Identification and characterization of a super-stable Cu–Zn SOD from leaves of turmeric (<Emphasis Type="Italic">Curcuma longa</Emphasis> L.)

We report a novel super stable superoxide dismutase (SOD) extracted from the leaves of Curcuma longa L.-a post-harvest waste. The scavenging activity of this SOD remains intact both in crude and purified forms before and after heating at boiling temperatures (80-100 degrees C) up to 20 min, autoclaving (6-20 bars up to 10 min) and microwaving (frequency of 2,450 megahertz (MHz) or million cycles per second for 1-3 min). This SOD has significant shelf life at room temperature (25-35 degrees C) and is stable for at least 18 months at 4 degrees C and with the retained activity of 82% at -10 degrees C and 88% at -20 degrees C without any infection or contamination. The heat stable enzyme is present both in cytoplasm and chloroplasts. The enzyme is also stable under wide range of pH, alcohol and SDS concentrations. The heat stability of this SOD protein is not due to any associated phenolic compound as no phenolic compound was bound to the novel thermo-stable SOD. The activity staining through native PAGE and purification of the enzyme protein have shown that this form of enzyme has a native molecular weight of 30.8 kDa and has two subunits of 15 kDa as shown by SDS PAGE. The characterized novel isoform is a Cu-Zn SOD as is indicated by its sensitivity to both H2O2 and KCN. Indian, US and PCT patents have been filed and products are being developed using this hyperthermophilic enzyme.     

Isocitrate dehydrogenase 1 R132C mutation occurs exclusively in microsatellite stable colorectal cancers with the CpG island methylator phenotype

The CpG Island Methylator Phenotype (CIMP) is fundamental to an important subset of colorectal cancer; however, its cause is unknown. CIMP is associated with microsatellite instability but is also found in BRAF mutant microsatellite stable cancers that are associated with poor prognosis. The isocitrate dehydrogenase 1 (IDH1) gene causes CIMP in glioma due to an activating mutation that produces the 2-hydroxyglutarate oncometabolite. We therefore examined IDH1 alteration as a potential cause of CIMP in colorectal cancer. The IDH1 mutational hotspot was screened in 86 CIMP-positive and 80 CIMP-negative cancers. The entire coding sequence was examined in 81 CIMP-positive colorectal cancers. Forty-seven cancers varying by CIMP-status and IDH1 mutation status were examined using Illumina 450K DNA methylation microarrays. The R132C IDH1 mutation was detected in 4/166 cancers. All IDH1 mutations were in CIMP cancers that were BRAF mutant and microsatellite stable (4/45, 8.9%). Unsupervised hierarchical cluster analysis identified an IDH1 mutation-like methylation signature in approximately half of the CIMP-positive cancers. IDH1 mutation appears to cause CIMP in a small proportion of BRAF mutant, microsatellite stable colorectal cancers. This study provides a precedent that a single gene mutation may cause CIMP in colorectal cancer, and that this will be associated with a specific epigenetic signature and clinicopathological features.     

Mathematical and computational modeling in biology at multiple scales

A variety of topics are reviewed in the area of mathematical and computational modeling in biology, covering the range of scales from populations of organisms to electrons in atoms. The use of maximum entropy as an inference tool in the fields of biology and drug discovery is discussed. Mathematical and computational methods and models in the areas of epidemiology, cell physiology and cancer are surveyed. The technique of molecular dynamics is covered, with special attention to force fields for protein simulations and methods for the calculation of solvation free energies. The utility of quantum mechanical methods in biophysical and biochemical modeling is explored. The field of computational enzymology is examined.     

Human metabolic phenotypes link directly to specific dietary preferences in healthy individuals

Individual human health is determined by a complex interplay between genes, environment, diet, lifestyle, and symbiotic gut microbial activity. Here, we demonstrate a new "nutrimetabonomic" approach in which spectroscopically generated metabolic phenotypes are correlated with behavioral/psychological dietary preference, namely, "chocolate desiring" or "chocolate indifferent". Urinary and plasma metabolic phenotypes are characterized by differential metabolic biomarkers, measured using 1H NMR spectroscopy, including the postprandial lipoprotein profile and gut microbial co-metabolism. These data suggest that specific dietary preferences can influence basal metabolic state and gut microbiome activity that in turn may have long-term health consequences to the host. Nutrimetabonomics appears as a promising approach for the classification of dietary responses in populations and personalized nutritional management.     

Top‐down systems biology integration of conditional prebiotic modulated transgenomic interactions in a humanized microbiome mouse model

Gut microbiome–host metabolic interactions affect human health and can be modified by probiotic and prebiotic supplementation. Here, we have assessed the effects of consumption of a combination of probiotics (Lactobacillus paracasei or L. rhamnosus) and two galactosyl‐oligosaccharide prebiotics on the symbiotic microbiome–mammalian supersystem using integrative metabolic profiling and modeling of multiple compartments in germ‐free mice inoculated with a model of human baby microbiota. We have shown specific impacts of two prebiotics on the microbial populations of HBM mice when co‐administered with two probiotics. We observed an increase in the populations of Bifidobacterium longum and B. breve, and a reduction in Clostridium perfringens, which were more marked when combining prebiotics with L. rhamnosus. In turn, these microbial effects were associated with modulation of a range of host metabolic pathways observed via changes in lipid profiles, gluconeogenesis, and amino‐acid and methylamine metabolism associated to fermentation of carbohydrates by different bacterial strains. These results provide evidence for the potential use of prebiotics for beneficially modifying the gut microbial balance as well as host energy and lipid homeostasis.     

Nutritional metabonomics: applications and perspectives

Nowadays, nutrition focuses on improving health of individuals through diet. Current nutritional research aims at health promotion, disease prevention, and performance improvement. Modern analytical platforms allow the simultaneous measurement of multiple metabolites providing new insights in the understanding of the functionalities of cells and whole organisms. Metabonomics, "the quantitative measurement of the dynamic multiparametric metabolic response of living systems to pathophysiological stimuli or genetic modifications", provides a systems approach to understanding global metabolic regulations of organisms. This concept has arisen from various applications of NMR and MS spectroscopies to study the multicomponent metabolic composition of biological fluids, cells, and tissues. The generated metabolic profiles are processed by multivariate statistics to maximize the recovery of information to be correlated with well-determined stimuli such as dietary intervention or with any phenotypic data or diet habits. Metabonomics is thus uniquely suited to assess metabolic responses to deficiencies or excesses of nutrients and bioactive components. Furthermore, metabonomics is used to characterize the metabolic phenotype of individuals integrating genetic polymorphism, metabolic interactions with commensal and symbiotic partners such as gut microflora, as well as environmental and behavioral factors including dietary preferences. This paper reports several experimental key aspects in nutritional metabonomics, reviews its applications employing targeted and holistic approach analysis for the study of the metabolic responses following dietary interventions. It also reports the assessment of intra- and inter-individual variability in animal and human populations. The potentialities of nutritional metabonomics for the discovery of new biomarkers and the characterization of metabolic phenotypes are discussed in a context of their possible utilizations for personalized nutrition to provide health maintenance at the individual level.     

Variation in the ribosomal internal transcribed spacers and 5.8S rDNA among five species of Acropora (Cnidaria; Scleractinia): patterns of variation consistent with reticulate evolution

The ITS sequences of Acropora spp. are the shortest so far identified in any metazoan and are among the shortest seen in eukaryotes; ITS1 was 70-80 bases, and ITS2 was 100-112 bases. The ITS sequences were also highly variable, but base composition and secondary structure prediction indicate that divergent sequence variants are unlikely to be pseudogenes. The pattern of variation was unusual in several other respects: (1) two distinct ITS2 types were detected in both A. hyacinthus and A. cytherea, species known to hybridize in vitro with high success rates, and a putative intermediate ITS2 form was also detected in A. cytherea; (2) A. valida was found to contain highly (29%) diverged ITS1 variants; and (3) A. longicyathus contained two distinct 5.8S rDNA types. These data are consistent with a reticulate evolutionary history for the genus Acropora.      

Glutamate 264 modulates the pH dependence of the NAD(+)-dependent D-lactate dehydrogenase.

Recently, we amplified the Lactobacillus bulgaricus NAD(+)-dependent D-lactate dehydrogenase gene by the polymerase chain reaction, cloned and overexpressed it in Escherichia coli (Kochhar, S., Chuard, N., and Hottinger, H. (1992) Biochem. Biophys. Res. Commun. 185, 705-712). Polymerase chain reaction-amplified DNA fragments may contain base changes resulting in mutant gene products. A comparison of specific activities of D-lactate dehydrogenase in the crude extracts of 50 recombinant clones indicated that one of the clones had drastically reduced enzyme activity. Nucleotide sequence analysis of the insert DNA showed an exchange of A to G at position 795 resulting in substitution of Glu264 to Gly in the D-lactate dehydrogenase. The purified mutant D-lactate dehydrogenase showed a shift of 2 units in its optimum pH toward the acidic range. The dependence of kcat/Km on the pH of the mutant enzyme showed that the pKa of the free enzyme was around 4, at least 2 pH units lower than that of the wild-type enzyme. Both the wild-type and the mutant enzyme at their respective optimum pH values showed similar kcat and Km values. The data suggest that the highly conserved Glu264 is not critical for enzyme catalysis, but it must be situated within hydrogen bonding distance to amino acid residue(s) involved in substrate binding as well as in catalysis.     

Comparative tests of ectoparasite species richness in seabirds

Background  

The diversity of parasites attacking a host varies substantially among different host species. Understanding the factors that explain these patterns of parasite diversity is critical to identifying the ecological principles underlying biodiversity. Seabirds (Charadriiformes, Pelecaniformes and Procellariiformes) and their ectoparasitic lice (Insecta: Phthiraptera) are ideal model groups in which to study correlates of parasite species richness. We evaluated the relative importance of morphological (body size, body weight, wingspan, bill length), life-history (longevity, clutch size), ecological (population size, geographical range) and behavioural (diving versus non-diving) variables as predictors of louse diversity on 413 seabird hosts species. Diversity was measured at the level of louse suborder, genus, and species, and uneven sampling of hosts was controlled for using literature citations as a proxy for sampling effort.     

An active center tryptophan residue in liquefying alpha-amylase from Bacillus amyloliquefaciens

Liquefying alpha-amylase from Bacillus amyloliquefaciens was inactivated on treatment with N-bromosuccinamide. Preincubation of the enzyme with either of the substrate, or competitive inhibitor provided significant protection against inactivation. The relationship between activity loss and the number of tryptophan residues modified, as well as presence of substrate/inhibitor in the reaction mixture, demonstrated that only one of three modifiable tryptophan residues is at or near the active center. The apparent Km of the modified enzyme for soluble starch increased manifold, thus implicating the sensitive tryptophan residue in the substrate binding region of the enzyme.