bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dextran sodium sulfate-induced colitis alters the proportion and composition of replicating gut bacteria
Authors: Beauchemin Eve T. , Hunter Claire , Maurice Corinne F. 
Published: February 2024

AbstractThe bacteria living in the human gut are essential for host health. Though the composition and metabolism of these bacteria is well described in both healthy hosts and those with intestinal disease, less is known about the activity of the gut bacteria prior to, and during, disease development – especially regarding gut bacterial replication. Here, we use a recently developed single-cell technique alongside existing metagenomics-based tools to identify, track, and quantify the replicating gut bacteria and their replication dynamics in the dextran sodium sulfate mouse model of colitis. We show that the proportion of replicating gut bacteria decreases when mice have the highest levels of inflammation and returns to baseline levels as mice begin recovering. We additionally report significant alterations in the composition of the total replicating gut bacterial community during colitis development. On the taxa level, we observe significant changes in the abundance of taxa such as the mucus-degradingAkkermansia muciniphilaand the poorly describedErysipelatoclostridiumgenus. We further demonstrate that many taxa exhibit variable replication rates during colitis, includingA. muciniphila. Lastly, we show that colitis development is positively correlated with increases in the presence and abundance of bacteria predicted to be fast replicators, suggesting that taxa with the potential to replicate quickly may have an advantage during intestinal inflammation. These data support the need for additional research using activity-based approaches to further characterize the gut bacterial response to intestinal inflammation and its consequences for both the host and the gut microbial community at large.ImportanceIt is well known that the bacteria living inside the gut are important for human health. Indeed, the type of bacteria which are present and their metabolism is different in healthy people versus those with intestinal disease. However, less is known about how these gut bacteria are replicating, especially as someone begins to develop intestinal disease. This is especially important as it is thought that the active gut bacteria may be more relevant to health. Here, we begin addressing this gap by using several complementary approaches to characterize the replicating gut bacteria in a mouse model of intestinal inflammation. We reveal which gut bacteria are replicating, and how quickly, as mice develop and recover from inflammation. This work can serve as a model for future research to identify how the active gut bacteria may be impacting health, or why these particular bacteria tend to thrive during intestinal inflammation.
Expression of the locus of enterocyte effacement genes during the invasion process of the atypical enteropathogenicEscherichia coli1711-4 strain of serotype O51:H40
Authors: Romão Fabiano T. , Santos Ana C. M. , Sperandio Vanessa , Hernandes Rodrigo T. , Gomes Tânia A. T. 
Published: February 2024

AbstractAtypical enteropathogenicEscherichia coli(aEPEC) is a significant cause of diarrhea in developing countries. Some aEPEC strains, including the Brazilian representative strain of serotype O51:H40 called aEPEC 1711-4, can use flagella to attach to, invade, and persist in T84 and Caco-2 intestinal cells. They can even translocate from the gut to extraintestinal sites in a rat model. Although various aspects of the virulence of this strain were studied and the requirement of the T3SS for the efficiency of the invasion process was demonstrated, the expression of the LEE genes during the invasion and intracellular persistence remains unclear. To address this, the expression of flagella and the different LEE operons was evaluated during kinetic experiments of the interaction of aEPEC 1711-4 with enterocytesin vitro. The genome of the strain was also sequenced. The results showed that flagella expression remained unchanged, but the expression ofeaeandescJincreased during the early interaction and invasion of aEPEC 1711-4 into Caco-2 cells, and there was no change 24 hours post-infection during the persistence period. The number of pedestal-like structures formed on HeLa cells also increased during the 24-hour analysis. No known gene related to the invasion process was identified in the genome of aEPEC 1711-4, which was shown to belong to the global EPEC lineage 10. These findings suggest that LEE components and the intimate adherence promoted by intimin are necessary for the invasion and persistence of aEPEC 1711-4, but the detailed mechanism needs further study.ImportanceAtypical enteropathogenicEscherichia coli(aEPEC) is a major cause of diarrhea, especially in developing countries, like Brazil. However, due to the genome heterogeneity of each clonal group, it is difficult to comprehend the pathogenicity of this strain fully. Among the aEPEC strains, 1711-4 can invade eukaryotic cellsin vitro, cross the gut barrier, and reach extraintestinal sites in animal models. By studying how different known aEPEC virulence factors are expressed during the invasion process, we can gain insight into the commonality of this phenotype among other aEPEC strains. This will help us develop preventive measures to control infections caused by invasive strains. No known virulence-encoding genes linked to the invasion process were found. Nevertheless, additional studies are still necessary to evaluate the role of other factors in this phenotype.
Bacterial community structure analysis onListeria monocytogenesinoculated spinach leaves is affected by PCR based methods to exclude chloroplast co-amplification
Authors: Culliney Paul , Schmalenberger Achim 
Published: February 2024

AbstractConsumption of ready-to-eat leafy vegetables has increased in popularity due to their anticipated health benefits, but their consumption also poses a potential health risk in the form of foodborne pathogens.Listeria monocytogenesis a ubiquitous pathogen that has been regularly found on leafy vegetables including spinach. Growth determining factors go beyond plant species and cultivation practice and may include the phyllosphere bacteriome to affect the growth potential ofL. monocytogenes. This study investigated the bacteriome of spinach leaves, stored under EURL challenge conditions for 9 days after inoculation withL. monocytogenesusing two methods of excluding chloroplast co-amplification (COMPETE, BLOCK) at the PCR step as well as a post-PCR chloroplast sequence filter option (CONTROL). While all three approaches have demonstrated a change of bacterial communities over time, the pPNA based BLOCK approach resulted in greater diversity similarities to the CONTROL option. The COMPETE solution with a specifically designed primer to prevent chloroplast amplification had a strong underrepresentation of the Planctomycetota phylum and to a lesser extend underrepresentation of Chloroflexi and Verrucomicrobiota due to the inheritance of the selected primer region that allowed to deselect chloroplast co-amplification. However, the COMPETE approach had the lowest level of chloroplast co-amplification. Higher growth potential ofL. monocytogenesfrom day 7 to 9 co-occurred with higher relative abundances of Pseudomonadaceae and lower numbers of Lactobacillales, suggesting that particular phylogenetic groups may support growth ofL. monocytogenes. While chloroplast co-amplification with spinach in the present study was relatively modest and a purely filter based chloroplast removal was sufficient, other leafy vegetables may require one of the tested co-amplification prevention solutions. While the COMPETE solution in the present study was linked to some amplification bias, the approach may be useful when otherwise co-amplification is very high and the demonstrated BLOCK approach with pPNA is insufficient.
DiffTopo: Fold exploration using coarse grained protein topology representations
Authors: Miao Yangyang , Correia Bruno 
Published: February 2024

AbstractA major challenge in the field of computational de novo protein design is the exploration of uncharted areas within protein structural space, i.e., generating “designable” protein structures that nature has not explored. However, the large degrees of freedom of protein structural backbones complicate the sampling process during protein design. In this work, we propose a new coarse grained protein structure representation method DiffTopo - an E(3) Equivariant 3D conditional diffusion model, which greatly increases the sampling efficiency. Combined with the RFdiffusion framework, novel protein folds can be generated rapidly, allowing for efficient exploration of the designable topology space. This opens up possibilities to solve the problem of generating new folds as well to functionalize de novo proteins through motif scaffolding, where functional or enzymatic sites can be introduced into novel protein frameworks.
Pediatric human nose organoids demonstrate greater susceptibility, epithelial responses, and cytotoxicity than adults during RSV infection
Authors: Aloisio Gina M. , Nagaraj Divya , Murray Ashley M. , Schultz Emily M. , McBride Trevor , Aideyan Letisha , Nicholson Erin G. , Henke David , Ferlic-Stark Laura , Rajan Anubama , Kambal Amal , Johnson Hannah L. , Mosa Elina , Stossi Fabio , Blutt Sarah E. , Piedra Pedro A. , Avadhanula Vasanthi 
Published: February 2024

AbstractRespiratory syncytial virus (RSV) is a common cause of respiratory infections, causing significant morbidity and mortality, especially in young children. Why RSV infection in children is more severe as compared to healthy adults is not fully understood. In the present study, we infect both pediatric and adult human nose organoid-air liquid interface (HNO-ALIs) cell lines with two contemporary RSV isolates and demonstrate how they differ in virus replication, induction of the epithelial cytokine response, cell injury, and remodeling. Pediatric HNO-ALIs were more susceptible to early RSV replication, elicited a greater overall cytokine response, demonstrated enhanced mucous production, and manifested greater cellular damage compared to their adult counterparts. Adult HNO-ALIs displayed enhanced mucus production and robust cytokine response that was well controlled by superior regulatory cytokine response and possibly resulted in lower cellular damage than in pediatric lines. Taken together, our data suggest substantial differences in how pediatric and adult upper respiratory tract epithelium responds to RSV infection. These differences in epithelial cellular response can lead to poor mucociliary clearance and predispose infants to a worse respiratory outcome of RSV infection.
Influenza A Virus Disruption of Dendritic Cell-Natural Killer Cell Crosstalk Impacts Activation of Helper and Cytotoxic T cell Subsets
Authors: Morson Connor A. , Uppalapati Chandana K. , Lopez Brina S. , Kronstad Lisa M. 
Published: February 2024

AbstractDendritic cells (DC) and Natural killer (NK) cells engage in reciprocal interactions to trigger an efficient innate immune response while governing the adaptive immune response. Here we used anex vivoautologous human primary immune cell co-culture of DCs and NK cells to investigate the impact of DC-NK cell crosstalk on activation of CD4+and CD8+naïve T cell responses to influenza A viral (IAV) infection. Using multiparameter flow cytometry, we observed that culturing T cells with DC and NK cells led to enhanced expression of CD69 and CD25 activation markers and increased proliferative ability of both CD4+and CD8+T cell subsets. Exposure of DCs to the pandemic A/California/07/2009 (H1N1) strain in NK cell co-culture led to a reduced frequency of CD4+CD69+, CD8+CD69+, CD4+CD25+, CD8+CD25+T cell subsets and a reduced expansion of CD4+T cells. The IAV-mediated curtailment of T cell activation was dependent on the ability of A/California/07/2009 (H1N1) to replicate as inactivation of the virus rescued expression of CD69, CD25 on both CD4+and CD8+T cell subsets and triggered expansion of CD4+T cells. Further, we discovered exposure of DCs to the A/Victoria/361/2011 (H3N2) IAV strain also significantly impaired expression of CD69 on CD4+and CD8+T cells and CD25 on CD8+T cells. In contrast with the A/California/07/2009 (H1N1 strain), inactivation of A/Victoria/361/2011 (H3N2) failed to fully restore T cell expression of CD69 and CD25 and proliferation. Collectively, these data demonstrate that IAV partially usurps the ability of DC-NK cell crosstalk to activate naïve CD4+and CD8+T cells in a strain-dependent manner. These data may inform the immunological signals required to trigger a potent cellular immune response to IAV, which may elicit broader and more durable protection than current inactivated vaccine platforms.
Optogenetic mapping of rhythmic phase-dependent excitability in the mouse striatum
Authors: Mohapatra Manish , Carmichael J. Eric , Smith Kyle S. , van der Meer Matthijs A. A. 
Published: February 2024

AbstractThe striatum is thought to switch flexibly between multiple converging inputs to support adaptive behavior. The “communication through coherence” (CTC) hypothesis is a potential mechanism to implement such a flexible switching. For CTC to work in the striatum, striatal excitability must show rhythmic fluctuations, such as those related to the phase of the striatal local field potential (LFP). To test this fundamental requirement, we delivered a constant input stimulus to ChR2-expressing striatal fast-spiking PV+ interneurons (FSIs) in head-fixed awake mice (PV-Cre:Ai-32, n = 18, 9 female), and determined whether the response to this stimulus varied with LFP phase. We found that approximately one-third (41.2%) of FSIs exhibited significant phase-dependent excitability in at least one LFP frequency band. Phase-dependent excitability was most prominent in the delta (2–5 Hz) frequency band, both in terms of prevalence (23.5% of FSIs sampled) and magnitude (phase modulation strength: 22% of average response). The most excitable phase tended to align with endogenous phase-locking, again most clearly in the delta band. These results bolster the functional relevance of the striatal field potential and spike-field relationships, and provide proof-of-principle support for the possibility of CTC in the striatum.Significance StatementThe striatum is thought to switch dynamically between multiple converging inputs. A leading idea for how this is accomplished is through communication through coherence (CTC). A fundamental, but previously untested, requirement for CTC to work is that striatum must show changes in excitability that depend on local field potential phase. We find that about one-third of striatal neurons show phase-dependent excitability, providing proof of principle for CTC-like switching in striatum.
Quantitative omnigenic model discovers interpretable genome-wide associations
Authors: Ružičková Natália , Hledík Michal , Tkačik Gašper 
Published: February 2024

AbstractAs their statistical power grows, genome-wide association studies (GWAS) have identified an increasing number of loci underlying quantitative traits of interest. These loci are scattered throughout the genome and are individually responsible only for small fractions of the total heritable trait variance. The recently proposed omnigenic model provides a conceptual framework to explain these observations by postulating that numerous distant loci contribute to each complex trait via effect propagation through intracellular regulatory networks. We formalize this conceptual framework by proposing the “quantitative omnigenic model” (QOM), a statistical model that combines prior knowledge of the regulatory network topology with genomic data. By applying our model to gene expression traits in yeast, we demonstrate that QOM achieves similar gene expression prediction performance to traditional GWAS with hundreds of times less parameters, while simultaneously extracting candidate causal and quantitative chains of effect propagation through the regulatory network for every individual gene. We estimate the fraction of heritable trait variance incis-and intrans-, break the latter down by effect propagation order, assess thetrans-variance not attributable to transcriptional regulation, and show that QOM correctly accounts for the low-dimensional structure of gene expression covariance. We furthermore demonstrate the relevance of QOM for systems biology, by employing it as a statistical test for the quality of regulatory network reconstructions, and linking it to the propagation of non-transcriptional (including environmental) effects.Significance statementGenetic variation leads to differences in traits implicated in health and disease. Identifying genetic variants associated with these traits is spearheaded by “genome-wide association studies” (GWAS) – statistically rigorous procedures whose power has grown with the number of genotyped samples. Nevertheless, GWAS have a substantial shortcoming: they are ill-equipped to detect the causal basis and reveal the complex systemic mechanisms of polygenic traits. Even a single genetic change can propagate throughout the entire genetic regulatory network causing a myriad of spurious detections, thereby significantly limiting GWAS usefulness. To this end, we propose a novel statistical approach that incorporates known regulatory network information with the potential to boost interpretability of state-of-the-art genomic analyses while simultaneously extracting systems biology insights.
First report and characterization of a plasmid-encodedblaSFO-1in a multi-drug resistantAeromonas hydrophilaclinical isolate
Authors: Skwor Troy , Jones Dan , Cahak Caitlin , Newton Ryan J 
Published: February 2024

AbstractAntibiotic resistance remains one of the most pressing public health issues facing the world today. At the forefront of this battle lies the ever-increasing identification of extended spectrum beta-lactamases and carbapenemases within human pathogens, conferring resistance towards broad-spectrum and last-resort anti-microbials. This study was prompted due to the identification of a pathogenicAeromonas hydrophilaisolate (strain MAH-4) collected from abdominal fluid, which presented a robust resistance pattern against second, third, and fourth generation cephalosporins, ertapenem, ciprofloxacin, gentamicin, levofloxacin and moxifloxacin, and beta lactam/beta-lactamase inhibitor combinations. Whole genome sequencing was performed and identified a 328 kb plasmid (pMAH4) encoding 10 antibiotic resistance genes, includingblaSFO-1,blaTEM-1,andblaOXA-1ofA. hydrophiaMAH-4. This is the first report of beta-lactamase SFO-1 within a clinical strain ofAeromonas. Due to the remarkable sequence identity of pMAH4 to plasmids associated withEnterobacteralesgenera likeKlebsiella, and the extensive capabilities ofAeromonasfor horizontal gene transfer, our identification of a clinical isolate encoding SFO-1 on a plasmid suggests ARG mobility betweenEnterobacteralesand non-Enterobacteralesspecies.
A detailed dissection of the expression, localization, structure, and diagnostic potential of cyst wall proteins of the eye pathogenAcanthamoeba
Authors: Kanakapura Sundararaj Bharath , Goyal Manish , Samuelson John 
Published: February 2024

ABSTRACTThe cyst wall of the eye pathogenAcanthamoeba castellaniicontains cellulose and chitin and has ectocyst and endocyst layers connected by conical ostioles. Previously, we used mass spectrometry of purified walls to identify an abundant laccase and three families of lectins (Jonah, Luke, and Leo). Here we show that frameshifts in the protein prediction in AmoebaDB, which incorrectly add 12 transmembrane helices, cause Jonah to mislocalize to a ring around ostioles rather than to the ectocyst layer. RT-PCR, double labels with GFP and RFP or mCherry, and promoter swaps show that ectocyst localization does not just correlate with but is caused by earlier expression, while localization in the endocyst layer and ostioles is caused by later expression. A chitin-binding domain from anEntamoebachitinase shows chitin forms thick fibrils in the ectocyst layer and a honeycomb in the endocyst layer. AlphaFold shows Ac wall proteins originate from bacteria by horizontal gene transfer (β-helical folds of Jonah and three cupredoxin-like domains of the laccase), share common ancestry with wall proteins of slime molds (β-jelly-roll folds of Luke), or are unique toAcanthamoeba(four disulfide knots of Leo). Ala mutations show linear arrays of aromatic amino acids in β-jelly-roll folds of Luke and disulfide knots of Leo are necessary for binding cellulose and proper localization of proteins in the cyst wall. Finally, rabbit antibodies to recombinant Jonah, Luke, Leo, and laccase efficiently detect calcoflour white-labeled cysts of 10 of 11Acanthamoebaisolates tested, suggesting all four proteins are excellent diagnostic targets.IMPORTANCEAcanthamoebaeare free-living amoeba in the soil and water that causeAcanthamoebakeratitis in under-resourced countries, where water for washing hands may be scarce.Acanthamoebais an emerging pathogen in the United States, because of its association with contact lens use. Here we show early expression during encystation causes a Jonah lectin and a laccase to localize to the outer layer of the cyst wall, while later expression cause Luke and Leo lectins to localize to the inner layer and the conical ostioles that connect the layers. We used structural predictions to identify the aromatic amino acids of Luke and Leo necessary for binding cellulose in the wall and to identify domains of Jonah and laccase useful for making recombinant proteins to immunize rabbits. Rabbit antibodies to Jonah, Luke, Leo, and laccase all efficiently detected cysts of tenAcanthamoebaisolates, including five T4 genotypes that cause most keratitis cases.