Protective effect of Tribulus terrestris linn on liver and kidney in cadmium intoxicated rats

Administration of cadmium (Cd) significantly increased the peroxidation markers such as malondialdehyde and protein carbonyls along with significant decrease in antioxidant markers such as super oxide dismutase and reduced glutathione in liver and kidney tissues. Cadmium also caused a significant alteration in hepatic and renal functional markers in serum viz. total protein, albumin, alanine transaminase, blood urea nitrogen and creatinine. Prominent pathological changes observed in liver were severe vascular and sinusoidal congestion with diffuse degenerative changes and mononuclear infiltration into peripheral areas, while the kidney showed vascular and glomerular congestion, cloudy swelling of tubular epithelium. Coadministration of ethonolic extract of T. terrestris or vitamin E along with Cd significantly reversed the Cd induced changes along with significant reduction in Cd load.     

Draft genome sequence of the sulfur-oxidizing bacterium "Candidatus Sulfurovum sediminum" AR, which belongs to the Epsilonproteobacteria

Sulfur-oxidizing bacteria are common microorganisms in a variety of sulfide-rich environments. They play important roles in the global sulfur cycle on earth. Here, we present a high-quality draft genome sequence of a sulfur-oxidizing bacterium, "Candidatus Sulfurovum sediminum" strain AR, which belongs to the class Epsilonproteobacteria and dominated an enrichment culture from a marine sediment collected off Svalbard, within the Arctic Circle. Its genome contains genes for sulfur oxidation and carbon fixation. The size of the draft genome is 2.12 Mb, and the G+C content is 39.4%.     

Insulin Signaling Regulates Mitochondrial Function in Pancreatic β-Cells

Insulin/IGF-I signaling regulates the metabolism of most mammalian tissues including pancreatic islets. To dissect the mechanisms linking insulin signaling with mitochondrial function, we first identified a mitochondria-tethering complex in β-cells that included glucokinase (GK), and the pro-apoptotic protein, BAD_S. Mitochondria isolated from β-cells derived from β-cell specific insulin receptor knockout (βIRKO) mice exhibited reduced BAD_S, GK and protein kinase A in the complex, and attenuated function. Similar alterations were evident in islets from patients with type 2 diabetes. Decreased mitochondrial GK activity in βIRKOs could be explained, in part, by reduced expression and altered phosphorylation of BAD_S. The elevated phosphorylation of p70S6K and JNK1 was likely due to compensatory increase in IGF-1 receptor expression. Re-expression of insulin receptors in βIRKO cells partially restored the stoichiometry of the complex and mitochondrial function. These data indicate that insulin signaling regulates mitochondrial function and have implications for β-cell dysfunction in type 2 diabetes.     

Matrix‐free UV‐laser desorption/ionization (LDI) mass spectrometric imaging at the single‐cell level: distribution of secondary metabolites of Arabidopsis thaliana and Hypericum species

The present paper describes matrix‐free laser desorption/ionisation mass spectrometric imaging (LDI‐MSI) of highly localized UV‐absorbing secondary metabolites in plant tissues at single‐cell resolution. The scope and limitations of the method are discussed with regard to plants of the genus Hypericum. Naphthodianthrones such as hypericin and pseudohypericin are traceable in dark glands on Hypericum leaves, placenta, stamens and styli; biflavonoids are also traceable in the pollen of this important phytomedical plant. The highest spatial resolution achieved, 10 μm, was much higher than that achieved by commonly used matrix‐assisted laser desorption/ionization (MALDI) imaging protocols. The data from imaging experiments were supported by independent LDI‐TOF/MS analysis of cryo‐sectioned, laser‐microdissected and freshly cut plant material. The results confirmed the suitability of combining laser microdissection (LMD) and LDI‐TOF/MS or LDI‐MSI to analyse localized plant secondary metabolites. Furthermore, Arabidopsis thaliana was analysed to demonstrate the feasibility of LDI‐MSI for other commonly occurring compounds such as flavonoids. The organ‐specific distribution of kaempferol, quercetin and isorhamnetin, and their glycosides, was imaged at the cellular level.     

Micropropagation of Withania coagulans (Stocks) Dunal: A Critically Endangered Medicinal Herb

An efficient micropropagation protocol has been developed for Withania coagulans, a highly endangered medicinal herb and an important natural source of withanolides. Prolific multiplication of axillary buds occurred from the nodal segments taken from adult plant, and cultured on MS medium enriched with BA (0.5 mg l^?1), Kn (0.5 mg l^?1) and PG (0.5 mg l^?1). Nodal segments and shoot tips of elongated microshoots also behaved the same way in cultures and formed multiple shoots through axillary bud multiplication. Addition of PG (0.5 mg l^?1) in the regeneration medium significantly improved induction and elongation of shoot buds. Elongated shoots were placed on filter paper bridges soaked in MS medium with CC (10 mg l^?1) and PG (0.5 mg l^?1) for the initial 7 days’ pulse treatment and thereafter, they were transferred to rooting medium containing IBA (0.25 mg l^?1) + PAA (0.5 mg l^?1) + CC (2 mg l^?1). This protocol has the capacity of producing 1000 plants from one nodal segment after 4 subcultures of 2 weeks each.     

Clinical Picture Of Arrhythmogenic Right Ventricular Dysplasia / Cardiomyopathy Patients From Indian Origin

Objective

Among the inherited cardiomyopathies, Arrhythmogenic right ventricular dysplasia/cardiomyopathy is unique with a peculiar pathology of fibro-fatty replacement. Studies have been carried out all over the world and several groups have reported clinical heterogeneity in manifestation of ARVD/C related symptoms. Present study is an attempt to identify the clinical profile of ARVD/C patients from Asian Indian origin.

Methods

31 patients in the span of three years were diagnosed with ARVD/C. Diagnosis was based on proposed task force criteria.

Results

The mean age at diagnosis was 32.9 ± 16.4 years with slight tilt in male to female ratio (1.46). About 80% cases had palpitations, syncope in 45.16% and dyspnea in 22.5%, whereas 16% of patients were asymptomatic. About 50% of patients revealed a family history of confirmed ARVD/C or sudden death of a family member without any known cause. ECG showed T-wave inversion in about 60% cases, prolongation of QRS was observed in 20% cases. RV dilatation was observed in 80% of patients and 66.7% showed systolic dysfunction. RV free wall motion abnormalities were found in 33% patients. Most of the early onset cases with less than 30 years of age showed family history indicative of ARVD/C. Familial study in three patients indicated early onset of condition in younger generations in two families.

Conclusions

ARVD/C in India shows relatively early age at onset when compared with other Asian populations with more than half of patients showing the disease below the age of 30 years. History in most of the early onset cases revealed family history indicating strong genetic influence.     

GrowMatch: An Automated Method for Reconciling In Silico/In Vivo Growth Predictions

Genome-scale metabolic reconstructions are typically validated by comparing in silico growth predictions across different mutants utilizing different carbon sources with in vivo growth data. This comparison results in two types of model-prediction inconsistencies; either the model predicts growth when no growth is observed in the experiment (GNG inconsistencies) or the model predicts no growth when the experiment reveals growth (NGG inconsistencies). Here we propose an optimization-based framework, GrowMatch, to automatically reconcile GNG predictions (by suppressing functionalities in the model) and NGG predictions (by adding functionalities to the model). We use GrowMatch to resolve inconsistencies between the predictions of the latest in silico Escherichia coli (iAF1260) model and the in vivo data available in the Keio collection and improved the consistency of in silico with in vivo predictions from 90.6% to 96.7%. Specifically, we were able to suggest consistency-restoring hypotheses for 56/72 GNG mutants and 13/38 NGG mutants. GrowMatch resolved 18 GNG inconsistencies by suggesting suppressions in the mutant metabolic networks. Fifteen inconsistencies were resolved by suppressing isozymes in the metabolic network, and the remaining 23 GNG mutants corresponding to blocked genes were resolved by suitably modifying the biomass equation of iAF1260. GrowMatch suggested consistency-restoring hypotheses for five NGG mutants by adding functionalities to the model whereas the remaining eight inconsistencies were resolved by pinpointing possible alternate genes that carry out the function of the deleted gene. For many cases, GrowMatch identified fairly nonintuitive model modification hypotheses that would have been difficult to pinpoint through inspection alone. In addition, GrowMatch can be used during the construction phase of new, as opposed to existing, genome-scale metabolic models, leading to more expedient and accurate reconstructions.     

CO Dehydrogenase Genes Found in Metagenomic Fosmid Clones from the Deep Mediterranean Sea

The use of carbon monoxide (CO) as a biological energy source is widespread in microbes. In recent years, the role of CO oxidation in superficial ocean waters has been shown to be an important energy supplement for heterotrophs (carboxydovores). The key enzyme CO dehydrogenase was found in both isolates and metagenomes from the ocean''s photic zone, where CO is continuously generated by organic matter photolysis. We have also found genes that code for both forms I (low affinity) and II (high affinity) in fosmids from a metagenomic library generated from a 3,000-m depth in the Mediterranean Sea. Analysis of other metagenomic databases indicates that similar genes are also found in the mesopelagic and bathypelagic North Pacific and on the surfaces of this and other oceanic locations (in lower proportions and similarities). The frequency with which this gene was found indicates that this energy-generating metabolism would be at least as important in the bathypelagic habitat as it is in the photic zone. Although there are no data about CO concentrations or origins deep in the ocean, it could have a geothermal origin or be associated with anaerobic metabolism of organic matter. The identities of the microbes that carry out these processes were not established, but they seem to be representatives of either Bacteroidetes or Chloroflexi.Carbon monoxide (CO) oxidation is a source of energy for a wide diversity of prokaryotes and is an important process within the global carbon cycle. There is a wide diversity of CO oxidation pathways among both archaea and bacteria (27, 28), and their wide distribution attests to both the ecological importance and ancient origin of CO oxidation. Most of these pathways are anaerobic (31, 40) and have been reported in both archaea and bacteria. However, aerobic CO oxidation is found only in a few groups of bacteria, specifically in many Actinobacteria and Proteobacteria spp. and in at least one Firmicutes sp. (for examples, see references 16, 17, 26, 35, 46, and 47). Classically, aerobic oxidation of CO has been known to be carried out in soils where, in addition to geological or anthropogenic emissions, there are local biological sources connected to plant roots and animals (15, 18, 19). However, more recently, the relevance of CO oxidation processes in the marine environment has also become clear, mostly from evidence from the fields of genomics and metagenomics (26, 42, 43).The aerobic oxidation of CO is very amenable to genomic analysis, since the genes involved are very characteristic, and their presence in marine bacterial genomes and in metagenomic databases can be considered diagnostic. The genes required for aerobic CO oxidation were first described in detail in chemolithoautotrophic Oligotropha carboxidovorans OM5 (10, 35, 36). The enzyme CO dehydrogenase (CODH) catalyzes the oxidation of CO and water to produce carbon dioxide, two electrons, and two protons (8, 11). The electrons are transferred to an electron transfer chain and used to generate a proton gradient across the membrane. Three genes, coxL, coxM, and coxS (for large, medium, and small subunits, respectively), encode the polypeptides for the CODH enzyme. Two heterotrimers, each composed of one CoxL, CoxM, and CoxS subunit, combine to form a functional aerobic CODH enzyme. The large subunit contains the molybdenum cofactor, the medium subunit binds flavin adenine dinucleotide, and the small subunit has two iron-sulfur clusters (13). In addition to these three genes, a number of other accessory genes have also been identified (CoxB, CoxC, CoxH, CoxD, CoxE, CoxF, CoxG, CoxI, and CoxK) that are believed to be required in the processes of regulation, posttranslational modification, and anchorage of the CODH complex to the cytoplasmic membrane. A number of these accessory genes are membrane-bound proteins themselves (CoxB, CoxC, CoxH, and CoxK), containing several transmembrane helices, and indeed, in O. carboxidovorans OM5, the CODH enzyme itself has been observed to associate with the inner cytoplasmic membrane.Based on sequence differences, genome organization, and catalytic properties, there are two types of aerobic molybdenum-based CODH (the anaerobic enzymes are a different class of genes) (20). Both forms can be readily differentiated from other molybdenum hydroxylases by phylogenetic analysis. Form I CODH (also called OMS, named after Oligotropha, Mycobacterium, and Pseudomonas) has been conclusively proven by mutagenesis experiments and X-ray crystallography (8, 32, 35) to be the key enzyme in aerobic CO oxidation by carboxydotrophic bacteria, i.e., those that can grow on CO as the sole carbon and energy source (at >10% CO concentration). The reaction mechanism has also been clearly defined. Form I CODH large-subunit CoxL can be readily diagnosed by its characteristic catalytic site motif AYXCSFR. Moreover, in all the organisms in which form I CODH genes have been identified so far, the genomic organization of the three subunits is always M→S→L. The organization of the accessory genes, however, may vary from organism to organism.There is much less known about the other form, form II CODH (or BMS, after Bradyrhizobium, Mesorhizobium, and Sinorhizobium), which was first described in Bradyrhizobium japonicum USDA 110 (23), a gram-negative bacterial strain and a nitrogen-fixing symbiont of soybeans. Form II CODH enables these bacteria to grow, albeit slowly, in the presence of CO as the sole carbon and energy source, but the rate of CO oxidation by form II CODH of B. japonicum USDA 110 is 10 to 1,000 times lower than that for form I CODH in O. carboxidovorans OM5 and Pseudomonas carboxydohydrogena OM5. The catalytic site of the form II CoxL large subunit is AYRGAGR. The genome organization of the form II subunits is S→L→M, different from that of form I. The number of accessory genes present along with these genes is also variable (20). Form II is often found as a paralogous copy of three subunits of form I, but without the accompanying set of CODH-related genes. This is not surprising, since in most cases, the genes appear to be already associated with the form I cluster elsewhere in the genome, like in Rhodothermus marinus DSM 4252, Dinoroseobacter shibae DFL 12, and Bradyrhizobium sp. strain BTAi1.The discovery of the role played by CODH in marine waters is relatively recent. First, it was found in the genome of Silicibacter pomeroyi DSS-3, a marine alphaproteobacterium of the Roseobacter cluster (26), which was concomitantly proven to be able to oxidize CO at low concentrations (as should be expected in marine waters). Later on the process, it was also found in metagenomic studies of surface waters for the Sargasso Sea metagenome project (26, 45). It has been proposed that many heterotrophic bacteria in surface waters are lithoheterotrophs and take advantage of the CO released by organic matter photolysis as an alternative energy source to supplement the scarce dissolved organic matter in a way akin to the photoheterotrophy mediated by proteorhodopsin or anoxygenic photosynthesis.We recently found evidence of a CODH presence deep in the Mediterranean Sea by the end sequencing of fosmids from a metagenomic library from a 3,000-m depth in the Ionian Sea (southeast of Sicily, Italy) (24). Here we present the analysis of nine fully sequenced fosmids that were chosen on the basis of the presence of CODH cluster genes at their ends. The results confirm the presence of complete CODH clusters, including one that has the gene sequence and cluster structure of a form I CODH. Although the source of CO deep in the ocean is unclear, the frequency in which these genes were found and the retrieval of similar sequences from the deep-ocean metagenomic database of the Hawaii Ocean Time-Series (HOT) station (7, 21) point toward an important contribution of this lithotrophic metabolism deep in the ocean, similarly relevant to that found in the surface waters.     

Textile dye degrading laccase from Pseudomonas desmolyticum NCIM 2112

A laccase requiring optimum temperature 60 °C, pH 4.0 for the activity and having apparent molecular weight 43,000 Da was purified from Pseudomonas desmolyticum NCIM 2112 by three steps, including heating, anion exchange, and molecular sieve chromatography. The purification fold and yield of laccase obtained through Biogel P100 were 45.75 and 19%, respectively. Staining of native gel with L-dopa showed dark brown color band indicating the presence of laccase. In relation to hydroquinone, the substrate specificity of laccase was in the following order: DAB > o-tolidine > ABTS > L-dopa. The absence of monophenolase activity in eluted fractions conformed that the purified protein is laccase. This laccase showed substrate dependent optimum pH character. Effect of inhibitor and metal ion on enzyme activity was analyzed. UV–vis analysis showed the decolorization of Direct Blue-6, Green HE4B and Red HE7B in the presence of laccase. The FTIR spectral comparison between the control dye sample and the metabolites extracted after decolorization by purified laccase have confirmed degradation of these dyes. This study contributes for the structural requirement of a dye to be degradable by P. desmolyticum laccase and is important in order to optimize potential bioremediation systems for industrial textile process water treatment.     

HIV‐1 IN alternative molecular recognition of DNA induced by raltegravir resistance mutations

Virologic failure during treatment with raltegravir, the first effective drug targeting HIV integrase, is associated with two exclusive pathways involving either Q148H/R/K, G140S/A or N155H mutations. We carried out a detailed analysis of the molecular and structural effects of these mutations. We observed no topological change in the integrase core domain, with conservation of a newly identified Ω‐shaped hairpin containing the Q148 residue, in particular. In contrast, the mutations greatly altered the specificity of DNA recognition by integrase. The native residues displayed a clear preference for adenine, whereas the mutant residues strongly favored pyrimidines. Raltegravir may bind to N155 and/or Q148 residues as an adenine bioisoster. This may account for the selected mutations impairing raltegravir binding while allowing alternative DNA recognition by integrase. This study opens up new opportunities for the design of integrase inhibitors active against raltegravir‐resistant viruses. Copyright © 2009 John Wiley & Sons, Ltd.