ARC: automated resource classifier for agglomerative functional classification of prokaryotic proteins using annotation texts.

Functional classification of proteins is central to comparative genomics. The need for algorithms tuned to enable integrative interpretation of analytical data is felt globally. The availability of a general,automated software with built-in flexibility will significantly aid this activity. We have prepared ARC (Automated Resource Classifier), which is an open source software meeting the user requirements of flexibility. The default classification scheme based on keyword match is agglomerative and directs entries into any of the 7 basic non-overlapping functional classes: Cell wall, Cell membrane and Transporters (C), Cell division (D), Information (I), Translocation (L), Metabolism (M), Stress(R), Signal and communication (S) and 2 ancillary classes: Others (O) and Hypothetical (H).The keyword library of ARC was built serially by first drawing keywords from Bacillus subtilis and Escherichia coli K12. In subsequent steps,this library was further enriched by collecting terms from archaeal representative Archaeoglobus fulgidus, Gene Ontology, and Gene Symbols. ARC is 94.04% successful on 6,75,663 annotated proteins from 348 prokaryotes. Three examples are provided to illuminate the current perspectives on mycobacterial physiology and costs of proteins in 333 prokaryotes. ARC is available at http://arc.igib.res.in.

Analysis of mycobacterial strains by two-dimensional gel electrophoresis.

This study pertains to analysis of the protein profile of different mycobacterial strains by two-dimensional gel electrophoresis (2DE). The strains were selected as they exhibit different phenotypic behaviour. TCA-acetone precipitated proteins were resolved by 2DE using immobilized pH gradient (IPG) strips. This study demonstrates that 2DE may be used as a tool for characterization of mycobacterial strains. Visual examination of the electrophoretograms was sufficient for characterization. Detailed characterization of specific proteins might lead to development of novel targets, diagnostic probes or sub-unit vaccine(s) against tuberculosis.

A comparative study on the effect of BCG-PSN and thymopeptides on T-lymphocyte subsets of normal and immunosuppressed mice / 华中科技大学学报（医学）（英德文版）

To compare the effects of polysaccharide nucleic acid fraction of bacillus calmette guerin (BCG-PSN) and thymopeptides on T-lymphocytes of normal and immunosuppressed mice, CD4+ and CD8+ T-lymphocyte subsets of single nucleic cell in thymus, spleen and peripheral blood were detected successively by flow cytometry after application of BCG-PSN and thymopeptides. Meanwhile, CD4+/CD8+ ratio was also calculated. The results showed that both BCG-PSN and thymopeptides could decrease the proportion of CD4+ CD8+ T-lymphocyte subsets in the thymus, at the same time increase CD4+ T-lymphocyte, CD8+ T-lymphocyte proportion in the three tissues. The fluctuation in amplitude was greater in thymopeptides group than that in BCG-PSN group. It is concluded that acting location of thymopeptides is in thymus, its stimulating action is stronger than that of BCG-PSN, while BCG-PSN not only accelerates the differentiation in thymus, but also has some direct stimulation to peripheral CD4+ T-lymphocytes, and can maintain CD4+/CD8+ ratio within normal range. So, BCG-PSN is safer.

Analise da conversao da reacao de mitsuda nas formas multibacilares da hanseniase / An analysis of mitsuda reactions conversion in multi-bacillar forms of hansen's disease

Com o objetivo de verificar o percentual de conversao imunologica atraves da reacao de Mitsuda e realizar a analise de fatores envolvidos nesse processo, selecionou-se ex-pacientes portadores de hanseniase atendidos na Fundacao Alfredo da Matta (Manaus-AM), com as seguintes caracteristicas: forma clinica multibacilar, reacao de Mitsuda negativo no diagnostico, alta por cura no periodo de 1989 a 1993, sem tratamento especifico anterior e que fizeram uso de esquemas poliquimioterapicos (PQT) com regularidade. Os participantes foram dispostos em dois grupos conforme esquema PQT: 22 haviam feito uso do esquema da OMS (PQT/OMS), isto e, ate negativacao baciloscopica, e 24 utilizaram o esquema de duracao fixa (PQT/DF), com ingestacao de 24 doses. Todos foram reavaliados, em 1997, atraves de exame clinico-dermatoneurologico, baciloscopia da pele, grau de incapacidade e aplicacao de novo reacao de Mitsuda com posterior leitura. Constatou-se que entre os individuos classificados como portadores de hanseniase Virchowiana nao ocorreu nenhuma variacao de resposta imunologica celular, medida pela reacao de Mitsuda. Entretanto, nas demais formas e principalmente nos pacientes que fizeram uso de PQT/DF, a conversao ocorreu com maior frequencia a medida que o paciente, na classificacao de Ridley e Jopling, estava mais proximo do polo imunocompetente. Em relacao ao Indice Baciloscopico verificou-se que a negativacao baciloscopica precoce pode ter enterferido na conversao da Reacao de Mitsuda. A correlacao dos dados retrospectivos e os obtidos na reavalicao contemporanea permitiu concluir que estas conversoes, embora frequentes, nao estao relacionadas com o esquema poliquimioterapico utilizado, a presenca ou nao de reacao reversa ou com o grau de incapacidade induzido pela hanseniase.

Tuberculosis: new strategies for the development of diagnostic tests and vaccines

New diagnostic tests and vaccines for tuberculosis are being developed by means of a strategy based on the study of antigens exclusive to Mycobacterium tuberculosis. These antigens were initially identified by Western blots using sera from active pulmonary tuberculosis patients against sonic extracts from M. tuberculosis and M. bovis BCG. Several proteins present in the M. tuberculosis but absent in the Mycobacterium bovis BCG sonic extracts were selected and are currently under investigation. One of these, denoted MTP40, has been extensively studied. The nucleotide sequence of the mtp40 gene has been obtained; hybridization studies have shown that this DNA fragment is exclusive to M. tuberculosis. Using this genomic fragment, a polymerase chain reaction (PCR)-based diagnostic test which allows the specific identification of a minimum of 10 fg of M. tuberculosis DNA was developed. The diagnostic assay is now being tested on uncultured clinical samples in order to determine its usefulness in routine diagnosis. Peptides synthesized from the derived sequence for the MTP40 protein and also from other M. tuberculosis proteins are now being studied as possible candidates for a new generation of synthetic vaccines against tuberculosis