Anvaya: a workflows environment for automated genome analysis

Anvaya is a workflow environment for automated genome analysis that provides an interface for several bioinformatics tools and databases, loosely coupled together in a coordinated system, enabling the execution of a set of analyses tools in series or in parallel. It is a client-server workflow environment that has an advantage over existing software as it enables extensive pre & post processing of biological data in an efficient manner. "Anvaya" offers the user, novel functionalities to carry out exhaustive comparative analysis via "custom tools," which are tools with new functionality not available in standard tools, and "built-in PERL parsers," which automate data-flow between tools that hitherto, required manual intervention. It also provides a set of 11 pre-defined workflows for frequently used pipelines in genome annotation and comparative genomics ranging from EST assembly and annotation to phylogenetic reconstruction and microarray analysis. It provides a platform that serves as a single-stop solution for biologists to carry out hassle-free and comprehensive analysis, without being bothered about the nuances involved in tool installation, command line parameters, format conversions required to connect tools and manage/process multiple data sets at a single instance.     

Ethanolic Zingiber officinale R. extract pretreatment alleviates isoproterenol-induced oxidative myocardial necrosis in rats

Ethanolic Z. officinale (ZO) extract (200 mg/kg) pretreatment for 20 days in isoproterenol (ISO)-treated rats significantly increased the levels of endogenous myocardial antioxidants (catalase, superoxide dismutase and tissue glutathione), decreased the levels of serum marker enzymes (lactate dehydrogenase, creatine kinase, aspartate transaminase and alanine transaminase) and increased myocardial lipid peroxides. Histological examination of rat's heart section confirmed myocardial injury with ISO administration and near normal pattern with ethanolic ZO extract pretreatment. The results of the present study, for the first time, provide clear evidence that the ethanolic ZO extract pretreatment enhances the antioxidant defense against ISO-induced oxidative myocardial injury in rats and exhibit cardioprotective property.     

Stem cell issue: Stem Cell Research Policies around the World

The proliferation of stem cell research, conflated with its ethical and moral implications, has led governments to attempt regulation of both the science and funding of stem cells. Due to a diversity of opinions and cultural viewpoints, no single policy or set of rules exist to govern stem cell research. Instead, each country has developed its own policy. The following map catalogs the general legal and political milleu regarding stem cell research by country.     

Identification of a Novel Abscisic Acid-Regulated Farnesol Dehydrogenase from Arabidopsis

In Arabidopsis (Arabidopsis thaliana), farnesylcysteine is oxidized to farnesal and cysteine by a membrane-associated thioether oxidase called farnesylcysteine lyase. Farnesol and farnesyl phosphate kinases have also been reported in plant membranes. Together, these observations suggest the existence of enzymes that catalyze the interconversion of farnesal and farnesol. In this report, Arabidopsis membranes are shown to possess farnesol dehydrogenase activity. In addition, a gene on chromosome 4 of the Arabidopsis genome (At4g33360), called FLDH, is shown to encode an NAD⁺-dependent dehydrogenase that oxidizes farnesol more efficiently than other prenyl alcohol substrates. FLDH expression is repressed by abscisic acid (ABA) but is increased in mutants with T-DNA insertions in the FLDH 5′ flanking region. These T-DNA insertion mutants, called fldh-1 and fldh-2, are associated with an ABA-insensitive phenotype, suggesting that FLDH is a negative regulator of ABA signaling.Isoprenylated proteins are modified at the C terminus via cysteinyl thioether linkage to either a 15-carbon farnesyl or a 20-carbon geranylgeranyl group (Clarke, 1992; Zhang and Casey, 1996; Rodríguez-Concepción et al., 1999; Crowell, 2000; Crowell and Huizinga, 2009). These modifications mediate protein-membrane and protein-protein interactions and are necessary for the proper localization and function of hundreds of proteins in eukaryotic cells. In Arabidopsis (Arabidopsis thaliana), the PLURIPETALA (PLP; At3g59380) and ENHANCED RESPONSE TO ABA1 (At5g40280) genes encode the α- and β-subunits of protein farnesyltransferase (PFT), respectively (Cutler et al., 1996; Pei et al., 1998; Running et al., 2004). These subunits form a heterodimeric zinc metalloenzyme that catalyzes the efficient transfer of a farnesyl group from farnesyl diphosphate to protein substrates with a C-terminal CaaX motif, where “C” is Cys, “a” is an aliphatic amino acid, and “X” is usually Met, Gln, Cys, Ala, or Ser (Fig. 1). The PLP and GERANYLGERANYL-TRANSFERASE BETA (At2g39550) genes encode the α- and β-subunits of protein geranylgeranyltransferase type 1 (PGGT1), respectively (Running et al., 2004; Johnson et al., 2005). These subunits form a distinct heterodimeric zinc metalloenzyme that catalyzes the efficient transfer of a geranylgeranyl group from geranylgeranyl diphosphate to protein substrates with a C-terminal CaaL motif, where “C” is Cys, “a” is an aliphatic amino acid, and “L” is Leu. A third protein prenyltransferase, called protein geranylgeranyltransferase type II or RAB geranylgeranyltransferase, catalyzes the dual geranylgeranylation of RAB proteins with a C-terminal XCCXX, XXCXC, XXCCX, XXXCC, XCXXX, or CCXXX motif, where “C” is Cys and “X” is any amino acid. However, RAB proteins must be associated with the RAB ESCORT PROTEIN to be substrates of RAB geranylgeranyltransferase. Plant protein prenylation has received considerable attention in recent years because of the meristem defects of Arabidopsis PFT mutants and the abscisic acid (ABA) hypersensitivity of Arabidopsis PFT and PGGT1 mutants (Cutler et al., 1996; Pei et al., 1998; Running et al., 1998, 2004; Johnson et al., 2005).Open in a separate windowFigure 1.Proposed metabolism of farnesal and farnesol as it relates to protein prenylation. The portion of the cycle shown in red is the subject of this article.Proteins that are prenylated by either PFT or PGGT1 undergo further processing in the endoplasmic reticulum (Crowell, 2000; Crowell and Huizinga, 2009). First, the aaX portion of the CaaX motif is removed by proteolysis (Fig. 1). This reaction is catalyzed by one of two CaaX endoproteases, which are encoded by the AtSTE24 (At4g01320) and AtFACE-2 (At2g36305) genes (Bracha et al., 2002; Cadiñanos et al., 2003). Second, the prenylated Cys residue at the new C terminus is methylated by one of two isoprenylcysteine methyltransferases (Fig. 1), which are encoded by the AtSTE14A (At5g23320) and AtSTE14B (ICMT; At5g08335) genes (Crowell et al., 1998; Crowell and Kennedy, 2001; Narasimha Chary et al., 2002; Bracha-Drori et al., 2008). A specific isoprenylcysteine methylesterase encoded by the Arabidopsis ICME (At5g15860) gene has also been described, demonstrating the reversibility of isoprenylcysteine methylation (Deem et al., 2006; Huizinga et al., 2008).Like all proteins, prenylated proteins have a finite half-life. However, unlike other proteins, prenylated proteins release farnesylcysteine (FC) or geranylgeranylcysteine (GGC) upon degradation. Mammals possess a prenylcysteine lyase enzyme that catalyzes the oxidative cleavage of FC and GGC (Zhang et al., 1997; Tschantz et al., 1999; Tschantz et al., 2001; Beigneux et al., 2002; Digits et al., 2002). This FAD-dependent thioether oxidase consumes molecular oxygen and generates hydrogen peroxide, Cys, and a prenyl aldehyde product (i.e. farnesal or geranylgeranial). In Arabidopsis, a similar lyase exists. However, the Arabidopsis enzyme, which is encoded by the FCLY (At5g63910) gene, is specific for FC (Fig. 1; Crowell et al., 2007; Huizinga et al., 2010). GGC is metabolized by a different mechanism.Plant membranes have been shown to contain farnesol kinase, geranylgeraniol kinase, farnesyl phosphate kinase, and geranylgeranyl phosphate kinase activities (Fig. 1; Thai et al., 1999). These membrane-associated kinases differ with respect to nucleotide specificity, suggesting that they are distinct enzymes (i.e. farnesol kinase and geranylgeraniol kinase can use CTP, UTP, or GTP as a phosphoryl donor, whereas farnesyl phosphate kinase and geranylgeranyl phosphate kinase exhibit specificity for CTP as a phosphoryl donor). However, it remains unclear if farnesol kinase is distinct from geranylgeraniol kinase or if farnesyl phosphate kinase is distinct from geranylgeranyl phosphate kinase. Nonetheless, it is clear that these kinases convert farnesol and geranylgeraniol to their monophosphate and diphosphate forms for use in isoprenoid biosynthesis, including sterol biosynthesis and protein prenylation.Because plants have the metabolic capability to generate farnesal from FC and farnesyl diphosphate from farnesol, we considered the possibility that plant membranes also contain an oxidoreductase capable of catalyzing the reduction of farnesal to farnesol and/or the oxidation of farnesol to farnesal (Fig. 1; Thai et al., 1999; Crowell et al., 2007). To date, the only reports of such an oxidoreductase are from the corpora allata glands of insects, where it participates in juvenile hormone synthesis, and black rot fungus-infected sweet potato (Ipomoea batatas; Baker et al., 1983; Inoue et al., 1984; Sperry and Sen, 2001; Mayoral et al., 2009). Insect farnesol dehydrogenase is an NADP⁺-dependent oxidoreductase that is encoded by a subfamily of short-chain dehydrogenase/reductase (SDR) genes (Mayoral et al., 2009). Farnesol dehydrogenase from sweet potato is a 90-kD, NADP⁺-dependent homodimer with broad specificity for prenyl alcohol substrates and is induced by wounding and fungus infection of potato roots (Inoue et al., 1984).Here, we extended previous work in which [1-³H]FC was shown to be oxidized to [1-³H]farnesal, and [1-³H]farnesal reduced to [1-³H]farnesol, in the presence of Arabidopsis membranes (Crowell et al., 2007). The reduction of [1-³H]farnesal to [1-³H]farnesol was abolished by pretreatment of Arabidopsis membranes with NADase, suggesting that sufficient NAD(P)H is present in Arabidopsis membranes to support the enzymatic reduction of farnesal to farnesol. In this report, we demonstrate the presence of farnesol dehydrogenase activity in Arabidopsis membranes using [1-³H]farnesol as a substrate. Moreover, we identify a gene on chromosome 4 of the Arabidopsis genome (At4g33360), called FLDH, that encodes an NAD⁺-dependent dehydrogenase with partial specificity for farnesol as a substrate. FLDH expression is repressed by exogenous ABA, and fldh mutants exhibit altered ABA signaling. Taken together, these observations suggest that ABA regulates farnesol metabolism in Arabidopsis, which in turn regulates ABA signaling.     

A simple method for the simultaneous isolation of stellate cells and hepatocytes from rat liver tissue

Hepatic stellate cells (HSCs), also referred to as Ito cells, perisinusiodal cells and fat-storing cells, have numerous vital functions. They are the main extracellular matrix-producing cells within the liver and are involved in the storage of retinol. HSCs are also known to secrete a number of liver mitogens. Current isolation techniques are cumbersome and most require a pronase digestion step, which destroys any hepatocytes present. We present a simple method for isolation and culture of hepatic stellate cells from the normally discarded washings from a two-step collagenase hepatocyte isolation, which has shown a yield of more than 1.5 × 10⁶ viable HSCs after 5 days in culture. The cells were positively identified as HSCs by staining for two intermediate filaments (desmin and GFAP) and observing their distinct morphology from other liver cell types. This efficient method allows rapid and consistent isolation of stellate cells to give a culture that may be passaged several times.     

Taq DNA polymerase slippage mutation rates measured by PCR and quasi-likelihood analysis: (CA/GT)n and (A/T)n microsatellites

During microsatellite polymerase chain reaction (PCR), insertion–deletion mutations produce stutter products differing from the original template by multiples of the repeat unit length. We analyzed the PCR slippage products of (CA)_n and (A)_n tracts cloned in a pUC18 vector. Repeat numbers varied from two to 14 (CA)_n and four to 12 (A)_n. Data was generated on approximately 10 single molecules for each clone type using two rounds of nested PCR. The size and peak areas of the products were obtained by capillary electrophoresis. A quasi- likelihood approach to the analysis of the data estimated the mutation rate/repeat/PCR cycle. The rate for (CA)_n tracts was 3.6 × 10^–3 with contractions 14 times greater than expansions. For (A)_n tracts the rate was 1.5 × 10^–2 and contractions outnumbered expansions by 5-fold. The threshold for detecting ‘stutter’ products was computed to be four repeats for (CA)_n and eight repeats for (A)_n or ~8 bp in both cases. A comparison was made between the computationally and experimentally derived threshold values. The threshold and expansion to contraction ratios are explained on the basis of the active site structure of Taq DNA polymerase and models of the energetics of slippage events, respectively.     

Temporal expression of fumonisin B(1)-induced tumor necrosis factor-alpha and interferon gamma in mice

Fumonisin B(1) (FB(1)), a toxic metabolite of Fusarium verticillioides, is a carcinogen and causative agent of various animal diseases. Our previous studies indicated the involvement of tumor necrosis factor-alpha (TNF alpha) in FB(1)-induced toxic responses. To further investigate the time-course of TNF alpha production and signaling, mice (four/group) were treated subcutaneously (s.c.) or per os (p.o.) with either vehicle or 25 mg/kg of FB(1) as a single dose and sacrificed at 0, 2, 4, 8, 12 and 24 h after treatment. The TNF alpha expression was increased in liver and kidney after both routes of FB(1) exposure without any alterations in spleen. The p.o.-route FB(1) treatment caused greater hepatotoxicity compared to the s.c. route, as depicted by increased alanine aminotransferase and aspartate aminotransferase level in plasma, observed only after p.o. FB(1) treatment. The increase in enzymes at 8 h after p.o. treatment correlated with the highest TNF alpha expression, also noted at 8 h after p.o. treatment, thus further confirming the involvement of TNF alpha in FB(1) toxicity. The interferon (IFN)-gamma expression was increased in liver at 4 h after p.o. FB(1) treatment, suggesting a possible combined role of TNF alpha and IFN gamma in their induction and hepatotoxicity.     

Impact of massive dose of vitamin A given to preschool children with acute diarrhoea on subsequent respiratory and diarrhoeal morbidity.

OBJECTIVE--To assess the impact of vitamin A supplementation on morbidity from acute respiratory tract infections and diarrhoea. DESIGN--Double blind randomised placebo controlled field trial. SETTING--An urban slum area in New Delhi, India. SUBJECTS--900 children aged 12-60 months attending a local health facility for acute diarrhoea of less than seven days'' duration randomly allocated to receive vitamin A 200,000 IU or placebo. MAIN OUTCOME MEASURES--Incidence and prevalence of acute lower respiratory tract infections and diarrhoea during the 90 days after termination of the enrolment diarrhoeal episode measured by twice weekly household surveillance. RESULTS--The incidence (relative risk 1.07; 95% confidence interval 0.92 to 1.26) and average number of days spent with acute lower respiratory tract infections were similar in the vitamin A supplementation and placebo groups. Among children aged 23 months or less there was a significant reduction in the incidence of measles (relative risk 0.06; 95% confidence interval 0.01 to 0.48). The incidence of diarrhoea was also similar (relative risk 0.95; 0.86 to 1.05) in the two groups. There was a 36% reduction in the mean daily prevalence of diarrhoea associated with fever in the vitamin A supplemented children older than 23 months. CONCLUSIONS--Results were consistent with a lack of impact on acute lower respiratory tract related mortality after vitamin A supplementation noted in other trials and a possible reduction in the severity of diarrhoea.     

Design,Synthesis and Pharmacological Screening of Novel Antihypertensive Agents Using Hybrid Approach

Eight derivatives of general formula 2-(2-(4-(3-((5-substituted methylene)-4-oxo-2-(phenylimino)thiazolidin-3-yl)-2-hydroxypropylamino)benzoyl)hydrazinyl)-2-oxoethyl nitrate were synthesized and tested for electrocardiographic, antiarrhythmic, vasorelaxing and antihypertensive activity as well as for in-vitro nitric oxide (NO) releasing ability. Compound 8b 2-(2-(4-(3-(5-benzyliden-4-oxo-2-(phenylimino)thiazolidin-3-yl)-2-hydroxypropylamino)benzoyl)hydrazinyl)-2-oxoethyl nitrate, was the most potent in this series. The pharmacological results suggested that the antiarrhythmic effects of these compounds were related to their adrenolytic properties which are believed to be due to the presence of the 5-(substituted)methylen-2-(phenylimino)thiazolidin-4-one moiety with less bulky, electron donating substituent on the phenyl ring at 5th position of the thiazolidin-4-one. In conclusion, most of the synthesized compounds were significantly potent as antiarrhythmic and antihypertensive; this might be due to the presence of different pharmacopores which might act at different locations with different mode of action. Further insights of the same can be obtained by doing investigation at receptor level. The potency of compounds 8a–8h were promising enough to continue further experiments.