Genome-scale CRISPR/Cas9 screening reveals the role of in colibactin-mediated cell cycle arrest.

Unlabelled: Colibactin is a genotoxic secondary metabolite produced by certain strains that populate the intestine and produces a specific mutational signature in human colonocytes. However, the host pathways involved in colibactin response remain unclear. To address this gap, we performed genome-wide CRISPR/Cas9 knockout screens and RNA sequencing utilizing live bacteria and a synthetic colibactin analog.

Potential of right ventricular function assessment with echocardiography in transcatheter aortic valve replacement.

Background: Right ventricular (RV) function assessment by echocardiography can be challenging due to its complex morphology. Also, increasing use of sedation rather than general anesthesia for transfemoral approach transcatheter aortic valve replacement (TAVR) reduces the need for intraoperative transesophageal echocardiography (TEE). Recent clinical studies have demonstrated the importance of 3-dimensional (3D) echocardiography and a longitudinal strain for RV function assessment.

The Microbiome Landscape of Adenomyosis: A Systematic Review.

Alterations in the microbiome composition have been identified in common gynecologic pathologies such as endometriosis carving a new frontier in diagnosis and treatment. We aimed to examine the existing literature on perturbations in the reproductive tract microbiome of individuals with adenomyosis informing future therapeutic targets. To examine the association between the reproductive tract microbiome composition among individuals with adenomyosis when compared to controls that can lead to new research evaluating novel mechanisms of action and treatment modalities.

Rethinking the Role of Teams and Training in Geopolitical Forecasting: The Effect of Uncontrolled Method Variance on Statistical Conclusions.

Using data from a geopolitical forecasting tournament, Mellers et al. (2014) [Psychological strategies for winning a geopolitical forecasting tournament. , 1106-1115] concluded that forecasting ability was improved by allowing participants to work in teams and providing them with probability training.

Metagenomic, metabolomic, and lipidomic shifts associated with fecal microbiota transplantation for recurrent infection.

Recurrent infection (rCDI) is an urgent public health threat, for which the last resort and lifesaving treatment is a fecal microbiota transplant (FMT). However, the exact mechanisms that mediate a successful FMT are not well-understood. Here, we use longitudinal stool samples collected from patients undergoing FMT to evaluate intra-individual changes in the microbiome, metabolome, and lipidome after successful FMTs relative to their baselines pre-FMT.

A memory-theoretic account of citation propagation.

Despite the common assumption that citations are indicative of an article's scientific merit, increasing evidence indicates that citation counts are largely driven by variables unrelated to quality. In this article, we treat people's decisions of what to cite as an instance of memory retrieval and show that observed citation patterns are well accounted for by a model of memory. The proposed exposure model anticipates that small alterations in factors that affect people's ability to retrieve to-be-cited articles from memory early in their life cycle are magnified over time and can lead to the emergence of highly cited papers.

Catalyzing communities of research rigour champions.

The biomedical sciences must maintain and enhance a research culture that prioritizes rigour and transparency. The US National Institute of Neurological Disorders and Stroke convened a workshop entitled 'Catalyzing Communities of Research Rigor Champions' that brought together a diverse group of leaders in promoting research rigour and transparency (identified as 'rigour champions') to discuss strategies, barriers and resources for catalyzing technical, cultural and educational changes in the biomedical sciences. This article summarizes 2 days of panels and discussions and provides an overview of critical barriers to research rigour, perspectives behind reform initiatives and considerations for stakeholders across science.

Glucagon-Like Peptide-1 Receptor Agonists Do Not Increase Aspiration During Upper Endoscopy in Patients With Diabetes.

Background & Aims: Glucagon-like peptide-1-receptor agonists (GLP1-RAs) have been associated with greater retention of gastric contents, however, there is minimal controlled, population-based data evaluating the potential adverse effects of GLP1-RA in the periprocedural setting. We aimed to determine if there is increased risk of aspiration and aspiration-related complications after upper endoscopy in patients using GLP1-RAs.

Methods: We used a nationwide commercial administrative claims database to conduct a retrospective cohort study of patients aged 18 to 64 with type 2 diabetes who underwent outpatient upper endoscopy from 2005 to 2021.

Offline Two-Dimensional Liquid Chromatography-Mass Spectrometry for Deep Annotation of the Fecal Metabolome Following Fecal Microbiota Transplantation.

Biological interpretation of untargeted LC-MS-based metabolomics data depends on accurate compound identification, but current techniques fall short of identifying most features that can be detected. The human fecal metabolome is complex, variable, incompletely annotated, and serves as an ideal matrix to evaluate novel compound identification methods. We devised an experimental strategy for compound annotation using multidimensional chromatography and semiautomated feature alignment and applied these methods to study the fecal metabolome in the context of fecal microbiota transplantation (FMT) for recurrent infection.

Delays in Colorectal Cancer Screening for Latino Patients: The Role of Immigrant Healthcare in Stemming the Rising Global Incidence of Colorectal Cancer.

The significant global burden of colorectal cancer accentuates disparities in access to preventive healthcare in most low- and middle-income countries (LMICs) as well as large sections of underserved populations within high-income countries. The barriers to colorectal cancer screening in economically transitioning Latin America are multiple. At the same time, immigration from these countries to the USA continues to increase.

Metagenomic, metabolomic, and lipidomic shifts associated with fecal microbiota transplantation for recurrent infection.

Recurrent infection (rCDI) is an urgent public health threat for which the last resort and lifesaving treatment is a fecal microbiota transplant (FMT). However, the exact mechanisms which mediate a successful FMT are not well understood. Here we use longitudinal stool samples collected from patients undergoing FMT to evaluate changes in the microbiome, metabolome, and lipidome after successful FMTs.

Colorectal Cancer Screening Programs in Latin America: A Systematic Review and Meta-Analysis.

Importance: Colorectal cancer (CRC) is a leading cause of cancer-related mortality globally, with increasing incidence and mortality in Latin America. CRC screening programs can reduce disease burden, but information on screening programs in Latin America is limited.

Objective: To describe characteristics (eg, type of program, uptake, neoplastic yield) of CRC screening programs in Latin America.

Using Multidimensional Separations to Distinguish Isomeric Amino Acid-Bile Acid Conjugates and Assess Their Presence and Perturbations in Model Systems.

Bile acids play key roles in nutrient uptake, inflammation, signaling, and microbiome composition. While previous bile acid analyses have primarily focused on profiling 5 canonical primary and secondary bile acids and their glycine and taurine amino acid-bile acid (AA-BA) conjugates, recent studies suggest that many other microbial conjugated bile acids (or MCBAs) exist. MCBAs are produced by the gut microbiota and serve as biomarkers, providing information about early disease onset and gut health.

Theoretical design of a space bioprocessing system to produce recombinant proteins.

Space-based biomanufacturing has the potential to improve the sustainability of deep space exploration. To advance biomanufacturing, bioprocessing systems need to be developed for space applications. Here, commercial technologies were assessed to design space bioprocessing systems to supply a liquid amine carbon dioxide scrubber with active carbonic anhydrase produced recombinantly.

The microbial genotoxin colibactin exacerbates mismatch repair mutations in colorectal tumors.

Certain Enterobacteriaceae strains contain a 54-kb biosynthetic gene cluster referred to as "pks" encoding the biosynthesis of a secondary metabolite, colibactin. Colibactin-producing E. coli promote colorectal cancer (CRC) in preclinical models, and in vitro induce a specific mutational signature that is also detected in human CRC genomes.

Offline Two-dimensional Liquid Chromatography-Mass Spectrometry for Deep Annotation of the Fecal Metabolome.

Compound identification is an essential task in the workflow of untargeted metabolomics since the interpretation of the data in a biological context depends on the correct assignment of chemical identities to the features it contains. Current techniques fall short of identifying all or even most observable features in untargeted metabolomics data, even after rigorous data cleaning approaches to remove degenerate features are applied. Hence, new strategies are required to annotate the metabolome more deeply and accurately.

Intestinal bacteria and colorectal cancer: etiology and treatment.

The etiology of colorectal cancer (CRC) is influenced by bacterial communities that colonize the gastrointestinal tract. These microorganisms derive essential nutrients from indigestible dietary or host-derived compounds and activate molecular signaling pathways necessary for normal tissue and immune function. Associative and mechanistic studies have identified bacterial species whose presence may increase CRC risk, including notable examples such as , Enterotoxigenic , and pks .

Bile salt hydrolases shape the bile acid landscape and restrict Clostridioides difficile growth in the murine gut.

Bile acids (BAs) mediate the crosstalk between human and microbial cells and influence diseases including Clostridioides difficile infection (CDI). While bile salt hydrolases (BSHs) shape the BA pool by deconjugating conjugated BAs, the basis for their substrate selectivity and impact on C. difficile remain elusive.