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.

     

Ultrastructural study of liver cells from rooks living in ecologically unfavorable areas

The ultrastructure of liver cells was studied in rooks (Corvus frugilegus) living in radioactive and chemical contamination areas. The ultrastructure of liver cells from rook as well as jackdaw (Corvus monedula) and hooded crow (Corvus cornix) (Corvidae family) from a conventionally clean area was studied as control. Control hepatocytes proved to contain a great number of mitochondria, many of which were swollen and had clear matrix and disorganized cristae. The cristae nearly lacked glycogen and had abundant lipid droplets, which often tightly contacted mitochondria. The cytoplasm of hepatocytes in birds from both ecologically unfavorable areas had numerous mitochondria with the same ultrastructure. In contrast to control, the hepatocyte cytoplasm: (1) contained a lot of glycogen; (2) there were many lipid droplets, which directly contacted glycogen granules; and (3) had more abundant peroxisomes. In addition to normal erythrocytes, the sinusoids contained erythrocytes with mitochondria, vesicles, and lipid droplets in their cytoplasm. Analysis of many micrographs of lipid droplets contacting glycogen granules, mitochondria, peroxisomes, and cisterns of smooth endoplasmic reticulum allowed us to propose that glycogen is synthesized via gluconeogenesis from glycerol and products of fatty acid oxidation in the liver cell cytoplasm of rooks from ecologically unfavorable areas as distinct from control.     

Maintenance of Plasmid Expression in vivo Depends Primarily on the CpG Contents of the Vector and Transgene

Molecular Biology - Plasmid-mediated gene therapy, being a safe and relatively inexpensive therapeutic strategy, is plagued by a fast silencing of transgene expression. The silencing severely...     

Improvement of nutrient absorption may enhance systemic oxidative stress in cystic fibrosis patients

BACKGROUND: The life expectancy of patients with cystic fibrosis (CF) is largely dependent on the pulmonary disease severity and progress. Malnutrition may be an important complicating factor in active and chronic lung disease. AIMS: The focus of this study was to investigate several inflammatory markers in pancreatic-insufficient CF patients with different enzyme treatment regimens. METHODS: CF patients with pancreatic insufficiency were examined at a time of symptomatic exacerbation of their lung disease. Group A (n = 11) regularly received microspheric enzymes. Group B (n = 8) were treated with enzymes during the hospitalization period only and demonstrated the presence of malnutrition. Inflammatory markers in the sputa (neutrophil elastase activity, interleukin-8 and tumour necrosis factor-alpha levels) and in the peripheral blood (plasma malondialdehyde (MDA), lymphocyte response to PHA, and the cell sensitivity to steroid suppression) have been investigated. RESULTS: During acute lung exacerbation, group B demonstrated reduced levels of lymphocyte proliferation. This parameter was normalized after combined antibiotic and pancreatic enzyme therapy. Simultaneously, plasma MDA in group B markedly increased following treatment. For this group, a significant positive linear association between values of plasma MDA and lymphocyte proliferation has been observed. For group A, neither the same correlation nor changes in MDA levels and lymphocyte proliferation have been found. CONCLUSIONS: Our data indicate that acute lung exacerbation in malnourished CF patients may be associated with alteration in T-lymphocyte activity. Adequate therapy normalizes lymphocyte function but results in systemic oxidative stress.