Identification and characterization of ethanol utilizing fungal flora of oil refinery contaminated soil

The indigenous fungal flora of three oil refinery contaminated sites (Bharuch, Valsad and Vadodara) of India has been documented in the present investigation. A total seventy-five fungal morphotypes were isolated from these sites and out of them, only fifteen isolates were capable of utilizing ethanol (0–8 %; v:v) as a sole source of carbon and energy for growth. Ten percent ethanol was completely lethal for the growth of all the isolated fungus. Biochemical characterization of the potent ethanol utilizing fungal isolates was studied based on substrate utilization profiles using BIOLOG phenotype microarray plates. Based on the morphological characters and Internal Transcribed Spacer region of ribosomal DNA, the fungal isolates were identified as Fusarium brachygibbosum, Fusarium equiseti, Fusarium acuminatum, Pencillium citrinum, Alternaria tenuissima, Septogloeum mori, Hypocrea lixii, Aureobasidium sp., Penicillium sp., and Fusarium sp. Intra-species genetic diversity among Fusarium sp. was evaluated by whole genome analysis with repetitive DNA sequences (ERIC, REP and BOX) based DNA fingerprinting. It was found that these fungus use alcohol dehydrogenase and acetaldehyde dehydrogenase enzymes based metabolism pathway to utilize ethanol for their growth and colonization.     

Molecular characterization and genetic diversity analysis of <Emphasis Type="Italic">Jatropha curcas</Emphasis> L. in India using RAPD and AFLP analysis

Jatropha curcas L. belongs to family Euphorbiaceae, native to South America and widely distributed in South and Central America, attained significant importance for its seed oil which can be converted to biodiesel, a renewable energy source alternative to conventional petro-diesel. Very few attempts were made to understand the extent of genetic diversity that exists in J. curcas. Therefore, the present investigation was undertaken to asses the genetic diversity among 28 diverse germplasm collected from distinct geographical areas in India. The overall percentage of polymorphism (PP) was found to be 50.70 and 60.95 by RAPD and AFLP, respectively. The mean PP was found to be 9.72 and 20.57 by RAPD and AFLP, respectively. The mean genetic similarity was observed to be 0.89 by RAPD and 0.88 by AFLP. Among the germplasm JCI20 found to be the most diverged one. The dendrogram analysis of RAPD and AFLP data showed good congruence, but better resolution and more polymorphism was observed with AFLP. When the dendrogram of RAPD was compared with AFLP dendrogram, the major clustering pattern was found to be similar; however, changes in minor grouping were observed. In both RAPD and AFLP analysis clustering of germplasm did not show any correlation with the geographical area of collection. Low genetic diversity observed in J. curcas and the clustering pattern indicates that the distribution of species might have happened through anthropogenic activity and warrants the need for widening the genetic base. The present study will provide pavement for further intra-population studies on narrow geographical areas, to understand the population genetic structure, phylogeography, molecular ecological studies. The marker information and the characterized germplasm help in further improvement of the species through marker assisted breeding programs.     

Downregulation of Apoptosis and Modulation of TGF-β1 by Sodium Selenate Prevents Streptozotocin-Induced Diabetic Rat Renal Impairment

To investigate whether sodium selenate treatment would impact on the onset of diabetic nephropathy, we examined blood glucose, serum biochemical components, and interrelationship between oxidative stress, TGF-β1, and apoptosis in streptozotocin (STZ) induced diabetic rats. Sixty male Wistar rats were divided into six groups. Group I (n = 10), normal control; Group II (n = 10), diabetic control; Group III (n = 10), sodium selenate (16 μmoles/kg) + diabetic; Group IV (n = 10), sodium selenate (32 μmoles/kg) + diabetic; Group V (n = 10), sodium selenate (16 μmoles/kg) control; and Group VI (n = 10), sodium selenate (32 μmoles/kg) control. Sodium selenate was administered via orogastric route for 10 weeks. In the diabetic group, diabetes was induced by single intraperitoneal injection of STZ (50 mg/kg). The levels of blood glucose were estimated and total cholesterol, high-density lipoprotein (HDL) cholesterol, triglycerides, creatinine, urea, and albumin were detected in serum. Antioxidant status was examined by measuring the superoxide dismutase (SOD), catalase, glutathione, and lipid peroxidation in kidney tissues. Histopathological studies were performed in the kidney tissue sections. The expression of TGF-β1 was estimated by the immunohistochemical analysis in kidneys. Apoptotic study in kidney was performed using the TdT-mediated dUTP nick end labeling technique. It was observed that blood glucose, serum, total cholesterol, HDL cholesterol, triglycerides, creatinine, urea, and albumin were significantly higher in diabetic control groups. Diabetic + sodium selenate (16 and 32 μmoles/kg) significantly reduced blood glucose, serum, total cholesterol, HDL cholesterol, triglycerides, creatinine, urea, and albumin levels. Selenium-treated groups significantly increased antioxidant enzyme activities (SOD, catalase, and glutathione) in kidneys of diabetic rats. All enzyme activities of selenium control groups did not differ compared with the normal control. Sodium selenate reduces significantly lipid peroxidation in diabetic rats. Cellular architecture of the diabetic rats was altered whereas sodium selenate administration rectifies the degenerative changes of the kidney. Profound immunopositivity of TGF-β1 was observed in the glomerular and tubulointerstitial cells of diabetic rat kidney. Immunopositivity of TGF-β1 was significantly reduced in both low and high dose of sodium-selenate-treated rats (P < 0.05, P < 0.01). High numbers of apoptotic cells were observed in diabetic rats whereas sodium selenate in both doses significantly reduces the incidence of apoptosis (P < 0.05, P < 0.01). We conclude herein that sodium selenate has the potential to play a significant role in limiting the renal impairment by altering the apoptosis and TGF-β1 in experimental diabetic rats.     

Lycopene as a natural protector against γ-radiation induced DNA damage,lipid peroxidation and antioxidant status in primary culture of isolated rat hepatocytes in vitro

The present study was designed to evaluate the radioprotective effect of lycopene, a naturally occurring dietary carotenoid, on γ-radiation induced toxicity in cultured rat hepatocytes. The cellular changes were estimated using lipid peroxidative indices like thiobarbituric acid reactive substances (TBARS), superoxide dismutase (SOD), catalase (CAT), glutathione peroxidase (GPx), reduced glutathione (GSH), ceruloplasmin, vitamins A, E, C and uric acid. The DNA damage was analysed by single cell gel electrophoresis (comet assay). The increase in the severity of DNA damage was observed with the increase in γ-radiation dose (1, 2 and 4 Gy) in cultured rat hepatocytes. TBARS were increased significantly whereas the levels of GSH, vitamins C, E and A, ceruloplasmin, uric acid and antioxidant enzymes were significantly decreased in γ-irradiated groups. The maximum damage to hepatocytes was observed at 4 Gy irradiation. Pretreatment with lycopene (1.86, 9.31 and 18.62 μM) showed a significant decrease in the levels of TBARS and DNA damage. The antioxidant enzymes increased significantly along with the levels of GSH, vitamins A, E, C, uric acid and ceruloplasmin. The maximum protection of hepatocytes was observed at 9.31 μM of lycopene pretreatment. Thus, our results show that pretreatment with lycopene offers protection against γ-radiation induced cellular damage and can be developed as an effective radioprotector during radiotherapy.     

Isolation and characterization of a novel <Emphasis Type="Italic">α</Emphasis>-amylase from a metagenomic library of Western Ghats of Kerala,India

In the present study, metagenomic library of Western Ghats soil sample was constructed in a fosmid vector (pCC1FOS) and screened for biocatalytic properties. The clones showed amylolytic activity on Luria-Bertani starch agar plates and one of them was studied in detail. The enzyme exhibited stability at elevated temperature with 60°C being the optimal temperature. The enzyme retained more than 30% activity after 60 min incubation at 80°C. It also showed more than 70% activity retention in 1.5 M NaCl solution. The pH optimum of the enzyme was at pH = 5.0. The enzyme possesses good activity in the presence of chelating and strong reducing agents with activity enhancements or retention being observed at 5 mM β-mercaptoethanol, dithiothreitol and N-bromosuccinimide. However, almost complete loss of activity was observed with 5 mM EDTA, while activity enhancement was observed upon incubation with Ca²⁺ suggesting it to be a Ca²⁺-dependent α-amylase, which was further confirmed by a thin-layer chromatography (TLC). The TLC run revealed that digestion pattern was similar to commercial α-amylase. The 16S rRNA gene sequence (GenBank accession number HQ680979) BLAST showed 95% similarities with Exiguobacterium sp. AFB-11 and AFB 18, with query sequence coverage of 99%.     

Differential and restricted expression of novel collagen VI chains in mouse

Recently, three novel collagen VI chains, α4, α5 and α6, were identified. These are thought to substitute for the collagen VI α3 chain, probably forming α1α2α4, α1α2α5 or α1α2α6 heterotrimers. The expression pattern of the novel chains is so far largely unknown. In the present study, we compared the tissue distribution of the novel collagen VI chains in mouse with that of the α3 chain by immunohistochemistry, immunoelectron microscopy and immunoblots. In contrast to the widely expressed α3 chain, the novel chains show a highly differential, restricted and often complementary expression. The α4 chain is strongly expressed in the intestinal smooth muscle, surrounding the follicles in ovary, and in testis. The α5 chain is present in perimysium and at the neuromuscular junctions in skeletal muscle, in skin, in the kidney glomerulus, in the interfollicular stroma in ovary and in the tunica albuginea of testis. The α6 chain is most abundant in the endomysium and perimysium of skeletal muscle and in myocard. Immunoelectron microscopy of skeletal muscle localized the α6 chain to the reticular lamina of muscle fibers. The highly differential and restricted expression points to the possibility of tissue-specific roles of the novel chains in collagen VI assembly and function.     

Development and validation of microsatellite markers for Karnal bunt (Tilletia indica) and loose smut (Ustilago segetum tritici) of wheat from related fungal species

Simple sequence repeats (SSRs) are preferred molecular markers because of their abundance, robustness, high reproducibility, high efficiency in detecting variation and suitability for high‐throughput analysis. In this study, an attempt was made to mine and analyse the SSRs from the genomes of two seed‐borne fungal pathogens, viz Ustilago maydis, which causes common smut of maize, and Tilletia horrida, the cause of rice kernel smut. After elimination of redundant sequences, 2,703 SSR loci of U. maydis were identified. Of the remaining SSRS, 44.5% accounted for di‐nucleotide repeats followed by 29.8% and 2.7% tri‐ and tetranucleotide repeats, respectively. Similarly, 2,638 SSR loci were identified in T. horrida, of which 20.2% were di‐nucleotide, 50.4% tri‐ and 20.5% tetra‐nucleotide repeats. A set of 65 SSRs designed from each fungus were validated, which yielded 23 polymorphic SSRs from Ustilago and 21 from Tilletia. These polymorphic SSR loci were also successfully cross‐amplified with the Ustilago segetum tritici and Tilletia indica. Principal coordinate analysis of SSR data clustered isolates according to their respective species. These newly developed and validated microsatellite markers may have immediate applications for detection of genetic variability and in population studies of bunt and smut of wheat and other related host plants. Moreover, this is first comprehensive report on molecular markers suitable for variability studies in wheat seed‐borne pathogens.     

Gene-based analysis of regionally enriched cortical genes in GWAS data sets of cognitive traits and psychiatric disorders

Background

Despite its estimated high heritability, the genetic architecture leading to differences in cognitive performance remains poorly understood. Different cortical regions play important roles in normal cognitive functioning and impairment. Recently, we reported on sets of regionally enriched genes in three different cortical areas (frontomedial, temporal and occipital cortices) of the adult rat brain. It has been suggested that genes preferentially, or specifically, expressed in one region or organ reflect functional specialisation. Employing a gene-based approach to the analysis, we used the regionally enriched cortical genes to mine a genome-wide association study (GWAS) of the Norwegian Cognitive NeuroGenetics (NCNG) sample of healthy adults for association to nine psychometric tests measures. In addition, we explored GWAS data sets for the serious psychiatric disorders schizophrenia (SCZ) (n = 3 samples) and bipolar affective disorder (BP) (n = 3 samples), to which cognitive impairment is linked.

Principal Findings

At the single gene level, the temporal cortex enriched gene RAR-related orphan receptor B (RORB) showed the strongest overall association, namely to a test of verbal intelligence (Vocabulary, P = 7.7E-04). We also applied gene set enrichment analysis (GSEA) to test the candidate genes, as gene sets, for enrichment of association signal in the NCNG GWAS and in GWASs of BP and of SCZ. We found that genes differentially expressed in the temporal cortex showed a significant enrichment of association signal in a test measure of non-verbal intelligence (Reasoning) in the NCNG sample.

Conclusion

Our gene-based approach suggests that RORB could be involved in verbal intelligence differences, while the genes enriched in the temporal cortex might be important to intellectual functions as measured by a test of reasoning in the healthy population. These findings warrant further replication in independent samples on cognitive traits.     

Characterization of silver nanoparticles synthesized by using marine isolate Streptomyces albidoflavus

Silver nanoparticles production by the green chemistry approach was investigated using an isolated marine actinomycetes strain. The isolated strain was identified as Streptomyces albidoflavus based on chemotaxonomic and ribotyping properties. The strain revealed production of silver nanoparticles both extracellular and intracellularly. Surface Plasmon Resonance analysis with the function of time revealed that particle synthesis by this strain is reaction time dependent. The produced particles were spherical shaped and monodispersive in nature and showed a single surface plasmon resonance peak at 410 nm. Size distribution histograms indicated production of 10-40- nm-size nanoparticles with a mean size of 14.5 nm. FT-IR spectra of nanopartilces showed N-H, C-H, and C-N stretching vibrations, denoting the presence of amino acid/ peptide compounds on the surface of silver nanoparticles produced by S. albidoflavus. Synthesized nanoparticles revealed a mean negative zeta potential and electrophoretic mobility of -8.5 mV and -0.000066 cm2/Vs, respectively. The nanoparticles produced were proteinaceous compounds as capping agents with -8.5 mV zeta potential and revealed antimicrobial activity against both Gram-negative and -positive bacterial strains. Owing to their small size, these particles have greater impact on industrial application spectra.