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https://www.readbyqxmd.com/read/29161754/the-sorghum-bicolor-reference-genome-improved-assembly-gene-annotations-a-transcriptome-atlas-and-signatures-of-genome-organization
#1
Ryan F McCormick, Sandra K Truong, Avinash Sreedasyam, Jerry Jenkins, Shengqiang Shu, David Sims, Megan Kennedy, Mojgan Amirebrahimi, Brock D Weers, Brian McKinley, Ashley Mattison, Daryl T Morishige, Jane Grimwood, Jeremy Schmutz, John E Mullet
Sorghum bicolor is a drought tolerant C4 grass used for production of grain, forage, sugar, and lignocellulosic biomass and a genetic model for C4 grasses due to its relatively small genome (~800 Mbp), diploid genetics, diverse germplasm, and colinearity with other C4 grass genomes. In this study, deep sequencing, genetic linkage analysis, and transcriptome data were used to produce and annotate a high-quality reference genome sequence. Reference genome sequence order was improved, 29.6 Mbp of additional sequence was incorporated, the number of genes annotated increased 24% to 34,211, average gene length and N50 increased, and error frequency was reduced 10-fold to 1 per 100 kbp...
November 21, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/29158639/mining-and-characterization-of-est-ssr-markers-for-zingiber-officinale-roscoe-with-transferability-to-other-species-of-zingiberaceae
#2
Praveen Awasthi, Ashish Singh, Gulfam Sheikh, Vidushi Mahajan, Ajai Prakash Gupta, Suphla Gupta, Yashbir S Bedi, Sumit G Gandhi
Zingiber officinale is a model spice herb, well known for its medicinal value. It is primarily a vegetatively propagated commercial crop. However, considerable diversity in its morphology, fiber content and chemoprofiles has been reported. The present study explores the utility of EST-derived markers in studying genetic diversity in different accessions of Z. officinale and their cross transferability within the Zingiberaceae family. A total of 38,115 ESTs sequences were assembled to generate 7850 contigs and 10,762 singletons...
October 2017: Physiology and Molecular Biology of Plants: An International Journal of Functional Plant Biology
https://www.readbyqxmd.com/read/29158527/azole-sensitivity-in-leptosphaeria-pathogens-of-oilseed-rape-the-role-of-lanosterol-14%C3%AE-demethylase
#3
Thomas R Sewell, Nichola J Hawkins, Henrik U Stotz, YongJu Huang, Steven L Kelly, Diane E Kelly, Bart Fraaije, Bruce D L Fitt
Lanosterol 14-α demethylase is a key enzyme intermediating the biosynthesis of ergosterol in fungi, and the target of azole fungicides. Studies have suggested that Leptosphaeria maculans and L. biglobosa, the causal agents of phoma stem canker on oilseed rape, differ in their sensitivity to some azoles, which could be driving pathogen frequency change in crops. Here we used CYP51 protein modelling and heterologous expression to determine whether there are interspecific differences at the target-site level...
November 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29157187/quantitative-weight-of-evidence-assessment-of-higher-tier-studies-on-the-toxicity-and-risks-of-neonicotinoid-insecticides-in-honeybees-1-methods
#4
Keith R Solomon, Gladys L Stephenson
A quantitative weight of evidence (QWoE) methodology was developed and used to assess many higher-tier studies on the effects of three neonicotinoid insecticides: clothianidin (CTD), imidacloprid (IMI), and thiamethoxam (TMX) on honeybees. A general problem formulation, a conceptual model for exposures of honeybees, and an analysis plan were developed. A QWoE methodology was used to characterize the quality of the available studies from the literature and unpublished reports of studies conducted by or for the registrants...
November 20, 2017: Journal of Toxicology and Environmental Health. Part B, Critical Reviews
https://www.readbyqxmd.com/read/29156391/optimal-allocation-of-physical-water-resources-integrated-with-virtual-water-trade-in-water-scarce-regions-a-case-study-for-beijing-china
#5
Quanliang Ye, Yi Li, La Zhuo, Wenlong Zhang, Wei Xiong, Chao Wang, Peifang Wang
This study provides an innovative application of virtual water trade in the traditional allocation of physical water resources in water scarce regions. A multi-objective optimization model was developed to optimize the allocation of physical water and virtual water resources to different water users in Beijing, China, considering the trade-offs between economic benefit and environmental impacts of water consumption. Surface water, groundwater, transferred water and reclaimed water constituted the physical resource of water supply side, while virtual water flow associated with the trade of five major crops (barley, corn, rice, soy and wheat) and three livestock products (beef, pork and poultry) in agricultural sector (calculated by the trade quantities of products and their virtual water contents)...
November 14, 2017: Water Research
https://www.readbyqxmd.com/read/29156288/determination-and-validation-of-soil-thresholds-for-cadmium-based-on-food-quality-standard-and-health-risk-assessment
#6
Changfeng Ding, Yibing Ma, Xiaogang Li, Taolin Zhang, Xingxiang Wang
Cadmium (Cd) is an environmental toxicant with high rates of soil-plant transfer. It is essential to establish an accurate soil threshold for the implementation of soil management practices. This study takes root vegetable as an example to derive soil thresholds for Cd based on the food quality standard as well as health risk assessment using species sensitivity distribution (SSD). A soil type-specific bioconcentration factor (BCF, ratio of Cd concentration in plant to that in soil) generated from soil with a proper Cd concentration gradient was calculated and applied in the derivation of soil thresholds instead of a generic BCF value to minimize the uncertainty...
November 17, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/29156275/agricultural-susceptibility-to-monsoon-variability-a-district-level-analysis-of-maharashtra-india
#7
Deepika Swami, Prashant Dave, Devanathan Parthasarathy
Indian Summer Monsoon (ISM) variability has always been a feature affecting Indian agriculture. However, nature of this variability is varying in the backdrop of climate change, and as a consequence, agriculture is getting significantly affected and subsequently threatening food security. To address the climate variability, most of the studies conducted so far have focused on a coarse scale such as Central India or Western Ghats. However, finer scale analysis for identification and quantification of the link between agriculture vulnerability and climate variables has not yet been attempted in a comprehensive manner...
November 17, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/29156057/prgdb-3-0-a-comprehensive-platform-for-prediction-and-analysis-of-plant-disease-resistance-genes
#8
Cristina M O Cruz, Andreu Paytuvi-Gallart, Antimo Di Donato, Vicky Sundesha, Giuseppe Andolfo, Riccardo Aiese Cigliano, Walter Sanseverino, Maria R Ercolano
The Plant Resistance Genes database (PRGdb; http://prgdb.org) has been redesigned with a new user interface, new sections, new tools and new data for genetic improvement, allowing easy access not only to the plant science research community but also to breeders who want to improve plant disease resistance. The home page offers an overview of easy-to-read search boxes that streamline data queries and directly show plant species for which data from candidate or cloned genes have been collected. Bulk data files and curated resistance gene annotations are made available for each plant species hosted...
November 16, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29153551/remote-sensing-based-deforestation-analysis-in-mahanadi-and-brahmaputra-river-basin-in-india-since-1985
#9
M D Behera, P Tripathi, P Das, S K Srivastava, P S Roy, C Joshi, P R Behera, J Deka, P Kumar, M L Khan, O P Tripathi, T Dash, Y V N Krishnamurthy
Land use and land cover (LULC) change has been recognized as a key driver of global climate change by influencing land surface processes. Being in constant change, river basins are always subjected to LULC changes, especially decline in forest cover to give way for agricultural expansion, urbanization, industrialization etc. We used on-screen digital interpretation technique to derive LULC maps from Landsat images at three decadal intervals i.e., 1985, 1995 and 2005 of two major river basins of India. Rain-fed, Mahanadi river basin (MRB) attributed to 55% agricultural area wherein glacier-fed, Brahmaputra river basin (BRB) had only 16% area under agricultural land...
November 15, 2017: Journal of Environmental Management
https://www.readbyqxmd.com/read/29153528/modeling-greenhouse-gas-emissions-from-dairy-farms
#10
C Alan Rotz
Dairy farms have been identified as an important source of greenhouse gas emissions. Within the farm, important emissions include enteric CH4 from the animals, CH4 and N2O from manure in housing facilities during long-term storage and during field application, and N2O from nitrification and denitrification processes in the soil used to produce feed crops and pasture. Models using a wide range in level of detail have been developed to represent or predict these emissions. They include constant emission factors, variable process-related emission factors, empirical or statistical models, mechanistic process simulations, and life cycle assessment...
November 15, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/29149288/overexpression-of-seipin1-increases-oil-in-hydroxy-fatty-acid-accumulating-seeds
#11
Daniel Lunn, James G Wallis, John Browse
While plant oils are an important source of food, plants also produce oils containing specialized fatty acids with chemical and physical properties valued in industry. Ricinoleic acid, a hydroxy-fatty acid (HFA) produced in the seed of castor (Ricinus communis), is of particular value with a wide range of applications. Since castor cultivation is currently successful only in tropic climates, and because castor seed contain the toxin ricin, there are ongoing efforts to develop a temperate crop capable of HFA biosynthesis...
November 15, 2017: Plant & Cell Physiology
https://www.readbyqxmd.com/read/29149280/whole-genome-re-sequencing-of-two-italian-tomato-landraces-reveals-sequence-variations-in-genes-associated-with-stress-tolerance-fruit-quality-and-long-shelf-life-traits
#12
Valentina Tranchida-Lombardo, Riccardo Aiese Cigliano, Irantzu Anzar, Simone Landi, Samuela Palombieri, Chiara Colantuono, Hamed Bostan, Pasquale Termolino, Riccardo Aversano, Giorgia Batelli, Maria Cammareri, Domenico Carputo, Maria Luisa Chiusano, Clara Conicella, Federica Consiglio, Nunzio D'Agostino, Monica De Palma, Antonio Di Matteo, Silvana Grandillo, Walter Sanseverino, Marina Tucci, Stefania Grillo
Tomato is a high value crop and the primary model for fleshy fruit development and ripening. Breeding priorities include increased fruit quality, shelf life and tolerance to stresses. To contribute towards this goal, we re-sequenced the genomes of Corbarino (COR) and Lucariello (LUC) landraces, which both possess the traits of plant adaptation to water deficit, prolonged fruit shelf-life and good fruit quality. Through the newly developed pipeline Reconstructor, we generated the genome sequences of COR and LUC using datasets of 65...
November 14, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/29148964/twenty-five-years-of-the-binary-power-law-for-characterizing-heterogeneity-of-disease-incidence
#13
Laurence V Madden, Gareth Hughes, Wanderson Bucker Moraes, Xiangming Xu, William W Turechek
Spatial pattern, an important epidemiological property of plant diseases, can be quantified at different scales using a range of methods. The spatial heterogeneity (or overdispersion) of disease incidence among sampling units is an especially important measure of small-scale pattern. As an alternative to Taylor's power law for the heterogeneity of counts with no upper bound, the binary power law (BPL) was proposed in 1992 as a model to represent the heterogeneity of disease incidence (number of plant units diseased out of n observed in each sampling unit, or the proportion diseased in each sampling unit)...
November 17, 2017: Phytopathology
https://www.readbyqxmd.com/read/29145463/the-chicken-or-the-egg-exploring-bi-directional-associations-between-newcastle-disease-vaccination-and-village-chicken-flock-size-in-rural-tanzania
#14
Julia de Bruyn, Peter C Thomson, Brigitte Bagnol, Wende Maulaga, Elpidius Rukambile, Robyn G Alders
Newcastle disease (ND) is a viral disease of poultry with global importance, responsible for the loss of a potential source of household nutrition and economic livelihood in many low-income food-deficit countries. Periodic outbreaks of this endemic disease result in high mortality amongst free-ranging chicken flocks and may serve as a disincentive for rural households to invest time or resources in poultry-keeping. Sustainable ND control can be achieved through vaccination using a thermotolerant vaccine administered via eyedrop by trained "community vaccinators"...
2017: PloS One
https://www.readbyqxmd.com/read/29144438/bioactive-components-in-moringa-oleifera-leaves-protect-against-chronic-disease
#15
REVIEW
Marcela Vergara-Jimenez, Manal Mused Almatrafi, Maria Luz Fernandez
Moringa Oleifera (MO), a plant from the family Moringacea is a major crop in Asia and Africa. MO has been studied for its health properties, attributed to the numerous bioactive components, including vitamins, phenolic acids, flavonoids, isothiocyanates, tannins and saponins, which are present in significant amounts in various components of the plant. Moringa Oleifera leaves are the most widely studied and they have shown to be beneficial in several chronic conditions, including hypercholesterolemia, high blood pressure, diabetes, insulin resistance, non-alcoholic liver disease, cancer and overall inflammation...
November 16, 2017: Antioxidants (Basel, Switzerland)
https://www.readbyqxmd.com/read/29142024/a-model-of-leaf-coordination-to-scale-up-leaf-expansion-from-the-organ-to-the-canopy
#16
Pierre Martre, Anaelle Dambreville
Process-based crop growth models are popular tools to analyze and understand the impact of crop management, genotype by environment interactions, or climate change. The ability to predict leaf area development is critical to predict crop growth, particularly under conditions of limited resources. Here, we aimed at deciphering growth coordination rules between wheat plant organs, i.e. between leaves within a stem, between laminae and sheaths, and between the mainstem and axillary tillers, to model the dynamics of canopy development...
November 15, 2017: Plant Physiology
https://www.readbyqxmd.com/read/29139077/spatiotemporal-patterns-and-source-attribution-of-nitrogen-pollution-in-a-typical-headwater-agricultural-watershed-in-southeastern-china
#17
Wenjun Chen, Bin He, Daniel Nover, Weili Duan, Chuan Luo, Kaiyan Zhao, Wen Chen
Excessive nitrogen (N) discharge from agriculture causes widespread problems in aquatic ecosystems. Knowledge of spatiotemporal patterns and source attribution of N pollution is critical for nutrient management programs but is poorly studied in headwaters with various small water bodies and mini-point pollution sources. Taking a typical small watershed in the low mountains of Southeastern China as an example, N pollution and source attribution were studied for a multipond system around a village using the Hydrological Simulation Program-Fortran (HSPF) model...
November 14, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/29138387/strategies-for-feeding-the-world-more-sustainably-with-organic-agriculture
#18
Adrian Muller, Christian Schader, Nadia El-Hage Scialabba, Judith Brüggemann, Anne Isensee, Karl-Heinz Erb, Pete Smith, Peter Klocke, Florian Leiber, Matthias Stolze, Urs Niggli
Organic agriculture is proposed as a promising approach to achieving sustainable food systems, but its feasibility is also contested. We use a food systems model that addresses agronomic characteristics of organic agriculture to analyze the role that organic agriculture could play in sustainable food systems. Here we show that a 100% conversion to organic agriculture needs more land than conventional agriculture but reduces N-surplus and pesticide use. However, in combination with reductions of food wastage and food-competing feed from arable land, with correspondingly reduced production and consumption of animal products, land use under organic agriculture remains below the reference scenario...
November 14, 2017: Nature Communications
https://www.readbyqxmd.com/read/29137937/design-synthesis-and-evaluation-of-3-arylidene-azetidin-2-ones-as-potential-antifungal-agents-against-alternaria-solani-sorauer
#19
Wang Delong, Wu Yongling, Wang Lanying, Feng Juntao, Zhang Xing
A new concise and facile method was explored to synthesize a collection of new 3-arylidene azetidin-2-ones, which could be regarded as the derivatives of the hybrid scaffold of bioactive natural cinnamamide and heterocycle azetidi-2-one. The structures of the synthesized compounds were characterized by (1)H, (13)C NMR, and MS; and their antifungal activity were evaluated against Alternaria solani Sorauer. These antifungal data were subjected to a quantitative structure-activity relationship (QSAR) analysis using Codessa software on the basis of the results from B3LYP/6-31G(d,p) quantum calculations...
November 4, 2017: Bioorganic & Medicinal Chemistry
https://www.readbyqxmd.com/read/29136323/increasing-canopy-photosynthesis-in-rice-can-be-achieved-without-a-large-increase-in-water-use-a-model-based-on-free-air-co2-enrichment
#20
Hiroki Ikawa, Charles P Chen, Martin Sikma, Mayumi Yoshimoto, Hidemitsu Sakai, Takeshi Tokida, Yasuhiro Usui, Hirofumi Nakamura, Keisuke Ono, Atsushi Maruyama, Tsutomu Watanabe, Tsuneo Kuwagata, Toshihiro Hasegawa
Achieving higher canopy photosynthesis rates is one of the keys to increasing future crop production; however, this typically requires additional water inputs because of increased water loss through the stomata. Lowland rice canopies presently consume a large amount of water, and any further increase in water usage may significantly impact local water resources. This situation is further complicated by changing environmental conditions such as rising atmospheric CO2 concentration ([CO2 ]). Here we modeled and compared evapotranspiration of fully developed rice canopies of a high-yielding rice cultivar (Oryza sativa L...
November 14, 2017: Global Change Biology
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