Continuing improvements in analytical technology along with an increased interest in performing comprehensive, quantitative metabolic profiling, is leading to increased interest pressures within the metabolomics community to develop centralized metabolite reference resources for certain clinically important biofluids, such as cerebrospinal fluid, urine and blood. As part of an ongoing effort to systematically characterize the human metabolome through the Human Metabolome Project, we have undertaken the task of characterizing the human serum metabolome. In doing so, we have combined targeted and non-targeted NMR, GC-MS and LC-MS methods with computer-aided literature mining to identify and quantify a comprehensive, if not absolutely complete, set of metabolites commonly detected and quantified (with today's technology) in the human serum metabolome. Our use of multiple metabolomics platforms and technologies allowed us to substantially enhance the level of metabolome coverage while critically assessing the relative strengths and weaknesses of these platforms or technologies. Tables containing the complete set of 4229 confirmed and highly probable human serum compounds, their concentrations, related literature references and links to their known disease associations are freely available at http://www.serummetabolome.ca.

Urine has long been a “favored” biofluid among metabolomics researchers. It is sterile, easy-to-obtain in large volumes, largely free from interfering proteins or lipids and chemically complex. However, this chemical complexity has also made urine a particularly difficult substrate to fully understand. As a biological waste material, urine typically contains metabolic breakdown products from a wide range of foods, drinks, drugs, environmental contaminants, endogenous waste metabolites and bacterial by-products. Many of these compounds are poorly characterized and poorly understood. In an effort to improve our understanding of this biofluid we have undertaken a comprehensive, quantitative, metabolome-wide characterization of human urine. This involved both computer-aided literature mining and comprehensive, quantitative experimental assessment/validation. The experimental portion employed NMR spectroscopy, gas chromatography mass spectrometry (GC-MS), direct flow injection mass spectrometry (DFI/LC-MS/MS), inductively coupled plasma mass spectrometry (ICP-MS) and high performance liquid chromatography (HPLC) experiments performed on multiple human urine samples. This multi-platform metabolomic analysis allowed us to identify 445 and quantify 378 unique urine metabolites or metabolite species. The different analytical platforms were able to identify (quantify) a total of: 209 (209) by NMR, 179 (85) by GC-MS, 127 (127) by DFI/LC-MS/MS, 40 (40) by ICP-MS and 10 (10) by HPLC. Our use of multiple metabolomics platforms and technologies allowed us to identify several previously unknown urine metabolites and to substantially enhance the level of metabolome coverage. It also allowed us to critically assess the relative strengths and weaknesses of different platforms or technologies. The literature review led to the identification and annotation of another 2206 urinary compounds and was used to help guide the subsequent experimental studies. An online database containing the complete set of 2651 confirmed human urine metabolite species, their structures (3079 in total), concentrations, related literature references and links to their known disease associations are freely available at http://www.urinemetabolome.ca.

The effect of NaCI on the endogenous levels of diamine, putrescine and polyamines, spermidine and spermine, was studied in the shoot system of salt-tolerant and salt-sensitive lines of rice (Oryza sativa L.) cultivars during three growth stages. Salt stress increased the levels of diamine and polyamine in varying degrees among nine rice cultivars investigated. Salt tolerant AU 1, Co43, and CSC1 were effective in maintaining high concentrations of spermidine and spermine, while the content of putrescine was not significantly altered in all the growth stages when plants were exposed to salinity. The salt sensitivity in rice was associated with excessive accumulation of putrescine and with low levels of spermidine and spermine in the shoot system of salt-sensitive cultivars Co36, CSC2, GR3, IR20, TKM4, and TKM9 under saline condition. One of the possible mechanisms of saline resistance was observed to be due to the highly increased polyamines against the low increase in diamines. Alternatively, the salt sensitivity could be due to high increase of diamines and an incapacity to maintain high levels of polyamines.Polyamines are the newest class of compounds to be considered recently as possible plant growth regulators. Specific information on polyamines in salt-stressed plants is scarce. Polyamines have been shown to inhibit senescence in oat protoplast (3) and in whole leaves ofa number ofplant species (1) and to inhibit stress-induced senescence ofbarley leaf discs through stabilization of thylakoid membranes (19 In contrast to halophytes, nonhalophytes vary more in their ability to control ion uptake and translocation of saline environments. The differences in ion regulation, mainly of Na+ and Cl-, cause specific nutritional imbalance that, together with metabolic reactions, is associated with salt tolerance of the species (1 1). Little is known about the physiological basis of the varietal differences of rice in salt tolerance. There is only limited information on the interrelation between salinity and polyamine metabolism of rice (20).Nine rice cultivars were employed in this study. In our earlier studies, varietal differences in salt tolerance in terms of vegetative shoot growth and yield were tested (13), followed by the studies to identify physiological differences in ion regulation and different facets of metabolism, ultimately accounting for salt tolerance and for changes in organic acid (14), enzymes (15), Chl (16), amino acids (17), and inorganic ions (13,14). Having understood some of the cellular and physiological processes that underlie salt tolerance of rice cultivars, as a part of our studies we have examined the changes in the endogenous levels of polyamines that may serve as markers for different phases of the growth response under NaCl saline conditions. The physiological significance of putrescine, spermidine, and spermine levels is discussed with salt tolerance and salt sensitivity of rice. MATERIALS AND METHODSThe seeds of rice (Oryza sativa L.) cultivars AU 1, Co43, CSC 1 (salt toler...

The pseudobulb of Oncidium orchid is a storage organ for supplying water, minerals and carbohydrates to the developing inflorescence. Different patterns of mannan, starch and pectin metabolism were observed in the pseudobulb of three developmental stages by histochemical staining and high performance anion exchange chromatographic (HPAEC) analysis. Copious pectin was strongly stained by ruthenium red in young pseudobulbs demonstrating that mannan and pectin were preferentially accumulated in the young pseudobulb sink at inflorescence pre-initiation stage. Concomitant with the emergence of the inflorescence, mannan and pectin decreased gradually and converted to starch. The starch, synthesized at the inflorescence developing stage, was eventually degraded at the floral development stage. A systematic survey on the subtractive EST (expression sequence tag) library of pseudobulb in the inflorescence pre-initiation stage revealed the presence of five groups of gene homologues related to sucrose, mannan, starch, pectin and other carbohydrate metabolism. The transcriptional level of 13 relevant genes related to carbohydrate metabolism was characterized from pseudobulbs of three different developmental stages. The specific activities of the enzymes encoded by these genes were also assayed. The expression profiles of these genes show that the transcriptional levels largely correlated with the enzyme activities, which were associated with the respective carbohydrate pools. These results demonstrated a novel functional profile of polysaccharide mobilization pathway as well as their relevant gene expression in the pseudobulb of Oncidium orchid during the flowering process.

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We investigated the alteration in l-ascorbate (AsA, reduced form) content and the expression pattern of its related genes during the phase transition in Oncidium orchid. During the vegetative growth, a high H2O2 level was associated with a high content of the reduced form of AsA. During the bolting period, the AsA content and H2O2 level were greatly reduced in parallel with increased expression of OgLEAFY, the gene encoding a key transcription factor integrating different flowering-inducing pathways. This observation suggests that reduced AsA content, due to it having been consumed in scavenging H2O2, is a prerequisite for mediating the phase transition in Oncidium. A survey of the AsA biosynthetic pathway revealed that the gene expression and enzymatic activities of the products of relevant genes of the galacturonate (GalUA) pathway, such as polygalacturonase (OgPG), pectin methylesterase (OgPME) and galacturonate reductase (OgGalUAR), were markedly decreased during the bolting period, as compared with during the vegetative stage. However, the genes whose products were involved in the Smirnoff-Wheeler pathway retained a similar expression level in the two growth stages. The data suggested that OgPME of the GalUA pathway was the pivotal gene in regulating AsA biosynthesis during the bolting period. Further elucidation by overexpressing OgPME in Arabidopsis demonstrated a considerable increase in AsA content, as well as a resulting delayed-flowering phenotype. Our results strongly imply that the reduced level of AsA, regulating bolting for phase transition, resulting in part from its consumption by scavenging H2O2, was mainly caused by the down-regulation of the GalUA pathway, not the Smirnoff-Wheeler pathway.

Highlights A total of 226 isolates were screened against three strains (cfNAV, cfCHA and cf8436) of C. falcatum by dual culture technique. Selected Twenty-Six bacteria characterized of morphology, biochemical activity, PGP activity, antifungal potential and 16S rRNA gene sequence. These isolates belonged to proteobacteria (13), firmicutes (10) and bacterioidetes (03) respectively. Ochrobactrum intermedium (TRD14), Acinetobacter sp (PK9), Bacillus sp (RSC29 and KR91) and Escherichia sp (VRE34) selected for green house study. The most promising results in suppression of the disease as well as plant growth were observed in treatment withVRE34. The plant height and stem diameter were increased from 13.27 ± 0.67 inches to 24.03 ± 1.40 inches and from 6.07 ± 0.45 mm to 9.87 ± 0.93 mm. Isolates identified in this study could be used as an alternative to chemical fungicides to control red rot pathogen of sugarcane plants. However, detailed investigations on their inoculations in the field to confirm its growth promotion potency and biocontrol efficacy under natural environmental and soil conditions shall make these strains as important bioinoculants for integrated disease management of red rot disease in sugarcane.

Costus pictus, belonging to the family Costaceae, is one of the valuable medicinal plants with its antidiabetic property. Despite ever-increasing demand from the pharmaceutical industry, this species is being less exploited at molecular level. Hence, an effort has been made in the present study to characterize the 15 accessions of C. pictus collected from different geographical regions of India through random amplified polymorphic DNA (RAPD) and inter-simple sequence repeats (ISSR) markers. A total of 25 RAPD and 20 ISSR primers were used in the present study. The RAPD analysis generated 343 loci, of which 124 were polymorphic with an average of 4.96 loci per primer. While, ISSR primers produced 177 loci, of which 77 were polymorphic with an average of 3.85 loci per primer. The similarity coefficients ranged from 0.86-0.99, 0.84-0.95 and 0.86-0.96 for RAPD, ISSR and combined RAPD-ISSR, respectively. The UPGMA dendrogram generated using these data showed low level of divergence among the accessions from South and West regions. Further, accession-specific bands were also revealed by RAPD and ISSR markers which might be contributed to specific trait. This investigation was an understanding of genetic variation within the C. pictus accessions. The present finding indicates that both the marker tools RAPD and ISSR combined or individually can be used in determining the genetic relationship between the accessions. It may be concluded that data of hereditary differences appeared among the C. pictus accessions could be utilized for their conservation and reproducing programs.