bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bifidobacterium breveUCC2003 induces a distinct global transcriptomic programme in neonatal murine intestinal epithelial cells
Authors: Kiu Raymond , Treveil Agatha , Harnisch Lukas C. , Caim Shabhonam , Leclaire Charlotte , van Sinderen Douwe , Korcsmaros Tamas , Hall Lindsay J. 
Published: March 2020

SummaryBifidobacteriumis an important gut microbiota member during early life that is associated with improved gut health. However, the underlying health-driving mechanisms are not well understood, particularly howBifidobacteriummay modulate the intestinal barrier via programming of intestinal epithelial cells (IECs). In this study, we sought to investigate the global impact of model strainBifidobacterium breveUCC2003 on the neonatal IEC transcriptome, including gene regulation and pathway modulation. Small IECs from two-week-old neonatal mice administeredB. breveUCC2003 for three consecutive days or PBS (control group) were subjected to global RNASeq, with various bioinformatic approaches used to determine differentially expressed genes, pathways and affected cell types between control and experimental groups. Whilst colonisation withB. brevehad minimal impacts on the neonatal microbiota, we observed extensive regulation of the IEC transcriptome; ~4,000 genes significantly up-regulated, including key genes associated with epithelial barrier function. Enrichment of cell differentiation and cell proliferation pathways were observed, along with an overrepresentation of stem cell marker genes, indicating an increase in the regenerative potential of the epithelial layer. Expression of distinct immune-associated pathway members (e.g. Toll-like Receptors) were also affected after neonatalB. brevecolonisation. In conclusion,B. breveUCC2003 plays a central role in driving universal transcriptomic changes in neonatal IECs that enhances cell replication, differentiation and growth, predominantly in the stem cell compartment. This study enhances our overall understanding of the benefits ofB. brevein driving intestinal epithelium homeostatic development during early life, with potential avenues to develop novel live biotherapeutic products.
Frisky CALF sometimes outruns LASSO
Authors: Jeffries Clark D. , Ford John R. , Tilson Jeffrey L. , Perkins Diana O. , Bost Darius M. , Filer Dayne L. , Wilhelmsen Kirk C. 
Published: March 2020

AbstractRegularized regression analysis is a mature analytic approach to identify weighted sums of variables that predict outcomes. Typically, the number of subjects (N) is smaller than the number of predictors (p). Here, we present a novel coarse approximation linear function (CALF) to frugally select important predictors, build linear models, and discover causality.CALF is a linear regression strategy applied to normalized data that employs only a few (such as 2 to 20) nonzero weights, each +1 or -1. Metrics can be Welch t-test p-value, area under curve (AUC) of receiver operating characteristic, or Pearson correlation, depending upon data type and user preferences. For quantitative approximations, a linear fit (adding an intercept value and rescaling ±1 weights by a common multiplier) can be added to optimize mean squared error (MSE).Real medical data of five types were used to generate examples with goals of binary classification or real variable approximation. Predictors considered were real, sets of integers, or ternary values of single nucleotide polymorphisms. When applied to real data, CALF approximations outperformed in p-value, AUC, correlation, or MSE a popular regularized linear regression algorithm, namely, basic LASSO. It appears that using LASSO without considering CALF might risk wasting resources.AvailabilityR version: Comprehensive R Archive (CRAN):https://cran.r-project.org/web/packages/CALF/index.htmlPython 3.x version: GitHub:https://github.com/jorufo/CALF_PythonContactclark_jeffries@med.unc.edu
A novel platform of RNA 2′-O-methylation high-throughput and site-specific quantification tools revealed its broad distribution on mRNA
Authors: Tang Yao , Wu Yifan , Wang Sainan , Lu Xiaolan , Gu Xiangwen , Li Yong , Yang Fan , Xu Ruilin , Wang Tao , Jiao Zichen , Wu Yan , Liu Liwei , Chen Jian-Qun , Wang Qiang , Chen Qihan 
Published: March 2020

AbstractRibose 2′-O-methylation is involved in critical biological processes, but its biological functions and significance in mRNAs remain largely unknown due to the lack of accurate and efficient identification tools. To overcome this gap, we established NJU-seq (an accurate high-throughput single-base method) and Nm-VAQ (a site-specific quantification tool). We identified thousands of new Nm sites on mRNA of human and mouse cell lines, in which 68 of 84 selected sites were further validated to be 2′-O-methylated more than 1%. Unlike rRNA, the methylated ratios of most validated mRNA Nm sites were lower than 30%. In addition, mRNA 2′-O-methylation was dynamic-changing according to the circumstance, which was presented with MHV infection. Furthermore, Nm sites of lung surgery samples revealed commonness of lung cancer pathogenesis, providing potential new diagnostic markers.
Accuracy and efficiency of germline variant calling pipelines for human genome data
Authors: Zhao Sen , Agafonov Oleg , Azab Abdulrahman , Stokowy Tomasz , Hovig Eivind 
Published: March 2020

AbstractAdvances in next-generation sequencing technology has enabled whole genome sequencing (WGS) to be widely used for identification of causal variants in a spectrum of genetic-related disorders, and provided new insight into how genetic polymorphisms affect disease phenotypes. The development of different bioinformatics pipelines has continuously improved the variant analysis of WGS data, however there is a necessity for a systematic performance comparison of these pipelines to provide guidance on the application of WGS-based scientific and clinical genomics. In this study, we evaluated the performance of three variant calling pipelines (GATK, DRAGEN™ and DeepVariant) using Genome in a Bottle Consortium, “synthetic-diploid” and simulated WGS datasets. DRAGEN™ and DeepVariant show a better accuracy in SNPs and indels calling, with no significant differences in their F1-score. DRAGEN™ platform offers accuracy, flexibility and a highly-efficient running speed, and therefore superior advantage in the analysis of WGS data on a large scale. The combination of DRAGEN™ and DeepVariant also provides a good balance of accuracy and efficiency as an alternative solution for germline variant detection in further applications. Our results facilitate the standardization of benchmarking analysis of bioinformatics pipelines for reliable variant detection, which is critical in genetics-based medical research and clinical application.
Pyocin efficacy in a murine model ofPseudomonas aeruginosasepsis
Authors: Six Anne , Mosbahi Khedidja , Barge Madhuri , Kleanthous Colin , Evans Thomas , Walker Daniel 
Published: March 2020

SynopsisBackgroundBloodstream infections with antibiotic resistantPseudomonas aeruginosaare common and increasingly difficult to treat. Pyocins are naturally occurring protein antibiotics produced byP. aeruginosathat have potential for human use.ObjectivesTo determine if pyocin treatment is effective in a murine model of sepsis withP. aeruginosa.MethodsRecombinant pyocins S5 and AP41 were purified tested for efficacy in aGalleria mellonellainfection model and a murine model ofP. aeruginosasepsis.ResultsBoth pyocins produced no adverse effects when injected alone into mice and showed good in vitro antipseudomonal activity. In an invertebrate model of sepsis usingGalleria mellonella, both pyocins significantly prolonged survival. Following injection into mice, both showed extensive distribution into different organs. When administered 5 hours after infection, both pyocins reduced mortality, with pyocin S5 being more effective than AP41.ConclusionsPyocins S5 and AP41 show in vivo biological activity and can improve survival in a murine model ofP. aeruginosainfection. They hold promise as novel antimicrobial agents for treatment of multi-drug resistant infections with this microbe.
Proliferation of HIV-infected renal epithelial cells following virus acquisition from infected macrophages
Authors: Hughes Kelly , Akturk Guray , Gnjatic Sacha , Chen Benjamin , Klotman Mary , Blasi Maria 
Published: March 2020

ABSTRACTObjectivesHIV-1 can infect and persist in different organs and tissues, resulting in the generation of multiple viral compartments and reservoirs. Increasing evidence supports the kidney as such a reservoir. Previous work demonstrated that HIV-1 infected CD4+ T-cells transfer virus to renal tubule epithelial (RTE) cells through cell-to-cell contact. In addition to CD4+ T-cells, macrophages represent the other major target of HIV-1. Renal macrophages induce and regulate inflammatory responses and are critical to homeostatic regulation of the kidney environment. Combined with their ability to harbor virus, macrophages may also play an important role in the spread of HIV-1 infection in the kidney.Design and MethodsMultiparametric histochemistry analysis was performed on kidney biopsies from individuals with HIV-1 associated nephropathy (HIVAN). Primary monocyte-derived macrophages were infected with a (GFP)-expressing replication competent HIV-1. HIV-1 transfer from macrophages to RTE cells was carried out in a co-culture system and evaluated by fluorescence-microscopy and flow-cytometry. Live imaging was performed to assess the fate of HIV-1 infected RTE cells over time.ResultsWe show that macrophages are abundantly present in the renal inflammatory infiltrate of individuals with HIVAN. We observed contact-dependent HIV-1 transfer from infected macrophages to both primary and immortalized renal cells. Live imaging of HIV-1 infected RTE cells revealed four different fates: proliferation, hypertrophy, latency and cell death.ConclusionsOur study suggests that macrophages may play a role in the dissemination of HIV-1 in the kidney and that proliferation of infected renal cells may contribute to HIV-1 persistence in this compartment.
Mapping the Location of Nucleosomes in Simian Virus 40 Chromatin Using the New England Biolabs FS Library Prep Kit
Authors: Milavetz Barry , Haugen Jacob , Rowbotham Kincaid 
Published: March 2020

AbstractThe location of nucleosomes in chromatin significantly impacts many biological processes including DNA replication, repair and gene expression. A number of techniques have been developed for mapping nucleosome locations in chromatin including MN-Seq (micrococcal nuclease digestion followed by next generation sequencing), ATAC-Seq (Tagamet chromatin fragmentation followed by next generation sequencing), and ChIP-Seq (chromatin immunoprecipitation and fragmentation followed by next generation sequencing). All of these techniques have been successfully used, but each with its own limitations. Recently, New England Biolabs has marketed a new kit, the NEBNext UltraII FS Library Prep kit, for preparing libraries for next generation sequencing from purified genomic DNA. This kit is based on a novel proprietary DNA fragmentation procedure which appears to cleave DNA that is not bound by proteins. Because DNA is fragmented directly in the FS kit, we tested whether the kit might also be useful for mapping the location of nucleosomes in chromatin. Using Simian Virus 40 (SV40) chromatin isolated at different times in an infection, we have compared nucleosome mapping using the NEB FS kit (FS-Seq) to MN-Seq, ATAC-Seq, and ChIP-Seq. Mapping nucleosomes using FS-Seq generated nucleosome profiles similar to those generated by ATAC-Seq and ChIP-Seq in regulatory regions of the SV40 genome. We conclude that FS-Seq is a simple, robust, cost-effective procedure for mapping nucleosomes in SV40 chromatin that should be useful for other forms of chromatin as well. We also present evidence that the FS kit may be useful for mapping the location of transcription factors in chromatin when sequencing reads between 75 and 99 base pairs in size are analyzed.
Evolutionarily conserved non-protein-coding regions in the chicken genome harbor functionally important variation
Authors: Groß Christian , Bortoluzzi Chiara , de Ridder Dick , Megens Hendrik-Jan , Groenen Martien AM , Reinders Marcel , Bosse Mirte 
Published: March 2020

AbstractThe availability of genomes for many species has advanced our understanding of the non-protein-coding fraction of the genome. Comparative genomics has proven to be an invaluable approach for the systematic, genome-wide identification of conserved non-protein-coding elements (CNEs). However, for many non-mammalian model species, including chicken, our capability to interpret the functional importance of variants overlapping CNEs has been limited by current genomic annotations, which rely on a single information type (e.g. conservation). We here studied CNEs in chicken using a combination of population genomics and comparative genomics. To investigate the functional importance of variants found in CNEs we develop a ch(icken) Combined Annotation-Dependent Depletion (chCADD), a variant effect prediction tool first introduced for humans and later on for mouse and pig. We show that 73 Mb of the chicken genome has been conserved across more than 280 million years of vertebrate evolution. The vast majority of the conserved elements are in non-protein-coding regions, which display SNP densities and allele frequency distributions characteristic of genomic regions constrained by purifying selection. By annotating SNPs with the chCADD score we are able to pinpoint specific subregions of the CNEs to be of higher functional importance, as supported by SNPs found in these subregions are associated with known disease genes in humans, mice, and rats. Taken together, our findings indicate that CNEs harbor variants of functional significance that should be object of further investigation along with protein-coding mutations. We therefore anticipate chCADD to be of great use to the scientific community and breeding companies in future functional studies in chicken.
SARS-CoV-2 and ORF3a: Non-Synonymous Mutations and Polyproline Regions
Authors: Issa Elio , Merhi Georgi , Panossian Balig , Salloum Tamara , Tokajian Sima 
Published: March 2020

AbstractThe effect of the rapid accumulation of non-synonymous mutations on the pathogenesis of SARS-CoV-2 is not yet known. To predict the impact of non-synonymous mutations and polyproline regions identified in ORF3a on the formation of B-cell epitopes and their role in evading the immune response, nucleotide and protein sequences of 537 available SARS-CoV-2 genomes were analyzed for the presence of non-synonymous mutations and polyproline regions. Mutations were correlated with changes in epitope formation. A total of 19 different non-synonymous amino acids substitutions were detected in ORF3a among 537 SARS-CoV-2 strains. G251V was the most common and identified in 9.9% (n=53) of the strains and was predicted to lead to the loss of a B-cell like epitope in ORF3a. Polyproline regions were detected in two strains (EPI_ISL_410486, France and EPI_ISL_407079, Finland) and affected epitopes formation. The accumulation of non-synonymous mutations and detected polyproline regions in ORF3a of SARS-CoV-2 could be driving the evasion of the host immune response thus favoring viral spread. Rapid mutations accumulating in ORF3a should be closely monitored throughout the COVID-19 pandemic.ImportanceAt the surge of the COVID-19 pandemic and after three months of the identification of SARS-CoV-2 as the disease-causing pathogen, nucleic acid changes due to host-pathogen interactions are insightful into the evolution of this virus. In this paper, we have identified a set of non-synonymous mutations in ORF3a and predicted their impact on B-cell like epitope formation. The accumulation of non-synonymous mutations in ORF3a could be driving protein changes that mediate immune evasion and favoring viral spread.
Ultrafast and accurate 16S microbial community analysis using Kraken 2
Authors: Lu Jennifer , Salzberg Steven L 
Published: March 2020

AbstractFor decades, 16S ribosomal RNA sequencing has been the primary means for identifying the bacterial species present in a sample with unknown composition. One of the most widely-used tools for this purpose today is the QIIME (Quantitative Insights Into Microbial Ecology) package. Recent results have shown that the newest release, QIIME 2, has higher accuracy than QIIME, MAPseq, and mothur when classifying bacterial genera from simulated human gut, ocean, and soil metagenomes, although QIIME 2 also proved to be the most computationally expensive method. Kraken, first released in 2014, has been shown to provide exceptionally fast and accurate classification for shotgun metagenomics sequencing projects. Bracken, released in 2016, then provided users with the ability to accurately estimate species or genus abundances using Kraken classification results. Kraken 2, which matches the accuracy and speed of Kraken 1, now supports 16S rRNA databases, allowing for direct comparisons to QIIME and similar systems. Here we show that, using the same simulated 16S rRNA metagenomic data as previous studies, Kraken 2 and Bracken are up to 300 times faster and also more accurate at 16S profiling than QIIME 2.
Detection of deleterious on-target effects after HDR-mediated CRISPR editing
Authors: Weisheit Isabel , Kroeger Joseph , Malik Rainer , Klimmt Julien , Crusius Dennis , Dannert Angelika , Dichgans Martin , Paquet Dominik 
Published: March 2020

SummaryCRISPR genome editing is a promising tool for translational research but can cause undesired editing outcomes, both on-target at the edited locus and off-target at other genomic loci. We investigated the occurrence of deleterious on-target effects in human stem cells after insertion of disease-related mutations by homology-directed repair (HDR). We identified large, mono-allelic genomic deletions and loss-of-heterozygosity that escaped standard quality controls in up to 40% of edited clones. To reliably detect such events, we developed simple, low-cost and universally applicable quantitative genotyping PCR (qgPCR) as well as sequencing-based tools and suggest their usage as additional quality controls after editing. This will help to ensure the integrity of edited loci and increase the reliability of CRISPR editing.
Mechano-bactericidal nanopillars require external forces to effectively kill bacteria
Authors: Valiei Amin , Lin Nicholas , Bryche Jean-Francois , McKay Geoffrey , Canva Michael , Charette Paul G. , Nguyen Dao , Moraes Christopher , Tufenkji Nathalie 
Published: March 2020

AbstractNanopillars are known to mechanically damage bacteria, suggesting a promising strategy for highly-effective anti-bacterial surfaces. However, the mechanisms underlying this phenomena remain unclear, which ultimately limits translational potential towards real-world applications. Using real-time and end-point analysis techniques, we demonstrate that in contrast to expectations, bacteria on multiple “mechano-bactericidal” surfaces remain viable, unless exposed to a moving air-liquid interface which caused considerable cell death. Reasoning that normal forces arising from surface tension may underlie mechano-bactericidal activity, we developed computational and experimental models to estimate, manipulate, and recreate the impact of these forces. Our experiments together demonstrate that nanopillar surfaces alone do not cause cell death, but require a critical level of external force to deform and rupture bacteria. These studies hence provide fundamental physical insight into the mechanisms by which nanopillar surfaces can serve as effective antibacterial strategies, and describe the use-conditions under which such nanotechnological approaches may provide practical value.Graphical Abstract
Recent loss of the Dim2 DNA methyltransferase decreases mutation rate in repeats and changes evolutionary trajectory in a fungal pathogen
Authors: Möller Mareike , Habig Michael , Lorrain Cécile , Feurtey Alice , Haueisen Janine , Fagundes Wagner C. , Alizadeh Alireza , Freitag Michael , Stukenbrock Eva H. 
Published: March 2020

AbstractDNA methylation is found throughout all domains of life, yet the extent and function of DNA methylation differ between eukaryotes. Strains of the plant pathogenic fungusZymoseptoria triticiappeared to lack cytosine DNA methylation (5mC) because gene amplification followed by Repeat-Induced Point mutation (RIP) resulted in the inactivation of thedim2DNA methyltransferase gene. 5mC is, however, present in closely related sister species. We demonstrate that inactivation ofdim2occurred recently as someZ. triticiisolates carry a functionaldim2gene. Moreover, we show thatdim2inactivation occurred by a different path than previously hypothesized. We mapped the genome-wide distribution of 5mC in strains with and without functionaldim2. Presence of functionaldim2correlates with high levels of 5mC in transposable elements (TEs), suggesting a role in genome defense. We identified low levels of 5mC in strains carrying inactivedim2alleles, suggesting that 5mC is maintained over time, presumably by an active Dnmt5 DNA methyltransferase. Integration of a functionaldim2allele in strains with mutateddim2restored normal 5mC levels, demonstratingde novocytosine methylation activity ofdim2. To assess the importance of 5mC for genome evolution, we performed an evolution experiment, comparing genomes of strains with high levels of 5mC to genomes of strains lackingdim2. We found that the presence ofdim2alters nucleotide composition by promoting C to T transitions (C→T) specifically at CpA (CA) sites during mitosis, likely contributing to TE inactivation. Our results show that 5mC density at TEs is a polymorphic trait inZ. triticipopulations that can impact genome evolution.Author SummaryCytosine DNA methylation (5mC) is known to silence transposable elements in fungi and thereby appears to contribute to genome stability. The genomes of plant pathogenic fungi are highly diverse, differing substantially in transposon content and distribution. Here, we show extensive differences of 5mC levels within a single species of an important wheat pathogen. These differences were caused by inactivation of the DNA methyltransferase Dim2 in the majority of studied isolates. Presence of widespread 5mC increased point mutation rates in regions with active or mutated transposable elements during mitosis. The mutation pattern is dependent on the presence of Dim2 and resembles a mitotic version of Repeat-Induced Point mutation (RIP). Thus, loss of 5mC may represent an evolutionary trade-off offering adaptive potential at the cost of transposon control.
TheHoja loca1Mutant and AUX/IAA Function in Phytomer Development
Authors: Richardson A. E. , Sluis A. , Hake S. 
Published: March 2020

AbstractPlant architecture is determined by the iterative building of phytomer units, each containing a portion of stem, an organ and an axillary meristem. Each phytomer can follow different developmental paths underpinning the complexity, and plasticity, of plant form. Auxin plays a central role in the coordination of phytomer development, regulating organ initiation and patterning across all axes. This diversity in auxin function results from changes in the activities and expression of auxin signaling components, including the AUX/IAA repressors. Higher land plants have multigene AUX/IAA families, which leads to functional redundancy. Dominant mutations, which prevent AUX/IAA degradation in response to auxin, have highlighted the importance of these proteins in fine-tuning organ development. Here we report a new dominant AUX/IAA mutant in maize,Hoja loca1(Oja).Ojahas a mutation in the degron motif of ZmIAA28 and specifically affects aerial organ initiation and leaf medio-lateral patterning, but phytomer initiation remains unchanged. Mutant phenotypes are variable and transcriptional profiling of individual meristems identified clusters of genes that may underpin the phenotypic differences. The unique phenotype ofOjaprovides evidence of species-specific sub-functionalization of the AUX/IAAs, and illustrates the crucial role of auxin signaling in the tight coordination of phytomer unit development.