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https://www.readbyqxmd.com/read/28108552/predicted-residual-error-sum-of-squares-of-mixed-models-an-application-to-genomic-prediction
#1
Shizhong Xu
Genomic prediction is a statistical method to predict phenotypes of polygenic traits using high throughput genomic data. Most diseases and behaviors in human and animals are polygenic traits. The majority of agronomic traits in crops are also polygenic. Accurate prediction of these traits can help medical professionals diagnose acute diseases and breeders to increase food products, and therefore, significantly contribute to human health and global food security. The best linear unbiased prediction (BLUP) is an important tool to analyze high throughput genomic data for prediction...
January 20, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28102548/the-shade-avoidance-syndrome-multiple-signals-and-ecological-consequences
#2
REVIEW
Carlos L Ballaré, Ronald Pierik
Plants use photoreceptor proteins to detect the proximity of other plants and to activate adaptive responses. Of these photoreceptors, phytochrome B (phyB), which is sensitive to changes in the red (R) to far-red (FR) ratio of sunlight, is the one that has been studied in greatest detail. The molecular connections between the proximity signal (low R:FR) and a model physiological response (increased elongation growth) have now been mapped in considerable detail in Arabidopsis seedlings. We briefly review our current understanding of these connections, and discuss recent progress in establishing the roles of other photoreceptors in regulating growth-related pathways in response to competition cues...
January 19, 2017: Plant, Cell & Environment
https://www.readbyqxmd.com/read/28102202/consistent-negative-response-of-us-crops-to-high-temperatures-in-observations-and-crop-models
#3
Bernhard Schauberger, Sotirios Archontoulis, Almut Arneth, Juraj Balkovic, Philippe Ciais, Delphine Deryng, Joshua Elliott, Christian Folberth, Nikolay Khabarov, Christoph Müller, Thomas A M Pugh, Susanne Rolinski, Sibyll Schaphoff, Erwin Schmid, Xuhui Wang, Wolfram Schlenker, Katja Frieler
High temperatures are detrimental to crop yields and could lead to global warming-driven reductions in agricultural productivity. To assess future threats, the majority of studies used process-based crop models, but their ability to represent effects of high temperature has been questioned. Here we show that an ensemble of nine crop models reproduces the observed average temperature responses of US maize, soybean and wheat yields. Each day >30 °C diminishes maize and soybean yields by up to 6% under rainfed conditions...
January 19, 2017: Nature Communications
https://www.readbyqxmd.com/read/28098774/learning-to-diagnose-cirrhosis-with-liver-capsule-guided-ultrasound-image-classification
#4
Xiang Liu, Jia Lin Song, Shuo Hong Wang, Jing Wen Zhao, Yan Qiu Chen
This paper proposes a computer-aided cirrhosis diagnosis system to diagnose cirrhosis based on ultrasound images. We first propose a method to extract a liver capsule on an ultrasound image, then, based on the extracted liver capsule, we fine-tune a deep convolutional neural network (CNN) model to extract features from the image patches cropped around the liver capsules. Finally, a trained support vector machine (SVM) classifier is applied to classify the sample into normal or abnormal cases. Experimental results show that the proposed method can effectively extract the liver capsules and accurately classify the ultrasound images...
January 13, 2017: Sensors
https://www.readbyqxmd.com/read/28096351/uncovering-hidden-variation-in-polyploid-wheat
#5
Ksenia V Krasileva, Hans A Vasquez-Gross, Tyson Howell, Paul Bailey, Francine Paraiso, Leah Clissold, James Simmonds, Ricardo H Ramirez-Gonzalez, Xiaodong Wang, Philippa Borrill, Christine Fosker, Sarah Ayling, Andrew L Phillips, Cristobal Uauy, Jorge Dubcovsky
Comprehensive reverse genetic resources, which have been key to understanding gene function in diploid model organisms, are missing in many polyploid crops. Young polyploid species such as wheat, which was domesticated less than 10,000 y ago, have high levels of sequence identity among subgenomes that mask the effects of recessive alleles. Such redundancy reduces the probability of selection of favorable mutations during natural or human selection, but also allows wheat to tolerate high densities of induced mutations...
January 17, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28095427/mobile-phones-and-mental-well-being-initial-evidence-suggesting-the-importance-of-staying-connected-to-family-in-rural-remote-communities-in-uganda
#6
Amber L Pearson, Elizabeth Mack, Judith Namanya
Due to the ubiquity of mobile phones around the globe, studies are beginning to analyze their influence on health. Prior work from developed countries highlights negative mental health outcomes related to overuse of mobile phones. However, there is little work on mental health impacts of mobile phone use or ownership in developing countries. This is an important gap to address because there are likely variations in mental health impacts of mobile phones between developing and developed countries, due to cultural nuances to phone use and distinct variations in financial models for obtaining mobile phone access in developing countries...
2017: PloS One
https://www.readbyqxmd.com/read/28095206/achieving-durable-resistance-against-plant-diseases-scenario-analysis-with-a-national-scale-spatially-explicit-model-for-a-wind-dispersed-plant-disease
#7
Marjolein Elisabeth Lof, Claude de Vallavieille-Pope, Wopke van der Werf
Genetic resistance in crops is a cornerstone of disease management in agriculture. Such genetic resistance is often rapidly broken due to selection for virulence in the pathogen population. Here we ask whether there are strategies that can prolong the useful life of plant resistance genes. In a modelling study, we compare four deployment strategies: gene pyramiding, sequential use, simultaneous use, and a mixed strategy. We developed a spatially explicit model for France and parameterized it for the fungal pathogen Puccinia striiformis f...
January 17, 2017: Phytopathology
https://www.readbyqxmd.com/read/28094805/the-genome-sequence-of-barbarea-vulgaris-facilitates-the-study-of-ecological-biochemistry
#8
Stephen L Byrne, Pernille Østerbye Erthmann, Niels Agerbirk, Søren Bak, Thure Pavlo Hauser, Istvan Nagy, Cristiana Paina, Torben Asp
The genus Barbarea has emerged as a model for evolution and ecology of plant defense compounds, due to its unusual glucosinolate profile and production of saponins, unique to the Brassicaceae. One species, B. vulgaris, includes two 'types', G-type and P-type that differ in trichome density, and their glucosinolate and saponin profiles. A key difference is the stereochemistry of hydroxylation of their common phenethylglucosinolate backbone, leading to epimeric glucobarbarins. Here we report a draft genome sequence of the G-type, and re-sequencing of the P-type for comparison...
January 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28093983/an-approach-towards-structure-based-antimicrobial-peptide-design-for-use-in-development-of-transgenic-plants-a-strategy-for-plant-disease-management
#9
Humaira Ilyas, Aritreyee Datta, Anirban Bhunia
Antimicrobial peptides (AMPs), also known as host defense peptides (HDPs), are ubiquitous and vital components of innate defense response that present themselves as potential candidates for drug design, aimed to control plant and animal diseases. Though their application for plant disease management has long been studied with natural AMPs, cytotoxicity and stability related shortcomings for the development of transgenic plants limits their usage. Newer technologies like molecular modelling, NMR spectroscopy and combinatorial chemistry allow screening for potent candidates and provide new avenues for the generation of rationally designed synthetic AMPs with multiple biological functions...
January 16, 2017: Current Medicinal Chemistry
https://www.readbyqxmd.com/read/28087768/the-rice-paradox-multiple-origins-but-single-domestication-in-asian-rice
#10
Jae Young Choi, Adrian E Platts, Dorian Q Fuller, Yue-Ie Hsing, Rod A Wing, Michael D Purugganan
The origin of domesticated Asian rice (Oryza sativa) has been a contentious topic, with conflicting evidence for either single or multiple domestication of this key crop species. We examined the evolutionary history of domesticated rice by analyzing de novo assembled genomes from domesticated rice and its wild progenitors. Our results indicate multiple origins, where each domesticated rice subpopulation (japonica, indica, and aus) arose separately from progenitor O. rufipogon and/or O. nivara Coalescence-based modeling of demographic parameters estimate that the first domesticated rice population to split off from O...
January 12, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28087663/evolution-and-structural-diversification-of-nictaba-like-lectin-genes-in-food-crops-with-a-focus-on-soybean-glycine-max
#11
Sofie Van Holle, Pierre Rougé, Els J M Van Damme
BACKGROUND AND AIMS: The Nictaba family groups all proteins that show homology to Nictaba, the tobacco lectin. So far, Nictaba and an Arabidopsis thaliana homologue have been shown to be implicated in the plant stress response. The availability of more than 50 sequenced plant genomes provided the opportunity for a genome-wide identification of Nictaba-like genes in 15 species, representing members of the Fabaceae, Poaceae, Solanaceae, Musaceae, Arecaceae, Malvaceae and Rubiaceae. Additionally, phylogenetic relationships between the different species were explored...
January 12, 2017: Annals of Botany
https://www.readbyqxmd.com/read/28080990/food-system-consequences-of-a-fungal-disease-epidemic-in-a-major-crop
#12
H Charles J Godfray, Daniel Mason-D'Croz, Sherman Robinson
Fungal diseases are major threats to the most important crops upon which humanity depends. Were there to be a major epidemic that severely reduced yields, its effects would spread throughout the globalized food system. To explore these ramifications, we use a partial equilibrium economic model of the global food system (IMPACT) to study a hypothetical severe but short-lived epidemic that reduces rice yields in the countries affected by 80%. We modelled a succession of epidemic scenarios of increasing severity, starting with the disease in a single country in southeast Asia and ending with the pathogen present in most of eastern Asia...
December 5, 2016: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/28078413/establishment-of-a-sandwich-enzyme-linked-immunosorbent-assay-for-specific-detection-of-bacillus-thuringiensis-bt-cry1ab-toxin-utilizing-a-monoclonal-antibody-produced-with-a-novel-hapten-designed-with-molecular-model
#13
Sa Dong, Xiao Zhang, Yuan Liu, Cunzheng Zhang, Yajing Xie, Jianfeng Zhong, Chongxin Xu, Xianjin Liu
Cry1Ab toxin is commonly expressed in genetically modified crops in order to control chewing pests. At present, the detection method with enzyme-linked immunosorbent assay (ELISA) based on monoclonal antibody cannot specifically detect Cry1Ab toxin for Cry1Ab's amino acid sequence and spatial structure are highly similar to Cry1Ac toxin. In this study, based on molecular design, a novel hapten polypeptide was synthesized and conjugated to keyhole limpet hemocyanin (KLH). Then, through animal immunization with this antigen, a monoclonal antibody named 2C12, showing high affinity to Cry1Ab and having no cross reaction with Cry1Ac, was produced...
January 11, 2017: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/28077090/gbs-based-single-dosage-markers-for-linkage-and-qtl-mapping-allow-gene-mining-for-yield-related-traits-in-sugarcane
#14
Thiago Willian Almeida Balsalobre, Guilherme da Silva Pereira, Gabriel Rodrigues Alves Margarido, Rodrigo Gazaffi, Fernanda Zatti Barreto, Carina Oliveira Anoni, Cláudio Benício Cardoso-Silva, Estela Araújo Costa, Melina Cristina Mancini, Hermann Paulo Hoffmann, Anete Pereira de Souza, Antonio Augusto Franco Garcia, Monalisa Sampaio Carneiro
BACKGROUND: Sugarcane (Saccharum spp.) is predominantly an autopolyploid plant with a variable ploidy level, frequent aneuploidy and a large genome that hampers investigation of its organization. Genetic architecture studies are important for identifying genomic regions associated with traits of interest. However, due to the genetic complexity of sugarcane, the practical applications of genomic tools have been notably delayed in this crop, in contrast to other crops that have already advanced to marker-assisted selection (MAS) and genomic selection...
January 11, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28073057/neonicotinoids-transference-from-the-field-to-the-hive-by-honey-bees-towards-a-pesticide-residues-biomonitor
#15
Niell Silvina, Jesús Florencia, Pérez Nicolás, Pérez Cecilia, Pareja Lucía, Silvana Abbate, Carrasco-Letelier Leonidas, Díaz Sebastián, Mendoza Yamandú, Cesio Verónica, Heinzen Horacio
The beehive as a quantitative monitor of pesticide residues applied over a soybean crop was studied through a semi field experiment of controlled exposure of honey bees to pesticides in macro tunnels. The distribution within exposed beehives of pesticides commonly used in soybean plantation, was assessed. Residue levels of insecticides in soybean leaves, honey bees, wax, honey and pollen were analyzed. The transference from pesticides present in the environment into the beehive was evidenced. The obtained results allow relating pesticide concentrations present in the environment with traces found in foraging bees...
January 7, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28072876/genetic-nature-of-elemental-contents-in-wheat-grains-and-its-genomic-prediction-toward-the-effective-use-of-wheat-landraces-from-afghanistan
#16
Alagu Manickavelu, Tomohiro Hattori, Shuhei Yamaoka, Kazusa Yoshimura, Youichi Kondou, Akio Onogi, Minami Matsui, Hiroyoshi Iwata, Tomohiro Ban
Profiling elemental contents in wheat grains and clarifying the underlying genetic systems are important for the breeding of biofortified crops. Our objective was to evaluate the genetic potential of 269 Afghan wheat landraces for increasing elemental contents in wheat cultivars. The contents of three major (Mg, K, and P) and three minor (Mn, Fe, and Zn) elements in wheat grains were measured by energy dispersive X-ray fluorescence spectrometry. Large variations in elemental contents were observed among landraces...
2017: PloS One
https://www.readbyqxmd.com/read/28070661/voltage-gated-sodium-channels-as-targets-for-pyrethroid-insecticides
#17
Linda M Field, T G Emyr Davies, Andrias O O'Reilly, Martin S Williamson, B A Wallace
The pyrethroid insecticides are a very successful group of compounds that have been used extensively for the control of arthropod pests of agricultural crops and vectors of animal and human disease. Unfortunately, this has led to the development of resistance to the compounds in many species. The mode of action of pyrethroids is known to be via interactions with the voltage-gated sodium channel. Understanding how binding to the channel is affected by amino acid substitutions that give rise to resistance has helped to elucidate the mode of action of the compounds and the molecular basis of their selectivity for insects vs mammals and between insects and other arthropods...
January 9, 2017: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/28069301/future-water-availability-in-the-largest-freshwater-mediterranean-lake-is-at-great-risk-as-evidenced-from-simulations-with-the-swat-model
#18
Tuba Bucak, Dennis Trolle, Hans Estrup Andersen, Hans Thodsen, Şeyda Erdoğan, Eti E Levi, Nur Filiz, Erik Jeppesen, Meryem Beklioğlu
Inter- and intra-annual water level fluctuations and changes in water flow regime are intrinsic characteristics of Mediterranean lakes. Additionally, considering climate change projections for the water-limited Mediterranean region, increased air temperatures and decreased precipitation are anticipated, leading to dramatic declines in lake water levels as well as severe water scarcity problems. The study site, Lake Beyşehir, the largest freshwater lake in the Mediterranean basin, is - like other Mediterranean lakes - threatened by climatic changes and over-abstraction of water for irrigated crop farming...
January 6, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28067005/phosphorus-in-agricultural-soils-drivers-of-its-distribution-at-the-global-scale
#19
Bruno Ringeval, Laurent Augusto, Hervé Monod, Dirk van Apeldoorn, Lex Bouwman, Xiaojuan Yang, David L Achat, Louise P Chini, Kristof Van Oost, Bertrand Guenet, Rong Wang, Bertrand Decharme, Thomas Nesme, Sylvain Pellerin
Phosphorus (P) availability in soils limits crop yields in many regions of the world, while excess of soil P triggers aquatic eutrophication in other regions. Numerous processes drive the global spatial distribution of P in agricultural soils, but their relative roles remain unclear. Here, we combined several global datasets describing these drivers with a soil P dynamics model to simulate the distribution of P in agricultural soils and to assess the contributions of the different drivers at the global scale...
January 9, 2017: Global Change Biology
https://www.readbyqxmd.com/read/28064178/linking-photosynthesis-and-leaf-n-allocation-under-future-elevated-co2-and-climate-warming-in-eucalyptus-globulus
#20
Robert E Sharwood, Kristine Y Crous, Spencer M Whitney, David S Ellsworth, Oula Ghannoum
Leaf-level photosynthetic processes and their environmental dependencies are critical for estimating CO2 uptake from the atmosphere. These estimates use biochemical-based models of photosynthesis that require accurate Rubisco kinetics. We investigated the effects of canopy position, elevated atmospheric CO2 [eC; ambient CO2 (aC)+240 ppm] and elevated air temperature (eT; ambient temperature (aT)+3 °C) on Rubisco content and activity together with the relationship between leaf N and V cmax (maximal Rubisco carboxylation rate) of 7 m tall, soil-grown Eucalyptus globulus trees...
January 7, 2017: Journal of Experimental Botany
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