Sensitivity and specificity of detection methods for erythropoietin doping in cyclists

Recombinant human erythropoietin (rHuEPO) is used as doping a substance. Anti-doping efforts include urine and blood testing and monitoring the athlete biological passport (ABP). As data on the performance of these methods are incomplete, this study aimed to evaluate the performance of two common urine assays and the ABP. In a randomized, double-blinded, placebo-controlled trial, 48 trained cyclists received a mean dose of 6000 IU rHuEPO (epoetin beta) or placebo by weekly injection for eight weeks. Seven timed urine and blood samples were collected per subject. Urine samples were analyzed by sarcosyl-PAGE and isoelectric focusing methods in the accredited DoCoLab in Ghent. A selection of samples, including any with false presumptive findings, underwent a second sarcosyl-PAGE confirmation analysis. Hematological parameters were used to construct a module similar to the ABP and analyzed by two evaluators from an Athlete Passport Management Unit. Sensitivity of the sarcosyl-PAGE and isoelectric focusing assays for the detection of erythropoietin abuse were 63.8% and 58.6%, respectively, with a false presumptive finding rate of 4.3% and 6%. None of the false presumptive findings tested positive in the confirmation analysis. Sensitivity was highest between 2 and 6 days after dosing, and dropped rapidly outside this window. Sensitivity of the ABP was 91.3%. Specificity of the urine assays was high; however, the detection window of rHuEPO was narrow, leading to questionable sensitivity. The ABP, integrating longitudinal data, is more sensitive, but there are still subjects that evade detection. Combining these methods might improve performance, but will not resolve all observed shortcomings

Metabolic engineering of Arabidopsis for butanetriol production using bacterial genes

Includes bibliographical references (pages 119-120).1,2,4-butanetriol (butanetriol) is a useful precursor for the synthesis of the energetic material butanetriol trinitrate and several pharmaceutical compounds. Bacterial synthesis of butanetriol from xylose or arabinose takes place in a pathway that requires four enzymes. To produce butanetriol in plants by expressing bacterial enzymes, we cloned native bacterial or codon optimized synthetic genes under different promoters into a binary vector and stably transformed Arabidopsis plants. Transgenic lines expressing introduced genes were analyzed for the production of butanetriol using gas chromatography coupled to mass spectrometry (GC-MS). Soil-grown transgenic plants expressing these genes produced up to 20 µg/g of butanetriol. To test if an exogenous supply of pentose sugar precursors would enhance the butanetriol level, transgenic plants were grown in a medium supplemented with either xylose or arabinose and the amount of butanetriol was quantified. Plants expressing synthetic genes in the arabinose pathway showed up to a forty-fold increase in butanetriol levels after arabinose was added to the medium. Transgenic plants expressing either bacterial or synthetic xylose pathways, or the arabinose pathway showed toxicity symptoms when xylose or arabinose was added to the medium, suggesting that a by-product in the pathway or butanetriol affected plant growth. Furthermore, the metabolite profile of plants expressing arabinose and xylose pathways was altered. Our results demonstrate that bacterial pathways that produce butanetriol can be engineered into plants to produce this chemical. This proof-of-concept study for phytoproduction of butanetriol paves the way to further manipulate metabolic pathways in plants to enhance the level of butanetriol production.Published with support from the Colorado State University Libraries Open Access Research and Scholarship Fund

A nematode demographics assay in transgenic roots reveals no significant impacts of the Rhg1 locus LRR-Kinase on soybean cyst nematode resistance

<p>Abstract</p> <p>Background</p> <p>Soybean cyst nematode (<it>Heterodera glycines</it>, SCN) is the most economically damaging pathogen of soybean (<it>Glycine max</it>) in the U.S. The <it>Rhg1 </it>locus is repeatedly observed as the quantitative trait locus with the greatest impact on SCN resistance. The Glyma18g02680.1 gene at the <it>Rhg1 </it>locus that encodes an apparent leucine-rich repeat transmembrane receptor-kinase (LRR-kinase) has been proposed to be the SCN resistance gene, but its function has not been confirmed. Generation of fertile transgenic soybean lines is difficult but methods have been published that test SCN resistance in transgenic roots generated with <it>Agrobacterium rhizogenes</it>.</p> <p>Results</p> <p>We report use of artificial microRNA (amiRNA) for gene silencing in soybean, refinements to transgenic root SCN resistance assays, and functional tests of the <it>Rhg1 </it>locus LRR-kinase gene. A nematode demographics assay monitored infecting nematode populations for their progress through developmental stages two weeks after inoculation, as a metric for SCN resistance. Significant differences were observed between resistant and susceptible control genotypes. Introduction of the <it>Rhg1 </it>locus LRR-kinase gene (genomic promoter/coding region/terminator; Peking/PI 437654-derived SCN-resistant source), into <it>rhg1</it>^-SCN-susceptible plant lines carrying the resistant-source <it>Rhg4</it>^{<it>+ </it>}locus, provided no significant increases in SCN resistance. Use of amiRNA to reduce expression of the LRR-kinase gene from the <it>Rhg1 </it>locus of Fayette (PI 88788 source of <it>Rhg1</it>) also did not detectably alter resistance to SCN. However, silencing of the LRR-kinase gene did have impacts on root development.</p> <p>Conclusion</p> <p>The nematode demographics assay can expedite testing of transgenic roots for SCN resistance. amiRNAs and the pSM103 vector that drives interchangeable amiRNA constructs through a soybean polyubiqutin promoter (Gmubi), with an intron-GFP marker for detection of transgenic roots, may have widespread use in legume biology. Studies in which expression of the <it>Rhg1 </it>locus LRR-kinase gene from different resistance sources was either reduced or complemented did not reveal significant impacts on SCN resistance.</p

Rice Bran Fermented with Saccharomyces boulardii Generates Novel Metabolite Profiles with Bioactivity

Emerging evidence supporting chronic disease fighting properties of rice bran has advanced the development of stabilized rice bran for human use as a functional food and dietary supplement. A global and targeted metabolomic investigation of stabilized rice bran fermented with Saccharomyces boulardii was performed in three rice varieties. Metabolites from S. boulardii-fermented rice bran were detected by gas chromatography−mass spectrometry (GC−MS) and assessed for bioactivity compared to nonfermented rice bran in normal and malignant lymphocytes. Global metabolite profiling revealed significant differences in the metabolome that led to discovery of candidate compounds modulated by S. boulardii fermentation. Fermented rice bran extracts from three rice varieties reduced growth of human B lymphomas compared to each variety’s nonfermented control and revealed that fermentation differentially altered bioactive compounds. These data support that integration of global and targeted metabolite analysis can be utilized for assessing health properties of rice bran phytochemicals that are enhanced by yeast fermentation and that differ across rice varieties

Metabolomic and Functional Genomic Analyses Reveal Varietal Differences in Bioactive Compounds of Cooked Rice

Emerging evidence supports that cooked rice (Oryza sativa L.) contains metabolites with biomedical activities, yet little is known about the genetic diversity that is responsible for metabolite variation and differences in health traits. Metabolites from ten diverse varieties of cooked rice were detected using ultra performance liquid chromatography coupled to mass spectrometry. A total of 3,097 compounds were detected, of which 25% differed among the ten varieties. Multivariate analyses of the metabolite profiles showed that the chemical diversity among the varieties cluster according to their defined subspecies classifications: indica, japonica, and aus. Metabolite-specific genetic diversity in rice was investigated by analyzing a collection of single nucleotide polymorphisms (SNPs) in genes from biochemical pathways of nutritional importance. Two classes of bioactive compounds, phenolics and vitamin E, contained nonsynonymous SNPs and SNPs in the 5′ and 3′ untranslated regions for genes in their biosynthesis pathways. Total phenolics and tocopherol concentrations were determined to examine the effect of the genetic diversity among the ten varieties. Per gram of cooked rice, total phenolics ranged from 113.7 to 392.6 µg (gallic acid equivalents), and total tocopherols ranged between 7.2 and 20.9 µg. The variation in the cooked rice metabolome and quantities of bioactive components supports that the SNP-based genetic diversity influenced nutritional components in rice, and that this approach may guide rice improvement strategies for plant and human health

Genetic basis of barley contributions to beer flavor

[EN] Barley malt is critical for the malting, brewing, and distilling industries, as it is one of the main ingredients of beer and some types of spirits. There is growing evidence that barley genotype - via malt - can impact the flavors of beers and spirits. However, information on the barley genes involved in these flavors is lacking. Therefore, we used quantitative trait locus (QTL) mapping of malt quality traits, beer sensory descriptors and metabolic compounds on a biparental population of doubled haploids derived from the cross of the cultivars Golden Promise and Full Pint. Putative candidate genes for QTLs were identified by alignment with the reference barley genome sequence. There were thirty-seven QTLs across all chromosomes except 4H, with three QTL clusters located on 3H (1 cluster) and 5H (2 clusters: mid-5H and end-5H). Those “hotspots” contained QTLs for multiple phenotypes. Several candidate genes that regulate plant metabolism were identified within the QTLs and included HvAlaAT, HvDep1, HvMKK3, HvGA20ox1 and HvGA20ox2. These genes are involved in seed dormancy and plant height. Alleles at these loci, and perhaps at physically linked loci, can have key downstream effects on malting quality, beer flavor, and abundance of volatile metabolitesSIResearch at Oregon State University was supported by the Agricultural Research Foundation Barley Progress Fund. At Colorado State University, research was supported by CSU’s College of Agricultural Sciences, with partial support from the American Malting Barley Associatio

Comparison of Machine Learning Algorithms for Predictive Modeling of Beef Attributes Using Rapid Evaporative Ionization Mass Spectrometry (REIMS) Data

Ambient mass spectrometry is an analytical approach that enables ionization of molecules under open-air conditions with no sample preparation and very fast sampling times. Rapid evaporative ionization mass spectrometry (REIMS) is a relatively new type of ambient mass spectrometry that has demonstrated applications in both human health and food science. Here, we present an evaluation of REIMS as a tool to generate molecular scale information as an objective measure for the assessment of beef quality attributes. Eight different machine learning algorithms were compared to generate predictive models using REIMS data to classify beef quality attributes based on the United States Department of Agriculture (USDA) quality grade, production background, breed type and muscle tenderness. The results revealed that the optimal machine learning algorithm, as assessed by predictive accuracy, was different depending on the classification problem, suggesting that a “one size fits all” approach to developing predictive models from REIMS data is not appropriate. The highest performing models for each classification achieved prediction accuracies between 81.5–99%, indicating the potential of the approach to complement current methods for classifying quality attributes in beef

Genetic basis of barley contributions to beer flavor

13 Pags.- 1 Fig.- 3 Tabls. © 2022 The Authors. Published by Elsevier Ltd. This is an open access article under the CC BY-NC-ND license.Barley malt is critical for the malting, brewing, and distilling industries, as it is one of the main ingredients of beer and some types of spirits. There is growing evidence that barley genotype - via malt - can impact the flavors of beers and spirits. However, information on the barley genes involved in these flavors is lacking. Therefore, we used quantitative trait locus (QTL) mapping of malt quality traits, beer sensory descriptors and metabolic compounds on a biparental population of doubled haploids derived from the cross of the cultivars Golden Promise and Full Pint. Putative candidate genes for QTLs were identified by alignment with the reference barley genome sequence. There were thirty-seven QTLs across all chromosomes except 4H, with three QTL clusters located on 3H (1 cluster) and 5H (2 clusters: mid-5H and end-5H). Those “hotspots” contained QTLs for multiple phenotypes. Several candidate genes that regulate plant metabolism were identified within the QTLs and included HvAlaAT, HvDep1, HvMKK3, HvGA20ox1 and HvGA20ox2. These genes are involved in seed dormancy and plant height. Alleles at these loci, and perhaps at physically linked loci, can have key downstream effects on malting quality, beer flavor, and abundance of volatile metabolites.Research at Oregon State University was supported by the Agricultural Research Foundation Barley Progress Fund. At Colorado State University, research was supported by CSU's College of Agricultural Sciences, with partial support from the American Malting Barley Association.Peer reviewe

Einkorn genomics sheds light on history of the oldest domesticated wheat

Einkorn (Triticum monococcum) was the first domesticated wheat species, and was central to the birth of agriculture and the Neolithic Revolution in the Fertile Crescent around 10,000 years ago$^{1,2}$. Here we generate and analyse 5.2-Gb genome assemblies for wild and domesticated einkorn, including completely assembled centromeres. Einkorn centromeres are highly dynamic, showing evidence of ancient and recent centromere shifts caused by structural rearrangements. Whole-genome sequencing analysis of a diversity panel uncovered the population structure and evolutionary history of einkorn, revealing complex patterns of hybridizations and introgressions after the dispersal of domesticated einkorn from the Fertile Crescent. We also show that around 1% of the modern bread wheat (Triticum aestivum) A subgenome originates from einkorn. These resources and findings highlight the history of einkorn evolution and provide a basis to accelerate the genomics-assisted improvement of einkorn and bread wheat

Euclid: I. Overview of the Euclid mission

The current standard model of cosmology successfully describes a variety of measurements, but the nature of its main ingredients,dark matter and dark energy, remains unknown. Euclid is a medium-class mission in the Cosmic Vision 2015–2025 programme of theEuropean Space Agency (ESA) that will provide high-resolution optical imaging, as well as near-infrared imaging and spectroscopy,over about 14 000 deg² of extragalactic sky. In addition to accurate weak lensing and clustering measurements that probe structureformation over half of the age of the Universe, its primary probes for cosmology, these exquisite data will enable a wide range ofscience. This paper provides a high-level overview of the mission, summarising the survey characteristics, the various data-processingsteps, and data products. We also highlight the main science objectives and expected performance