Managerial and environmental determinants of clinical mastitis in Danish dairy herds

Background  

Several management and environmental factors are known as contributory causes of clinical mastitis in dairy herd. The study objectives were to describe the structure of herd-specific mastitis management and environmental factors and to assess the relevance of these herd-specific indicators to mastitis incidence rate.     

Fine-tuning the space, time, and host distribution of mycobacteria in wildlife

Background  

We describe the diversity of two kinds of mycobacteria isolates, environmental mycobacteria and Mycobacterium bovis collected from wild boar, fallow deer, red deer and cattle in Do?ana National Park (DNP, Spain), analyzing their association with temporal, spatial and environmental factors.     

Environmental distribution of prokaryotic taxa

Background  

The increasing availability of gene sequences of prokaryotic species in samples extracted from all kind of locations allows addressing the study of the influence of environmental patterns in prokaryotic biodiversity. We present a comprehensive study to address the potential existence of environmental preferences of prokaryotic taxa and the commonness of the specialist and generalist strategies. We also assessed the most significant environmental factors shaping the environmental distribution of taxa.     

Sample phenotype clusters in high-density oligonucleotide microarray data sets are revealed using Isomap,a nonlinear algorithm

Background  

Life processes are determined by the organism's genetic profile and multiple environmental variables. However the interaction between these factors is inherently non-linear [1]. Microarray data is one representation of the nonlinear interactions among genes and genes and environmental factors. Still most microarray studies use linear methods for the interpretation of nonlinear data. In this study, we apply Isomap, a nonlinear method of dimensionality reduction, to analyze three independent large Affymetrix high-density oligonucleotide microarray data sets.     

Detection of a highly prevalent and potentially virulent strain of <Emphasis Type="Italic">Pseudomonas aeruginosa</Emphasis> from nosocomial infections in a medical center

Background  

We correlated genotypes, virulence factors and antimicrobial susceptibility patterns of nosocomially identified Pseudomonas aeruginosa isolates from clinical specimens to those of environmental isolates encountered in the same units of a medical center. Antibiotic susceptibility testing, RAPD analysis and detection of enzymatic activities of extracellular virulence factors, were done on these isolates.     

Improved human disease candidate gene prioritization using mouse phenotype

Background  

The majority of common diseases are multi-factorial and modified by genetically and mechanistically complex polygenic interactions and environmental factors. High-throughput genome-wide studies like linkage analysis and gene expression profiling, tend to be most useful for classification and characterization but do not provide sufficient information to identify or prioritize specific disease causal genes.     

Correlation between structure and temperature in prokaryotic metabolic networks

Background  

In recent years, an extensive characterization of network structures has been made in an effort to elucidate design principles of metabolic networks, providing valuable insights into the functional organization and the evolutionary history of organisms. However, previous analyses have not discussed the effects of environmental factors (i.e., exogenous forces) in shaping network structures. In this work, we investigate the effect of temperature, which is one of the environmental factors that may have contributed to shaping structures of metabolic networks.     

Presence of virulence markers in environmental Vibrio vulnificus strains

Aims

This work aims to demonstrate the presence of several genes and factors associated with virulence in strains isolated from the environment at Pueblo Viejo Lagoon, State of Veracruz, Mexico.

Methods and Results

In this study, we investigated the production of V. vulnificus virulence factors, as cytolysin (haemolysin), RTX toxin, metalloprotease, siderophores, capsular polysaccharide, adhesion structures (like type IV pili), and polar and lateral flagella, involved in swimming and swarming (or, at least, the presence of genes encoding some of them) in 40 strains of V. vulnificus isolated from water and food. The results indicate that strains of environmental origin possess potential virulence characteristics.

Conclusions

Caution should be exercised when consuming raw shellfish (especially by those more susceptible risk groups).

Significance and Impact of the Study

This is the first work focused on the evaluation of V. vulnificus virulence factors in Mexico.     

Salinity appears to be the main factor shaping spatial COI diversity of Corbicula lineages within the Chinese Yangtze River Basin

Aim

To date, few studies have examined the phylogenetics of Corbicula clams in their native range and the environmental parameters influencing their distribution, although this could provide great insights into the biological adaptation and invasion dynamics of Corbicula clams. We sought to identify the genetic lineages of native Corbicula clams and elucidate the environmental factors shaping the distributions of identified lineages.

Location

China, mainly the Yangtze River Basin.

Methods

The alignment comprised 558 COI sequences including samples from China and 222 COI sequences from published studies. This dataset was used to generate phylogenetic trees and compare population diversity. We used dbRDA method to assess the relationship between these COI data and environmental factors measured to identify the important factors affecting Corbicula's distribution.

Results

The COI phylogenetic tree delineated the monophyly of 3 major COI clades and 77 distinct COI haplotypes in the Yangtze River Basin. The invasive lineage C/S (FW17) was not identified in our sampling in China, while invasive lineages A/R (FW5 = Hap6), B (FW1 = Hap17) and Rlc (FW4 = Hap43) were identified, abundant and widely distributed in the middle and lower reaches of Yangtze River. Focusing on populations from Yangtze River Basin, both the COI haplotype and nucleotide diversity in the lakes along the Yangtze River increased with longitude, except for the river mouth population. The AMOVA tests showed significant differentiation between the middle and lower reaches of the Yangtze River and among populations. The dbRDA results suggested that the parameter chloride explained most of the spatial COI haplotype distribution variation in the Yangtze River Basin, with the three invasive lineages tolerating broad fluctuations of salinity (chloride levels ranging from 4 to 60 mg/L).

Conclusions

The Corbicula COI haplotypes found within the Yangtze River Basin had distinct distribution preferences, with the invasive androgenetic lineages being the most abundant and widely distributed. Genetic diversity was higher in this native region than in invaded areas in Europe and America, while it decreased with increasing distance from the river mouth. Salinity appeared to be the main environmental factor shaping the COI haplotype distribution of Corbicula lineages within their native range.     

Incorporating gene co-expression network in identification of cancer prognosis markers

Background  

Extensive biomedical studies have shown that clinical and environmental risk factors may not have sufficient predictive power for cancer prognosis. The development of high-throughput profiling technologies makes it possible to survey the whole genome and search for genomic markers with predictive power. Many existing studies assume the interchangeability of gene effects and ignore the coordination among them.     

A systematic review of population based epidemiological studies in Myasthenia Gravis

Background  

The aim was to collate all myasthenia gravis (MG) epidemiological studies including AChR MG and MuSK MG specific studies. To synthesize data on incidence rate (IR), prevalence rate (PR) and mortality rate (MR) of the condition and investigate the influence of environmental and technical factors on any trends or variation observed.     

A model of gene-gene and gene-environment interactions and its implications for targeting environmental interventions by genotype

Background  

The potential public health benefits of targeting environmental interventions by genotype depend on the environmental and genetic contributions to the variance of common diseases, and the magnitude of any gene-environment interaction. In the absence of prior knowledge of all risk factors, twin, family and environmental data may help to define the potential limits of these benefits in a given population. However, a general methodology to analyze twin data is required because of the potential importance of gene-gene interactions (epistasis), gene-environment interactions, and conditions that break the 'equal environments' assumption for monozygotic and dizygotic twins.     

PADB : Published Association Database

Background  

Although molecular pathway information and the International HapMap Project data can help biomedical researchers to investigate the aetiology of complex diseases more effectively, such information is missing or insufficient in current genetic association databases. In addition, only a few of the environmental risk factors are included as gene-environment interactions, and the risk measures of associations are not indexed in any association databases.     

A comparative study of cultural methods for the detection of Salmonella in feed and feed ingredients

Background  

Giardia duodenalis is a ubiquitous protozoan parasite that has emerged as a significant opportunistic human pathogen. G. duodenalis may have a deleterious effect on animal growth and performance, therefore its potential as a production limiting organism should not be discounted. We therefore undertook this study to determine management and environmental factors in feedlots that influence the prevalence and environmental load of G. duodenalis cysts in fecal material deposited by feedlot cattle in the central and western United States.     

Community-wide analysis of microbial genome sequence signatures

Background  

Analyses of DNA sequences from cultivated microorganisms have revealed genome-wide, taxa-specific nucleotide compositional characteristics, referred to as genome signatures. These signatures have far-reaching implications for understanding genome evolution and potential application in classification of metagenomic sequence fragments. However, little is known regarding the distribution of genome signatures in natural microbial communities or the extent to which environmental factors shape them.     

Life cycle energy consumption and CO2 emission of an office building in China

Purpose  

Building is one of the main factors of energy use and greenhouse gas emissions. Reducing energy consumption and carbon dioxide (CO₂) emission from building is urgent for environmental protection and sustainable development. The objective of this study is to develop a life cycle assessment (LCA) model for an office building in China to assess its energy consumption and CO₂ emission, determine the whole life cycle phases, and the significant environmental aspects that contribute most to the impact.     

Assessing drug distribution in tissues expressing P-glycoprotein through physiologically based pharmacokinetic modeling: model structure and parameters determination

Background  

The expression and activity of P-glycoproteins due to genetic or environmental factors may have a significant impact on drug disposition, drug effectiveness or drug toxicity. Hence, characterization of drug disposition over a wide range of conditions of these membrane transporters activities is required to better characterize drug pharmacokinetics and pharmacodynamics. This work aims to improve our understanding of the impact of P-gp activity modulation on tissue distribution of P-gp substrate.     

Functional comparison of plasma-membrane Na<Superscript>+</Superscript>/H<Superscript>+</Superscript> antiporters from two pathogenic <Emphasis Type="Italic">Candida</Emphasis> species

Background  

The virulence of Candida species depends on many environmental conditions. Extracellular pH and concentration of alkali metal cations belong among important factors. Nevertheless, the contribution of transporters mediating the exchange of alkali metal cations for protons across the plasma membrane to the cell salt tolerance and other physiological properties of various Candida species has not been studied so far.