Importing statistical measures into Artemis enhances gene identification in the <Emphasis Type="Italic">Leishmania</Emphasis> genome project

Background

Seattle Biomedical Research Institute (SBRI) as part of the Leishmania Genome Network (LGN) is sequencing chromosomes of the trypanosomatid protozoan species Leishmania major. At SBRI, chromosomal sequence is annotated using a combination of trained and untrained non-consensus gene-prediction algorithms with ARTEMIS, an annotation platform with rich and user-friendly interfaces.

Results

Here we describe a methodology used to import results from three different protein-coding gene-prediction algorithms (GLIMMER, TESTCODE and GENESCAN) into the ARTEMIS sequence viewer and annotation tool. Comparison of these methods, along with the CODON USAGE algorithm built into ARTEMIS, shows the importance of combining methods to more accurately annotate the L. major genomic sequence.

Conclusion

An improvised and powerful tool for gene prediction has been developed by importing data from widely-used algorithms into an existing annotation platform. This approach is especially fruitful in the Leishmania genome project where there is large proportion of novel genes requiring manual annotation.

     

The dynamics of vegetation on and around <Emphasis Type="Italic">Formica rufa</Emphasis> nests

The species composition and structure of plant communities related to the activity of Formica rufa ants were studied in green moss pine forests located in Nerusso-Desnyanskoe Polesye (Bryansk Province). Four types of microsites were established and examined: (1) the mound of an active ant nest, (2) the soil bank around an active ant nest, (3) the mound of an abandoned nest, and (4) the soil bank around an abandoned nest. The background plant community was considered as the fifth type. According to MRPP method, all pairs of microsites except (3–4) were different both in plant species composition and species abundance. The microsites created by Formica rufa increase the habitat capacity and β diversity of the plant communities due to the appearance of meadow species requiring richer soils.     

The role of persistence and virulence factors in microecological changes in a humans

The patterns of persistence and virulence factors expression in the representatives of human microbial biocenosis depends on a complex of the environmental conditions: influence of microbes-symbionts, biotope peculiarities, properties of microorganisms located within eukaryotes. Interactions of symbionts in pairs "indigen-indigen" isolated from mucous membrane of tonsils in healthy persons, did not lead to changes in expression of pathogenic properties. Interinfluence in pairs "pathogen-indigen" and "indigen-indigen", isolated from patients with chronic tonsilitis were accompanied by an increase of anti-lysozyme, hemolytic and lecithovitellase activities. Migration of strains of non-enzymatized gram-negative bacteria (NEYNB) from nasal into tympanic cavity in experimental acute purulent otitis is connected with an earlier increase of their number in the nasal cavity and the expression of anti-lysozyme activity. In acute and chronic pyoderma, expression of ALA is more marked in bacteria from a perifocal damage in contrast to focal damage of normal skin. In conditions of interaction between erythrocytes and staphylococcal clones with different levels of expression of pathogenic factors, differences were observed in dynamics of hemolytic and anti-hemoglobin activities.     

Characterization of 13 newly isolated strains of anaerobic, cellulolytic, thermophilic bacteria

Characteristics of 13 newly isolated thermophilic, anaerobic, and cellulolytic strains were compared with previously described strains of Clostridium thermocellum: ATCC 27405 and JW20 (ATCC 31549). Colony morphology, antibiotic sensitivity, fermentation end-products, and cellulose degradation were documented. All 13 strains were sensitive to erythromycin (5 μg/ml) and chloramphenicol (25 μg/ml), and all strains but one were sensitive to kanamycin (20 μg/ml). Polymerase chain reaction (PCR) amplification using primers based on gene sequences from C. thermocellum ATCC 27405 was successful for all 13 strains in the case of the hydrogenase gene and 11 strains in the case of phosphotransacetylase/acetate kinase genes. Ten strains amplified a product of the expected size with primers developed to be specific for C. thermocellum 16SrRNA primers. Two of the 13 strains did not amplify any product with the PCR primers designed for the phosphotransacetylase/acetate kinase and 16SrRNA primers. A MboI-like GATC- recognizing restriction activity was present in all of the five strains examined. The results of this study have several positive implications with respect to future development of a transformation system for cellulolytic thermophiles. Journal of Industrial Microbiology & Biotechnology (2001) 27, 275–280. Received 12 September 2000/ Accepted in revised form 20 November 2000     

Molecular and epidemiologic characteristics of HIV-infection outbreak in the Irkutsk region

The genetic analysis of the variants of human immunodeficiency virus of type 1 (HIV-I) circulating among drug addicts in the Irkutsk region was carried out. The results of serological tests and comparative evaluation of electrophoretic mobility of heteroduplexes (HMA) revealed that all 74 samples under study belonged to subtype A. Genetic differences between these viruses did not exceed 2%. Thus, it was the variant of subtype A prevalent in CIS countries which caused the outbreak of HIV infection among drug addicts in the Irkutsk region, but not viruses of subtypes B, C or A/E typical for this risk group in relatively nearby China.     

A genetic analysis of variants of the human immunodeficiency virus type 1 (HIV-1) circulating among drug abusers in Moscow and Moscow Province

The genetic analysis of the variants of human immunodeficiency virus of type 1 (HIV-1), circulating among drug addicts in Moscow and Moscow Province, has been carried out. The serological analysis of 122 blood specimens taken from HIV-infected drug addicts, residing in Moscow and 22 settlements of the Moscow region, has shown that in this region HIV-1 variant of subtype A spreads among drug addicts. These data have been confirmed by the results of the analysis of 44 specimens, made with the use of the method of the heteroduplex mobility assay for gene env. As revealed in this study, HIV-1 variants spreading at present among drug addicts in Moscow and the Moscow region are genetically related to viruses of subtype A, detected earlier in this group of risk in other regions of Russia, the Ukraine, Belarus and other countries of Eastern Europe.     

Interaction of bacteria and red blood cells

The interaction of staphylococci, streptococci, meningococci, enterobacteria, leptospires and other microorganisms with red blood cells is considered. Three forms of the interaction of bacteria and red blood cells are discussed: adhesion, the influence of secretory factors on red blood cells, the action of pathogenic bacteria on hemoglobin. The applied aspects of the interaction of bacteria and red blood cells in the human body are presented in accordance with the results of clinical and laboratory studies.     

Andrenocorticotropin and β-lipotropin in the hypothalamus

Adrenocorticotropin and β-lipotropin (β-LPH) have been localized by immunoperoxidase methods in nerve cells and fibers of the hypothalamus and brain stem of the ewe. 6-μm sections were immunostained first for either ACTH or β-LPH. The reaction products and the antibody complexes were then eluted completely from the tissue, and the same section was immunostained for the second peptide. Absorption of the primary antisera with a variety of peptide fragments of ACTH and β-LPH demonstrated, immunocytochemically as well as by radioimmunoassay, that the ACTH and β-LPH antisera were directed to the COOH- and NH(2)-termini of the peptides, respectively. Neither antiserum recognized any portion of the heterologous peptide. In the sequential staining procedure on the same tissue section, preincubation of the antisera with the homologous peptide abolished the staining, whereas preincubation with the heterologous peptide did not affect it, regardless of the order followed. Every nerve cell in the arcuate nucleus that contained ACTH also contained β-LPH, but β-LPH cells appeared, probably falsely, to be twice as numerous as ACTH cells. β-LPH-positive fibers in and beyond the hypothalamus were also more numerous and stained more intensively than ACTH fibers. The salient exception was fibers in the infundibular zona externa, where the opposite was true. Our observations establish that ACTH and β-LPH are contained in the same nerve cells They stongly favor biosynthesis in brain, probably from a common precursor molecule, as has been demonstrated in the pituitary gland. The complexity of the cytologic distribution pattern described suggests that the two peptides are not processed in the same manner by the nerve cell.