Enhanced degradation of gamma-irradiated lignocelluloses by a new xylanolytic Flavobacterium sp. isolated from soil

An extracellular chitosanase produced by Rhodotorula gracilis CFR-1 that catalyses a limited degradation of chitosan with no detectable generation of glucosamine or reducing groups was identified. Ultracentrifugation, polyacrylamide gel electrophoresis and gel permeation studies suggest that chitosan of average molecular mass 36000 Da was reduced by the enzymic catalysis to nearly one-fourth this size without further hydrolysis of the products. The enzyme, produced constitutively by this yeast, was partially purified and some of its properties were studied.     

Evaluating the effectiveness of conservation site networks under climate change: accounting for uncertainty

We forecasted potential impacts of climate change on the ability of a network of key sites for bird conservation (Important Bird Areas; IBAs) to provide suitable climate for 370 bird species of current conservation concern in two Asian biodiversity hotspots: the Eastern Himalaya and Lower Mekong. Comparable studies have largely not accounted for uncertainty, which may lead to inappropriate conclusions. We quantified the contribution of four sources of variation (choice of general circulation models, emission scenarios and species distribution modelling methods and variation in species distribution data) to uncertainty in forecasts and tested if our projections were robust to these uncertainties. Declines in the availability of suitable climate within the IBA network by 2100 were forecast as ‘extremely likely’ for 45% of species, whereas increases were projected for only 2%. Thus, we predict almost 24 times as many ‘losers’ as ‘winners’. However, for no species was suitable climate ‘extremely likely’ to be completely lost from the network. Considerable turnover (median = 43%, 95% CI = 35–69%) in species compositions of most IBAs were projected by 2100. Climatic conditions in 47% of IBAs were projected as ‘extremely likely’ to become suitable for fewer priority species. However, no IBA was forecast to become suitable for more species. Variation among General Circulation Models and Species Distribution Models contributed most to uncertainty among forecasts. This uncertainty precluded firm conclusions for 53% of species and IBAs because 95% confidence intervals included projections of no change. Considering this uncertainty, however, allows robust recommendations concerning the remaining species and IBAs. Overall, while the IBA network will continue to sustain bird conservation, climate change will modify which species each site will be suitable for. Thus, adaptive management of the network, including modified site conservation strategies and facilitating species' movement among sites, is critical to ensure effective future conservation.     

Purification and characterization of a novel thermo-active amidase from Geobacillus subterraneus RL-2a

A thermostable amidase produced by Geobacillus subterraneus RL-2a was purified to homogeneity, with a yield of 9.54 % and a specific activity of 48.66 U mg^?1. The molecular weight of the native enzyme was estimated to be 111 kDa. The amidase of G. subterraneus RL-2a is constitutive in nature, active at a broad range of pH (4.5–11.5) and temperature (40–90 °C) and has a half-life of 5 h and 54 min at 70 °C. Inhibition of enzyme activity was observed in the presence of metal ions, such as Co²⁺, Hg²⁺, Cu²⁺, Ni²⁺, and thiol reagents. The presence of mid-chain aliphatic and amino acid amides enhances the enzymatic activity. The acyl transferase activity was detected with propionamide, butyramide and nicotinamide. The enzyme showed moderate stability toward toluene, carbon tetrachloride, benzene, ethylene glycol except acetone, ethanol, butanol, propanol and dimethyl sulfoxide. The K _m and V _max of the purified amidase with nicotinamide were 6.02 ± 0.56 mM and 132.6 ± 4.4 μmol min^?1 mg^?1 protein by analyzing Michaelis–Menten kinetics. The results of MALDI-TOF analysis indicated that this amidase has homology with the amidase of Geobacillus sp. C56-T3 (gi|297530427). It is the first reported wide-spectrum thermostable amidase from a thermophilic G. subterraneus.     

Predicting the distributions of predator (snow leopard) and prey (blue sheep) under climate change in the Himalaya

Future climate change is likely to affect distributions of species, disrupt biotic interactions, and cause spatial incongruity of predator–prey habitats. Understanding the impacts of future climate change on species distribution will help in the formulation of conservation policies to reduce the risks of future biodiversity losses. Using a species distribution modeling approach by MaxEnt, we modeled current and future distributions of snow leopard (Panthera uncia) and its common prey, blue sheep (Pseudois nayaur), and observed the changes in niche overlap in the Nepal Himalaya. Annual mean temperature is the major climatic factor responsible for the snow leopard and blue sheep distributions in the energy‐deficient environments of high altitudes. Currently, about 15.32% and 15.93% area of the Nepal Himalaya are suitable for snow leopard and blue sheep habitats, respectively. The bioclimatic models show that the current suitable habitats of both snow leopard and blue sheep will be reduced under future climate change. The predicted suitable habitat of the snow leopard is decreased when blue sheep habitats is incorporated in the model. Our climate‐only model shows that only 11.64% (17,190 km²) area of Nepal is suitable for the snow leopard under current climate and the suitable habitat reduces to 5,435 km² (reduced by 24.02%) after incorporating the predicted distribution of blue sheep. The predicted distribution of snow leopard reduces by 14.57% in 2030 and by 21.57% in 2050 when the predicted distribution of blue sheep is included as compared to 1.98% reduction in 2030 and 3.80% reduction in 2050 based on the climate‐only model. It is predicted that future climate may alter the predator–prey spatial interaction inducing a lower degree of overlap and a higher degree of mismatch between snow leopard and blue sheep niches. This suggests increased energetic costs of finding preferred prey for snow leopards – a species already facing energetic constraints due to the limited dietary resources in its alpine habitat. Our findings provide valuable information for extension of protected areas in future.     

BJ-1108, a 6-Amino-2,4,5-Trimethylpyridin-3-ol Analog,Inhibits Serotonin-Induced Angiogenesis and Tumor Growth through PI3K/NOX Pathway

5-Hydroxytryptamine (5-HT) induces proliferation of cancer cells and vascular cells. In addition to 5-HT production by several cancer cells including gastrointestinal and breast cancer, a significant level of 5-HT is released from activated platelets in the thrombotic environment of tumors, suggesting that inhibition of 5-HT signaling may constitute a new target for antiangiogenic anticancer drug discovery. In the current study we clearly demonstrate that 5-HT-induced angiogenesis was mediated through the 5-HT₁ receptor-linked Gβγ/Src/PI3K pathway, but not through the MAPK/ERK/p38 pathway. In addition, 5-HT induced production of NADPH oxidase (NOX)-derived reactive oxygen species (ROS). In an effort to develop new molecularly targeted anticancer agents against 5-HT action in tumor growth, we demonstrate that BJ-1108, a derivative of 6-amino-2,4,5-trimethylpyridin-3-ol, significantly inhibited 5-HT-induced angiogenesis. In addition, BJ-1108 induced a significant reduction in the size and weight of excised tumors in breast cancer cell-inoculated CAM assay, showing proportionate suppression of tumor growth along with inhibition of angiogenesis. In human umbilical vein endothelial cells (HUVECs), BJ-1108 significantly suppressed 5-HT-induced ROS generation and phosphorylation of PI3K/Akt but not of Src. Unlike NOX inhibitors, BJ-1108, which showed better antioxidant activity than vitamin C, barely suppressed superoxide anion induced by mevalonate or geranylgeranyl pyrophosphate which directly activates NOX without help from other signaling molecules in HUVECs, implying that the anti-angiogenic action of BJ-1108 was not mediated through direct action on NOX activation, or free radical scavenging activity. In conclusion, BJ-1108 inhibited 5-HT-induced angiogenesis through PI3K/NOX signaling but not through Src, ERK, or p38.     

Mitochondrial DNA genomes of five major Helicoverpa pest species from the Old and New Worlds (Lepidoptera: Noctuidae)

Five species of noctuid moths, Helicoverpa armigera, H. punctigera, H. assulta, H. zea, and H. gelotopoeon, are major agricultural pests inhabiting various and often overlapping global distributions. Visual identification of these species requires a great deal of expertise and misidentification can have repercussions for pest management and agricultural biosecurity. Here, we report on the complete mitochondrial genomes of H. assulta assulta and H. assulta afra, H. gelotopoeon, H. punctigera, H. zea, and H. armigera armigera and H. armigera conferta’ assembled from high‐throughput sequencing data. This study significantly increases the mitogenome resources for these five agricultural pests with sequences assembled from across different continents, including an H. armigera individual collected from an invasive population in Brazil. We infer the phylogenetic relationships of these five Helicoverpa species based on the 13 mitochondrial DNA protein‐coding genes (PCG's) and show that two publicly available mitogenomes of H. assulta ( KP015198 and KR149448 ) have been misidentified or incorrectly assembled. We further consolidate existing PCR‐RFLP methods to cover all five Helicoverpa pest species, providing an updated method that will contribute to species differentiation and to future monitoring efforts of Helicoverpa pest species across different continents. We discuss the value of Helicoverpa mitogenomes to assist with species identification in view of the context of the rapid spread of H. armigera in the New World. With this work, we provide the molecular resources necessary for future studies of the evolutionary history and ecology of these species.     

Conserved amino acid residues within the amino-terminal domain of ClpB are essential for the chaperone activity

ClpB from Escherichia coli is a member of a protein-disaggregating multi-chaperone system that also includes DnaK, DnaJ, and GrpE. The sequence of ClpB contains two ATP-binding domains that are enclosed between the amino-terminal and carboxyl-terminal regions. The N-terminal sequence region does not contain known functional sequence motifs. Here, we performed site-directed mutagenesis of four polar residues within the N-terminal domain of ClpB (Thr7, Ser84, Asp103 and Glu109). These residues are conserved in several ClpB homologs. We found that the mutations, T7A, S84A, D103A, and E109A did not significantly affect the secondary structure and thermal stability of ClpB, nor did they inhibit the self-association of ClpB, its basal ATPase activity, or the enhanced rate of the ATP hydrolysis by ClpB in the presence of poly-L-lysine. We observed, however, that three mutations, T7A, D103A, and E109A, reduced the casein-induced activation of the ClpB ATPase. The same three mutant ClpB variants also showed low chaperone activity in the luciferase reactivation assay. We found, however, that the four ClpB mutants, as well as the wild-type, bound similar amounts of inactivated luciferase. In summary, we have identified three essential amino acid residues within the N-terminal region of ClpB that participate in the coupling between a protein-binding signal and the ATP hydrolysis, and also support the chaperone activity of ClpB.     

The inositol polyphosphate 5-phosphatases and the apurinic/apyrimidinic base excision repair endonucleases share a common mechanism for catalysis

Inositol polyphosphate 5-phosphatases (5-phosphatase) hydrolyze the 5-position phosphate from the inositol ring of phosphatidylinositol-derived signaling molecules; however, the mechanism of catalysis is only partially characterized. These enzymes play critical roles in regulating cell growth, apoptosis, intracellular calcium oscillations, and post-synaptic vesicular trafficking. The UCLA fold recognition server (threader) predicted that the conserved 300-amino acid catalytic domain, common to all 5-phosphatases, adopts the fold of the apurinic/apyrimidinic (AP) base excision repair endonucleases. PSI-BLAST searches of GENPEPT, using the amino acid sequence of AP endonuclease exonuclease III, identified all members of the 5-phosphatase family with highly significant scores. A sequence alignment between exonuclease III and all known 5-phosphatases revealed six highly conserved motifs containing residues that corresponded to the catalytic residues in the AP endonucleases. Mutation of each of these residues to alanine in the mammalian 43-kDa, or yeast Inp52p 5-phosphatase, resulted in complete loss of enzyme activity. We predict the 5-phosphatase enzymes share a similar mechanism of catalysis to the AP endonucleases, consistent with other common functional similarities such as an absolute requirement for magnesium for activity. Based on this analysis, functional roles have been assigned to conserved residues in all 5-phosphatase enzymes.     

Antioxidative metabolism in down syndrome

Down syndrome is the most common cause of mental retardation, affecting 1 in 700–800 liveborn infants. Although numerous biochemical abnormalities accompanying the syndrome have not yet been completely clarified, the antioxidant defense system enzymes have shown to be altered due to increased gene dosage on chromosome 21 and overproduction of superoxide dismutase (SOD-1 or Cu/Zn SOD). The purpose of this study was to investigate the activities of SOD-1 and glutathione peroxidase (GSH-Px) enzymes and the levels of their cofactors zinc (Zn), copper (Cu) and selenium (Se) in plasma of 20 Down syndrome patients. In comparison with age and sex-matched controls (n=15), plasma GSH-Px, SOD, and Cu levels were significantly decreased in the patient group, but Zn and Se concentrations remained unchanged. This study was presented as a poster in 29th Annual Meeting of European Society of Human Genetics held in Genoa in May, 1997.