In Silico analysis of the lateral organ junction (LOJ) gene and promoter of Arabidopsis thaliana

A T-DNA based promoter trapped mutant has led to the identification of a novel lateral organ junction specific promoter upstream of the pentatricopeptide repeat (PPR) protein coding gene LOJ in Arabidopsis thaliana by our laboratory. Various in silico based prediction tools are employed to characterize the upstream sequence of the LOJ gene. Out of numerous cis-elements detected in the LOJ promoter a few are considered important based on the expression pattern of the LOJ gene. These elements would provide a basis for designing experiments for more accurate promoter function annotation. A comparative search for conserved elements in the 5'-upstream region of a few genes involved in lateral organ development and meristem related expression reveals a few common relevant regulatory motifs. The coding region of the LOJ gene is intron-less and contains 19 PPR units. Based on in silico analysis, LOJ protein is predicted to be hydrophobic in nature and targeted to mitochondria. A partial 3D model of LOJ protein has been suggested using a homology-based modeling program.     

BTXpred: prediction of bacterial toxins

This paper describes a method developed for predicting bacterial toxins from their amino acid sequences. All the modules, developed in this study, were trained and tested on a non-redundant dataset of 150 bacterial toxins that included 77 exotoxins and 73 endotoxins. Firstly, support vector machines (SVM) based modules were developed for predicting the bacterial toxins using amino acids and dipeptides composition and achieved an accuracy of 96.07% and 92.50%, respectively. Secondly, SVM based modules were developed for discriminating entotoxins and exotoxins, using amino acids and dipeptides composition and achieved an accuracy of 95.71% and 92.86%, respectively. In addition, modules have been developed for classifying the exotoxins (e.g. activate adenylate cyclase, activate guanylate cyclase, neurotoxins) using hidden Markov models (HMM), PSI-BLAST and a combination of the two and achieved overall accuracy of 95.75%, 97.87% and 100%, respectively. Based on the above study, a web server called 'BTXpred' has been developed, which is available at http://www.imtech.res.in/raghava/btxpred/. Supplementary information is available at http://www.imtech.res.in/raghava/btxpred/supplementary.html.     

A comparative study of predation of three aquatic heteropteran bugs on Culex quinquefasciatus larvae

The aquatic bugs Anisops bouvieri Kirkaldy 1704 (Heteroptera: Notonectidae), Diplonychus (=Sphaerodema) rusticus Fabricius 1781, and Diplonychus annulatus Fabricius 1781 (Heteroptera: Belostomatidae) are common members of the freshwater insect communities of the East Calcutta Wetlands along the eastern fringe of Kolkata, India. These insects are established predators of dipteran larvae and other organisms. A comparative account of their predatory efficiency was made using larvae of Culex quinquefasciatus Say 1823 in the laboratory. It was revealed that a single adult of A. bouvieri could consume 28–34 fourth-instar mosquito larvae per day, D. rusticus 11–87 fourth-instar mosquito larvae per day, and D. annulatus 33–122 fourth-instar mosquito larvae per day, depending upon the prey and predator densities. The mean predation rate of A. bouvieri and D. annulatus remained stable over a 6-day feeding period but varied for D. rusticus. The predatory impact (PI) values were 14.77–17.31, 46.9–55.73, and 61.74–72.72 larvae/day for A. bouvieri, D. rusticus, and D. annulatus, respectively. Compared to these, the clearance rate (CR) value range was 9.06–13.25 for A. bouvieri, 13.64–15.99 for D. rusticus, and 13.50–16.52 larvae l/day/predator for D. annulatus. The values of mutual interference, “m,” remained 0.06–0.78 for A. bouvieri, 0.003–0.25 for D. rusticus, and 0.09–0.27 for D. annulatus, and did not vary between the days. The difference in predatory efficiency, CR, and PI values varied significantly among the three predators, indicating the possible difference in the function as predators occupying the same guild. It can be assumed that these predators play an important role in larval population regulation of mosquitoes and thereby impart an effect on species composition and interactions in the aquatic insect communities of the wetlands and other similar habitats where they occur.     

The Role of the Mammalian DNA End-processing Enzyme Polynucleotide Kinase 3’-Phosphatase in Spinocerebellar Ataxia Type 3 Pathogenesis

DNA strand-breaks (SBs) with non-ligatable ends are generated by ionizing radiation, oxidative stress, various chemotherapeutic agents, and also as base excision repair (BER) intermediates. Several neurological diseases have already been identified as being due to a deficiency in DNA end-processing activities. Two common dirty ends, 3’-P and 5’-OH, are processed by mammalian polynucleotide kinase 3’-phosphatase (PNKP), a bifunctional enzyme with 3’-phosphatase and 5’-kinase activities. We have made the unexpected observation that PNKP stably associates with Ataxin-3 (ATXN3), a polyglutamine repeat-containing protein mutated in spinocerebellar ataxia type 3 (SCA3), also known as Machado-Joseph Disease (MJD). This disease is one of the most common dominantly inherited ataxias worldwide; the defect in SCA3 is due to CAG repeat expansion (from the normal 14–41 to 55–82 repeats) in the ATXN3 coding region. However, how the expanded form gains its toxic function is still not clearly understood. Here we report that purified wild-type (WT) ATXN3 stimulates, and by contrast the mutant form specifically inhibits, PNKP’s 3’ phosphatase activity in vitro. ATXN3-deficient cells also show decreased PNKP activity. Furthermore, transgenic mice conditionally expressing the pathological form of human ATXN3 also showed decreased 3’-phosphatase activity of PNKP, mostly in the deep cerebellar nuclei, one of the most affected regions in MJD patients’ brain. Finally, long amplicon quantitative PCR analysis of human MJD patients’ brain samples showed a significant accumulation of DNA strand breaks. Our results thus indicate that the accumulation of DNA strand breaks due to functional deficiency of PNKP is etiologically linked to the pathogenesis of SCA3/MJD.     

Cell disruption methods for improving lipid extraction efficiency in unicellular microalgae

Identification of cost‐effective cell disruption methods to facilitate lipid extraction from microalgae represents a crucial step in identifying promising biofuel‐producing species. Various cell disruption methods including autoclaving, microwave, osmotic shock, and pasteurization were tested in the microalgae Chlorococcum sp. MCC30, Botryococcus sp. MCC31, Botryococcus sp. MCC32, and Chlorella sorokiniana MIC‐G5. Lipid content (on dry weight basis) from the four cultures on day 7 ranged from 11.15 to 48.33%, and on day 14 from 11.42 to 44.26%. Among the methods tested, enhanced lipid extraction was achieved through osmotic shock (15% NaCl) for Botryococcus sp. MCC32, microwave (6 min) for Botryococcus sp. MCC31, osmotic shock (5% NaCl) for Chlorella sorokiniana MIC‐G5 and microwave (2 min) for Chlorococcum sp. MCC30. The highest palmitate (16:0) contents (25.64% and 34.20%) were recorded with osmotic shock (15% NaCl) treatment for Botryococcus sp. MCC32 and microwave (6 min) for Botryococcus sp. MCC31, respectively. Two strains, along with their respective cell disruption methods, were identified as promising oil blends or nutraceuticals due to their high unsaturated fatty acid (UFA) content: Botryococcus sp. MCC31 (37.6% oleic acid content; 39.37% UFA) after autoclaving and Botryococcus sp. MCC32 after osmotic shock of 15% NaCl treatment (19.95% oleic acid content; 38.17% UFA).     

Modified high-density lipoprotein modulates aldosterone release through scavenger receptors via extra cellular signal-regulated kinase and Janus kinase-dependent pathways

A proliferation-inducing ligand (APRIL) is overexpressed in most tumor cells and tissues, especially in tumors of the alimentary system, such as colorectal cancer (CRC), gastric cancer, and liver cancer. RNA interference (RNAi) has been proved to be a powerful tool for gene knockdown and holds great promise for the treatment of cancer. In this study, the efficacy of RNAi targeting APRIL was analyzed via relevant experiments on human CRC xenografted in BALB/c nude mice. Both the mRNA and protein levels of APRIL were examined after intratumoral injection of APRIL small interfering RNA (siRNA). Meanwhile, pathological tools were utilized to observe the alterations on the aspects of proliferation, metastasis, apoptosis and cellular necrosis by means of detecting proliferating cell nuclear antigen, Ki-67, MMP-2, MMP-9, TIMP-3, TIMP-4, Bcl-2, Bax and Bcl-xL of CRC. In addition, terminal deoxyribonucleotidyl transferase-mediated dUTP-digoxigenin nick end-labeling (TUNEL) and hematoxylin and eosin staining were also conducted to examine cell apoptosis and necrosis. It was found that grafted human colorectal tumor growth and metastasis were obviously inhibited while tumor cell apoptosis and necrosis were induced after in vivo APRIL siRNA injection into nude mice. The data indicated that silencing of the APRIL gene using RNAi may serve as a novel therapeutic strategy for treatment of CRC.     

Crystal structure of Staphylococcal dual specific inositol monophosphatase/NADP(H) phosphatase (SAS2203) delineates the molecular basis of substrate specificity

Inositol monophosphatase (IMPase) family of proteins are Mg(2+) activated Li(+) inhibited class of ubiquitous enzymes with promiscuous substrate specificity. Herein, the molecular basis of IMPase substrate specificity is delineated by comparative crystal structural analysis of a Staphylococcal dual specific IMPase/NADP(H) phosphatase (SaIMPase - I) with other IMPases of different substrate compatibility, empowered by in silico docking and Escherichia coli SuhB mutagenesis analysis. Unlike its eubacterial and eukaryotic NADP(H) non-hydrolyzing counterparts, the composite structure of SaIMPase - I active site pocket exhibits high structural resemblance with archaeal NADP(H) hydrolyzing dual specific IMPase/FBPase. The large and shallow SaIMPase - I active site cleft efficiently accommodate large incoming substrates like NADP(H), and therefore, justifies the eminent NADP(H) phosphatase activity of SaIMPase - I. Compared to other NADP(H) non-hydrolyzing IMPases, the profound difference in active site topology as well as the unique NADP(H) recognition capability of SaIMPase - I stems from the differential length and orientation of a distant helix α4 (in human and bovine α5) and its preceding loop. We identified the length of α4 and its preceding loop as the most crucial factor that regulates IMPase substrate specificity by employing a size exclusion mechanism. Hence, in SaIMPase - I, the substrate promiscuity is a gain of function by trimming the length of α4 and its preceding loop, compared to other NADP(H) non-hydrolyzing IMPases. This study thus provides a biochemical - structural framework revealing the length and orientation of α4 and its preceding loop as the predisposing factor for the determination of IMPase substrate specificity.     

Dimethylsulphopropionate (DMSP) and proline from the surface of the brown alga Fucus vesiculosus inhibit bacterial attachment

It was demonstrated previously that polar and non-polar surface extracts of the brown alga Fucus vesiculosus collected during winter from the Kiel Bight (Germany) inhibited bacterial attachment at natural concentrations. The present study describes the bioassay-guided identification of the active metabolites from the polar fraction. Chromatographic separation on a size-exclusion liquid chromatography column and bioassays identified an active fraction that was further investigated using nuclear magnetic resonance spectroscopy and mass spectrometry. This fraction contained the metabolites dimethylsulphopropionate (DMSP), proline and alanine. DMSP and proline caused the anti-attachment activity. The metabolites were further quantified on the algal surface together with its associated boundary layer. DMSP and proline were detected in the range 0.12-1.08 ng cm(-2) and 0.09-0.59 ng cm(-2), respectively. These metabolites were tested in the concentration range from 0.1 to 1000 ng cm(-2) against the attachment of five bacterial strains isolated from algae and sediment co-occurring with F. vesiculosus. The surface concentrations for 50% inhibition of attachment of these strains were always <0.38 ng cm(-2) for DMSP and in four cases <0.1 ng cm(-2) for proline, while one strain required 1.66 ng cm(-2) of proline for 50% inhibition. Two further bacterial strains that had been directly isolated from F. vesiculosus were also tested, but proved to be the least sensitive. This study shows that DMSP and proline have an ecologically relevant role as surface inhibitors against bacterial attachment on F. vesiculosus.