High throughput profile-profile based fold recognition for the entire human proteome

BACKGROUND: In order to maintain the most comprehensive structural annotation databases we must carry out regular updates for each proteome using the latest profile-profile fold recognition methods. The ability to carry out these updates on demand is necessary to keep pace with the regular updates of sequence and structure databases. Providing the highest quality structural models requires the most intensive profile-profile fold recognition methods running with the very latest available sequence databases and fold libraries. However, running these methods on such a regular basis for every sequenced proteome requires large amounts of processing power.In this paper we describe and benchmark the JYDE (Job Yield Distribution Environment) system, which is a meta-scheduler designed to work above cluster schedulers, such as Sun Grid Engine (SGE) or Condor. We demonstrate the ability of JYDE to distribute the load of genomic-scale fold recognition across multiple independent Grid domains. We use the most recent profile-profile version of our mGenTHREADER software in order to annotate the latest version of the Human proteome against the latest sequence and structure databases in as short a time as possible. RESULTS: We show that our JYDE system is able to scale to large numbers of intensive fold recognition jobs running across several independent computer clusters. Using our JYDE system we have been able to annotate 99.9% of the protein sequences within the Human proteome in less than 24 hours, by harnessing over 500 CPUs from 3 independent Grid domains. CONCLUSION: This study clearly demonstrates the feasibility of carrying out on demand high quality structural annotations for the proteomes of major eukaryotic organisms. Specifically, we have shown that it is now possible to provide complete regular updates of profile-profile based fold recognition models for entire eukaryotic proteomes, through the use of Grid middleware such as JYDE.

Stability of plasmid profile of highly virulent races of Xanthomonas campestris pv. malvacearum during storage and subculturing

Four races of Xanthomonas campestris pv. mal-vacearum (Xcm) viz. races 23, 27 and 32 (isolated from Gossypium hirsutum) and race 23b (from Gossypium barbadense) were studied. The plasmid profile of the natural isolates showed four plasmids in races 23 and 23b (ca. 60, 40, 23, 8.2 kb), five in race 27 (ca. 60, 40, 23, 8.2 and 3.7 kb) and six in race 32 (ca. 60, 40, 23, 8.2, 3.7 and 1.6 kb). Continuously sub-cultured laboratory isolates of the Xcm races resulted in the loss of all but two plasmids, ca. 60 and 40 kb in size. When the laboratory isolates were passed through cotton (Gossypium hirsutum), they regained certain plasmids so that four plasmids were found in race 23 and 23b (ca. 60, 40, 23 and 8.2 kb), five in race 27 (ca. 60, 40, 23, 8.2 and 3.7 kb) and six in race 32 (ca. 60, 40, 23, 8.2, 3.7 and 1.6 kb), which was more or less similar to the original isolates. The isolates recovered from cotton maintained their plasmid profile (except for minor changes in the miniplasmids) after storage for six months at -70degreesC in 50% glycerol. It is suggested that plasmid profiles among highly virulent races of Xcm are unstable during repeated sub-culturing at room temperature, resulting in rapid loss of some plasmids. However, when the cultures were sub-cultured and stored at -70degreesC the plasmid profile was fairly stable except for the miniplasmids (ca. 3.7 and 1.6 kb).

Modulation of the fecal microflora profile and immune function by a novel trans-galactooligosaccharide mixture (B-GOS) in healthy elderly volunteers

Background: Aging is associated with reduced numbers of beneficial colonic bifidobacteria and impaired immunity. Galactooligosaccharides (GOSs) stimulate the growth of bifidobacteria in younger adults, but little is known about their effects in the elderly and their immunomodulatory capacity. Objective: We assessed the effect of a prebiotic GOS mixture (B-GOS) on immune function and fecal microflora composition in healthy elderly subjects. Design: In a double-blind, placebo-controlled, crossover study, 44 elderly subjects were randomly assigned to receive either a placebo or the B-GOS treatment (5.5 g/d). Subjects consumed the treatments for 10 wk, and then went through a 4-wk washout period, before switching to the other treatment for the final 10 wk. Blood and fecal samples were collected at the beginning, middle (5 wk), and end of the test period. Predominant bacterial groups were quantified, and phagocytosis, natural killer (NK) cell activity, cytokine production, plasma cholesterol, and HDL cholesterol were measured. Results: B-GOS significantly increased the numbers of beneficial bacteria, especially bifidobacteria, at the expense of less beneficial groups compared with the baseline and placebo. Significant increases in phagocytosis, NK cell activity, and the production of antiinflammatory cytokine interleukin-10 (IL-10) and significant reduction in the production of proinflammatory cytokines (IL-6, IL-1 beta , and tumor necrosis factor-alpha) were also observed. B-GOS exerted no effects on total cholesterol or HDL-cholesterol production, however. Conclusions: B-GOS administration to healthy elderly persons resulted in positive effects on both the microflora composition and the immune response. Therefore, B-GOS may be a useful dietary candidate for the enhancement of gastrointestinal health and immune function in elderly persons. Am J Clin Nutr 2008; 88: 1438-46.

Effects of dairy products naturally enriched with cis-9,trans-11 conjugated linoleic acid on the blood lipid profile in healthy middle-aged men

Background: Interest in the development of dairy products naturally enriched in conjugated linoleic acid (CLA) exists. However, feeding regimens that enhance the CLA content of milk also increase concentrations of trans-18:1 fatty acids. The implications for human health are not yet known. Objective: This study investigated the effects of consuming dairy products naturally enriched in cis-9,trans-11 CLA (and trans-11 18:1) on the blood lipid profile, the atherogenicity of LDL, and markers of inflammation and insulin resistance in healthy middle-aged men. Design: Healthy middle-aged men (n = 32) consumed ultra-heat-treated milk, butter, and cheese that provided 0.151 g/d (control) or 1.421 g/d (modified) cis-9,trans-11 CLA for 6 wk. This was followed by a 7-wk washout and a crossover to the other treatment. Results: Consumption of dairy products enriched with cis-9,trans-11 CLA and trans-11 18:1 did not significantly affect body weight, inflammatory markers, insulin, glucose, triacylglycerols, or total, LDL, and HDL cholesterol but resulted in a small increase in the ratio of LDL to HDL cholesterol. The modified dairy products changed LDL fatty acid composition but had no significant effect on LDL particle size or the susceptibility of LDL to oxidation. Overall, increased consumption of full-fat dairy products and naturally derived trans fatty acids did not cause significant changes in cardiovascular disease risk variables, as may be expected on the basis of current health recommendations. Conclusion: Dairy products naturally enriched with cis-9,trans-11 CLA and trans-11 18: 1 do not appear to have a significant effect on the blood lipid profile.

Volatile flavour profile of goat meat extracted by three widely used techniques

Three procedures for the isolation of volatiles from grilled goat meat were compared: dynamic headspace entrainment on Tenax TA, simultaneous steam distillation-extraction, and solid-phase microextraction. Headspace entrainment on Tenax TA extracted the highest number of Maillard-derived volatile compounds. Two hundred and three volatile components were identified: 159 are reported for the first time in goat meat. Most of the volatiles detected (155) were lipid oxidation products, such as hydrocarbons, aldehydes, alcohols, ketones, carboxylic acids and esters. Forty-eight Maillard-derived compounds were identified. comprising pyrazines, pyrroles, thiophenes, furanthiol derivatives, alkyl and alicyclic sulphides, pyridines, and thiazoles. Some reported character impact compounds of cooked meat, e.g., 12-methyltridecanal, (EE)-2,4-decadienal, methional, and dimethyl trisulphide were identified in the volatile profile of goat meat, together with a series of C-2 to C-5 alkylformylcyclopentenes, which have been reported in cooked chicken, pork, beef and lamb, as being important for the characteristic flavour impression of different animal species. (C) 2009 Published by Elsevier Ltd.

Effect of a simulated kilning regime on the profile and antioxidant activity of the free phenolic acids extracted from green malt

Free phenolic acids were extracted from a laboratory-produced sample of green malt. Aliquots of the phenolic acid extract were heated from 25 to 110°C over 27 h, representative of a commercial kilning regime. Samples were taken at regular intervals throughout heating and were assessed for changes in antioxidant activity by both the 2,2(prime)-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) radical-cation scavenging (ABTS(^•+)) and the ferric-reducing antioxidant potential (FRAP) assays. Changes in the profile of the phenolic acids of the extracts were determined by HPLC. Overall, there was a decrease in both antioxidant activity level and the level of phenolic acids, but as the temperature increased from 80 to 100°C, there was an increase in both the antioxidant activity level and the level of detected phenolic acids.

Effect of heat treatment on the antioxidant activity, color, and free phenolic acid profile of malt

Green malt was kilned at 95 degrees C following two regimens: a standard regimen (SKR) and a rapid regimen (RKR). Both resulting malts were treated further in a tray dryer heated to 120 degrees C, as was green malt previously dried to 65 degrees C (TDR). Each regimen was monitored by determining the color, antioxidant activity (by both ABTS(center dot+) and FRAP methods), and polyphenolic profile. SKR and RKR malts exhibited decreased L* and increased b* values above approximately 80 degrees C. TDR malts changed significantly less, and color did not develop until 110 degrees C, implying that different chemical reactions lead to color in those malts. Antioxidant activity increased progressively with each regimen, although with TDR malts this became significant only at 110-120 degrees C. The RKR malt ABTS(center dot+) values were higher than those of the SKR malt. The main phenolics, that is, ferulic, p-coumaric, and vanillic acids, were monitored throughout heating. Ferulic acid levels increased upon heating to 80 degrees C for SKR and to 70 degrees C for RKR, with subsequent decreases. However, the levels for TDR malts did not increase significantly. The increase in free phenolics early in kilning could be due to enzymatic release of bound phenolics and/or easier extractability due to changes in the matrix. The differences between the kilning regimens used suggest that further modification of the regimens could lead to greater release of bound phenolics with consequent beneficial effects on flavor stability in beer and, more generally, on human health.

Evaluation by volatile profile of the synergistic antioxidant effect between bovine serum albumin and virgin olive oil phenolic compounds in an oil-in-water emulsion

THE OXIDATIVE STABILITY OF OIL-IN-WATER EMULSIONS, CONTAINING BOVINE SERUM ALBUMIN (BSA) AND VIRGIN OLIVE OIL PHENOLIC COMPOUNDS, WAS STUDIED BY THE DETERMINATION OF THE FORMATION OF VOLATILE OXIDATION PRODUCTS. FOUR OIL-IN-WATER EMULSIONS WITH AND WITHOUT PHENOLS ISOLATED FROM VIRGIN OLIVE OIL AND BSA WERE PREPARED. THESE MODEL SYSTEMS WERE STORED AT 60 degrees C TO ACCELERATE LIPID OXIDATION. VOLATILE OXIDATION PRODUCTS WERE MONITORED EVERY THREE DAYS BY HEADSPACE SOLID-PHASE MICROEXTRACTION COUPLED WITH GAS CHROMATOGRAPHY. ALTHOUGH INDIVIDUALLY OLIVE OIL PHENOLIC COMPOUNDS AND BSA SHOWED A SIGNIFICANT ANTIOXIDANT ACTIVITY, THE COMBINATION OF THESE COMPONENTS SHOWED A VERY GOOD SYNERGY, QUANTIFIED AS 127%. IN FACT, THE EMULSION CONTAINING BOTH PHENOLIC COMPOUNDS AND BSA SHOWED A VERY LOW LEVEL OF OXIDATIVE DETERIORATION AFTER 45 DAYS STORAGE.

Identification of hepatic molecular mechanisms of action of alpha-tocopherol using global gene expression profile analysis in rats

The recent discovery that vitamin E (VE) regulates gene activity at the transcriptional level indicates that VE may exert part of its biological effects by mechanisms which may be independent of its well-recognised antioxidant function. The objective of this study was the identification of hepatic vitamin E-sensitive genes and examination of the effects of VE on their corresponding biological endpoints. Two groups of male rats were randomly assigned to either a VE-sufficient diet or to a control diet deficient in VE for 290 days. High-density oligonucleotide microarrays comprising over 7000 genes were used to assess the transcriptional response of the liver. Differential gene expression was monitored over a period of 9 months, at four different time-points, and rats were individually profiled. This experimental strategy identified several VE-sensitive genes, which were chronically altered by dietary VE. VE supplementation down-regulated scavenger receptor CD36, coagulation factor IX and 5-alpha-steroid reductase type 1 mRNA levels while hepatic gamma glutamyl-cysteinyl synthetase was significantly up-regulated. Measurement of the corresponding biological endpoints such as activated partial thromboplastin time, plasma dihydrotestosterone and hepatic glutathione substantiated the gene chip data which indicated that dietary VE plays an important role in a range of metabolic processes within the liver. (C) 2004 Elsevier B.V. All rights reserved.

Determination of some water-soluble aroma precursors in goat meat and their enrolment on flavour profile of goat meat

Selected water-soluble precursors, including sugars, free amino acids and nucleotides, were quantified in raw and cooked goat meat, as a part of a study which the main aim was to better understand the aroma formation in goat meat. When compared with the same precursors in beef, lamb and chicken, levels in goat meat were generally similar, except for fructose and glycine, which were present at higher concentrations in goat meat. Fructose, glucose, IMP, and cysteine suffered the greatest losses during the cooking process and seem to be most involved in aroma formation in goat meat. The effects of these precursor changes on the volatile compound composition and formation process of them on cooked goat meat are discussed.