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Find video protocols related to scientific articles indexed in Pubmed.
Borneo and Indochina are Major Evolutionary Hotspots for Southeast Asian Biodiversity.
Syst. Biol.
PUBLISHED: 07-28-2014
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Tropical Southeast (SE) Asia harbors extraordinary species richness and in its entirety comprises four of the Earth's 34 biodiversity hotspots. Here, we examine the assembly of the SE Asian biota through time and space. We conduct meta-analyses of geological, climatic, and biological (including 61 phylogenetic) data sets to test which areas have been the sources of long-term biological diversity in SE Asia, particularly in the pre-Miocene, Miocene, and Plio-Pleistocene, and whether the respective biota have been dominated by in situ diversification, immigration and/or emigration, or equilibrium dynamics. We identify Borneo and Indochina, in particular, as major "evolutionary hotspots" for a diverse range of fauna and flora. Although most of the region's biodiversity is a result of both the accumulation of immigrants and in situ diversification, within-area diversification and subsequent emigration have been the predominant signals characterizing Indochina and Borneo's biota since at least the early Miocene. In contrast, colonization events are comparatively rare from younger volcanically active emergent islands such as Java, which show increased levels of immigration events. Few dispersal events were observed across the major biogeographic barrier of Wallace's Line. Accelerated efforts to conserve Borneo's flora and fauna in particular, currently housing the highest levels of SE Asian plant and mammal species richness, are critically required.
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An O-methyltransferase modifies accumulation of methylated anthocyanins in seedlings of tomato.
Plant J.
PUBLISHED: 05-19-2014
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Anthocyanins contribute to the appearance of fruit by conferring to them a red, blue or purple colour. In a food context, they have also been suggested to promote consumer health. In purple tomato tissues, such as hypocotyls, stems and purple fruits, various anthocyanins accumulate. These molecules have characteristic patterns of modification, including hydroxylations, methylations, glycosylations and acylations. The genetic basis for many of these modifications has not been fully elucidated, and nor has their role in the functioning of anthocyanins. In this paper, AnthOMT, an O-methyltransferase (OMT) mediating the methylation of anthocyanins, has been identified and functionally characterized using a combined metabolomics and transcriptomics approach. Gene candidates were selected from the draft tomato genome, and their expression was subsequently monitored in a tomato seedling system comprising three tissues and involving several time points. In addition, we also followed gene expression in wild-type red and purple transgenic tomato fruits expressing Rosea1 and Delila transcription factors. Of the 57 candidates identified, only a single OMT gene showed patterns strongly correlating with both accumulation of anthocyanins and expression of anthocyanin biosynthesis genes. This candidate (AnthOMT) was compared to a closely related caffeoyl CoA OMT by recombinant expression in Escherichia coli, and then tested for substrate specificity. AnthOMT showed a strong affinity for glycosylated anthocyanins, while other flavonoid glycosides and aglycones were much less preferred. Gene silencing experiments with AnthOMT resulted in reduced levels of the predominant methylated anthocyanins. This confirms the role of this enzyme in the diversification of tomato anthocyanins.
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The towering orogeny of New Guinea as a trigger for arthropod megadiversity.
Nat Commun
PUBLISHED: 04-29-2014
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Early studies on Melanesian mountain systems provided insights for fundamental evolutionary and ecological concepts. These island-like systems are thought to provide opportunities in the form of newly formed, competition-free niches. Here we show that a hyperdiverse radiation of freshwater arthropods originated in the emerging central New Guinea orogen, out of Australia, about 10 million years ago. Further diversification was mainly allopatric, with repeated more recent colonization of lowlands as they emerged in the form of colliding oceanic island arcs, continental fragments and the Papuan Peninsula, as well as recolonization of the central orogen. We unveil a constant and ongoing process of lineage accumulation while the carrying capacity of the island is about to be reached, suggesting that lineage diversification speed now exceeds that of landmass/new ecological opportunity formation. Therefore, the central orogeny of New Guinea acts as a motor of diversification for the entire region.
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Validation of an oligonucleotide ligation assay for quantification of human immunodeficiency virus type 1 drug-resistant mutants by use of massively parallel sequencing.
J. Clin. Microbiol.
PUBLISHED: 04-16-2014
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Global HIV treatment programs need sensitive and affordable tests to monitor HIV drug resistance. We compared mutant detection by the oligonucleotide ligation assay (OLA), an economical and simple test, to massively parallel sequencing. Nonnucleoside reverse transcriptase inhibitor (K103N, V106M, Y181C, and G190A) and lamivudine (M184V) resistance mutations were quantified in blood-derived plasma RNA and cell DNA specimens by OLA and 454 pyrosequencing. A median of 1,000 HIV DNA or RNA templates (range, 163 to 1,874 templates) from blood specimens collected in Mozambique (n = 60) and Kenya (n = 51) were analyzed at 4 codons in each sample (n = 441 codons assessed). Mutations were detected at 75 (17%) codons by OLA sensitive to 2.0%, at 71 codons (16%; P = 0.78) by pyrosequencing using a cutoff value of ? 2.0%, and at 125 codons (28%; P < 0.0001) by pyrosequencing sensitive to 0.1%. Discrepancies between the assays included 15 codons with mutant concentrations of ?2%, one at 8.8% by pyrosequencing and not detected by OLA, and one at 69% by OLA and not detected by pyrosequencing. The latter two cases were associated with genetic polymorphisms in the regions critical for ligation of the OLA probes and pyrosequencing primers, respectively. Overall, mutant concentrations quantified by the two methods correlated well across the codons tested (R(2) > 0.8). Repeat pyrosequencing of 13 specimens showed reproducible detection of 5/24 mutations at <2% and 6/6 at ? 2%. In conclusion, the OLA and pyrosequencing performed similarly in the quantification of nonnucleoside reverse transcriptase inhibitor and lamivudine mutations present at >2% of the viral population in clinical specimens. While pyrosequencing was more sensitive, detection of mutants below 2% was not reproducible.
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Plant metabolomics is not ripe for environmental risk assessment.
Trends Biotechnol.
PUBLISHED: 03-16-2014
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Metabolomics separates and detects small molecules and helps determine the composition of plant materials. This makes it appear to be a possible contributor to environmental risk assessment (ERA) of transgenic plants. Here we argue that, despite important advances in the technology, limited annotation and our limited knowledge of the role of metabolites in plant-environment interactions means that metabolomics is not yet ripe for ERA.
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Polycistronic expression of a ?-carotene biosynthetic pathway in Saccharomyces cerevisiae coupled to ?-ionone production.
J. Biotechnol.
PUBLISHED: 02-04-2014
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The flavour and fragrance compound ?-ionone, which naturally occurs in raspberry and many other fruits and flowers, is currently produced by synthetic chemistry. This study describes a synthetic biology approach for ?-ionone production from glucose by Saccharomyces cerevisiae that is partially based on polycistronic expression. Experiments with model proteins showed that the T2A sequence of the Thosea asigna virus mediated efficient production of individual proteins from a single transcript in S. cerevisiae. Subsequently, three ?-carotene biosynthesis genes from the carotenoid-producing ascomycete Xanthophyllomyces dendrorhous (crtI, crtE and crtYB) were expressed in S. cerevisiae from a single polycistronic construct. In this construct, the individual crt proteins were separated by T2A sequences. Production of the individual proteins from the polycistronic construct was confirmed by Western blot analysis and by measuring the production of ?-carotene. To enable ?-ionone production, a carotenoid-cleavage dioxygenase from raspberry (RiCCD1) was co-expressed in the ?-carotene producing strain. In glucose-grown cultures with a second phase of dodecane, ?-ionone and geranylacetone accumulated in the organic phase. Thus, by introducing a polycistronic construct encoding a fungal carotenoid pathway and an expression cassette encoding a plant dioxygenase, a novel microbial production system has been established for a fruit flavour compound.
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An ecological function and services approach to total maximum daily load (TMDL) prioritization.
Environ Monit Assess
PUBLISHED: 01-17-2014
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Prioritizing total maximum daily load (TMDL) development starts by considering the scope and severity of water pollution and risks to public health and aquatic life. Methodology using quantitative assessments of in-stream water quality is appropriate and effective for point source (PS) dominated discharge, but less so in watersheds with mostly nonpoint source (NPS) related impairments. For NPSs, prioritization in TMDL development and implementation of associated best management practices should focus on restoration of ecosystem physical functions, including how restoration effectiveness depends on design, maintenance and placement within the watershed. To refine the approach to TMDL development, regulators and stakeholders must first ask if the watershed, or ecosystem, is at risk of losing riparian or other ecologically based physical attributes and processes. If so, the next step is an assessment of the spatial arrangement of functionality with a focus on the at-risk areas that could be lost, or could, with some help, regain functions. Evaluating stream and wetland riparian function has advantages over the traditional means of water quality and biological assessments for NPS TMDL development. Understanding how an ecosystem functions enables stakeholders and regulators to determine the severity of problem(s), identify source(s) of impairment, and predict and avoid a decline in water quality. The Upper Reese River, Nevada, provides an example of water quality impairment caused by NPS pollution. In this river basin, stream and wetland riparian proper functioning condition (PFC) protocol, water quality data, and remote sensing imagery were used to identify sediment sources, transport, distribution, and its impact on water quality and aquatic resources. This study found that assessments of ecological function could be used to generate leading (early) indicators of water quality degradation for targeting pollution control measures, while traditional in-stream water quality monitoring lagged in response to the deterioration in ecological functions.
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Metabolomics in melon: a new opportunity for aroma analysis.
Phytochemistry
PUBLISHED: 01-10-2014
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Cucumis melo fruit is highly valued for its sweet and refreshing flesh, however the flavour and value are also highly influenced by aroma as dictated by volatile organic compounds (VOCs). A simple and robust method of sampling VOCs on polydimethylsiloxane (PDMS) has been developed. Contrasting cultivars of C. melo subspecies melo were investigated at commercial maturity: three cultivars of var. Cantalupensis group Charentais (cv. Cézanne, Escrito, and Dalton) known to exhibit differences in ripening behaviour and shelf-life, as well as one cultivar of var. Cantalupensis group Ha'Ogan (cv. Noy Yisre'el) and one non-climacteric cultivar of var. Inodorus (cv. Tam Dew). The melon cultivar selection was based upon fruits exhibiting clear differences (cv. Noy Yisre'el and Tam Dew) and similarities (cv. Cézanne, Escrito, and Dalton) in flavour. In total, 58 VOCs were detected by thermal desorption (TD)-GC-MS which permitted the discrimination of each cultivar via Principal component analysis (PCA). PCA indicated a reduction in VOCs in the non-climacteric cv. Tam Dew compared to the four Cantalupensis cultivars. Within the group Charentais melons, the differences between the short, mid and long shelf-life cultivars were considerable. ¹H NMR analysis led to the quantification of 12 core amino acids, their levels were 3-10-fold greater in the Charentais melons, although they were reduced in the highly fragrant cv. Cézanne, indicating their role as VOC precursors. This study along with comparisons to more traditional labour intensive solid phase micro-extraction (SPME) GC-MS VOC profiling data has indicated that the high-throughput PDMS method is of great potential for the assessment of melon aroma and quality.
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Control of anthocyanin and non-flavonoid compounds by anthocyanin-regulating MYB and bHLH transcription factors in Nicotiana benthamiana leaves.
Front Plant Sci
PUBLISHED: 01-01-2014
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Coloration of plant organs such as fruit, leaves and flowers through anthocyanin production is governed by a combination of MYB and bHLH type transcription factors (TFs). In this study we introduced Rosea1 (ROS1, a MYB type) and Delila (DEL, a bHLH type), into Nicotiana benthamiana leaves by agroinfiltration. ROS1 and DEL form a pair of well-characterized TFs from Snapdragon (Antirrhinum majus), which specifically induce anthocyanin accumulation when expressed in tomato fruit. In N. benthamiana, robust induction of a single anthocyanin, delphinidin-3-rutinoside (D3R) was observed after expression of both ROS1 and DEL. Surprisingly in addition to D3R, a range of additional metabolites were also strongly and specifically up-regulated upon expression of ROS1 and DEL. Except for the D3R, these induced compounds were not derived from the flavonoid pathway. Most notable among these are nornicotine conjugates with butanoyl, hexanoyl, and octanoyl hydrophobic moieties, and phenylpropanoid-polyamine conjugates such as caffeoyl putrescine. The defensive properties of the induced molecules were addressed in bioassays using the tobacco specialist lepidopteran insect Manduca sexta. Our study showed that the effect of ROS1 and DEL expression in N. benthamiana leaves extends beyond the flavonoid pathway. Apparently the same transcription factor may regulate different secondary metabolite pathways in different plant species.
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Diversity of global rice markets and the science required for consumer-targeted rice breeding.
PLoS ONE
PUBLISHED: 01-01-2014
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With the ever-increasing global demand for high quality rice in both local production regions and with Western consumers, we have a strong desire to understand better the importance of the different traits that make up the quality of the rice grain and obtain a full picture of rice quality demographics. Rice is by no means a 'one size fits all' crop. Regional preferences are not only striking, they drive the market and hence are of major economic importance in any rice breeding / improvement strategy. In this analysis, we have engaged local experts across the world to perform a full assessment of all the major rice quality trait characteristics and importantly, to determine how these are combined in the most preferred varieties for each of their regions. Physical as well as biochemical characteristics have been monitored and this has resulted in the identification of no less than 18 quality trait combinations. This complexity immediately reveals the extent of the specificity of consumer preference. Nevertheless, further assessment of these combinations at the variety level reveals that several groups still comprise varieties which consumers can readily identify as being different. This emphasises the shortcomings in the current tools we have available to assess rice quality and raises the issue of how we might correct for this in the future. Only with additional tools and research will we be able to define directed strategies for rice breeding which are able to combine important agronomic features with the demands of local consumers for specific quality attributes and hence, design new, improved crop varieties which will be awarded success in the global market.
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A historical perspective of influenza A(H1N2) virus.
Emerging Infect. Dis.
PUBLISHED: 01-01-2014
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The emergence and transition to pandemic status of the influenza A(H1N1)A(H1N1)pdm09) virus in 2009 illustrated the potential for previously circulating human viruses to re-emerge in humans and cause a pandemic after decades of circulating among animals. Within a short time of the initial emergence of A(H1N1)pdm09 virus, novel reassortants were isolated from swine. In late 2011, a variant (v) H3N2 subtype was isolated from humans, and by 2012, the number of persons infected began to increase with limited person-to-person transmission. During 2012 in the United States, an A(H1N2)v virus was transmitted to humans from swine. During the same year, Australia recorded its first H1N2 subtype infection among swine. The A(H3N2)v and A(H1N2)v viruses contained the matrix protein from the A(H1N1)pdm09 virus, raising the possibility of increased transmissibility among humans and underscoring the potential for influenza pandemics of novel swine-origin viruses. We report on the differing histories of A(H1N2) viruses among humans and animals.
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Investigating the Transport Dynamics of Anthocyanins from Unprocessed Fruit and Processed Fruit Juice from Sour Cherry (Prunus cerasus L.) across Intestinal Epithelial Cells.
J. Agric. Food Chem.
PUBLISHED: 11-14-2013
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Anthocyanins can contribute to human health through preventing a variety of diseases. The uptake of these compounds from food and the parameters determining uptake efficiency within the human body are still poorly understood. Here we have employed a Caco-2 cell based system to investigate the transport of key antioxidant food components from sour cherry (Prunus cerasus L.) across the intestinal epithelial barrier. Anthocyanins and (-)-epicatechin were supplied in three contrasting matrices: fruit, processed fruit cherry juice, and polyphenolic fractions obtained by solid-phase extraction. Results show that both compound types behave differently. Fruit or juice matrices display comparable transport across the epithelial cell layer. The juice supplements sucrose and citric acid, which are regularly added to processed foods, have a positive effect on stability and transport. Polyphenolic fractions display a lower transport efficiency, relative to that of the fruit or juice, indicating the importance of food matrix components for intestinal absorption of polyphenols.
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Molecular Layer Deposition on Carbon Nanotubes.
ACS Nano
PUBLISHED: 08-23-2013
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Molecular layer deposition (MLD) techniques were used to deposit conformal coatings on bulk quantities of carbon nanotubes (CNTs). Several metalcone MLD chemistries were employed, including alucone (trimethylaluminum/glycerol and trimethylaluminum/ethylene glycol), titanicone (TiCl4/glycerol), and zincone (diethyl zinc/glycerol). The metalcone MLD films grew directly on the CNTs and MLD initiation did not require atomic layer deposition (ALD) of an adhesion layer. Transmission electron microscopy revealed that MLD formed three-dimensional conformal deposits throughout a CNT scaffold. Mechanical testing was also performed on sheets of CNT networks coated by MLD. Youngs Modulus values improved from an initial value of 510 MPa for uncoated CNT sheet to values that ranged from 2.2 GPa, for 10 nm of glycerol alucone (AlGL), to 8.7 GPa for a composite 5 nm AlGL + 5 nm Al2O3 coating.
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NON-smoky glycosyltransferase1 prevents the release of smoky aroma from tomato fruit.
Plant Cell
PUBLISHED: 08-16-2013
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Phenylpropanoid volatiles are responsible for the key tomato fruit (Solanum lycopersicum) aroma attribute termed "smoky." Release of these volatiles from their glycosylated precursors, rather than their biosynthesis, is the major determinant of smoky aroma in cultivated tomato. using a combinatorial omics approach, we identified the non-smoky glycosyltransferase1 (NSGT1) gene. Expression of NSGT1 is induced during fruit ripening, and the encoded enzyme converts the cleavable diglycosides of the smoky-related phenylpropanoid volatiles into noncleavable triglycosides, thereby preventing their deglycosylation and release from tomato fruit upon tissue disruption. In an nsgt1/nsgt1 background, further glycosylation of phenylpropanoid volatile diglycosides does not occur, thereby enabling their cleavage and the release of corresponding volatiles. Using reverse genetics approaches, the NSGT1-mediated glycosylation was shown to be the molecular mechanism underlying the major quantitative trait locus for smoky aroma. Sensory trials with transgenic fruits, in which the inactive nsgt1 was complemented with the functional NSGT1, showed a significant and perceivable reduction in smoky aroma. NSGT1 may be used in a precision breeding strategy toward development of tomato fruits with distinct flavor phenotypes.
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Paleo-drainage basin connectivity predicts evolutionary relationships across three Southeast Asian biodiversity hotspots.
Syst. Biol.
PUBLISHED: 02-07-2013
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Understanding factors driving diversity across biodiversity hotspots is critical for formulating conservation priorities in the face of ongoing and escalating environmental deterioration. While biodiversity hotspots encompass a small fraction of Earths land surface, more than half the worlds plants and two-thirds of terrestrial vertebrate species are endemic to these hotspots. Tropical Southeast (SE) Asia displays extraordinary species richness, encompassing four biodiversity hotspots, though disentangling multiple potential drivers of species richness is confounded by the regions dynamic geological and climatic history. Here, we use multilocus molecular genetic data from dense multispecies sampling of freshwater fishes across three biodiversity hotspots, to test the effect of Quaternary climate change and resulting drainage rearrangements on aquatic faunal diversification. While Cenozoic geological processes have clearly shaped evolutionary history in SE Asian halfbeak fishes, we show that paleo-drainage re-arrangements resulting from Quaternary climate change played a significant role in the spatiotemporal evolution of lowland aquatic taxa, and provide priorities for conservation efforts.
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Changes in polyphenol content during production of grape juice concentrate.
Food Chem
PUBLISHED: 01-10-2013
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The production of grape juice concentrate on an industrial scale was evaluated and samples from the main steps of processing have been collected and analyzed. The sampling steps included the selection and washing of grapes (Nevsehir Patlak variety), pressing in order to obtain the juice separate from the seed and the skin fraction, pasteurization, clarification, filtration, evaporation, and filling-packing at 27°C with a Brix of 45°. Samples from each of the processing steps were analyzed by a number of spectrophotometric analyses. A series of anthocyanin compounds was identified using HPLC-MS, and the fate of anthocyanins, quercetin rutinoside and procyanidins was followed using HPLC. The results indicate that the removal of seed and fruit skin removes most of the procyanidins and anthocyanins, while subsequent clarification and filtration treatments further reduce the anthocyanin content.
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The flavonoid pathway in tomato seedlings: transcript abundance and the modeling of metabolite dynamics.
PLoS ONE
PUBLISHED: 01-01-2013
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Flavonoids are secondary metabolites present in all terrestrial plants. The flavonoid pathway has been extensively studied, and many of the involved genes and metabolites have been described in the literature. Despite this extensive knowledge, the functioning of the pathway in vivo is still poorly understood. Here, we study the flavonoid pathway using both experiments and mathematical models. We measured flavonoid metabolite dynamics in two tissues, hypocotyls and cotyledons, during tomato seedling development. Interestingly, the same backbone of interactions leads to very different accumulation patterns in the different tissues. Initially, we developed a mathematical model with constant enzyme concentrations that described the metabolic networks separately in both tissues. This model was unable to fit the measured flavonoid dynamics in the hypocotyls, even if we allowed unrealistic parameter values. This suggested us to investigate the effect of transcript abundance on flavonoid accumulation. We found that the expression of candidate flavonoid genes varies considerably with time. Variation in transcript abundance results in enzymatic variation, which could have a large effect on metabolite accumulation. Candidate transcript abundance was included in the mathematical model as representative for enzyme concentration. We fitted the resulting model to the flavonoid dynamics in the cotyledons, and tested it by applying it to the data from hypocotyls. When transcript abundance is included, we are indeed able to explain flavonoid dynamics in both tissues. Importantly, this is possible under the biologically relevant restriction that the enzymatic properties estimated by the model are conserved between the tissues.
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Metalcones: hybrid organic-inorganic films fabricated using atomic and molecular layer deposition techniques.
J Nanosci Nanotechnol
PUBLISHED: 11-22-2011
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Hybrid organic-inorganic films can be deposited using atomic layer deposition (ALD) and molecular layer deposition (MLD) techniques. A special set of hybrid organic-inorganic films based on metal precursors and various organic alcohols yields metal alkoxide films that can be described as "metalcones." Many metalcone films are possible such as the "alucones" and "zincones" based on the reaction of trimethylaluminum and diethylzinc, respectively, with various organic alcohols such as ethylene glycol (EG). This paper reviews the previous work on metalcone MLD and discusses a variety of new metalcone systems. "Titanicones" are grown using TiCl4 and glycerol or EG and "zircones" are grown using zirconium tetra-tert-butoxide and EG. In addition, the organic alcohol can also be varied to change the properties within one metalcone family. For example, the glycerol triol precursor allows for more cross-linking and higher toughness in alucones than the EG diol precursor. Alloys can also be formed by combining metalcone MLD and metal oxide ALD. By varying the relative number of cycles of MLD and ALD, the composition and properties of the hybrid organic-inorganic films can be tuned from pure metalcone MLD to pure metal oxide ALD.
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Plant metabolomics and its potential for systems biology research background concepts, technology, and methodology.
Meth. Enzymol.
PUBLISHED: 09-28-2011
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The "metabolome" comprises the entire complement of small molecules in a plant or any other organism. It represents the ultimate phenotype of cells, deduced from the perturbation of gene expression and the modulation of protein function, as well as environmental cues. Extensive advances over the past decade, regarding the high-throughput (HTP) nature of "omics" research, have given birth to the expectation that a type of "systems level" overview may soon be possible. Having such a global overview of the molecular organization of a plant in the context of a particular set of genetic or environmental conditions, be it at cell, organ, or whole plant level, would clearly be very powerful. Currently, we are far from achieving this goal; however, within our hands, plant metabolomics is an HTP and informative "omics" approach to both sample generation and data generation, as well as raw data preprocessing, statistical analysis, and biological interpretation. Within this chapter, we aim to describe the great attention given to experimental design to ensure that the correct sample set and control are included and to, thereby, enable reliable statistical analysis of the data. For as comprehensive metabolite coverage as possible, we advocate the use of multiparallel approaches; thus, we describe a step-by-step standardized method for Nuclear magnetic resonance spectroscopy, as well as discussing with reference to standardized methodologies the techniques of gas chromatography-time of flight/mass spectrometry, and liquid chromatography-mass spectrometry.
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Ecosystem ecology meets adaptive management: food web response to a controlled flood on the Colorado River, Glen Canyon.
Ecol Appl
PUBLISHED: 09-24-2011
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Large dams have been constructed on rivers to meet human demands for water, electricity, navigation, and recreation. As a consequence, flow and temperature regimes have been altered, strongly affecting river food webs and ecosystem processes. Experimental high-flow dam releases, i.e., controlled floods, have been implemented on the Colorado River, U.S.A., in an effort to reestablish pulsed flood events, redistribute sediments, improve conditions for native fishes, and increase understanding of how dam operations affect physical and biological processes. We quantified secondary production and organic matter flows in the food web below Glen Canyon dam for two years prior and one year after an experimental controlled flood in March 2008. Invertebrate biomass and secondary production declined significantly following the flood (total biomass, 55% decline; total production, 56% decline), with most of the decline driven by reductions in two nonnative invertebrate taxa, Potamopyrgus antipodarum and Gammarus lacustris. Diatoms dominated the trophic basis of invertebrate production before and after the controlled flood, and the largest organic matter flows were from diatoms to the three most productive invertebrate taxa (P. antipodarum, G. lacustris, and Tubificida). In contrast to invertebrates, production of rainbow trout (Oncorhynchus mykiss) increased substantially (194%) following the flood, despite the large decline in total secondary production of the invertebrate assemblage. This counterintuitive result is reconciled by a post-flood increase in production and drift concentrations of select invertebrate prey (i.e., Chironomidae and Simuliidae) that supported a large proportion of trout production but had relatively low secondary production. In addition, interaction strengths, measured as species impact values, were strongest between rainbow trout and these two taxa before and after the flood, demonstrating that the dominant consumer-resource interactions were not necessarily congruent with the dominant organic matter flows. Our study illustrates the value of detailed food web analysis for elucidating pathways by which dam management may alter production and strengths of species interactions in river food webs. We suggest that controlled floods may increase production of nonnative rainbow trout, and this information can be used to help guide future dam management decisions.
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Quantity and quality: unifying food web and ecosystem perspectives on the role of resource subsidies in freshwaters.
Ecology
PUBLISHED: 07-30-2011
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Although the study of resource subsidies has emerged as a key topic in both ecosystem and food web ecology, the dialogue over their role has been limited by separate approaches that emphasize either subsidy quantity or quality. Considering quantity and quality together may provide a simple, but previously unexplored, framework for identifying the mechanisms that govern the importance of subsidies for recipient food webs and ecosystems. Using a literature review of > 90 studies of open-water metabolism in lakes and streams, we show that high-flux, low-quality subsidies can drive freshwater ecosystem dynamics. Because most of these ecosystems are net heterotrophic, allochthonous inputs must subsidize respiration. Second, using a literature review of subsidy quality and use, we demonstrate that animals select for high-quality food resources in proportions greater than would be predicted based on food quantity, and regardless of allochthonous or autochthonous origin. This finding suggests that low-flux, high-quality subsidies may be selected for by animals, and in turn may disproportionately affect food web and ecosystem processes (e.g., animal production, trophic energy or organic matter flow, trophic cascades). We then synthesize and review approaches that evaluate the role of subsidies and explicitly merge ecosystem and food web perspectives by placing food web measurements in the context of ecosystem budgets, by comparing trophic and ecosystem production and fluxes, and by constructing flow food webs. These tools can and should be used to address future questions about subsidies, such as the relative importance of subsidies to different trophic levels and how subsidies may maintain or disrupt ecosystem stability and food web interactions.
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International measles incidence and immunization coverage.
J. Infect. Dis.
PUBLISHED: 06-14-2011
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Measles is exquisitely sensitive to immunization programs. We investigated the decline in measles incidence after immunization with 1 or 2 doses of measles-containing vaccine (MCV), with or without supplementary immunization activities (SIAs). Using data from the World Health Organization, we modeled the impact of measles immunization using a negative binomial regression model. All countries offer measles immunization, and 192 of 193 countries offer a second dose of MCV (MCV2), using either a routine second dose, SIAs, or both. The incidence of measles fell from a median of 70.9 cases/100,000/year when coverage with a first dose of MCV (MCV1) was in the range of 0%-39% to a median of .9 cases/100,000/year when MCV1 coverage was 90%-100%, in both cases with no MCV2. Further reductions followed the introduction of MCV2 and SIAs. Modeling showed that each 1% increase in MCV1 coverage was followed by a 2.0% decrease in incidence in the same and following years (95% confidence interval [CI], 2.0%-1.9%, and 2.1%-1.9%, respectively). For a second dose, a rise of 1% in MCV2 coverage was followed by a decrease in measles incidence by .4% (95% CI, .3%-.5%) in the same year and .3% (95% CI, .2%-.5%) in the following year. SIAs were followed by decreases of measles incidence by 40.3% (95% CI, 46.3%-33.8%) in the same year and 45.2% (95% CI, 51.1%-48.7%) in the following year. A herd immunity effect was demonstrated with MCV1 coverage of >80%, and SIAs are an extraordinarily effective strategy for measles control.
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Having a yarn about smoking: using action research to develop a no smoking policy within an Aboriginal Health Organisation.
Health Policy
PUBLISHED: 06-05-2011
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This article reports on a culturally appropriate process of development of a smoke-free workplace policy within the peak Aboriginal Controlled Community Health Organisation in Victoria, Australia. Smoking is acknowledged as being responsible for at least 20% of all deaths in Aboriginal communities in Australia, and many Aboriginal health workers smoke.
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Community-wide assessment of protein-interface modeling suggests improvements to design methodology.
J. Mol. Biol.
PUBLISHED: 05-26-2011
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The CAPRI (Critical Assessment of Predicted Interactions) and CASP (Critical Assessment of protein Structure Prediction) experiments have demonstrated the power of community-wide tests of methodology in assessing the current state of the art and spurring progress in the very challenging areas of protein docking and structure prediction. We sought to bring the power of community-wide experiments to bear on a very challenging protein design problem that provides a complementary but equally fundamental test of current understanding of protein-binding thermodynamics. We have generated a number of designed protein-protein interfaces with very favorable computed binding energies but which do not appear to be formed in experiments, suggesting that there may be important physical chemistry missing in the energy calculations. A total of 28 research groups took up the challenge of determining what is missing: we provided structures of 87 designed complexes and 120 naturally occurring complexes and asked participants to identify energetic contributions and/or structural features that distinguish between the two sets. The community found that electrostatics and solvation terms partially distinguish the designs from the natural complexes, largely due to the nonpolar character of the designed interactions. Beyond this polarity difference, the community found that the designed binding surfaces were, on average, structurally less embedded in the designed monomers, suggesting that backbone conformational rigidity at the designed surface is important for realization of the designed function. These results can be used to improve computational design strategies, but there is still much to be learned; for example, one designed complex, which does form in experiments, was classified by all metrics as a nonbinder.
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A De in the life of cholera.
Indian J. Med. Res.
PUBLISHED: 03-19-2011
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The 50-year commemoration of S.N. Des seminal 1959 publication in Nature provides an opportunity to reflect on scientific discovery, recognition, and public health. Des paper marked the first major conceptual advance in cholera research since 1884, when Robert Koch definitively identified Der Kommabazillus as the aetiological agent of cholera. Unfortunately, Koch reported that systemic toxinosis and multi-organ failure led to severe dehydrating diarrhoea, thereby mistaking cause for effect. As a consequence, while work on other microbial pathogens advanced into the development of vaccines and therapeutics, cholera research languished as scientists injected animals parenterally in decades of futile effort to develop an animal model of diarrhoea. This fundamental misconception in cholera pathogenesis was swept away when S.N. De used ligated loops of rabbit ileum to demonstrate lumenal fluid accumulation in the presence of Vibrio cholerae culture filtrates. After some delay, Des observation of a diarrhoeagenic exotoxin became the founding principle of modern cholera research, vaccination, and treatment; and a burst of discovery saw V. cholerae transformed into the enteric pathogen best understood at the molecular level. The scientific basis for orally administering vaccines to induce mucosal immunity was established, and the success of oral rehydration, what has been described as one of the 20 th centurys most important medical advances, was explained. Nobel laureate Joshua Lederberg wrote of Des iconoclastic creativity, experimental skill, and observational mastery, and many other leaders in the field concurred. De was nominated for the Nobel Prize in Physiology or Medicine more than once. But despite the passage of half a century from Des work, cholera remains a frustrating problem: we are clearly missing something. In reviewing the scientific and programmatic impact of S.N. De on cholera, it is clear that a defining victory against the disease is achievable, but only if basic scientific discoveries are relentlessly driven towards progress in public health.
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Best practices for clinical pathology testing in carcinogenicity studies.
Toxicol Pathol
PUBLISHED: 02-04-2011
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The Society of Toxicologic Pathology (STP) and American Society for Veterinary Clinical Pathology (ASCVP) convened a Clinical Pathology in Carcinogenicity Studies Working Group to recommend best practices for inclusion of clinical pathology testing in carcinogenicity studies. Regulatory guidance documents and literature were reviewed, and veterinary pathologists from North America, Japan, and Europe were surveyed regarding current practices, perceived value, and recommendations for clinical pathology testing in carcinogenicity studies. For two-year rodent carcinogenicity studies, the Working Group recommends that clinical pathology testing be limited to collection of blood smears at scheduled and unscheduled sacrifices to be examined only if indicated to aid in the diagnosis of possible hematopoietic neoplasia following histopathologic evaluation. Additional clinical pathology testing is most appropriately used to address specific issues from prior toxicity studies or known test article-related class effects. Inadequate data were available to make a recommendation concerning clinical pathology testing for alternative six-month carcinogenicity assays using genetically modified mice, although the Working Group suggests that it may be appropriate to use the same approach as for two-year carcinogenicity studies since the study goal is the same.
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Extensive metabolic cross-talk in melon fruit revealed by spatial and developmental combinatorial metabolomics.
New Phytol.
PUBLISHED: 01-28-2011
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• Variations in tissue development and spatial composition have a major impact on the nutritional and organoleptic qualities of ripe fleshy fruit, including melon (Cucumis melo). To gain a deeper insight into the mechanisms involved in these changes, we identified key metabolites for rational food quality design. • The metabolome, volatiles and mineral elements were profiled employing an unprecedented range of complementary analytical technologies. Fruits were followed at a number of time points during the final ripening process and tissues were collected across the fruit flesh from rind to seed cavity. Approximately 2000 metabolite signatures and 15 mineral elements were determined in an assessment of temporal and spatial melon fruit development. • This study design enabled the identification of: coregulated hubs (including aspartic acid, 2-isopropylmalic acid, ?-carotene, phytoene and dihydropseudoionone) in metabolic association networks; global patterns of coordinated compositional changes; and links of primary and secondary metabolism to key mineral and volatile fruit complements. • The results reveal the extent of metabolic interactions relevant to ripe fruit quality and thus have enabled the identification of essential candidate metabolites for the high-throughput screening of melon breeding populations for targeted breeding programmes aimed at nutrition and flavour improvement.
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Using an integrated automated system to optimize retention and increase frequency of blood donations.
Transfusion
PUBLISHED: 12-24-2010
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This study examines the impact of an integrated, automated phone system to reinforce retention and increase frequency of donations among blood donors.
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Nitrous oxide emission from denitrification in stream and river networks.
Proc. Natl. Acad. Sci. U.S.A.
PUBLISHED: 12-20-2010
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Nitrous oxide (N(2)O) is a potent greenhouse gas that contributes to climate change and stratospheric ozone destruction. Anthropogenic nitrogen (N) loading to river networks is a potentially important source of N(2)O via microbial denitrification that converts N to N(2)O and dinitrogen (N(2)). The fraction of denitrified N that escapes as N(2)O rather than N(2) (i.e., the N(2)O yield) is an important determinant of how much N(2)O is produced by river networks, but little is known about the N(2)O yield in flowing waters. Here, we present the results of whole-stream (15)N-tracer additions conducted in 72 headwater streams draining multiple land-use types across the United States. We found that stream denitrification produces N(2)O at rates that increase with stream water nitrate (NO(3)(-)) concentrations, but that <1% of denitrified N is converted to N(2)O. Unlike some previous studies, we found no relationship between the N(2)O yield and stream water NO(3)(-). We suggest that increased stream NO(3)(-) loading stimulates denitrification and concomitant N(2)O production, but does not increase the N(2)O yield. In our study, most streams were sources of N(2)O to the atmosphere and the highest emission rates were observed in streams draining urban basins. Using a global river network model, we estimate that microbial N transformations (e.g., denitrification and nitrification) convert at least 0.68 Tg·y(-1) of anthropogenic N inputs to N(2)O in river networks, equivalent to 10% of the global anthropogenic N(2)O emission rate. This estimate of stream and river N(2)O emissions is three times greater than estimated by the Intergovernmental Panel on Climate Change.
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Importance of trimethylaluminum diffusion in three-step ABC molecular layer deposition using trimethylaluminum, ethanolamine, and maleic anhydride.
Langmuir
PUBLISHED: 11-30-2010
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Hybrid organic-inorganic films were grown by molecular layer deposition (MLD) with a three-step ABC reaction sequence using (A) trimethylaluminum (TMA), (B) ethanolamine (EA), and (C) maleic anhydride (MA) at 90 °C. Very large steady state mass gains of 1854-4220 ng/(cm(2) cycle) were measured depending on reaction conditions. These mass gains are much larger than typical mass gains for surface reactions. The quartz crystal microbalance (QCM) mass profiles during the TMA reaction were consistent with TMA diffusion into and out of the ABC films. The ABC mass gains per cycle also displayed a strong dependence on the TMA dose and purge times that was consistent with the effects of TMA diffusion. Multiple dose experiments conducted at 130 °C revealed that the ABC reactions were self-limiting for thin ABC films. For thicker ABC films, increased TMA diffusion into the ABC film led to non-self-limiting behavior. Numerical modeling assuming Fickian diffusion for TMA diffusing into and out of the ABC film could fit the QCM mass profiles. The results all indicate that TMA diffusion into the ABC MLD film plays a key role in the thin film growth. In addition, X-ray reflectivity (XRR) measurements revealed that the ABC films were exceptionally smooth.
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The effect of industrial food processing on potentially health-beneficial tomato antioxidants.
Crit Rev Food Sci Nutr
PUBLISHED: 11-26-2010
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Increasing desires from both consumers and producers to understand better which nutritive components are present in our food and how these are influenced by industrial processing strategies is resulting in extra research involving the use of state-of-the-art technologies to generate novel biochemical information. In this review, attention has been focused on tomato as this is a product eaten right across the world both as fresh produce and after having been processed in a wide variety of ways. There is a particular interest in tomato as it is a major component in the so-called "Mediterranean diet" which has recently been associated with a healthier lifestyle. Tomatoes are rich sources of a variety of nutritional compounds and especially some key antioxidant components such as the carotenoid lycopene, vitamin C, and a range of polyphenols. The potentially protective properties of these antioxidants are of great interest and the consumer has already become aware of their potential importance. Surveying the literature has revealed that much research has been done on the biochemical composition of tomato and its products. However, it remains difficult to make clear conclusions on optimizing the processing strategy. Many, apparently conflicting, findings have been reported and consequently, in this review, we have drawn attention to these and have attempted to clarify their cause. Finally, a range of recommendations has been made as to how future research might be performed in order to generate more concrete conclusions enabling recommendations towards more optimized processing strategies.
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Reported waterborne outbreaks of gastrointestinal disease in Australia are predominantly associated with recreational exposure.
Aust N Z J Public Health
PUBLISHED: 11-03-2010
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To examine the frequency and circumstances of reported waterborne outbreaks of gastroenteritis in Australia.
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International recommendations for training future toxicologic pathologists participating in regulatory-type, nonclinical toxicity studies.
Toxicol Pathol
PUBLISHED: 08-17-2010
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The International Federation of Societies of Toxicologic Pathologists (IFSTP) proposes a common global framework for training future toxicologic pathologists who will support regulatory-type, nonclinical toxicology studies. Optimally, trainees should undertake a scientific curriculum of at least five years at an accredited institution leading to a clinical degree (veterinary medicine or medicine). Trainees should then obtain four or more years of intensive pathology practice during a residency and/or on-the-job "apprenticeship," at least two years of which must be focused on regulatory-type toxicologic pathology topics. Possession of a recognized pathology qualification (i.e., certification) is highly recommended. A nonclinical pathway (e.g., a graduate degree in medical biology or pathology) may be possible if medically trained pathologists are scarce, but this option is not optimal. Regular, lifelong continuing education (peer review of nonclinical studies, professional meetings, reading, short courses) will be necessary to maintain and enhance ones understanding of current toxicologic pathology knowledge, skills, and tools. This framework should provide a rigorous yet flexible way to reliably train future toxicologic pathologists to generate, interpret, integrate, and communicate data in regulatory-type, nonclinical toxicology studies.
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International recommendations for training future toxicologic pathologists participating in regulatory-type, nonclinical toxicity studies.
J Toxicol Pathol
PUBLISHED: 06-20-2010
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The International Federation of Societies of Toxicologic Pathologists (IFSTP) proposes a common global framework for training future toxicologic pathologists who will support regulatory-type nonclinical toxicology studies. Trainees optimally should undertake a scientific curriculum of at least 5 years at an accredited institution leading to a clinical degree (veterinary medicine or medicine). Trainees should then obtain 4 or more years of intensive pathology practice during a residency and/or on-the-job "apprenticeship," at least 2 years of which must be focused on regulatory-type toxicologic pathology topics. Possession of a recognized pathology qualification (i.e., certification) is highly recommended. A non-clinical pathway (e.g., a graduate degree in medical biology or pathology) may be possible if medically trained pathologists are scarce, but this option is not optimal. Regular, lifelong continuing education (peer review of nonclinical studies, professional meetings, reading, short courses) will be necessary to maintain and enhance ones understanding of current toxicologic pathology knowledge, skills, and tools. This framework should provide a rigorous yet flexible way to reliably train future toxicologic pathologists to generate, interpret, integrate, and communicate data in regulatory-type, nonclinical toxicology studies.
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International recommendations for training future toxicologic pathologists participating in regulatory-type, nonclinical toxicity studies.
Exp. Toxicol. Pathol.
PUBLISHED: 05-10-2010
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The International Federation of Societies of Toxicologic Pathologists (IFSTP) proposes a common global framework for training future toxicologic pathologists who will support regulatory-type - nonclinical toxicology studies. Trainees optimally should undertake a scientific curriculum of at least 5 years at an accredited institution leading to a clinical degree (veterinary medicine or medicine). Trainees should then obtain 4 or more years of intensive pathology practice during a residency and/or on-the-job "apprenticeship," at least 2 years of which must be focused on regulatory-type toxicologic pathology topics. Possession of a recognized pathology qualification (i.e., certification) is highly recommended. A nonclinical pathway (e.g., a graduate degree in medical biology or pathology) may be possible if medically trained pathologists are scarce, but this option is not optimal. Regular, lifelong continuing education (peer review of nonclinical studies, professional meetings, reading, short courses) will be necessary to maintain and enhance ones understanding of current toxicologic pathology knowledge, skills, and tools. This framework should provide a rigorous yet flexible way to reliably train future toxicologic pathologists to generate, interpret, integrate, and communicate data in regulatory-type, nonclinical toxicology studies.
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Plant molecular stress responses face climate change.
Trends Plant Sci.
PUBLISHED: 03-24-2010
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Environmental stress factors such as drought, elevated temperature, salinity and rising CO? affect plant growth and pose a growing threat to sustainable agriculture. This has become a hot issue due to concerns about the effects of climate change on plant resources, biodiversity and global food security. Plant adaptation to stress involves key changes in the -omic architecture. Here, we present an overview of the physiological and molecular programs in stress adaptation focusing on how genes, proteins and metabolites change after individual and multiple environmental stresses. We address the role which -omics research, coupled to systems biology approaches, can play in future research on plants seemingly unable to adapt as well as those which can tolerate climatic change.
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Linking calcification by exotic snails to stream inorganic carbon cycling.
Oecologia
PUBLISHED: 01-08-2010
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Biotic calcification is rarely considered in freshwater C budgets, despite calculations suggesting that calcifying animals can alter inorganic C cycling. Most studies that have quantified biocalcification in aquatic ecosystems have not directly linked CO(2) fluxes from biocalcification with whole-ecosystem rates of inorganic C cycling. The freshwater snail, Melanoides tuberculata, has achieved a high abundance and 37.4 g biomass m(-2) after invading Kelly Warm Springs in Grand Teton National Park. This high biomass suggests that introduced populations of Melanoides may alter ecosystem processes. We measured Melanoides growth rates and biomass to calculate the production of biomass, shell mass, and CO(2). We compared Melanoides biomass and inorganic C production with ecosystem C pools and fluxes, as well as with published rates of CO(2) production by other calcifying organisms. Melanoides calcification in Kelly Warm Springs produced 12.1 mmol CO(2) m(-2) day(-1) during summer months. We measured high rates of gross primary productivity and respiration in Kelly Warm Springs (-378 and 533 mmol CO(2) m(-2) day(-1), respectively); CO(2) produced from biocalcification increased net CO(2) production in Kelly Warm Springs from 155 to 167 mmol CO(2) m(-2) day(-1). This rate of CO(2) production via biocalcification is within the published range of calcification by animals. But these CO(2) fluxes are small when compared to ecosystem C fluxes from stream metabolism. The influence of animals is relative to ecosystem processes, and should always be compared with ecosystem fluxes to quantify the importance of a specific animal in its environment.
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A role for differential glycoconjugation in the emission of phenylpropanoid volatiles from tomato fruit discovered using a metabolic data fusion approach.
Plant Physiol.
PUBLISHED: 11-04-2009
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A role for differential glycoconjugation in the emission of phenylpropanoid volatiles from ripening tomato fruit (Solanum lycopersicum) upon fruit tissue disruption has been discovered in this study. Application of a multiinstrumental analytical platform for metabolic profiling of fruits from a diverse collection of tomato cultivars revealed that emission of three discriminatory phenylpropanoid volatiles, namely methyl salicylate, guaiacol, and eugenol, took place upon disruption of fruit tissue through cleavage of the corresponding glycoconjugates, identified putatively as hexose-pentosides. However, in certain genotypes, phenylpropanoid volatile emission was arrested due to the corresponding hexose-pentoside precursors having been converted into glycoconjugate species of a higher complexity: dihexose-pentosides and malonyl-dihexose-pentosides. This glycoside conversion was established to occur in tomato fruit during the later phases of fruit ripening and has consequently led to the inability of red fruits of these genotypes to emit key phenylpropanoid volatiles upon fruit tissue disruption. This principle of volatile emission regulation can pave the way to new strategies for controlling tomato fruit flavor and taste.
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Multi-scale landscape factors influencing stream water quality in the state of Oregon.
Environ Monit Assess
PUBLISHED: 10-23-2009
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Enterococci bacteria are used to indicate the presence of human and/or animal fecal materials in surface water. In addition to human influences on the quality of surface water, a cattle grazing is a widespread and persistent ecological stressor in the Western United States. Cattle may affect surface water quality directly by depositing nutrients and bacteria, and indirectly by damaging stream banks or removing vegetation cover, which may lead to increased sediment loads. This study used the State of Oregon surface water data to determine the likelihood of animal pathogen presence using enterococci and analyzed the spatial distribution and relationship of biotic (enterococci) and abiotic (nitrogen and phosphorous) surface water constituents to landscape metrics and others (e.g. human use, percent riparian cover, natural covers, grazing, etc.). We used a grazing potential index (GPI) based on proximity to water, land ownership and forage availability. Mean and variability of GPI, forage availability, stream density and length, and landscape metrics were related to enterococci and many forms of nitrogen and phosphorous in standard and logistic regression models. The GPI did not have a significant role in the models, but forage related variables had significant contribution. Urban land use within stream reach was the main driving factor when exceeding the threshold (> or =35 cfu/100 ml), agriculture was the driving force in elevating enterococci in sites where enterococci concentration was <35 cfu/100 ml. Landscape metrics related to amount of agriculture, wetlands and urban all contributed to increasing nutrients in surface water but at different scales. The probability of having sites with concentrations of enterococci above the threshold was much lower in areas of natural land cover and much higher in areas with higher urban land use within 60 m of stream. A 1% increase in natural land cover was associated with a 12% decrease in the predicted odds of having a site exceeding the threshold. Opposite to natural land cover, a one unit change in each of manmade barren and urban land use led to an increase of the likelihood of exceeding the threshold by 73%, and 11%, respectively. Change in urban land use had a higher influence on the likelihood of a site exceeding the threshold than that of natural land cover.
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Evaluation of a breastfeeding assessment score in a diverse population.
J Hum Lact
PUBLISHED: 09-16-2009
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A previous study performed in a predominately suburban population developed a breastfeeding assessment score (BAS) that was designed to predict, prior to hospital discharge, those mothers who would discontinue breastfeeding within the first 10 days of age. The purpose of the present study was to assess the BAS in a more diverse population. Patients were solicited from 3 urban hospitals serving patients primarily supported by public funding. Results of the present study with 1182 mother-infant pairs confirmed that 5 variables scored on a 0-2 scale (maternal age, previous breastfeeding experience, latching difficulty, breastfeeding interval, number bottles) remained highly significant for predicting discontinuation of breastfeeding. The data also demonstrate that the BAS is inversely related to the risk of cessation of breastfeeding at 7 to 10 days of age. Those at an early risk of cessation of breastfeeding, identified by the BAS, may benefit from early identification and a lactation consultation.
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Users perceptions of remote trauma telesonography.
J Telemed Telecare
PUBLISHED: 07-11-2009
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We established a pilot tele-ultrasound system between a rural referring hospital and a tertiary care trauma centre to facilitate telementoring during acute trauma resuscitations. Over a 12-month period, 23 tele-ultrasound examinations were completed. The clinical protocol examined both the Focused Assessment with Sonography for Trauma (FAST) and the Extended FAST (EFAST) for pneumothoraxes. Twenty of the examinations were conducted during acute trauma resuscitations and three during live patient simulations. FAST examinations were completed in all 23 cases and EFAST examinations in 17 cases. There were 18 clinical users, of whom 14 completed a survey (76% response rate). Overall, 93% of respondents were either satisfied or very satisfied with the telemedicine interaction and agreed or strongly agreed that the technology could potentially benefit injured patients in the far north of Canada. In addition, 93% of the respondents felt that the project had improved collegiality between the two institutions involved. The majority of respondents (71%) agreed or strongly agreed that the project had improved their ultrasound skills. We believe that as further experience is obtained, tele-ultrasound will prove to be an important aid to the care of remotely injured and ill patients.
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Characterization of Rhamnosidases from Lactobacillus plantarum and Lactobacillus acidophilus.
Appl. Environ. Microbiol.
PUBLISHED: 04-03-2009
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Lactobacilli are known to use plant materials as a food source. Many such materials are rich in rhamnose-containing polyphenols, and thus it can be anticipated that lactobacilli will contain rhamnosidases. Therefore, genome sequences of food-grade lactobacilli were screened for putative rhamnosidases. In the genome of Lactobacillus plantarum, two putative rhamnosidase genes (ram1(Lp) and ram2(Lp)) were identified, while in Lactobacillus acidophilus, one rhamnosidase gene was found (ramA(La)). Gene products from all three genes were produced after introduction into Escherichia coli and were then tested for their enzymatic properties. Ram1(Lp), Ram2(Lp), and RamA(La) were able to efficiently hydrolyze rutin and other rutinosides, while RamA(La) was, in addition, able to cleave naringin, a neohesperidoside. Subsequently, the potential application of Lactobacillus rhamnosidases in food processing was investigated using a single matrix, tomato pulp. Recombinant Ram1(Lp) and RamA(La) enzymes were shown to remove the rhamnose from rutinosides in this material, but efficient conversion required adjustment of the tomato pulp to pH 6. The potential of Ram1(Lp) for fermentation of plant flavonoids was further investigated by expression in the food-grade bacterium Lactococcus lactis. This system was used for fermentation of tomato pulp, with the aim of improving the bioavailability of flavonoids in processed tomato products. While import of flavonoids into L. lactis appeared to be a limiting factor, rhamnose removal was confirmed, indicating that rhamnosidase-producing bacteria may find commercial application, depending on the technological properties of the strains and enzymes.
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Not just a grain of rice: the quest for quality.
Trends Plant Sci.
PUBLISHED: 02-18-2009
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A better understanding of the factors that contribute to the overall grain quality of rice (Oryza sativa) will lay the foundation for developing new breeding and selection strategies for combining high quality, with high yield. This is necessary to meet the growing global demand for high quality rice while offering producing countries additional opportunities for generating higher export revenues. Several recent developments in genetics, genomics, metabolomics and phenomics are enhancing our understanding of the pathways that determine several quality traits. New research strategies, as well as access to the draft of the rice genome, will not only advance our understanding of the molecular mechanisms that lead to quality rice but will also pave the way for efficient and targeted grain improvement.
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Countering tumor-induced immunosuppression during immunotherapy for pancreatic cancer.
Expert Opin Biol Ther
PUBLISHED: 02-17-2009
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Vaccines for pancreatic cancer have been challenged by a number of factors, especially the immunosuppressive microenvironment within the tumor that allows for escape from immune surveillance.
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Quantifying structural physical habitat attributes using LIDAR and hyperspectral imagery.
Environ Monit Assess
PUBLISHED: 01-23-2009
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Structural physical habitat attributes include indices of stream size, channel gradient, substrate size, habitat complexity, and riparian vegetation cover and structure. The Environmental Monitoring and Assessment Program (EMAP) is designed to assess the status and trends of ecological resources at different scales. High-resolution remote sensing provides unique capabilities in detecting a variety of features and indicators of environmental health and condition. LIDAR is an airborne scanning laser system that provides data on topography, channel dimensions (width, depth), slope, channel complexity (residual pools, volume, morphometric complexity, hydraulic roughness), riparian vegetation (height and density), dimensions of riparian zone, anthropogenic alterations and disturbances, and channel and riparian interaction. Hyperspectral aerial imagery offers the advantage of high spectral and spatial resolution allowing for the detection and identification of riparian vegetation and natural and anthropogenic features at a resolution not possible with satellite imagery. When combined, or fused, these technologies comprise a powerful geospatial data set for assessing and monitoring lentic and lotic environmental characteristics and condition.
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Phosphorus-mediated changes in life history traits of the invasive New Zealand mudsnail (Potamopyrgus antipodarum).
Oecologia
PUBLISHED: 01-04-2009
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Understanding the mechanisms that species use to succeed in new environments is vital to predicting the extent of invasive species impacts. Food quality is potentially important because it can affect population dynamics by affecting life history traits. The New Zealand mudsnail, Potamopyrgus antipodarum, is a worldwide invader. We examined how mudsnail growth rate and fecundity responded to the C:P ratio of algal food in laboratory conditions. Mudsnails fed low-P algae (C:P 1,119) grew more slowly, matured later, produced smaller offspring, and grew to a smaller adult size than snails reared on algae with high levels of P. A relatively small increase in algal C:P (203-270) significantly increased mudsnail age at maturity. We suggest that the relatively high body P requirements of mudsnails make them susceptible to allocation trade-offs between growth and reproduction under P-limited conditions. The elemental composition of algae varies greatly in nature, and over half of the rock biofilms in streams surveyed within the introduced range of mudsnails in the Greater Yellowstone Area had C:P ratios above which could potentially pose P limitation of life history traits. High growth rate and fecundity are common traits of many species that become invasive and are also associated with high-P demands. Therefore, fast-growing consumers with high P demands, such as mudsnails, are potentially more sensitive to P limitation suggesting that limitation of growth and reproduction by food quality is an important factor in understanding the resource demands of invasive species.
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De novo production of the flavonoid naringenin in engineered Saccharomyces cerevisiae.
Microb. Cell Fact.
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Flavonoids comprise a large family of secondary plant metabolic intermediates that exhibit a wide variety of antioxidant and human health-related properties. Plant production of flavonoids is limited by the low productivity and the complexity of the recovered flavonoids. Thus to overcome these limitations, metabolic engineering of specific pathway in microbial systems have been envisaged to produce high quantity of a single molecules.
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Correlation of rutin accumulation with 3-O-glucosyl transferase and phenylalanine ammonia-lyase activities during the ripening of tomato fruit.
Plant Foods Hum Nutr
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In tomato, the predominant flavonoid is quercetin-3-rutinoside (rutin). In this study, we aim to investigate the phenylalanine ammonia-lyase (PAL) and the quercetin-3-O-glucosyl transferase (3-GT) reactions in the formation of rutin during tomato fruit ripening. Tomatoes of the Moneymaker variety at different development stages (green, breaker, turning, pink, red, and deep red) were divided into flesh and peel fractions. In each sample, both the content of rutin and the enzymatic activities for PAL and 3-GT were recorded. The highest activities of PAL were recorded in the peel of turning fruit (3,000 ?kat/mg fresh weight). In fruit flesh, maximal activity was observed in red fruit (917.3 ?kat/mg). For both tissues, PAL activity strongly decreased at the final (deep red) fruit stage. The activity of 3-GT in peel peaked in the turning fruit stage (50.7 pkat/mg), while in flesh maximal activity (33.4 pkat/mg) was observed in green fruit, which rapidly declined at the turning stage. Higher levels of rutin were detected in the tomato peel compared to the flesh part with the highest level being found at the green stage. The relation of PAL and 3-GT activities to rutin content is also evaluated.
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Food webs: reconciling the structure and function of biodiversity.
Trends Ecol. Evol. (Amst.)
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The global biodiversity crisis concerns not only unprecedented loss of species within communities, but also related consequences for ecosystem function. Community ecology focuses on patterns of species richness and community composition, whereas ecosystem ecology focuses on fluxes of energy and materials. Food webs provide a quantitative framework to combine these approaches and unify the study of biodiversity and ecosystem function. We summarise the progression of food-web ecology and the challenges in using the food-web approach. We identify five areas of research where these advances can continue, and be applied to global challenges. Finally, we describe what data are needed in the next generation of food-web studies to reconcile the structure and function of biodiversity.
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The biogeography of Sulawesi revisited: is there evidence for a vicariant origin of taxa on Wallaces "anomalous island"?
Evolution
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Sulawesi, the largest island in the Indonesian biodiversity hotspot region Wallacea, hosts a diverse endemic fauna whose origin has been debated for more than 150 years. We use a comparative approach based on dated phylogenies and geological constraints to test the role of vicariance versus dispersal in the origin of Sulawesi taxa. Most divergence time estimates for the split of Sulawesi lineages from their sister groups postdate relevant tectonic vicariant events, suggesting that the island was predominantly colonized by dispersal. Vicariance cannot be refuted for 20% of the analyzed taxa, though. Although vicariance across Wallaces Line was only supported for one arthropod taxon, divergence time estimates were consistent with a "tectonic dispersal" vicariance hypothesis from the East in three (invertebrate and vertebrate) taxa. Speciation on Sulawesi did not occur before the Miocene, which is consistent with geological evidence for more extensive land on the island from that time. The Pliocene onset of periodic sea-level changes may have played a role in increasing the potential for dispersal to Sulawesi. A more extensive taxon sampling in Wallacea will be crucial for refining our understanding of the regions biogeography and for testing hypotheses on the origin of taxa on its most important island.
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Bacterial communities in women with bacterial vaginosis: high resolution phylogenetic analyses reveal relationships of microbiota to clinical criteria.
PLoS ONE
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Bacterial vaginosis (BV) is a common condition that is associated with numerous adverse health outcomes and is characterized by poorly understood changes in the vaginal microbiota. We sought to describe the composition and diversity of the vaginal bacterial biota in women with BV using deep sequencing of the 16S rRNA gene coupled with species-level taxonomic identification. We investigated the associations between the presence of individual bacterial species and clinical diagnostic characteristics of BV.
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Diabetes prevalence and determinants in adults in China mainland from 2000 to 2010: a systematic review.
Diabetes Res. Clin. Pract.
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To systematically review trends in diabetes mellitus (DM) prevalence in adults in China over the last 10 years and to identify the determinants of these trends.
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Activity of pomalidomide in patients with immunoglobulin light-chain amyloidosis.
Blood
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Immunoglobulin light-chain (AL) amyloidosis is a rare, incurable plasma cell disorder. Its therapy has benefited immensely from the expanding drug armamentarium available for multiple myeloma. Pomalidomide in combination with weekly dexamethasone (Pom/dex) is active among patients with relapsed myeloma. In the present study, we explored the Pom/dex combination in patients with previously treated AL. Patients were eligible for this prospective phase 2 trial if they had had at least one prior regimen and if they had reasonably preserved organ function. Patients were treated with oral Pom/dex. Thirty-three patients were enrolled. The median age was 66 years. Median time from diagnosis to on-study was 37 months. Eighty-two percent had cardiac involvement. The confirmed hematologic response rate was 48%, with a median time to response of 1.9 months. Organ improvement was documented in 5 patients. The median overall and progression-free survival rates were 28 and 14 months, respectively; the 1-year overall and progression-free survival rates were 76% and 59%, respectively. There was a discordance between the hematologic response and the N-terminal pro-brain natriuretic peptide response. The most common grade 3-5 adverse events, regardless of attribution, were neutropenia and fatigue. We conclude that pomalidomide appears to be a valuable drug covering an unmet clinical need in patients with previously treated AL. The trial is registered at www.clinicaltrials.gov as NCT00558896.
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High-performance liquid chromatography-mass spectrometry analysis of plant metabolites in brassicaceae.
Methods Mol. Biol.
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The Brassicaceae family comprises a variety of plant species that are of high economic importance as -vegetables or industrial crops. This includes crops such as Brassica rapa (turnip, Bok Choi), B. oleracea (cabbages, broccoli, cauliflower, etc.), and B. napus (oil seed rape), and also includes the famous genetic model of plant research, Arabidopsis thaliana (thale cress). Brassicaceae plants contain a large variety of interesting secondary metabolites, including glucosinolates, hydroxycinnamic acids, and flavonoids. These metabolites are also of particular importance due to their proposed positive effects on human health. Next to these well-known groups of phytochemicals, many more metabolites are of course also present in crude extracts prepared from Brassica and Arabidopsis plant material.High-pressure liquid chromatography coupled to mass spectrometry (HPLC-MS), especially if combined with a high mass resolution instrument such as a QTOF MS, is a powerful approach to separate, detect, and annotate metabolites present in crude aqueous-alcohol plant extracts. Using an essentially unbiased procedure that takes into account all metabolite mass signals from the raw data files, detailed information on the relative abundance of hundreds of both known and, as yet, unknown semipolar metabolites can be obtained. These comprehensive metabolomics data can then be used to, for instance, identify genetic markers regulating metabolic composition, determine effects of (a)biotic stress or specific growth conditions, or establish metabolite changes occurring upon food processing or storage.This chapter describes in detail a procedure for preparing crude extracts and performing comprehensive HPLC-QTOF MS-based profiling of semi-polar metabolites in Brassicaceae plant material. Compounds present in the extract can be (partially or completely) annotated based on their accurate mass, their MS/MS fragments and on other specific chemical characteristics such as retention time and UV-absorbance spectrum.
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Solid phase micro-extraction GC-MS analysis of natural volatile components in melon and rice.
Methods Mol. Biol.
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The natural fragrance compounds produced by plants play key roles in the long-term fitness and survival of these plants as well as being of direct/indirect benefit to man. Almost all plant fragrances, either pleasant or unpleasant, comprise many different compounds, from different chemical classes and can indeed be highly complex in composition involving several hundred types of volatile molecule. Analyzing these mixtures and identifying their main (bio)active components is of importance in both fundamental and applied science. Gas Chromatography-Mass Spectrometry (GC-MS) plays a central role here. GC-MS has regularly been used for fragrance analysis and different extraction/adsorption and detection protocols have been designed specifically for plant materials. In this chapter, two methods are presented for two highly contrasting plant organs-a melon fruit and rice grains. Metabolomics analyses of these important food crops are already helping us understand better which components are most important in determining the flavour of these important food crops and how we might go about producing new "designer" crops which are even tastier than the existing ones.
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Practical applications of metabolomics in plant biology.
Methods Mol. Biol.
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The technologies being developed for the large-scale, essentially unbiased analysis of the small molecules present in organic extracts made from plant materials are greatly changing our way of thinking about what is possible in plant biology. A range of different separation and detection techniques are being refined and expanded and their combination with advanced data management and data analysis approaches is already giving plant scientists far deeper insights into the complexity of plant metabolism and plant metabolic composition than was imaginable just a few years ago. This field of "metabolomics", while still in its infancy, has nevertheless already been welcomed with open arms by the plant science community, partly because of these said advantages but also because of the broad potential applicability of the approaches in both fundamental and applied science. The diversity in application already ranges from understanding the considerable complexity of primary metabolic networks in Arabidopsis, to the changes which occur in the biochemical composition of foods occurring, for example, during the Pasteurization of tomato purée for long-term storage or the boiling of Basmati rice for direct consumption. The insights being gained are revealing valuable information on the strict control yet flexible nature of plant metabolic networks in many different systems. This volume aims to give a comprehensive overview of the approaches available for the performance of a "typical" plant metabolomics experiment, the choice of analytical techniques and to offer warnings on the potential pitfalls in experimental design and execution.
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JoVE Visualize is a tool created to match the last 5 years of PubMed publications to methods in JoVE's video library.

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