PubMed Health⌕ Search

Biomedical subjects

Robert D Hall

Publications and source records attributed to Robert D Hall.

14 recordsLinked to original sources
PubMed2007

Metabolomic profiling of natural volatiles: headspace trapping: GC-MS.

Plants are a fabulously rich source of naturally volatile metabolites, which are derived from a range of contrasting biochemical pathways (e.g., mono-, di-, and sesquiterpenoids, benzoates, alcohols, esters). Such volatiles may immediately be released from the plant or they may be stored, e.g., in glycosylated form for release later "on demand." Certain roles for these molecules have already been determined in that they can function as attractants (e.g., to pollinators, seed dispersers, and others) or as protectants (repellants, pathogen inhibitors, and so on). The flavor and fragrance of plant materials to humans and other animals are also, to a great extent, determined by natural volatiles. Other more sophisticated roles have also been elucidated where plant volatiles have been shown to be involved either as signal molecules to attract the predators of damaging herbivorous insects or potentially even as signal molecules warning other plants of imminent danger. As such, detailed knowledge of these components can be valuable in relation to breeding crop varieties for enhanced product quality or for achieving improved resistance to pathogens and insects. Furthermore, knowledge of the metabolites can result in a corresponding knowledge of the genes responsible for their synthesis and this can lead to dedicated strategies for their in vitro production through, e.g., reverse genetics in heterologous microbial expression systems in fermentors for the production of high-value fine chemicals. Various analytical techniques based on gas chromatography-mass spectrometry have been devised for the analysis of this complex group of metabolites. Two of these key methods are detailed in this chapter.

Arabidopsis↗
PubMed2006

The genetics of plant metabolism.

Variation for metabolite composition and content is often observed in plants. However, it is poorly understood to what extent this variation has a genetic basis. Here, we describe the genetic analysis of natural variation in the metabolite composition in Arabidopsis thaliana. Instead of focusing on specific metabolites, we have applied empirical untargeted metabolomics using liquid chromatography-time of flight mass spectrometry (LC-QTOF MS). This uncovered many qualitative and quantitative differences in metabolite accumulation between A. thaliana accessions. Only 13.4% of the mass peaks were detected in all 14 accessions analyzed. Quantitative trait locus (QTL) analysis of more than 2,000 mass peaks, detected in a recombinant inbred line (RIL) population derived from the two most divergent accessions, enabled the identification of QTLs for about 75% of the mass signals. More than one-third of the signals were not detected in either parent, indicating the large potential for modification of metabolic composition through classical breeding.

Arabidopsis↗
PubMed2006

Alignment and statistical difference analysis of complex peptide data sets generated by multidimensional LC-MS.

A method for high-resolution proteomics analyses of complex protein mixtures is presented using multidimensional HPLC coupled to MS (MDLC-MS). The method was applied to identify proteins that are differentially expressed during fruit ripening of tomato. Protein extracts from red and green tomato fruits were digested by trypsin. The resulting highly complex peptide mixtures were separated by strong cation exchange chromatography (SCX), and subsequently analyzed by RP nano-LC coupled to quadrupole-TOF MS. For detailed quantitative comparison, triplicate RP-LC-MS runs were performed for each SCX fraction. The resulting data sets were analyzed using MetAlign software for noise and data reduction, multiple alignment and statistical variance analysis. For each RP-LC-MS chromatogram, up to 7000 mass components were detected. Peak intensity data were compared by multivariate and statistical analysis. This revealed a clear separation between the green and red tomato samples, and a clear separation of the different SCX fractions. MS/MS spectra were collected using the data-dependent acquisition mode from a selected set of differentially detected peptide masses, enabling the identification of proteins that were differentially expressed during ripening of tomato fruits. Our approach is a highly sensitive method to analyze proteins in complex mixtures without the need of isotope labeling.

Cation Exchange Resins↗
PubMed2006

Plant metabolomics: from holistic hope, to hype, to hot topic.

In a short time, plant metabolomics has gone from being just an ambitious concept to being a rapidly growing, valuable technology applied in the stride to gain a more global picture of the molecular organization of multicellular organisms. The combination of improved analytical capabilities with newly designed, dedicated statistical, bioinformatics and data mining strategies, is beginning to broaden the horizons of our understanding of how plants are organized and how metabolism is both controlled but highly flexible. Metabolomics is predicted to play a significant, if not indispensable role in bridging the phenotype-genotype gap and thus in assisting us in our desire for full genome sequence annotation as part of the quest to link gene to function. Plants are a fabulously rich source of diverse functional biochemicals and metabolomics is also already proving valuable in an applied context. By creating unique opportunities for us to interrogate plant systems and characterize their biochemical composition, metabolomics will greatly assist in identifying and defining much of the still unexploited biodiversity available today.

Biotechnology↗
PubMed2005

Antioxidants in raspberry: on-line analysis links antioxidant activity to a diversity of individual metabolites.

The presence of antioxidant compounds can be considered as a quality parameter for edible fruit. In this paper, we studied the antioxidant compounds in raspberry (Rubus idaeus) fruits by high-performance liquid chromatography (HPLC) coupled to an on-line postcolumn antioxidant detection system. Both developmental and genetic factors were assessed by comparing fruits from a single cultivar of different ripening stages and by comparing ripe fruits of 14 raspberry cultivars, respectively. The HPLC-separated antioxidant compounds were identified using HPLC-photodiode array coupled to mass spectrometry (quadrupole time-of-flight tandem mass spectrometry), using a reference lock mass for determining accurate masses. The dominant antioxidants could be classified as anthocyanins, ellagitannins, and proanthocyanidin-like tannins. During fruit ripening, some anthocyanins were newly produced, while others, like cyanidin-3-glucoside, were already present early in fruit development. The level of tannins, both ellagitannins and proanthocyanidin-like tannins, was reduced strongly during fruit ripening. Among the 14 cultivars, major differences (>20-fold) were observed in the levels of pelagonidin type anthocyanins and some proanthocyanidin type tannins. The content of ellagitannins varied approximately 3-fold. The findings presented here suggest that the content of individual health-promoting compounds varies significantly in raspberry, due to both developmental and genetic factors. This information will assist in the future development and identification of raspberry lines with enhanced health-promoting properties.

Anthocyanins↗
PubMed2005

Identification and dietary relevance of antioxidants from raspberry.

In this paper we review the current literature on antioxidants from fruit of red raspberry (Rubus idaeus) and place these in context concerning what is known from other food species. The review concentrates on the methods of antioxidant testing, the diversity of antioxidants in raspberry, effects of ripeness, cultivar, storage and processing techniques, and the bioavailability of raspberry antioxidants in humans after eating the fruit. It is clear that raspberry, like several other fruits and vegetables such as tomato, strawberry, kiwi and broccoli, represents a valuable contrasting source of potentially healthy compounds and can represent an important component of a balanced diet.

Animals↗
PubMed2005

A novel approach for nontargeted data analysis for metabolomics. Large-scale profiling of tomato fruit volatiles.

To take full advantage of the power of functional genomics technologies and in particular those for metabolomics, both the analytical approach and the strategy chosen for data analysis need to be as unbiased and comprehensive as possible. Existing approaches to analyze metabolomic data still do not allow a fast and unbiased comparative analysis of the metabolic composition of the hundreds of genotypes that are often the target of modern investigations. We have now developed a novel strategy to analyze such metabolomic data. This approach consists of (1) full mass spectral alignment of gas chromatography (GC)-mass spectrometry (MS) metabolic profiles using the MetAlign software package, (2) followed by multivariate comparative analysis of metabolic phenotypes at the level of individual molecular fragments, and (3) multivariate mass spectral reconstruction, a method allowing metabolite discrimination, recognition, and identification. This approach has allowed a fast and unbiased comparative multivariate analysis of the volatile metabolite composition of ripe fruits of 94 tomato (Lycopersicon esculentum Mill.) genotypes, based on intensity patterns of >20,000 individual molecular fragments throughout 198 GC-MS datasets. Variation in metabolite composition, both between- and within-fruit types, was found and the discriminative metabolites were revealed. In the entire genotype set, a total of 322 different compounds could be distinguished using multivariate mass spectral reconstruction. A hierarchical cluster analysis of these metabolites resulted in clustering of structurally related metabolites derived from the same biochemical precursors. The approach chosen will further enhance the comprehensiveness of GC-MS-based metabolomics approaches and will therefore prove a useful addition to nontargeted functional genomics research.

Automation↗
PubMed2005

Tuber on a chip: differential gene expression during potato tuber development.

Potato tuber development has proven to be a valuable model system for studying underground sink organ formation. Research on this topic has led to the identification of many genes involved in this complex process and has aided in the unravelling of the mechanisms underlying starch synthesis. However, less attention has been paid to the biochemical pathways of other important metabolites or to the changing metabolic fluxes occurring during potato tuber development. In this paper, we describe the construction of a potato complementary DNA (cDNA) microarray specifically designed for genes involved in processes related to tuber development and tuber quality traits. We present expression profiles of 1315 cDNAs during tuber development where the predominant profiles were strong up- and down-regulation. Gene expression profiles showing transient increases or decreases were less abundantly represented and followed more moderate changes, mainly during tuber initiation. In addition to the confirmation of gene expression patterns during tuber development, many novel differentially expressed genes were identified and are considered as candidate genes for direct involvement in potato tuber development. A detailed analysis of starch metabolism genes provided a unique overview of expression changes during tuber development. Characteristic expression profiles were often clearly different between gene family members. A link between differential gene expression during tuber development and potato tissue specificity is described. This dataset provides a firm basis for the identification of key regulatory genes in a number of metabolic pathways that may provide researchers with new tools to achieve breeding goals for use in industrial applications.

Journal Article↗
PubMed2005

The light-hyperresponsive high pigment-2dg mutation of tomato: alterations in the fruit metabolome.

Overall metabolic modifications between fruit of light-hyperresponsive high-pigment (hp) tomato (Lycopersicon esculentum) mutant plants and isogenic nonmutant (wt) control plants were compared. Targeted metabolite analyses, as well as large-scale nontargeted mass spectrometry (MS)-based metabolite profiling, were used to phenotype the differences in fruit metabolite composition. Targeted high-performance liquid chromatography with photodiode array detection (HPLC-PDA) metabolite analyses showed higher levels of isoprenoids and phenolic compounds in hp-2dg fruit. Nontargeted GC-MS profiling of red fruits produced 25 volatile compounds that showed a 1.5-fold difference between the genotypes. Analyses of red fruits using HPLC coupled to high-resolution quadrupole time-of-flight mass spectrometry (LC-QTOF-MS) in both ESI-positive and ESI-negative mode generated, respectively, 6168 and 5401 mass signals, of which 142 and 303 showed a twofold difference between the genotypes. hp-2dg fruits are characterized by overproduction of many metabolites, several of which are known for their antioxidant or photoprotective activities. These metabolites may now be more closely implicated as resources recruited by plants to respond to and manage light stress. The similarity in metabolic alterations in fruits of hp-1 and hp-2 mutant plants helps us to understand how hp mutations affect cellular processes.

Ascorbic Acid↗
PubMed2005

Relative abundance of tree hole-breeding mosquitoes in Boone County, Missouri, USA, with emphasis on the vector potential of Aedes triseriatus for canine heartworm, Dirofilaria immitis (Spirurida: Filariidae).

Aedes (Protomacleaya) triseriatus currently shares its habitat in the USA with the introduced species Aedes (Finlaya) japonicus and Aedes (Stegomyia) albopictus. In the late 1980s, before the introduction of these 2 species, Ae. triseriatus was the dominant tree hole- and artificial container-breeding mosquito in central Missouri. Aedes triseriatus represented 89% of the mosquito immatures collected from water-filled tree holes and artificial containers at 3 forested field sites in central Missouri, from May to October, 1986 to 1988. Laboratory-reared female Ae. triseriatus were able to support larval development of Dirofilaria immitis (canine heartworm) to the infective 3rd larval stage. A blood meal from a microfilaremic Collie-mix dog was sufficient to infect adult female mosquitoes, indicating that Ae. triseriatus is a possible vector of canine heartworm in central Missouri. Confirmation of the vector status of this species depends on the yet-to-be observed transmission of D. immitis by Ae. triseriatus in the field, possibly by experimental infection of dogs by wild-caught mosquitoes. Defining the role of this species in epizootic outbreaks could contribute toward accurate risk assessment as the abundance of Ae. triseriatus increases and decreases in response to the success of Ae. albopictus, Ae. japonicus, or other introduced container-breeding mosquitoes.

Aedes↗
PubMed2005

Does carcass enrichment alter community structure of predaceous and parasitic arthropods? A second test of the arthropod saturation hypothesis at the Anthropology Research Facility in Knoxville, Tennessee.

In a second test of an arthropod saturation hypothesis, we analyzed if the on-campus Anthropology Research Facility (ARF) at the University of Tennessee, Knoxville, with its 20+ yr history of carcass enrichment, is comparable to non-enriched sites in community structure of predatory and parasitic arthropods that prey upon the sarcosaprophagous fauna. Over a 12-day period in June 1998, using pitfall traps and sweep nets, 10,065 predaceous, parasitic, and hematophagous (blood-feeding) arthropods were collected from freshly euthanized pigs (Sus scrofa L.) placed at ARF and at three surrounding sites various distances away (S2-S4). The community structure of these organisms was comparable in most paired-site tests with respect to species composition, colonization rates, and evenness of pitfall-trap abundances on a per carcass basis. Site differences were found in rarefaction tests of both sweep-net and pitfall-trap taxa and in tests of taxonomic evenness and ranked abundances of sweep-net samples. Despite these differences, no evidence was found that the predatory/parasitic fauna at ARF was impoverished with fewer but larger populations as a result of carcass enrichment. Comparison of the sarcosaprophagous and predatory/parasitic faunas revealed a tighter (and more predictable) linkage between carrion feeders (sarcosaprovores) and their carrion than between carrion feeders and their natural enemies (predators and parasitoids), leading us to conclude that ARF is more representative of surrounding sites with respect to the sarcosaprovore component than to the predatory/parasitic component within the larger carrion-arthropod community.

Animals↗
PubMed2003

Carcass enrichment does not alter decay rates or arthropod community structure: a test of the arthropod saturation hypothesis at the anthropology research facility in Knoxville, Tennessee.

In a test of an arthropod saturation hypothesis, we asked if the 30-yr history of carcass enrichment at the Anthropology Research Facility, Knoxville TN, has altered carcass decay rates or community structure of sarcosaprophagous arthropods, compared with three local nonenriched sites. Over a 12-d period in 1998, using pitfall traps and sweep nets, we sampled a total of 81,000 invertebrates from freshly euthanized pigs (Sus scrofa L.) placed in these sites. From this number, we sorted 69,286 forensically important (sarcosaprophagous) arthropods. The community structure of these organisms, as measured by species and individuals accumulation curves, rarefaction, and nonparametric correlation, was comparable in all four sites in taxonomic similarity, colonization rates, aerial species richness, and ranked abundances of forensically important taxa on a per carcass basis. Measures of carcass decay rate, remaining carcass weight (%) and periodic weight loss, also were similar. In most cases, carcass surface temperatures and maggot mass temperatures were also statistically indistinguishable. Probability-based results and posthoc power analyses of these variables led us to conclude that the sarcosaprophagous arthropod community of the Anthropology Research Facility is representative of surrounding sites.

Animal Feed↗
PubMed2002

Factors influencing cDNA microarray hybridization on silylated glass slides.

cDNA microarray technology is becoming the technique of choice for studying gene expression and gene expression patterns. Although experimental protocols are available, only limited methodological information on microarray manufacture, hybridization, and signal interpretation has been published. The aim of this paper is to provide more insight into the practical aspects of microarray construction and hybridization. The influence of the size, composition, and concentration of the spotted DNA fragments on the final hybridization signal and the effect of hybridization volume, sample concentration, and sample depletion have been tested and are discussed.

Amines↗