Enzymes with new biochemical properties in the pectinolytic complex produced by Aspergillus niger MIUG 16

A comprehensive study on the purification and characterization of pectinolytic enzymes produced by Aspergillus niger MIUG 16 on raw materials solid-state fermentation is reported. Five pectinolytic enzymes were purified using a combination of chromatographic techniques. The properties of these homogenous enzymes were analyzed. The purified enzymes were classified with respect to their biochemical properties and substrate specificity. Among these proteins, one revealed polygalacturonase activity, another appeared to be a pectin methylesterase and three were identified as pectate lyases. The capacity of the fungus A. niger to produce pectate lyases with optimum pH in acidic domain was reported for the first time.     

Ethanol-induced alterations of the antioxidant defense system in rat kidney

We report here the effects of chronic ethanol consumption on the antioxidant defense system in rat kidney. Thirty-two male Wistar rats were randomly divided in two identical groups and were treated as follows: control group (water for fluid) and the ethanol-fed group (2 g/kg body weight/24 h). The animals were sacrificed after 10 weeks, and respectively 30 weeks of ethanol consumption, and the renal tissue was isolated and analyzed. Results revealed that kidney alcohol dehydrogenase activities increased significantly after ethanol administration, but the electrophoretic pattern of alcohol dehydrogenase isoforms was unmodified. The SDS polyacrylamidegel electrophoretic study of kidney proteins has revealed the appearance of two new protein bands after long-term ethanol consumption. The kidney reduced glutathione/oxidized glutathione ratio decreased, indicating an oxidative stress response due to ethanol ingestion. The malondialdehyde contents and xanthine oxidase activities were unchanged. The antioxidant enzymatic defense system showed a different response during the two periods of ethanol administration. After 10 weeks, catalase, glutathione peroxidase, glutathione reductase, and glucose-6-phosphate dehydrogenase were activated, while superoxide dismutase, glutathione transferase, and gamma-glutamyltranspeptidase levels were stationary. After 30 weeks, superoxide dismutase and glutathione peroxidase activities were unmodified, but catalase, glutathione transferase, gamma-glutamyltranspeptidase, glutathione reductase, and glucose-6-phosphate dehydrogenase activities were significantly increased. Remarkable changes have been registered after 30 weeks of ethanol administration for glutathione reductase and glucose-6-phosphate dehydrogenase activities, including an increase by 106 and 216' of control values, respectively. These results showed specific changes in rat kidney antioxidant system and glutathione status as a consequence of long-term ethanol administration.     

Ethanol‐induced alterations of the antioxidant defense system in rat kidney

We report here the effects of chronic ethanol consumption on the antioxidant defense system in rat kidney. Thirty‐two male Wistar rats were randomly divided in two identical groups and were treated as follows: control group (water for fluid) and the ethanol‐fed group (2 g/kg body weight/24 h). The animals were sacrificed after 10 weeks, and respectively 30 weeks of ethanol consumption, and the renal tissue was isolated and analyzed. Results revealed that kidney alcohol dehydrogenase activities increased significantly after ethanol administration, but the electrophoretic pattern of alcohol dehydrogenase isoforms was unmodified. The SDS polyacrylamidegel electrophoretic study of kidney proteins has revealed the appearance of two new protein bands after long‐term ethanol consumption. The kidney reduced glutathione/oxidized glutathione ratio decreased, indicating an oxidative stress response due to ethanol ingestion. The malondialdehyde contents and xanthine oxidase activities were unchanged. The antioxidant enzymatic defense system showed a different response during the two periods of ethanol administration. After 10 weeks, catalase, glutathione peroxidase, glutathione reductase, and glucose‐6‐phosphate dehydrogenase were activated, while superoxide dismutase, glutathione transferase, and γ‐glutamyltranspeptidase levels were stationary. After 30 weeks, superoxide dismutase and glutathione peroxidase activities were unmodified, but catalase, glutathione transferase, γ‐glutamyltranspeptidase, glutathione reductase, and glucose‐6‐phosphate dehydrogenase activities were significantly increased. Remarkable changes have been registered after 30 weeks of ethanol administration for glutathione reductase and glucose‐6‐phosphate dehydrogenase activities, including an increase by 106 and 216' of control values, respectively. These results showed specific changes in rat kidney antioxidant system and glutathione status as a consequence of long‐term ethanol administration. © 2005 Wiley Periodicals, Inc. J Biochem Mol Toxicol 19:386‐395, 2005; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/jbt.20101     

Environmental temperature and 17-ketosteroidogenesis in sheep

Investigations were performed on the fractionation of the urinary 17-ketosteroids of 6 castrated rams kept in constant general conditions and diet, 44 assays were performed during 3 winter months.Comparison of the hormone assais with the fluctuation in environmental temperature showed there to be a positive correlation between temperature under 0°C and 11-oxy-17-ketosteroid excretion and negative correlation with dehydro-epiandrosterone and aldosterone + etiocholanolone excretion. There was an inverse response when the temperature was over 0°C. The different response of cortisteroidogenesis to experimental and natural conditions is discussed in relation to high and low temperature.

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Zusammenfassung Die 17-Ketosteroide im Harn von 6 kastrierten Hammeln, die unter konstanten Bedingungen und Ernährung lebten, wurden während 3 Monaten im Winter untersucht. Die Korrelation der Hormonmengen mit den Veränderungen der Umgebungstemperatur ergab: (1) Bei Temperaturen unter 0°C war die Ausscheidung von 11-Oxy-17-Ketosteroid erhöht und die von Dehydro-Epiandrosteron und Aldosteron mit Atiocholanolon vermindert; (2) die umgekehrte Beziehung ergab sich bei Temperaturen über 0°C. Die verschiedenen Reaktionen der Kortikosteroidgenese auf natürliche und experimentelle Bedingungen in Beziehung auf hohe und niedrige Temperaturen werden diskutiert.

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Resume On a examiné durant trois mois d'hiver les 17-kétostéroïdes recueillis dans l'urine de 6 moutons châtrés. Ceux-ci vivaient dans des conditions extérieures identiques et recevaient la même nourriture. La corrélation établie entre les quantités d'hormones et les fluctuations de la température ambiante a donné les résultats suivants: (1) Par température inférieure à 0°C, la sécrétion de 11-Oxy-17-Kétostéroïde augmente alors que celles de déhydro-épiandrostérone et de aldostérone +étiocholandone diminuent; (2) l'effet opposé se produit par températures supérieures à 0°C. On discute les diverses réactions de la sécrétion de cortistéroïde à des températures élevées ou basses et cela dans des conditions naturelles et expérimentales.

     

BitTorious: global controlled genomics data publication,research and archiving via BitTorrent extensions

Background

Centralized silos of genomic data are architecturally easier to initially design, develop and deploy than distributed models. However, as interoperability pains in EHR/EMR, HIE and other collaboration-centric life sciences domains have taught us, the core challenge of networking genomics systems is not in the construction of individual silos, but the interoperability of those deployments in a manner embracing the heterogeneous needs, terms and infrastructure of collaborating parties. This article demonstrates the adaptation of BitTorrent to private collaboration networks in an authenticated, authorized and encrypted manner while retaining the same characteristics of standard BitTorrent.

Results

The BitTorious portal was sucessfully used to manage many concurrent domestic Bittorrent clients across the United States: exchanging genomics data payloads in excess of 500GiB using the uTorrent client software on Linux, OSX and Windows platforms. Individual nodes were sporadically interrupted to verify the resilience of the system to outages of a single client node as well as recovery of nodes resuming operation on intermittent Internet connections.

Conclusions

The authorization-based extension of Bittorrent and accompanying BitTorious reference tracker and user management web portal provide a free, standards-based, general purpose and extensible data distribution system for large ‘omics collaborations.     

Design of a bovine low-density SNP array optimized for imputation

The Illumina BovineLD BeadChip was designed to support imputation to higher density genotypes in dairy and beef breeds by including single-nucleotide polymorphisms (SNPs) that had a high minor allele frequency as well as uniform spacing across the genome except at the ends of the chromosome where densities were increased. The chip also includes SNPs on the Y chromosome and mitochondrial DNA loci that are useful for determining subspecies classification and certain paternal and maternal breed lineages. The total number of SNPs was 6,909. Accuracy of imputation to Illumina BovineSNP50 genotypes using the BovineLD chip was over 97% for most dairy and beef populations. The BovineLD imputations were about 3 percentage points more accurate than those from the Illumina GoldenGate Bovine3K BeadChip across multiple populations. The improvement was greatest when neither parent was genotyped. The minor allele frequencies were similar across taurine beef and dairy breeds as was the proportion of SNPs that were polymorphic. The new BovineLD chip should facilitate low-cost genomic selection in taurine beef and dairy cattle.     

On the electrical conductivity of rhodopsin solutions

Measurements were made on the conductivity of digitonin extracts of frog rhodopsin with and without previous light exposure. The light-dark difference in conductivity is observed at low concentrations of rhodopsin and detergent.     

JADE: An approach for interconnecting bioinformatics databases

To achieve the integration of biological data available on the World Wide Web and maintained in diverse sources such as GDB, Genbank or Acedb, we have developed a software called Jade. Jade allows programmers to create analytic tools and graphical user interfaces for one or more existing bioinformatics data sources. These tools can then be interchanged, compared and reused without making modifications in the data sources themselves. The system is implemented in the Java programming language and will run equally well on Macintosh, Windows or Unix workstations. Jade is free and can be used immediately by all interested parties.     

Association of SNPs in EGR3 and ARC with Schizophrenia Supports a Biological Pathway for Schizophrenia Risk

We have previously hypothesized a biological pathway of activity-dependent synaptic plasticity proteins that addresses the dual genetic and environmental contributions to schizophrenia. Accordingly, variations in the immediate early gene EGR3, and its target ARC, should influence schizophrenia susceptibility. We used a pooled Next-Generation Sequencing approach to identify variants across these genes in U.S. populations of European (EU) and African (AA) descent. Three EGR3 and one ARC SNP were selected and genotyped for validation, and three SNPs were tested for association in a replication cohort. In the EU group of 386 schizophrenia cases and 150 controls EGR3 SNP rs1877670 and ARC SNP rs35900184 showed significant associations (p = 0.0078 and p = 0.0275, respectively). In the AA group of 185 cases and 50 controls, only the ARC SNP revealed significant association (p = 0.0448). The ARC SNP did not show association in the Han Chinese (CH) population. However, combining the EU, AA, and CH groups revealed a highly significant association of ARC SNP rs35900184 (p = 2.353 x 10⁻⁷; OR [95% CI] = 1.54 [1.310–1.820]). These findings support previously reported associations between EGR3 and schizophrenia. Moreover, this is the first report associating an ARC SNP with schizophrenia and supports recent large-scale GWAS findings implicating the ARC complex in schizophrenia risk. These results support the need for further investigation of the proposed pathway of environmentally responsive, synaptic plasticity-related, schizophrenia genes.