The whole genome of a pigment-producing isolate from a lake in northern India, Pseudogulbenkiania ferrooxidans strain EGD-HP2, has been sequenced to study the spectrum of biosynthesis of secondary metabolites. The genome annotation data revealed an operon for violacein, which showed homology with the reported operon of a Chromobacterium sp., and also a quinone cofactor.

Background: Oral submucous fibrosis (OSF) is an oral potentially malignant disorder depicting extensive fibrosis of the submucosa affecting most parts of the oral cavity, including pharynx and upper third of the oesophagus. Despite its high potentially malignant nature, transformation of the epithelium towards malignancy in the background of fibrosis has not been studied extensively till date. Hypoxia Inducible Factor-1α (HIF-1α) is a master transcription factor that is induced by hypoxia and has found to be significantly associated with both fibrosis and malignancy. Aim: To test the hypothesis of differential expression of HIF-1α in malignant transformation of OSF. Materials and methods: Fifteen samples each of Normal Mucosa (NOM), OSF and Oral Squamous Cell Carcinoma (OSCC) making total of 45 tissues were studied by formalin fixed Haematoxylin and Eosin (H&E)-stained sections and frozen fixed for Reverse Transcription Polymerase Chain Reaction (RT-PCR). The relationship between differential HIF-1α messenger RNA expression level and oral epithelial dysplasia, inter incisal opening and grade of OSCC was studied. Conclusions: An upregulation of HIF-1α expression level is positively correlated with oral carcinogenesis and grade of OSCC, whereas downregulation is associated with fibrosis. Hence, it can be used as both diagnostic as well as a prognostic marker.

All the genetic potential and the intelligence a bacteria can showcase in a given environment are embedded in its genome. In this study, we have presented systematic guidelines to understand a bacterial genome with the relevant set of in silico tools using a novel bacteria as an example. This study presents a multi-dimensional approach from genome annotation to tracing genes and their network of metabolism operating in an organism. It also shows how the sequence can be used to mine the enzymes and construction of its 3-dimensional structure so that its functional behavior can be predicted and compared. The discriminating algorithm allows analysis of the promoter region and provides the insight in the regulation of genes in spite of the similarity in its sequences. The ecological niche specific bacterial behavior and adapted altered physiology can be understood through the presence of secondary metabolite, antibiotic resistance genes, and viral genes; and it helps in the valorization of genetic information for developing new biological application/processes. This study provides an in silico work plan and necessary steps for genome analysis of novel bacteria without any rigorous wet lab experiments.

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