Spatial pattern indicates an influence of barnacle and ascidian aggregations on the surrounding benthic assemblage

Joint clusters of solitary ascidians Styela spp., Bolthenia echinata (L.), Molgula spp. and barnacles Balanus crenatus Bruguiere in the White Sea subtidal often develop on shells or stones partially buried into muddy sediment. To assess the structuring role of these suspension-feeders' aggregations, we examined the spatial patterns of the surrounding infaunal assemblage. Pairs of cores obtained close to clusters (Close ones) and 20-25 cm away from them (Distant ones) were compared, the distance corresponding to the average distance observed between aggregations. These pairs were spatially grouped in replicas (blocks) tens of meters from each other. Out of 10 dominating invertebrate species found around the clusters (84 in total), 5 demonstrated significant difference in density (N) close to aggregations and between them. All the five, including polychaets Scoloplos armiger (Muller, Orbiniidae), Aricidea nolani (Eliason, Paraonidae), Heteromastus filiformis Zachs (Capitellidae), Chaetozone setosa Malmgren (Cirratulidae) and undetermined oligochaets, were associated with Close cores. Total abundance of polychaets, oligochaets, crustaceans and bivalves was also different in Close and Distant cores and indicated significant correlations (of either sign) with biomass estimates for barnacles and ascidians in each block. Individual mean body weight (IMW) in pairs of cores was different for 3 of 10 dominants, maldanid polychaets being larger close to clusters, and cirratulids being larger between them. For several taxa the difference, observed in both parameters (N and IMW), significantly varied between the replicas.Filter-feeding activity and faeces production are regarded as the main possible factors explaining the effect of barnacles and ascidians presence, since the spatial pattern observed corresponds with feeding types of the infaunal taxa studied. Average distance between the clusters was short enough, which allows us to conclude that the spatial distribution pattern of benthic infaunal species within the research area strongly depends on barnacle and ascidian aggregations mosaic.     

Diversity of LTR retrotransposons and their role in genome reorganization

Current views of retrotransposons possessing long terminal repeats (LTRs) are described. The existing classification and element types isolated by genome organization are considered. Experimental data are summarized to demonstrate that the replicative cycle of a retrotransposon is not restricted to a single cell and that LTR retrotransposons are transferred between somatic cells with a rate comparable with the element transposition rate within the genome of one cell. The major mechanisms mediating the role of LTR retrotransposons in reorganization of the genome are considered with regard to the strategies of their horizontal and vertical transfer.__________Translated from Genetika, Vol. 41, No. 4, 2005, pp. 542–548.Original Russian Text Copyright © 2005 by Syomin, Ilyin.     

Copper-induced liver fibrosis affects the behavior of bone marrow cells in primary culture

Background

The present study investigated the effects of low-molecular-weight components of bovine colostrum (LMCC), which were administered per os, on the differentiation, growth, and survival of cells obtained from the bone marrow of rats in primary culture.

Methods

Bone marrow cells (BMCs) were obtained from both the rat femurs and were cultured in medium 199 supplemented with antibiotics (8% streptomycin and 8% gentamycin) and 20% inactivated fetal calf serum. In addition, the number of BMCs was counted and their morphotypes were determined.

Results

Animals were treated with copper (Cu) sulfate to induce liver fibrosis. Subsequent treatment with LMCC eliminated growth inhibition and normalized the bodyweight and temperature of animals with Cu-induced liver fibrosis. The number of lymphocytes in the bone marrow of animals with Cu-induced liver fibrosis was significantly higher than that in the bone marrow of control animals. The number of neutrophils in untreated animals with liver fibrosis and LMCC-treated animals with liver fibrosis was lower than that in control animals. Neutrophils obtained from untreated animals with liver fibrosis and LMCC-treated animals with liver fibrosis underwent two-times faster degradation in vitro than neutrophils obtained from control animals.

Conclusions

Our results indicate that LMCC affects the distribution of different morphological types of BMCs but does not prevent their degradation in vitro, which was two-times faster than that of BMCs obtained from control animals.

     

Tools for comparative protein structure modeling and analysis

The following resources for comparative protein structure modeling and analysis are described (http://salilab.org): MODELLER, a program for comparative modeling by satisfaction of spatial restraints; MODWEB, a web server for automated comparative modeling that relies on PSI-BLAST, IMPALA and MODELLER; MODLOOP, a web server for automated loop modeling that relies on MODELLER; MOULDER, a CPU intensive protocol of MODWEB for building comparative models based on distant known structures; MODBASE, a comprehensive database of annotated comparative models for all sequences detectably related to a known structure; MODVIEW, a Netscape plugin for Linux that integrates viewing of multiple sequences and structures; and SNPWEB, a web server for structure-based prediction of the functional impact of a single amino acid substitution.     

High-throughput siRNA-based functional target validation

The drug discovery process pursued by major pharmaceutical companies for many years starts with target identification followed by high-throughput screening (HTS) with the goal of identifying lead compounds. To accomplish this goal, significant resources are invested into automation of the screening process or HTS. Robotic systems capable of handling thousands of data points per day are implemented across the pharmaceutical sector. Many of these systems are amenable to handling cell-based screening protocols as well. On the other hand, as companies strive to develop innovative products based on novel mechanisms of action(s), one of the current bottlenecks of the industry is the target validation process. Traditionally, bioinformatics and HTS groups operate separately at different stages of the drug discovery process. The authors describe the convergence and integration of HTS and bioinformatics to perform high-throughput target functional identification and validation. As an example of this approach, they initiated a project with a functional cell-based screen for a biological process of interest using libraries of small interfering RNA (siRNA) molecules. In this protocol, siRNAs function as potent gene-specific inhibitors. siRNA-mediated knockdown of the target genes is confirmed by TaqMan analysis, and genes with impacts on biological functions of interest are selected for further analysis. Once the genes are confirmed and further validated, they may be used for HTS to yield lead compounds.