Ecological Trait-Based Digital Categorization of Microbial Genomes for Denitrification Potential.

Microorganisms encode proteins that function in the transformations of useful and harmful nitrogenous compounds in the global nitrogen cycle. The major transformations in the nitrogen cycle are nitrogen fixation, nitrification, denitrification, anaerobic ammonium oxidation, and ammonification. The focus of this report is the complex biogeochemical process of denitrification, which, in the complete form, consists of a series of four enzyme-catalyzed reduction reactions that transforms nitrate to nitrogen gas.

Bioinformatics Investigations of Universal Stress Proteins from Mercury-Methylating .

The presence of methylmercury in aquatic environments and marine food sources is of global concern. The chemical reaction for the addition of a methyl group to inorganic mercury occurs in diverse bacterial taxonomic groups including the Gram-negative, sulfate-reducing family that inhabit extreme aquatic environments. The availability of whole-genome sequence datasets for members of the presents opportunities to understand the microbial mechanisms that contribute to methylmercury production in extreme aquatic environments.

Integrating Datasets on Public Health and Clinical Aspects of Sickle Cell Disease for Effective Community-Based Research and Practice.

Sickle cell disease (SCD) is a genetic disease that has multiple aspects including public health and clinical aspects. The goals of the research study were to (1) understand the public health aspects of sickle cell disease, and (2) understand the overlap between public health aspects and clinical aspects that can inform research and practice beneficial to stakeholders in sickle cell disease management. The approach involved the construction of datasets from textual data sources produced by experts on sickle cell disease including from landmark publications published in 2020 on sickle cell disease in the United States.

Knowledge Visualizations to Inform Decision Making for Improving Food Accessibility and Reducing Obesity Rates in the United States.

The aim of this article is to promote the use of knowledge visualization frameworks in the creation and transfer of complex public health knowledge. The accessibility to healthy food items is an example of complex public health knowledge. The United States Department of Agriculture Food Access Research Atlas (FARA) dataset contains 147 variables for 72,864 census tracts and includes 16 food accessibility variables with binary values (0 or 1).

Harnessing Knowledge for Improving Access to Fruits and Vegetables at Farmers Markets: Interactive Data Visualization to Inform Food Security Programs and Policy.

High consumption of fruits and vegetables leads to decreased risk of various chronic diseases, including obesity and cardiovascular disease. Community-level barriers to access fruits and vegetables include the high cost, limited availability, and transportation. Farmers markets are a priority strategy for improving community access to fresh fruits and vegetables.

Arsenicosis in bladder pathology and schistosomiasis in Eggua, Nigeria.

Background: Chronic schistosomiasis and arsenic exposure through drinking water are some of the risk factors for bladder cancer. To determine the association of schistosomiasis and arsenicosis with bladder pathologies, 122 individuals from Eggua in southwest Nigeria were recruited for this study.

Methods: Prevalence of schistosomiasis was determined by urine microscopy and PCR.

Metabolite profiling for biomarkers in Schistosoma haematobium infection and associated bladder pathologies.

Background: Metabolic fingerprinting analysis can offer insights into underlying reactions in a biological system; hence it is crucial to the understanding of disease pathogenesis and could provide useful tools for discovering biomarkers. We sought to examine the urine and plasma metabolome in individuals affected by urogenital schistosomiasis and its associated-bladder pathologies.

Methodology: Blood and midstream urine were obtained from volunteers who matched our inclusion criteria among residents from Eggua, southwestern Nigeria.

Correction: The microbiome in urogenital schistosomiasis and induced bladder pathologies.

[This corrects the article DOI: 10.1371/journal.pntd.

Plant Phenology Supports the Multi-emergence Hypothesis for Ebola Spillover Events.

Ebola virus disease outbreaks in animals (including humans and great apes) start with sporadic host switches from unknown reservoir species. The factors leading to such spillover events are little explored. Filoviridae viruses have a wide range of natural hosts and are unstable once outside hosts.

The microbiome in urogenital schistosomiasis and induced bladder pathologies.

Background: Human schistosomiasis is a highly prevalent neglected tropical disease (NTD) caused by Schistosoma species. Research on the molecular mechanisms influencing the outcomes of bladder infection by Schistosoma haematobium is urgently needed to develop new diagnostics, therapeutics and infection prevention strategies. The objective of the research study was to determine the microbiome features and changes in urine during urogenital schistosomiasis and induced bladder pathologies.

Transcriptomic and macroevolutionary evidence for phenotypic uncoupling between frog life history phases.

Anuran amphibians undergo major morphological transitions during development, but the contribution of their markedly different life-history phases to macroevolution has rarely been analysed. Here we generate testable predictions for coupling versus uncoupling of phenotypic evolution of tadpole and adult life-history phases, and for the underlying expression of genes related to morphological feature formation. We test these predictions by combining evidence from gene expression in two distantly related frogs, Xenopus laevis and Mantidactylus betsileanus, with patterns of morphological evolution in the entire radiation of Madagascan mantellid frogs.

Genomic Evidence for Bacterial Determinants Influencing Obesity Development.

Obesity is a major global public health problem requiring multifaceted interventional approaches including dietary interventions with probiotic bacteria. High-throughput genome sequencing of microbial communities in the mammalian gastrointestinal system continues to present diverse protein function information to understand the bacterial determinants that influence obesity development. The goal of the research reported in this article was to identify biological processes in probiotic bacteria that could influence the mechanisms for the extraction of energy from diet in the human gastrointestinal system.

Secondary Data Analytics of Aquaporin Expression Levels in Glioblastoma Stem-Like Cells.

Glioblastoma is the most common brain tumor in adults in which recurrence has been attributed to the presence of cancer stem cells in a hypoxic microenvironment. On the basis of tumor formation in vivo and growth type in vitro, two published microarray gene expression profiling studies grouped nine glioblastoma stem-like (GS) cell lines into one of two groups: full (GSf) or restricted (GSr) stem-like phenotypes. Aquaporin-1 (AQP1) and aquaporin-4 (AQP4) are water transport proteins that are highly expressed in primary glial-derived tumors.

Evaluative profiling of arsenic sensing and regulatory systems in the human microbiome project genomes.

The influence of environmental chemicals including arsenic, a type 1 carcinogen, on the composition and function of the human-associated microbiota is of significance in human health and disease. We have developed a suite of bioinformatics and visual analytics methods to evaluate the availability (presence or absence) and abundance of functional annotations in a microbial genome for seven Pfam protein families: As(III)-responsive transcriptional repressor (ArsR), anion-transporting ATPase (ArsA), arsenical pump membrane protein (ArsB), arsenate reductase (ArsC), arsenical resistance operon transacting repressor (ArsD), water/glycerol transport protein (aquaporins), and universal stress protein (USP). These genes encode function for sensing and/or regulating arsenic content in the bacterial cell.

Proteomics-Based Identification of Differentially Abundant Proteins from Human Keratinocytes Exposed to Arsenic Trioxide.

Introduction: Arsenic is a widely distributed environmental toxicant that can cause multi-tissue pathologies. Proteomic assays allow for the identification of biological processes modulated by arsenic in diverse tissue types.

Method: The altered abundance of proteins from HaCaT human keratinocyte cell line exposed to arsenic was quantified using a label-free LC-MS/MS mass spectrometry workflow.

A candidate multimodal functional genetic network for thermal adaptation.

Vertebrate ectotherms such as reptiles provide ideal organisms for the study of adaptation to environmental thermal change. Comparative genomic and exomic studies can recover markers that diverge between warm and cold adapted lineages, but the genes that are functionally related to thermal adaptation may be difficult to identify. We here used a bioinformatics genome-mining approach to predict and identify functions for suitable candidate markers for thermal adaptation in the chicken.

Geminin overexpression promotes imatinib sensitive breast cancer: a novel treatment approach for aggressive breast cancers, including a subset of triple negative.

Breast cancer is the second leading cause of cancer-related deaths in women. Triple negative breast cancer (TNBC) is an aggressive subtype that affects 10-25% mostly African American women. TNBC has the poorest prognosis of all subtypes with rapid progression leading to mortality in younger patients.

Application of universal stress proteins in probing the dynamics of potent degraders in complex terephthalate metagenome.

The culture-independent strategies to study microbial diversity and function have led to a revolution in environmental genomics, enabling fundamental questions about the distribution of microbes and their influence on bioremediation to be addressed. In this research we used the expression of universal stress proteins as a probe to determine the changes in degrading microbial population from a highly toxic terephthalate wastewater to a less toxic activated sludge bioreactor. The impact of relative toxicities was significantly elaborated at the levels of genus and species.

Identification of Functional Regulatory Residues of the β -Lactam Inducible Penicillin Binding Protein in Methicillin-Resistant Staphylococcus aureus.

Resistance to methicillin by Staphylococcus aureus is a persistent clinical problem worldwide. A mechanism for resistance has been proposed in which methicillin resistant Staphylococcus aureus (MRSA) isolates acquired a new protein called β -lactam inducible penicillin binding protein (PBP-2'). The PBP-2' functions by substituting other penicillin binding proteins which have been inhibited by β -lactam antibiotics.

Inferences on the biochemical and environmental regulation of universal stress proteins from Schistosomiasis parasites.

Background: Human schistosomiasis is a freshwater snail-transmitted disease caused by parasitic flatworms of the Schistosoma genus. Schistosoma haematobium, Schistosoma mansoni, and Schistosoma japonicum are the three major species infecting humans. These parasites undergo a complex developmental life cycle, in which they encounter a plethora of environmental signals.

Functional Annotation Analytics of Bacillus Genomes Reveals Stress Responsive Acetate Utilization and Sulfate Uptake in the Biotechnologically Relevant Bacillus megaterium.

Bacillus species form an heterogeneous group of Gram-positive bacteria that include members that are disease-causing, biotechnologically-relevant, and can serve as biological research tools. A common feature of Bacillus species is their ability to survive in harsh environmental conditions by formation of resistant endospores. Genes encoding the universal stress protein (USP) domain confer cellular and organismal survival during unfavorable conditions such as nutrient depletion.

Drug Target Exploitable Structural Features of Adenylyl Cyclase Activity in Schistosoma mansoni.

The draft genome sequence of the parasitic flatworm Schistosoma mansoni (S. mansoni), a cause of schistosomiasis, encodes a predicted guanosine triphosphate (GTP) binding protein tagged Smp_059340.1.

Knowledge building insights on biomarkers of arsenic toxicity to keratinocytes and melanocytes.

Exposure to inorganic arsenic induces skin cancer and abnormal pigmentation in susceptible humans. High-throughput gene transcription assays such as DNA microarrays allow for the identification of biological pathways affected by arsenic that lead to initiation and progression of skin cancer and abnormal pigmentation. The overall purpose of the reported research was to determine knowledge building insights on biomarker genes for arsenic toxicity to human epidermal cells by integrating a collection of gene lists annotated with biological information.

Cytotoxicity patterns of arsenic trioxide exposure on HaCaT keratinocytes.

Background: Arsenic is a ubiquitous environmental toxicant, and abnormalities of the skin are the most common outcomes of long-term, low-dose, chronic arsenic exposure. If the balance between keratinocyte proliferation, differentiation, and death is perturbed, pathologic changes of the epidermis may result, including psoriasis, atopic dermatitis, and certain forms of ichthyosis. Therefore, research investigations using in vitro human epidermal cells could help elucidate cellular and molecular processes in keratinocytes affected by arsenic.