bluuebunny/crossref_metadata_2025_split huggingface dataset:
Three orphan histidine kinases inhibit Clostridioides difficile sporulation
Authors: Edwards Adrianne N. , Wetzel Daniela , DiCandia Michael A. , McBride Shonna M. 
Published: November 2021

ABSTRACTThe ability of the anaerobic gastrointestinal pathogen, Clostridioides difficile, to survive outside the host relies on the formation of dormant endospores. Spore formation is contingent on the activation of a conserved transcription factor, Spo0A, by phosphorylation. Multiple kinases and phosphatases regulate Spo0A activity in other spore-forming organisms; however, these factors are not well conserved in C. difficile. Previously, we discovered that deletion of a conserved phosphotransfer protein, CD1492, increases sporulation, indicating that CD1492 inhibits C. difficile spore formation. In this study, we investigate the functions of additional conserved orphan phosphotransfer proteins, CD2492, CD1579, and CD1949 which are hypothesized to regulate Spo0A phosphorylation. Disruption of the conserved phosphotransfer protein, CD2492, also increased sporulation frequency, similarly to the CD1492 mutant, and in contrast to a previous study. A CD1492 CD2492 mutant phenocopied the sporulation and gene expression patterns of the single mutants, suggesting that these proteins function in the same genetic pathway to repress sporulation. Deletion of the conserved CD1579 phosphotransfer protein also variably increased sporulation frequency; however, knockdown of CD1949 expression did not influence sporulation. We provide evidence that CD1492, CD2492 and CD1579 function as phosphatases, as mutation of the conserved histidine residue for phosphate transfer abolished CD2492 function, and expression of the CD1492 or CD2492 histidine site-directed mutants or the wild-type CD1579 allele in a parent strain resulted in a dominant negative hypersporulation phenotype. Altogether, at least three phosphotransfer proteins, CD1492, CD2492 and CD1579 (herein, PtpA, PtpB and PtpC) repress C. difficile sporulation initiation by regulating activity of Spo0A.IMPORTANCEThe formation of inactive spores is critical for the long-term survival of the gastrointestinal pathogen Clostridioides difficile. The onset of sporulation is controlled by the master regulator of sporulation, Spo0A, which is activated by phosphorylation. Multiple kinases and phosphatases control Spo0A phosphorylation; however, this regulatory pathway is not defined in C. difficile. We show that two conserved phosphotransfer proteins, CD1492 (PtpA) and CD2492 (PtpB), function in the same regulatory pathway to repress sporulation by preventing Spo0A phosphorylation. We show that another conserved phosphotransfer protein, CD1579 (PtpC), also represses sporulation, and we eliminate the possibility that a fourth orphan histidine kinase protein, CD1949, impacts C. difficile sporulation. These results support the idea that C. difficile inhibits sporulation initiation through multiple phosphatases.
Replication protein Rep provides selective advantage to viruses in the presence of CRISPR-Cas immunity
Authors: Zhang Weijia , Bhoobalan-Chitty Yuvaraj , Zhai Xichuan , Hui Yan , Hansen Lars Hestbjerg , Deng Ling , Peng Xu 
Published: November 2021

AbstractProkaryotic viruses express anti-CRISPR (Acr) proteins to inhibit the host adaptive immune system, CRISPR-Cas. While the virus infection biology was shown to be strongly dependent on the relative strengths of the host CRISPR-Cas and viral Acrs, little is known about the role of the core processes of viral life cycle (replication, packaging etc) in defence/anti-defence arms race. Here, we demonstrate the selective advantage provided by a replication initiator, Rep, in the context of CRISPR-Acr interactions. First, we developed a two-host based CRISPR-Cas genome editing tool for the deletion of highly conserved and thus potentially important viral genes. Using this strategy, we deleted a highly conserved Rep-coding gene, gp16, from the genome of Sulfolobus islandicus rod-shaped virus 2 (SIRV2). The knockout mutant (Δgp16) produced around 4 fold less virus in a CRISPR-null host, suggesting that Rep is the major contributor to replication initiation in Rudiviridae. Indeed, DNA sequencing revealed Rep-dependent replication initiation from the viral genome termini, in addition to Rep-independent replication initiation from non-terminal sites. Intriguingly, the lack of Rep showed a profound effect on virus propagation in a host carrying CRISPR-Cas immunity. Accordingly, the co-infecting parental virus (rep-containing) outcompeted the Δgp16 mutant much more quickly in CRISPR-containing host than in CRISPR-null host, demonstrating a selective advantage provided by Rep in the presence of host CRISPR-Cas immunity. Despite the non-essentiality, rep is carried by all known members of Rudiviridae, which is likely an evolutionary outcome driven by the ubiquitous presence of CRISPR-Cas in Sulfolobales.ImportanceCRISPR-Cas and anti-CRISPR proteins are accessary to prokaryotes and their viruses respectively. To date, research has been focused on their diversity, molecular mechanisms and application in genome editing. How CRISPR-Acr arms race influence the evolution of viral core genes involved in the basic virus life cycle remained a gap of knowledge so far. This study provides the first evidence that CRISPR-Acr arms race poses a selection pressure on the efficiency of viral genome replication, forcing viruses to evolve highly productive replication machineries..
Genetic regulation of serum IgA levels and susceptibility to common immune, infectious, kidney, and cardio-metabolic traits
Authors: Liu Lili , Khan Atlas , Sanchez-Rodriguez Elena , Zanoni Francesca , Li Yifu , Steers Nicholas , Balderes Olivia , Zhang Junying , Krithivasan Priya , LeDesma Robert A. , Fischman Clara , Hebbring Scott J. , Harley John B. , Moncrieffe Halima , Kottyan Leah C. , Namjou-Khales Bahram , Walunas Theresa L. , Knevel Rachel , Raychaudhuri Soumya , Karlson Elizabeth W. , Denny Joshua C. , Stanaway Ian B. , Crosslin David , Rauen Thomas , Floege Jürgen , Eitner Frank , Moldoveanu Zina , Reily Colin , Knoppova Barbora , Hall Stacy , Sheff Justin T. , Julian Bruce A. , Wyatt Robert J. , Suzuki Hitoshi , Xie Jingyuan , Chen Nan , Zhou Xujie , Zhang Hong , Hammarström Lennart , Viktorin Alexander , Magnusson Patrik K. E. , Shang Ning , Hripcsak George , Weng Chunhua , Rundek Tatjana , Elkind Mitchell S. V. , Oelsner Elizabeth C. , Barr R. Graham , Ionita-Laza Iuliana , Novak Jan , Gharavi Ali G. , Kiryluk Krzysztof 
Published: November 2021

AbstractImmunoglobulin A (IgA) mediates mucosal responses to food antigens and the intestinal microbiome and has a known role in susceptibility to mucosal pathogens, celiac disease, inflammatory bowel disease, and IgA nephropathy. We performed genetic analyses of serum IgA levels in 41,263 individuals of diverse ancestries. We observed unexpected variability in IgA levels across major ancestral populations, with African ancestry being reproducibly associated with higher serum IgA levels compared to other ancestries. The trans-ethnic GWAS analysis identified 20 genome-wide significant loci associated with serum IgA levels, including nine known and 11 novel loci. Systematic co-localization analysis with blood and primary immune cell expression QTLs prioritized candidate genes for 14 of 20 loci. Most GWAS loci encoded genes that produce immune defects and IgA abnormalities when genetically manipulated in mice. We uncovered positive genetic correlations of serum IgA levels with IgA nephropathy, type 2 diabetes and body mass index, as well as negative genetic correlations with celiac disease, inflammatory bowel disease, several infections, and intestinal microbiome diversity. Our findings provide novel insights into the genetic regulation of IgA production and its potential role in human disease.
Humoral immune response after COVID-19 infection or BNT162b2 vaccine among older adults: evolution over time and protective thresholds
Authors: Meyer Maxence , Constancias Florentin , Worth Claudia , Meyer Anita , Muller Marion , Boussuge Alexandre , Kaltenbach Georges , Schmitt Elise , Chayer Saïd , Velay Aurélie , Vogel Thomas , Fafi-Kremer Samira , Karcher Patrick 
Published: November 2021

ABSTRACTINTRODUCTIONThe objectives of this study were to assess the dynamics of the SARS-CoV-2 anti-RBD IgG response over time among older people after COVID-19 infection or vaccination and its comparison with speculative levels of protection assumed by current data.METHODSFrom November 2020 to October 2021, we included geriatric patients with serological test results for COVID-19.We considered antibody titre thresholds thought to be high enough to protect against SARS-CoV-2 infection: 141 BAU/ml for protection/vaccine efficacy > 89.3%.Three cohorts are presented. A vaccine group (n=34) that received two BNT162b2/Comirnaty injections 21 days apart, a group of natural COVID-19 infection (n=32) and a third group who contracted COVID-19 less than 15 days after the first BNT162b2/Comirnaty injection (n=17).RESULTS83 patients were included, the median age was 87 (81-91) years.In the vaccine group at 1 month since the first vaccination, the median BAU/ml with IQR was 620 (217-1874) with 87% of patients above the threshold of 141 BAU/ml. Seven months after the first vaccination the BAU/ml was 30 (19-58) with 9.5% of patients above the threshold of 141 BAU/ml.In the natural COVID-19 infection group, at 1 month since the date of first symptom onset, the median BAU/ml was 798 (325-1320) with 86.7% of patients above the threshold of 141 BAU/ml and fell to 88 (37-385) with 42.9% of patients above the threshold of 141 BAU/ml at 2 months. The natural infection group was vaccinated three months after the infection. Five months after the end of the vaccination cycle the BAU/ml was 2048 (471-4386) with 83.3% of patients above the threshold of 141 BAU/ml.DISCUSSIONOn the humoral level, this supports the clinical results describing the decrease in vaccine protection over time.
Low neutralizing antibody titers against the Mu variant of SARS-CoV-2 in BNT162b2 vaccinated individuals
Authors: Álvarez-Díaz Diego A. , Muñoz Ana Luisa , Tavera-Rodríguez Pilar , Herrera-Sepúlveda María T. , Ruiz-Moreno Hector Alejandro , Laiton-Donato Katherine , Franco-Muñoz Carlos , Pelaez-Carvajal Dioselina , Cuellar Diego , Muñoz-Ramirez Alejandra M. , Galindo Marisol , Arias-Ramirez Edgar J. , Mercado-Reyes Marcela 
Published: November 2021

SummaryBackgroundGlobal surveillance programs for the virus that causes COVID-19 are showing the emergence of variants with mutations in the Spike protein, including the Mu variant, recently declared a Variant of Interest (VOI) by the World Health Organization. Genomic and laboratory surveillance is important in these types of variants because they may be more infectious or less susceptible to antiviral treatments and vaccine-induced antibodies.ObjectivesTo evaluate the sensitivity of the Mu variant (B.1.621) to neutralizing antibodies induced by the BNT162b2 vaccine.Study designThree of the most predominant SARS-CoV-2 variants in Colombia during the epidemiological peaks of 2021 were isolated. Microneutralization assays were performed by incubating 120 TCDI50 of each SARS-CoV-2 isolate with five 2-fold serial dilutions of sera from 14 BNT162b2 vaccinated volunteers. The MN50 titer was calculated by the Reed-Muench formulaResultsThe three isolated variants were Mu, a Variant of Interest (VOI), Gamma, a variant of concern (VOC), and B.1.111 that lacks genetic markers associated with greater virulence. At the end of August, the Mu and Gamma variants were widely distributed in Colombia. Mu was predominant (49%), followed by Gamma (25%). In contrast, B.1.111 became almost undetectable. The evaluation of neutralizing antibodies suggests that patients vaccinated with BNT162-2 generate neutralizing antibody titers against the Mu variant at significantly lower concentrations relative to B.1.111 and Gamma.ConclusionsThis study shows the importance of continuing with surveillance programs of emerging variants as well as the need to evaluate the neutralizing antibody response induced by other vaccines circulating in the country against Mu and other variants with high epidemiological impact.HighlightsMu and Gamma variants represented 49% and 25% of cases in Colombia by August 2021.Increased proportion of SARS-COV-2 cases were mostly associated with Mu variant, despite being detected simultaneously with the VOC GammaThe Mu variant remarkably escapes from neutralizing antibodies elicited by the BNT162b2-vaccineLaboratory studies of neutralizing antibodies are useful to determine the efficacy of SARS-CoV-2 vaccines against VOC and VOI.
Smart soils to observe hidden rhizosphere processes
Authors: Patko Daniel , Yang Qizhi , Liu Yangminghao , Falireas Panagiotis , Briou Benoit , Tawade Bhausaheb V , George Timothy S , Daniell Tim J , MacDonald Michael P , Ladmiral Vincent , Ameduri Bruno , Dupuy Lionel X 
Published: November 2021

SummaryAgriculture must reduce green-house gas emission and pollution, produce safer and healthier food, closer to home, reducing waste whilst delivering more diverse diets to a growing world population. Soils could enable this transformation, but unfortunately, they have a hugely complex and opaque structure and studies of its myriad of mechanisms are difficult. Here, the fabrication of smart soils for the screening of below-ground bio-processes is demonstrated. Particles were generated from fluoropolymer waste with functionalisation converting them into sensors able to report on key chemical dynamics. Tailored functionalization was obtained by radical terpolymerisation to improve growth conditions and sensing capabilities. The study demonstrates the potential for the development of accelerated genetic or agrochemical screens and could pave the way for improved models for rhizosphere dynamics.
Glyphosate and its formulations Roundup Bioflow and RangerPro alter bacterial and fungal community composition in the rat caecum microbiome
Authors: Mesnage Robin , Panzacchi Simona , Bourne Emma , Mein Charles A , Perry Melissa J , Hu Jianzhong , Chen Jia , Mandrioli Daniele , Belpoggi Fiorella , Antoniou Michael N 
Published: November 2021

AbstractThe potential health consequences of glyphosate-induced gut microbiome alterations have become a matter of intense debate. As part of a multifaceted study investigating toxicity, carcinogenicity and multigenerational effects of glyphosate and its commercial herbicide formulations, we assessed changes in bacterial and fungal populations in the caecum microbiota of rats exposed prenatally until adulthood (13 weeks after weaning) to three doses of glyphosate (0.5, 5, 50 mg/kg body weight/day), or to the formulated herbicide products Roundup Bioflow and RangerPro at the same glyphosate-equivalent doses. Caecum bacterial microbiota were evaluated by 16S rRNA sequencing whilst the fungal population was determined by ITS2 amplicon sequencing. Results showed that both fungal and bacterial diversity were affected by the Roundup formulations in a dose-dependent manner, whilst glyphosate alone significantly altered only bacterial diversity. At taxa level, a reduction in Bacteroidota abundance, marked by alterations in the levels of Alloprevotella, Prevotella and Prevotellaceae UCG-003, was concomitant to increased levels of Firmicutes (e.g., Romboutsia, Dubosiella, Eubacterium brachy group or Christensenellaceae) and Actinobacteria (e.g., Enterorhabdus, Adlercreutzia, or Asaccharobacter). Treponema and Mycoplasma also had their levels reduced by the pesticide treatments. Analysis of fungal composition indicated that the abundance of the rat gut commensal Ascomycota Kazachstania was reduced while the abundance of Gibberella, Penicillium, Claviceps, Cornuvesica, Candida, Trichoderma and Sarocladium were increased by exposure to the Roundup formulations, but not to glyphosate. Altogether, our data suggest that glyphosate and its Roundup RangerPro and Bioflow caused profound changes in caecum microbiome composition by affecting the fitness of major commensals, which in turn reduced competition and allowed opportunistic fungi to grow in the gut, in particular in animals exposed to the herbicide formulations. This further indicates that changes in gut microbiome composition might influence the long-term toxicity, carcinogenicity and multigenerational effects of glyphosate-based herbicides.
Swarm learning for decentralized artificial intelligence in cancer histopathology
Authors: Saldanha Oliver Lester , Quirke Philip , West Nicholas P. , James Jacqueline A. , Loughrey Maurice B. , Grabsch Heike I. , Salto-Tellez Manuel , Alwers Elizabeth , Cifci Didem , Laleh Narmin Ghaffari , Seibel Tobias , Gray Richard , Hutchins Gordon G. A. , Brenner Hermann , Yuan Tanwei , Brinker Titus J. , Chang-Claude Jenny , Khader Firas , Schuppert Andreas , Luedde Tom , Foersch Sebastian , Muti Hannah Sophie , Trautwein Christian , Hoffmeister Michael , Truhn Daniel , Kather Jakob Nikolas 
Published: November 2021

AbstractArtificial Intelligence (AI) can extract clinically actionable information from medical image data. In cancer histopathology, AI can be used to predict the presence of molecular alterations directly from routine histopathology slides. However, training robust AI systems requires large datasets whose collection faces practical, ethical and legal obstacles. These obstacles could be overcome with swarm learning (SL) where partners jointly train AI models, while avoiding data transfer and monopolistic data governance. Here, for the first time, we demonstrate the successful use of SL in large, multicentric datasets of gigapixel histopathology images comprising over 5000 patients. We show that AI models trained using Swarm Learning can predict BRAF mutational status and microsatellite instability (MSI) directly from hematoxylin and eosin (H&E)-stained pathology slides of colorectal cancer (CRC). We trained AI models on three patient cohorts from Northern Ireland, Germany and the United States of America and validated the prediction performance in two independent datasets from the United Kingdom using SL-based AI models. Our data show that SL enables us to train AI models which outperform most locally trained models and perform on par with models which are centrally trained on the merged datasets. In addition, we show that SL-based AI models are data efficient and maintain a robust performance even if only subsets of local datasets are used for training. In the future, SL can be used to train distributed AI models for any histopathology image analysis tasks, overcoming the need for data transfer and without requiring institutions to give up control of the final AI model.
TK216 targets microtubules in Ewing sarcoma cells
Authors: Povedano Juan Manuel , Li Vicky , Lake Katherine E. , Bai Xin , Rallabandi Rameshu , Kim Jiwoong , Xie Yang , De Brabander Jef K. , McFadden David G. 
Published: November 2021

ABSTRACTEwing sarcoma (EWS) is a pediatric malignancy driven by the EWSR1-FLI1 fusion protein formed by the chromosomal translocation t(11;22). The small molecule TK216 was developed as a first-in-class direct EWSR1-FLI1 inhibitor and is in phase II clinical trials in combination with vincristine for EWS patients. However, TK216 exhibits anti-cancer activity against cancer cell lines and xenografts that do not express EWSR1-FLI1, and the mechanism underlying cytotoxicity remains unresolved. We apply a forward genetics screening platform utilizing engineered hypermutation in EWS cell lines and identify recurrent mutations in TUBA1B, encoding α-tubulin, that prove sufficient to drive resistance to TK216. Using reconstituted microtubule (MT) polymerization in vitro and cell-based chemical probe competition assays, we demonstrate that TK216 acts as an MT destabilizing agent. This work defines the mechanism of cytotoxicity of TK216, explains the synergy observed with vincristine, and calls for a reexamination of ongoing clinical trials with TK216.
A Time-calibrated Firefly (Coleoptera: Lampyridae) Phylogeny: Using Genomic Data for Divergence Time Estimation
Authors: Höhna Sebastian , Lower Sarah E. , Duchen Pablo , Catalán Ana 
Published: November 2021

AbstractFireflies (Coleoptera: Lampyridae) consist of over 2,000 described extant species. A well-resolved phylogeny of fireflies is important for the study of their population genetics, bioluminescence, evolution, and conservation. We used a recently published anchored hybrid enrichment dataset (AHE; 436 loci for 88 Lampyridae species and 10 outgroup species) and state-of-the-art statistical methods (the fossilized birth-death-range process implemented in a Bayesian framework) to estimate a time-calibrated phylogeny of Lampyridae. Unfortunately, estimating calibrated phylogenies using AHE and the latest and most robust time-calibration strategies is not possible because of computational constraints. As a solution, we subset the full dataset by applying three different strategies: (i) using the most complete loci, (ii) using the most homogeneous loci, and (iii) using the loci with the highest accuracy to infer the well established Photinus clade. The estimated topology using the three data subsets agreed on almost all major clades and only showed minor discordance within less supported nodes. The estimated divergence times overlapped for all nodes that are shared between the topologies. Thus, divergence time estimation is robust as long as the topology inference is robust and any well selected data subset suffices. Additionally, we observed an un-expected amount of gene tree discordance between the 436 AHE loci. Our assessment of model adequacy showed that standard phylogenetic substitution models are not adequate for any of the 436 AHE loci which is likely to bias phylogenetic inferences. We performed a simulation study to explore the impact of (a) incomplete lineage sorting, (b) uniformly distributed and systematic missing data, and (c) systematic bias in the position of highly variable and conserved sites. For our simulated data, we observed less gene tree variation which shows that the empirically observed amount of gene tree discordance for the AHE dataset is unexpected and needs further investigation.