bluuebunny/crossref_metadata_2025_split huggingface dataset:
A technical pipeline for screening microbial communities as a function of substrate specificity through single cell fluorescent imaging
Authors: Leivers Shaun , Lagos Leidy , La Rosa Sabina Leanti , Westereng Bjørge 
Published: May 2021

ABSTRACTThe study of specific glycan uptake and metabolism has been shown to be an effective tool in aiding with the continued unravelling of the complexities in the human gut microbiome. To this aim fluorescent labelling of glycans may provide a powerful route towards target. In this study, we successfully used the fluorescent label 2-aminobenzamide (2-AB), most commonly employed for enhancing the detection of protein anchored glycans, to monitor and study microbial degradation of labelled glycans. Both single strain and co-cultured fermentations of microbes from the common human-gut derived Bacteroides genus, were able to grow when supplemented with 2-AB labelled glycans of different monosaccharide composition, degrees of acetylation and polymerization. Utilizing a multifaceted approach that combines chromatography, mass spectrometry, microscopy and flow cytometry techniques, it was possible to comprehensively track the metabolism of the labelled glycans in both supernatants and at a single cell level. We envisage this combination of complimentary techniques will help further the understanding of substrate specificity and the role it plays within microbial communities.IMPORTANCEInformation on how bacterial consortia utilize polysaccharides at strain level, whilst progressing rapidly in recent years still lacks a suitable way to study the vast range of ornamentations and structural motifs found in the natural glycans we consume in everyday life. As multi-omic approaches commonly require complex and costly analysis, a screening platform, as described in our work, could be seen as both a complementary and essential new tool in the understanding of microbial polysaccharide metabolism. Our study demonstrates a fast and efficient glycan labelling technique composed of several integrated procedures and advanced analytical methodologies. Chromatography and mass spectrometry are applied in the tracking of metabolized labelled glycans whilst microscopy and flow cytometry are used in the visualization of labelled bacteria at a single cell level.
The globular C1q receptor is required for epidermal growth factor receptor signaling during Candida albicans infection
Authors: Phan Quynh T. , Lin Jianfeng , Solis Norma V. , Eng Michael , Swidergall Marc , Wang Feng , Li Shan , Gaffen Sarah L. , Chou Tsui-Fen , Filler Scott G. 
Published: May 2021

ABSTRACTDuring oropharyngeal candidiasis, Candida albicans activates the epidermal growth factor receptor (EGFR), which induces oral epithelial cells to both endocytose the fungus and synthesize proinflammatory mediators that orchestrate the host immune response. To elucidate the signaling pathways that are stimulated when C. albicans interacts with EGFR, we analyzed the proteins that associate with EGFR when C. albicans infects human oral epithelial cells. We identified 1214 proteins that were associated with EGFR in C. albicans-infected cells. We investigated the function of seven of these proteins that either showed increased association with EGFR in response to C. albicans or that mediated the interaction of other microbial pathogens with epithelial cells. Among these proteins, EGFR was found to associate with WW domain-binding protein 2, toll-interacting protein, interferon-induced transmembrane protein 3, and the globular C1q receptor (gC1qR) in viable epithelial cells. Each of these proteins was required for maximal endocytosis of C. albicans and they all regulated fungal-induced production of IL-1β and/or IL-8, either positively or negatively. gC1qR functioned as a key coreceptor with EGFR. Interacting with the C. albicans Als3 invasin, gC1qR was required for the fungus to stimulate both EGFR and the ephrin type-A receptor 2. The combination of gC1qR and EGFR was necessary for maximal endocytosis of C. albicans and secretion of IL-1β, IL-8, and GM-CSF. Thus, this work provides an atlas of proteins that associate with EGFR and identifies several that play a central role in the response of human oral epithelial cells to C. albicans infection.IMPORTANCEOral epithelial cells play a key role in the pathogenesis of oropharyngeal candidiasis. In addition to being target host cells for C. albicans adherence and invasion, they secrete proinflammatory cytokines and chemokines that recruit T cells and activated phagocytes to foci of infection. It is known that C. albicans activates EGFR on oral epithelial cells, which induces these cells to endocytose the organism and stimulates them to secrete proinflammatory mediators. To elucidate the EGFR signaling pathways that govern these responses, we analyzed the epithelial cell proteins that associate with EGFR in C. albicans-infected epithelial cells. We identified four proteins that physically associate with EGFR and that regulate different aspects of the epithelial response to C. albicans. One of these is gC1qR, which is required for C. albicans to activate EGFR, induce endocytosis, and stimulate the secretion of proinflammatory mediators, indicating that gC1qR functions as a key co-receptor with EGFR.
Recovery from the COVID-19 pandemic by mass vaccination: emergent lessons from the United States and India
Authors: Michael Edwin , Newcomb Ken , Mubayi Anuj , Mahmood Imran 
Published: May 2021

AbstractThe advent of vaccinations has heightened global optimism that the end of the SARS-CoV-2 pandemic could be in sight. However, concerns, including the impact of variations in the rates of vaccination between countries, raise questions about the use of mass vaccination for accomplishing a quick recovery from the contagion. Here, we used a SEIR-based model calibrated to data on the pandemic and vaccinations reported for the United States (US) and India to gain strategic insights into using mass vaccinations for ending COVID-19. We estimate that while up to 65% of the US population is already immune to the virus due to the recent rapid mass vaccinations carried out, only 13% of the Indian population may be immune currently owing to a slow rate of vaccination and the effect of a stricter lockdown imposed to curb the first wave of the pandemic. We project that due to the higher immune to susceptible ratio already achieved in the US, the pandemic will only decline if the present rates of vaccinations and social mitigations are continued and remain effective. By contrast, the recent loosening of social measures coupled with a slow rate of vaccination is the chief reason for the virus resurgence in India, with only immediate lockdowns coupled with ramping up of vaccinations providing the means to control the present wave. These results highlight that using mass vaccination to achieve a speedy recovery from the SARS-CoV-2 pandemic will depend crucially on the ability to carry out national vaccinations as rapidly as possible.
Epigenetic Patterns in a Complete Human Genome
Authors: Gershman Ariel , Sauria Michael E.G. , Hook Paul W. , Hoyt Savannah J. , Razaghi Roham , Koren Sergey , Altemose Nicolas , Caldas Gina V. , Vollger Mitchell R. , Logsdon Glennis A. , Rhie Arang , Eichler Evan E. , Schatz Michael C. , O’Neill Rachel J. , Phillippy Adam M. , Miga Karen H. , Timp Winston 
Published: May 2021

ABSTRACTThe completion of the first telomere-to-telomere human genome, T2T-CHM13, enables exploration of the full epigenome, removing limitations previously imposed by the missing reference sequence. Existing epigenetic studies omit unassembled and unmappable genomic regions (e.g. centromeres, pericentromeres, acrocentric chromosome arms, subtelomeres, segmental duplications, tandem repeats). Leveraging the new assembly, we were able to measure enrichment of epigenetic marks with short reads using k-mer assisted mapping methods. This granted array-level enrichment information to characterize the epigenetic regulation of these satellite repeats. Using nanopore sequencing data, we generated base level maps of the most complete human methylome ever produced. We examined methylation patterns in satellite DNA and revealed organized patterns of methylation along individual molecules. When exploring the centromeric epigenome, we discovered a distinctive dip in centromere methylation consistent with active sites of kinetochore assembly. Through long-read chromatin accessibility measurements (nanoNOMe) paired to CUT&RUN data, we found the hypomethylated region was extremely inaccessible and paired to CENP-A/B binding. With long-reads we interrogated allele-specific, longrange epigenetic patterns in complex macro-satellite arrays such as those involved in X chromosome inactivation. Using the single molecule measurements we can clustered reads based on methylation status alone distinguishing epigenetically heterogeneous and homogeneous areas. The analysis provides a framework to investigate the most elusive regions of the human genome, applying both long and short-read technology to grant new insights into epigenetic regulation.
Quadratic and adaptive computations yield an efficient representation of song in Drosophila auditory receptor neurons
Authors: Clemens Jan , Murthy Mala 
Published: May 2021

AbstractSensory neurons encode information using multiple nonlinear and dynamical transformations. For instance, auditory receptor neurons in Drosophila adapt to the mean and the intensity of the stimulus, change their frequency tuning with sound intensity, and employ a quadratic nonlinearity. While these computations are considered advantageous in isolation, their combination can lead to a highly ambiguous and complex code that is hard to decode. Combining electrophysiological recordings and computational modelling, we investigate how the different computations found in auditory receptor neurons in Drosophila combine to encode behaviorally-relevant acoustic signals like the courtship song.The computational model consists of a quadratic filter followed by a divisive normalization stage and reproduces population neural responses to artificial and natural sounds. For general classes of sounds, like band-limited noise, the representation resulting from these highly nonlinear computations is highly ambiguous and does not allow for a recovery of information about the frequency content and amplitude pattern. However, for courtship song, the code is simple and efficient: The quadratic filter improves the representation of the song envelope while preserving information about the song’s fine structure across intensities. Divisive normalization renders the presentation of the song envelope robust to the relatively slow fluctuations in intensity that arise during social interactions, while preserving information about the species-specific fast fluctuations of the envelope.Overall, we demonstrate how a sensory system can benefit from adaptive and nonlinear computations while minimizing concomitant costs arising from ambiguity and complexity of readouts by adapting the code for behaviorally-relevant signals.
TIGER: The gene expression regulatory variation landscape of human pancreatic islets
Authors: Alonso Lorena , Piron Anthony , Morán Ignasi , Guindo-Martínez Marta , Bonàs-Guarch Sílvia , Atla Goutham , Miguel-Escalada Irene , Royo Romina , Puiggròs Montserrat , Garcia-Hurtado Xavier , Suleiman Mara , Marselli Lorella , Esguerra Jonathan L.S. , Turatsinze Jean-Valéry , Torres Jason M. , Nylander Vibe , Chen Ji , Eliasson Lena , Defrance Matthieu , Amela Ramon ,   MAGIC, Mulder Hindrik , Gloyn Anna L. , Groop Leif , Marchetti Piero , Eizirik Decio L. , Ferrer Jorge , Mercader Josep M. , Cnop Miriam , Torrents David 
Published: May 2021

AbstractGWAS have identified more than 700 genetic signals associated with type 2 diabetes (T2D). To gain insight into the underlying molecular mechanisms, we created the Translational human pancreatic Islet Genotype tissue-Expression Resource (TIGER), aggregating >500 human islet RNA-seq and genotyping datasets. We imputed genotypes using 4 reference panels and meta-analyzed cohorts to improve coverage of expression quantitative trait loci (eQTL) and developed a method to combine allele-specific expression across samples (cASE). We identified >1 million islet eQTLs (56% novel), of which 53 colocalize with T2D signals (60% novel). Among them, a low-frequency allele that reduces T2D risk by half increases CCND2 expression. We identified 8 novel cASE colocalizations, among which an SLC30A8 T2D associated variant. We make all the data available through the open-access TIGER portal (http://tiger.bsc.es), which represents a comprehensive human islet genomic data resource to elucidate how genetic variation affects islet function and translate this into therapeutic insight and precision medicine for T2D.
Desmin intermediate filaments and tubulin detyrosination stabilize growing microtubules in the cardiomyocyte
Authors: Salomon Alexander K. , Phyo Sai Aung , Okami Naima , Heffler Julie , Robison Patrick , Bogush Alexey I. , Prosser Benjamin L. 
Published: May 2021

AbstractIn heart failure, an increased abundance of post-translationally detyrosinated microtubules stiffens the cardiomyocyte and impedes its contractile function. Detyrosination promotes interactions between microtubules, desmin intermediate filaments and the sarcomere to increase cytoskeletal stiffness, yet the mechanism by which this occurs is unknown. We hypothesized that detyrosination may regulate the growth and shrinkage of dynamic microtubules to facilitate interactions with desmin and the sarcomere. Through a combination of biochemical assays and direct observation of growing microtubule plus-ends in adult cardiomyocytes, we find that desmin is required to stabilize growing microtubules at the sarcomere Z-disk, where desmin also rescue shrinking microtubules from continued depolymerization. Further, reducing detyrosination (tyrosination) promotes frequent depolymerization and inefficient growth of microtubules. This is concomitant with tyrosination promoting the interaction of microtubules with the depolymerizing protein complex of end-binding protein 1 (EB1) and CAP-Gly domain containing linker protein 1 (CLIP1/CLIP170). The futile growth of tyrosinated microtubules reduces their opportunity for stabilizing interactions at the Z-disk, coincident with tyrosination globally reducing microtubule lifetimes and stability. These data provide a model for how intermediate filaments and tubulin detyrosination establish long-lived and physically reinforced microtubules in the cardiomyocyte, and inform on the mechanism of action for therapies that target microtubules for the treatment of cardiac disease.
Engineering improved Cas13 effectors for targeted post-transcriptional regulation of gene expression
Authors: Charles Emeric J , Kim Shin Eui , Knott Gavin J. , Smock Dylan , Doudna Jennifer , Savage David F. 
Published: May 2021

SummaryCas13 is a family of unique RNA-targeting CRISPR-Cas effectors, making it an appealing tool for probing and perturbing RNA function. However only a few Cas13 homologs have been shown to mediate robust RNA targeting in human cells, suggesting that unknown elements may be limiting their efficacy. Furthermore, many Cas13 enzymes show high degrees of toxicity upon targeting and have not been shown to mediate specific knockdown in other cell types such as E. coli. Here, we show that catalytically inactive Cas13 enzymes can be repurposed for efficient translational repression in bacteria with no associated growth defects. To achieve this advance, we carried out a directed evolution screen to engineer functional Cas13a variants, and identified a number of stabilizing mutations, which enabled efficient post transcriptional knockdown of gene expression. In vitro characterization of the resulting engineered Lbu Cas13a mutant, termed eLbu, revealed both stabilization and altered cleavage kinetics. Finally, we show that eLbu can be used for efficient exon skipping in human cells. This work represents the first demonstration of targeted translational repression in E. coli using a CRISPR enzyme, as well as the first directed evolution of a Cas13 enzyme. Such a platform could allow for engineering other aspects of this protein family to obtain more robust RNA targeting tools.
Single-cell phenotypic characteristics of phenotypic resistance under recurring antibiotic exposure inEscherichia coli
Authors: Kollerová Silvia , Jouvet Lionel , Smelková Julia , Zunk-Parras Sara , Rodríguez-Rojas Alexandro , Steiner Ulrich K. 
Published: May 2021

AbstractDespite increasing interest, non-heritable, phenotypic drug resistance, such as tolerance and persistence towards antibiotics, remains less characterized compared to genetic resistance. Non-heritable drug resistance challenges antibiotic treatment and have implications towards heritable resistance evolution. Phenotypically resistant cells have commonly been characterized as growth arrested cells prior and during antibiotic application that quickly resume growth post-application. Here, we add novel combinations of characteristics of phenotypic resistantE. colisingle cells—that are of particular interest towards genetically fixed resistance—, and contrast those to susceptible cells of the isoclonal initial population by exposure to different levels of recurrent antibiotic. We find that phenotypic resistant cells reduced their growth rate by about 50% compared to growth rates prior to antibiotic exposure, but cells do not go into near growth arrest. The growth reduction is induced by antibiotic exposure and not caused by a stochastic switch or predetermined state as frequently described. Cells exhibiting constant intermediate growth survived best under antibiotic exposure and, contrary to expectations, selection did not primarily act on fast growing cells. Our findings support diverse modes of phenotypic resistance, and we revealed resistant cell characteristics that supports acclaims of an underappreciated role of phenotypic resistant cells towards resistance evolution.
Environment, rather thanHematodiniumparasitization, determines collateral disease contraction in a crustacean host
Authors: Davies Charlotte E. , Thomas Jessica E. , Malkin Sophie H. , Batista Frederico M. , Rowley Andrew F. , Coates Christopher J. 
Published: May 2021

AbstractHost, pathogen, and environment are determinants of the disease triangle, the latter being a key driver of disease outcomes and persistence within a community. The dinoflagellate genusHematodiniumis detrimental to crustaceans globally – considered to suppress the innate defences of hosts, making them more susceptible to co-infections. Evidence supporting immune-suppression is largely anecdotal and sourced from diffuse accounts of compromised decapods. We used a population of shore crabs (Carcinus maenas), whereHematodiniumsp. is endemic, to determine the extent of collateral infections across two distinct environments (open water, semi- closed dock). Using a multi-resource approach (PCR, histology, haematology, population genetics, eDNA), we identified 162Hematodinium-positive crabs and size/sex-matched these to 162Hematodinium-free crabs out of 1,191 analysed. Crabs were interrogated for additional disease-causing agents; haplosporidians, microsporidians, mikrocytids,Vibriospp., fungi,Sacculina, trematodes, and haemolymph bacterial loads. We found no significant differences in occurrence, severity or composition of collateral infections betweenHematodinium-positive andHematodinium-free crabs at either site, but crucially, we recorded site-restricted blends of pathogens. We found no gross signs of host cell immune reactivity towardHematodiniumin the presence or absence of other pathogens. We contendHematodiniumsp. is an immune-evader rather than immune-suppressor, which suggests an evolutionary drive toward latency in this environmentally plastic host.
Reduced sensitivity of infectious SARS-CoV-2 variant B.1.617.2 to monoclonal antibodies and sera from convalescent and vaccinated individuals
Authors: Planas Delphine , Veyer David , Baidaliuk Artem , Staropoli Isabelle , Guivel-Benhassine Florence , Rajah Maaran Michael , Planchais Cyril , Porrot Françoise , Robillard Nicolas , Puech Julien , Prot Matthieu , Gallais Floriane , Gantner Pierre , Velay Aurélie , Le Guen Julien , Kassis-Chikhani Najibi , Edriss Dhiaeddine , Belec Laurent , Seve Aymeric , Péré Hélène , Courtellemont Laura , Hocqueloux Laurent , Fafi-Kremer Samira , Prazuck Thierry , Mouquet Hugo , Bruel Timothée , Simon-Lorière Etienne , Rey Felix A. , Schwartz Olivier 
Published: May 2021

AbstractThe SARS-CoV-2 B.1.617 lineage emerged in October 2020 in India1–6. It has since then become dominant in some indian regions and further spread to many countries. The lineage includes three main subtypes (B1.617.1, B.1617.2 and B.1.617.3), which harbour diverse Spike mutations in the N-terminal domain (NTD) and the receptor binding domain (RBD) which may increase their immune evasion potential. B.1.617.2 is believed to spread faster than the other versions. Here, we isolated infectious B.1.617.2 from a traveller returning from India. We examined its sensitivity to monoclonal antibodies (mAbs) and to antibodies present in sera from COVID-19 convalescent individuals or vaccine recipients, in comparison to other viral lineages. B.1.617.2 was resistant to neutralization by some anti-NTD and anti-RBD mAbs, including Bamlanivimab, which were impaired in binding to the B.1.617.2 Spike. Sera from convalescent patients collected up to 12 months post symptoms and from Pfizer Comirnaty vaccine recipients were 3 to 6 fold less potent against B.1.617.2, relative to B.1.1.7. Sera from individuals having received one dose of AstraZeneca Vaxzevria barely inhibited B.1.617.2. Thus, B.1.617.2 spread is associated with an escape to antibodies targeting non-RBD and RBD Spike epitopes.
Tannic Acid Inhibits α-Synuclein Amyloid Fibril Formation via Binding to the Monomer N-terminal Domain
Authors: Stoeber Jonathan , Williams Jonathan K. , Moghe Prabhas V. , Baum Jean 
Published: May 2021

Abstractα-Synuclein (αS) is an intrinsically disordered protein (IDP) that aggregates into amyloid fibrils during the progression of Parkinson’s Disease and other synucleinopathies. The N-terminal domain (residues 1-60) is now understood to play a critical role in the initial nucleation of aggregation, as well as a pivotal role in the monomer-fibril interaction underlying amyloid seeding. Here we report on the interaction between αS and the polyphenol tannic acid (TA), where a combination of solution NMR, atomic force microscopy (AFM), and ThT assays have identified that TA targets the αS N-terminal domain to inhibit amyloid fibril formation in a pH dependent manner. This work highlights the importance of targeting the N-terminus of αS to arrest fibril formation, and suggests the importance of including polyphenolic moieties in future amyloid inhibitors.