Structural basis of hypoxic gene regulation by the Rv0081 transcription factor of Mycobacterium tuberculosis.

The transcription factor Rv0081 of Mycobacterium tuberculosis controls hypoxic gene expression and acts as a regulatory hub in the latent phase of tuberculosis (TB) infection. We report here the crystal structure of Rv0081 at 2.9 Å resolution revealing that it belongs to the well-known ArsR/SmtB family proteins.

Attenuation of Tumor Suppressive Function of FBXO16 Ubiquitin Ligase Activates Wnt Signaling In Glioblastoma.

Glioblastoma (GBM) is one of the most aggressive and lethal types of brain tumor. Despite the advancements in conventional or targeted therapies, median survival of GBM patients is less than 12 months. Amongst various signaling pathways aberrantly activated in glioma, active Wnt/β-catenin signaling pathway is one of the crucial oncogenic players.

Breast cancer stem cells: Biology and therapeutic implications.

Breast cancer remains to be a dreadful disease even with several advancements in radiation and chemotherapies, owing to the drug resistance and tumor relapse caused by breast cancer stem cells. Cancer stem cells are a minute population of cells of solid tumors which show self-renewal and differentiation properties as well as tumorigenic potential. Several signaling pathways including Notch, Hippo, Wnt and Hedgehog and tumor-stroma exchanges play a critical role in the self-renewal and differentiation of cancer stem cells in breast cancer.

Efflux pumps and antimicrobial resistance: Paradoxical components in systems genomics.

Efflux pumps play a major role in the increasing antimicrobial resistance rendering a large number of drugs of no use. Large numbers of pathogens are becoming multidrug resistant due to inadequate dosage and use of the existing antimicrobials. This leads to the need for identifying new efflux pump inhibitors.

Engineering riboswitch in L. major: From prediction to conceptualization.

Post-transcriptional gene regulation is a vital process to regulate expression of the key genes in the eukaryotic cell. Such processes are essential for pathogens which reside inside the host cell. One such pathogen is Leishmania major, which causes cutaneous leishmaniasis.

Systems-synthetic biology in understanding the complexities and simple devices in immunology.

Systems and synthetic biology in the coming era has the ability to manipulate, stimulate and engineer cells to counteract the pathogenic immune response. The inherent biological complexities associated with the creation of a device allow capitalizing the biotechnological resources either by simply administering a recombinant cytokine or just reprogramming the immune cells. The strategy outlined, adopted and discussed may mark the beginning with promising therapeutics based on the principles of synthetic immunology.

TryTransDB: A web-based resource for transport proteins in Trypanosomatidae.

TryTransDB is a web-based resource that stores transport protein data which can be retrieved using a standalone BLAST tool. We have attempted to create an integrated database that can be a one-stop shop for the researchers working with transport proteins of Trypanosomatidae family. TryTransDB (Trypanosomatidae Transport Protein Database) is a web based comprehensive resource that can fire a BLAST search against most of the transport protein sequences (protein and nucleotide) from Trypanosomatidae family organisms.

Transcription Factor Target Gene Network governs the Logical Abstraction Analysis of the Synthetic Circuit in Leishmaniasis.

With the advent of synthetic biology in medicine many synthetic or engineered proteins have made their way to therapeutics and diagnostics. In this paper, the downstream gene network of CD14-TNF-EGFR pathway in leishmaniasis, a tropical disease, is reconstructed. Network analysis showed that NFkB links the signaling and gene network, used as a point of intervention through a synthetic circuit embedded within the negative autoregulatory feedback loop.

Receptor tyrosine kinases (RTKs) in breast cancer: signaling, therapeutic implications and challenges.

Breast cancer is a multifactorial disease and driven by aberrant regulation of cell signaling pathways due to the acquisition of genetic and epigenetic changes. An array of growth factors and their receptors is involved in cancer development and metastasis. Receptor Tyrosine Kinases (RTKs) constitute a class of receptors that play important role in cancer progression.

Dataset generated for Dissection of mechanisms of Trypanothione Reductase and Tryparedoxin Peroxidase through dynamic network analysis and simulations in leishmaniasis.

Leishmaniasis is the second largest parasitic killer disease caused by the protozoan parasite , transmitted by the bite of sand flies. It's endemic in the eastern India with 165.4 million populations at risk with the current drug regimen.

Fungal Planet description sheets: 558-624.

Novel species of fungi described in this study include those from various countries as follows: : (incl. gen. nov.

Computational design of molecular motors as nanocircuits in Leishmaniasis.

Cutaneous leishmaniasis is the most common form of leishmaniasis, caused by and is spread by the bite of a sandfly This species infects the macrophages and dendritic cells Due to multi-drug resistance, there is a need for a new therapeutic technique. Recently, a novel molecular motor of , Myosin XXI, was classified and characterized. In addition, the drug resistance in this organism has been linked with the overexpression of ABC transporters.

Genome modularity and synthetic biology: Engineering systems.

Whole genome sequencing projects running in various laboratories around the world has generated immense data. A systematic phylogenetic analysis of this data shows that genome complexity goes on decreasing as it evolves, due to its modular nature. This modularity can be harnessed to minimize the genome further to reduce it with the bare minimum essential genes.

Angiogenic Gene Signature Derived from Subtype Specific Cell Models Segregate Proneural and Mesenchymal Glioblastoma.

Intertumoral molecular heterogeneity in glioblastoma identifies four major subtypes based on expression of molecular markers. Among them, the two clinically interrelated subtypes, proneural and mesenchymal, are the most aggressive with proneural liable for conversion to mesenchymal upon therapy. Using two patient-derived novel primary cell culture models (MTA10 and KW10), we developed a minimal but unique four-gene signature comprising genes vascular endothelial growth factor A (VEGF-A), vascular endothelial growth factor B (VEGF-B) and angiopoietin 1 (ANG1), angiopoietin 2 (ANG2) that effectively segregated the proneural (MTA10) and mesenchymal (KW10) glioblastoma subtypes.

Changes in structure and function of bacterial communities during coconut leaf vermicomposting.

To understand bacterial community dynamics during the vermicomposting of lignin-rich coconut leaves using an indigenous isolate of an epigeic earthworm, Eudrilus sp., we employed amplicon-based pyrosequencing of the V1 to V3 region of the 16S rRNA genes. Total community DNA was isolated from two separate vermicomposting tanks in triplicate at four different stages of the process: pre-decomposition (15th day), initial vermicomposting (45th day), 50-70% vermicomposting (75th day) and mature vermicompost (105th day).

Molecular docking and molecular dynamics simulation study of inositol phosphorylceramide synthase - inhibitor complex in leishmaniasis: Insight into the structure based drug design.

Inositol phosphorylceramide synthase (IPCS) has emerged as an important, interesting and attractive target in the sphingolipid metabolism of IPCS catalyzes the conversion of ceramide to IPC which forms the most predominant sphingolipid in . IPCS has no mammalian equivalent and also plays an important role in maintaining the infectivity and viability of the parasite. The present study explores the possibility of targeting IPCS; development of suitable inhibitors for the same would serve as a treatment strategy for the infectious disease leishmaniasis.

Biological Activity of Coumarin Derivatives as Anti-Leishmanial Agents.

Cutaneous leishmaniasis affects nearly 0.7 to 1.3 million people annually.

LmSmdB: an integrated database for metabolic and gene regulatory network in Leishmania major and Schistosoma mansoni.

A database that integrates all the information required for biological processing is essential to be stored in one platform. We have attempted to create one such integrated database that can be a one stop shop for the essential features required to fetch valuable result. LmSmdB (L.

Tumor exosomes: cellular postmen of cancer diagnosis and personalized therapy.

Nanosized (30-150 nm) extracellular vesicles 'exosomes' are secreted by cells for intercellular communication during normal and pathological conditions. Exosomes carry biomacromolecules from cell-of-origin and, therefore, represent molecular bioprint of the cell. Tumor-derived exosomes or TDEx modulate tumor microenvironment by transfer of macromolecules locally as well as at distant metastatic sites.

Cancer stem cell-vascular endothelial cell interactions in glioblastoma.

Glioblastoma (GBM), a higher grade glial tumor, is highly aggressive, therapy resistant and often shows poor patient prognosis due to frequent recurrence. These features of GBM are attributed to presence of a significantly smaller proportion of glioma stem cells (GSCs) that are endowed with self-renewal ability, multi-potent nature and show resistance to therapy in patients. GSCs preferably take shelter close to tumor vasculature due to paracrine need of soluble factors secreted by endothelial cells (ECs) of vasculature.

The crux and crust of ebolavirus: Analysis of genome sequences and glycoprotein gene.

The recent 2013-15 epidemic of Ebola virus disease (EVD) has initiated extensive sequencing and analysis of ebolavirus genomes. All ebolavirus genomes available until December 2014 have been collated and analyzed in this study to obtain phylogenetic relationship and uncover the variations amongst them. The terminal 'leader' and 'trailer' nucleotide sequences of the genomes were omitted and analysis of the intermediate region accommodating the sole seven genes (hepta-CDS region) of the virus showed relative stability of the genome, including the ones isolated from the current epidemic.