bluuebunny/crossref_metadata_2025_split huggingface dataset:
A fast machine-learning-guided primer design pipeline for selective whole genome amplification
Authors: Yu Jane A. , Oppler Zachary J. , Mitchell Matthew W. , Song Yun S. , Brisson Dustin 
Published: April 2022

AbstractAddressing many of the major outstanding questions in the fields of microbial evolution and pathogenesis will require analyses of populations of microbial genomes. Although population genomic studies provide the analytical resolution to investigate evolutionary and mechanistic processes at fine spatial and temporal scales – precisely the scales at which these processes occur – microbial population genomic research is currently hindered by the practicalities of obtaining sufficient quantities of the relatively pure microbial genomic DNA necessary for next-generation sequencing. Here we present swga2.0, an optimized and parallelized pipeline to design selective whole genome amplification (SWGA) primer sets. Unlike previous methods, swga2.0 incorporates active and machine learning methods to evaluate the amplification efficacy of individual primers and primer sets. Additionally, swga2.0 optimizes primer set search and evaluate strategies, including parallelization at each stage of the pipeline, to dramatically decrease program runtime from weeks to minutes. Here we describe the swga2.0 pipeline, including the empirical data used to identify primer and primer set characteristics, that improve amplification performance. Additionally, we evaluated the novel swga2.0 pipeline by designing primers sets that successfully amplify Prevotella melaninogenica, an important component of the lung microbiome in cystic fibrosis patients, from samples dominated by human DNA.
Age-related changes of deep-brain neurophysiological activity
Authors: Hinault T. , Baillet S. , Courtney SM. 
Published: April 2022

AbstractCognitive decline with age is associated with brain atrophy and reduced brain activations, but the underlying neurophysiological mechanisms are unclear, especially in deeper brain structures primarily affected by healthy aging or neurodegenerative processes. Here, we characterize time-resolved, resting-state magnetoencephalography activity of the hippocampus and subcortical brain regions in a large cohort of healthy young and older volunteers from the Cam-CAN open repository. The data show age-related changes in both rhythmic and arrhythmic signal strength and temporal variability in multiple deeper brain regions, including the hippocampus, striatum, and thalamus. We observe a slowing of neural activity in deeper brain regions, which echoes previous reports of cortical slowing. We also report reduced occipito-parietal alpha peak associated with increased theta-band activity and signal variability in the hippocampus, an effect that may reflect compensatory processes as theta activity and variability were more strongly expressed when cognitive performances are preserved. Overall, this study advances the understanding of the biological nature of inter-individual variability in aging. The data provide new insight of how hippocampus and subcortical neurophysiological activity evolve with biological age, and highlight frequency-specific effects associated with cognitive decline vs. cognitive maintenance.
The distribution of the Lansing Effect across animal species
Authors: Ivimey-Cook Edward , Shorr Sarema , Moorad Jacob 
Published: April 2022

AbstractMaternal senescence is a reduction in individual performance associated with an increase in its mother’s age at conception. When manifested on adult lifespan, this is known as the ‘Lansing Effect’. Single-species studies report both maternal age-related increases and decreases in adult lifespan, but no comprehensive review of the literature has yet determined if the Lansing Effect is a widespread phenomenon. To address this knowledge gap, we performed a meta-analysis of maternal aging rates taken from all available published studies. We recovered 74 estimates from 20 studies representing 14 species. All studies taken together suggest a propensity for a Lansing Effect with an estimated average effect of maternal age on adult lifespan of between -22% to -17% (the lifespan response to an increase in maternal age expressed in the same time units), depending upon our specific choice of model. We failed to find a significant effect of animal class or insect order, but given the oversampling of insect species in the published literature and the paucity of vertebrate studies, we infer that only rotifers and insects demonstrate a tendency for expressing the phenomenon.
Rac rather than Rho drives the early transcriptional response to extracellular matrix stiffness and mediates repression of ATF3
Authors: Dang Irène , Bae Yongho , Brazzo Joseph A. , Assoian Richard K 
Published: April 2022

SUMMARYThe Rho family GTPases, Rac and Rho, play critical roles in transmitting mechanical information contained within the extracellular matrix (ECM) to the cell. Rac and Rho have well described roles in regulating stiffness-dependent actin remodeling, proliferation and motility. However, much less is known about the relative roles of these GTPases in stiffness-dependent transcription, particularly at the genome-wide level. Here, we selectively inhibited Rac and Rho in mouse embryonic fibroblasts cultured on deformable substrata and used RNA sequencing to elucidate and compare the contribution of these GTPases to the early transcriptional response to ECM stiffness. Surprisingly, we found that Rac activation is almost exclusively responsible for the initial transcriptional response to ECM stiffness. We also identified Activating Transcription Factor 3 (ATF3) as a major target of stiffness/Rac signaling and show that ATF3 repression by ECM stiffness connects the stiffness-dependent activation of Rac to the induction of cyclin D1.
Tackling RecalcitrantPseudomonas aeruginosaInfections In Critical Illness via Anti-virulence Monotherapy
Authors: Singh Vijay K. , Almpani Marianna , Maura Damien , Kitao Tomoe , Ferrari Livia , Fontana Stefano , Bergamini Gabriella , Calcaterra Elisa , Pignaffo Chiara , Negri Michele , de Oliveira Pereira Thays , Skinner Frances , Gkikas Manos , Andreotti Danielle , Felici Antonio , Déziel Eric , Lépine Francois , Rahme Laurence G. 
Published: April 2022

AbstractIntestinal barrier derangement allows intestinal bacteria and their products to translocate to the systemic circulation.Pseudomonas aeruginosa(PA) superimposed infection in critically ill patients increases gut permeability and leads to gut-driven sepsis.PAinfections are challenging due to multi-drug resistance (MDR), biofilms, and/or antibiotic tolerance. Inhibition of the quorum-sensing transcriptional regulator MvfR(PqsR) is a desirable anti-PAstrategy as MvfR controls multiple acute and chronic virulence functions. Here we show that MvfR promotes intestinal permeability and report novel potent anti-MvfR compounds, the N-Aryl Malonamides (NAMs) resulting from extensive structure-activity-relationship studies and thorough assessment of the inhibition of MvfR-controlled virulence functions. This novel class of anti-virulence non-native ligand-based agents has a half-maximal inhibitory concentration in the nanomolar range and strong target engagement. Using a NAM lead in monotherapy protects murine intestinal barrier function, abolishes MvfR-regulated small molecules, ameliorates bacterial dissemination, and lowers inflammatory cytokines. This study demonstrates the importance of MvfR inPA-driven intestinal permeability. It underscores the utility of anti-MvfR agents in maintaining gut mucosal integrity, which should be part of any successful strategy to prevent/treatPAinfections and associated gut-derived sepsis in critical illness settings. NAMs provide for the development of crucial preventive/therapeutic monotherapy options against untreatable MDRPAinfections.
Receptor-like kinases FER and SRK mediate Lotus japonicus freezing tolerance and climate adaptation
Authors: Mustamin Yusdar , Akyol Turgut Yigit , Gordon Max , Manggabarani Andi Madihah , Isomura Yoshiko , Kawamura Yasuko , Bamba Masaru , Williams Cranos , Andersen Stig Uggerhøj , Sato Shusei 
Published: April 2022

ABSTRACTMany plant species have succeeded in colonizing a wide range of diverse climates through local adaptation, but the underlying molecular genetics remain obscure. We previously found that winter survival was a direct target of selection during colonization of Japan by the perennial legume Lotus japonicus and identified associated candidate genes. Here, we show that two of these, the FERONIA-receptor like kinase (LjFER) and a novel S-receptor-like kinase (LjSRK) are required for non-acclimated freezing tolerance and show haplotype-dependent cold-responsive expression. Our work demonstrates that recruiting a conserved growth regulator, FER, and a novel receptor-like kinase, SRK, into the set of cold-responsive genes has contributed to freezing tolerance and local climate adaptation in L. japonicus, offering new functional genetic insight into perennial herb evolution.
miRNA408 and its encoded peptide, miPEP408, regulate arsenic stress response in Arabidopsis
Authors: Kumar Ravi Shankar , Sinha Hiteshwari , Datta Tapasya , Asif Mehar Hasan , Trivedi Prabodh Kumar 
Published: April 2022

ABSTRACTMicroRNAs (miRNAs) are small non-coding RNAs that play a central role in regulating various developmental and biological processes. The expression of miRNAs is differentially modulated in response to various stresses. Based on the recent findings, it has been shown that some of the pri-miRNAs encode small regulatory peptides, microRNA-encoded peptides (miPEP). miPEPs are reported to regulate the growth and development of plants by modulating corresponding miRNA expression; however, the role of these peptides in different stresses has not been explored yet. Here, we reported that pri-miR408 encodes a small peptide, miPEP408, that regulates the expression of miR408, its targets, and associated phenotype in Arabidopsis. Plants overexpressing miR408 showed severe sensitivity under low sulphur (LS), Arsenite As(III) and LS+As(III) stress, while miR408 mutant developed through the CRISPR/Cas9 approach showed tolerance. Transgenic lines showed phenotypic alteration and modulation in the expression of genes involved in the sulphur reduction pathway and affect sulphate and glutathione accumulation. Similar to miR408 overexpressing lines, the exogenous application of synthetic miPEP408 or miPEP408 overexpression led to sensitivity in plants under LS, As(III) and combined LS+As(III) stress compared to control. This study suggests the involvement of miR408 and miPEP408 in heavy metal and nutrient deficiency responses.One-sentence summarymiR408 and peptide encoded by miR408, miPEP408, regulate arsenic stress and low sulphur responses in Arabidopsis.
The localization of PHRAGMOPLAST ORIENTING KINESIN1 at the division site depends on two microtubule binding proteins TANGLED1 and AUXIN-INDUCED-IN-ROOT-CULTURES9 in Arabidopsis
Authors: Mills Alison M. , Morris Victoria H. , Rasmussen Carolyn G 
Published: April 2022

AbstractProper plant growth and development requires spatial coordination of cell divisions. Two unrelated microtubule-binding proteins, TANGLED1 (TAN1) and AUXIN-INDUCED-IN-ROOT-CULTURES9 (AIR9), are together required for normal growth and division-plane orientation in Arabidopsis. tan1 air9 double mutants have synthetic growth and division-plane orientation defects while single mutants lack obvious defects. Here we show that the division-site localized protein, PHRAGMOPLAST-ORIENTING-KINESIN1 (POK1), was aberrantly lost from the division site during metaphase and telophase in tan1 air9 mutants. Since TAN1 and POK1 interact via the first 132 amino acids of TAN1 (TAN11-132), we assessed its localization and function in the tan1 air9 double mutant. TAN11-132 rescued tan1 air9 mutant phenotypes and localized to the division site in telophase. However, replacing six amino-acid residues within TAN11-132 that disrupts POK1-TAN1 interaction in the yeast-two-hybrid system caused loss of both rescue and division-site localization of TAN11-132 in tan1 air9 mutants. Full-length TAN1 with the same alanine substitutions had defects in phragmoplast guidance and reduced TAN1 and POK1 localization at the division site but rescued most tan1 air9 mutant phenotypes. Together, these data suggest that TAN1 and AIR9 are required for POK1 localization, and yet unknown proteins may stabilize TAN1-POK1 interactions.One sentence summarySpecific amino acids within TAN1 are required for its correct localization and function partially through interaction with POK1; both TAN1 and AIR9 mediate POK1 division site localization.
A toolbox for systematic discovery of stable and transient protein interactors in baker’s yeast
Authors: Fenech Emma J. , Cohen Nir , Kupervaser Meital , Gazi Zohar , Schuldiner Maya 
Published: April 2022

AbstractIdentification of both stable and transient interactions is essential for understanding protein function and regulation. While assessing stable interactions is more straightforward, capturing transient ones is challenging. In recent years, sophisticated tools have emerged to improve transient interactor discovery, with many harnessing the power of evolved biotin ligases for proximity labelling. However, biotinylation-based methods have lagged behind in the model eukaryote, Saccharomyces cerevisiae, possibly due to the presence of several abundant, endogenously biotinylated proteins. In this study, we optimised robust biotin- ligation methodologies in yeast and increased their sensitivity by creating a bespoke technique for downregulating endogenous biotinylation which we term ABOLISH (Auxin- induced BiOtin LIgase diminiSHing). We used the endoplasmic reticulum insertase complex (EMC) to demonstrate our approaches and uncover new substrates. To make these tools available for systematic probing of both stable and transient interactions, we generated five full-genome collections of strains in which every yeast protein is tagged with each of the tested biotinylation machineries; some on the background of the ABOLISH system. This comprehensive toolkit enables functional interactomics of the entire yeast proteome.
Two types of human TCR differentially regulate reactivity to self and non-self antigens
Authors: Trofimov Assya , Brouillard Philippe , Larouche Jean-David , Séguin Jonathan , Laverdure Jean-Philippe , Brasey Ann , Ehx Gregory , Roy Denis-Claude , Busque Lambert , Lachance Silvy , Lemieux Sébastien , Perreault Claude 
Published: April 2022

SUMMARYBased on analyses of TCR sequences from over 1,000 individuals, we report that the TCR repertoire is composed of two ontogenically and functionally distinct types of TCRs. Their production is regulated by variations in thymic output and terminal deoxynucleotidyl transferase (TDT) activity. Neonatal TCRs derived from TDT-negative progenitors persist throughout life, are highly shared among subjects, and are polyreactive to self and microbial antigens. Thus, >50% of cord blood TCRs are responsive to SARS-CoV2 and other common pathogens. TDT- dependent TCRs present distinct structural features and are less shared among subjects. TDT- dependent TCRs are produced in maximal numbers during infancy when thymic output and TDT activity reach a summit, are more abundant in subjects with AIRE mutations, and seem to play a dominant role in graft-versus-host disease. Factors decreasing thymic output (age, male sex) negatively impact TCR diversity. Males compensate for their lower repertoire diversity via hyperexpansion of selected TCR clonotypes.
Ligand Binding Prediction using Protein Structure Graphs and Residual Graph Attention Networks
Authors: Pandey Mohit , Radaeva Mariia , Mslati Hazem , Garland Olivia , Fernandez Michael , Ester Martin , Cherkasov Artem 
Published: April 2022

AbstractMotivationComputational prediction of ligand-target interactions is a crucial part of modern drug discovery as it helps to bypass high costs and labor demands of in vitro and in vivo screening. As the wealth of bioactivity data accumulates, it provides opportunities for the development of deep learning (DL) models with increasing predictive powers. Conventionally, such models were either limited to the use of very simplified representations of proteins or ineffective voxelization of their 3D structures. Herein, we present the development of the PSG-BAR (Protein Structure Graph –Binding Affinity Regression) approach that utilizes 3D structural information of the proteins along with 2D graph representations of ligands. The method also introduces attention scores to selectively weight protein regions that are most important for ligand binding.ResultsThe developed approach demonstrates the state-of-the-art performance on several binding affinity benchmarking datasets. The attention-based pooling of protein graphs enables identification of surface residues as critical residues for protein-ligand binding. Finally, we validate our model predictions against an experimental assay on a viral main protease (Mpro)– the hallmark target of SARS-CoV-2 coronavirus.AvailabilityThe code for PSG-BAR is made available athttps://github.com/diamondspark/PSG-BARContactacherkasov@prostatecentre.com
Integrated Genomics Approaches Identify Transcriptional Mediators and Epigenetic Responses to Afghan Desert Particulate Matter in Small Airway Epithelial Cells
Authors: Gupta Arnav , Sasse Sarah K. , Berman Reena , Gruca Margaret A. , Dowell Robin D. , Chu Hong Wei , Downey Gregory P. , Gerber Anthony N. 
Published: April 2022

AbstractMilitary Deployment to Southwest Asia and Afghanistan and exposure to toxic airborne particulates has been associated with an increased risk of developing respiratory disease, collectively termed deployment-related respiratory diseases (DRRD). Our knowledge about how particulates mediate respiratory disease is limited, precluding the appropriate recognition or management. Central to this limitation is the lack of understanding of how exposures translate into dysregulated cell identity with dysregulated transcriptional programs. The small airway epithelium is involved in both the pathobiology of DRRD and fine particulate matter deposition. To characterize small airway epithelial cell epigenetic and transcriptional responses to Afghan desert particulate matter (APM) and investigate the functional interactions of transcription factors that mediate these responses, we applied two genomics assays, the assay for transposase accessible chromatin with sequencing (ATAC-seq) and Precision Run-on sequencing (PRO-seq). We identified activity changes in a series of transcriptional pathways as candidate regulators of susceptibility to subsequent insults, including signal-dependent pathways, such as loss of cytochrome P450 or P53/P63, and lineage-determining transcription factors, such as GRHL2 loss or TEAD3 activation. We further demonstrated that TEAD3 activation was unique to APM exposure despite similar inflammatory responses when compared with wood smoke particle exposure and that P53/P63 program loss was uniquely positioned at the intersection of signal-dependent and lineage-determining transcriptional programs. Our results establish the utility of an integrated genomics approach in characterizing responses to exposures and identify genomic targets for the advanced investigation of the pathogenesis of DRRD.
Humanization and Expression of IgG and IgM Antibodies in Plants as Potential Diagnostic Reagents for Valley Fever
Authors: Jugler Collin , Grill Francisca J. , Grys Thomas E. , Lake Douglas F. , Chen Qiang 
Published: April 2022

AbstractMonoclonal antibodies (mAbs) are important proteins used in many life science applications, from diagnostics to therapeutics. High demand for mAbs for different applications urges the development of rapid and reliable recombinant production platforms. Plants provide a quick and inexpensive system for producing recombinant mAbs. Moreover, when paired with an established platform for mAb discovery, plants can easily be tailored to produce mAbs of different isotypes against the same target. Here, we demonstrate that a hybridoma-generated mouse mAb against chitinase 1 (CTS1), an antigen fromCoccidioidesspp., can be biologically engineered for use with serologic diagnostic test kits for coccidioidomycosis (Valley Fever) using plant expression. The original mouse IgG was modified and recombinantly produced in plants as IgG and IgM isotypes with human kappa, gamma, and mu constant regions. The two mAb isotypes produced in plants were shown to maintain target antigen recognition to CTS1 using similar reagents as the Food and Drug Administration (FDA)-approved Valley Fever diagnostic kits. As none of the currently approved kits provide antibody dilution controls, humanization of antibodies that bind to CTS1, a major component of the diagnostic antigen preparation, may provide a solution to the lack of consistently reactive antibody controls for Valley Fever diagnosis. Furthermore, our work provides a foundation for reproducible and consistent production of recombinant mAbs engineered to have a specific isotype for use in diagnostic assays.
Conserved FimK truncation coincides with increased expression of type 3 fimbriae and cultured bladder epithelial cell association in Klebsiella quasipneumoniae
Authors: Venkitapathi Sundharamani , Wijesundara Yalini H. , Herbert Fabian C. , Gassensmith Jeremiah J. , Zimmern Philippe E. , De Nisco Nicole J. 
Published: April 2022

AbstractKlebsiella spp. commonly cause both uncomplicated urinary tract infection (UTI) and recurrent UTI (rUTI). Klebsiella quasipneumoniae, a relatively newly defined species of Klebsiella, has been shown to be metabolically distinct from Klebsiella pneumoniae, but its urovirulence mechanisms have not been defined. K. pneumoniae uses both type 1 and type 3 fimbriae to attach to host epithelial cells. The type 1 fimbrial operon is well-conserved between Escherichia coli and K. pneumoniae with the exception of fimK, which is unique to Klebsiella spp. FimK contains an N-terminal DNA binding domain and a C-terminal phosphodiesterase (PDE) domain that has been hypothesized to cross-regulate type 3 fimbriae expression via modulation of cellular levels of cyclic di-GMP. Here, we find that a conserved premature stop codon in K. quasipneumoniae fimK results in truncation of the C-terminal PDE domain and that the bladder epithelial cell association and invasion of uropathogenic K. quasipneumoniae strain KqPF9 is dependent on type 3 but not type 1 fimbriae. Further, we show that basal expression of both type 1 and type 3 fimbrial operons as well as bladder epithelial cell association is elevated in KqPF9 relative to uropathogenic K. pneumoniae TOP52 and that complementation of KqPF9ΔfimK with the TOP52 fimK allele reduced type 3 fimbrial expression and bladder epithelial cell attachment. Taken together these data suggest that the C-terminal PDE of FimK can modulate type 3 fimbrial expression in K. pneumoniae and its absence in K. quasipneumoniae may lead to a loss of type 3 fimbrial cross-regulation.ImportanceK. quasipneumoniae is often indicated as the cause of many opportunistic infections including urinary tract infection (UTI), which affects >50% of women worldwide. However, virulence mechanisms of K. quasipneumoniae remain uninvestigated. Prior to this work, K. quasipneumoniae and K. pneumoniae had only been distinguished phenotypically by metabolic differences. This work contributes to the understanding of K. quasipneumoniae virulence phenotypes by evaluating the contribution of type 1 and type 3 fimbriae, which are critical colonization factors encoded by all Klebsiella spp., to K. quasipneumoniae bladder epithelial cell attachment. We identify clear phenotypic differences in both bladder epithelial cell attachment between uropathogenic K. pneumoniae and K. quasipneumoniae. Importantly, we find that a structural difference in the fimbrial regulatory gene fimK may contribute to differential co-regulation of type 1 and type 3 fimbriae between the two Klebsiella species.