Genome-wide screening of mariner-like elements (MLEs) in the silkworm Bombyx mori has revealed the presence of five different types of MLEs (Bmmar1, Bmmar2, Bmmar3, Bmmar4 and Bmmar5). We isolated and characterized sixty copies of the MLEs representing the five Bmmar types. Their nucleotide sequences, nucleotide compositions, deduced transposase sequences, codon preferences, and the copy numbers showed extensive variations. Phylogenetic analysis of the sequences revealed that Bmmar1, Bmmar2, and Bmmar3 have been in the B. mori genome for a long time, while Bmmar4 is probably a recent invader of the genome. Because of the long-term association of Bmmar1 and Bmmar2 with the genome, highly mutated miniature Bmmar1 and Bmmar2 are widespread in the genome, and the footprints of these elements are also present in different silkworm genes. However, miniature copies of Bmmar4 were not detected. This recently acquired element has very few mutations. None of the characterized copies had functional transposase open reading frames. They essentially exist as fossils in the genome.

Stomach cancer is the second leading cause of cancer death and fourth most common cancer in the world. Deregulated transcription programs and signaling pathways are the major driving forces involved in the initiation and progression of cancer. Identification of the dysregulated transcription programs and genes from the transcriptome of gastric tumors would pave the way for i) the identification of major dysregulations involved in gastric cancer, ii) stratification of tumors, and iii) development of targeted therapies. Specificity protein (SP1) is a transcription factor and aberrant expression of SP1 is known to confer proliferative and metastatic advantage to tumor cells. The role of SP1 mediated expression in gastric cancer was investigated in the genome-wide mRNA profile of gastric cancer cell line upon SP1 silencing. Gene-set based cumulative expression analysis of the available SP1 regulated gene-sets revealed the involvement of certain SP1 target genes in a sub-set of gastric tumors while the another group of genes in another sub-set. This shows the bi-modal involvement of different SP1 regulated genes in different subtypes of gastric tumors. The expression of a set of SP1 genes were found positively correlated with the oncogenic signatures of MYC, E2F and mTOR signaling with their elevated expression in intestinal type tumors. Another category of SP1 genes, which are up-regulated upon SP1 silencing were found expressed in diffuse type tumors along with the activated VEGFA, OCT4, and TGF-β signaling. These results reveal that SP1 transcriptionally activates the genes involved in intestinal type and represses the genes involved in diffuse type gastric tumors. This shows the dual role of SP1 regulated transcription in sub-sets of gastric tumors and warrant further investigation in diagnostic and therapeutic contexts.

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Objective: Characterization of novel 'Indian Bison Type' bio-type of Mycobacterium avium subspecies paratuberculosis (MAP) strain 'S5' (goat origin) was done through six MAP cultural filtrate proteins (CFPs) genes (MAP 1693c, MAP 2168c, MAP Mod D, MAP 85c, MAP Pep AN and MAP Pep AC) encoding for above six recombinant CFPs. Material and Methods: Six immunogenic MAP CFPs genes (1693c, 2168c, ModD, 85c, Pep AN and Pep AC) were cloned and were confirmed by restriction digestions and sequencing. Evolutionary Analysis of the six genes was done using phylogenetic tree constructions and Sequence Identity plot. Results and Discussion: Sequence analysis of six CFPs genes was studied extensively for their genetic composition, mutations and other variations in their open reading frames. Good percentage of homology has been found among the global biotypes/strains of the MAP along with the MAP strain 'S5' and a novel biotype (Indian Bison Type) of goat origin and other Indian isolates. Aligned sequences of the six genes have been submitted to NCBI. Genebank accessioned by following IDs (MG753462, MG753463, MG753464, MG753465, MG753466 and MG753467). However, certain insertions, deletions within the genes still required to be explored to identify the nature of the disease in Indian scenario with respect to genotypic influences in geographical entity. Mutations were observed in four genes of MAP 'S5' strain, 2168c, Mod D, Pep AN and Pep AC. Phylogenetic tree analysis of MAP 'S5' genes showed 1693c and 2168c genes were taxonomically distant, on contrary Mod D, Pep AN were located taxonomically closer, 85C was present as out group of the first branch and Pep AC slightly away. Conclusion: The study helped to understand molecular diversity and homology of CFPs genes of MAP 'S5' with other strains. Mutations may lead to modulations in the functions of the MAP metabolism thereby influencing the virulence and host response to the disease.

A search for the presence of mariner-like elements in the Labeo rohita genome by polymerase chain reaction led to the amplification of a partial DNA sequence coding for a putative transmembrane domain of gonadotropin hormone receptor. The amplified DNA sequence shows a high degree of homology to the available turkey and human luteinizing and follicle stimulating hormone receptor coding sequences. This is the first report on cloning such sequences of piscine origin.