Intelligent Access to Sequence and Structure Databases (IASSD) ? an interface for accessing information from major web databases

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Legacy Effects of Oil Road Reclamation on Soil Biology and Plant Community Composition

Following the unprecedented oil drilling presently occurring in western North Dakota, thousands of kilometers of oil roads must be reclaimed to an acceptable post‐extraction condition. This study assessed the soil biological and plant communities of nine decommissioned oil roads reclaimed during three periods between 1983 and 2002 in the Little Missouri National Grasslands of western North Dakota. We hypothesized that time‐since‐reclamation would positively affect soil biological and plant communities and, consequently, success of reclamation at older sites. To assess this hypothesis, we measured soil enzyme activity, soil microbial community composition, plant community composition, and soil physical and chemical properties along a gradient extending from road‐center to adjacent native prairie for the nine roads. Time‐since‐reclamation did not affect soil and plant properties measured, indicating that older reclamations are not more similar to native prairie than reclamations occurring more recently. A strong gradient between samples from road‐center and native prairie was identified with univariate and ordination analyses, indicating that soil and plant communities of reclaimed oil roads do not resemble those of the surrounding prairie. Soil organic matter (SOM) was identified as the most significantly affected soil property, being 30% lower on reclaimed roads than prairie. The relationship between SOM, microbial community, and plant community suggests that incorporating additional SOM could hasten reclamation as a result of improving the physical environment for plants and providing a labile carbon and energy source for the soil microbial community which, in turn, will enhance the nutrient and physical conditions for plant growth.     

Sleeping Beauty Mouse Models Identify Candidate Genes Involved in Gliomagenesis

Genomic studies of human high-grade gliomas have discovered known and candidate tumor drivers. Studies in both cell culture and mouse models have complemented these approaches and have identified additional genes and processes important for gliomagenesis. Previously, we found that mobilization of Sleeping Beauty transposons in mice ubiquitously throughout the body from the Rosa26 locus led to gliomagenesis with low penetrance. Here we report the characterization of mice in which transposons are mobilized in the Glial Fibrillary Acidic Protein (GFAP) compartment. Glioma formation in these mice did not occur on an otherwise wild-type genetic background, but rare gliomas were observed when mobilization occurred in a p19Arf heterozygous background. Through cloning insertions from additional gliomas generated by transposon mobilization in the Rosa26 compartment, several candidate glioma genes were identified. Comparisons to genetic, epigenetic and mRNA expression data from human gliomas implicates several of these genes as tumor suppressor genes and oncogenes in human glioblastoma.     

Identification of Th1/Th2 regulatory switch to promote healing response during leishmaniasis: a computational approach

Leishmania devices its survival strategy by suppressing the host’s immune functions. The antigen molecules produced by Leishmania interferes with the host’s cell signaling cascades and consequently changes the protein expression pattern of the antigen-presenting cell (APC). This creates an environment suitable for the switching of the T-cell responses from a healing Th1 response to a non-healing Th2 response that is favorable for the continued survival of the parasite inside the host APC. Using a reconstructed signaling network of the intracellular and intercellular reactions between a Leishmania infected APC and T-cell, we propose a computational model to predict the inhibitory effect of the Leishmania infected APC on the T-cell and to identify the regulators of this Th1-/Th2-switching behavior as observed during Leishmania infection. In this work, we hypothesize that a complete removal of the parasite could only be achieved with a simultaneous up-regulation of the healing Th1 response and stimulation of nitric oxide (NO) production from the APCs, and downregulation of the non-healing Th2 response and thereby propose several unique combinations of protein molecules that could elicit this anti-Leishmania immune response. Our results indicate that TLR3 may play a positive role in eliciting NO synthesis, while TLR2 may be responsible for inhibiting an anti-Leishmania immune response. Also, TLR3 overexpression (in the APC), when combined with SHP2 inhibition (in the T cell), produces an anti-Leishmania response that is better than the conventional IFN-gamma or IL12 treatment. A similar anti-Leishmania response is also obtained in another combination where TLR3 (in APC) is overexpressed, and SHC and MKP (of T cell) are inhibited and activated, respectively. Through our study, we also observe that Leishmania infection may induce an upregulation of IFN-beta production from the APC that may lead to an upregulation of the RAP1 and SOCS3 proteins inside the T cell, the potential inhibitors of MAPK and JAK-STAT signaling pathways, respectively, via the TYK2-mediated pathway. This study not only enhances our knowledge in understanding the Th1/Th2 regulatory switch to promote healing response during leishmaniasis but also helps to identify novel combinations of proteins as potential immunomodulators.     

Industrial Whey Utilization as a Medium Supplement for Biphasic Growth and Bacteriocin Production by Probiotic Lactobacillus casei LA-1

The ability of probiotic Lactobacillus casei LA-1 for bacteriocin production using industrial by-products, such as whey, as supplement in growth medium has been demonstrated for the first time. Whey was investigated as a sole carbon source in cooperation with other components to substitute expensive nutrients as MRS for economical bacteriocin production. Industrial whey-supplemented MRS medium was then selected as to determine the effect of four variables (temperature, initial pH, incubation time, and whey concentration) by response surface methodology on bacteriocin production. Statistical analysis of results showed that two variables have a significant effect on bacteriocin production. Response surface data showed maximum bacteriocin production of 6,132.33?AU/mL at an initial pH of 7.12, temperature 34.29?°C, and whey concentration 13.74?g/L. The production of bacteriocin started during the exponential growth phase, reaching maximum values at stationary phase, and a biphasic growth and production pattern was observed. Our current work demonstrates that this approach of utilization of whey as substitution in costly medium as MRS has great promise for cost reduction in industry for the production of novel biological metabolic product that can be utilized as a food preservative.     

Evidence of indigenous NAH plasmid of naphthalene degrading Pseudomonas putida PpG7 strain implicated in limonin degradation

A well characterized naphthalene-degrading strain, Pseudomonas putida PpG7 was observed to utilize limonin, a highly-oxygenated triterpenoid compound as a sole source of carbon and energy. Limonin concentrations evidenced a 64% reduction over 48 h of growth in batch cultures. Attempts were made to acquire a plasmid-less derivative via various methods (viz. Ethidium Bromide, SDS, elevated temperature & mitomycin C), among which the method involving mitomycin C (20 ug/ml) proved successful. Concomitant with the loss of plasmid in P. putida PpG7 strain, the cured derivative was identified as a lim- phenotype. The lim+ phenotype could be conjugally transferred to the cured derivative. Based on the results of curing with mitomycin C, conjugation studies and presence of ndo gene encoding naphthalene 1,2 dioxygenase, it was demonstrated that genes for the limonin utilization were encoded on an 83 kb indigenous transmissible Inc. P9 NAH plasmid in Pseudomonas putida PpG7 strain.     

Single‐nucleotide polymorphism (A118G) in exon 1 of OPRM1 gene causes alteration in downstream signaling by mu‐opioid receptor and may contribute to the genetic risk for addiction

The opioid receptor mu1 (OPRM1) mediates the action of morphine. Although genetic background plays an important role in the susceptibility toward abuse of drugs as evident from familial, adoption and twin studies, association of specific single‐nucleotide polymorphisms of OPRM1 gene with narcotic addiction is to be established. Here, we demonstrate the involvement of A118G polymorphism of exon1 of human OPRM1 gene (hOPRM1), with heroin and alcohol addiction, in a population in eastern India. Statistical analysis exhibited a significant association of G allele with both heroin and alcohol addiction with a risk factor of P_trend < 0.05. The functional significance of G allele in A118G single‐nucleotide polymorphisms was evaluated by studying the regulation of protein kinase A (PKA), pCREB, and pERK1/2 by morphine in Neuro 2A cells, stably transfected with either wild type or A118G mutant hOPRM1. Unlike acute morphine treatment, both chronic morphine exposure and withdrawal precipitated by naloxone were differentially regulated by A118 and G118 receptor isoforms when both PKA and pERK1/2 activities were compared. Results suggest that the association of A118G polymorphism to heroin and alcohol addiction may be because of the altered regulation of PKA and pERK1/2 during opioid and alcohol exposures.     

Adrenal steroids act as inhibitory modulators of thyrofollicular cell morphology and proliferation in neonatal chicks (Gallus domesticus)

In the present study the effects of adrenal corticoids, both natural and synthetic, namely cortisol and dexamethasone respectively, was observed on the thyroid gland cell morphology and proliferation in neonatal male chicks (Gallus domesticus). Cortisol was injected at a dose of 4 mg/100 g body weight and dexamethasone at a dose of 1 mg/100 g b.w. subcutaneously daily for fifteen consecutive days. The control birds were similarly injected with normal saline at a daily dose of 0.2 ml per bird for the same time period. The results indicated that both cortisol and dexamethasone caused a significant decrease in thyrofollicular cell height. On the contrary, a significant increase in the ratio of the follicular diameter to the number of nuclei per follicle i.e. D/N value was observed in both cortisol and dexamethasone treated chicks. It was also observed that both cortisol and dexamethasone induced suppression of mitotic activity, as evidenced from a significant decrease in mitotic percentage compared with the control chicks. The present authors' studies thus indicate that adrenal corticoids act as inhibitory modulators of thyroid follicular activity as regards karyomorphology and cell proliferation.