Deploying QTL-seq for rapid delineation of a potential candidate gene underlying major trait-associated QTL in chickpea

A rapid high-resolution genome-wide strategy for molecular mapping of major QTL(s)/gene(s) regulating important agronomic traits is vital for in-depth dissection of complex quantitative traits and genetic enhancement in chickpea. The present study for the first time employed a NGS-based whole-genome QTL-seq strategy to identify one major genomic region harbouring a robust 100-seed weight QTL using an intra-specific 221 chickpea mapping population (desi cv. ICC 7184 × desi cv. ICC 15061). The QTL-seq-derived major SW QTL (CaqSW1.1) was further validated by single-nucleotide polymorphism (SNP) and simple sequence repeat (SSR) marker-based traditional QTL mapping (47.6% R² at higher LOD >19). This reflects the reliability and efficacy of QTL-seq as a strategy for rapid genome-wide scanning and fine mapping of major trait regulatory QTLs in chickpea. The use of QTL-seq and classical QTL mapping in combination narrowed down the 1.37 Mb (comprising 177 genes) major SW QTL (CaqSW1.1) region into a 35 kb genomic interval on desi chickpea chromosome 1 containing six genes. One coding SNP (G/A)-carrying constitutive photomorphogenic9 (COP9) signalosome complex subunit 8 (CSN8) gene of these exhibited seed-specific expression, including pronounced differential up-/down-regulation in low and high seed weight mapping parents and homozygous individuals during seed development. The coding SNP mined in this potential seed weight-governing candidate CSN8 gene was found to be present exclusively in all cultivated species/genotypes, but not in any wild species/genotypes of primary, secondary and tertiary gene pools. This indicates the effect of strong artificial and/or natural selection pressure on target SW locus during chickpea domestication. The proposed QTL-seq-driven integrated genome-wide strategy has potential to delineate major candidate gene(s) harbouring a robust trait regulatory QTL rapidly with optimal use of resources. This will further assist us to extrapolate the molecular mechanism underlying complex quantitative traits at a genome-wide scale leading to fast-paced marker-assisted genetic improvement in diverse crop plants, including chickpea.     

Prognostic significance of cyclooxygenase-2 and response to chemotherapy in invasive ductal breast carcinoma patients by real time surface plasmon resonance analysis

Cyclooxygenase-2 (COX-2), an inducible enzyme, has been implicated in the progression and angiogenesis of breast cancer. The aim of the study is to quantify the concentration of COX-2 and its association with clinico-pathological parameters and response to treatment in patients with invasive ductal carcinoma receiving both neo-adjuvant and adjuvant chemotherapy. The level of COX-2 was estimated using a novel biosensor-based surface plasmon resonance technique in serum of 84 patients with breast cancer (48 patients of neo-adjuvant chemotherapy and 36 patients of adjuvant chemotherapy) and 40 age- and gender-matched normal individuals. A significant increase in COX-2 level was observed in patients compared with normal individuals (p>0.0001). The COX-2 level in serum was found to be significantly higher in patients with lymph node involvement (p<0.0061). 68% (33/48) of the patients receiving neo-adjuvant chemotherapy showed significantly (p<0.0025) reduced COX-2 levels. This study shows significant decrease of COX-2 level in patients with breast cancer treated with both neo-adjuvant and adjuvant chemotherapy. Estimation of COX-2 level in serum may serve as a tumor biomarker in patients with breast cancer.     

Mammalian antimicrobial peptide influences control of cutaneous Leishmania infection

Cathelicidin-type antimicrobial peptides (CAMP) are important mediators of innate immunity against microbial pathogens acting through direct interaction with and disruption of microbial membranes and indirectly through modulation of host cell migration and activation. Using a mouse knock-out model in CAMP we studied the role of this host peptide in control of dissemination of cutaneous infection by the parasitic protozoan Leishmania. The presence of pronounced host inflammatory infiltration in lesions and lymph nodes of infected animals was CAMP-dependent. Lack of CAMP expression was associated with higher levels of IL-10 receptor expression in bone marrow, splenic and lymph node macrophages as well as higher anti-inflammatory IL-10 production by bone marrow macrophages and spleen cells but reduced production of the pro-inflammatory cytokines IL-12 and IFN-γ by lymph nodes. Unlike wild-type mice, local lesions were exacerbated and parasites were found largely disseminated in CAMP knockouts. Infection of CAMP knockouts with parasite mutants lacking the surface metalloprotease virulence determinant resulted in more robust disseminated infection than in control animals suggesting that CAMP activity is negatively regulated by parasite surface proteolytic activity. This correlated with the ability of the protease to degrade CAMP in vitro and co-localization of CAMP with parasites within macrophages. Our results highlight the interplay of antimicrobial peptides and Leishmania that influence the host immune response and the outcome of infection.     

F2Dock: fast Fourier protein-protein docking

The functions of proteins are often realized through their mutual interactions. Determining a relative transformation for a pair of proteins and their conformations which form a stable complex, reproducible in nature, is known as docking. It is an important step in drug design, structure determination, and understanding function and structure relationships. In this paper, we extend our nonuniform fast Fourier transform-based docking algorithm to include an adaptive search phase (both translational and rotational) and thereby speed up its execution. We have also implemented a multithreaded version of the adaptive docking algorithm for even faster execution on multicore machines. We call this protein-protein docking code F2Dock (F2 = Fast Fourier). We have calibrated F2Dock based on an extensive experimental study on a list of benchmark complexes and conclude that F2Dock works very well in practice. Though all docking results reported in this paper use shape complementarity and Coulombic-potential-based scores only, F2Dock is structured to incorporate Lennard-Jones potential and reranking docking solutions based on desolvation energy .     

Single-particle reconstruction using L(2)-gradient flow

In this paper, we present an iterative algorithm for reconstructing a three-dimensional density function from a set of two dimensional electron microscopy images. By minimizing an energy functional consisting of a fidelity term and a regularization term, an L²-gradient flow is derived. The flow is integrated by a finite element method in the spatial direction and an explicit Euler scheme in the temporal direction. Our method compares favorably with those of the weighted back projection, Fourier method, algebraic reconstruction technique and simultaneous iterative reconstruction technique.     

Megafaunal community structure of Andaman seamounts including the Back-arc Basin--a quantitative exploration from the Indian Ocean

Species rich benthic communities have been reported from some seamounts, predominantly from the Atlantic and Pacific Oceans, but the fauna and habitats on Indian Ocean seamounts are still poorly known. This study focuses on two seamounts, a submarine volcano (cratered seamount--CSM) and a non-volcano (SM2) in the Andaman Back-arc Basin (ABB), and the basin itself. The main purpose was to explore and generate regional biodiversity data from summit and flank (upper slope) of the Andaman seamounts for comparison with other seamounts worldwide. We also investigated how substratum types affect the megafaunal community structure along the ABB. Underwater video recordings from TeleVision guided Gripper (TVG) lowerings were used to describe the benthic community structure along the ABB and both seamounts. We found 13 varieties of substratum in the study area. The CSM has hard substratum, such as boulders and cobbles, whereas the SM2 was dominated by cobbles and fine sediment. The highest abundance of megabenthic communities was recorded on the flank of the CSM. Species richness and diversity were higher at the flank of the CSM than other are of ABB. Non-metric multi-dimensional scaling (nMDS) analysis of substratum types showed 50% similarity between the flanks of both seamounts, because both sites have a component of cobbles mixed with fine sediments in their substratum. Further, nMDS of faunal abundance revealed two groups, each restricted to one of the seamounts, suggesting faunal distinctness between them. The sessile fauna corals and poriferans showed a significant positive relation with cobbles and fine sediments substratum, while the mobile categories echinoderms and arthropods showed a significant positive relation with fine sediments only.     

An alkali-thermotolerant extracellular protease from a newly isolated Streptomyces sp. DP2

Of six alkalitolerant, extracellular protease producing bacterial strains isolated, DP2 displayed maximum activity. This organism was designated as Streptomyces sp. DP2 and identified as Streptomyces ambofaciens. Maximum protease yield was observed after 48 hours of submerged fermentation using various carbon and nitrogen sources. Fructose was found to be the best substrate for protease production, followed by maltose, lactose and wheat bran. Mustard cake is reported for the first time as the most ideal nitrogen source although soybean meal also gave comparable yield. The protease produced by Streptomyces sp. DP2 exhibited extensive activity over a broad pH range (4–12) with maximum activity at pH 8, and was active over a broad range of elevated temperatures (50–100°C), and possessed thermostability at 60–90°C for up to 1 hour. Enzyme activity was reduced by EDTA (25%), SDS (16%), and PMSF (6%). This novel alkaline protease has both alkali- and thermostability that may have industrial significance.