Kalign – an accurate and fast multiple sequence alignment algorithm

Background  

The alignment of multiple protein sequences is a fundamental step in the analysis of biological data. It has traditionally been applied to analyzing protein families for conserved motifs, phylogeny, structural properties, and to improve sensitivity in homology searching. The availability of complete genome sequences has increased the demands on multiple sequence alignment (MSA) programs. Current MSA methods suffer from being either too inaccurate or too computationally expensive to be applied effectively in large-scale comparative genomics.     

Protein tyrosine phosphatases and the immune response

Reversible tyrosine phosphorylation of proteins is a key regulatory mechanism for numerous important aspects of eukaryotic physiology and is catalysed by kinases and phosphatases. Together, cells of the immune system express at least half of the 107 protein tyrosine phosphatase (PTP) genes in the human genome, most of which encode multidomain proteins that contain protein- and phospholipid-interaction domains. Here, we discuss the diverse but specific, and important, roles that PTPs have in immune cells, focusing mainly on T and B cells, and we highlight recent evidence that even subtle alterations in PTPs can cause immune dysfunction and human disease.     

Removal of C-terminal SRC kinase from the immune synapse by a new binding protein

The Csk tyrosine kinase negatively regulates the Src family kinases Lck and Fyn in T cells. Engagement of the T-cell antigen receptor results in a removal of Csk from the lipid raft-associated transmembrane protein PAG/Cbp. Instead, Csk becomes associated with an approximately 72-kDa tyrosine-phosphorylated protein, which we identify here as G3BP, a phosphoprotein reported to bind the SH3 domain of Ras GTPase-activating protein. G3BP reduced the ability of Csk to phosphorylate Lck at Y505 by decreasing the amount of Csk in lipid rafts. As a consequence, G3BP augmented T-cell activation as measured by interleukin-2 gene activation. Conversely, elimination of endogenous G3BP by RNA interference increased Lck Y505 phosphorylation and reduced TCR signaling. In antigen-specific T cells, endogenous G3BP moved into a intracellular location adjacent to the immune synapse, but deeper inside the cell, upon antigen recognition. Csk colocalization with G3BP occurred in this "parasynaptic" location. We conclude that G3BP is a new player in T-cell-antigen receptor signaling and acts to reduce the amount of Csk in the immune synapse.     

Synthesis and characterization of hexadecadienyl compounds with a conjugated diene system,sex pheromone of the persimmon fruit moth and related compounds

Hexadecadien-1-ol and the derivatives (acetate and aldehyde) with a conjugated diene system have recently been identified from a pheromone gland extract of the persimmon fruit moth (Stathmopoda masinissa), a pest insect of persimmon fruits distributed in East Asia. The alcohol and acetate showed their base peaks at m/z 79 in a GC-MS analysis by electron impact ionization, but the aldehyde produced a unique base peak at m/z 84, suggesting a 4,6-diene structure. To confirm this inference, four geometrical isomers of each 4,6-hexadecadienyl compound were synthesized by two different routes in which one of two double bonds was furnished in a highly stereoselective manner. Separation of the two isomers synthesized together by each route was facilely accomplished by preparative HPLC. Their mass spectra coincided well with those of natural components, indicating that they were available for use as authentic standards for determining the configuration of the natural pheromone. Furthermore, other hexadecadienyl compounds, including the conjugated diene system between the 3- and 10-positions, were synthesized to accumulate the spectral data of pheromone candidates. 5,7-Hexadecadienal interestingly showed the base peak at m/z 80; meanwhile, the base peaks of its alcohol and acetate were detected at m/z 79 like the corresponding 4,6-dienes. The base peaks of all 6,8-, 7,9-, and 8,10-dienes universally appeared at m/z 67 like 9,11-, 10,12-, and 13,15-dienes, the spectra of which have already been published. Although 3,5-hexadecadienal was not prepared, base peaks at m/z 67 and 79 were recorded for the alcohol and acetate, respectively.     

Resveratrol reverses tumor-promoter-induced inhibition of gap-junctional intercellular communication

The naturally occurring stilbene/alexin trans-resveratrol (trans-3,5, 4'-trihydroxystilbene) is a promising agent for the prevention of cancer. We investigated the effect of resveratrol on gap-junctional intercellular communication (GJIC) in WB-F344 rat liver epithelial cells because inhibition of GJIC is an important mechanism of tumor promotion. Seventeen to 50 microM resveratrol increased GJIC significantly by a factor of 1.3 compared with solvent vehicle controls, when the WB-F344 cells were exposed to resveratrol for 6 h. Most tumor promoters, including the phorbol ester TPA and the insecticide DDT, block GJIC. Resveratrol at 17-50 microM also significantly prevented down-regulation of GJIC by TPA and DDT, by a factor of 2.7 and 1.8, respectively. This recovery of GJIC from TPA inhibition was partly correlated with hindered hyperphosphorylation of Cx43. In conclusion, resveratrol was found to enhance GJIC and counteract the effects of tumor promoters on GJIC, and this is likely a mechanism that contributes to the antipromotional and anticarcinogenic properties of resveratrol.     

Phylogenetic relationships of the tribe Operophterini (Lepidoptera, Geometridae): a case study of the evolution of female flightlessness

A molecular phylogenetic analysis was conducted in order to reconstruct the evolution of female flightlessness in the geometrid tribe Operophterini (Lepidoptera, Geometridae, Larentiinae). DNA variation in four nuclear gene regions, segments D1 and D2 of 28S rRNA, elongation factor 1α , and wingless , was examined from 22 species representing seven tribes of Larentiinae and six outgroup species. Direct optimization was used to infer a phylogenetic hypothesis from the combined sequence data set. The results obtained confirmed that Operophterini (including Malacodea ) is a monophyletic group, and Perizomini is its sister group. Within Operophterini, the genus Malacodea is the sister group to the genera Operophtera and Epirrita , which form a monophyletic group. This relationship is also supported by morphological data. The results suggest that female flightlessness has evolved independently twice: first in the lineage of Malacodea and, for the second time, in the lineage of Operophtera after its separation from the lineage of Epirrita . An alternative reconstruction (i.e. recovery of flight ability in an ancestor of Epirrita ) appears unlikely for various reasons. The similarities shared by Epirrita with a basal representative of Perizomini, Perizoma didymatum , allow the proposal of a sequence of evolutionary events that has led to flightlessness. It is likely that the transition to female flightlessness in the two lineages of Operophterini occurred after the colonization of stable forest habitats, followed by the evolution of a specific set of permissive traits, including larval polyphagy, limited importance of adult feeding, and adult flight during the cold months of the season.  © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 92 , 241–252.     

Sample storage conditions induce post-collection biases in microbiome profiles

Background

Here we investigated the influence of different stabilization and storage strategies on the quality and composition of the fecal microbial community. Namely, same-day isolated murine DNA was compared to samples stored for 1 month in air at ambient temperature, with or without preservative buffers (i.e. EDTA and lysis buffer), different temperatures (i.e. 4?°C, ??20?°C, and???80?°C), and hypoxic conditions.

Results

Only storage in lysis buffer significantly reduced DNA content, yet without integrity loss. Storage in EDTA affected alpha diversity the most, which was also reflected in cluster separation. Distinct changes were also seen in the phyla and bacterial species abundance per storage strategy. Metabolic function analysis showed 22 pathways not significantly affected by storage conditions, whereas the tyrosine metabolism pathway was significantly changed in all strategies except by EDTA.

Conclusion

Each long-term storage strategy introduced a unique post-collection bias, which is important to take into account when interpreting data.