Nuclear and plastid haplotypes suggest rapid diploid and polyploid speciation in the N Hemisphere <Emphasis Type="BoldItalic">Achillea millefolium</Emphasis>complex (Asteraceae)

Background  

Species complexes or aggregates consist of a set of closely related species often of different ploidy levels, whose relationships are difficult to reconstruct. The N Hemisphere Achillea millefolium aggregate exhibits complex morphological and genetic variation and a broad ecological amplitude. To understand its evolutionary history, we study sequence variation at two nuclear genes and three plastid loci across the natural distribution of this species complex and compare the patterns of such variations to the species tree inferred earlier from AFLP data.     

Influence of plant diversity and elevated atmospheric carbon dioxide levels on belowground bacterial diversity

Background  

Changes in aboveground plant species diversity as well as variations of environmental conditions such as exposure of ecosystems to elevated concentrations of atmospheric carbon dioxide may lead to changes in metabolic activity, composition and diversity of belowground microbial communities, both bacterial and fungal.     

Structure of <Emphasis Type="Italic">Arabidopsis thaliana</Emphasis> 5-methylthioribose kinase reveals a more occluded active site than its bacterial homolog

Background  

Metabolic variations exist between the methionine salvage pathway of humans and a number of plants and microbial pathogens. 5-Methylthioribose (MTR) kinase is a key enzyme required for methionine salvage in plants and many bacteria. The absence of a mammalian homolog suggests that MTR kinase is a good target for the design of specific herbicides or antibiotics.     

Two common nonsynonymous paraoxonase 1 (<Emphasis Type="Italic">PON1</Emphasis>) gene polymorphisms and brain astrocytoma and meningioma

Background  

Human serum paraoxonase 1 (PON1) plays a major role in the metabolism of several organophosphorus compounds. The enzyme is encoded by the polymorphic gene PON1, located on chromosome 7q21.3. Aiming to identify genetic variations related to the risk of developing brain tumors, we investigated the putative association between common nonsynonymous PON1 polymorphisms and the risk of developing astrocytoma and meningioma.     

Synthesis and characterization of core-shell Fe<Subscript>3</Subscript>O<Subscript>4</Subscript>-gold-chitosan nanostructure

Background  

Fe₃O₄-gold-chitosan core-shell nanostructure can be used in biotechnological and biomedical applications such as magnetic bioseparation, water and wastewater treatment, biodetection and bioimaging, drug delivery, and cancer treatment.     

Variation in DNA methylation patterns of grapevine somaclones (<Emphasis Type="Italic">Vitis vinifera L</Emphasis>.)

Background  

In traditional vine areas, the production should present a typicity that partly depends on the grapevine variety. Therefore, vine improvement is considered difficult because of the limited choice in the natural variability of the cultivars within the limits of their characteristics. A possibility to circumvent this problem is the use of somatic variability. In vitro somatic embryogenesis and organogenesis can lead to genotypic and phenotypic variations, described as somaclonal variation, that could be useful for the selection of improved grapevine genotypes.     

Predicting the phenotypic effects of non-synonymous single nucleotide polymorphisms based on support vector machines

Background  

Human genetic variations primarily result from single nucleotide polymorphisms (SNPs) that occur approximately every 1000 bases in the overall human population. The non-synonymous SNPs (nsSNPs) that lead to amino acid changes in the protein product may account for nearly half of the known genetic variations linked to inherited human diseases. One of the key problems of medical genetics today is to identify nsSNPs that underlie disease-related phenotypes in humans. As such, the development of computational tools that can identify such nsSNPs would enhance our understanding of genetic diseases and help predict the disease.     

Environmental assessment of the Atlantic mackerel (<Emphasis Type="Italic">Scomber scombrus</Emphasis>) season in the Basque Country. Increasing the timeline delimitation in fishery LCA studies

Purpose  

The purpose of this study was to evaluate the environmental impacts linked to fish extraction on a temporal basis, in order to analyze the effect that stock abundance variations may have on reporting environmental burdens. Inventory data for the North-East Atlantic Mackerel (NEAM) fishing season were collected over an 8-year period and used to carry out a life cycle assessment (LCA). The selected fishery corresponds to the Basque coastal purse seining fleet.     

A non-sense mutation in the putative anti-mutator gene <Emphasis Type="Italic">ada/alkA</Emphasis> of <Emphasis Type="Italic">Mycobacterium tuberculosis</Emphasis> and <Emphasis Type="Italic">M. bovis</Emphasis> isolates suggests convergent evolution

Background  

Previous studies have suggested that variations in DNA repair genes of W-Beijing strains may have led to transient mutator phenotypes which in turn may have contributed to host adaptation of this strain family. Single nucleotide polymorphism (SNP) in the DNA repair gene mutT1 was identified in MDR-prone strains from the Central African Republic. A Mycobacteriumtuberculosis H37Rv mutant inactivated in two DNA repair genes, namely ada/alkA and ogt, was shown to display a hypermutator phenotype. We then looked for polymorphisms in these genes in Central African Republic strains (CAR).     

Widespread pyocyanin over-production among isolates of a cystic fibrosis epidemic strain

Background  

Some isolates of the Liverpool cystic fibrosis epidemic strain of Pseudomonas aeruginosa exhibit an unusual virulence-related phenotype, characterized by over-production of quorum sensing-regulated exoproducts such as pyocyanin and LasA protease. Our aim was to determine the prevalence of this unusual phenotype amongst isolates of the epidemic strain, and to study other intraclonal phenotypic and genotypic variations.     

Using Generalized Procrustes Analysis (GPA) for normalization of cDNA microarray data

Background  

Normalization is essential in dual-labelled microarray data analysis to remove non-biological variations and systematic biases. Many normalization methods have been used to remove such biases within slides (Global, Lowess) and across slides (Scale, Quantile and VSN). However, all these popular approaches have critical assumptions about data distribution, which is often not valid in practice.     

Mixture models for analysis of melting temperature data

Background  

In addition to their use in detecting undesired real-time PCR products, melting temperatures are useful for detecting variations in the desired target sequences. Methodological improvements in recent years allow the generation of high-resolution melting-temperature (T_m) data. However, there is currently no convention on how to statistically analyze such high-resolution T_m data.     

Aspects of coverage in medical DNA sequencing

Background  

DNA sequencing is now emerging as an important component in biomedical studies of diseases like cancer. Short-read, highly parallel sequencing instruments are expected to be used heavily for such projects, but many design specifications have yet to be conclusively established. Perhaps the most fundamental of these is the redundancy required to detect sequence variations, which bears directly upon genomic coverage and the consequent resolving power for discerning somatic mutations.     

Metabolic response of <Emphasis Type="Italic">Geobacter sulfurreducens</Emphasis> towards electron donor/acceptor variation

Background  

Geobacter sulfurreducens is capable of coupling the complete oxidation of organic compounds to iron reduction. The metabolic response of G. sulfurreducens towards variations in electron donors (acetate, hydrogen) and acceptors (Fe(III), fumarate) was investigated via ¹³C-based metabolic flux analysis. We examined the ¹³C-labeling patterns of proteinogenic amino acids obtained from G. sulfurreducens cultured with ¹³C-acetate.     

Normalization method for metabolomics data using optimal selection of multiple internal standards

Background  

Success of metabolomics as the phenotyping platform largely depends on its ability to detect various sources of biological variability. Removal of platform-specific sources of variability such as systematic error is therefore one of the foremost priorities in data preprocessing. However, chemical diversity of molecular species included in typical metabolic profiling experiments leads to different responses to variations in experimental conditions, making normalization a very demanding task.     

Comparative analysis of the <Emphasis Type="Italic">Saccharomyces cerevisiae</Emphasis> and <Emphasis Type="Italic">Caenorhabditis elegans</Emphasis> protein interaction networks

Background  

Protein interaction networks aim to summarize the complex interplay of proteins in an organism. Early studies suggested that the position of a protein in the network determines its evolutionary rate but there has been considerable disagreement as to what extent other factors, such as protein abundance, modify this reported dependence.     

Swarming and complex pattern formation in <Emphasis Type="Italic">Paenibacillus vortex</Emphasis> studied by imaging and tracking cells

Background  

Swarming motility allows microorganisms to move rapidly over surfaces. The Gram-positive bacterium Paenibacillus vortex exhibits advanced cooperative motility on agar plates resulting in intricate colonial patterns with geometries that are highly sensitive to the environment. The cellular mechanisms that underpin the complex multicellular organization of such a simple organism are not well understood.     

<Emphasis Type="Italic">Gen</Emphasis><Superscript><Emphasis Type="Italic">Htr</Emphasis></Superscript>: a tool for comparative assessment of genetic heterogeneity in microbial genomes generated by massive short-read sequencing

Background  

Microevolution is the study of short-term changes of alleles within a population and their effects on the phenotype of organisms. The result of the below-species-level evolution is heterogeneity, where populations consist of subpopulations with a large number of structural variations. Heterogeneity analysis is thus essential to our understanding of how selective and neutral forces shape bacterial populations over a short period of time. The Solexa Genome Analyzer, a next-generation sequencing platform, allows millions of short sequencing reads to be obtained with great accuracy, allowing for the ability to study the dynamics of the bacterial population at the whole genome level. The tool referred to as Gen ^Htr was developed for genome-wide heterogeneity analysis.     

Cloning and characterization of a 9-lipoxygenase gene induced by pathogen attack from <Emphasis Type="Italic">Nicotiana benthamiana</Emphasis>for biotechnological application

Background  

Plant lipoxygenases (LOXs) have been proposed to form biologically active compounds both during normal developmental stages such as germination or growth as well as during responses to environmental stress such as wounding or pathogen attack. In our previous study, we found that enzyme activity of endogenous 9-LOX in Nicotiana benthamiana was highly induced by agroinfiltration using a tobacco mosaic virus (TMV) based vector system.     

Polymorphism in the flanking regions of the PbGP43 gene from the human pathogen Paracoccidioides brasiliensis: search for protein binding sequences and poly(A) cleavage sites

Background  

Paracoccidioides brasiliensis is a thermo-dimorphic fungus that causes paracoccidiodomycosis (PCM). Glycoprotein gp43 is the fungal main diagnostic antigen, which can also protect against murine PCM and interact with extracellular matrix proteins. It is structurally related to glucanases, however not active, and whose expression varies considerably. We have presently studied polymorphisms in the PbGP43 flanking regions to help understand such variations.