Winter York 
Published: April 2018

ABSTRACTAnimal individuals show patterns of behavior that are stable within individuals but different among individuals. Such individual differences are potentially associated with differences in foraging efficiency and in fitness. Furthermore, behavioral responses may be correlated in specific suites of so called behavioral syndromes that are consistent across different contexts and with time. Here we present a field investigation on individual differences between wild, free-flying nectarivorous bats (Glossophaga commissarisi) in the foraging context. We further investigated how individual differences effect foraging performance, and we examined their interdependence within hypothesized behavioral syndrome structures. Free-ranging bats were individually identified as they visited an array of 24 artificial flowers with nectar of high or low sugar concentration. We found that three behavioral measures of foraging behavior were individually stable over the two-month observation period. We investigated the link between individual behavioral measures and measures of foraging performance using generalized linear mixed models. Individual measures of foraging performance showed significant repeatability, and we found evidence that bats making more visits per bout tend to be slower in learning to avoid unprofitable flowers. We used a multi-response generalized linear mixed model to estimate between-individual correlations and compare hypothesized syndrome structures. There were no clear patterns of between-individual correlations among the behavioral measures in our study, despite the measures exhibiting significant repeatability. This may indicate that foraging performance depends on multiple individual behavior dimensions that are not adequately described by simple models of behavior syndromes.
Cycles of gene expression and genome response during mammalian tissue regeneration
Authors: Rib Leonor , Villeneuve Dominic , Praz Viviane , Hernandez Nouria , Guex Nicolas , Herr Winship ,   CycliX Consortium
Published: April 2018

AbstractBackgroundCompensatory liver hyperplasia — or regeneration — induced by two-thirds partial hepatectomy (PH) permits the study of synchronized activation of mammalian gene expression, particularly in relation to cell proliferation. Here, we measured genomic transcriptional responses and mRNA accumulation changes after PH and sham surgeries.ResultsDuring the first 10–20 hours, the PH- and sham-surgery responses were very similar, including parallel early activation of cell-division-cycle genes. After 20 hours, however, whereas post-PH livers continued with a robust and coordinate cell-division-cycle gene-expression response before returning to the resting state by one week, sham-surgery livers returned directly to a resting gene-expression state. Localization of RNA polymerase II (Pol II), and trimethylated histone H3 lysine 4 (H3K4me3) and 36 (H3K36me3) on genes dormant in the resting liver and activated during the PH response revealed a general de novo promoter Pol II recruitment and H3K4me3 increase during the early 10–20 hour phase followed by Pol II elongation and H3K36me3 accumulation in gene bodies during the later proliferation phase. H3K36me3, generally appearing at the first-internal exon, was preceded 5′ by H3K36me2; 3′ of the first-internal exon, in about half of genes H3K36me3 predominated and in the other half H3K36me2 and H3K36me3 co-existed. Further, we observed some unusual gene profiles with abundant Pol II but little evident H3K4me3 or H3K36me3 modification, indicating that these modifications are neither universal nor essential partners to Pol II transcription.ConclusionsPH and sham surgical procedures on mice reveal striking early post-operatory gene expression similarities followed by synchronized mRNA accumulation and epigenetic histone mark changes specific to PH.
PII1: a protein involved in starch initiation that determines granule number and size in Arabidopsis chloroplast
Authors: Vandromme Camille , Spriet Corentin , Dauvillée David , Courseaux Adeline , Putaux Jean-Luc , Wychowski Adeline , Facon Maud , D’Hulst Christophe , Wattebled Fabrice 
Published: April 2018

AbstractThe initiation of starch granule formation is still poorly understood. However, soluble starch synthase 4 (SS4) appears to be a major component of this process since it is required to synthetize the correct number of starch granules in the chloroplasts of Arabidopsis thaliana plants. A yeast-2-hybrid screen allowed the identification of several putative SS4 interacting partners. We identified the product of At4g32190 locus as a chloroplast-targeted PROTEIN INVOLVED IN STARCH INITIATION (named PII1). Arabidopsis mutants devoid of PII1 display an alteration of starch initiation process and accumulate, on average, one starch granule per plastid instead of the 5 to 7 granules found in plastids of wild-type plants. These granules are larger than in wild type and they remain flat and lenticular. pii1 mutants display wild-type growth rates and accumulate standard starch amounts. Moreover, starch characteristics, such as amylopectin chain length distribution, remain unchanged. Our results reveal the involvement of PII1 in starch priming process in Arabidopsis leaves through interaction with SS4.
Adaptive protein evolution through length variation in short tandem repeats
Authors: Reinar William B. , Greulich Anne , Stø Ida M. , Knutsen Jonfinn B. , Reitan Trond , Tørresen Ole K. , Jentoft Sissel , Butenko Melinka A. , Jakobsen Kjetill S. 
Published: April 2018

AbstractIntrinsically disordered protein regions are of high importance for temperature sensing and immune responses in plants. Tracts of identical amino acids accumulate in these regions and can vary in length over generations due to expansions and retractions of short tandem repeats at the genomic level. However, little attention has been paid to what extent length variation is shaped by natural selection. By environmental association analysis on 2,514 length variable tracts in 770 whole-genome sequenced wildArabidopsis thalianawe show that length variation in glutamine and asparagine amino acid homopolymers, as well as in interaction hotspots, correlate with local bio-climatic habitat. We determined experimentally that the promoter activity of a light-stress gene depended on polyglutamine length variants in a disordered transcription factor. Our results show that length variations impact protein function and are substantially shaped by natural selection. Length variants modulating protein function at a global genomic scale has implications for understanding protein evolution and eco-evolutionary biology.
Rescue of a developmental arrest caused by aC. elegansheat-shock transcription-factor mutation by loss of ribosomal S6-kinase activity
Authors: Chisnell Peter , Richard Parenteau T. , Tank Elizabeth , Ashrafi Kaveh , Kenyon Cynthia 
Published: April 2018

AbstractThe widely conserved heat-shock response, regulated by heat shock transcription factors, is not only essential for cellular stress resistance and adult longevity, but also for proper development. However, the genetic mechanisms by which heat-shock transcription factors regulate development are not well understood. InC. elegans, we conducted an unbiased genetic screen to identify mutations that could ameliorate the developmental arrest phenotype of a heat-shock factor mutant. Here we show that loss of the conserved translational activatorrsks-1/S6-Kinase, a downstream effector of TOR kinase, can rescue the developmental-arrest phenotype of hsf-1partial loss-of-function mutants. Unexpectedly, we show that the rescue is not likely caused by reduced translation, nor to activation of any of a variety of stress-protective genes and pathways. Our findings identify an as-yet unexplained regulatory relationship between the heat-shock transcription factor and the TOR pathway duringC. elegans’development.
Single cell RNA sequencing reveals a novel, microglia-like cell type in cerebrospinal fluid during virologically suppressed HIV
Authors: Farhadian Shelli F. , Mehta Sameet S. , Zografou Chrysoula , Pappalardo Jenna , Chiarella Jennifer , Hafler David A. , Spudich Serena S. 
Published: April 2018

AbstractCentral nervous system (CNS) immune activation in an important driver of neuronal injury during several neurodegenerative and neuroinflammatory diseases. During HIV infection, CNS immune activation is associated with high rates of neurocognitive impairment, even with sustained long-term suppressive antiretroviral therapy (ART). However, the cellular subsets that drive immune activation and neuronal damage in the CNS during HIV infection and neurological conditions remain unknown, in part because CNS cells are difficult to access in living humans. Using single cell RNA sequencing (scRNA-seq) on cerebrospinal fluid (CSF) and blood from adults with HIV, we identified a rare (<5% of cells) subset of myeloid cells in CSF presenting a gene expression signature consistent with neurodegenerative disease associated microglia. This highlights the power of scRNA-seq of CSF to identify rare CNS immune cell subsets that may perpetuate neuronal injury during HIV infection and other conditions.
Hydrogen-deuterium exchange coupled to top- and middle-down mass spectrometry enables high-resolution measurements of histone tail dynamics before and after nucleosome assembly
Authors: Karch Kelly R. , Coradin Mariel , Zandarashvili Levani , Kan Zhong-Yuan , Gerace Morgan , Englander S. Walter , Black Ben E. , Garcia Benjamin A. 
Published: April 2018

AbstractUntil recently, a major limitation of hydrogen deuterium exchange mass spectrometry (HDX-MS) was that resolution of deuterium localization information was limited to the length of the peptide generated during proteolysis. Recently, however, it has been demonstrated that electron transfer dissociation (ETD) allows for preservation of deuterium label in the gas phase and therefore can be used to obtain more resolved information. To date, this technology has remained mostly limited to single, small, already well-characterized model proteins. Here, we optimize, expand, and adapt HDX-MS/MS capabilities to accommodate histone and nucleosomal complexes on top-down (TD) HDX-MS/MS and middle-down (MD) HDX-MS/MS platforms and demonstrate that near site-specific resolution of deuterium localization can be obtained with high reproducibility. We are able to study histone tail dynamics in unprecedented detail, which have evaded rigorous analysis by traditional structural biology techniques for decades, revealing important novel insights into chromatin biology. This work represents the first heterogeneous protein complex and protein-DNA complex to be analyzed by TD- and MD-HDX-MS/MS, respectively. Together, the results of these studies highlight the versatility, reliability, and reproducibility of ETD-based HDX-MS/MS methodology to interrogate large protein and protein/DNA complexes.
Molecular Strategy for Blocking Isopeptide Bond Formation in Nascent Pilin Proteins
Authors: Rivas-Pardo Jaime Andrés , Badilla Carmen L. , Tapia-Rojo Rafael , Alonso-Caballero Álvaro , Fernández Julio M. 
Published: April 2018

ABSTRACTBacteria anchor to their host cells through their adhesive pili, which must resist the large mechanical stresses induced by the host as it attempts to dislodge the pathogens. The pili of Gram-positive bacteria are constructed as a single polypeptide made of hundreds of pilin repeats, which contain intramolecular isopeptide bonds strategically located in the structure to prevent their unfolding under force, protecting the pilus from degradation by extant proteases and oxygen radicals. Here, we demonstrate the design of a short peptide that blocks the formation of the isopeptide bond present in the pilin Spy0128 from the human pathogen Streptococcus pyogenes, resulting in mechanically labile pilin domains. We use a combination of protein engineering and AFM force spectroscopy to demonstrate that the peptide blocks the formation of the native isopeptide bond and compromises the mechanics of the domain. While an intact Spy0128 is inextensible at any force, peptide-modified Spy0128 pilins readily unfold at very low forces, marking the abrogation of the intramolecular isopeptide bond as well as the absence of a stable pilin fold. We propose that isopeptide-blocking peptides could be further developed as a novel type of highly-specific anti-adhesive antibiotics to treat Gram-positive pathogens.SignificanceAt the onset of an infection, Gram-positive bacteria adhere to host cells through their pili, filamentous structures built by hundreds of repeats of pilin proteins. These proteins can withstand large mechanical challenges without unfolding, remaining anchored to the host and resisting cleavage by proteases and oxygen radicals present in the targeted tissues. The key structural component that gives pilins mechanical resilience are internal isopeptide bonds, strategically placed so that pilins become inextensible structures. We target this bond by designing a blocking peptide that interferes with its formation during folding. We demonstrate that peptide-modified pilins lack mechanical stability and extend at low forces. We propose this strategy as a rational design of mechanical antibiotics, targeting the Achilles’ Heel of bacterial adhesion.
Gain of Function Analysis Reveals Non-Redundant Roles for theYersinia pestisType III Secretion System Effectors YopJ, YopT, and YpkA
Authors: Palace Samantha G. , Proulx Megan K. , Szabady Rose L. , Goguen Jon D. 
Published: April 2018

AbstractVirulence ofYersinia pestisin mammals requires the type III secretion system, which delivers seven effector proteins into the cytoplasm of host cells to undermine immune responses. All seven of these effectors are conserved acrossY. pestisstrains, but three – YopJ, YopT, and YpkA – are apparently dispensable for virulence. Some degree of functional redundancy between effector proteins would explain both observations. Here, we use a combinatorial genetic approach to define the minimal subset of effectors required for full virulence in mice following subcutaneous infection. We found that aY. pestisstrain lacking YopJ, YopT, and YpkA is attenuated for virulence in mice, and that addition of any one of these effectors to this strain increases lethality significantly. YopJ, YopT, and YpkA likely contribute to virulence via distinct mechanisms. YopJ is uniquely able to cause macrophage cell deathin vitroand to suppress accumulation of inflammatory cells to foci of bacterial growth in deep tissue, whereas YopT and YpkA cannot. The synthetic phenotypes that emerge when YopJ, YopT, and YpkA are removed in combination provide evidence that each enhancesY. pestisvirulence, and that YopT and YpkA act through a mechanism distinct from that of YopJ.
Map segmentation, automated model-building and their application to the Cryo-EM Model Challenge
Authors: Terwilliger Thomas C. , Adams Paul D. , Afonine Pavel V. , Sobolev Oleg V. 
Published: April 2018

AbstractA recently-developed method for identifying a compact, contiguous region representing the unique part of a density map was applied to 218 cryo-EM maps with resolutions of 4.5 Å or better. The key elements of the segmentation procedure are (1) identification of all regions of density above a threshold and (2) choice of a unique set of these regions, taking symmetry into consideration, that maximize connectivity and compactness. This segmentation approach was then combined with tools for automated map sharpening and model-building to generate models for the 12 maps in the 2016 cryo-EM model challenge in a fully automated manner. The resulting models have completeness from 24% to 82% and RMS distances from reference interpretations of 0.6 Å to 2.1 Å.
GnasR201C Induces Murine Pancreatic Cystic Neoplasms through Suppression of YAP1 Signaling and Transcriptional Reprogramming
Authors: Ideno Noboru , Yamaguchi Hiroshi , Ghosh Bidyut , Gupta Sonal , Okumura Takashi , Fisher Catherine G , Wood Laura D , Singhi Aatur D. , Nakamura Masafumi , Gutkind J Silvio , Maitra Anirban 
Published: April 2018

ABSTRACTBackground & AimsSomatic “hotspot” mutations of GNAS, which encodes for the alpha subunit of stimulatory G-protein, are present in ~60% of intraductal papillary mucinous neoplasms (IPMNs) of the pancreas. There are currently no cognate animal models that recapitulate the biology of mutant Gnas-induced IPMNs, and the underlying mechanisms that lead to the cystic pathway of neoplasia in the pancreas remain unknown.MethodsWe generated p48-Cre; LSL-KrasG12D; Rosa26R-LSL-rtTA-TetO-GnasR201C mice (Kras; Gnas mice) where pancreas-specific GnasR201C expression was induced by doxycycline administration. In this model, mutant Kras is constitutively expressed, and control mice were produced through absence of doxycycline. Separate cohorts of mice were utilized for timed necropsies and for Kaplan-Meier survival analysis. Isogenic cell lines (with doxycycline inducible mutant Gnas expression) were propagated from the resulting pancreatic ductal adenocarcinoma (PDAC).ResultsCo-expression of KrasG12D and GnasR201C resulted in the development of pancreatic cystic lesions resembling human IPMNs in 100% of mice, with higher grades of epithelial dysplasia observed over time. Approximately one-third of Kras; Gnas mice developed PDAC at a median of 38 weeks post doxycycline induction. GnasR201C did not accelerate oncogenic transformation with KrasG12D, but rather, reprogrammed Ras-induced neoplasms towards a well-differentiated phenotype. GnasR201C induction led to activation of the inhibitory Hippo kinase cascade and cytoplasmic sequestration of phosphorylated YAP1 protein, a phenomenon that was also observed in human IPMN with GNAS mutations.ConclusionsGNASR201C functions not as a traditional oncogene, but rather as an “oncomodulator” of KRAS-mediated pancreatic neoplasia, through suppression of YAP1 and transcriptional reprogramming towards a differentiated (large ductal) phenotype.
Exploring sex differences in the prevention of ethanol drinking by naltrexone in dependent rats during abstinence
Authors: Matzeu A , Terenius L , Martin-Fardon R 
Published: April 2018

AbstractBackgroundDespite considerable efforts, few drugs are available for the treatment of alcohol (ethanol [EtOH]) use disorders (AUDs). Ethanol directly or indirectly modulates several aspects of the central nervous system, including neurotransmitter/neuromodulator systems. Relapse vulnerability is a challenge for the treatment of EtOH addiction. Ethanol withdrawal symptoms create motivational states that lead to compulsive EtOH drinking and relapse even after long periods of abstinence. Among the therapeutics to treat AUDs, naltrexone (NTX) is a pharmacological treatment for relapse. The goal of the present study was to evaluate the effect of NTX on EtOH drinking in EtOH-dependent male and female rats during abstinence.MethodsWistar rats (males and females) were first trained to orally self-administer 10% EtOH. Half of them were then made dependent by chronic intermittent EtOH (CIE) vapor exposure, and the other half were exposed to air. Using this model, rats exhibit somatic and motivational signs of withdrawal. At the end of EtOH vapor (or air) exposure, the rats were tested for the effects of NTX (10 mg/kg, p.o.) on EtOH self-administration at three abstinence time points: acute abstinence (8 h, A-Abst), late abstinence (2 weeks, L-Abst), and protracted abstinence (6 weeks, P-Abst).ResultsNTX decreased EtOH intake in nondependent rats, regardless of sex and abstinence time point. In post-dependent rats, the effects of NTX improved with a longer abstinence time (i.e., L-Abst and P-Abst) in males, whereas it similarly reduced EtOH drinking in females at all abstinence points.ConclusionsThe data suggest that the therapeutic efficacy of NTX depends on the time of intervention during abstinence and sex. The data further suggest that EtOH dependence induces different neuroadaptations in male and female rats, reflected by differential effects of NTX. The results underscore the significance of considering the duration of EtOH abstinence and sex for the development of pharmacotherapeutic treatments for AUD.
Joint single-cell DNA accessibility and protein epitope profiling reveals environmental regulation of epigenomic heterogeneity
Authors: Chen Xingqi , Litzenburger Ulrike M. , Wei Yuning , Schep Alicia N. , LaGory Edward L. , Choudhry Hani , Giaccia Amato J. , Greenleaf William J. , Chang Howard Y. 
Published: April 2018

AbstractHere we introduce Protein-indexed Assay of Transposase Accessible Chromatin with sequencing (Pi-ATAC) that combines single-cell chromatin and proteomic profiling. In conjunction with DNA transposition, the levels of multiple cell surface or intracellular protein epitopes are recorded by index flow cytometry and positions in arrayed microwells, and then subject to molecular barcoding for subsequent pooled analysis. Pi-ATAC simultaneously identifies the epigenomic and proteomic heterogeneity in individual cells. Pi-ATAC reveals a casual link between transcription factor abundance and DNA motif access, and deconvolute cell types and states in the tumor microenvironmentin vivo. We identify a dominant role for hypoxia, marked by HIF1α protein, in the tumor microvenvironment for shaping the regulome in a subset of epithelial tumor cells.
HDAC11 Deficiency Prevents High-Fat Diet-Induced Obesity and Metabolic Syndrome
Authors: Sun Lei , Marin De Evsikova Caralina , Bian Ka , Achille Alexandra , Telles Elphine , Seto Edward 
Published: April 2018

Significance StatementObesity is a serious and widespread health problem which has become a growing concern in many societies. Most currently available weight-loss medications do not work for everyone, and the effects decline over time. Thus, there is an urgent need to identify new molecular targets to improve drug development for the treatment of obesity and obesity-related diseases. In this study, we discovered that the histone deacetylase 11 (HDAC11) enzyme is a key regulator of metabolism and obesity, and the absence of HDAC11 prevents obesity in mice. Our findings will facilitate the development of novel therapeutics to treat obesity by targeting HDAC11.AbstractObesity and its associated metabolic syndromes are the consequence of susceptible genes and obesogenic environments. We report here that histone deacetylase 11 (HDAC11) plays a critical role in the development of obesity and in metabolic homeostasis. HDAC11 knockout mice display resistance to high-fat diet-induced obesity and associated syndromes by enhancing glucose tolerance and insulin sensitivity, attenuating hypercholesterolemia and hyperinsulinemia, and blocking hepatosteatosis and liver damage. Mechanistically, HDAC11 deficiency boosts energy expenditure through promoting thermogenic capacity, which attributes to the elevation of uncoupling protein 1 (UCP1) expression and activity in brown adipose tissue. Moreover, loss of HDAC11 stimulates mitochondrial oxidation, elevates plasma adiponectin, and activates the adiponectin-AdipoR-AMPK pathway in the liver, which may contribute to a reversal in hepatosteatosis. These findings establish HDAC11 as a key regulator of metabolism and indicate that HDAC11 inhibitors may hold promise for treating overweight and obesity-related diseases.