Clinical and Virological Features of SARS-CoV-2 Variants during the Four Waves of the Pandemic in the Mexican Southeast.

We conducted a retrospective study using a population of patients who were hospitalized at Dr. Juan Graham Casasus Hospital in Villahermosa (Tabasco, Mexico) and had a positive RT-PCR test for SARS-CoV-2 between June 2020 and January 2022. We analyzed all medical records, including demographic data, SARS-CoV-2 exposure history, underlying comorbidities, symptoms, signs at admission, laboratory findings during the hospital stay, outcome, and whole-genome sequencing data.

SARS-CoV-2 Genome Variations in Viral Shedding of an Immunocompromised Patient with Non-Hodgkin's Lymphoma.

Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing coronavirus disease 2019 (COVID-19) is the most transmissible ß-coronavirus in history, affecting all population groups. Immunocompromised patients, particularly cancer patients, have been highlighted as a reservoir to promote accumulation of viral mutations throughout persistent infection.

Case Presentation: We aimed to describe the clinical course and SARS-CoV-2 mutation profile for 102 days in an immunocompromised patient with non-Hodgkin's lymphoma and COVID-19.

Analytical Performances of the COVISTIX Antigen Rapid Test for SARS-CoV-2 Detection in an Unselected Population (All-Comers).

The performance and validity of the COVISTIX rapid antigen test for the detection of SARS-CoV-2 were evaluated in an unselected population. Additionally, we assessed the influence of the Omicron SARS-CoV-2 variant in the performance of this antigen rapid test. Swab samples were collected at two point-of-care facilities in Mexico City from individuals that were probable COVID-19 cases, as they were either symptomatic or asymptomatic persons at risk of infection due to close contact with SARS-CoV-2 positive cases.

Early Genomic, Epidemiological, and Clinical Description of the SARS-CoV-2 Omicron Variant in Mexico City.

Omicron is the most mutated SARS-CoV-2 variant-a factor that can affect transmissibility, disease severity, and immune evasiveness. Its genomic surveillance is important in cities with millions of inhabitants and an economic center, such as Mexico City. Results.

Lovastatin as a supplement to mitigate rumen methanogenesis: an overview.

Methane from enteric fermentation is the gas with the greatest environmental impact emitted by ruminants. Lovastatin (Lv) addition to feedstocks could be a strategy to mitigate rumen methane emissions via decreasing the population of methanogenic archaea (MA). Thus, this paper provides the first overview of the effects of Lv supplementation, focusing on the inhibition of methane production, rumen microbiota, and ruminal fermentation.

The transcriptome of early GGT/KRT19-positive hepatocellular carcinoma reveals a downregulated gene expression profile associated with fatty acid metabolism.

Hepatocellular carcinoma expressing hepatobiliary progenitor markers, is considered of poor prognosis. By using a hepatocarcinogenesis model, laser capture microdissection, and RNA-Sequencing analysis, we identified an expression profile in GGT/KRT19-positive experimental tumors; 438 differentially expressed genes were found in early and late nodules along with increased collagen deposition. Dysregulated genes were involved in Fatty Acid Metabolism, RXR function, and Hepatic Stellate Cells Activation.

The Evolutionary Landscape of SARS-CoV-2 Variant B.1.1.519 and Its Clinical Impact in Mexico City.

The SARS-CoV-2 pandemic is one of the most concerning health problems around the globe. We reported the emergence of SARS-CoV-2 variant B.1.

SARS-CoV-2 positivity rates in asymptomatic workers at a cancer referral center in Mexico City: A prospective observational study in the context of adapting hospitals back to regular practice.

Background: Healthcare workers are at increased risk of SARS-CoV-2 infection. The positivity rates in hospitals that do not receive patients with COVID-19, such as the National Cancer Institute (INCan) in Mexico, and the associated factors are unknown.

Objective: To assess the incidence and factors associated with SARS-CoV-2 infection in health workers at INCan.

Gut dsDNA virome shows diversity and richness alterations associated with childhood obesity and metabolic syndrome.

Changes in the human gut microbiome are associated with obesity and metabolic syndrome, but the role of the gut virome in both diseases remains largely unknown. We characterized the gut dsDNA virome of 28 school-aged children with healthy normal-weight (NW, n = 10), obesity (O, n = 10), and obesity with metabolic syndrome (OMS, n = 8), using metagenomic sequencing of virus-like particles (VLPs) from fecal samples. The virome classification confirmed the bacteriophages' dominance, mainly composed of Caudovirales.

Intestinal microbiota fingerprint in subjects with irritable bowel syndrome responders to a low FODMAP diet.

Irritable Bowel Syndrome (IBS) is a functional gastrointestinal disorder characterized by abdominal pain and altered bowel habit. IBS patients report that FODMAP (Fermentable Oligosaccharides, Disaccharides, Monosaccharides, and Polyols) diet induce or exacerbate their symptoms. It has been reported that low-FODMAP diet (LFD) improves the symptoms in 50%-80% of IBS patients.

Saliva is a reliable and accessible source for the detection of SARS-CoV-2.

Objectives: The aim of this study was to investigate the feasibility of saliva sampling as a non-invasive and safer tool to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and to compare its reproducibility and sensitivity with nasopharyngeal swab samples (NPS). The use of sample pools was also investigated.

Methods: A total of 2107 paired samples were collected from asymptomatic healthcare and office workers in Mexico City.

Effect of Dietary Magnesium Content on Intestinal Microbiota of Rats.

Background: Magnesium is a mineral that modulates several physiological processes. However, its relationship with intestinal microbiota has been scarcely studied. Therefore, this study aimed to assess the role of dietary magnesium content to modulate the intestinal microbiota of Wistar male rats.

Relevance of epidemiological surveillance in travelers: an imported case of Leishmania tropica in Mexico.

We report the case of a patient with cutaneous leishmaniasis who showed a rapidly progressing ulcerative lesion after traveling to multiple countries where different Leishmania species are endemic. Diagnosis of Leishmania tropica, an exotic species in Mexico was established by using serological and molecular tools.

Metatranscriptomic analysis to define the Secrebiome, and 16S rRNA profiling of the gut microbiome in obesity and metabolic syndrome of Mexican children.

Background: In the last decade, increasing evidence has shown that changes in human gut microbiota are associated with diseases, such as obesity. The excreted/secreted proteins (secretome) of the gut microbiota affect the microbial composition, altering its colonization and persistence. Furthermore, it influences microbiota-host interactions by triggering inflammatory reactions and modulating the host's immune response.

Doing More with Less: A Comparison of 16S Hypervariable Regions in Search of Defining the Shrimp Microbiota.

The shrimp has become the most valuable traded marine product in the world, and its microbiota plays an essential role in its development and overall health status. Massive high-throughput sequencing techniques using several hypervariable regions of the 16S rRNA gene are broadly applied in shrimp microbiota studies. However, it is essential to consider that the use of different hypervariable regions can influence the obtained data and the interpretation of the results.

Functional and taxonomic classification of a greenhouse water drain metagenome.

Microbiome sequencing has become the standard procedure in the study of new ecological and human-constructed niches. To our knowledge, this is the first report of a metagenome from the water of a greenhouse drain. We found that the greenhouse is not a diverse niche, mainly dominated by and Rodobacterales.

A novel approach for human whole transcriptome analysis based on absolute gene expression of microarray data.

Background: In spite of the emergence of RNA sequencing (RNA-seq), microarrays remain in widespread use for gene expression analysis in the clinic. There are over 767,000 RNA microarrays from human samples in public repositories, which are an invaluable resource for biomedical research and personalized medicine. The absolute gene expression analysis allows the transcriptome profiling of all expressed genes under a specific biological condition without the need of a reference sample.

Microbiome of Pacific Whiteleg shrimp reveals differential bacterial community composition between Wild, Aquacultured and AHPND/EMS outbreak conditions.

Crustaceans form the second largest subphylum on Earth, which includes Litopeneaus vannamei (Pacific whiteleg shrimp), one of the most cultured shrimp worldwide. Despite efforts to study the shrimp microbiota, little is known about it from shrimp obtained from the open sea and the role that aquaculture plays in microbiota remodeling. Here, the microbiota from the hepatopancreas and intestine of wild type (wt) and aquacultured whiteleg shrimp and pond sediment from hatcheries were characterized using sequencing of seven hypervariable regions of the 16S rRNA gene.

Secretome Prediction of Two Clinical Isolates Reveals Their High Antigenic Density and Potential Drug Targets.

The Excreted/Secreted (ES) proteins play important roles during invasion, virulence, and survival inside the host and they are a major source of immunogenic proteins. However, the molecular complexity of the bacillus cell wall has made difficult the experimental isolation of the total bacterial ES proteins. Here, we reported the genomes of two Beijing genotype clinical isolates obtained from patients from Vietnam (isolate 46) and South Africa (isolate 48).

RNA-Seq analysis of the multipartite genome of Rhizobium etli CE3 shows different replicon contributions under heat and saline shock.

Background: Regulation of transcription is essential for any organism and Rhizobium etli (a multi-replicon, nitrogen-fixing symbiotic bacterium) is no exception. This bacterium is commonly found in the rhizosphere (free-living) or inside of root-nodules of the common bean (Phaseolus vulgaris) in a symbiotic relationship. Abiotic stresses, such as high soil temperatures and salinity, compromise the genetic stability of R.

RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units).

RegulonDB (http://regulondb.ccg.unam.

Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli.

Despite almost 40 years of molecular genetics research in Escherichia coli a major fraction of its Transcription Start Sites (TSSs) are still unknown, limiting therefore our understanding of the regulatory circuits that control gene expression in this model organism. RegulonDB (http://regulondb.ccg.