bluuebunny/crossref_metadata_2025_split huggingface dataset:
A pan-genome method to determine core regions of theBacillus subtilisandEscherichia coligenomes
Authors: Sutton Granger , Fogel Gary B. , Abramson Bradley , Brinkac Lauren , Michael Todd , Liu Enoch S. , Thomas Sterling 
Published: June 2020

AbstractSynthetic engineering of bacteria to produce industrial products is a burgeoning field of research and application. In order to optimize genome design, designers need to understand which genes are essential, which are optimal for growth, and locations in the genome that will be tolerated by the organism when inserting engineered cassettes. We present a pan-genome based method for the identification of core regions in a genome that are strongly conserved at the species level. We show that these core regions are very likely to contain all or almost all essential genes. We assert that synthetic engineers should avoid deleting or inserting into these core regions unless they understand and are manipulating the function of the genes in that region. Similarly, if the designer wishes to streamline the genome, non-core regions and in particular low penetrance genes would be good targets for deletion. Care should be taken to remove entire cassettes with similar penetrance of the genes within cassettes as they may harbor toxin/antitoxin genes which need to be removed in tandem. The bioinformatic approach introduced here saves considerable time and effort relative to knockout studies on single isolates of a given species and captures a broad understanding of the conservation of genes that are core to a species.ImportanceThe pan-genome approach presented in this paper can be used to determine core regions of a genome and has many possible applications. Synthetic engineering design can be informed by which genes/regions are more conserved (core) versus less conserved. The level of conservation of adjacent non-core genes tends to define cassettes of genes which may be part of a pathway or system that can inform researchers about possible functional significance. The pattern of gene presence across the different genomes of a species can inform the understanding of evolution and horizontal gene acquisition. The approach saves considerable time and effort relative to laboratory methods used to identify essential genes in species.
MHC class I and II genes in Serpentes
Authors: Olivieri D.N. , Mirete-Bachiller S. , Gambón-Deza F. 
Published: June 2020

AbstractGenes of the major class I and II histocompatibility complex have been extensively studied in mammals. Studies of these antigens in reptiles are very scarce. Here we describe the characteristics of these genes in the suborder Serpentes. We identified the presence of a much larger number of molecules of class I and beta chains of class II than found in mammals. Snakes only have one gene for the class II alpha chain. In these species, class I genes can be classified into two types. Approximately half of the genes lack 10 amino acids in theα1 domain, producing a structural alteration in the interaction region with the T lymphocyte receptor. In the genome ofThamnophis elegans, two haplotypes of an individual were studied revealing a different number and location of class I genes between these haplotypes. The results indicate that in these species, the diversity in the MHC is generated by the presence or absence of genes, independent of the presence of alleles.
Disentangling interactions among mercury, immunity, and infection in a Neotropical bat community
Authors: Becker Daniel J. , Speer Kelly A. , Korstian Jennifer M. , Volokhov Dmitriy V. , Droke Hannah F. , Brown Alexis M. , Baijnauth Catherene L. , Padgett-Stewart Ticha , Broders Hugh G. , Plowright Raina K. , Rainwater Thomas R. , Fenton M. Brock , Simmons Nancy B. , Chumchal Matthew M. 
Published: June 2020

AbstractContaminants such as mercury are pervasive and can have immunosuppressive effects on wildlife. Impaired immunity could be important for forecasting pathogen spillover risks, as many land-use changes that generate mercury contamination also bring wildlife into close contact with humans and domestic animals. However, the interactions among contaminants, immunity, and infection are difficult to study in natural systems, and empirical tests of possible directional relationships remain rare.We capitalized on extreme mercury variation in a diverse bat community in Belize to test association among contaminants, immunity, and infection. By comparing a previous dataset of bats sampled in 2014 with new data from 2017, representing a period of rapid agricultural land conversion, we first confirmed bat species more reliant on aquatic prey had higher fur mercury. Bats in the agricultural habitat also had higher mercury in recent years. We then tested covariation between mercury and cellular immunity and determined if such relationships mediated associations between mercury and common bacterial pathogens. As bat ecology can dictate exposure to mercury and pathogens, we also assessed species-specific patterns in mercury–infection relationships.Across the bat community, individuals with higher mercury had fewer neutrophils but not lymphocytes, suggesting stronger associations with innate immunity. However, the odds of infection for hemoplasmas andBartonellaspp. were generally lowest in bats with high mercury, and relationships between mercury and immunity did not mediate infection patterns. Mercury also showed species- and clade-specific relationships with infection, being associated with especially low odds for hemoplasmas inPteronotus mesoamericanusandDermanura phaeotis.ForBartonellaspp., mercury was associated with particularly low odds in the genusPteronotusbut high odds in the Stenodermatinae.Synthesis and application:Lower general infection risk in bats with high mercury despite weaker innate defense suggests contaminant-driven loss of pathogen habitat (i.e., anemia) or vector mortality as possible causes. Greater attention to these potential pathways could help disentangle relationships among contaminants, immunity, and infection in anthropogenic habitats and help forecast disease risks. Our results also suggest contaminants may increase infection risk in some taxa but not others, emphasizing the importance of considering surveillance and management at different phylogenetic scales.
A Rat Model of a Focal Mosaic Expression of PCDH19 Replicates Human Brain Developmental Abnormalities and Behaviors
Authors: Cwetsch Andrzej W , Narducci Roberto , Bolla Maria , Pinto Bruno , Perlini Laura , Bassani Silvia , Passafaro Maria , Cancedda Laura 
Published: June 2020

AbstractPCDH19 gene-related epilepsy or epileptic encephalopathy, early infantile, 9 (EIEE9) is an infantile onset epilepsy syndrome characterized by psychiatric (including autistic) sensory and cognitive impairment of varying degrees. EIEE9 is caused by X-linked PCDH19 protein loss of function. Due to random X-chromosome inactivation, EIEE9-affected females present a mosaic population of healthy and Pcdh19-mutant cells. Unfortunately, no mouse models recapitulate to date both the brain histological and behavioural deficits present in people with EIEE9. Thus, the search for a proper understanding of the disease, and possible future treatment is hampered. By inducing a focal mosaicism of Pcdh19 expression usingin uteroelectroporation in rat, we found here that Pcdh19 signaling in specific brain areas is implicated in neuronal migration, as well as in core behaviors related to autism and cognitive function.
Co-occupancy analysis reveals novel transcriptional synergies for axon growth
Authors: Venkatesh Ishwariya , Mehra Vatsal , Wang Zimei , Simpson Matthew T. , Eastwood Erik , Chakraborty Advaita , Beine Zac , Gross Derek , Cabahug Michael , Olson Greta , Blackmore Murray G. 
Published: June 2020

AbstractTranscription factors (TFs) act as powerful levers to regulate neural physiology and can be targeted to improve cellular responses to injury or disease. Because TFs often depend on cooperative activity, a major challenge is to identify and deploy optimal sets. Here we developed a novel bioinformatics pipeline, centered on TF co-occupancy of regulatory DNA, and used it to predict factors that potentiate the effects of pro-regenerative Klf6. High content screens of neurite outgrowth identified cooperative activity by 12 candidates, and systematic testing in an animal model of corticospinal tract (CST) damage substantiated three novel instances of pairwise cooperation. Combined Klf6 and Nr5a2 drove the strongest growth, and transcriptional profiling of CST neurons identified Klf6/Nr5a2-responsive gene networks involved in macromolecule biosynthesis and DNA repair. These data identify novel TF combinations that promote enhanced CST growth, clarify the transcriptional correlates, and provide a bioinformatics roadmap to detect TF synergy.
Longitudinal isolation of potent near-germline SARS-CoV-2-neutralizing antibodies from COVID-19 patients
Authors: Kreer Christoph , Zehner Matthias , Weber Timm , Rohde Cornelius , Halwe Sandro , Ercanoglu Meryem S. , Gieselmann Lutz , Korenkov Michael , Gruell Henning , Schommers Philipp , Vanshylla Kanika , Di Cristanziano Veronica , Janicki Hanna , Brinker Reinhild , Ashurov Artem , Krähling Verena , Kupke Alexandra , Cohen-Dvashi Hadas , Koch Manuel , Lederer Simone , Pfeifer Nico , Wolf Timo , Vehreschild Maria J.G.T. , Wendtner Clemens , Diskin Ron , Becker Stephan , Klein Florian 
Published: June 2020

SUMMARYThe SARS-CoV-2 pandemic has unprecedented implications for public health, social life, and world economy. Since approved drugs and vaccines are not available, new options for COVID-19 treatment and prevention are highly demanded. To identify SARS-CoV-2 neutralizing antibodies, we analysed the antibody response of 12 COVID-19 patients from 8 to 69 days post diagnosis. By screening 4,313 SARS-CoV-2-reactive B cells, we isolated 255 antibodies from different time points as early as 8 days post diagnosis. Among these, 28 potently neutralized authentic SARS-CoV-2 (IC100as low as 0.04 μg/ml), showing a broad spectrum of V genes and low levels of somatic mutations. Interestingly, potential precursors were identified in naïve B cell repertoires from 48 healthy individuals that were sampled before the COVID-19 pandemic. Our results demonstrate that SARS-CoV-2 neutralizing antibodies are readily generated from a diverse pool of precursors, fostering the hope of rapid induction of a protective immune response upon vaccination.
DNA methylation reveals distinct cells of origin for pancreatic neuroendocrine carcinomas (PanNECs) and pancreatic neuroendocrine tumors (PanNETs)
Authors: Simon Tincy , Riemer Pamela , Detjen Katharina , Di Domenico Annunziata , Bormann Felix , Menne Andrea , Khouja Slim , Monjé Nanna , Childs Liam H. , Lenze Dido , Leser Ulf , Jarosch Armin , Rossner Florian , Morkel Markus , Blüthgen Nils , Pavel Marianne , Horst David , Capper David , Marinoni Ilaria , Perren Aurel , Mamlouk Soulafa , Sers Christine 
Published: June 2020

AbstractPancreatic Neuroendocrine Carcinomas (PanNECs) are high-grade, poorly-differentiated tumors grouped together with Pancreatic Neuroendocrine Tumors (PanNETs) and placed within the Pancreatic Neuroendocrine Neoplasms (PanNENs) WHO tumor classification. Despite recent studies suggesting the endocrine origin of low-grade PanNETs, high-grade PanNEC origin remains unknown. DNA methylation analysis using the Illumina 850K beadchip array was conducted on 57 PanNEN samples, including 14 PanNECs. Distinct methylation profiles separated PanNEN samples into two major groups, clearly distinguishing high-grade PanNECs from other PanNETs including high-grade NETG3. DNA mutations, copy number changes and Immunohistochemistry of pancreatic cell-type markers PDX1, ARX and SOX9 were utilized to further characterize PanNECs and their hierarchical cell of origin in the pancreas. Phylo-epigenetic and cell-type signature features using methylation data from normal alpha, beta, acinar and ductal adult cells indicate an exocrine cell of origin for PanNECs, thus separating them in cell lineage from other PanNENs of endocrine origin. Our study provides a robust and clinically relevant method relying on methylation profiles to clearly distinguish PanNECs from PanNETG3s to improve patient stratification and treatment.
The alternative sigma factor σXmediates competence shut-off at the cell pole inStreptococcus pneumoniae
Authors: Johnston Calum , Soulet Anne-Lise , Berge Matthieu , Prudhomme Marc , De Lemos David , Polard Patrice 
Published: June 2020

SummaryBacterial competence for genetic transformation is a well-known species-specific differentiation program driving genome plasticity, antibiotic resistance and virulence in many pathogens. How competence regulation is spatiotemporally integrated in the cell is ill-defined. Here, we unraveled the localization dynamics of the key regulators that master the two intertwined transcription waves controlling competence inStreptococcus pneumoniae. The first wave relies on a stress-inducible phosphorelay system, made up of the ComD and ComE proteins, and the second is directed by an alternative sigma factor, σX, which includes in its regulon the DprA protein that turns off competence through interaction with phosphorylated ComE. Remarkably, we found that ComD, σXand DprA stably co-localize at a single cell pole over the competence period. In contrast, ComE assembles into dynamic patches in the cell periphery, colocalizing temporarily with DprA and ComD at the pole. Furthermore, we provide evidence that σXdirectly conveys DprA polar anchoring. Through this protein targeting function, σXis shown to be actively involved in the timely shut-off of the competence cycle, hence preserving cell fitness. Altogether, this study unveils an unprecedented role for a bacterial transcription σ factor in spatially coordinating the negative feedback loop of its own genetic circuit.
Hierarchical Model for the Role of J-Domain Proteins in Distinct Cellular Functions
Authors: Sugimoto Shinya , Yamanaka Kunitoshi , Niwa Tatsuya , Kinjo Yuki , Mizunoe Yoshimitsu , Ogura Teru 
Published: June 2020

ABSTRACTInEscherichia coli, the major bacterial Hsp70 system consists of DnaK, three J-domain proteins (JDPs: DnaJ, CbpA, and DjlA), and one nucleotide exchange factor (NEF: GrpE). JDPs determine substrate specificity for the Hsp70 system; however, knowledge on their specific role in bacterial cellular functions is limited. In this study, we demonstrated the role of JDPs in bacterial survival during heat stress and the DnaK-regulated formation of curli—extracellular amyloid fibers involved inE. colibiofilm formation. Genetic analysis with a complete set of JDP-null mutant strains demonstrated that only DnaJ is essential for survival at high temperature, while DnaJ and CbpA are indispensable in DnaK regulation of curli production. Additionally, we found that DnaJ and CbpA are involved in the expression of the master regulator CsgD through the folding of MlrA; this keeps CsgA in a translocation-competent state by preventing its aggregation in the cytoplasm. Our findings support a hierarchical model wherein the role of JDPs in the Hsp70 system differs according to individual cellular functions.
Cancer exosomes harbor diverse hypoxia-targeted mRNAs and contribute toward tumor angiogenesis
Authors: Zhang Pan , Lim Su Bin , Jiang Kuan , Chew Ti Weng , Low Boon Chuan , Lim Chwee Teck 
Published: June 2020

AbstractExosomes are extracellular vesicles of endosome origin secreted by various cells. The exosomal cargo, especially proteins and microRNAs, have been extensively investigated for their roles in intercellular communication and as biomarkers for clinical applications. However, the understanding of types and functions of exosomal mRNAs remains limited. Here, we evaluated the mRNAs of 61 hypoxia-targeted genes in exosomes by quantitative reverse transcription PCR (RT-qPCR). Among these 61 mRNAs, 14.8% of them were detected in the MCF10A-derived exosomes, 42.6% in the MCF7-derived exosomes, and 49.2% in the MDA-MB-231-derived exosomes, many of which are differentially regulated in response to hypoxic stress in a cell-line dependent manner. Consequently, 30 exosomal mRNAs are identified as cancer related biomarkers as they are present in cancer cell-derived exosomes and absent in MCF10A-derived exosomes. Co-culture of MDA-MB-231 cells with HUVECs shows uptake of MDA-MB-231 secreted exosomes by the Human umbilical vein endothelial cells (HUVECs). Subsequently, the cancer exosomal VEGFA mRNAs were translated within the HUVECs into proteins that promoted VEGFR-dependent angiogenesis. This finding provides novel insights into how cancer cells can directly contribute towards angiogenesis. RNA-seq also shows that cancer exosomes can upregulate epithelial-mesenchymal transition-related and metabolism-related genes. The transcripts of these genes are found present in the cancer exosomes, suggesting that the uptake of exosomal mRNAs at least partially contributed to the upregulation of the corresponding mRNAs. This study shows that cancer exosomes harbor diverse mRNAs, some of which can act as promising biomarkers as well as contribute towards reprogramming of recipient cells.
Molecular switch architecture drives response properties
Authors: Ghusinga Khem Raj , Jones Roger D. , Jones Alan M. , Elston Timothy C. 
Published: June 2020

AbstractMany intracellular signaling pathways are composed of molecular switches, proteins that transition between two states—onandoff. Typically, signaling is initiated when an external stimulus activates its cognate receptor that in turn causes downstream switches to transition fromofftoonusing one of the following mechanisms: activation, in which the transition rate from theoffstate to theonstate increases; derepression, in which the transition rate from theonstate to theoffstate decreases; and concerted, in which activation and derepression operate simultaneously. We use mathematical modeling to compare these signaling mechanisms in terms of their dose-response curves, response times, and abilities to process upstream fluctuations. Our analysis elucidates several general principles. First, activation increases the sensitivity of the pathway, whereas derepression decreases sensitivity. Second, activation generates response times that decrease with signal strength, whereas derepression causes response times to increase with signal strength. These opposing features allow the concerted mechanism to not only show dose-response alignment, but also to decouple the response time from stimulus strength. However, these potentially beneficial properties come at the expense of increased susceptibility to up-stream fluctuations. In addition to above response metrics, we also examine the effect of receptor removal on switches governed by activation and derepression. We find that if inactive (active) receptors are preferentially removed then activation (derepression) exhibits a sustained response whereas derepression (activation) adapts. In total, we show how the architecture of molecular switches govern their response properties. We also discuss the biological implications of our findings.
Molecular diversity of glutamatergic and GABAergic synapses from multiplexed fluorescence imaging
Authors: Danielson Eric , de Arce Karen Perez , Cimini Beth , Wamhoff Eike-Christian , Singh Shantanu , Cottrell Jeffrey R , Carpenter Anne E. , Bathe Mark 
Published: June 2020

AbstractNeuronal synapses contain hundreds of different protein species important for regulating signal transmission. Characterizing differential expression profiles of proteins within synapses in distinct regions of the brain has revealed a high degree of synaptic diversity defined by unique molecular organization. Multiplexed imaging ofin vitroneuronal culture models at single synapse resolution offers new opportunities for exploring synaptic reorganization in response to chemical and genetic perturbations. Here, we combine 12-color multiplexed fluorescence imaging with quantitative image analysis and machine learning to identify novel synaptic subtypes within excitatory and inhibitory synapses based on the expression profiles of major synaptic components. We characterize differences in the correlated expression of proteins within these subtypes and we examine how the distribution of these synapses is modified following induction of synaptic plasticity. Under chronic suppression of neuronal activity, phenotypic characterization revealed coordinated increases in both excitatory and inhibitory protein levels without changes in the distribution of synaptic subtypes, suggesting concerted events targeting glutamatergic and GABAergic synapses. Our results offer molecular insight into the mechanisms of synaptic plasticity.
Heart Slice Culture System Reliably Demonstrates Clinical Drug-Related Cardiotoxicity
Authors: Miller Jessica M. , Meki Moustafa H. , Ou Qinghui , George Sharon A. , Gams Anna , Abouleisa Riham R. E. , Tang Xian-Liang , Ahern Brooke M. , Giridharan Guruprasad A. , El-Baz Ayman , Hill Bradford G. , Satin Jonathan , Conklin Daniel J. , Moslehi Javid , Bolli Roberto , Ribeiro Alexandre J. S. , Efimov Igor R. , Mohamed Tamer M. A. 
Published: June 2020

AbstractThe limited availability of human heart tissue and its complex cell composition are major limiting factors for reliable testing drug efficacy, toxicity and understanding mechanism. Recently, we developed a functional human and pig heart slice biomimetic culture system that fully preserves the viability and functionality of 300 µm heart slices for 6 days. Here, we tested the reliability of this culture system in delineating the mechanisms of known anti-cancer drugs that cause cardiomyopathy. We tested three anti-cancer drugs (doxorubicin, trastuzumab, and sunitinib) associated with different mechanisms leading to cardiotoxicity at three concentrations and assessed the effect of these drugs on heart slice viability, structure, function and transcriptome. Slices incubated with any of these drugs for 48 h showed significant loss in viability, cardiomyocyte structure and functionality. Mechanistically, RNA sequencing demonstrated a significant downregulation of cardiac genes and upregulation of oxidative response in doxorubicin-treated tissues. Trastuzumab treatment caused major downregulation in cardiac muscle contraction-related genes, consistent with its clinically known direct effect on cardiomyocytes. Interestingly, sunitinib treatment resulted in significant downregulation of angiogenesis-related genes in line with its mechanism of action. Heart slices are not only able to demonstrate the expected toxicity of doxorubicin and trastuzumab similar to hiPS-derived-cardiomyocytes; they are superior in detecting sunitinib cardiotoxicity phenotypes and mechanism in the clinically relevant concentration range, 100 nM – 1 µM. These results indicate that heart slice tissue culture models have the potential to become a reliable platform for testing drug toxicity and mechanism of action.