Ancient origin of a Western Mediterranean radiation of subterranean beetles

Background  

Cave organisms have been used as models for evolution and biogeography, as their reduced above-ground dispersal produces phylogenetic patterns of area distribution that largely match the geological history of mountain ranges and cave habitats. Most current hypotheses assume that subterranean lineages arose recently from surface dwelling, dispersive close relatives, but for terrestrial organisms there is scant phylogenetic evidence to support this view. We study here with molecular methods the evolutionary history of a highly diverse assemblage of subterranean beetles in the tribe Leptodirini (Coleoptera, Leiodidae, Cholevinae) in the mountain systems of the Western Mediterranean.     

CAVER: a new tool to explore routes from protein clefts, pockets and cavities

Background  

The main aim of this study was to develop and implement an algorithm for the rapid, accurate and automated identification of paths leading from buried protein clefts, pockets and cavities in dynamic and static protein structures to the outside solvent.     

Comparative genotypic and pathogenic examination of <Emphasis Type="Italic">Campylobacter concisus</Emphasis>isolates from diarrheic and non-diarrheic humans

Background  

Campylobacter concisus is an emerging enteric pathogen, yet it is commonly isolated from feces and the oral cavities of healthy individuals. This genetically complex species is comprised of several distinct genomospecies which may vary in pathogenic potential.     

Enhanced inhibition of Aspergillus niger on sedge (Lepironia articulata) treated with heat‐cured lime oil

Aims

This study aimed to examine heat curing effect (30–100°C) on antifungal activities of lime oil and its components (limonene, p‐cymene, β‐pinene and α‐pinene) at concentrations ranging from 100 to 300 μl ml^?1 against Aspergillus niger in microbiological medium and to optimize heat curing of lime oil for efficient mould control on sedge (Lepironia articulata).

Methods and Results

Broth dilution method was employed to determine lime oil minimum inhibitory concentration, which was at 90 μl ml^?1 with heat curing at 70°C. Limonene, a main component of lime oil, was an agent responsible for temperature dependencies of lime oil activities observed. Response surface methodology was used to construct the mathematical model describing a time period of zero mould growth on sedge as functions of heat curing temperature and lime oil concentration. Heat curing of 90 μl ml^?1 lime oil at 70°C extended a period of zero mould growth on sedge to 18 weeks under moist conditions.

Conclusions

Heat curing at 70°C best enhanced antifungal activity of lime oil against A. niger both in medium and on sedge.

Significance and Impact of the Study

Heat curing of lime oil has potential to be used to enhance the antifungal safety of sedge products.     

Predicting gene ontology functions from protein's regional surface structures

Background  

Annotation of protein functions is an important task in the post-genomic era. Most early approaches for this task exploit only the sequence or global structure information. However, protein surfaces are believed to be crucial to protein functions because they are the main interfaces to facilitate biological interactions. Recently, several databases related to structural surfaces, such as pockets and cavities, have been constructed with a comprehensive library of identified surface structures. For example, CASTp provides identification and measurements of surface accessible pockets as well as interior inaccessible cavities.     

A phylogenetic estimate for golden moles (Mammalia,Afrotheria, Chrysochloridae)

Background  

Golden moles (Chrysochloridae) are small, subterranean, afrotherian mammals from South Africa and neighboring regions. Of the 21 species now recognized, some (e.g., Chrysochloris asiatica, Amblysomus hottentotus) are relatively common, whereas others (e.g., species of Chrysospalax, Cryptochloris, Neamblysomus) are rare and endangered. Here, we use a combined analysis of partial sequences of the nuclear GHR gene and morphological characters to derive a phylogeny of species in the family Chrysochloridae.     

Osteoblastic differentiation and stress response of human mesenchymal stem cells exposed to alternating current electric fields

Background  

Electric fields are integral to many biological events, from maintaining cellular homeostasis to embryonic development to healing. The application of electric fields offers substantial therapeutic potential, while optimal dosing regimens and the underlying mechanisms responsible for the positive clinical impact are poorly understood.     

Enzymatic transesterification of Jatropha oil

Background  

Transesterification of Jatropha oil was carried out in t-butanol solvent using immobilized lipase from Enterobacter aerogenes. The presence of t-butanol significantly reduced the negative effects caused by both methanol and glycerol. The effects of various reaction parameters on transesterification of Jatropha oil were studied.     

Comparison of different treatment options for palm oil production waste on a life cycle basis

Background, aim, and scope  

Globally, 45 million metric tonnes of palm oil has been produced in 2009. The production of 1 t crude palm oil requires 5 t of fresh fruit bunches (FFB). On average, processing of 1 t FFB in palm oil mills generates 230 kg empty fruit bunches (EFB) and 650 kg palm oil mill effluent (POME) as residues. These residues cause considerable environmental burdens, particularly greenhouse gas emissions. In order to reduce those emissions, four waste management options are compared in the present study using 1,000 kg of FFB as functional unit.     

A modified scoring system to describe gross pathology in the rabbit model of tuberculosis

Background  

The rabbit model is an ideal means to study the pathogenesis of tuberculosis due to its semblance to the disease in humans. We have previously described the results using a bronchoscopic route of infection with live bacilli as a reliable means of generating lung cavities in sensitized rabbits. The role of sensitization in the development of disease outcomes has been well established in several animal models. We have described here the varying gross pathology that result from lack of sensitization with heat-killed M. bovis prior to high-dose bronchoscopic infection with live bacilli.     

Microsatellite analysis of Damask rose (<Emphasis Type="Italic">Rosa damascena</Emphasis> Mill.) accessions from various regions in Iran reveals multiple genotypes

Background  

Damask roses (Rosa damascena Mill.) are mainly used for essential oil production. Previous studies have indicated that all production material in Bulgaria and Turkey consists of only one genotype. Nine polymorphic microsatellite markers were used to analyze the genetic diversity of 40 accessions of R. damascena collected across major and minor rose oil production areas in Iran.     

Determination of GHG contributions by subsystems in the oil palm supply chain using the LCA approach

Purpose  

With increasing attention on sustainable development, the environmental and social relevance of palm oil production are now important trade issues. The life cycle assessment (LCA) study of Malaysian oil palm products from mineral soils including palm biodiesel was aimed to provide baseline information on the environmental performance of the industry for drawing up policies pertaining to the sustainable production. The share of greenhouse gas (GHG) contribution by the various subsystems in the oil palm supply chain is considered here.     

Visualization of three-way comparisons of omics data

Background  

Density plot visualizations (also referred to as heat maps or color maps) are widely used in different fields including large-scale omics studies in biological sciences. However, the current color-codings limit the visualizations to single datasets or pairwise comparisons.     

LAMINA: a tool for rapid quantification of leaf size and shape parameters

Background  

An increased understanding of leaf area development is important in a number of fields: in food and non-food crops, for example short rotation forestry as a biofuels feedstock, leaf area is intricately linked to biomass productivity; in paleontology leaf shape characteristics are used to reconstruct paleoclimate history. Such fields require measurement of large collections of leaves, with resulting conclusions being highly influenced by the accuracy of the phenotypic measurement process.     

A possible alternative method for collecting mosquito larvae in rice fields

Background  

Rice fields are efficient breeding places for malaria vectors in Madagascar. In order to establish as easily as possible if a rice field is an effective larval site for anophelines, we compared classical dipping versus a net as methods of collecting larvae.     

Substance P scavenger enhances antioxidant defenses and prevents prothrombotic effects on the rat lung after acute exposure to oil smoke

Background  

Airborne particulate matter, from cooking oil, smoking, engine exhaust and other sources, is associated with the development of atherosclerosis and myocardial infarction. In order to explore the cellular and molecular events following exposure of rats to lard oil smoke, we measured the generation of reactive oxygen species (ROS), substance P, cellular adhesion molecules, and thrombosis in relation to inhibitors of substance P, the NK-1 receptor, and antioxidants.     

Prediction of β-barrel membrane proteins by searching for restricted domains

Background  

The identification of β-barrel membrane proteins out of a genomic/proteomic background is one of the rapidly developing fields in bioinformatics. Our main goal is the prediction of such proteins in genome/proteome wide analyses.     

Soil-Behaviour of Phytophthora clandestina

Investigations were undertaken to study the nature and behaviour of P. clandestina in soil. The pathogen was recovered only from soil sievings 250–499 μm and 500 μm–0.99 mm, containing small root fragments. In soil the introduced inoculum of the fungus was incapable of saprophytically and competitively colonizing the dead cotyledons of subterranean clover used as bait material. Exposure of the inoculum to increasing numbers of microbes by adding greater proportions of nonsterile fields, oil to the growth medium of the plant had no significant effect on survival rate and fresh shoot weight of subterranean clover. However, microbes present in the field soil reduced the severity of root rot of subterranean clover. P. clandestina was, able to spread between 15–30 mm through pasteurized soil within a period of 20 days.     

Proteome analysis of soybean leaves,hypocotyls and roots under salt stress

Background  

Salinity is one of the most widespread agricultural problems in arid and semi-arid regions that makes fields unproductive, and soil salinization is a serious problem in the entire world. To determine the effects of salt stress on soybean seedlings, a proteomic technique was used.