Showing papers by "Agriculture and Agri-Food Canada published in 2015"

The Top 10 oomycete pathogens in molecular plant pathology

Abstract: Oomycetes form a deep lineage of eukaryotic organisms that includes a large number of plant pathogens which threaten natural and managed ecosystems. We undertook a survey to query the community for their ranking of plant-pathogenic oomycete species based on scientific and economic importance. In total, we received 263 votes from 62 scientists in 15 countries for a total of 33 species. The Top 10 species and their ranking are: (1) Phytophthora infestans; (2, tied) Hyaloperonospora arabidopsidis; (2, tied) Phytophthora ramorum; (4) Phytophthora sojae; (5) Phytophthora capsici; (6) Plasmopara viticola; (7) Phytophthora cinnamomi; (8, tied) Phytophthora parasitica; (8, tied) Pythium ultimum; and (10) Albugo candida. This article provides an introduction to these 10 taxa and a snapshot of current research. We hope that the list will serve as a benchmark for future trends in oomycete research.

Human gut Bacteroidetes can utilize yeast mannan through a selfish mechanism

Abstract: Yeasts, which have been a component of the human diet for at least 7,000 years, possess an elaborate cell wall α-mannan The influence of yeast mannan on the ecology of the human microbiota is unknown Here we show that yeast α-mannan is a viable food source for the Gram-negative bacterium Bacteroides thetaiotaomicron, a dominant member of the microbiota Detailed biochemical analysis and targeted gene disruption studies support a model whereby limited cleavage of α-mannan on the surface generates large oligosaccharides that are subsequently depolymerized to mannose by the action of periplasmic enzymes Co-culturing studies showed that metabolism of yeast mannan by B thetaiotaomicron presents a 'selfish' model for the catabolism of this difficult to breakdown polysaccharide Genomic comparison with B thetaiotaomicron in conjunction with cell culture studies show that a cohort of highly successful members of the microbiota has evolved to consume sterically-restricted yeast glycans, an adaptation that may reflect the incorporation of eukaryotic microorganisms into the human diet

Spent coffee grounds: A review on current research and future prospects

Abstract: Spent coffee ground (SCG) contains large amounts of organic compounds (i.e. fatty acids, amino acids, polyphenols, minerals and polysaccharides) that justify its valorization. Earlier innovation explored the extraction of specific components such as oil, flavor, terpenes, and alcohols as value-added products. However, by-products of coffee fruit and bean processing can also be considered as potential functional ingredients for the food industry. There is an urgent need for practical and innovative ideas to use this low cost SCG and exploit its full potential increasing the overall sustainability of the coffee agro-industry.

One fungus, which genes? Development and assessment of universal primers for potential secondary fungal DNA barcodes.

Abstract: Primer development and testing by partners in the European Consortium of Microbial Resource Centres (EMbaRC) was supported through funding of the European Community’s Seventh Framework Programme (FP7, 2007–2013), Research Infrastructures action, under grant agreement no. FP7-228310. Part of sequencing work in CBS was supported by Fonds Economische Structuurversterking (FES), Dutch Ministry of Education, Culture and Science grant BEK/BPR-2009/137964-U). WM and VR were supported by research grant NH&MRC #APP1031952. Genome mining at CBS and AAFC, and primer development and testing at AAFC, were supported by grants from the A.P. Sloan Foundation Programme on the Microbiology of the Built Environment. We acknowledge the Deanship of Scientific Research (DSR), King Abdulaziz University, under grant No. 1-965/1434 HiCi for technical and financial support. AY was supported by Fundacao para a Ciencia e a Tecnologia (Portugal), project PTDC/BIA-BIC/4585/2012. MPM was supported by grant CGL2012-359 (Spain).

Protein Oxidation in Processed Meat: Mechanisms and Potential Implications on Human Health.

Abstract: Processed meats represent a large percentage of muscle foods consumed in the western world Various processing steps affect the physicochemical properties of the meat, compromise its nutritional components, or produce some compounds that are of health concern Hence, the impact of oxidation on human health and the aging process and the influence of diet on these harmful reactions are of growing interest Past decades have seen more focus on lipid oxidation, microbial deterioration, and pathogenicity, as well as production of carcinogenic compounds during meat processing The oxidation of protein, which is a major component in meat systems, has received less attention Protein oxidation has been defined as a covalent modification of protein induced either directly by reactive species or indirectly by reaction with secondary by-products of oxidative stress Not only are these modifications critical for technological and sensory properties of muscle foods, they may have implications on human health and safety when consumed Cooking, for example, has been observed to increase free radical generation while it also decreases the antioxidant protection systems in meat, both of which contribute to protein oxidation Many other meat processing techniques, as well as other emerging technologies, may significantly affect protein oxidation and protein overall quality This paper explores the current understanding of meat processing techniques and their possible effects on the status of protein oxidation and nutritional value, as well as their possible implications on human health

Identification of loci governing eight agronomic traits using a GBS-GWAS approach and validation by QTL mapping in soya bean

Abstract: Soya bean is a major source of edible oil and protein for human consumption as well as animal feed. Understanding the genetic basis of different traits in soya bean will provide important insights for improving breeding strategies for this crop. A genome-wide association study (GWAS) was conducted to accelerate molecular breeding for the improvement of agronomic traits in soya bean. A genotyping-by-sequencing (GBS) approach was used to provide dense genome-wide marker coverage (>47,000 SNPs) for a panel of 304 short-season soya bean lines. A subset of 139 lines, representative of the diversity among these, was characterized phenotypically for eight traits under six environments (3 sites × 2 years). Marker coverage proved sufficient to ensure highly significant associations between the genes known to control simple traits (flower, hilum and pubescence colour) and flanking SNPs. Between one and eight genomic loci associated with more complex traits (maturity, plant height, seed weight, seed oil and protein) were also identified. Importantly, most of these GWAS loci were located within genomic regions identified by previously reported quantitative trait locus (QTL) for these traits. In some cases, the reported QTLs were also successfully validated by additional QTL mapping in a biparental population. This study demonstrates that integrating GBS and GWAS can be used as a powerful complementary approach to classical biparental mapping for dissecting complex traits in soya bean.

Evolution and Classification of Cannabis sativa (Marijuana, Hemp) in Relation to Human Utilization

Abstract: Cannabis sativa has been employed for thousands of years, primarily as a source of a stem fiber (both the plant and the fiber termed “hemp”) and a resinous intoxicant (the plant and its drug preparations commonly termed “marijuana”). Studies of relationships among various groups of domesticated forms of the species and wild-growing plants have led to conflicting evolutionary interpretations and different classifications, including splitting C. sativa into several alleged species. This review examines the evolving ways Cannabis has been used from ancient times to the present, and how human selection has altered the morphology, chemistry, distribution and ecology of domesticated forms by comparison with related wild plants. Special attention is given to classification, since this has been extremely contentious, and is a key to understanding, exploiting and controlling the plant. Differences that have been used to recognize cultivated groups within Cannabis are the results of disruptive selection for characteristics selected by humans. Wild-growing plants, insofar as has been determined, are either escapes from domesticated forms or the results of thousands of years of widespread genetic exchange with domesticated plants, making it impossible to determine if unaltered primeval or ancestral populations still exist. The conflicting approaches to classifying and naming plants with such interacting domesticated and wild forms are examined. It is recommended that Cannabis sativa be recognized as a single species, within which there is a narcotic subspecies with both domesticated and ruderal varieties, and similarly a non-narcotic subspecies with both domesticated and ruderal varieties. An alternative approach consistent with the international code of nomenclature for cultivated plants is proposed, recognizing six groups: two composed of essentially non-narcotic fiber and oilseed cultivars as well as an additional group composed of their hybrids; and two composed of narcotic strains as well as an additional group composed of their hybrids.

Dissecting the molecular network of virus-plant interactions: the complex roles of host factors.

Abstract: A successful infection by a plant virus results from the complex molecular interplay between the host plant and the invading virus. Thus, dissecting the molecular network of virus-host interactions advances the understanding of the viral infection process and may assist in the development of novel antiviral strategies. In the past decade, molecular identification and functional characterization of host factors in the virus life cycle, particularly single-stranded, positive-sense RNA viruses, have been a research focus in plant virology. As a result, a number of host factors have been identified. These host factors are implicated in all the major steps of the infection process. Some host factors are diverted for the viral genome translation, some are recruited to improvise the viral replicase complexes for genome multiplication, and others are components of transport complexes for cell-to-cell spread via plasmodesmata and systemic movement through the phloem. This review summarizes current knowledge about host factors and discusses future research directions.

Phytogenic Compounds as Alternatives to In-Feed Antibiotics: Potentials and Challenges in Application

Abstract: This article summarizes current experimental knowledge on the efficacy, possible mechanisms and feasibility in the application of phytogenic products as feed additives for food-producing animals. Phytogenic compounds comprise a wide range of plant-derived natural bioactive compounds and essential oils are a major group. Numerous studies have demonstrated that phytogenic compounds have a variety of functions, including antimicrobial/antiviral, antioxidative and anti-inflammation effects and improvement in the palatability of feed and gut development/health. However, the mechanisms underlying their functions are still largely unclear. In the past, there has been a lack of consistency in the results from both laboratory and field studies, largely due to the varied composition of products, dosages, purities and growing conditions of animals used. The minimal inhibitory concentration (MIC) of phytogenic compounds required for controlling enteric pathogens may not guarantee the best feed intake, balanced immunity of animals and cost-effectiveness in animal production. The lipophilic nature of photogenic compounds also presents a challenge in effective delivery to the animal gut and this can partially be resolved by microencapsulation and combination with other compounds (synergistic effect). Interestingly, the effects of photogenic compounds on anti-inflammation, gut chemosensing and possible disruption of bacterial quorum sensing could explain a certain number of studies with different animal species for the better production performance of animals that have received phytogenic feed additives. It is obvious that phytogenic compounds have good potential as an alternative to antibiotics in feed for food animal production and the combination of different phytogenic compounds appears to be an approach to improve the efficacy and safety of phytogenic compounds in the application. It is our expectation that the recent development of high-throughput and “omics” technologies can significantly advance the studies on the mechanisms underlying phytogenic compounds’ functions and, therefore, guide the effective use of the compounds.

Disease Resistance Gene Analogs (RGAs) in Plants

Abstract: Plants have developed effective mechanisms to recognize and respond to infections caused by pathogens. Plant resistance gene analogs (RGAs), as resistance (R) gene candidates, have conserved domains and motifs that play specific roles in pathogens’ resistance. Well-known RGAs are nucleotide binding site leucine rich repeats, receptor like kinases, and receptor like proteins. Others include pentatricopeptide repeats and apoplastic peroxidases. RGAs can be detected using bioinformatics tools based on their conserved structural features. Thousands of RGAs have been identified from sequenced plant genomes. High-density genome-wide RGA genetic maps are useful for designing diagnostic markers and identifying quantitative trait loci (QTL) or markers associated with plant disease resistance. This review focuses on recent advances in structures and mechanisms of RGAs, and their identification from sequenced genomes using bioinformatics tools. Applications in enhancing fine mapping and cloning of plant disease resistance genes are also discussed.

Plant Translation Factors and Virus Resistance

Abstract: Plant viruses recruit cellular translation factors not only to translate their viral RNAs but also to regulate their replication and potentiate their local and systemic movement. Because of the virus dependence on cellular translation factors, it is perhaps not surprising that many natural plant recessive resistance genes have been mapped to mutations of translation initiation factors eIF4E and eIF4G or their isoforms, eIFiso4E and eIFiso4G. The partial functional redundancy of these isoforms allows specific mutation or knock-down of one isoform to provide virus resistance without hindering the general health of the plant. New possible targets for antiviral strategies have also been identified following the characterization of other plant translation factors (eIF4A-like helicases, eIF3, eEF1A and eEF1B) that specifically interact with viral RNAs and proteins and regulate various aspects of the infection cycle. Emerging evidence that translation repression operates as an alternative antiviral RNA silencing mechanism is also discussed. Understanding the mechanisms that control the development of natural viral resistance and the emergence of virulent isolates in response to these plant defense responses will provide the basis for the selection of new sources of resistance and for the intelligent design of engineered resistance that is broad-spectrum and durable.

Achievements and Challenges in Improving the Nutritional Quality of Food Legumes

Abstract: Quality aspects of food crops have globally important market economic and health repercussions in the current climate of food security. Grain legumes have high potential for the nutritional quality improvement of foods, but limited data on manipulating seed quality is available as the primary focus has been hitherto on phenotypic and agronomic trait improvement. This has resulted in a lack of innovation and low attractiveness of legume food products that, with the emergence of novel food habits, have together contributed to reduced legume food consumption. This trend now needs to be challenged and circumvented. In this review we have assessed the key factors affecting the nutritional quality of legume seeds such as protein, starch, dietary fiber, natural antioxidant compounds and anti-nutritional factors. All have been reviewed with emphasis on how these components might influence consumer acceptance and functional properties of legume based food products. Biofortification approaches and technological pro...

Diversifying crop rotations with pulses enhances system productivity.

Abstract: Agriculture in rainfed dry areas is often challenged by inadequate water and nutrient supplies. Summerfallowing has been used to conserve rainwater and promote the release of nitrogen via the N mineralization of soil organic matter. However, summerfallowing leaves land without any crops planted for one entire growing season, creating lost production opportunity. Additionally, summerfallowing has serious environmental consequences. It is unknown whether alternative systems can be developed to retain the beneficial features of summerfallowing with little or no environmental impact. Here, we show that diversifying cropping systems with pulse crops can enhance soil water conservation, improve soil N availability, and increase system productivity. A 3-yr cropping sequence study, repeated for five cycles in Saskatchewan from 2005 to 2011, shows that both pulse- and summerfallow-based systems enhances soil N availability, but the pulse system employs biological fixation of atmospheric N2, whereas the summerfallow-system relies on ‘mining’ soil N with depleting soil organic matter. In a 3-yr cropping cycle, the pulse system increased total grain production by 35.5%, improved protein yield by 50.9%, and enhanced fertilizer-N use efficiency by 33.0% over the summerfallow system. Diversifying cropping systems with pulses can serve as an effective alternative to summerfallowing in rainfed dry areas.

Range expansion of the invasive brown marmorated stinkbug, Halyomorpha halys: an increasing threat to field, fruit and vegetable crops worldwide

Abstract: The brown marmorated stink bug, Halyomorpha halys (Hemiptera: Pentatomidae), has emerged as a harmful invasive insect pest in North America and Europe in the 1990s and 2000s, respectively. Native to eastern Asia, this highly polyphagous pest (>120 different host plants) is spreading rapidly worldwide, notably through human activities. The increasing global importance of the pest suggests that more coordinated actions are needed to slow its spread and mitigate negative effects in invaded areas. Prevention of large-scale outbreaks will require accurate identification and effective mitigation tools to be rapidly developed and widely implemented. In this short review, we update the current distribution of H. halys, discuss potential geographic range expansion based on passive and active dispersal and provide insight on the economic, environmental and social impact associated with H. halys.

Increased mobilization of aged carbon to rivers by human disturbance

Abstract: Most dissolved organic carbon in rivers originates from young carbon in soils and vegetation. A global radiocarbon data set suggests that human disturbance is also introducing aged carbon to rivers and to active carbon cycling.

Animal models to study acute and chronic intestinal inflammation in mammals

Abstract: Acute and chronic inflammatory diseases of the intestine impart a significant and negative impact on the health and well-being of human and non-human mammalian animals. Understanding the underlying mechanisms of inflammatory disease is mandatory to develop effective treatment and prevention strategies. As inflammatory disease etiologies are multifactorial, the use of appropriate animal models and associated metrics of disease are essential. In this regard, animal models used alone or in combination to study acute and chronic inflammatory disease of the mammalian intestine paired with commonly used inflammation-inducing agents are reviewed. This includes both chemical and biological incitants of inflammation, and both non-mammalian (i.e. nematodes, insects, and fish) and mammalian (i.e. rodents, rabbits, pigs, ruminants, dogs, and non-human primates) models of intestinal inflammation including germ-free, gnotobiotic, as well as surgical, and genetically modified animals. Importantly, chemical and biological incitants induce inflammation via a multitude of mechanisms, and intestinal inflammation and injury can vary greatly according to the incitant and animal model used, allowing studies to ascertain both long-term and short-term effects of inflammation. Thus, researchers and clinicians should be aware of the relative strengths and limitations of the various animal models used to study acute and chronic inflammatory diseases of the mammalian intestine, and the scope and relevance of outcomes achievable based on this knowledge. The ability to induce inflammation to mimic common human diseases is an important factor of a successful animal model, however other mechanisms of disease such as the amount of infective agent to induce disease, invasion mechanisms, and the effect various physiologic changes can have on inducing damage are also important features. In many cases, the use of multiple animal models in combination with both chemical and biological incitants is necessary to answer the specific question being addressed regarding intestinal disease. Some incitants can induce acute responses in certain animal models while others can be used to induce chronic responses; this review aims to illustrate the strengths and weaknesses in each animal model and to guide the choice of an appropriate acute or chronic incitant to facilitate intestinal disease.

Mapping trends in novel and emerging food processing technologies around the world

Abstract: This paper discusses novel technologies and their applications in the world. Two surveys were independently designed and conducted by a North American (Survey 1) and by a European group (Survey 2). The respondents were food professionals from industry, academia and government. The questions sought to identify novel technologies either applied now or with the potential to be commercialised in 5–10 years, commercialisation factors, associated regulations and limitations. In Survey 1, HPP (80%), microwave (88%) and UV (84%) were the main technologies applied now and anticipated in the next 5 years. PEF was third instead of UV in Survey 2. The main drivers were higher quality products (94%), product safety (92%) and shelf life (91%). HPP and microwaves were identified as main technologies now and in the next 10 years. There were geographical differences with North America finding UV and radiation, and Europe finding PEF of more importance now. Cold plasma and PEF were anticipated to be more important in Europe in 10 years' time while HPP, microwave and UV remained more important to North America. Industrial relevance The emerging technologies mentioned in the survey have been developing since the early 20th century or before. However, they are not adopted on any large scale such as canning or heat pasteurisation. This study was conducted on a worldwide scale to determine current uses for emerging technologies in different food sectors. Some technologies are deemed of more commercial importance in certain countries than others. HPP and microwave heating are the two main technologies currently on commercial applications. PEF is more popular in Europe, especially the Netherlands where a commercial scale unit exists. On the contrary, microwave technology seems to be popular in all countries but the Netherlands. UV and radiation are more important in North America than Europe. Pressure and CO 2 is only deemed to be of commercial importance in North America.