| 1. |
- Das, Sarbashis, et al.
(författare)
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Genetic heterogeneity revealed by sequence analysis of Mycobacterium tuberculosis isolates from extra-pulmonary tuberculosis patients.
- 2013
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Ingår i: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 14, s. 404-
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Tuberculosis remains a major public health problem. Clinical tuberculosis manifests often as pulmonary and occasionally as extra-pulmonary tuberculosis. The emergence of drug resistant tubercle bacilli and its association with HIV is a formidable challenge to curb the spread of tuberculosis. There have been concerted efforts by whole genome sequencing and bioinformatics analysis to identify genomic patterns and to establish a relationship between the genotype of the organism and clinical manifestation of tuberculosis. Extra-pulmonary TB constitutes 15-20 percent of the total clinical cases of tuberculosis reported among immunocompetent patients, whereas among HIV patients the incidence is more than 50 percent. Genomic analysis of M. tuberculosis isolates from extra pulmonary patients has not been explored.RESULTS: The genomic DNA of 5 extra-pulmonary clinical isolates of M. tuberculosis derived from cerebrospinal fluid, lymph node fine needle aspirates (FNAC) / biopsies, were sequenced. Next generation sequencing approach (NGS) was employed to identify Single Nucleotide Variations (SNVs) and computational methods used to predict their consequence on functional genes. Analysis of distribution of SNVs led to the finding that there are mixed genotypes in patient isolates and that many SNVs are likely to influence either gene function or their expression. Phylogenetic relationship between the isolates correlated with the origin of the isolates. In addition, insertion sites of IS elements were identified and their distribution revealed a variation in number and position of the element in the 5 extra-pulmonary isolates compared to the reference M. tuberculosis H37Rv strain.CONCLUSIONS: The results suggest that NGS sequencing is able to identify small variations in genomes of M. tuberculosis isolates including changes in IS element insertion sites. Moreover, variations in isolates of M. tuberculosis from non-pulmonary sites were documented. The analysis of our results indicates genomic heterogeneity in the clinical isolates.
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| 2. |
- Das, Sarbashis, et al.
(författare)
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Identification of hot and cold spots in genome of Mycobacterium tuberculosis using Shewhart Control Charts.
- 2012
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Ingår i: Scientific reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 2, s. 297-
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Tidskriftsartikel (refereegranskat)abstract
- The organization of genomic sequences is dynamic and undergoes change during the process of evolution. Many of the variations arise spontaneously and the observed genomic changes can either be distributed uniformly throughout the genome or be preferentially localized to some regions (hot spots) compared to others. Conversely cold spots may tend to accumulate very few variations or none at all. In order to identify such regions statistically, we have developed a method based on Shewhart Control Chart. The method was used for identification of hot and cold spots of single-nucleotide variations (SNVs) in Mycobacterium tuberculosis genomes. The predictions have been validated by sequencing some of these regions derived from clinical isolates. This method can be used for analysis of other genome sequences particularly infectious microbes.
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| 3. |
- Hon, Chung-Chau, et al.
(författare)
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Quantification of stochastic noise of splicing and polyadenylation in Entamoeba histolytica.
- 2013
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Ingår i: Nucleic Acids Research. - : Oxford University Press (OUP). - 0305-1048 .- 1362-4962. ; 41:3, s. 1936-52
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Tidskriftsartikel (refereegranskat)abstract
- Alternative splicing and polyadenylation were observed pervasively in eukaryotic messenger RNAs. These alternative isoforms could either be consequences of physiological regulation or stochastic noise of RNA processing. To quantify the extent of stochastic noise in splicing and polyadenylation, we analyzed the alternative usage of splicing and polyadenylation sites in Entamoeba histolytica using RNA-Seq. First, we identified a large number of rarely spliced alternative junctions and then showed that the occurrence of these alternative splicing events is correlated with splicing site sequence, occurrence of constitutive splicing events and messenger RNA abundance. Our results implied the majority of these alternative splicing events are likely to be stochastic error of splicing machineries, and we estimated the corresponding error rates. Second, we observed extensive microheterogeneity of polyadenylation cleavage sites, and the extent of such microheterogeneity is correlated with the occurrence of constitutive cleavage events, suggesting most of such microheterogeneity is likely to be stochastic. Overall, we only observed a small fraction of alternative splicing and polyadenylation isoforms that are unlikely to be solely stochastic, implying the functional relevance of alternative splicing and polyadenylation in E. histolytica is limited. Lastly, we revised the gene models and annotated their 3'UTR in AmoebaDB, providing valuable resources to the community.
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| 4. |
- Pettersson, B M Fredrik, et al.
(författare)
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Draft Genome Sequence of Saccharopolyspora rectivirgula.
- 2014
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Ingår i: Genome Announcements. - 2169-8287. ; 2:1
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Tidskriftsartikel (refereegranskat)abstract
- We have sequenced the genome of Saccharopolyspora rectivirgula, the causative agent of farmer's lung disease. The draft genome consists of 182 contigs totaling 3,977,051 bp, with a GC content of 68.9%.
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| 5. |
- Pettersson, B. M. Fredrik, et al.
(författare)
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Identification and expression of stressosomal proteins in Mycobacterium marinum under various growth and stress conditions
- 2013
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Ingår i: FEMS Microbiology Letters. - : Oxford University Press (OUP). - 0378-1097 .- 1574-6968. ; 342:2, s. 98-105
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Tidskriftsartikel (refereegranskat)abstract
- Like other bacteria, Mycobacterium spp. have developed different strategies in response to environmental changes such as nutrient limitations and other different stress situations. We have identified candidate genes (rsb genes) from Mycobacterium marinum involved in the regulation of the activity of the alternative sigma factor, sigma F. This is a homolog of the master regulator of general stress response, sigma B, and the sporulation-specific sigma factor, sigma F, in Bacillus subtilis. The organization of these genes in M.marinum and B.subtilis is similar. Transcriptome and qRT-PCR data show that these genes are indeed expressed in M.marinum and that the levels of expression vary with growth phase and exposure to stress. In particular, cold stress caused a significant rise in the expression of all identified rsb and sigF genes. We discuss these data in relation to what is currently known for other Mycobacterium spp.
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