A new metabolomics analysis technique: steady-state metabolic network dynamics analysis

With the recent advances in experimental technologies, such as gas chromatography and mass spectrometry, the number of metabolites that can be measured in biofluids of individuals has markedly increased. Given a set of such measurements, a very common task encountered by biologists is to identify the metabolic mechanisms that lead to changes in the concentrations of given metabolites and interpret the metabolic consequences of the observed changes in terms of physiological problems, nutritional deficiencies, or diseases. In this paper, we present the steady-state metabolic network dynamics analysis (SMDA) approach in detail, together with its application in a cystic fibrosis study. We also present a computational performance evaluation of the SMDA tool against a mammalian metabolic network database. The query output space of the SMDA tool is exponentially large in the number of reactions of the network. However, (i) larger numbers of observations exponentially reduce the output size, and (ii) exploratory search and browsing of the query output space is provided to allow users to search for what they are looking for.     

Zinc-dependent changes in ESR signals, NADPH oxidase and plasma membrane permeability in cotton roots

The effect of Zn²⁺ on the plasma membrane permeability and superoxide radical (O₂^-) formation in roots was studied with cotton ( Gossypium hirsutum L. cv. Delta-pine 15/21) plants grown in nutrient solution with different Zn²⁺ supply. Compared to Zn-sufficient plants, the plasma membrane permeability of Zn-deficient plants was increased as indicated by a 3-, 5- and 2.5-fold increase in root cell leakage of K⁺, NO₃^- and organic carbon compounds, respectively. Resupply of Zn²⁺ to Zn-deficient plants for 12 h substantially decreased this leakage. The effects of Zn²⁺ on membrane permeability were closely correlated with the levels of O₂^- measured by electron spin resonance (ESR) spectroscopy in the microsomal membrane fraction and in the cytosol fraction of root cells. The amplitudes of the O₂^- -derived Tiron ESR signal also coincided with a O₂^- -generating oxidase activity which was strongly dependent on the presence of NADPH and FAD. The results suggest that Zn²⁺ directly affects the integrity of the plasma membrane, at least in part, by interfering with O₂^- generation by a membrane-bound NADPH oxidase.     

Zinc deficiency enhanced NAD(P)H-dependent superoxider radical production in plasma membrane vesicles isolated from roots of bean plants

The production of superoxide radical (O₂^–) was studiedin plasma membrane vesicles isolated by aqueous polymer two-phasepartitioning from roots of zinc-sufficient and zinc-deficientbean (Phaseolus vulgaris L. cv. Prélude) plants. Thetwo populations of vesicles were highly enriched in plasma membraneand had similar composition as evidenced by the specific membranemarker enzymes. Vesicles from zinc-deficient roots showed higherrates of NAD(P)H oxidation compared to vesicles from zinc-sufficientplants. The NAD(P)H-dependent formation of O₂^– in plasmamembrane vesicles was also highly increased by zinc deficiency.For both activities, a higher response to zinc deficiency wasobserved when NADPH was used as electron source. Re-supply ofzinc to deficient plants for 24 h substantially decreased therates of NAD(P)H oxidation and 0₂^– production in isolatedvesicles. The NADPH-dependent O₂^– generation was stronglystimulated by FAD and showed a high pH optimum; it was scarcelyaffected by Triton X-100 or even inhibited in the presence ofFAD and was almost insensitive to Antimycin A. The results suggest the presence at the plasma membrane of beanroots of an O₂^– generating activity, preferentially utilizingNADPH, which is affected by the zinc nutritional status of theplant. This finding, together with previous observations oncytosolic and microsomal fractions prepared from zinc-deficientroots of different plants, is consistent with a role of zincin membrane stabilization by controlling the level of oxidizingO₂ species. Key words: NAD(P)H oxidase, superoxide radical, plasma membrane, zinc deficiency     

Diterpenes from the berries of Juniperus excelsa

From the hexane extract of berries of Juniperus excelsa, one new and four known diterpenes were isolated besides a known sesquiterpene. The structures of the known diterpenes were identified as isopimaric, isocommunic, (-)ent-trans communic and sandracopimaric acids, along with the sesquiterpene 4a-hydroxycedrol and the new compound which was elucidated as 3 alpha-acetoxylabda-8(17),13(16),14-trien-19-oic acid (juniperexcelsic acid). Cytotoxic activity of the hexane extract was investigated against a panel of cell line and found highly active against LNCaP, KB-V (+VLB) and KB-V (-VLB) cell lines. Furthermore, the hexane and methanol extracts, and the new compound were found to be moderately active against Mycobacterium tuberculosis.     

Quantitative trait loci associated with soybean seed weight and composition under different phosphorus levels

Seed size and composition are important traits in food crops and can be affected by nutrient availability in the soil. Phosphorus (P) is a non‐renewable, essential macronutrient, and P deficiency limits soybean (Glycine max) yield and quality. To investigate the associations of seed traits in low‐ and high‐P environments, soybean recombinant inbred lines (RILs) from a cross of cultivars Fiskeby III and Mandarin (Ottawa) were grown under contrasting P availability environments. Traits including individual seed weight, seed number, and intact mature pod weight were significantly affected by soil P levels and showed transgressive segregation among the RILs. Surprisingly, P treatments did not affect seed composition or weight, suggesting that soybean maintains sufficient P in seeds even in low‐P soil. Quantitative trait loci (QTLs) were detected for seed weight, intact pods, seed volume, and seed protein, with five significant QTLs identified in low‐P environments and one significant QTL found in the optimal‐P environment. Broad‐sense heritability estimates were 0.78 (individual seed weight), 0.90 (seed protein), 0.34 (seed oil), and 0.98 (seed number). The QTLs identified under low P point to genetic regions that may be useful to improve soybean performance under limiting P conditions.     

Plant nutrition research: Priorities to meet human needs for food in sustainable ways

The world population is expanding rapidly and will likely be 10 billion by the year 2050. Limited availability of additional arable land and water resources, and the declining trend in crop yields globally make food security a major challenge in the 21st century. According to the projections, food production on presently used land must be doubled in the next two decades to meet food demand of the growing world population. To achieve the required massive increase in food production, large enhancements in application of fertilizers and improvements of soil fertility are indispensable approaches. Presently, in many developing countries, poor soil fertility, low levels of available mineral nutrients in soil, improper nutrient management, along with the lack of plant genotypes having high tolerance to nutrient deficiencies or toxicities are major constraints contributing to food insecurity, malnutrition (i.e., micronutrient deficiencies) and ecosystem degradation. Plant nutrition research provides invaluable information highly useful in elimination of these constraints, and thus, sustaining food security and well-being of humans without harming the environment. The fact that at least 60% of cultivated soils have growth-limiting problems with mineral-nutrient deficiencies and toxicities, and about 50% of the world population suffers from micronutrient deficiencies make plant nutrition research a major promising area in meeting the global demand for sufficient food production with enhanced nutritional value in this millennium. Integration of plant nutrition research with plant genetics and molecular biology is indispensable in developing plant genotypes with high genetic ability to adapt to nutrient deficient and toxic soil conditions and to allocate more micronutrients into edible plant products such as cereal grains.