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author:("gogo, madhura")
1.  Prevalence and Identification of Burkholderia pseudomallei and Near-Neighbor Species in the Malabar Coastal Region of India 
PLoS Neglected Tropical Diseases  2016;10(9):e0004956.
Accurate identification of pathogens with biowarfare importance requires detection tools that specifically differentiate them from near-neighbor species. Burkholderia pseudomallei, the causative agent of a fatal disease melioidosis, is one such biothreat agent whose differentiation from its near-neighbor species is always a challenge. This is because of its phenotypic similarity with other Burkholderia species which have a wide spread geographical distribution with shared environmental niches. Melioidosis is a major public health concern in endemic regions including Southeast Asia and northern Australia. In India, the disease is still considered to be emerging. Prevalence surveys of this saprophytic bacterium in environment are under-reported in the country. A major challenge in this case is the specific identification and differentiation of B. pseudomallei from the growing list of species of Burkholderia genus. The objectives of this study included examining the prevalence of B. pseudomallei and near-neighbor species in coastal region of South India and development of a novel detection tool for specific identification and differentiation of Burkholderia species. Briefly, we analyzed soil and water samples collected from Malabar coastal region of Kerala, South India for prevalence of B. pseudomallei. The presumptive Burkholderia isolates were identified using recA PCR assay. The recA PCR assay identified 22 of the total 40 presumptive isolates as Burkholderia strains (22.72% and 77.27% B. pseudomallei and non-pseudomallei Burkholderia respectively). In order to identify each isolate screened, we performed recA and 16S rDNA sequencing. This two genes sequencing revealed that the presumptive isolates included B. pseudomallei, non-pseudomallei Burkholderia as well as non-Burkholderia strains. Furthermore, a gene termed D-beta hydroxybutyrate dehydrogenase (bdha) was studied both in silico and in vitro for accurate detection of Burkholderia genus. The optimized bdha based PCR assay when evaluated on the Burkholderia isolates of this study, it was found to be highly specific (100%) in its detection feature and a clear detection sensitivity of 10 pg/μl of purified gDNA was recorded. Nucleotide sequence variations of bdha among interspecies, as per in silico analysis, ranged from 8 to 29% within the target stretch of 730 bp highlighting the potential utility of bdha sequencing method in specific detection of Burkholderia species. Further, sequencing of the 730 bp bdha PCR amplicon of each Burkholderia strain isolated could differentiate the species and the data was comparable with recA sequence data of the strains. All sequencing results obtained were submitted to NCBI database. Bayesian phylogenetic analysis of bdha in comparison with recA and 16S rDNA showed that the bdha gene provided comparable identification of Burkholderia species.
Author Summary
With the growing list of Burkholderia species, which represents a genus of bacteria with economical, health and biowarfare importance, the need for specific and efficient detection systems is also growing. Burkholderia pseudomallei is reported to be endemic in India. However, limited prevalence studies have been conducted in the country to determine the presence of this pathogen in environment. The high level of phenotypic and genotypic similarities of this bacterium with other species of the genus stands as a difficult challenge to differentiate them. Several molecular detection systems have been reported in this field, with a range of identification potential restricted to Burkholderia cepacia complex. The present study addresses the former mentioned challenges by performing a surveillance study in Malabar coastal region of South India wherein we encountered 22 strains of Burkholderia. Furthermore, we determined the utility of a novel gene for specific detection of the whole Burkholderia genus by developing a novel bdha based PCR assay. The study design includes extensive bioinformatic analyses and comparative genomics for the development of the described compound detection tool. The study also includes the evaluation of the genus-specific gene of its efficiency in specifically identifying the Burkholderia species by nucleotide sequencing based method. The novel genus-specific gene is also evaluated for its role in phylogeny of Burkholderia species in comparison with that of earlier reported recA and 16S rDNA genes.
PMCID: PMC5025242  PMID: 27632353
2.  Computational identification and analysis of MADS box genes in Camellia sinensis 
Bioinformation  2015;11(3):115-121.
MADS (Minichromosome Maintenance1 Agamous Deficiens Serum response factor) box genes encode transcription factors and they play a key role in growth and development of flowering plants. There are two types of MADS box genes- Type I (serum response factor (SRF)-like) and Type II (myocyte enhancer factor 2 (MEF2)-like). Type II MADS box genes have a conserved MIKC domain (MADS DNA-binding domain, intervening domain, keratin-like domain, and c-terminal domain) and these were extensively studied in plants. Compared to other plants very little is known about MADS box genes in Camellia sinensis. The present study aims at identifying and analyzing the MADS-box genes present in Camellia sinensis. A comparative bioinformatics and phylogenetic analysis of the Camellia sinensis sequences along with Arabidopsis thaliana MADS box sequences available in the public domain databases led to the identification of 16 genes which were orthologous to Type II MADS box gene family members. The protein sequences were classified into distinct clades which are associated with the conserved function of flower and seed development. The identified genes may be used for gene expression and gene manipulation studies to elucidate their role in the development and flowering of tea which may pave the way to improve the crop productivity.
PMCID: PMC4403032  PMID: 25914445
Bioinformatics; Crop productivity; Flowering; MADS box genes; Tea; Transcription factor
3.  Prevalence of Cataract in an Older Population in India 
Ophthalmology  2011;118(2-19):272-278.e2.
To describe the prevalence of cataract in older people in 2 areas of north and south India.
Population-based, cross-sectional study.
Randomly sampled villages were enumerated to identify people aged ≥60 years. Of 7518 enumerated people, 78% participated in a hospital-based ophthalmic examination.
The examination included visual acuity measurement, dilatation, and anterior and posterior segment examination. Digital images of the lens were taken and graded by type and severity of opacity using the Lens Opacity Classification System III (LOCS III).
Main Outcome Measures
Age- and gender-standardized prevalence of cataract and 95% confidence intervals (CIs). We defined type of cataract based on the LOCS III grade in the worse eye of: ≥4 for nuclear cataract, ≥3 for cortical cataract, and ≥2 for posterior subcapsular cataract (PSC). Any unoperated cataract was based on these criteria or ungradable dense opacities. Any cataract was defined as any unoperated or operated cataract.
The prevalence of unoperated cataract in people aged ≥60 was 58% in north India (95% CI, 56–60) and 53% (95% CI, 51–55) in south India (P = 0.01). Nuclear cataract was the most common type: 48% (95% CI, 46–50) in north India and 38% (95% CI, 37–40) in south India (P<0.0001); corresponding figures for PSC were 21% (95% CI, 20–23) and 17% (95% CI, 16–19; P = 0.003), respectively, and for cortical cataract 7.6% (95% CI, 7–9) and 10.2% (95% CI, 9–11; P<0.004). Bilateral aphakia/pseudophakia was slightly higher in the south (15.5%) than in the north (13.2%; P<0.03). The prevalence of any cataracts was similar in north (73.8%) and south India (71.8%). The prevalence of unoperated cataract increased with age and was higher in women than men (odds ratio [OR], 1.8). Aphakia/pseudophakia was also more common in women, either unilateral (OR, 1.2; P<0.02) or bilateral (OR, 1.3; P<0.002).
We found high rates of unoperated cataract in older people in north and south India. Posterior subcapsular cataract was more common than in western studies. Women had higher rates of cataract, which was not explained by differential access to surgery.
Financial Disclosure(s)
The authors have no proprietary or commercial interest in any of the materials discussed in this article.
PMCID: PMC3146699  PMID: 20801514

Results 1-3 (3)