Showing papers by "Agriculture and Agri-Food Canada published in 2014"
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University of Évry Val d'Essonne1, Crops Research Institute2, Agriculture and Agri-Food Canada3, Fujian Agriculture and Forestry University4, J. Craig Venter Institute5, Plant Genome Mapping Laboratory6, University of Giessen7, French Alternative Energies and Atomic Energy Commission8, Institut national de la recherche agronomique9, National Research Council10, Australian Centre for Plant Functional Genomics11, University of Cologne12, Purdue University13, University of California, Berkeley14, University of British Columbia15, Fondation Jean Dausset Centre d'Etude du Polymorphisme Humain16, Huazhong Agricultural University17, Hunan Agricultural University18, Chungnam National University19, University of Arizona20, University of York21, University of Missouri22, Southern Cross University23, University of Western Australia24, Centre national de la recherche scientifique25
TL;DR: The polyploid genome of Brassica napus, which originated from a recent combination of two distinct genomes approximately 7500 years ago and gave rise to the crops of rape oilseed, is sequenced.
Abstract: Oilseed rape (Brassica napus L.) was formed ~7500 years ago by hybridization between B. rapa and B. oleracea, followed by chromosome doubling, a process known as allopolyploidy. Together with more ancient polyploidizations, this conferred an aggregate 72× genome multiplication since the origin of angiosperms and high gene content. We examined the B. napus genome and the consequences of its recent duplication. The constituent An and Cn subgenomes are engaged in subtle structural, functional, and epigenetic cross-talk, with abundant homeologous exchanges. Incipient gene loss and expression divergence have begun. Selection in B. napus oilseed types has accelerated the loss of glucosinolate genes, while preserving expansion of oil biosynthesis genes. These processes provide insights into allopolyploid evolution and its relationship with crop domestication and improvement.
1,743 citations
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Crops Research Institute1, Australian Centre for Plant Functional Genomics2, Agriculture and Agri-Food Canada3, Purdue University4, Plant Genome Mapping Laboratory5, Southwest University6, University of York7, Seoul National University8, Southern Cross University9, University of Missouri10, Centre national de la recherche scientifique11, Huazhong Agricultural University12, Hunan Agricultural University13, University of Queensland14, National Research Council15, Central University, India16, Sahmyook University17, King Abdulaziz University18
TL;DR: A draft genome sequence of Brassica oleracea is described, comparing it with that of its sister species B. rapa to reveal numerous chromosome rearrangements and asymmetrical gene loss in duplicated genomic blocks.
Abstract: Polyploidization has provided much genetic variation for plant adaptive evolution, but the mechanisms by which the molecular evolution of polyploid genomes establishes genetic architecture underlying species differentiation are unclear Brassica is an ideal model to increase knowledge of polyploid evolution Here we describe a draft genome sequence of Brassica oleracea, comparing it with that of its sister species B rapa to reveal numerous chromosome rearrangements and asymmetrical gene loss in duplicated genomic blocks, asymmetrical amplification of transposable elements, differential gene co-retention for specific pathways and variation in gene expression, including alternative splicing, among a large number of paralogous and orthologous genes Genes related to the production of anticancer phytochemicals and morphological variations illustrate consequences of genome duplication and gene divergence, imparting biochemical and morphological variation to B oleracea This study provides insights into Brassica genome evolution and will underpin research into the many important crops in this genus
884 citations
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TL;DR: New combinations for accepted species presently lacking an Aspergillus name are introduced and an updated accepted species list for the genus is provided, now containing 339 species.
793 citations
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TL;DR: The nomenclatural list is updated and a standard working method for species descriptions and identifications to be adopted by laboratories working on Penicillium is recommended, thereby supplying a verified set of sequences for each species of the genus.
599 citations
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Western Kentucky University1, Cooperative Institute for Research in Environmental Sciences2, University of Nebraska–Lincoln3, Purdue University4, University of Queensland5, Pennsylvania State University6, Cooperative Institute for Research in the Atmosphere7, Agriculture and Agri-Food Canada8, John Deere9, Oak Ridge National Laboratory10, University of Alabama in Huntsville11, University of Delaware12, University of Georgia13, Chinese Academy of Sciences14, University of Colorado Boulder15, Texas A&M University16, Tuskegee University17
TL;DR: In this article, the authors provide an overview and synthesis of some of the most notable types of land cover changes and their impacts on climate, including agriculture, deforestation and afforestation, desertification, and urbanization.
Abstract: Land cover changes (LCCs) play an important role in the climate system. Research over recent decades highlights the impacts of these changes on atmospheric temperature, humidity, cloud cover, circulation, and precipitation. These impacts range from the local- and regional-scale to sub-continental and global-scale. It has been found that the impacts of regional-scale LCC in one area may also be manifested in other parts of the world as a climatic teleconnection. In light of these findings, this article provides an overview and synthesis of some of the most notable types of LCC and their impacts on climate. These LCC types include agriculture, deforestation and afforestation, desertification, and urbanization. In addition, this article provides a discussion on challenges to, and future research directions in, assessing the climatic impacts of LCC.
560 citations
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TL;DR: Genotyping-by-sequencing (GBS) has been developed and applied in sequencing multiplexed samples that combine molecular marker discovery and genotyping and has been successfully used in implementing genome-wide association study (GWAS), genomic diversity study, genetic linkage analysis, molecular markers discovery and genomic selection under a large scale of plant breeding programs.
Abstract: Marker-assisted selection (MAS) refers to the use of molecular markers to assist phenotypic selections in crop improvement. Several types of molecular markers, such as single nucleotide polymorphism (SNP), have been identified and effectively used in plant breeding. The application of next-generation sequencing (NGS) technologies has led to remarkable advances in whole genome sequencing, which provides ultra-throughput sequences to revolutionize plant genotyping and breeding. To further broaden NGS usages to large crop genomes such as maize and wheat, genotyping-by-sequencing (GBS) has been developed and applied in sequencing multiplexed samples that combine molecular marker discovery and genotyping. GBS is a novel application of NGS protocols for discovering and genotyping SNPs in crop genomes and populations. The GBS approach includes the digestion of genomic DNA with restriction enzymes followed by the ligation of barcode adapter, PCR amplification and sequencing of the amplified DNA pool on a single lane of flow cells. Bioinformatic pipelines are needed to analyze and interpret GBS datasets. As an ultimate MAS tool and a cost-effective technique, GBS has been successfully used in implementing genome-wide association study (GWAS), genomic diversity study, genetic linkage analysis, molecular marker discovery and genomic selection under a large scale of plant breeding programs.
500 citations
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Lehigh University1, University of Hawaii at Manoa2, Bowdoin College3, University of Eastern Finland4, University of Exeter5, Eton College6, Stockholm University7, University of Southampton8, Queen Mary University of London9, University of Wisconsin–La Crosse10, University of Gloucestershire11, University of Toulouse12, Adam Mickiewicz University in Poznań13, University of Toronto14, Université du Québec à Montréal15, Lund University16, University of California, Los Angeles17, United States Geological Survey18, University of Copenhagen19, University of Helsinki20, University of Nottingham21, Laval University22, Geological Survey of Finland23, University of Aberdeen24, McGill University25, Columbia University26, Université de Montréal27, Champlain College28, Agriculture and Agri-Food Canada29, University of Guelph30, University of Amsterdam31, Southern Illinois University Carbondale32, Chinese Academy of Sciences33
TL;DR: In this paper, the authors present results from the most comprehensive compilation of Holocene peat soil properties with associated carbon and nitrogen accumulation rates for northern peatlands, which consists of 268 peat cores from 215 sites located north of 45°N.
Abstract: Here, we present results from the most comprehensive compilation of Holocene peat soil properties with associated carbon and nitrogen accumulation rates for northern peatlands. Our database consists of 268 peat cores from 215 sites located north of 45°N. It encompasses regions within which peat carbon data have only recently become available, such as the West Siberia Lowlands, the Hudson Bay Lowlands, Kamchatka in Far East Russia, and the Tibetan Plateau. For all northern peatlands, carbon content in organic matter was estimated at 42 ± 3% (standard deviation) for Sphagnum peat, 51 ± 2% for non-Sphagnum peat, and at 49 ± 2% overall. Dry bulk density averaged 0.12 ± 0.07 g/cm3, organic matter bulk density averaged 0.11 ± 0.05 g/cm3, and total carbon content in peat averaged 47 ± 6%. In general, large differences were found between Sphagnum and non-Sphagnum peat types in terms of peat properties. Time-weighted peat carbon accumulation rates averaged 23 ± 2 (standard error of mean) g C/m2/yr during the Holocene on the basis of 151 peat cores from 127 sites, with the highest rates of carbon accumulation (25-28 g C/m2/yr) recorded during the early Holocene when the climate was
404 citations
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TL;DR: The results offer some scope for the refinement of manure retention coefficients used in crop management guidelines and for the improvement of SOC change factors for national GHG inventories by taking into account manure-C input.
Abstract: The impact of animal manure application on soil organic carbon (SOC) stock changes is of interest for both agronomic and environmental purposes. There is a specific need to quantify SOC change for use in national greenhouse gas (GHG) emission inventories. We quantified the response of SOC stocks to manure application from a large worldwide pool of individual studies and determined the impact of explanatory factors such as climate, soil properties, land use and manure characteristics. Our study is based on a meta-analysis of 42 research articles totaling 49 sites and 130 observations in the world. A dominant effect of cumulative manure-C input on SOC response was observed as this factor explained at least 53% of the variability in SOC stock differences compared to mineral fertilized or unfertilized reference treatments. However, the effects of other determining factors were not evident from our data set. From the linear regression relating cumulative C inputs and SOC stock difference, a global manure-C retention coefficient of 12% ± 4 (95% Confidence Interval, CI) could be estimated for an average study duration of 18 years. Following an approach comparable to the Intergovernmental Panel on Climate Change, we estimated a relative SOC change factor of 1.26 ± 0.14 (95% CI) which was also related to cumulative manure-C input. Our results offer some scope for the refinement of manure retention coefficients used in crop management guidelines and for the improvement of SOC change factors for national GHG inventories by taking into account manure-C input. Finally, this study emphasizes the need to further document the long-term impact of manure characteristics such as animal species, especially pig and poultry, and manure management systems, in particular liquid vs. solid storage.
376 citations
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Agriculture and Agri-Food Canada1, National Research Council2, J. Craig Venter Institute3, Centre national de la recherche scientifique4, University of Queensland5, University of Missouri6, University of Warwick7, University of Western Australia8, Plant Genome Mapping Laboratory9, Southern Cross University10, University of York11
TL;DR: Differential expression of the triplicated syntelogs and cytosine methylation levels across the sub-genomes suggest residual marks of the genome dominance that led to the current genome architecture, and epigenetic mechanisms play a role in the functional diversification of duplicate genes.
Abstract: Background: Brassica oleracea is a valuable vegetable species that has contributed to human health and nutrition for hundreds of years and comprises multiple distinct cultivar groups with diverse morphological and phytochemical attributes. In addition to this phenotypic wealth, B. oleracea offers unique insights into polyploid evolution, as it results from multiple ancestral polyploidy events and a final Brassiceae-specific triplication event. Further, B. oleracea represents one of the diploid genomes that formed the economically important allopolyploid oilseed, Brassica napus. A deeper understanding of B. oleracea genome architecture provides a foundation for crop improvement strategies throughout the Brassica genus. Results: We generate an assembly representing 75% of the predicted B. oleracea genome using a hybrid Illumina/ Roche 454 approach. Two dense genetic maps are generated to anchor almost 92% of the assembled scaffolds to nine pseudo-chromosomes. Over 50,000 genes are annotated and 40% of the genome predicted to be repetitive, thus contributing to the increased genome size of B. oleracea compared to its close relative B. rapa. A snapshot of both the leaf transcriptome and methylome allows comparisons to be made across the triplicated sub-genomes, which resulted from the most recent Brassiceae-specific polyploidy event. Conclusions: Differential expression of the triplicated syntelogs and cytosine methylation levels across the sub-genomes suggest residual marks of the genome dominance that led to the current genome architecture. Although cytosine methylation does not correlate with individual gene dominance, the independent methylation patterns of triplicated copies suggest epigenetic mechanisms play a role in the functional diversification of duplicate genes.
362 citations
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TL;DR: Pesticide applications, including broad-spectrum insecticides, have increased in response to H. halys infestations, potentially negatively influencing populations of beneficial arthropods and increasing secondary pest outbreaks.
Abstract: Brown marmorated stink bug, Halyomorpha halys Stal, is an invasive, herbivorous insect species that was accidentally introduced to the United States from Asia. First discovered in Allentown, PA, in 1996, H. halys has now been reported from at least 40 states in the United States. Additional invasions have been detected in Canada, Switzerland, France, Germany, Italy, and Lichtenstein, suggesting this invasive species could emerge as a cosmopolitan pest species. In its native range, H. halys is classified as an outbreak pest; however, in North America, H. halys has become a major agricultural pest across a wide range of commodities. H. halys is a generalist herbivore, capable of consuming >100 different species of host plants, often resulting in substantial economic damage; its feeding damage resulted in US$37 million of losses in apple in 2010, but this stink bug species also attacks other fruit, vegetable, field crop, and ornamental plant species. H. halys has disrupted integrated pest management programs for multiple cropping systems. Pesticide applications, including broad-spectrum insecticides, have increased in response to H. halys infestations, potentially negatively influencing populations of beneficial arthropods and increasing secondary pest outbreaks. H. halys is also challenging because it affects homeowners as a nuisance pest; the bug tends to overwinter in homes and outbuildings. Although more research is required to better understand the ecology and biology of H. halys , we present its life history, host plant damage, and the management options available for this invasive pest species.
326 citations
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TL;DR: The first chromosome-scale high-quality reference genome sequence is generated for C. sativa and annotated 89,418 protein-coding genes, representing a whole-genome triplication event relative to the crucifer model Arabidopsis thaliana.
Abstract: Camelina sativa is an oilseed with desirable agronomic and oil-quality attributes for a viable industrial oil platform crop. Here we generate the first chromosome-scale high-quality reference genome sequence for C. sativa and annotated 89,418 protein-coding genes, representing a whole-genome triplication event relative to the crucifer model Arabidopsis thaliana. C. sativa represents the first crop species to be sequenced from lineage I of the Brassicaceae. The well-preserved hexaploid genome structure of C. sativa surprisingly mirrors those of economically important amphidiploid Brassica crop species from lineage II as well as wheat and cotton. The three genomes of C. sativa show no evidence of fractionation bias and limited expression-level bias, both characteristics commonly associated with polyploid evolution. The highly undifferentiated polyploid genome of C. sativa presents significant consequences for breeding and genetic manipulation of this industrial oil crop.
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TL;DR: Distribution maps indicate neonicotinoid use is increasing and becoming more widespread with concerns for environmental loading, while frequently detected neonicsotinoid concentrations in Prairie wetlands suggest high persistence and transport into wetlands.
Abstract: Neonicotinoids currently dominate the insecticide market as seed treatments on Canada's major Prairie crops (e.g., canola). The potential impact to ecologically significant wetlands in this dominantly agro-environment has largely been overlooked while the distribution of use, incidence and level of contamination remains unreported. We modelled the spatial distribution of neonicotinoid use across the three Prairie Provinces in combination with temporal assessments of water and sediment concentrations in wetlands to measure four active ingredients (clothianidin, thiamethoxam, imidacloprid and acetamiprid). From 2009 to 2012, neonicotinoid use was increasing; by 2012, applications covered an estimated ∼11 million hectares (44% of Prairie cropland) with >216,000 kg of active ingredients. Thiamethoxam, followed by clothianidin, were the dominant seed treatments by mass and area. Areas of high neonicotinoid use were identified as high density canola or soybean production. Water sampled four times from 136 wetlands (spring, summer, fall 2012 and spring 2013) across four rural municipalities in Saskatchewan similarly revealed clothianidin and thiamethoxam in the majority of samples. In spring 2012 prior to seeding, 36% of wetlands contained at least one neonicotinoid. Detections increased to 62% in summer 2012, declined to 16% in fall, and increased to 91% the following spring 2013 after ice-off. Peak concentrations were recorded during summer 2012 for both thiamethoxam (range:
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TL;DR: The status of acaricide resistance in cattle ticks from different parts of the world is summarized and modes of action of currently used acaricides, mechanism of resistance development, contributory factors for the development and spread of resistance, management of resistant strains and strategies to prolong the effect of the available acar pesticides are reviewed.
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Institut national de la recherche agronomique1, Commonwealth Scientific and Industrial Research Organisation2, University of Wisconsin-Madison3, United States Department of Agriculture4, Rural Development Administration5, Agriculture and Agri-Food Canada6, University of Sydney7, Empresa Brasileira de Pesquisa Agropecuária8, Columbia University9, West Virginia University10, Chinese Academy of Sciences11
TL;DR: GlobalSoilMap as mentioned in this paper is a digital soil map that aims to provide a fine-resolution global grid of soil functional properties with estimates of their associated uncertainties, including stores and fluxes in soils of water, carbon, nutrients, and solutes.
Abstract: Soil scientists are being challenged to provide assessments of soil condition from local through to global scales. A particular issue is the need for estimates of the stores and fluxes in soils of water, carbon, nutrients, and solutes. This review outlines progress in the development and testing of GlobalSoilMap —a digital soil map that aims to provide a fine-resolution global grid of soil functional properties with estimates of their associated uncertainties. A range of methods can be used to generate the fine-resolution spatial estimates depending on the availability of existing soil surveys, environmental data, and point observations. The system has an explicit geometry for estimating point and block estimates of soil properties continuously down the soil profile. This geometry is necessary to ensure mass balance when stores and fluxes are computed. It also overcomes some limitations with existing systems for characterizing soil variation with depth. GlobalSoilMap has been designed to enable delivery of soil data via Web services. This review provides an overview of the system's technical specifications including the minimum data set. Examples from contrasting countries and environments are then presented to demonstrate the robustness of the technical specifications. GlobalSoilMap provides the means for supplying soil information in a format and resolution compatible with other fundamental data sets from remote sensing, terrain analysis, and other systems for mapping, monitoring, and forecasting biophysical processes. The initial research phase of the core project is nearing completion and attention is now shifting toward establishing the institutional and governance arrangements necessary to complete a full global coverage and maintaining the operational version of the GlobalSoilMap . This will be a grand and rewarding challenge for the soil science profession in the coming years.
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TL;DR: There was a significantly greater effect for both LDL and total cholesterol in subjects with diabetes compared with those without (although based on few studies), and there was no significant effect of OBG on high-density lipoprotein (HDL) cholesterol or triglycerides.
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TL;DR: The move towards understanding of anaerobic fungi using -omics based (genomic, transcriptomic and proteomic) approaches is starting to yield valuable insights into the unique cellular processes, evolutionary history, metabolic capabilities and adaptations that exist within the Neocallimastigomycota.
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University of Gothenburg1, University of Malaya2, Mae Fah Luang University3, Franklin & Marshall College4, Chinese Academy of Sciences5, University of Warsaw6, Kaiserslautern University of Technology7, Wageningen University and Research Centre8, Royal Botanic Gardens9, Agriculture and Agri-Food Canada10, United States Department of Agriculture11, Landcare Research12, Department of Agriculture, Fisheries and Forestry13, World Agroforestry Centre14, University of Melbourne15, Universiti Putra Malaysia16, Leibniz Association17, University of Jena18
TL;DR: This study provides phylogenetic synopses for 25 groups of plant pathogenic fungi in the Ascomycota, BasidiomyCota, Mucormycotina (Fungi), and Oomycota using recent molecular data, up-to-date names, and the latest taxonomic insights.
Abstract: Many fungi are pathogenic on plants and cause significant damage in agriculture and forestry. They are also part of the natural ecosystem and may play a role in regulating plant numbers/density. Morphological identification and analysis of plant pathogenic fungi, while important, is often hampered by the scarcity of discriminatory taxonomic characters and the endophytic or inconspicuous nature of these fungi. Molecular (DNA sequence) data for plant pathogenic fungi have emerged as key information for diagnostic and classification studies, although hampered in part by non-standard laboratory practices and analytical methods. To facilitate current and future research, this study provides phylogenetic synopses for 25 groups of plant pathogenic fungi in the Ascomycota, Basidiomycota, Mucormycotina (Fungi), and Oomycota, using recent molecular data, up-to-date names, and the latest taxonomic insights. Lineage-specific laboratory protocols together with advice on their application, as well as general observations, are also provided. We hope to maintain updated backbone trees of these fungal lineages over time and to publish them jointly as new data emerge. Researchers of plant pathogenic fungi not covered by the present study are invited to join this future effort. Bipolaris, Botryosphaeriaceae, Botryosphaeria, Botrytis, Choanephora, Colletotrichum, Curvularia, Diaporthe, Diplodia, Dothiorella, Fusarium, Gilbertella, Lasiodiplodia, Mucor, Neofusicoccum, Pestalotiopsis, Phyllosticta, Phytophthora, Puccinia, Pyrenophora, Pythium, Rhizopus, Stagonosporopsis, Ustilago and Verticillium are dealt with in this paper.
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TL;DR: Fluorescence spectroscopy studies confirmed that resveratrol was encapsulated in the inner core of the nanoemulsions, which provides protection against chemical degradation, and the developed systems also demonstrated the capability of nanoemulsion-based delivery systems in sustained release of resver atrol from dialysis bags compared to the unencapsulated compound.
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TL;DR: In this article, a field study with comparisons of three mulching areas and two ridge-furrow shapes was conducted for two years (2009 and 2010) to assess evapotranspiration, water use efficiency, and tuber yields in the semi-arid Northwest China.
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TL;DR: The carbon footprint of alternative wheat production systems suited to semiarid environments is quantified and it is found that integrating improved farming practices lowers wheat carbon footprint effectively, averaging −256 kg CO2 eq ha−1 per year.
Abstract: Wheat is one of the world's most favoured food sources, reaching millions of people on a daily basis However, its production has climatic consequences Fuel, inorganic fertilizers and pesticides used in wheat production emit greenhouse gases that can contribute negatively to climate change It is unknown whether adopting alternative farming practices will increase crop yield while reducing carbon emissions Here we quantify the carbon footprint of alternative wheat production systems suited to semiarid environments We find that integrating improved farming practices (that is, fertilizing crops based on soil tests, reducing summerfallow frequencies and rotating cereals with grain legumes) lowers wheat carbon footprint effectively, averaging -256 kg CO2 eq ha(-1) per year For each kg of wheat grain produced, a net 0027-0377 kg CO2 eq is sequestered into the soil With the suite of improved farming practices, wheat takes up more CO2 from the atmosphere than is actually emitted during its production
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TL;DR: In this paper, a case study of the statistical evaluation was conducted for the DSSAT Cropping System Model (CSM) using 10 experimental datasets for maize, peanut, soybean, wheat and potato from Brazil, China, Ghana, and the USA.
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TL;DR: The potential of anaerobic digestion to degrade antibiotics in livestock manure contributes to a more sustainable and environment-friendly livestock breeding and further investigations are required to assess the degradation of antibiotics during psychrophilic anaer aerobic digestion.
Abstract: Degrading antibiotics discharged in the livestock manure in a well-controlled bioprocess contributes to a more sustainable and environment-friendly livestock breeding. Although most antibiotics remain stable during manure storage, anaerobic digestion can degrade and remove them to various extents depending on the concentration and class of antibiotic, bioreactor operating conditions, type of feedstock and inoculum sources. Generally, antibiotics are degraded during composting > anaerobic digestion > manure storage > soil. Manure matrix variation influences extraction, quantification, and degradation of antibiotics, but it has not been well investigated. Fractioning of manure-laden antibiotics into liquid and solid phases and its effects on their anaerobic degradation and the contribution of abiotic (physical and chemical) versus biotic degradation mechanisms need to be quantified for various manures, antibiotics types, reactor designs and temperature of operations. More research is required to determine the kinetics of antibiotics' metabolites degradation during anaerobic digestion. Further investigations are required to assess the degradation of antibiotics during psychrophilic anaerobic digestion.
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TL;DR: The cpn 60-based investigation of the vaginal microbiome demonstrated that in healthy women most vaginal microbiomes remained stable through their menstrual cycle, with little variation in diversity and only modest fluctuations in species richness.
Abstract: The vaginal microbial community plays a vital role in maintaining women’s health. Understanding the precise bacterial composition is challenging because of the diverse and difficult-to-culture nature of many bacterial constituents, necessitating culture-independent methodology. During a natural menstrual cycle, physiological changes could have an impact on bacterial growth, colonization, and community structure. The objective of this study was to assess the stability of the vaginal microbiome of healthy Canadian women throughout a menstrual cycle by using cpn 60-based microbiota analysis. Vaginal swabs from 27 naturally cycling reproductive-age women were collected weekly through a single menstrual cycle. Polymerase chain reaction (PCR) was performed to amplify the universal target region of the cpn 60 gene and generate amplicons representative of the microbial community. Amplicons were pyrosequenced, assembled into operational taxonomic units, and analyzed. Samples were also assayed for total 16S rRNA gene content and Gardnerella vaginalis by quantitative PCR and screened for the presence of Mollicutes by using family and genus-specific PCR. Overall, the vaginal microbiome of most women remained relatively stable throughout the menstrual cycle, with little variation in diversity and only modest fluctuations in species richness. Microbiomes between women were more different than were those collected consecutively from individual women. Clustering of microbial profiles revealed the expected groupings dominated by Lactobacillus crispatus, Lactobacillus iners, and Lactobacillus jensenii. Interestingly, two additional clusters were dominated by either Bifidobacterium breve or a heterogeneous mixture of nonlactobacilli. Direct G. vaginalis quantification correlated strongly with its pyrosequencing-read abundance, and Mollicutes, including Mycoplasma hominis, Ureaplasma parvum, and Ureaplasma urealyticum, were detected in most samples. Our cpn 60-based investigation of the vaginal microbiome demonstrated that in healthy women most vaginal microbiomes remained stable through their menstrual cycle. Of interest in these findings was the presence of Bifidobacteriales beyond just Gardnerella species. Bifidobacteriales are frequently underrepresented in 16S rRNA gene-based studies, and their detection by cpn 60-based investigation suggests that their significance in the vaginal community may be underappreciated.
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TL;DR: The aim of this study was to identify isolates to species level and describe the new species found, and to create a reliable reference sequence database to be used for next-generation sequencing projects.
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TL;DR: The properties of some bioactive molecules, like those found in cranberry, which have shown interesting polyvalent antibacterial and immuno-stimulatory activities are described here.
Abstract: The use of antibiotics in food-producing animals has significantly increased animal health by lowering mortality and the incidence of diseases. Antibiotics also have largely contributed to increase productivity of farms. However, antibiotic usage in general and relevance of non-therapeutic antibiotics in feed (growth promoters) need to be reevaluated especially because bacterial pathogens of humans and animals have developed and shared a variety of antibiotic resistance mechanisms that can easily spread within microbial communities. In Canada, poultry production involves more than 2,600 regulated chicken producers. There are several antibiotics approved as feed additives available for poultry farmers. Feed recipes and mixtures greatly vary geographically and from one farm to another, making links between use of a specific antibiotic feed additive and production yields or selection of specific antibiotic-resistant bacteria difficult to establish. Many on-farm studies have revealed the widespread presence of antibiotic-resistant bacteria in broiler chickens. While sporadic reports linked the presence of antibiotic-resistant organisms to the use of feed supplemented with antibiotics, no recent studies could clearly demonstrate the benefit of antimicrobial growth promoters on performance and production yields. With modern biosecurity and hygienic practices, there is a genuine concern that intensive utilization of antibiotics or use of antimicrobial growth promoters in feed might no longer be useful. Public pressure and concerns about food and environmental safety (antibiotic residues, antibiotic-resistant pathogens) have driven researchers to actively look for alternatives to antibiotics. Some of the alternatives include pre- and probiotics, organic acids and essential oils. We will describe here the properties of some bioactive molecules, like those found in cranberry, which have shown interesting polyvalent antibacterial and immuno-stimulatory activities.
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TL;DR: In this article, the effects of genetic manipulation on amylose levels in plants, enzymatic hydrolysis, physical treatments, chemical modifications, exposure to γ-rays, and the effect of lipid complexation on the RS content of starches from various botanical sources were compared.
Abstract: Research involving resistant starch (RS) is becoming more prominent. RS has the ability to modulate postprandial blood-glucose levels and can be fermented by the colonic microflora to produce short-chain fatty acids, which exert positive health benefits on the consumer such as increased colonic blood flow to ease colonic inflammation and a decreased risk of colon and/or other cancers. This paper reviews the effects of genetic manipulation on amylose levels in plants, enzymatic hydrolysis, physical treatments, chemical modifications, exposure to γ-rays, and the effects of lipid complexation on the RS content of starches from various botanical sources. All treatments reviewed increased the RS content; however, select treatments (namely genetic manipulation, enzymatic debranching, hydrothermal treatments, high hydrostatic pressure, most chemical modifications, γ-irradiation exposure, as well as lipid complexation) were more effective to varying degrees than were extrusion and mineral acid treatments. Various methods commonly used for measuring RS were compared. Additionally, the effects of food matrix components were also examined to gauge their effectiveness at inhibiting or enhancing RS formation, with lipids and gums known to be the most effective at enhancing (or apparently enhancing) RS. This review draws largely, but not exclusively, from research published post 2009.
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TL;DR: In this paper, a review of P NMR studies of soil has been presented, including pre-and post-extraction treatments, the physical state of the soil sample at the time of extraction, extraction length, extraction ratio, soil/extractant ratio, P recovery, P in residues, methods to concentrate extracts, redissolving samples for ³¹P NMR experiments, and the use of the internal standard methylene diphosphonic acid.
Abstract: Phosphorus nuclear magnetic resonance (³¹P NMR) spectroscopy is an important tool for the study of soil P and has significantly advanced our knowledge of soil P forms, particularly organic P; however, it must be used correctly to provide meaningful results. This review covers the ³¹P NMR studies of soil published from 2005 to 2013. The first part discusses preparing samples for ³¹P NMR, including extractants, pre- and post-extraction treatments, the physical state of the soil sample at the time of extraction, extraction length, the soil/extractant ratio, P recovery, P in residues, methods to concentrate extracts, redissolving samples for ³¹P NMR experiments, the use of the internal standard methylene diphosphonic acid, and the potential for degradation with any of these steps. The second part of this review focuses on NMR experiment parameters, including delay times, proton decoupling, and experiment length. Potential concerns in these areas are noted, and suggestions are given for procedures to optimize the information obtained from a ³¹P NMR experiment.
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TL;DR: The moisture sorption behavior of TPS is described in GAB and BET models, from which monolayer moisture content and specific area are derived, and current studies on surface tension, gas permeability, crystallinity, and so on of the TPS are also reviewed.
Abstract: Canola Council of Canada, Winnipeg, Manitoba, Canada The rising costs of nonrenewable feedstocks and environmental concerns with their industrial usage have encouraged the study and development of renewable products, including thermoplastic starch (TPS). Starch is an abundant, plant-based biodegradable material with interesting physicochemical characteristics that can be exploited, and this has received attention for development of TPS products. Starch exhibits usable thermoplastic properties when plasticizers, elevated temperatures, and shear are present. The choice of plasticizer has an effect on TPS, even when these have similar plasticization principles. Most TPS have glass transition temperature, Tg, in the range of approximately -75 to 10°C. Glassy transition of TPS is detected by differential scanning calorimeter (DSC) and thermodynamic analyzer (DMA), although DMA has been found to be more sensitive and effective. TPS has low tensile properties, typically below 6 MPa in tensile strength (TS). The addition of synthetic polymers, nanoclay, and fiber can improve TS and water-resistance ability. The moisture sorption behavior of TPS is described in GAB and BET models, from which monolayer moisture content and specific area are derived. Current studies on surface tension, gas permeability, crystallinity, and so on of the TPS are also reviewed.
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Charles Sturt University1, University of Canberra2, University of Wollongong3, New South Wales Department of Primary Industries4, University of Western Australia5, Commonwealth Scientific and Industrial Research Organisation6, International Crops Research Institute for the Semi-Arid Tropics7, Agriculture and Agri-Food Canada8
TL;DR: The results indicate that genetic diversity for shatter resistance genes in B. napus is limited; breeders will need to target the introduction of useful alleles especially from genotypes of other related species of Brassica, such as those that have been identified.
Abstract: Resistance to pod shattering (shatter resistance) is a target trait for global rapeseed (canola, Brassica napus L.), improvement programs to minimise grain loss in the mature standing crop, and during windrowing and mechanical harvest. We describe the genetic basis of natural variation for shatter resistance in B. napus and show that several quantitative trait loci (QTL) control this trait. To identify loci underlying shatter resistance, we used a novel genotyping-by-sequencing approach DArT-Seq. QTL analysis detected a total of 12 significant QTL on chromosomes A03, A07, A09, C03, C04, C06, and C08; which jointly account for approximately 57% of the genotypic variation in shatter resistance. Through Genome-Wide Association Studies, we show that a large number of loci, including those that are involved in shattering in Arabidopsis, account for variation in shatter resistance in diverse B. napus germplasm. Our results indicate that genetic diversity for shatter resistance genes in B. napus is limited; many of the genes that might control this trait were not included during the natural creation of this species, or were not retained during the domestication and selection process. We speculate that valuable diversity for this trait was lost during the natural creation of B. napus. To improve shatter resistance, breeders will need to target the introduction of useful alleles especially from genotypes of other related species of Brassica, such as those that we have identified.
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TL;DR: In this article, the effects of contact time and temperature on the adsorption of methylene blue (MB) onto monolithic graphene oxide (GO) gels were investigated, and the results showed that MB absorption mechanisms can be different for these two gels.