Crowd sourcing a new paradigm for interactome driven drug target identification in Mycobacterium tuberculosis

A decade since the availability of Mycobacterium tuberculosis (Mtb) genome sequence, no promising drug has seen the light of the day. This not only indicates the challenges in discovering new drugs but also suggests a gap in our current understanding of Mtb biology. We attempt to bridge this gap by carrying out extensive re-annotation and constructing a systems level protein interaction map of Mtb with an objective of finding novel drug target candidates. Towards this, we synergized crowd sourcing and social networking methods through an initiative 'Connect to Decode' (C2D) to generate the first and largest manually curated interactome of Mtb termed 'interactome pathway' (IPW), encompassing a total of 1434 proteins connected through 2575 functional relationships. Interactions leading to gene regulation, signal transduction, metabolism, structural complex formation have been catalogued. In the process, we have functionally annotated 87% of the Mtb genome in context of gene products. We further combine IPW with STRING based network to report central proteins, which may be assessed as potential drug targets for development of drugs with least possible side effects. The fact that five of the 17 predicted drug targets are already experimentally validated either genetically or biochemically lends credence to our unique approach.     

Kappaphycus alvarezii as a source of bioethanol

The present study describes production of bio-ethanol from fresh red alga, Kappaphycus alvarezii. It was crushed to expel sap - a biofertilizer - while residual biomass was saccharified at 100 °C in 0.9 N H₂SO₄. The hydrolysate was repeatedly treated with additional granules to achieve desired reducing sugar concentration. The best yields for saccharification, inclusive of sugar loss in residue, were 26.2% and 30.6% (w/w) at laboratory (250 g) and bench (16 kg) scales, respectively. The hydrolysate was neutralized with lime and the filtrate was desalted by electrodialysis. Saccharomyces cerevisiae (NCIM 3523) was used for ethanol production from this non-traditional bio-resource. Fermentation at laboratory and bench scales converted ca. 80% of reducing sugar into ethanol in near quantitative selectivity. A petrol vehicle was successfully run with E10 gasoline made from the seaweed-based ethanol. Co-production of ethanol and bio-fertilizer from this seaweed may emerge as a promising alternative to land-based bio-ethanol.     

‘Inverted’ analogs of the antibiotic gramicidin S with an improved biological profile

A series of gramicidin S derivatives 4–15 are presented that have four ornithine residues as polar protonated side chains and two central hydrophobic amino acids with unaltered turn regions. These peptides were screened against human erthrocytes and our standard panel of Gram negative- and Gram positive bacteria, including four MRSA strains. Based on the antibacterial- and hemolytic data, peptides 13 and 14 have an improved biological profile compared to the clinically applied topical antibiotic gramicidin S.     

Evidence for mouse sulfhydryl oxidase‐assisted cross‐linking of major seminal vesicle proteins

Copulatory plug formation in animals is a general phenomenon by which competition is reduced among rival males. In mouse, the copulatory plug formation results from the coagulation of highly viscous seminal vesicle secretion (SVS) that is rich in proteins, such as dimers of SVS I, SVS I + II + III, and SVS II. These high‐molecular‐weight complexes (HMWCs) are also reported to be the bulk of proteins in the copulatory plug of the female mouse following copulation. In addition, mouse SVS contributes to the existence of sulfhydryl oxidase (Sox), which mediates the disulfide bond formation between cysteine residues. In this study, flavin adenine dinucleotide (FAD)‐dependent Sox was purified from mouse SVS using ion exchange and high‐performance liquid chromatography. The purified enzyme was identified to be Sox, based on western blot analysis with Sox antiserum and its capability of oxidizing dithiothreitol as substrate. The pH optima and thermal stability of the enzyme were determined. Among the metal ions tested, zinc showed an inhibitory effect on Sox activity. A prosthetic group of the enzyme was identified as FAD. The K_m and V_max of the enzyme was also determined. In addition to purification and biochemical characterization of seminal vesicle Sox, the major breakthrough of this study was proving its cross‐linking activity among SVS I–III monomers to form HMWCs in SVS.     

Protein trafficking in response to DNA damage

Human cells are prone to a range of natural environmental stresses and administered agents that damage or modify DNA, resulting in a cellular response typified by either cell death, or a cell cycle arrest, to permit repair of the genomic damage. DNA damage often elicits movement of proteins from one subcellular location to another, and the redistribution of proteins involved in genomic maintenance into distinct nuclear DNA repair foci is well documented. In this review, we discuss the DNA damage-induced trafficking of proteins to and from other distinct subcellular organelles including the nucleolus, mitochondria, Golgi complex and centrosome. The extent of intracellular transport suggests a dynamic and possibly co-ordinated role for protein trafficking in the DNA damage response.     

Activation of ATM kinase by ROS generated during ionophore-induced mitophagy in human T and B cell malignancies

Molecular and Cellular Biochemistry - Ataxia telangiectasia mutated (ATM), a critical DNA damage sensor, also possesses non-nuclear functions owing to its presence in extra-nuclear compartments,...     

Is predation of juvenile crown-of-thorns seastars (Acanthaster cf. solaris) by peppermint shrimp (Lysmata vittata) dependent on age,size, or diet?

Coral Reefs - Outbreaks of crown-of-thorns seastars (CoTS) are one of the leading causes of coral decline on Indo-Pacific coral reefs. Predator removal has been proposed to be a possible mechanism...     

Predicting non-native insect impact: focusing on the trees to see the forest

Non-native organisms have invaded novel ecosystems for centuries, yet we have only a limited understanding of why their impacts vary widely from minor to severe. Predicting the impact of non-established or newly detected species could help focus biosecurity measures on species with the highest potential to cause widespread damage. However, predictive models require an understanding of potential drivers of impact and the appropriate level at which these drivers should be evaluated. Here, we used non-native, specialist herbivorous insects of forest ecosystems to test which factors drive impact and if there were differences based on whether they used woody angiosperms or conifers as hosts. We identified convergent and divergent patterns between the two host types indicating fundamental similarities and differences in their interactions with non-native insects. Evolutionary divergence time between native and novel hosts was a significant driver of insect impact for both host types but was modulated by different factors in the two systems. Beetles in the subfamily Scolytinae posed the highest risk to woody angiosperms, and different host traits influenced impact of specialists on conifers and woody angiosperms. Tree wood density was a significant predictor of host impact for woody angiosperms with intermediate densities (0.5–0.6 mg/mm³) associated with highest risk, whereas risk of impact was highest for conifers that coupled shade tolerance with drought intolerance. These results underscore the importance of identifying the relevant levels of biological organization and ecological interactions needed to develop accurate risk models for species that may arrive in novel ecosystems.

     

In silico analyses reveal common cellular pathways affected by loss of heterozygosity (LOH) events in the lymphomagenesis of Non-Hodgkin’s lymphoma (NHL)

Background

The analysis of cellular networks and pathways involved in oncogenesis has increased our knowledge about the pathogenic mechanisms that underlie tumour biology and has unmasked new molecular targets that may lead to the design of better anti-cancer therapies. Recently, using a high resolution loss of heterozygosity (LOH) analysis, we identified a number of potential tumour suppressor genes (TSGs) within common LOH regions across cases suffering from two of the most common forms of Non-Hodgkin’s lymphoma (NHL), Follicular Lymphoma (FL) and Diffuse Large B-cell Lymphoma (DLBCL). From these studies LOH of the protein tyrosine phosphatase receptor type J (PTPRJ) gene was identified as a common event in the lymphomagenesis of these B-cell lymphomas. The present study aimed to determine the cellular pathways affected by the inactivation of these TSGs including PTPRJ in FL and DLBCL tumourigenesis.

Results

Pathway analytical approaches identified that candidate TSGs located within common LOH regions participate within cellular pathways, which may play a crucial role in FL and DLBCL lymphomagenesis (i.e., metabolic pathways). These analyses also identified genes within the interactome of PTPRJ (i.e. PTPN11 and B2M) that when inactivated in NHL may play an important role in tumourigenesis. We also detected genes that are differentially expressed in cases with and without LOH of PTPRJ, such as NFATC3 (nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 3). Moreover, upregulation of the VEGF, MAPK and ERBB signalling pathways was also observed in NHL cases with LOH of PTPRJ, indicating that LOH-driving events causing inactivation of PTPRJ, apart from possibly inducing a constitutive activation of these pathways by reduction or abrogation of its dephosphorylation activity, may also induce upregulation of these pathways when inactivated. This finding implicates these pathways in the lymphomagenesis and progression of FL and DLBCL.

Conclusions

The evidence obtained in this research supports findings suggesting that FL and DLBCL share common pathogenic mechanisms. Also, it indicates that PTPRJ can play a crucial role in the pathogenesis of these B-cell tumours and suggests that activation of PTPRJ might be an interesting novel chemotherapeutic target for the treatment of these B-cell tumours.

Electronic supplementary material

The online version of this article (doi: 10.1186/1471-2164-15-390) contains supplementary material, which is available to authorized users.