A model of evolution and structure for multiple sequence alignment

We have developed a phylogeny-aware progressive alignment method that recognizes insertions and deletions as distinct evolutionary events and thus avoids systematic errors created by traditional alignment methods. We now extend this method to simultaneously model regional heterogeneity and evolution. This novel method can be flexibly adapted to alignment of nucleotide or amino acid sequences evolving under processes that vary over genomic regions and, being fully probabilistic, provides an estimate of regional heterogeneity of the evolutionary process along the alignment and a measure of local reliability of the solution. Furthermore, the evolutionary modelling of substitution process permits adjusting the sensitivity and specificity of the alignment and, if high specificity is aimed at, leaving sequences unaligned when their divergence is beyond a meaningful detection of homology.     

MALIDUP: a database of manually constructed structure alignments for duplicated domain pairs

We describe MALIDUP (manual alignments of duplicated domains), a database of 241 pairwise structure alignments for homologous domains originated by internal duplication within the same polypeptide chain. Since duplicated domains within a protein frequently diverge in function and thus in sequence, this would be the first database of structurally similar homologs that is not strongly biased by sequence or functional similarity. Our manual alignments in most cases agree with the automatic structural alignments generated by several commonly used programs. This carefully constructed database could be used in studies on protein evolution and as a reference for testing structure alignment programs. The database is available at http://prodata.swmed.edu/malidup.     

Killing bacteria present on surfaces in films or in droplets using microwave UV lamps

The killing of bacteria on surfaces by two types of UV sources generated by microwave radiation is described. In both cases, UV radiation is produced by gas-discharge electrodeless lamps (Ar/Hg) excited by microwaves generated by a power supply from a standard domestic microwave oven. For UV lamp excitation, one of these sources makes use of a coaxial line with a truncated outer electrode that allows the excitation of gases and gaseous mixtures over a wide range of pressures at a comparatively low microwave power. In the second source, UV lamps are placed inside a microwave oven. Ultraviolet generated by the two sources was used to destroy vegetative Escherichia coli bacteria dispersed in thin films and in droplets on surfaces. Two types of UV lamps were used in the study. The first was constructed of quartz that filtered UV below 200 nm preventing the dissociation of oxygen in air and, hence, ozone production. The second type of tube was transparent to UV below 200 nm facilitating ozone production in air surrounding it. It was shown that bacterial cells dispersed in films on surfaces are killed more rapidly than cells present in droplets when using the lamps producing ozone and UV radiation. The UV sources described can effect rapid killing and constitute a cost-effective treatment of food and other surfaces, and, the destruction of airborne viruses and bacteria. The lamps can also be utilised for the rapid eradication of microorganisms in liquids.     

Natural variation in four human collagen genes across an ethnically diverse population

Collagens are members of one of the most important families of structural proteins in higher organisms. There are 28 types of collagens encoded by 43 genes in humans that fall into several different functional protein classes. Mutations in the major fibrillar collagen genes lead to osteogenesis imperfecta (COL1A1 and COL1A2 encoding the chains of Type I collagen), chondrodysplasias (COL2A1 encoding the chains of Type II collagen), and vascular Ehlers-Danlos syndrome (COL3A1 encoding the chains of Type III collagen). Over the past 2 decades, mutations in these collagen genes have been catalogued, in hopes of understanding the molecular etiology of diseases caused by these mutations, characterizing the genotype-phenotype relationships, and developing robust models predicting the molecular and clinical outcomes. To achieve these goals better, it is necessary to understand the natural patterns of variation in collagen genes in human populations. We screened exons, flanking intronic regions, and conserved noncoding regions for variations in COL1A1, COL1A2, COL2A1, and COL3A1 in 48 individuals from each of four ethnically diverse populations. We identified 459 single-nucleotide polymorphisms (SNPs), more than half of which were novel and not found in public databases. Of the 52 SNPs found in coding regions, 15 caused amino acid substitutions while 37 did not. Although the four collagens have similar gene and protein structures, they have different molecular evolutionary characteristics. For example, COL1A1 appears to have been under substantially stronger negative selection than the rest. Phylogenetic analysis also suggests that the four genes have very different evolutionary histories among the different ethnic groups. Our observations suggest that the study of collagen mutations and their relationships with disease phenotypes should be performed in the context of the genetic background of the subjects.     

DNA methylation in mouse embryonic stem cells and development

Mammalian development is associated with considerable changes in global DNA methylation levels at times of genomic reprogramming. Normal DNA methylation is essential for development but, despite considerable advances in our understanding of the DNA methyltransferases, the reason that development fails when DNA methylation is deficient remains unclear. Furthermore, although much is known about the enzymes that cause DNA methylation, comparatively little is known about the mechanisms or significance of active demethylation in early development. In this review, we discuss the roles of the various DNA methyltransferases and their likely functions in development.     

Evaluation of a fully automated method to measure the critical removal stress of adult barnacles

A computer-controlled force gauge designed to measure the adhesive strength of barnacles on test substrata is described. The instrument was evaluated with adult barnacles grown in situ on Silastic T2(R)-coated microscope slides and epoxy replicas adhered to the same substratum with synthetic adhesive. The force per unit area required to detach the barnacles (critical removal stress) using the new automated system was comparable to that obtained with ASTM D5618 (1994) (0.19 and 0.28 MPa compared with 0.18 and 0.27 MPa for two batches of barnacles). The automated method showed a faster rate of force development compared with the manual spring force gauge used for ASTM D5618 (1994). The new instrument was as accurate and precise at determining surface area as manual delineation used with ASTM D5618 (1994). The method provided significant advantages such as higher throughput speed, the ability to test smaller barnacles (which took less time to grow) and to control the force application angle and speed. The variability in measurements was lower than previously reported, suggesting an improved ability to compare the results obtained by different researchers.     

Molecular basis of resistance to cytochrome bc1 inhibitors

Inhibitors of the mitochondrial respiratory chain enzyme cytochrome bc ₁ (respiratory complex III) have been developed as antimicrobial agents. They are used in agriculture to control plant pathogenic fungi and in medicine against human pathogens, such as the malaria parasite Plasmodium falciparum , or Pneumocystis jiroveci (an opportunistic pathogenic fungus life-threatening in immuno-compromised patients). These respiratory inhibitors are thus effective against a broad range of important pathogens. Unfortunately, the problem of acquired resistance has rapidly emerged. A growing number of pathogen isolates resistant to inhibitor treatment have been reported, and this resistance is often linked to mutation within cytochrome b , one of the essential catalytic subunits of the complex. Saccharomyces cerevisiae is an invaluable model in order to assess the impact of the mutations on the sensitivity to the drugs, on the respiratory capacity and the fitness of cells. In this minireview, the inhibitors, their mode of action, and the mutations implicated in resistance and studied in yeast are briefly reviewed. Four mutations that are of particular importance in medicine and in agriculture are briefly reviewed and described in more detail and the molecular basis of resistance and of evolution of the mutations is discussed succinctly.     

Determination and validation of principal gene products

MOTIVATION: Alternative splicing has the potential to generate a wide range of protein isoforms. For many computational applications and for experimental research, it is important to be able to concentrate on the isoform that retains the core biological function. For many genes this is far from clear. RESULTS: We have combined five methods into a pipeline that allows us to detect the principal variant for a gene. Most of the methods were based on conservation between species, at the level of both gene and protein. The five methods used were the conservation of exonic structure, the detection of non-neutral evolution, the conservation of functional residues, the existence of a known protein structure and the abundance of vertebrate orthologues. The pipeline was able to determine a principal isoform for 83% of a set of well-annotated genes with multiple variants.