HIV, the gut microbiome and clinical outcomes, a systematic review.

Background: Effective antiretroviral therapy (ART) has improved the life expectancy of people with HIV (PWH). However, this population is now experiencing accelerated age-related comorbidities, contributed to by chronic immune activation and inflammation, with dysbiosis of the gut microbiome also implicated.

Method: We conducted a systematic literature search of PubMed, Embase, Scopus, Cochrane reviews and international conference abstracts for articles that examined for the following non-communicable diseases (NCDs); cardiovascular disease, cancer, frailty, metabolic, bone, renal and neurocognitive disease, in PWH aged >18 years.

A genome-scale metabolic model of a globally disseminated hyperinvasive M1 strain of .

is responsible for a range of diseases in humans contributing significantly to morbidity and mortality. Among more than 200 serotypes of , serotype M1 strains hold the greatest clinical relevance due to their high prevalence in severe human infections. To enhance our understanding of pathogenesis and discovery of potential therapeutic approaches, we have developed the first genome-scale metabolic model (GEM) for a serotype M1 strain, which we name iYH543.

The oral microbiome is associated with HPA axis response to a psychosocial stressor.

Intense psychosocial stress during early life has a detrimental effect on health-disease balance in later life. Simultaneously, despite its sensitivity to stress, the developing microbiome contributes to long-term health. Following stress exposure, HPA-axis activation regulates the "fight or flight" response with the release of glucose and cortisol.

Multimodality imaging for the evaluation and management of patients with long-term (durable) left ventricular assist devices.

Left ventricular assist devices (LVADs) are gaining increasing importance as therapeutic strategy in advanced heart failure (HF), not only as bridge to recovery or to transplant but also as destination therapy. Even though long-term LVADs are considered a precious resource to expand the treatment options and improve clinical outcome of these patients, these are limited by peri-operative and post-operative complications, such as device-related infections, haemocompatibility-related events, device mis-positioning, and right ventricular failure. For this reason, a precise pre-operative, peri-operative, and post-operative evaluation of these patients is crucial for the selection of LVAD candidates and the management LVAD recipients.

Exercise and endometriosis-is there a promising future? A narrative review.

Background: Endometriosis is the leading cause of chronic pelvic pain in women of reproductive age with debilitating effects on quality of life, yet no cure exists. Exercise yields the potential in providing women with a non-invasive, non-pharmacological method of symptom control.

Aim(s): Present up-to-date knowledge regarding how exercise may contribute to the management of endometriosis-related symptoms.

Anorexia Nervosa in vivo cytokine production: a systematic review.

Introduction: The underlying psychobiology that contributes to Anorexia Nervosa (AN) onset and disease progression remains unclear. New research is emerging suggesting a possible link between inflammation and a variety of mental illnesses. Alterations of cytokines may play a role in the pathogenesis of AN.

Preparation of Genomic DNA Using a Chloroform Extraction and Ethanol Precipitation Method, Followed by Additional Cleanup and Quantification Steps.

In this protocol, we describe the isolation of genomic DNA (gDNA) from strains using a chloroform extraction and ethanol precipitation method. This gDNA-isolation method is well-suited for downstream whole-genome sequencing applications when working with strains that contain plasmids, as only a small amount of plasmid DNA is isolated along with the gDNA. Similar to other gDNA isolation methods for Gram-positive bacteria, the first step in the procedure is a mechanical lysis (e.

Agar Plate-Based Method for the Selection of Antibiotic-Resistant Bacterial Strains.

Identifying the molecular mechanisms underlying antibiotic resistance is important, as it can reveal key information on the mode of action of a drug and provide insights for the development of novel or improved antimicrobials. Here, we describe an agar-based method for the selection of bacterial strains with increased antibiotic resistance, and how the increase in resistance can be confirmed by a spot-plating assay. As a specific example, we describe the selection of strains with increased resistance to oxacillin; however, the protocol can be easily adapted and used with other bacteria and antibiotics.

Preparation of Genomic DNA Using Promega Nuclei Lysis and Protein Precipitation Solutions, Followed by Additional Cleanup and Quantification Steps.

In this protocol, we describe the isolation of genomic DNA (gDNA) from using the Promega Nuclei Lysis and Protein Precipitation solutions. Gram-positive bacteria such as are harder to lyse than Gram-negative bacteria. Hence, the first step in the procedure for isolating gDNA from Gram-positive bacteria consists of a mechanical lysis step (e.

Selection of Antibiotic-Resistant Bacterial Strains and Identification of Genomic Alterations by Whole-Genome Sequencing: Using and Oxacillin Resistance as an Example.

Here, we discuss methods for the selection of antibiotic-resistant bacteria and the use of high-throughput whole-genome sequencing for the identification of the underlying mutations. We comment on sample requirements and the choice of specific DNA preparation methods depending on the strain used and briefly introduce a workflow we use for the selection of strains with increased oxacillin resistance and identification of genomic alterations.

Bacterial Whole-Genome-Resequencing Analysis: Basic Steps Using the CLC Genomics Workbench Software.

In this protocol, we describe the basic steps for bacterial genome resequencing analysis using the QIAGEN CLC Genomics Workbench software. More specifically, we present how a reference genome sequence can be generated from Illumina reads of a wild-type reference bacterial strain and how this reference genome sequence can then be used to identify genomic alterations in mutant strains. As specific examples, Illumina reads from the RN4220 strain will be used to generate a consensus reference genome based on the publicly available NCTC8325 genome sequence.

Small-Scale Illumina Library Preparation Using the Illumina Nextera XT DNA Library Preparation Kit.

Here, we describe a protocol for a scaled-down version of a genomic DNA (gDNA)-fragmentation and tagmentation reaction using the Illumina Nextera XT DNA Library Preparation Kit. Using as an example which has a genome size of ∼3 Mb, we show how 24 different samples can be pooled for a typical paired-end Illumina high-throughput sequencing run using the MiSeq Reagent V2 300-cycle kit, with which it is possible to sequence 5.1 Gb of DNA.

Initial symptoms and three months follow-up after acute COVID-19 in outpatients: An international prospective cohort study.

Background: Most studies on long-term follow-up of patients with COVID-19 focused on hospitalised patients. No prospective study with structured follow-up has been performed in non-hospitalised patients with COVID-19.

Objectives: To assess long-COVID and post-COVID (WHO definition: symptomatic at least 12 weeks), describe lingering symptoms, their impact on daily activities, and general practice visits and explore risk factors for symptom duration in outpatients.

A Mixed Methods Study Identifying the Competencies of Health Care Simulation Technicians.

Introduction: Health care simulation technicians (HSTs), also referred to as simulation operations specialists, are essential to the delivery of simulation-based education. The HST role draws on a broad range of knowledge, skills, and attitude competencies. However, because of the neoteric nature of the HST role and the ambiguity surrounding the core responsibilities of the position, it has proved difficult to identify the competencies required to perform this role successfully.

Whole-body metabolic modelling predicts isoleucine dependency of SARS-CoV-2 replication.

We aimed at investigating host-virus co-metabolism during SARS-CoV-2 infection. Therefore, we extended comprehensive sex-specific, whole-body organ resolved models of human metabolism with the necessary reactions to replicate SARS-CoV-2 in the lung as well as selected peripheral organs. Using this comprehensive host-virus model, we obtained the following key results: 1.

NMR Metabolomics Reveal Urine Markers of Microbiome Diversity and Identify Benzoate Metabolism as a Mediator between High Microbial Alpha Diversity and Metabolic Health.

Microbial metabolites measured using NMR may serve as markers for physiological or pathological host-microbe interactions and possibly mediate the beneficial effects of microbiome diversity. Yet, comprehensive analyses of gut microbiome data and the urine NMR metabolome from large general population cohorts are missing. Here, we report the associations between gut microbiota abundances or metrics of alpha diversity, quantified from stool samples using 16S rRNA gene sequencing, with targeted urine NMR metabolites measures from 951 participants of the Study of Health in Pomerania (SHIP).

The gut microbial metabolite formate exacerbates colorectal cancer progression.

The gut microbiome is a key player in the immunomodulatory and protumorigenic microenvironment during colorectal cancer (CRC), as different gut-derived bacteria can induce tumour growth. However, the crosstalk between the gut microbiome and the host in relation to tumour cell metabolism remains largely unexplored. Here we show that formate, a metabolite produced by the CRC-associated bacterium Fusobacterium nucleatum, promotes CRC development.

The Role of MicroRNAs in Endothelial Cell Senescence.

Cellular senescence is a complex, dynamic process consisting of the irreversible arrest of growth and gradual deterioration of cellular function. Endothelial senescence affects the cell's ability to repair itself, which is essential for maintaining vascular integrity and leads to the development of endothelial dysfunction, which has an important role in the pathogenesis of cardiovascular diseases. Senescent endothelial cells develop a particular, senescence-associated secretory phenotype (SASP) that detrimentally affects both surrounding and distant endothelial cells, thereby facilitating the ageing process and development of age-related disorders.

Microbiome Modelling Toolbox 2.0: efficient, tractable modelling of microbiome communities.

Motivation: Constraint-Based Reconstruction and Analysis (COBRA) is a widely used approach for the interrogation and stratification of microbiome samples, yet applications to large-scale cohorts are hampered by limited scalability and efficiency of simulations.

Results: We substantially improved the computation speed and scalability of a previous implementation for the construction and interrogation of personalized constraint-based microbiome models as well as implemented additional functionalities for analysis and visualization.

Availability And Implementation: Microbiome Modelling Toolbox and tutorials are freely available as part of the COBRA Toolbox at https://git.

The global case fatality rate of coronavirus disease 2019 by continents and national income: A meta-analysis.

The aim of this study is to provide a more accurate representation of COVID-19's case fatality rate (CFR) by performing meta-analyses by continents and income, and by comparing the result with pooled estimates. We used multiple worldwide data sources on COVID-19 for every country reporting COVID-19 cases. On the basis of data, we performed random and fixed meta-analyses for CFR of COVID-19 by continents and income according to each individual calendar date.