Showing papers by "Agriculture and Agri-Food Canada published in 2016"

Dietary polyphenols, oxidative stress and antioxidant and anti-inflammatory effects

Abstract: Phenolic compounds including phenolic acids, flavonoids and proanthocyanidins are widely distributed in plants as a protective mechanism against biotic and abiotic stresses. Fruits, vegetables, grains, spices and herbs are the richest source of dietary polyphenols. High intake of these foods has been linked to lowered risk of most common degenerative and chronic diseases that are known to be caused by oxidative stress. This review intends to summarize briefly recent progress on the chemistry and biochemistry of dietary polyphenols, their antioxidant and anti-inflammatory activities, and the underlying molecular mechanisms of their involvement in inflammation mediated metabolic diseases are also discussed. Perspectives for future research are also briefly discussed.

Current knowledge and perspectives of Paenibacillus : a review

Abstract: Isolated from a wide range of sources, the genus Paenibacillus comprises bacterial species relevant to humans, animals, plants, and the environment. Many Paenibacillus species can promote crop growth directly via biological nitrogen fixation, phosphate solubilization, production of the phytohormone indole-3-acetic acid (IAA), and release of siderophores that enable iron acquisition. They can also offer protection against insect herbivores and phytopathogens, including bacteria, fungi, nematodes, and viruses. This is accomplished by the production of a variety of antimicrobials and insecticides, and by triggering a hypersensitive defensive response of the plant, known as induced systemic resistance (ISR). Paenibacillus-derived antimicrobials also have applications in medicine, including polymyxins and fusaricidins, which are nonribosomal lipopeptides first isolated from strains of Paenibacillus polymyxa. Other useful molecules include exo-polysaccharides (EPS) and enzymes such as amylases, cellulases, hemicellulases, lipases, pectinases, oxygenases, dehydrogenases, lignin-modifying enzymes, and mutanases, which may have applications for detergents, food and feed, textiles, paper, biofuel, and healthcare. On the negative side, Paenibacillus larvae is the causative agent of American Foulbrood, a lethal disease of honeybees, while a variety of species are opportunistic infectors of humans, and others cause spoilage of pasteurized dairy products. This broad review summarizes the major positive and negative impacts of Paenibacillus: its realised and prospective contributions to agriculture, medicine, process manufacturing, and bioremediation, as well as its impacts due to pathogenicity and food spoilage. This review also includes detailed information in Additional files 1, 2, 3 for major known Paenibacillus species with their locations of isolation, genome sequencing projects, patents, and industrially significant compounds and enzymes. Paenibacillus will, over time, play increasingly important roles in sustainable agriculture and industrial biotechnology.

Assessment of the SMAP Passive Soil Moisture Product

Abstract: The National Aeronautics and Space Administration (NASA) Soil Moisture Active Passive (SMAP) satellite mission was launched on January 31, 2015. The observatory was developed to provide global mapping of high-resolution soil moisture and freeze-thaw state every two to three days using an L-band (active) radar and an L-band (passive) radiometer. After an irrecoverable hardware failure of the radar on July 7, 2015, the radiometer-only soil moisture product became the only operational soil moisture product for SMAP. The product provides soil moisture estimates posted on a 36 km Earth-fixed grid produced using brightness temperature observations from descending passes. Within months after the commissioning of the SMAP radiometer, the product was assessed to have attained preliminary (beta) science quality, and data were released to the public for evaluation in September 2015. The product is available from the NASA Distributed Active Archive Center at the National Snow and Ice Data Center. This paper provides a summary of the Level 2 Passive Soil Moisture Product (L2_SM_P) and its validation against in situ ground measurements collected from different data sources. Initial in situ comparisons conducted between March 31, 2015 and October 26, 2015, at a limited number of core validation sites (CVSs) and several hundred sparse network points, indicate that the V-pol Single Channel Algorithm (SCA-V) currently delivers the best performance among algorithms considered for L2_SM_P, based on several metrics. The accuracy of the soil moisture retrievals averaged over the CVSs was 0.038 m3/m3 unbiased root-mean-square difference (ubRMSD), which approaches the SMAP mission requirement of 0.040 m3/m3.

Regulated deficit irrigation for crop production under drought stress. A review

Abstract: Agriculture consumes more than two thirds of the total freshwater of the planet. This issue causes substantial conflict in freshwater allocation between agriculture and other economic sectors. Regulated deficit irrigation (RDI) is key technology because it helps to improve water use efficiency. Nonetheless, there is a lack of understanding of the mechanisms with which plants respond to RDI. In particular, little is known about how RDI might increase crop production while reducing the amount of irrigation water in real-world agriculture. In this review, we found that RDI is largely implemented through three approaches: (1) growth stage-based deficit irrigation, (2) partial root-zone irrigation, and (3) subsurface dripper irrigation. Among these, partial root-zone irrigation is the most popular and effective because many field crops and some woody crops can save irrigation water up to 20 to 30 % without or with a minimal impact on crop yield. Improved water use efficiency with RDI is mainly due to the following: (1) enhanced guard cell signal transduction network that decreases transpiration water loss, (2) optimized stomatal control that improves the photosynthesis to transpiration ratio, and (3) decreased evaporative surface areas with partial root-zone irrigation that reduces soil evaporation. The mechanisms involved in the plant response to RDI-induced water stress include the morphological traits, e.g., increased root to shoot ratio and improved nutrient uptake and recovery; physiological traits, e.g., stomatal closure, decreased leaf respiration, and maintained photosynthesis; and biochemical traits, e.g., increased signaling molecules and enhanced antioxidation enzymatic activity.

Nanotechnologies for increasing the crop use efficiency of fertilizer-micronutrients

Abstract: Billions of people and many soils across the planet suffer from micronutrient (MN) deficiencies impairing human health. In general, fertilization of deficient soils, according to soil test, with MNs alone and in combination with nitrogen, phosphorous, and potassium (NPK) baseline treatment increases crop yield. The soil applied fertilizer-MN use efficiency (MUE) by crops is <5 % due to a lack of synchronization between the fertilizer-MN release and their crop demand during growth. Nanotechnology and biotechnology have the potential to play a prominent place in transforming agricultural systems and food production worldwide in the coming years. MNs added in microcapsules and nanocapsules, nanomaterials (NMs), and nanoparticles (NPs) are taken up and translocated within plants when grown to maturity, increasing crop yield and MN concentration in plants. Noteworthy, many of the effects of NPs and NMs on crop yield and quality, human health, and associated environmental risks remain to be explored. Increasing MUE requires synchronizing the release of nutrients from fertilizers with crop demand during the growing season. Development of intelligent MN fertilizer delivery platforms (IMNDP) may be possible on the basis of elucidating communication signals between plant roots and soil microorganisms. Important benefits from the development and farm adoption of intelligent MN delivery platforms include increased MUE, reduced fertilizer use, and minimal toxicity and environmental impacts. This article proposes for the first time a novel model for IMNDP to enhance MUE and food quality by enabling the synchronization of MN release from fertilizers according to crop demand.

Cover crops to increase soil microbial diversity and mitigate decline in perennial agriculture. A review

Abstract: Commercial perennial agriculture is prone to declining productivity due to negative plant-soil feedback. An alternative to costly and environmentally harmful conventional treatment such as soil fumigation could be to manipulate soil microbial diversity through careful selection and management of cover crop mixtures. Although cover crops are already used in these systems for other reasons, their capacity to influence soil biota is unexploited. Here, we examine the role of plant diversity and identity on plant-soil feedbacks in the context of perennial agriculture. We identify key microorganisms involved in these feedbacks and explore plant-based strategies for mitigating decline of perennial crop plants. We conclude that (1) increasing plant diversity increases soil microbial diversity, minimizing the proliferation of soil-borne pathogens; (2) populations of beneficial microbes can be increased by increasing plant functional group richness, e.g., legumes, C4 grasses, C3 grasses, and non-leguminous forbs; (3) brassicas suppress fungal pathogens and promote disease-suppressive bacteria; (4) native plants may further promote beneficial soil microbiota; and (5) frequent tillage, herbicide use, and copper fungicides can harm populations of beneficial microbes and, in some cases, contribute to greater crop decline. Non-crop vegetation management is a viable and cost-effective means of minimizing crop decline in perennial monocultures but is in need of more direct experimental investigation in perennial agroecosystems.

Potato Production, Usage, and Nutrition--A Review.

Abstract: Potato is an economically important staple crop prevailing all across the world with successful large-scale production, consumption, and affordability with easy availability in the open market. Potatoes provide basic nutrients such as-carbohydrates, dietary fiber (skin), several vitamins, and minerals (e.g., potassium, magnesium, iron). On occasion exposures to raw and cooked potatoes impart allergic reactions. Dietary intake of potatoes, especially colored potatoes, play an important role in the production of antioxidant defense system by providing essential nutrient antioxidants, such as vitamins, β-carotene, polyphenols, and minerals. This may help lower the incidence of wide range of chronic and acute disease processes (like hypertension, heart diseases, cancer, neurodegenerative, and other diseases). However, retention of nutrients in potatoes is affected by various cooking and processing methods. Cooking at elevated temperature also produces acrylamide-a suspected carcinogen. Independent and/or collaborative studies have been conducted and reported on the various pathways leading to the formation of acrylamide in heat processed foods. This article reviews the latest research on potato production, consumption, nature of phytochemicals and their health benefits, and allergic reactions to children. Also included is the discovery of acrylamide in processed starch-rich foods including potatoes, mechanism of formation, detection methodologies, and mitigation steps to reduce acrylamide content in food.

Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database

Abstract: Microbial inhabitants of soils are important to ecosystem and planetary functions, yet there are large gaps in our knowledge of their diversity and ecology. The ‘Biomes of Australian Soil Environments’ (BASE) project has generated a database of microbial diversity with associated metadata across extensive environmental gradients at continental scale. As the characterisation of microbes rapidly expands, the BASE database provides an evolving platform for interrogating and integrating microbial diversity and function. BASE currently provides amplicon sequences and associated contextual data for over 900 sites encompassing all Australian states and territories, a wide variety of bioregions, vegetation and land-use types. Amplicons target bacteria, archaea and general and fungal-specific eukaryotes. The growing database will soon include metagenomics data. Data are provided in both raw sequence (FASTQ) and analysed OTU table formats and are accessed via the project’s data portal, which provides a user-friendly search tool to quickly identify samples of interest. Processed data can be visually interrogated and intersected with other Australian diversity and environmental data using tools developed by the ‘Atlas of Living Australia’. Developed within an open data framework, the BASE project is the first Australian soil microbial diversity database. The database will grow and link to other global efforts to explore microbial, plant, animal, and marine biodiversity. Its design and open access nature ensures that BASE will evolve as a valuable tool for documenting an often overlooked component of biodiversity and the many microbe-driven processes that are essential to sustain soil function and ecosystem services.

Unraveling Anthocyanin Bioavailability for Human Health

Abstract: This review considers the bioavailability of health-protective anthocyanin pigments from foods, in light of the multiple molecular structures and complicated traffic patterns taken by anthocyanins both as flavonoid metabolites and as phenolic acid metabolites within the body. Anthocyanins have generally been considered to have notoriously poor bioavailability, based on the very low levels typically detected in routine human blood draws after ingestion. Although some investigations have assessed anthocyanin bioavailability solely based on the measurement of parent anthocyanins or phenolic acid breakdown products, more recent research has increasingly revealed the presence, qualitative diversity, relatively high concentrations, and tenacity of molecular intermediates of anthocyanins that retain the unique flavonoid C6-C3-C6 backbone structure. We argue that the persistence of anthocyanin metabolites suggests enterohepatic recycling, leading to prolonged residence time, and supports the notion that anthocyanins are far more bioavailable than previously suggested.

Concerted genomic targeting of H3K27 demethylase REF6 and chromatin-remodeling ATPase BRM in Arabidopsis

Abstract: Yuhai Cui and colleagues report that the H3K27 demethylase REF6 targets genomic loci containing a specific DNA motif via its zinc-finger domains. They show that REF6 facilitates the recruitment of BRM and that deleting the DNA motif from a target gene in Arabidopsis makes it inaccessible to REF6.

Legacy effects of soil moisture on microbial community structure and N2O emissions

Abstract: Soil moisture is a strong determinant of microbial activity exerting dominant control over gaseous and liquid diffusion rates and affecting O2 and substrate availability. Often, measures of microbial community structure and soil moisture status fail to inform our understanding of soil processes, particularly those that are governed by complex feedbacks between substrate availability and environmental conditions (e.g. nitrogen transformations). Nitrous oxide (N2O) emissions, although conceptually regulated by soil moisture, are notoriously difficult to predict based on soil water content and nutrient status. Here, we studied agricultural soils under wetting, drying, and static moisture conditions to assess the impact of current and previous moisture on bacterial 16S rRNA composition; transcription of amoA, hao, norB, and nosZ; and net N2O production. Microbial community composition was dependent on previous moisture. As soils dried, bacterial rRNA contained fewer and more evenly distributed genera. We hypothesize that this was linked to the evenness of resource distribution as controlled by differences in substrate diffusion in wetting vs. drying conditions. N2O flux depended on previous, as well as current, soil moisture status and this legacy effect was greatest at 80% water filled pore space. Overall, we found that previous moisture affected microbial activity, transcription, composition and ultimately, N2O emissions. Our study demonstrates that, for soil microorganisms and processes, it is not only what soil moisture is, but also what it was that is important.

A high-density SNP genotyping array for Brassica napus and its ancestral diploid species based on optimised selection of single-locus markers in the allotetraploid genome

Abstract: Key message TheBrassica napusIllumina array provides genome-wide markers linked to the available genome sequence, a significant tool for genetic analyses of the allotetraploidB. napusand its progenitor diploid genomes.

Plant Virus-Insect Vector Interactions: Current and Potential Future Research Directions.

Abstract: Acquisition and transmission by an insect vector is central to the infection cycle of the majority of plant pathogenic viruses. Plant viruses can interact with their insect host in a variety of ways including both non-persistent and circulative transmission; in some cases, the latter involves virus replication in cells of the insect host. Replicating viruses can also elicit both innate and specific defense responses in the insect host. A consistent feature is that the interaction of the virus with its insect host/vector requires specific molecular interactions between virus and host, commonly via proteins. Understanding the interactions between plant viruses and their insect host can underpin approaches to protect plants from infection by interfering with virus uptake and transmission. Here, we provide a perspective focused on identifying novel approaches and research directions to facilitate control of plant viruses by better understanding and targeting virus–insect molecular interactions. We also draw parallels with molecular interactions in insect vectors of animal viruses, and consider technical advances for their control that may be more broadly applicable to plant virus vectors.

Reinventing potato as a diploid inbred line-based crop

Abstract: The third most important food crop worldwide, potato (Solanum tuberosum L.) is a tetraploid outcrossing species propagated from tubers. Breeders have long been challenged by polyploidy, heterozygosity, and asexual reproduction. It has been assumed that tetraploidy is essential for high yield, that the creation of inbred potato is not feasible, and that propagation by seed tubers is ideal. In this paper, we question those assumptions and propose to convert potato into a diploid inbred line–based crop propagated by true seed. Although a conversion of this magnitude is unprecedented, the possible genetic gains from a breeding system based on inbred lines and the seed production benefits from a sexual propagation system are too large to ignore. We call on leaders of public and private organizations to come together to explore the feasibility of this radical and exciting new strategy in potato breeding. S.H. Jansky, USDA–ARS Vegetable Crops Research Unit, Dep. of Horticulture, Univ. of Wisconsin, 1575 Linden Dr., Madison, WI; A.O. Charkowski, Dep. of Plant Pathology, Univ. of Wisconsin, Madison, WI; D.S. Douches, Dep. of Plant, Soil, and Microbial Sciences, Mich. State Univ., East Lansing, MI; G. Gusmini, Pepsico, St. Paul, MN; C. Richael, Simplot Plant Sciences, Boise, ID; P.C. Bethke and D.M. Spooner, USDA–ARS Vegetable Crops Research Unit, Dep. of Horticulture, Univ. of Wisconsin, Madison, WI; R.G. Novy, USDA– ARS Small Grains and Potato Germplasm Research Unit, Aberdeen, ID; H. De Jong, Agriculture and Agri-Food Canada, Fredericton, New Brunswick, Canada (retired); W.S. De Jong, School of Integrative Plant Sciences, Cornell Univ., Ithaca, NY; J.B. Bamberg USDA–ARS, Dep. of Horticulture, Univ. of Wisconsin, Madison, WI, and US Potato Genebank, Sturgeon Bay, WI; A.L. Thompson, Dep. of Plant Sciences, North Dakota State Univ.; B. Bizimungu, Agriculture and Agri-Food Canada, Fredericton, New Brunswick, Canada; D.G. Holm, Dep. of Horticulture and Landscape Architecture, Colorado State Univ., San Luis Valley Research Center, Center, CO; C.R. Brown, USDA– ARS, Prosser, WA; K.G. Haynes, USDA–ARS, Beltsville, MD; V.R. Sathuvalli, Dep. of Crop and Soil Science, Oregon State Univ., Hermiston Agricultural Research and Extension Center, Hermiston, OR; R.E. Veilleux, Dep. of Horticulture, Virginia Tech, Blacksburg, VA; J.C. Miller, Jr., Dep. of Horticultural Sciences, Texas AM J.M. Bradeen, Dep. of Plant Pathology, Univ. of Minnesota, St. Paul, MN; J. Jiang, Dep. of Horticulture, Univ. of Wisconsin, Madison, WI. G. Gusmini is an employee of PepsiCo, Inc.; the views expressed in this presentation are those of the author and do not necessarily reflect the position or policy of PepsiCo Inc. C. Richael is an employee of Simplot Plant Sciences; the views expressed in this presentation are those of the author and do not necessarily reflect the position or policy of Simplot Plant Sciences. Received 3 Dec. 2015. Accepted 25 Jan. 2016. *Corresponding author (shelley.jansky@ars. usda.gov; shjansky@wisc.edu). Abbreviations: CIP, International Potato Center; ILs, introgression lines; RILs, recombinant inbred lines; TPS, true potato seed. Published in Crop Sci. 56:1412–1422 (2016). doi: 10.2135/cropsci2015.12.0740 © Crop Science Society of America | 5585 Guilford Rd., Madison, WI 53711 USA This is an open access article distributed under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). Published July 7, 2016

Alleviation of Drought Stress and Metabolic Changes in Timothy (Phleum pratense L.) Colonized with Bacillus subtilis B26.

Abstract: Drought is a major limiting factor of crop productivity worldwide and its incidence is predicted to increase under climate change. Drought adaptation of cool-season grasses is thus a major challenge to secure the agricultural productivity under current and future climate conditions. Endophytes are non-pathogenic plant-associated bacteria that can play an important role in conferring resistance and improving plant tolerance to drought. In this study, the effect of inoculation of the bacterial endophyte Bacillus subtilis strain B26 on growth, water status, photosynthetic activity and metabolism of timothy (Phleum pratense L.) subjected to drought stress was investigated under controlled conditions. Under both drought-stress and non-stressed conditions, strain B26 successfully colonized the internal tissues of timothy and had a positive impact on plant growth. Exposure of inoculated plant to a 8-wk drought-stress led to significant increase in shoot and root biomass by 26.6 and 63.8%, and in photosynthesis and stomatal conductance by 55.2 and 214.9% respectively, compared to non-inoculated plants grown under similar conditions. There was a significant effect of the endophyte on plant metabolism; higher levels of several sugars, notably sucrose and fructans and an increase of key amino acids such as, asparagine, glutamic acid and glutamine were recorded in shoots and roots of colonized plants compared to non-colonized ones. The accumulation of the non-protein amino acid GABA in shoots of stressed plants and in roots of stressed and unstressed plants was increased in the presence of the endophyte. Taken together, our results indicate that B. subtilis B26 improves timothy growth under drought stress through the modification of osmolyte accumulation in roots and shoots. These results will contribute to the development of a microbial agent to improve the yield of grass species including forage crops and cereals exposed to environmental stresses.

High Molecular Weight Barley β-Glucan Alters Gut Microbiota Toward Reduced Cardiovascular Disease Risk

Abstract: The physiological cholesterol-lowering benefits of β-glucan have been well documented, however, whether modulation of gut microbiota by β-glucan is associated with these physiological effects remains unknown. The objectives of this study were therefore to determine the impact of β-glucan on the composition of gut microbiota in mildly hypercholesterolemic individuals and to identify if the altered microbiota are associated with bioactivity of β-glucan in improving risk factors of cardiovascular disease (CVD). Using a randomized, controlled crossover study design, individuals received for 5-week either a treatment breakfast containing 3g high molecular weight (HMW), 3g low molecular weight (LMW), 5g LMW barley β-glucan or wheat and rice (WR). The American Heart Association (AHA) diet served as the background diet for all treatment groups. Phases were separated by 4-week washout periods. Fecal samples were collected at the end of each intervention phase and subjected to Illumina sequencing of 16S rRNA genes. Results revealed that at the phylum level, supplementation of 3g/d HMW β-glucan increased Bacteroidetes and decreased Firmicutes abundances compared to control (P < 0.001). At the genus level, consumption of 3g/d HMW β-glucan increased Bacteroides (P < 0.003), tended to increase Prevotella (P < 0.1) but decreased Dorea (P < 0.1), whereas diets containing 5g LMW β-glucan and 3g LMW β-glucan failed to alter the gut microbiota composition. Bacteroides, Prevotella, and Dorea composition correlated (P < 0.05) with shifts of CVD risk factors, including body mass index, waist circumference, blood pressure, as well as triglyceride levels. Our data suggest that consumption of HMW β-glucan favourably alters the composition of the gut microbiota and this altered microbiota profile associates with a reduction of CVD risk markers. Together, our study suggests that β-glucan induced shifts in gut microbiota in a MW-dependent manner and that might be one of the underlying mechanisms responsible for the physiological benefits of β-glucan.

Effects of Ultraviolet Light and High‐Pressure Processing on Quality and Health‐Related Constituents of Fresh Juice Products

Abstract: Fresh juices are highly popular beverages in the global food market. They are perceived as wholesome, nutritious, all-day beverages. For a fast growing category of premium juice products such as cold-pressed juices, minimal-processing nonthermal techniques such as ultraviolet (UV) light and high-pressure processing (HPP) are expected to be used to extend shelf-life while retaining physicochemical, nutritional, and sensory characteristics with reduced microbial loads. Also, UV light and HPP are approved by regulatory agencies and recognized as one of the simplest and very environmentally friendly ways to destroy pathogenic organisms. One of the limitations to their more extensive commercial application lies in the lack of comparative effects on nutritional and quality-related compounds in juice products. This review provides a comparative analysis using 92 studies (UV light: 42, HPP: 50) mostly published between 2004 and 2015 to evaluate the effects of reported UV light and HPP processing conditions on the residual content or activity of bioactive compounds such as vitamins, polyphenols, antioxidants, and oxidative enzymes in 45 different fresh fruit and vegetable juices (low-acid, acid, and high-acid categories). Also, the effects of UV light and HPP on color and sensory characteristics of juices are summarized and discussed.

RGAugury: a pipeline for genome-wide prediction of resistance gene analogs (RGAs) in plants

Abstract: Resistance gene analogs (RGAs), such as NBS-encoding proteins, receptor-like protein kinases (RLKs) and receptor-like proteins (RLPs), are potential R-genes that contain specific conserved domains and motifs. Thus, RGAs can be predicted based on their conserved structural features using bioinformatics tools. Computer programs have been developed for the identification of individual domains and motifs from the protein sequences of RGAs but none offer a systematic assessment of the different types of RGAs. A user-friendly and efficient pipeline is needed for large-scale genome-wide RGA predictions of the growing number of sequenced plant genomes. An integrative pipeline, named RGAugury, was developed to automate RGA prediction. The pipeline first identifies RGA-related protein domains and motifs, namely nucleotide binding site (NB-ARC), leucine rich repeat (LRR), transmembrane (TM), serine/threonine and tyrosine kinase (STTK), lysin motif (LysM), coiled-coil (CC) and Toll/Interleukin-1 receptor (TIR). RGA candidates are identified and classified into four major families based on the presence of combinations of these RGA domains and motifs: NBS-encoding, TM-CC, and membrane associated RLP and RLK. All time-consuming analyses of the pipeline are paralleled to improve performance. The pipeline was evaluated using the well-annotated Arabidopsis genome. A total of 98.5, 85.2, and 100 % of the reported NBS-encoding genes, membrane associated RLPs and RLKs were validated, respectively. The pipeline was also successfully applied to predict RGAs for 50 sequenced plant genomes. A user-friendly web interface was implemented to ease command line operations, facilitate visualization and simplify result management for multiple datasets. RGAugury is an efficiently integrative bioinformatics tool for large scale genome-wide identification of RGAs. It is freely available at Bitbucket: https://bitbucket.org/yaanlpc/rgaugury .

Bound Phenolics of Quinoa Seeds Released by Acid, Alkaline, and Enzymatic Treatments and Their Antioxidant and α-Glucosidase and Pancreatic Lipase Inhibitory Effects.

Abstract: Unextractable phenolics from plant foods and their role in health benefits have become increasingly important. Meal residues of three quinoa seeds free of fat and extractable phenolics were subjected to acid, alkaline, and enzymatic hydrolyses. The total and individual phenolic compounds released were analyzed, and 19 phenolics, predominantly phenolic acids and several flavonoids, were identified. The concentration of bound phenolics was highest in black quinoa followed by red and white, regardless of the hydrolysis method. Higher phenolic contents also showed stronger antioxidant activities and inhibition of α-glucosidase and pancreatic lipase activities. Carbohydrases, that is, pectinase, xylanase and feruloyl esterase, which effectively liberated bound phenolics are known to be secreted by colonic bacteria, suggesting potential antioxidant and anti-inflammatory effects by these compounds in the large intestine during colonic fermentation. These results can also be applied to treat foods high in bound phenolics to enhance bioaccessibility.

Microbial biotransformation of DON: molecular basis for reduced toxicity

Abstract: Bacteria are able to de-epoxidize or epimerize deoxynivalenol (DON), a mycotoxin, to deepoxy-deoxynivalenol (deepoxy-DON or DOM-1) or 3-epi-deoxynivalenol (3-epi-DON), respectively. Using different approaches, the intestinal toxicity of 3 molecules was compared and the molecular basis for the reduced toxicity investigated. In human intestinal epithelial cells, deepoxy-DON and 3-epi-DON were not cytotoxic, did not change the oxygen consumption or impair the barrier function. In intestinal explants, exposure for 4 hours to 10 μM DON induced intestinal lesions not seen in explants treated with deepoxy-DON and 3-epi-DON. A pan-genomic transcriptomic analysis was performed on intestinal explants. 747 probes, representing 323 genes, were differentially expressed, between DON-treated and control explants. By contrast, no differentially expressed genes were observed between control, deepoxy-DON and 3-epi-DON treated explants. Both DON and its biotransformation products were able to fit into the pockets of the A-site of the ribosome peptidyl transferase center. DON forms three hydrogen bonds with the A site and activates MAPKinases (mitogen-activated protein kinases). By contrast deepoxy-DON and 3-epi-DON only form two hydrogen bonds and do not activate MAPKinases. Our data demonstrate that bacterial de-epoxidation or epimerization of DON altered their interaction with the ribosome, leading to an absence of MAPKinase activation and a reduced toxicity.

The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence

Abstract: The yellow potato cyst nematode, Globodera rostochiensis, is a devastating plant pathogen of global economic importance. This biotrophic parasite secretes effectors from pharyngeal glands, some of which were acquired by horizontal gene transfer, to manipulate host processes and promote parasitism. G. rostochiensis is classified into pathotypes with different plant resistance-breaking phenotypes. We generate a high quality genome assembly for G. rostochiensis pathotype Ro1, identify putative effectors and horizontal gene transfer events, map gene expression through the life cycle focusing on key parasitic transitions and sequence the genomes of eight populations including four additional pathotypes to identify variation. Horizontal gene transfer contributes 3.5 % of the predicted genes, of which approximately 8.5 % are deployed as effectors. Over one-third of all effector genes are clustered in 21 putative ‘effector islands’ in the genome. We identify a dorsal gland promoter element motif (termed DOG Box) present upstream in representatives from 26 out of 28 dorsal gland effector families, and predict a putative effector superset associated with this motif. We validate gland cell expression in two novel genes by in situ hybridisation and catalogue dorsal gland promoter element-containing effectors from available cyst nematode genomes. Comparison of effector diversity between pathotypes highlights correlation with plant resistance-breaking. These G. rostochiensis genome resources will facilitate major advances in understanding nematode plant-parasitism. Dorsal gland promoter element-containing effectors are at the front line of the evolutionary arms race between plant and parasite and the ability to predict gland cell expression a priori promises rapid advances in understanding their roles and mechanisms of action.

Salt stress (NaCl) affects plant growth and branch pathways of carotenoid and flavonoid biosyntheses in Solanum nigrum

Abstract: In this study, we set out to investigate the effect of sodium chloride (NaCl) on carotenoid and flavonoid production by the black nightshade (Solanum nigrum L.). The study was carried out under green chamber conditions using seedlings subjected to 0, 50, 100 and 150 mM NaCl for 3 weeks. The negative effect of NaCl on dry biomass production of roots and leaves were accompanied by a significant restriction in K+, Ca2+ and Mg2+ ion uptake and by an increase in Na+ ion concentrations, the effects of which were most pronounced at the highest NaCl level. Salt stress also induced oxidative stress, according to the amplified levels of thiobarbituric acid reactive substances and relative ion leakage ratio. Expression of some related carotenoid (phytoene synthase 2 and β-lycopene cyclase) and flavonoids genes (phenylalanine ammonialyase, chalcone synthase and flavonol synthase) were induced by NaCl, followed enhanced production of β-carotene, lutein, and quercetin 3-β-d-glucoside. At the highest NaCl level (150 mM NaCl), quercetin 3-β-d-glucoside synthesis came at the expense of reduced β-carotene and lutein, while salt stress treatment affected leaf antioxidant activities to a great extent relative to the control. Our data suggest that the potential antioxidant properties of carotenoids and flavonoids and their related key genes may be efficiently involved in the restriction of salt-induced oxidative damages.

Antimicrobial usage and resistance in beef production

Abstract: Antimicrobials are critical to contemporary high-intensity beef production. Many different antimicrobials are approved for beef cattle, and are used judiciously for animal welfare, and controversially, to promote growth and feed efficiency. Antimicrobial administration provides a powerful selective pressure that acts on the microbial community, selecting for resistance gene determinants and antimicrobial-resistant bacteria resident in the bovine flora. The bovine microbiota includes many harmless bacteria, but also opportunistic pathogens that may acquire and propagate resistance genes within the microbial community via horizontal gene transfer. Antimicrobial-resistant bovine pathogens can also complicate the prevention and treatment of infectious diseases in beef feedlots, threatening the efficiency of the beef production system. Likewise, the transmission of antimicrobial resistance genes to bovine-associated human pathogens is a potential public health concern. This review outlines current antimicrobial use practices pertaining to beef production, and explores the frequency of antimicrobial resistance in major bovine pathogens. The effect of antimicrobials on the composition of the bovine microbiota is examined, as are the effects on the beef production resistome. Antimicrobial resistance is further explored within the context of the wider beef production continuum, with emphasis on antimicrobial resistance genes in the food chain, and risk to the human population.

The pathogenesis of necrotic enteritis in chickens: what we know and what we need to know: a review.

Abstract: This review summarizes advances in understanding the pathogenesis of necrotic enteritis of chickens caused by netB-positive Clostridium perfringens. The discovery of NetB as the essential toxin trigger for the disease was followed by recognition that it forms part of a large plasmid-encoded 42 kb pathogenicity locus (NELoc-1). While the locus is critical for toxin production, it likely has additional functions related to colonization and degradation of the mucus barrier, which are essential both to multiplication and to bringing NetB close to the intestinal epithelium. Two "chitinases" (glycoside hydrolases (GHs)) present on NELoc-1 are predicted to be involved in mucin degradation, as is the large carbohydrate-binding metalloprotease, shown to be involved in mucinase activity in other clostridia. A second pathogenicity locus found in netB-positive C. perfringens, NELoc-2, also encodes a GH likely involved in mucin degradation. Upon reaching a sufficient cell density on the intestinal mucosa, the Agr-like quorum-sensing system is triggered, which in turn up-regulates the VirR/VirS regulon. This regulon includes NetB. Where NetB initiates damage is unresolved, but it may be deep in the intestinal mucosa, rather than superficially. As the disease progresses, C. perfringens line what remains of the intestinal epithelium in large numbers. This likely involves a number of different bacterial adhesins, including additional NELoc-1-encoded bacterial surface proteins, some of which may adhere to epithelial cell ligands exposed by bacterial sialidases. Further studies of the pathogenesis of necrotic enteritis should lead to development of novel ways to control the infection.

Back to the future of soil metagenomics

Abstract: Direct extraction and characterization of microbial community DNA through PCR amplicon surveys and metagenomics has revolutionized the study of environmental microbiology and microbial ecology. In particular, metagenomic analysis of nucleic acids provides direct access to the genomes of the “uncultivated majority.” Accelerated by advances in sequencing technology, microbiologists have discovered more novel phyla, classes, genera, and genes from microorganisms in the first decade and a half of the twenty-first century than since these “many very little living animalcules” were first discovered by van Leeuwenhoek (Table 1). The unsurpassed diversity of soils promises continued exploration of a range of industrial, agricultural, and environmental functions. The ability to explore soil microbial communities with increasing capacity offers the highest promise for answering many outstanding who, what, where, when, why, and with whom questions such as: Which microorganisms are linked to which soil habitats? How do microbial abundances change with changing edaphic conditions? How do microbial assemblages interact and influence one another synergistically or antagonistically? What is the full extent of soil microbial diversity, both functionally and phylogenetically? What are the dynamics of microbial communities in space and time? How sensitive are microbial communities to a changing climate? What is the role of horizontal gene transfer in the stability of microbial communities? Do highly diverse microbial communities confer resistance and resilience in soils?

Canola/rapeseed protein-functionality and nutrition

Abstract: Protein rich meal is a valuable co-product of canola/rapeseed oil extraction. Seed storage proteins that include cruciferin (11S) and napin (2S) dominate the protein complement of canola while oleosins, lipid transfer proteins and other minor proteins of non-storage nature are also found. Although oil-free canola meal contains 36–40% protein on a dry weight basis, non-protein components including fibre, polymeric phenolics, phytates and sinapine, etc . of the seed coat and cellular components make protein less suitable for food use. Separation of canola protein from non-protein components is a technical challenge but necessary to obtain full nutritional and functional potential of protein. Process conditions of raw material and protein preparation are critical of nutritional and functional value of the final protein product. The storage proteins of canola can satisfy many nutritional and functional requirements for food applications. Protein macromolecules of canola also provide functionalities required in applications beyond edible uses; there exists substantial potential as a source of plant protein and a renewable biopolymer. Available information at present is mostly based on the protein products that can be obtained as mixtures of storage protein types and other chemical constituents of the seed; therefore, full potential of canola storage proteins is yet to be revealed.