Lectindb: a plant lectin database

Lectins, a class of carbohydrate-binding proteins, are now widely recognized to play a range of crucial roles in many cell-cell recognition events triggering several important cellular processes. They encompass different members that are diverse in their sequences, structures, binding site architectures, quaternary structures, carbohydrate affinities, and specificities as well as their larger biological roles and potential applications. It is not surprising, therefore, that the vast amount of experimental data on lectins available in the literature is so diverse, that it becomes difficult and time consuming, if not impossible to comprehend the advances in various areas and obtain the maximum benefit. To achieve an effective use of all the data toward understanding the function and their possible applications, an organization of these seemingly independent data into a common framework is essential. An integrated knowledge base ( Lectindb, http://nscdb.bic.physics.iisc.ernet.in ) together with appropriate analytical tools has therefore been developed initially for plant lectins by collating and integrating diverse data. The database has been implemented using MySQL on a Linux platform and web-enabled using PERL-CGI and Java tools. Data for each lectin pertain to taxonomic, biochemical, domain architecture, molecular sequence, and structural details as well as carbohydrate and hence blood group specificities. Extensive links have also been provided for relevant bioinformatics resources and analytical tools. Availability of diverse data integrated into a common framework is expected to be of high value not only for basic studies in lectin biology but also for basic studies in pursuing several applications in biotechnology, immunology, and clinical practice, using these molecules.     

A genome-wide screen for essential yeast genes that affect telomere length maintenance

Telomeres are structures composed of repetitive DNA and proteins that protect the chromosomal ends in eukaryotic cells from fusion or degradation, thus contributing to genomic stability. Although telomere length varies between species, in all organisms studied telomere length appears to be controlled by a dynamic equilibrium between elongating mechanisms (mainly addition of repeats by the enzyme telomerase) and nucleases that shorten the telomeric sequences. Two previous studies have analyzed a collection of yeast deletion strains (deleted for nonessential genes) and found over 270 genes that affect telomere length (Telomere Length Maintenance or TLM genes). Here we complete the list of TLM by analyzing a collection of strains carrying hypomorphic alleles of most essential genes (DAmP collection). We identify 87 essential genes that affect telomere length in yeast. These genes interact with the nonessential TLM genes in a significant manner, and provide new insights on the mechanisms involved in telomere length maintenance. The newly identified genes span a variety of cellular processes, including protein degradation, pre-mRNA splicing and DNA replication.     

A murine pneumonia model to study pathogenesis of <Emphasis Type="Italic">Stenotrophomonas maltophilia</Emphasis>

Early attempts to develop an animal model of infection appeared to support the hypothesis that Stenotrophomonas maltophilia does not cause serious sepsis when bacteria are intravenously administered to mice. This species has also been implicated in an increasing number of infections such as, bacteremia, endocarditis, ophthalmological syndromes, skin lesions, urinary, respiratory tract and gastrointestinal infections. Despite this clinical importance, the mechanisms involved in the pathogenesis of S. maltophilia infections have not been elucidated and the virulence factors of importance in the pathogenesis of S. maltophilia associated pulmonary infection remain to be characterized. The purpose of this study was to establish an infection model using 5 clinical isolates of S. maltophilia in a mouse pneumonia model. All strains were able to establish themselves in respiratory tract with peak of infection occurring at 24 h post infection. The strains were able to cause neutrophil influx, were taken up and intracellularly killed by alveolar macrophages except Sm2 that persisted for a slightly longer time in the macrophages. All strains were resistant to lytic action of serum and survived in blood confirming their ability to cause bacteremia. The strains were cleared from spleen and liver by 7th and 4th day but caused tissue damage that was measured in terms of lipid peroxidation, lactate dehydrogenase activity and histopathological examination of lung tissue homogenate. All strains caused interstitial pneumonitis in lungs of mice.     

QPath: a method for querying pathways in a protein-protein interaction network

Background  

Sequence comparison is one of the most prominent tools in biological research, and is instrumental in studying gene function and evolution. The rapid development of high-throughput technologies for measuring protein interactions calls for extending this fundamental operation to the level of pathways in protein networks.     

A genetic discontinuity in root-nodulating bacteria of cultivated pea in the Indian trans-Himalayas

Evolutionary relationships of 120 root‐nodulating bacteria isolated from the nodules of Pisum sativum cultivated at 22 different locations of the trans‐Himalayan valleys of Lahaul and Spiti in the state of Himachal Pradesh of India were studied using 16S rRNA gene PCR‐RFLP, ERIC‐PCR, sequencing of 16S rRNA, atpD, recA, nodC and nifH genes, carbon‐source utilization pattern (BIOLOG?), and whole‐cell fatty acid profiling. The results demonstrated that all isolates belonged to Rhizobium leguminosarum symbiovar viciae (Rlv). Isolates from the two valleys were clearly separated on the basis of ERIC fingerprints, carbon‐source utilization pattern, and whole‐cell fatty acid methyl esters. Phylogenetic analysis of atpD, recA, nodC and nifH genes revealed a common Rlv sublineage in Spiti valley. Lahaul valley isolates were represented by three sequence types of atpD and recA genes, and four sequence types of nodC and nifH genes. Genotypes from the two valleys were completely distinct, except for two Lahaul isolates that shared nodC and nifH sequences with Spiti isolates but were otherwise more similar to other Lahaul isolates. Isolates from the two highest Spiti valley sites (above 4000 m) had a distinctive whole‐cell fatty acid profile. Spiti valley isolates are closely related to Rlv sublineages from Xinjiang and Shanxi provinces in China, while Lahaul valley isolates resemble cosmopolitan strains of the western world. The high mountain pass between these valleys represents a boundary between two distinct microbial populations.     

Immunization with Th-CTL fusion peptide and cytosine-phosphate-guanine DNA in transgenic HLA-A2 mice induces recognition of HIV-infected T cells and clears vaccinia virus challenge

We evaluated immunogenicity of a novel Th-CTL fusion peptide composed of the pan DR Th epitope and a CTL epitope derived from HIV-pol in two transgenic HLA-A*0201/K(b) mouse models. The immunogenicity of peptides of this structure is highly dependent on coadministered cytosine-phosphate-guanine DNA. Initial evaluations of peptide-specific immunity are based on results of chromium release assay, intracellular cytokine, and tetramer staining. Significant cytotoxic T cell responses are found upon a single immunization with as low as 0.1 nmol both peptide and cytosine-phosphate-guanine DNA. Splenocytes from immunized mice recognize naturally processed HIV-pol expressed from vaccinia virus (pol-VV). Translation of immunologic criteria into more relevant assays was pursued using systemic challenge of immunized mice with pol-VV. Only mice receiving both peptide and DNA together successfully cleared upward of 6 logs of virus from ovaries, compared with controls. Challenge with pol-VV by intranasal route of intranasal immunized mice showed a significant reduction in the levels of VV in lung compared with naive mice. A convincing demonstration of the relevance of these vaccines is the robust lysis of HIV-infected Jurkat T cells (JA2/R7/Hyg) by immune splenocytes from peptide- and DNA-immunized mice. This surprisingly effective immunization merits consideration for clinical evaluation, because it succeeded in causing immune recognition and lysis of cells infected with its target virus and reduction in titer of highly pathogenic VV.     

Role of mouse spleen cell HMG proteins and their poly-ADP-ribosylation in betelnut induced carcinogenesis

The role of high mobility group (HMG) proteins and their poly-ADP-ribosylation (PAR) in betel nut induced initiation of carcinogenesis in mice has been studied. A known carcinogen, diethylnitrosamine (DEN) was used as a positive control. Swiss albino mice were chronically exposed to aqueous extract of betel nut (AEBN) or DEN at low doses for up to 4 weeks. The poly-ADP-ribosylation (PAR) of spleen cell HMG proteins was monitored using [32P]-NAD+. Parallel to this, chromatin was subjected to DNase I cleavage and the organizational state of the chromatin was monitored. The PAR of HMG proteins showed a marked progressive reduction at different times following AEBN- or DEN treatment. HMG proteins isolated from the control and carcinogen treated mice were allowed to reassociate with the untreated spleen cells chromatin. The reassociated chromatin showed progressive relaxation in its superstructure. The results suggest that under the influence of potential carcinogens AEBN or DEN, the mouse spleen cell HMG proteins created molecular conditions favourable to initiation of cancer.