Metatranscriptomics-based metabolic modeling of patient-specific urinary microbiome during infection.

Urinary tract infections (UTIs) are among the most common bacterial infections and are increasingly complicated by multidrug resistance (MDR). While Escherichia coli is frequently implicated, the contribution of broader microbial communities remains less understood. Here, we integrate metatranscriptomic sequencing with genome-scale metabolic modeling to characterize active metabolic functions of patient-specific urinary microbiomes during acute UTI.

Metabolic modeling elucidates phenformin and atpenin A5 as broad-spectrum antiviral drugs against RNA viruses.

The SARS-CoV-2 pandemic has reemphasized the urgent need for broad-spectrum antiviral therapies. We developed a computational workflow using scRNA-Seq data to assess cellular metabolism during viral infection. With this workflow we predicted the capacity of cells to sustain SARS-CoV-2 virion production in patients and found a tissue-wide induction of metabolic pathways that support viral replication.

Reconstructing the transcriptional regulatory network of probiotic is enabled by transcriptomics and machine learning.

Unlabelled: , a probiotic microbe instrumental to human health and sustainable food production, adapts to diverse environmental shifts via dynamic gene expression. We applied the independent component analysis (ICA) to 117 RNA-seq data sets to decode its transcriptional regulatory network (TRN), identifying 35 distinct signals that modulate specific gene sets. Our findings indicate that the ICA provides a qualitative advancement and captures nuanced relationships within gene clusters that other methods may miss.

Parkinson's Disease and the Metal-Microbiome-Gut-Brain Axis: A Systems Toxicology Approach.

Parkinson's Disease (PD) is a neurodegenerative disease, leading to motor and non-motor complications. Autonomic alterations, including gastrointestinal symptoms, precede motor defects and act as early warning signs. Chronic exposure to dietary, environmental heavy metals impacts the gastrointestinal system and host-associated microbiome, eventually affecting the central nervous system.

Medical Device Sterilization and Reprocessing in the Era of Multidrug-Resistant (MDR) Bacteria: Issues and Regulatory Concepts.

The emergence of multidrug-resistant (MDR) bacteria threatens humans in various health sectors, including medical devices. Since formal classifications for medical device sterilization and disinfection were established in the 1970's, microbial adaptation under adverse environmental conditions has evolved rapidly. MDR microbial biofilms that adhere to medical devices and recurrently infect patients pose a significant threat in hospitals.

COVID-19 through Adverse Outcome Pathways: Building networks to better understand the disease - 3rd CIAO AOP Design Workshop.

On April 28-29, 2021, 50 scientists from different fields of expertise met for the 3rd online CIAO workshop. The CIAO project “Modelling the Pathogenesis of COVID-19 using the Adverse Outcome Pathway (AOP) framework” aims at building a holistic assembly of the available scientific knowledge on COVID-19 using the AOP framework. An individual AOP depicts the disease progression from the initial contact with the SARS-CoV-2 virus through biological key events (KE) toward an adverse outcome such as respiratory distress, anosmia or multiorgan failure.

Recurrent Urinary Tract Infections: Unraveling the Complicated Environment of Uncomplicated rUTIs.

Urinary tract infections (UTIs) are frequent in humans, affecting the upper and lower urinary tract. Present diagnosis relies on the positive culture of uropathogenic bacteria from urine and clinical markers of inflammation of the urinary tract. The bladder is constantly challenged by adverse environmental stimuli which influence urinary tract physiology, contributing to a dysbiotic environment.

Longitudinal Multi-omics Analyses Identify Responses of Megakaryocytes, Erythroid Cells, and Plasmablasts as Hallmarks of Severe COVID-19.

Temporal resolution of cellular features associated with a severe COVID-19 disease trajectory is needed for understanding skewed immune responses and defining predictors of outcome. Here, we performed a longitudinal multi-omics study using a two-center cohort of 14 patients. We analyzed the bulk transcriptome, bulk DNA methylome, and single-cell transcriptome (>358,000 cells, including BCR profiles) of peripheral blood samples harvested from up to 5 time points.

Profiling the Gene Expression and DNA Methylation in the Mouse Brain after Ischemic Preconditioning.

Ischemic preconditioning (IPC) is a phenomenon in which a short-term sublethal ischemic exposure induces tolerance to a subsequent lethal ischemic insult; however, the detailed mechanism underlying IPC-induced neuroprotection remains obscure. Here, we applied middle cerebral artery occlusion, a preconditioning ischemic insult mouse model, to investigate the molecular mechanism underlying cerebral IPC. RNA sequencing and whole-genome bisulfite sequencing were performed to explore the gene expression profile and DNA methylation changes after cerebral IPC treatment.

Quality antenatal care protects against low birth weight in 42 poor counties of Western China.

Limited data exist related to low birth weight (LBW) incidence and risk factors in Western China. This paper aims to assess LBW and its relationship with antenatal care (ANC) in the poor counties of Western China. A community-based study in rural Western China was conducted in 2011.

The dietary diversity and stunting prevalence in minority children under 3 years old: a cross-sectional study in forty-two counties of Western China.

As a key indicator of childhood malnutrition, few studies have focused on stunting in relation to various socio-economic factors in which disadvantaged groups face in China. We conducted a community-based cross-sectional study incorporating forty-two rural counties in seven western provinces of China in 2011. In total, 5196 children aged 6-23 months were included.

Messenger RNA sequencing reveals similar mechanisms between neonatal and acute respiratory distress syndrome.

Hypoxemia and hypercarbia resulting from a lack of surfactant is considered to be the primary mechanism underlying neonatal respiratory distress syndrome (NRDS). Surfactant replacement therapy may mitigate the symptoms of the disease by decreasing the surface tension of alveoli and facilitating inflation. However, surfactant serves an additional role in immunological processes.

Human microbiome versus food-borne pathogens: friend or foe.

As food safety advances, there is a great need to maintain, distribute, and provide high-quality food to a much broader consumer base. There is also an ever-growing "arms race" between pathogens and humans as food manufacturers. The human microbiome is a collective organ of microbes that have found community niches while associating with their host and other microorganisms.