PATRIC: The VBI PathoSystems Resource Integration Center

The PathoSystems Resource Integration Center (PATRIC) is one of eight Bioinformatics Resource Centers (BRCs) funded by the National Institute of Allergy and Infection Diseases (NIAID) to create a data and analysis resource for selected NIAID priority pathogens, specifically proteobacteria of the genera Brucella, Rickettsia and Coxiella, and corona-, calici- and lyssaviruses and viruses associated with hepatitis A and E. The goal of the project is to provide a comprehensive bioinformatics resource for these pathogens, including consistently annotated genome, proteome and metabolic pathway data to facilitate research into counter-measures, including drugs, vaccines and diagnostics. The project's curation strategy has three prongs: ‘breadth first’ beginning with whole-genome and proteome curation using standardized protocols, a ‘targeted’ approach addressing the specific needs of researchers and an integrative strategy to leverage high-throughput experimental data (e.g. microarrays, proteomics) and literature. The PATRIC infrastructure consists of a relational database, analytical pipelines and a website which supports browsing, querying, data visualization and the ability to download raw and curated data in standard formats. At present, the site warehouses complete sequences for 17 bacterial and 332 viral genomes. The PATRIC website () will continually grow with the addition of data, analysis and functionality over the course of the project

A Synthetic Uric Acid Analog Accelerates Cutaneous Wound Healing in Mice

Wound healing is a complex process involving intrinsic dermal and epidermal cells, and infiltrating macrophages and leukocytes. Excessive oxidative stress and associated inflammatory processes can impair wound healing, and antioxidants have been reported to improve wound healing in animal models and human subjects. Uric acid (UA) is an efficient free radical scavenger, but has a very low solubility and poor tissue penetrability. We recently developed novel UA analogs with increased solubility and excellent free radical-scavenging properties and demonstrated their ability to protect neural cells against oxidative damage. Here we show that the uric acid analog (6, 8 dithio-UA, but not equimolar concentrations of UA or 1, 7 dimethyl-UA) modified the behaviors of cultured vascular endothelial cells, keratinocytes and fibroblasts in ways consistent with enhancement of the wound healing functions of all three cell types. We further show that 6, 8 dithio-UA significantly accelerates the wound healing process when applied topically (once daily) to full-thickness wounds in mice. Levels of Cu/Zn superoxide dismutase were increased in wound tissue from mice treated with 6, 8 dithio-UA compared to vehicle-treated mice, suggesting that the UA analog enhances endogenous cellular antioxidant defenses. These results support an adverse role for oxidative stress in wound healing and tissue repair, and provide a rationale for the development of UA analogs in the treatment of wounds and for modulation of angiogenesis in other pathological conditions

Quality of life, psychological morbidity and family stress in elderly residing in the community

Este estudo procurou investigar as relações existentes entre morbilidade psicológica, stress familiar e qualidade de vida (QV) da pessoa idosa. A amostra foi constituída por 126 idosos. Os instrumentos utilizados foram: The Lawton Instrumental Activities of Daily Living (IADL), Quality of Life (WHOQOL-Bref), Geriatric Anxiety Inventory (GSI), Geriatric Depression Scale (GDS); e Index of Family Relations (IFR). Os resultados revelaram a importância da idade, estado civil, escolaridade e número de patologias assim como o género na capacidade funcional, morbilidade, stress familiar e QV. Ao nível dos preditores, a depressão foi a variável que mais contribuiu para a QV. Não foram encontradas variáveis moderadoras no modelo. A discussão e implicações dos resultados são abordadas bem como a intervenção psicológica nesta população.This study sought to understand the relationships among psychological morbidity, family stress and quality of life (QL) of elderly. The sample consisted of 126 elderly. The following instruments were used: the Lawton Instrumental Activities of Daily Living (IADL); Quality of Life (WHOQOL-Bref), Geriatric Anxiety Inventory (GSI), Geriatric Depression Scale (GDS), and the Index of Family Relations (IFR). Results revealed the importance of age, marital status, education and number of pathologies as well as gender on functional capacity, morbidity, family stress and QV. In terms of predictors, depression was the variable that contributed the most to QL. There were no moderating variables in the model. Discussion and implications of results are addressed as well as psychological interventions.(undefined

Rickettsia Phylogenomics: Unwinding the Intricacies of Obligate Intracellular Life

BACKGROUND: Completed genome sequences are rapidly increasing for Rickettsia, obligate intracellular alpha-proteobacteria responsible for various human diseases, including epidemic typhus and Rocky Mountain spotted fever. In light of phylogeny, the establishment of orthologous groups (OGs) of open reading frames (ORFs) will distinguish the core rickettsial genes and other group specific genes (class 1 OGs or C1OGs) from those distributed indiscriminately throughout the rickettsial tree (class 2 OG or C2OGs). METHODOLOGY/PRINCIPAL FINDINGS: We present 1823 representative (no gene duplications) and 259 non-representative (at least one gene duplication) rickettsial OGs. While the highly reductive (approximately 1.2 MB) Rickettsia genomes range in predicted ORFs from 872 to 1512, a core of 752 OGs was identified, depicting the essential Rickettsia genes. Unsurprisingly, this core lacks many metabolic genes, reflecting the dependence on host resources for growth and survival. Additionally, we bolster our recent reclassification of Rickettsia by identifying OGs that define the AG (ancestral group), TG (typhus group), TRG (transitional group), and SFG (spotted fever group) rickettsiae. OGs for insect-associated species, tick-associated species and species that harbor plasmids were also predicted. Through superimposition of all OGs over robust phylogeny estimation, we discern between C1OGs and C2OGs, the latter depicting genes either decaying from the conserved C1OGs or acquired laterally. Finally, scrutiny of non-representative OGs revealed high levels of split genes versus gene duplications, with both phenomena confounding gene orthology assignment. Interestingly, non-representative OGs, as well as OGs comprised of several gene families typically involved in microbial pathogenicity and/or the acquisition of virulence factors, fall predominantly within C2OG distributions. CONCLUSION/SIGNIFICANCE: Collectively, we determined the relative conservation and distribution of 14354 predicted ORFs from 10 rickettsial genomes across robust phylogeny estimation. The data, available at PATRIC (PathoSystems Resource Integration Center), provide novel information for unwinding the intricacies associated with Rickettsia pathogenesis, expanding the range of potential diagnostic, vaccine and therapeutic targets

Exposure to extreme heat and precipitation events associated with increased risk of hospitalization for asthma in Maryland, U.S.A.

Several studies have investigated the association between asthma exacerbations and exposures to ambient temperature and precipitation. However, limited data exists regarding how extreme events, projected to grow in frequency, intensity, and duration in the future in response to our changing climate, will impact the risk of hospitalization for asthma. The objective of our study was to quantify the association between frequency of extreme heat and precipitation events and increased risk of hospitalization for asthma in Maryland between 2000 and 2012. We used a time-stratified case-crossover design to examine the association between exposure to extreme heat and precipitation events and risk of hospitalization for asthma (ICD-9 code 493, n = 115,923). Occurrence of extreme heat events in Maryland increased the risk of same day hospitalization for asthma (lag 0) by 3 % (Odds Ratio (OR): 1.03, 95 % Confidence Interval (CI): 1.00, 1.07), with a considerably higher risk observed for extreme heat events that occur during summer months (OR: 1.23, 95 % CI: 1.15, 1.33). Likewise, summertime extreme precipitation events increased the risk of hospitalization for asthma by 11 % in Maryland (OR: 1.11, 95 % CI: 1.06, 1.17). Across age groups, increase in risk for asthma hospitalization from exposure to extreme heat event during the summer months was most pronounced among youth and adults, while those related to extreme precipitation event was highest among ≤4 year olds. Exposure to extreme heat and extreme precipitation events, particularly during summertime, is associated with increased risk of hospitalization for asthma in Maryland. Our results suggest that projected increases in frequency of extreme heat and precipitation event will have significant impact on public health.https://doi.org/10.1186/s12940-016-0142-

A review of dengue's historical and future health risk from a changing climate

Purpose of review: The purpose of this review is to summarize research articles that provide risk estimates for the historical and future impact that climate change has had upon dengue published from 2007 through 2019. Recent findings: Findings from 30 studies on historical health estimates, with the majority of the studies conducted in Asia, emphasized the importance of temperature, precipitation, and relative humidity, as well as lag effects, when trying to understand how climate change can impact the risk of contracting dengue. Furthermore, 35 studies presented findings on future health risk based upon climate projection scenarios, with a third of them showcasing global level estimates and findings across the articles emphasizing the need to understand risk at a localized level as the impacts from climate change will be experienced inequitably across different geographies in the future. Dengue is one of the most rapidly spreading viral diseases in the world, with ~390 million people infected worldwide annually. Several factors have contributed towards its proliferation, including climate change. Multiple studies have previously been conducted examining the relationship between dengue and climate change, both from a historical and a future risk perspective. We searched the U.S. National Institute of Environmental Health (NIEHS) Climate Change and Health Portal for literature (spanning January 2007 to September 2019) providing historical and future health risk estimates of contracting dengue infection in relation to climate variables worldwide. With an overview of the evidence of the historical and future health risk posed by dengue from climate change across different regions of the world, this review article enables the research and policy community to understand where the knowledge gaps are and what areas need to be addressed in order to implement localized adaptation measures to mitigate the health risks posed by future dengue infection

At-Line Sampling and Characterization of Pyrolytic Vapors from Biomass Feedstock Blends Using SPME-GC/MS-PCA: Influence of Char on Fast Pyrolysis

Solid-phase microextraction (SPME) coupled with gas chromatography–mass spectrometry (GC–MS) analysis was used for the at-line sampling of pyrolytic vapors produced during the fast pyrolysis of biomass. The pure and binary blends of switchgrass (SWG) and pine harvest residues (PT6) were used as biomass feedstocks. Sequential SPME sampling allowed for monitoring of changes in the pyrolysis vapors as char accumulated in the fluid bed. The relative concentration and composition of the pyrolysis vapors desorbed from the SPME fibers were investigated using GC–MS, and the resulting chromatograms were analyzed using principal component analysis (PCA) to compare the composition of the pyrolysis vapors over the course of the pyrolysis run. The chemical compositions of both carbohydrate and lignin fragments varied as the char builds up in the reactor bed. Fragments derived from cellulose and hemicelluloses included anhydrosugars, furans, and light-oxygenated compounds. Lignin fragments included methoxyphenols, phenolic ketones, aldehydes, and low-molecular-weight aromatics. The composition of the carbohydrate fragments changed more than those of the lignin fragments as the char built up in the fluid bed. This combination of SPME-GC/MS-PCA was a novel, easy, and effective method for measuring the composition and changes in the composition of pyrolysis vapors during the fast pyrolysis process. This work also highlighted the effect of char build-up on the composition of the overall pyrolysis vapors