ProPr54 web server: predicting σ promoters and regulon with a hybrid convolutional and recurrent deep neural network.

σ serves as an unconventional sigma factor with a distinct mechanism of transcription initiation, which depends on the involvement of a transcription activator. This unique sigma factor σ is indispensable for orchestrating the transcription of genes crucial to nitrogen regulation, flagella biosynthesis, motility, chemotaxis and various other essential cellular processes. Currently, no comprehensive tools are available to determine σ promoters and regulon in bacterial genomes.

Synechococsins: Lanthipeptides acting as defensive signals to disarm offensive competitors?

Synechococsins represent a diverse group of class II lanthipeptides from the prochlorosin family, produced by the marine picocyanobacterium Synechococcus. A single strain can produce multiple SyncA peptides through modification by SyncM, a bifunctional lanthipeptide synthetase. Despite the prevalence of these lanthipeptides in nature, their biological functions remain elusive, even for the most studied group, Prochlorococcus MIT9313.

Activation of the Innate Immune System in Brain-Dead Donors Can Be Reduced by Luminal Intestinal Preservation During Organ Procurement Surgery - A Porcine Model.

Organs obtained from brain dead donors can have suboptimal outcomes. Activation of the innate immune system and translocation of intestinal bacteria could be causative. Thirty two pigs were assigned to control, brain death (BD), BD + luminal intestinal polyethylene glycol (PEG), and BD + luminal intestinal University of Wisconsin solution (UW) groups.

Coronary Connector Facilitated Total Endoscopic Coronary Artery Bypass: An Ex Vivo Feasibility Study.

Objective: Totally endoscopic coronary artery bypass (TECAB) procedures pose significant challenges, motivating the development of Octocon, an automated endoscopic connector designed for coronary anastomoses in off-pump and endoscopic settings. This feasibility study aimed to assess Octocon's functionality and maneuverability in closed-chest conditions during robot-assisted TECAB simulations.

Methods: The Octocon deployment comprises a 3-step procedure.

Bismuth-based drugs sensitize Pseudomonas aeruginosa to multiple antibiotics by disrupting iron homeostasis.

Pseudomonas aeruginosa infections are difficult to treat due to rapid development of antibiotic drug resistance. The synergistic combination of already-in-use drugs is an alternative to developing new antibiotics to combat antibiotic-resistant bacteria. Here we demonstrate that bismuth-based drugs (bismuth subsalicylate, colloidal bismuth subcitrate) in combination with different classes of antibiotics (tetracyclines, macrolides, quinolones, rifamycins and so on) can eliminate multidrug-resistant P.

Cost Analysis of Robot-Assisted Versus On-Pump and Off-Pump Coronary Artery Bypass Grafting: A Single-Center Surgical and 30-Day Outcomes Comparison.

Objective: Throughout Europe, the interest in implementing robot-assisted minimally invasive direct coronary artery bypass (RA-MIDCAB) has been growing. However, concerns about additional costs have emerged concurrently. In this analysis, we aim to provide a comparison of the cumulative perioperative costs of RA-MIDCAB, on-pump coronary artery bypass grafting (CABG), and off-pump CABG (OPCAB).

Automated tools for identifying the causes of anaemia in general practices are particularly advantageous for patients who do not fit the typical profile.

Background: The Dutch guideline algorithm for the analysis of anaemia in patients of general practitioners (GPs) was programmed in a Clinical Decision Support system (CDS-anaemia) to support the process of diagnosing the cause of anaemia in the laboratory. This research aims to assess the supplementary benefit provided by the automated algorithm in various demographic categories, including different sexes, age groups and severities of anaemia, in comparison to the manual diagnostic approach employed by GPs.

Methods: This was a retrospective cohort study of 5399 primary care patients where the cause of anaemia was diagnosed by GPs with or without the aid of CDS-anaemia within the age groups 18-44, 45-64, 65-79 and 80 and older.

A systematic comparison of natural product potential, with an emphasis on RiPPs, by mining of bacteria of three large ecosystems.

The implementation of several global microbiome studies has yielded extensive insights into the biosynthetic potential of natural microbial communities. However, studies on the distribution of several classes of ribosomally synthesized and post-translationally modified peptides (RiPPs), non-ribosomal peptides (NRPs) and polyketides (PKs) in different large microbial ecosystems have been very limited. Here, we collected a large set of metagenome-assembled bacterial genomes from marine, freshwater and terrestrial ecosystems to investigate the biosynthetic potential of these bacteria.

Food safety and biological control; genomic insights and antimicrobial potential of Bacillus velezensis FB2 against agricultural fungal pathogens.

Development of natural, broad-spectrum, and eco-friendly bio-fungicides is of high interest in the agriculture and food industries. In this context, Bacillus genus has shown great potential for producing a wide range of antimicrobial metabolites against various pathogens. A Bacillus velezensis strain FB2 was isolated from an agricultural field of National Institute for Biotechnology and Genetic Engineering (NIBGE) Faisalabad, Pakistan, exhibiting good antifungal properties.

A Nationwide Study of Clinical Outcomes After Robot-Assisted Coronary Artery Bypass Surgery and Hybrid Revascularization in the Netherlands.

Objective: Robot-assisted minimally invasive direct coronary artery bypass (RA-MIDCAB) surgery and hybrid coronary revascularization (HCR) are minimally invasive alternative strategies to conventional coronary artery bypass surgery in patients with isolated left anterior descending (LAD) stenosis or multivessel coronary disease. We analyzed a large, multicenter data-set based on the Netherlands Heart Registration including all patients undergoing RA-MIDCAB.

Methods: We included 440 consecutive patients who underwent RA-MIDCAB with the left internal thoracic artery to LAD between January 2016 and December 2020.

The effectiveness of an automated algorithm as a tool for investigating the cause of anaemia in undiagnosed patients from general practitioners.

Background: The Dutch guideline algorithm for the analysis of anaemia in patients of general practitioners (GPs) was programmed in a Clinical Decision Support system (CDS-anaemia) to support the process of diagnosing the cause of anaemia in the laboratory. This study investigates the diagnostic yield of the automated anaemia algorithm compared to that of the manual work up by the GP.

Methods: This retrospective population-based study consisted of 2697 people ≥18 years.

Staphylococcus aureus populations from the gut and the blood are not distinguished by virulence traits-a critical role of host barrier integrity.

Background: The opportunistic pathogen Staphylococcus aureus is an asymptomatically carried member of the microbiome of about one third of the human population at any given point in time. Body sites known to harbor S. aureus are the skin, nasopharynx, and gut.

Differential Virulence of Aggregatibacter actinomycetemcomitans Serotypes Explained by Exoproteome Heterogeneity.

Aggregatibacter actinomycetemcomitans () is a Gram-negative bacterial pathogen associated with periodontitis and nonoral diseases like rheumatoid arthritis and Alzheimer´s disease. isolates with the serotypes a, b, and c are globally most prevalent. Importantly, isolates displaying these serotypes have different clinical presentations.

Connections between Exoproteome Heterogeneity and Virulence in the Oral Pathogen Aggregatibacter actinomycetemcomitans.

Aggregatibacter actinomycetemcomitans is a Gram-negative bacterial pathogen associated with severe periodontitis and nonoral diseases. Clinical isolates of A. actinomycetemcomitans display a rough (R) colony phenotype with strong adherent properties.

FUNAGE-Pro: comprehensive web server for gene set enrichment analysis of prokaryotes.

Recent advances in the field of high throughput (meta-)transcriptomics and proteomics call for easy and rapid methods enabling to explore not only single genes or proteins but also extended biological systems. Gene set enrichment analysis is commonly used to find relations in a set of genes and helps to uncover the biological meaning in results derived from high-throughput data. The basis for gene set enrichment analysis is a solid functional classification of genes.

Minimally invasive surgery or stenting for left anterior descending artery disease - -analysis.

Minimally invasive direct coronary artery bypass (MIDCAB) surgery and percutaneous coronary intervention (PCI) are both well-established minimally invasive revascularization strategies in patients with proximal left anterior descending (LAD) lesions. We aimed to evaluate the 20-years' experience by performing a systematic review and -analysis comparing MIDCAB versus PCI in adults with proximal LAD disease. We searched MEDLINE, EMBASE and Cochrane on October 1st, 2021 for articles published in the year 2000 or later.

Human milk oligosaccharides and non-digestible carbohydrates reduce pathogen adhesion to intestinal epithelial cells by decoy effects or by attenuating bacterial virulence.

This work investigated the effects of different chemical structures of human milk oligosaccharides (hMOs) and non-digestible carbohydrates (NDCs) on pathogen adhesion by serving as decoy receptors. Pre-exposure of pathogens to inulins and low degree of methylation (DM) pectin prevented binding to gut epithelial Caco2-cells, but effects were dependent on the molecules' chemistry, pathogen strain and growth phase. Pre-exposure to 3-fucosyllactose increased E.

G-Quadruplex DNA as a Target in Pathogenic Bacteria: Efficacy of an Extended Naphthalene Diimide Ligand and Its Mode of Action.

Guanidine DNA quadruplex (G4-DNA) structures convey a distinctive layer of epigenetic information that is critical for regulating key biological activities and processes as transcription, replication, and repair in living cells. The information regarding their role and use as therapeutic drug targets in bacteria is still scarce. Here, we tested the biological activity of a G4-DNA ligand library, based on the naphthalene diimide (NDI) pharmacophore, against both Gram-positive and Gram-negative bacteria.

Identification, Isolation, and Characterization of Medipeptins, Antimicrobial Peptides From EDOX.

The plant microbiome is a vastly underutilized resource for identifying new genes and bioactive compounds. Here, we used sp. EDOX, isolated from the leaf endosphere of a tomato plant grown on a small farm in the Netherlands.

Elucidating the mechanism by which synthetic helper peptides sensitize Pseudomonas aeruginosa to multiple antibiotics.

The emergence and rapid spread of multi-drug resistant (MDR) bacteria pose a serious threat to the global healthcare. There is an urgent need for new antibacterial substances or new treatment strategies to deal with the infections by MDR bacterial pathogens, especially the Gram-negative pathogens. In this study, we show that a number of synthetic cationic peptides display strong synergistic antimicrobial effects with multiple antibiotics against the Gram-negative pathogen Pseudomonas aeruginosa.

Draft Genome Sequences of a Bacillus subtilis Strain, a Bacillus velezensis Strain, a Strain, and an Acinetobacter baumannii Strain, All Isolated from the Phyllosphere of Lactuca sativa or Solanum lycopersicum.

Four strains isolated from tomato and lettuce phyllosphere were sequenced in order to investigate the presence of novel antimicrobial gene clusters and to get a better understanding of plant microbe interactions. These strains comprise two strains, one strain, and one strain.

Transcriptomic analysis of stress response to novel antimicrobial coatings in a clinical MRSA strain.

Multi-drug resistant pathogens such as methicillin-resistant Staphylococcus aureus (MRSA) cause nosocomial infections that can have deleterious effects on human health. Thus, it is imperative to find solutions to treat these detrimental infections as well as to control their spread. We tested the effect of two different antimicrobial materials, functionalised graphene oxide (GOX), and AGXX® coated on cellulose fibres, on the growth and transcriptome of the clinical MRSA strain S.

Exoproteomic profiling uncovers critical determinants for virulence of livestock-associated and human-originated ST398 strains.

Staphylococcus aureus: with the sequence type (ST) 398 was previously associated with livestock carriage. However, in recent years livestock-independent ST398 has emerged, representing a potential health risk for humans especially in nosocomial settings. Judged by whole-genome sequencing analyses, the livestock- and human originated strains belong to two different ST398 clades but, to date, it was not known to what extent these clades differ in terms of actual virulence.