Tradescantia-Micronucleus (Trad-MCN) tests on 140 health-related agents

The Tradescantia-Micronucleus (Trad-MCN) test is a simple short-term bioassay for various gaseous and liquid forms of chemical agents, and physical agents such as radiation. 140 agents, directly or indirectly related to human health, were screened for their mutagenicity. Plant cuttings of young inflorescences, in which the pollen mother cells undergo various stages of meiosis, were maintained in nutrient solution for experimentation. Treatments were made either by absorption of the soluble agents through the stem, by diffusion of gaseous agents through the leaves and buds, by exposure to internal/external radiation or by in situ exposure to air pollutants. Micronuclei formed from damaged chromosomes served as the indicators of mutagenicity. Results of 140 agents tested are listed in 9 different categories. (1) Carcinogens/mutagens, (2) common beverages, (3) common chemicals, (4) drugs, (5) pesticides, (6) common household chemicals, (7) radiation and radioisotopes, (8) in situ monitoring, (9) complex environmental mixtures. Out of 140 agents tested, 52 showed positive, 20 showed borderline positive responses and 5 showed strong toxicity. Test results of 41 agents in the present study showed 67% congruity with Ames test results found in the literature.     

Ecosystem quality in LCIA: status quo,harmonization, and suggestions for the way forward

Purpose

Life cycle impact assessment (LCIA) results are used to assess potential environmental impacts of different products and services. As part of the UNEP-SETAC life cycle initiative flagship project that aims to harmonize indicators of potential environmental impacts, we provide a consensus viewpoint and recommendations for future developments in LCIA related to the ecosystem quality area of protection (AoP). Through our recommendations, we aim to encourage LCIA developments that improve the usefulness and global acceptability of LCIA results.

Methods

We analyze current ecosystem quality metrics and provide recommendations to the LCIA research community for achieving further developments towards comparable and more ecologically relevant metrics addressing ecosystem quality.

Results and discussion

We recommend that LCIA development for ecosystem quality should tend towards species-richness-related metrics, with efforts made towards improved inclusion of ecosystem complexity. Impact indicators—which result from a range of modeling approaches that differ, for example, according to spatial and temporal scale, taxonomic coverage, and whether the indicator produces a relative or absolute measure of loss—should be framed to facilitate their final expression in a single, aggregated metric. This would also improve comparability with other LCIA damage-level indicators. Furthermore, to allow for a broader inclusion of ecosystem quality perspectives, the development of an additional indicator related to ecosystem function is recommended. Having two complementary metrics would give a broader coverage of ecosystem attributes while remaining simple enough to enable an intuitive interpretation of the results.

Conclusions

We call for the LCIA research community to make progress towards enabling harmonization of damage-level indicators within the ecosystem quality AoP and, further, to improve the ecological relevance of impact indicators.

     

Mitochondrial gene divergence of Colombian Drosophila pseudoobscura

Isolated populations of drosophila pseudoobscura, separated from North American populations by about 2,400 km, were found in Colombia in 1960. We compared for sequences of the small ribosomal RNA (srRNA) gene on the mitochondria between North American and Colombian D. pseudoobscura in order to clarify the age of the Colombian isolates. The North American populations were not genetically different from each other but were genetically different from the Colombian populations. The Mexican strains represent the area from which the Colombian founders might have come. The estimated net nucleotide divergence between Mexican and Colombian D. pseudoobscura indicates that the Colombian population is not an ancient lineage. Phylogenies using both distance and parsimony methodologies reinforced this conclusion. The Colombian samples group together with both methods but, according to the bootstrap analysis, not significantly. It appears that the populations have not been separated long enough for their DNA sequences to show much divergence.      

HotPatch: a statistical approach to finding biologically relevant features on protein surfaces

We describe a fully automated algorithm for finding functional sites on protein structures. Our method finds surface patches of unusual physicochemical properties on protein structures, and estimates the patches' probability of overlapping functional sites. Other methods for predicting the locations of specific types of functional sites exist, but in previous analyses, it has been difficult to compare methods when they are applied to different types of sites. Thus, we introduce a new statistical framework that enables rigorous comparisons of the usefulness of different physicochemical properties for predicting virtually any kind of functional site. The program's statistical models were trained for 11 individual properties (electrostatics, concavity, hydrophobicity, etc.) and for 15 neural network combination properties, all optimized and tested on 15 diverse protein functions. To simulate what to expect if the program were run on proteins of unknown function, as might arise from structural genomics, we tested it on 618 proteins of diverse mixed functions. In the higher-scoring top half of all predictions, a functional residue could typically be found within the first 1.7 residues chosen at random. The program may or may not use partial information about the protein's function type as an input, depending on which statistical model the user chooses to employ. If function type is used as an additional constraint, prediction accuracy usually increases, and is particularly good for enzymes, DNA-interacting sites, and oligomeric interfaces. The program can be accessed online (at http://hotpatch.mbi.ucla.edu).     

R5 Strains of Human Immunodeficiency Virus Type 1 from Rapid Progressors Lacking X4 Strains Do Not Possess X4-Type Pathogenicity in Human Thymus

Some individuals infected with only R5 strains of human immunodeficiency virus type 1 progress to AIDS as quickly as individuals harboring X4 strains. We determined that three R5 viruses were much less pathogenic than an X4 virus in SCID-hu Thy/Liv mice, suggesting that R5 virus-mediated rapid disease progression is associated with host, not viral, factors.     

The Tyrosine Kinase Inhibitor Genistein Increases Endogenous Dopamine Release from Normal and Weaver Mutant Mouse Striatal Slices

Abstract: Protein tyrosine kinases that are known to have major roles in the control of cell growth and transformation are abundant and have numerous phosphoprotein substrates in the adult CNS. Although less well characterized than serine/threonine kinases, tyrosine kinases are also concentrated in the synapse. The effect of genistein, a selective inhibitor of tyrosine kinase activity, was examined on the in vitro release of endogenous dopamine (DA) from superfused mouse striatal slices. Fractional release of DA was significantly increased over basal release levels by genistein (100 and 200 µ M ). The effect was concentration dependent and rapidly reversible on washout of the kinase inhibitor. No significant change from basal release levels was observed with two structural analogues of genistein that do not inhibit tyrosine kinase activity at the same concentration. We have previously described alterations in basal and evoked DA release from the striatum of the weaver ( wv/wv ) mutant mouse, and genotypic differences in fractional release were also observed with genistein stimulation. The total evoked release was 25–50% greater from the wv/wv striatum. These results suggest a modulatory role for tyrosine kinase activity in neurotransmitter release and perhaps an alteration of kinase-regulated mechanisms in the DA-deficient wv/wv striatum.     

GTC: A web server for integrating systems biology data with web tools and desktop applications

Gaggle Tool Creator (GTC) is a web application which provides access to public annotation, interaction, orthology, and genomic data for hundreds of organisms, and enables instant analysis of the data using many popular web-based and desktop applications.     

The role of the Vlax Roma in shaping the European Romani maternal genetic history

The Roma are comprised of many founder groups of common Indian origins but different socio-cultural characteristics. The Vlax Roma are one of the founder Roma populations characterized by a period of bondage in the historic Romanian principalities, and by the archaic Romanian language. Demographic history suggests different migration routes of Roma populations, especially after their arrival in Mesopotamia and the eastern boundary of the Byzantine Empire. Although various genetic studies of uniparental genetic markers showed a connection between Roma genetic legacy and their migration routes, precise sampling of Roma populations elucidates this relationship in more detail. In this study, we analyzed mitochondrial DNA of 384 Croatian Vlax Roma from two geographic locations in the context of 734 European Roma samples. Our results show that Roma migration routes are marked with two Near-Eastern haplogroups, X2 and U3, whose inverse proportional incidence clearly separates the Balkan and the Vlax Roma from other Roma populations that reached Europe as part of the first migration wave. Spatial and temporal characteristics of these haplogroups indicate a possibility of their admixture with Roma populations before arrival in Europe. Distribution of haplogroup M35 indicates that all Vlax Roma populations descend from one single founder population that might even reach back to the original ancestral Indian population. Founder effects followed by strict endogamy rules can be traced from India to contemporary small, local communities, as in the case of two Croatian Vlax Roma populations that show clear population differentiation despite similar origins and shared demographic history.     

Development of a cost-effective high-throughput process of microsatellite analysis involving miniaturized multiplexed PCR amplification and automated allele identification

Background

Microsatellites are nucleotide sequences of tandem repeats occurring throughout the genome, which have been widely used in genetic linkage analysis, studies of loss of heterozygosity, determination of lineage and clonality, and the measurement of genome instability or the emergence of drug resistance reflective of mismatch repair deficiency. Such analyses may involve the parallel evaluation of many microsatellite loci, which are often limited by sample DNA, are labor intensive, and require large data processing.

Results

To overcome these challenges, we developed a cost-effective high-throughput approach of microsatellite analysis, in which the amplifications of microsatellites are performed in miniaturized, multiplexed polymerase chain reaction (PCR) adaptable to 96 or 384 well plates, and accurate automated allele identification has been optimized with a collective reference dataset of 5,508 alleles using the GeneMapper software.

Conclusions

In this investigation, we have documented our experience with the optimization of multiplex PCR conditions and automated allele identification, and have generated a unique body of data that provide a starting point for a cost-effective, high-throughput process of microsatellite analysis using the studied markers.