Prophage-DB: a comprehensive database to explore diversity, distribution, and ecology of prophages.

Background: Viruses that infect prokaryotes (phages) constitute the most abundant group of biological agents, playing pivotal roles in microbial systems. They are known to impact microbial community dynamics, microbial ecology, and evolution. Efforts to document the diversity, host range, infection dynamics, and effects of bacteriophage infection on host cell metabolism are extremely underexplored.

Insights into the lemon (Citrus limon) epiphytic microbiome: impact of the biocontrol yeast Clavispora lusitaniae 146.

Background: Postharvest lemons are affected by several fungal infections, and as alternatives to chemical fungicides for combating these infections, different microbial biocontrol agents have been studied, with the Clavispora lusitaniae 146 strain standing out. Although strain 146 has proven to be an effective agent, the influence of a microbial biological control agent on the postharvest lemon microbiome has not been studied until now. Thus, this study aimed to evaluate how the epiphytic microbiome of postharvest lemons is affected by the application of the biocontrol yeast C.

Tissue-specific resistance and susceptibility to the tomato brown rugose fruit virus (ToBRFV) conferred by Solanum pennellii loci.

Background: Plant breeding research heavily relies on wild species, which harbor valuable traits for modern agriculture. This work employed a new introgression population derived from Solanum pennellii (LA5240), a wild tomato native to Peru, composed of 1,900 genotyped backcross inbred lines (BILs_BC2S6) in the tomato inbreds LEA and TOP cultivated genetic backgrounds. This Peruvian accession was found resistant to the most threatening disease of tomatoes today, caused by the tobamovirus tomato brown rugose fruit virus (ToBRFV).

Scoring of swine lung images: a comparison between a computer vision system and human evaluators.

Cranioventral pulmonary consolidation (CVPC) is a common lesion observed in the lungs of slaughtered pigs, often associated with Mycoplasma (M.) hyopneumoniae infection. There is a need to implement simple, fast, and valid CVPC scoring methods.

SARS-CoV-2 excretion and genetic evolution in nasopharyngeal and stool samples from primary immunodeficiency and immunocompetent pediatric patients.

Background: Primary Immunodeficiency disorders (PID) can increase the risk of severe COVID-19 and prolonged infection. This study investigates the duration of SARS-CoV-2 excretion and the genetic evolution of the virus in pediatric PID patients as compared to immunocompetent (IC) patients.

Materials And Methods: A total of 40 nasopharyngeal and 24 stool samples were obtained from five PID and ten IC children.

Genomic analysis and replication kinetics of the closely related EHV-1 neuropathogenic 21P40 and abortigenic 97P70 strains.

Varicellovirus equidalpha 1, formerly known as Equid alphaherpesvirus 1 (EHV-1), is highly prevalent and can lead to various problems, such as respiratory problems, abortion, neonatal foal death, and neurological disorders. The latter is known as equine herpes myeloencephalopathy (EHM). Cases of EHM have significantly increased since the beginning of the twenty-first century.

Pathogen delivery route impacts disease severity in experimental Mycoplasma ovipneumoniae infection of domestic lambs.

M. ovipneumoniae is a respiratory pathogen that can cause mild to moderate pneumonia and reduced productivity in domestic lambs. However, studies on both natural and experimental M.

Time-dependent, patient-centered perceptions of quality measures for total joint arthroplasty: a cross-sectional, choice modeling study.

Background: As value-based care arrangements continue to assess quality of care and costs, comprehensive and patient-centered definitions of quality of care are required. While patient-reported outcome measures are increasingly integrated into quality assessments following total joint arthroplasty (TJA), patient perceptions of quality paired with the phase of surgical care has not been described. The purpose of this study was to assess how TJA patients perceive measures of quality of care and assess if these perceptions change based on the phase of care.

"Sichuanvirus", a novel bacteriophage viral genus, able to lyse carbapenem-resistant Klebsiella pneumoniae.

Background: Carbapenem-resistant Klebsiella pneumoniae (CRKP) is a severe threat for human health and urgently needs new therapeutic approaches. Lytic bacteriophages (phages) are promising clinically viable therapeutic options against CRKP. We attempted to isolate lytic phages against CRKP of sequence type 11 and capsular type 64 (ST11-KL64), the predominant type in China.

Understanding the clinical and molecular epidemiological characteristics of carbapenem-resistant Acinetobacter baumannii infections within intensive care units of three teaching hospitals.

Background: Carbapenem-resistant Acinetobacter baumannii (CRAB) is recognized as a common clinical conditional pathogen with bla gene-mediated multidrug-resistance that is a significant threat to public health safety. Timely and effective infection control measures are needed to prevent their spread.

Methods: We conducted a retrospective study of CRAB patients at three teaching hospitals from 2019 to 2022.

Synergistic effects of PGPRs and fertilizer amendments on improving the yield and productivity of Canola (Brassica napus L.).

Background: Organic fertilizers are safer and more eco-friendly than chemical fertilizers; hence, organic fertilizers can be used to support sustainable farming. The effects of PGPRs are manifold in agriculture, especially in monoculture crops, where the soil needs to be modified to increase germination, yield, and disease resistance. The objective of this study was to assess the effects of PGPRs combined with fertilizer on the yield and productivity of canola.

Genetic determinants of silver nanoparticle resistance and the impact of gamma irradiation on nanoparticle stability.

Background: One of the main issues facing public health with microbial infections is antibiotic resistance. Nanoparticles (NPs) are among the best alternatives to overcome this issue. Silver nanoparticle (AgNPs) preparations are widely applied to treat multidrug-resistant pathogens.

Associations between changes in the gut microbiota and liver cirrhosis: a systematic review and meta-analysis.

Objective: Summaries of the relationships between the microbiota and liver cirrhosis and their conclusions are not consistent. This study describes microbial differences in patients with liver cirrhosis by performing a meta-analysis.

Methods: We searched PubMed, Embase, Web of Science, and the Cochrane Library and collected related articles published before March 10, 2024.

Optimization and characterization studies of poultry waste valorization for peptone production using a newly Egyptian Bacillus subtilis strain.

Valorization of poultry waste is a significant challenge addressed in this study, which aimed to produce cost-effective and sustainable peptones from poultry waste. The isolation process yielded the highly potent proteolytic B.subtilis isolate P6, identified through 16S rRNA gene sequencing to share 94% similarity with the B.

Deciphering the nature and statistical optimization of antimicrobial metabolites of two endophytic bacilli.

In this study, Allium sativum, garlic, was selected to isolate endophytic bacteria and to evaluate the antimicrobial, antiviral, antioxidant, and cytotoxic activities of their produced metabolites followed by identification of the biosynthetic gene cluster of the antimicrobial metabolites using Oxford Nanopore Technology (ONT). Two bacterial isolates, C6 and C11, were found to have a broad-spectrum antagonistic effect against four standard microbial strains and were molecularly identified using 16 S ribosomal RNA sequence analysis and deposited in a local culture collection as B. velezensis CCASU-C6, and B.

Genome Analysis of Coxsackievirus A4 Identified from Herpangina Children in Northern China.

Sporadic epidemics of coxsackievirus A4 (CVA4) have been reported worldwide. However, the lack of the whole genome sequence has restricted the study of the gene characterization and evolution of CVA4. In this study, four whole genome sequences and 17 VP1 sequences of CVA4 identified from Linyi, northern China, in summer 2024 were used for genetic characterization and phylogenetic analysis.

Malassezia polysorbatinonusus sp. nov., a Novel Isolate from a Japanese Patient with Seborrheic Dermatitis.

We describe a novel Malassezia species named Malassezia polysorbatinonusus, isolated from a Japanese patient with seborrheic dermatitis. The internal transcribed spacer (ITS) region of the isolate (LSEM 4845) were only 94.7% identical to those of M.

Laparoscopic pancreatic enucleation: how far should we go for parenchyma preservation? A study by the French National Association of Surgery.

Background: Pancreatic enucleation is indicated for selected patients and tumours with very low oncological risk to preserve a maximum of healthy pancreatic parenchyma. Minimally invasive pancreatic enucleation (MIPE) is increasingly performed. This study aims to assess the impact of tumor location and center experience on textbook outcomes (TBO) in patients undergoing MIPE.

A Dual-Color Fluorescence-Based Ratiometric Assay to Measure Endocytic Trafficking of Surface Proteins.

Many membrane proteins on the cell surface are constantly internalized from, and re-delivered to, the plasma membrane. This endocytic cycling, which relies on accurate SNARE-mediated fusion of vesicles containing cargo proteins, is highly important for the function of many proteins such as signaling receptors. While the SNARE proteins that mediate fusion during specific events, such as neurotransmitter and hormone release, in mammalian cells has been heavily studied, the SNARE proteins that mediate surface delivery of specific cargo such as the receptors for these released factors are still not known.

Molecular Dynamics Simulations of the SNARE Complex Interacting with Synaptotagmin, Complexin, and Lipid Bilayers.

Molecular dynamics (MD) simulations enable in silico investigation of the dynamic behavior of proteins and protein complexes. Here, we describe MD simulations of the SNARE bundle forming the complex with the neuronal proteins Synaptotagmin-1 (Syt1) and Complexin (Cpx). Syt1 is the synaptic vesicle (SV) protein that serves as the neuronal calcium sensor and triggers synaptic fusion upon calcium binding, and this process is promoted and accelerated by Cpx.

The diagnostic accuracy of ultrasound in assessing anterior cruciate ligament tears: a systematic review and meta-analysis.

Background: Advances in technology and affordability of ultrasound (US) have expanded its use in the evaluation of musculoskeletal injuries. However, US accuracy for diagnosing anterior cruciate ligament (ACL) injuries remains inconsistently reported in the literature.

Hypothesis/purpose: Systematically review the literature and perform a meta-analysis to statistically evaluate the accuracy of US in diagnosing ACL tears.

Differential roles of human CD4 and CD8 regulatory T cells in controlling self-reactive immune responses.

Here we analyzed the relative contributions of CD4 regulatory T cells expressing Forkhead box protein P3 (FOXP3) and CD8 regulatory T cells expressing killer cell immunoglobulin-like receptors to the control of autoreactive T and B lymphocytes in human tonsil-derived immune organoids. FOXP3 and GZMB respectively encode proteins FOXP3 and granzyme B, which are critical to the suppressive functions of CD4 and CD8 regulatory T cells. Using CRISPR-Cas9 gene editing, we were able to achieve a reduction of ~90-95% in the expression of these genes.

Shallow-water mussels (Mytilus galloprovincialis) adapt to deep-sea environment through transcriptomic and metagenomic insights.

Recent studies have unveiled the deep sea as a rich biosphere, populated by species descended from shallow-water ancestors post-mass extinctions. Research on genomic evolution and microbial symbiosis has shed light on how these species thrive in extreme deep-sea conditions. However, early adaptation stages, particularly the roles of conserved genes and symbiotic microbes, remain inadequately understood.