bluuebunny/crossref_metadata_2025_split huggingface dataset:
The predicted acetoin dehydrogenase pathway represses sporulation ofClostridioides difficile
Authors: Wetzel Daniela , Rizvi Arshad , Edwards Adrianne N. , McBride Shonna M. 
Published: July 2023

ABSTRACTClostridioides difficileis a major gastrointestinal pathogen that is transmitted as a dormant spore. As an intestinal pathogen,C. difficilemust contend with variable environmental conditions, including fluctuations in pH and nutrient availability. Nutrition and pH both influence growth and spore formation, but how pH and nutrition jointly influence sporulation are not known. In this study, we investigated the dual impact of pH and pH-dependent metabolism onC. difficilesporulation. Specifically, we examined the impacts of pH and the metabolite acetoin onC. difficilegrowth and sporulation. We found that expression of the predicted acetoin dehydrogenase operon,acoRABCL, was pH-dependent and regulated by acetoin. Regulation of theC. difficile acolocus is distinct from other characterized systems and appears to involve a co-transcribed DeoR-family regulator rather than the sigma54-dependent activator. In addition, anacoAnull mutant produced significantly more spores and initiated sporulation earlier than the parent strain. However, unlike other Firmicutes, growth and culture density ofC. difficilewas not increased by acetoin availability or disruption of theacopathway. Together, these results indicate that acetoin, pH, and theacopathway play important roles in nutritional repression of sporulation inC. difficile, but acetoin metabolism does not support cell growth as a stationary phase energy source.IMPORTANCEClostridioides difficile,orC. diff, is an anaerobic bacterium that lives within the gut of many mammals and causes infectious diarrhea.C. difficileis able to survive outside of the gut and transmit to new hosts by forming dormant spores. It is known that the pH of the intestine and the nutrients available both affect the growth and sporulation ofC. diffiicile,but the specific conditions that result in sporulation in the host are not clear. In this study, we investigated how pH and the metabolite acetoin affect the ability ofC. difficileto grow, proliferate, and form spores. We found that a mutant lacking the predicted acetoin metabolism pathway form more spores, but their growth is not impacted. These results show thatC. difficileuses acetoin differently than many other species and that acetoin has an important role as an environmental metabolite that influences spore formation.
A Non-Coding Variant inSLC15A4Modulates Enhancer Activity and Lysosomal Deacidification Linked to Lupus Susceptibility
Authors: Singh Manish Kumar , Maiti Guru Prashad , Reddy-Rallabandi HariKrishna , Fazel-Najafabadi Mehdi , Looger Loren L. , Nath Swapan K. 
Published: July 2023

AbstractSystemic lupus erythematosus (SLE) is a complex autoimmune disease with a strong genetic basis. Despite the identification of several single nucleotide polymorphisms (SNPs) near theSLC15A4gene that are significantly associated with SLE across multiple populations, specific causal SNP(s) and molecular mechanisms responsible for disease susceptibility are unknown. To address this gap, we employed bioinformatics, expression quantitative trait loci (eQTLs), and 3D chromatin interaction analysis to nominate a likely functional variant, rs35907548, in an active intronic enhancer ofSLC15A4. Through luciferase reporter assays followed by chromatin immunoprecipitation (ChIP)-qPCR, we observed significant allele-specific enhancer effects of rs35907548 in diverse cell lines. The rs35907548 risk allele T is associated with increased regulatory activity and target gene expression, as shown by eQTLs and chromosome conformation capture (3C)-qPCR. The latter revealed long-range chromatin interactions between the rs35907548 enhancer and the promoters ofSLC15A4, GLTLD1, and an uncharacterized lncRNA. The enhancer-promoter interactions and expression effects were validated by CRISPR/Cas9 knock-out (KO) of the locus in HL60 promyeloblast cells. KO cells also displayed dramatically dysregulated endolysosomal pH regulation. Together, our data show that the rs35907548 risk allele affects multiple aspects of cellular physiology and may directly contribute to SLE.
Unraveling cell differentiation mechanisms through topological exploration of single-cell developmental trajectories
Authors: Flores-Bautista Emanuel , Thomson Matt 
Published: July 2023

AbstractUnderstanding the circuits that control cell differentiation is a fundamental problem in developmental biology. Single-cell RNA sequencing has emerged as a powerful tool for investigating this problem. However, the reconstruction of developmental trajectories is based on the assumption that cell states traverse a tree-like structure, which may bias our understanding of critical developmental mechanisms. To address this limitation, we developed a framework, TopGen, that enables identifying topological signatures of functional biological circuits as persistent homology groups in transcriptome space. First, we show that TopGen can identify genetic drivers of topological structures in simulated datasets. We then applied our approach to more than ten single-cell developmental atlases and found that topological transcriptome spaces are predominantly path-connected and only sometimes simply connected. Finally, we applied TopGen to analyze gene expression patterns in topological loops representing stem-like, transdifferentiation, and convergent cell circuits, found inC. elegans, H. vulgaris, andN. vectensis, respectively. Our results show that some essential differentiation mechanisms use non-trivial topological motifs, and that these motifs can be conserved in a cell-type–specific manner. Thus, our approach to studying the topological properties of developmental transcriptome atlases opens new possibilities for understanding cell development and differentiation.
An adaptive biomolecular condensation response is conserved across environmentally divergent species
Authors: Kik Samantha Keyport , Christopher Dana , Glauninger Hendrik , Hickernell Caitlin Wong , Bard Jared A. M. , Ford Michael , Sosnick Tobin R. , Drummond D. Allan 
Published: July 2023

AbstractCells must sense and respond to sudden maladaptive environmental changes—stresses—to survive and thrive. Across eukaryotes, stresses such as heat shock trigger conserved responses: growth arrest, a specific transcriptional response, and biomolecular condensation of protein and mRNA into structures known as stress granules under severe stress. The composition, formation mechanism, adaptive significance, and even evolutionary conservation of these condensed structures remain enigmatic. Here we provide an unprecedented view into stress-triggered condensation, its evolutionary conservation and tuning, and its integration into other well-studied aspects of the stress response. Using three morphologically near-identical budding yeast species adapted to different thermal environments and diverged by up to 100 million years, we show that proteome-scale biomolecular condensation is tuned to species-specific thermal niches, closely tracking corresponding growth and transcriptional responses. In each species, poly(A)-binding protein—a core marker of stress granules—condenses in isolation at species-specific temperatures, with conserved molecular features and conformational changes modulating condensation. From the ecological to the molecular scale, our results reveal previously unappreciated levels of evolutionary selection in the eukaryotic stress response, while establishing a rich, tractable system for further inquiry.
Reliable protein-protein docking with AlphaFold, Rosetta, and replica-exchange
Authors: Harmalkar Ameya , Lyskov Sergey , Gray Jeffrey J. 
Published: July 2023

AbstractDespite the recent breakthrough of AlphaFold (AF) in the field of protein sequence-to-structure prediction, modeling protein interfaces and predicting protein complex structures remains challenging, especially when there is a significant conformational change in one or both binding partners. Prior studies have demonstrated that AF-multimer (AFm) can predict accurate protein complexes in only up to 43% of cases.1In this work, we combine AlphaFold as a structural template generator with a physics-based replica exchange docking algorithm to better sample conformational changes. Using a curated collection of 254 available protein targets with both unbound and bound structures, we first demonstrate that AlphaFold confidence measures (pLDDT) can be repurposed for estimating protein flexibility and docking accuracy for multimers. We incorporate these metrics within our ReplicaDock 2.0 protocol2to complete a robust in-silico pipeline for accurate protein complex structure prediction. AlphaRED (AlphaFold-initiated Replica Exchange Docking) successfully docks failed AF predictions including 97 failure cases in Docking Benchmark Set 5.5. AlphaRED generates CAPRI acceptable-quality or better predictions for 63% of benchmark targets. Further, on a subset of antigen-antibody targets, which is challenging for AFm (20% success rate), AlphaRED demonstrates a success rate of 43%. This new strategy demonstrates the success possible by integrating deep-learning based architectures trained on evolutionary information with physics-based enhanced sampling. The pipeline is available atgithub.com/Graylab/AlphaRED.
Epigenomic Analyses Identify FOXM1 As a Key Regulator of Anti-Tumor Immune Response in Esophageal Adenocarcinoma
Authors: Ziman Benjamin , Yang Qian , Zheng Yueyuan , Sheth Megha , Nam Chehyun , Zhao Hua , Sinha Uttam K , Lin De-Chen 
Published: July 2023

AbstractUnlike most cancer types, the incidence of esophageal adenocarcinoma (EAC) has rapidly escalated in the western world over recent decades. Using whole genome bisulfite sequencing (WGBS), we identify the transcription factor (TF) FOXM1 as an important epigenetic regulator of EAC. FOXM1 plays a critical role in cellular proliferation and tumor growth in EAC patient-derived organoids and cell line models. We identify ERBB2 as an upstream regulator of the expression and transcriptional activity of FOXM1. Unexpectedly, Gene Set Enrichment Analysis (GSEA) unbiased screen reveals a prominent anti-correlation between FOXM1 and immune response pathways. Indeed, syngeneic mouse models show that FOXM1 inhibits the infiltration of CD8+T cells into the tumor microenvironment. Consistently, FOXM1 suppresses CD8+T cell chemotaxisin vitroand antigen-dependent CD8+T cell killing. This study characterizes FOXM1 as a significant EAC-promoting TF and elucidates its novel function in regulating anti-tumor immune response.
Multiplexed functional assessments ofMYH7variants in human cardiomyocytes at scale
Authors: Friedman Clayton E. , Fayer Shawn , Pendyala Sriram , Chien Wei-Ming , Tran Linda , Chao Leslie S. , McKinstry Ashley , Ahmed Dania , Loiben Alexander , Farris Stephen D. , Stempien-Otero April , Jonlin Erica , Murry Charles E. , Starita Lea M. , Fowler Douglas M. , Yang Kai-Chun 
Published: July 2023

AbstractBackgroundSingle, autosomal-dominant missense mutations inMYH7, which encodes a sarcomeric protein (MHC-β) in cardiac and skeletal myocytes, are a leading cause of hypertrophic cardiomyopathy and are clinically-actionable. However, ∼75% ofMYH7variants are of unknown significance (VUS), causing diagnostic challenges for clinicians and emotional distress for patients. Deep mutational scans (DMS) can determine variant effect at scale, but have only been utilized in easily-editable cell lines. While human induced pluripotent stem cells (hiPSCs) can be differentiated to numerous cell types that enable the interrogation of variant effect in a disease-relevant context, DMS have not been executed using diploid hiPSC derivates. However, CRaTER enrichment has recently enabled the pooled generation of a saturated five positionMYH7variant hiPSC library suitable for DMS for the first time.ResultsAs a proof-of-concept, we differentiated thisMYH7variant hiPSC library to cardiomyocytes (hiPSC-CMs) for multiplexed assessment of MHC-β variant abundance by massively parallel sequencing (VAMP-seq) and hiPSC-CM survival. We confirm MHC-β protein loss occurs in a failing human heart with a pathogenicMYH7mutation. We find the multiplexed assessment of MHC-β abundance and hiPSC-CM survival both accurately segregate all pathogenic variants from synonymous controls. Overall, functional scores of 68 amino acid substitutions across these independent assays are ∼50% consistent.ConclusionsThis study leverages hiPSC differentiation into disease-relevant cardiomyocytes to enable multiplexed assessments ofMYH7missense variants at scale for the first time. This proof-of-concept demonstrates the ability to DMS previously restricted, clinically-actionable genes to reduce the burden of VUS on patients and clinicians.
Mistletoe as a Therapeutic Option in Cancer Patients: a scoping review protocol
Authors: Cordeiro Milena Mendes , Malta Felipe Aguiar Pupo Seabra , Gonçalves Daniela Caetano 
Published: July 2023

ABSTRACTObjectiveThis scoping review aims to identify, map and provide an overview of the studies investigating the therapeutic use of Viscum Album L. (mistletoe) in cancer patients. By identifying pivotal patterns and research gaps in the existing literature on Viscum therapy, this review intends to offer valuable insights and supportive information to better inform future research efforts in this field.IntroductionCancer exerts a significant impact on global mortality, posing numerous challenges to public policies. The disease progression and the conventional treatment itself presents multifaceted health adversities to subjects. In response to these complexities, researchers have been exploring non-conventional therapeutic approaches, including phytotherapy. Mistletoe, a widely-used herbal medicine in oncology, is currently undergoing investigation for its potential adjuvant roles in both curative and palliative cancer care.Inclusion criteriaWe will consider studies that include individuals with cancer, irrespective of participant’s age or cancer type/stage, and who were subjected/exposed to interventions based on or incorporating Viscum album L. The review will consider clinical, quasi-experimental, and analytical observational studies, with no limitations on the time of intervention/exposure, treatment stage or geographic region.MethodsThis review will follow the methodological guidance of the JBI Manual for Evidence Synthesis for scoping reviews. The searches will be conducted in the following databases: MEDLINE (via PubMed), CENTRAL (via Cochrane Library), Embase (via Elsevier), Scopus, Web of Science Core Collection, CINAHL (via EBSCO), LILACS and SciELO. The search strategy will be adapted to the specificities of each of these databases, using thesaurus terms and synonyms related to the intervention (mistletoe) and the population (cancer), without restrictions on language or date of publication. The search for unpublished studies will be done in Google Scholar, preprint servers (medRxiv and bioRxiv) and trial registry platforms (Clinical Trials and International Clinical Trials Registry Platform), along grey literature in OpenGrey. Initially, eligibility criteria will be screened by two independent reviewers, assessing article titles and abstracts. Following finishing the full reading and inclusion determination, data extraction will be carried out by two independent reviewers. The results will be presented in narrative form and through tables and graphs.
A Scoping Review of Interventions to De-implement Potentially Harmful Nonsteroidal Anti-inflammatory Drugs (NSAIDs) in Healthcare Settings
Authors: Rockwell Michelle S. , Oyese Emma G. , Singh Eshika , Vinson Matthew , Yim Isaiah , Turner Jamie K. , Epling John W. 
Published: July 2023

ABSTRACTObjectivesPotentially harmful nonsteroidal anti-inflammatory drugs (NSAIDs) utilization persists at undesirable rates throughout the world. The purpose of this paper is to review the literature on interventions to de-implement potentially harmful NSAIDs in healthcare settings and to suggest directions for future research.DesignScoping reviewData SourcesPubMed, CINAHL, Embase, Cochrane Central, and Google Scholar (2000-2022)Study SelectionStudies reporting on the effectiveness of interventions to systematically reduce potentially harmful NSAID utilization in healthcare settings.Data ExtractionUsing Covidence systematic review software, we extracted study and intervention characteristics, including the effectiveness of interventions in reducing NSAID utilization.ResultsFrom 7,818 articles initially identified, 68 were included in the review. Most studies took place in European countries (45.6%) or the U.S. (35.3%), with randomized controlled trial as the most common design (55.9%). The majority of studies (76.2%) reported a reduction in the utilization of potentially harmful NSAIDs. Interventions were largely clinician-facing (76.2%) and delivered in primary care (60.2%). Academic detailing, clinical decision support or electronic medical record interventions, performance reports, and pharmacist review were frequent approaches employed. NSAID use was most commonly classified as potentially harmful based on patients’ age (55.8%) or history of gastrointestinal disorders (47.1%) or kidney disease (38.2%). Only 7.4% of interventions focused on over-the-counter NSAIDs in addition to prescription. Few studies (5.9%) evaluated pain or quality of life following NSAIDs discontinuation.ConclusionMany varied interventions are effective in de-implementing potentially harmful NSAIDs in healthcare settings. Efforts to adapt, scale, and disseminate these interventions are needed. In addition, future interventions should address over-the-counter NSAIDs, which are broadly available and widely used. Evaluating unintended consequences of interventions, including patient-focused outcomes, is another important priority.What is already known on this topic–NSAIDs are overutilized by high-risk patients at persistent rates. Interventions to reduce potentially harmful NSAIDs prescribing and over-the-counter (OTC) NSAIDs use are needed.What this study adds–More than 50 studies published internationally from 2000 to 2022 (three quarters of those reviewed) reported on interventions effective in de-implementing potentially harmful NSAIDs. We extracted and summarized characteristics of studies and of interventions to identify research gaps and priorities for future research.How this study might affect research, practice or policy–In light of the large number of effective interventions on record, implementation and dissemination efforts should be the priority of future work.
Adjunctive Vasopressors in Patients with Septic Shock: Protocol for a Systematic Review and Meta-Analysis
Authors: Bauer Seth R. , Wieruszewski Patrick M. , Bissell Brittany D. , Dugar Siddharth , Sacha Gretchen L. , Sato Ryota , Siuba Matthew T. , Schleicher Mary , Vachharajani Vidula , Falck-Ytter Yngve , Morgan Rebecca L. 
Published: July 2023

AbstractBackgroundOver one-third of patients with septic shock have adjunctive vasopressors added to first-line vasopressors. However, no randomized trial has detected improved mortality with adjunctive vasopressors. Published systematic reviews and meta-analysis have sought to inform the use of adjunctive vasopressors, yet each published review has limitations that hinder its interpretation. This review aims to overcome the limitations of previous reviews by systematically synthesizing the direct evidence for adjunctive vasopressor therapy use in adult patients with septic shock.MethodsWe will conduct a systematic review and meta-analysis of randomized controlled trials evaluating adjunctive vasopressors (vasopressin analogues, angiotensin II, hydroxocobalamin, methylene blue, and catecholamine analogues) in adult patients with septic shock. Relevant studies will be identified through comprehensive searches of MEDLINE, Embase, CENTRAL, and reference lists of previous systematic reviews. Only randomized trials comparing adjunctive vasopressors (>75% of subjects on vasopressors at enrollment) to standard care vasopressors in adults with septic shock (>75% of subjects having septic shock) will be included. Titles and abstracts will be screened, full-text articles assessed for eligibility, and data extracted from included studies. Outcomes of interest include short-term mortality, intermediate-term mortality, kidney replacement therapy, digital/peripheral ischemia, and venous thromboembolism. Pairwise meta-analysis using a random-effects model will be utilized to estimate the risk ratio for the outcomes. Risk of bias will be adjudicated with the Cochrane Risk of Bias 2 tool, and GRADE will be used to rate the certainty of the body of evidence.DiscussionAlthough adjunctive vasopressors are commonly used in patients with septic shock their effect on patient-important outcomes is unclear. This study is planned to use rigorous systematic review methodology, including strict adhere to established guidelines, in order to overcome limitations of previously-published reviews and inform clinical practice and treatment guidelines for the use of adjunctive vasopressors in adults with septic shock.Systematic review registrationPROSPERO CRD4202327984
Bacterial pathogens deliver water/solute-permeable channels as a virulence strategy
Authors: Nomura Kinya , Andreazza Felipe , Cheng Jie , Dong Ke , Zhou Pei , He Sheng Yang 
Published: July 2023

SUMMARYMany animal and plant pathogenic bacteria utilize a type III secretion system to deliver effector proteins into the host cell1,2. Elucidation of how these effector proteins function in the host cell is critical for understanding infectious diseases in animals and plants3–5. The widely conserved AvrE/DspE-family effectors play a central role in the pathogenesis of diverse phytopathogenic bacteria6. These conserved effectors are involved in the induction of “water-soaking” and host cell death that are conducive to bacterial multiplication in infected tissues. However, the exact biochemical functions of AvrE/DspE-family effectors have been recalcitrant to mechanistic understanding for three decades. Here we show that AvrE/DspE-family effectors fold into a β-barrel structure that resembles bacterial porins. Expression of AvrE and DspE inXenopusoocytes results in (i) inward and outward currents, (ii) permeability to water and (iii) osmolarity-dependent oocyte swelling and bursting. Liposome reconstitution confirmed that the DspE channel alone is sufficient to allow the passage of small molecules such as fluorescein dye. Targeted screening of chemical blockers based on the predicted pore size (15-20 Å) of the DspE channel identified polyamidoamine (PAMAM) dendrimers as inhibitors of the DspE/AvrE channels. Remarkably, PAMAMs broadly inhibit AvrE/DspE virulence activities inXenopusoocytes and duringErwinia amylovoraandPseudomonas syringaeinfections. Thus, we have unraveled the enigmatic function of a centrally important family of bacterial effectors with significant conceptual and practical implications in the study of bacterial pathogenesis.