Faculty of Agricultural and Food Sciences

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Open Access
Respiratory Symptoms and Lung Function in Poultry Confinement Workers in Western Canada
(2003-1-1) Kirychuk, Shelley P; Senthilselvan, Ambikaipakan; Dosman, James A; Juorio, Victor; Feddes, John JR; Willson, Philip; Classen, Henry; Reynolds, Stephen J; Guenter, Wilhelm; Hurst, Thomas S
OBJECTIVE: To determine whether poultry production methods impact respiratory health, and whether poultry farmers have more respiratory symptoms and lower lung function than comparison control groups.DESIGN: Cross-sectional study.SETTING: Provinces of Saskatchewan, Alberta and Manitoba during the winters of 1997 to 1999. POPULATION: Three hundred three poultry workers, 241 grain farmers and 206 nonfarming control subjects were studied. Poultry workers were further classified according to the poultry housing type in which they worked, ie, workers who worked with poultry raised on the floor (floor-based operations), which included broiler/roaster, broiler/breeder and turkey operations (n=181), and workers who worked with poultry raised in a caged setting (cage-based operations), which included egg operations (n=122).INTERVENTIONS: Subjects completed a respiratory health questionnaire, which included questions on the poultry operation and work habits, and participated in lung function testing.MAIN RESULTS: Overall, this study indicated that poultry workers report greater prevalences of current and chronic respiratory symptoms than control populations, and that the type of production method (cage-based versus floor-based) appears to influence the prevalence of respiratory symptoms and lung function values. Workers from cage-based operations report greater prevalences of current cough and wheeze, as well as lower mean values for forced expiratory volume in the first second (FEV1), forced expiratory flow at 25% to 75% of vital capacity (FEF25-75) and FEV1/FVC than workers from floor-based facilities. Workers from cage-based facilities also reported greater prevalences of current and chronic cough and phlegm, as well as significantly lower FEF25-75 and FEV1/FVC values than nonfarming control subjects. Furthermore, grain farmers had lower FVC and FEV1 values than nonfarmers.CONCLUSIONS: The results suggest that the type of poultry production system (ie, floor- versus cage-based) appears to have an effect on the respiratory response of workers from these facilities. Further studies are required to understand the physiological mechanisms of respiratory dysfunction and the relationships concerning workplace exposure among poultry workers.
Open Access
Age-related Changes in p56lck Protein Levels and Phenotypic Distribution of T Lymphocytes in Young Rats
(2005-03) Hosea, Heather J.; Rector, Edward S.; Taylor, Carla G.
p56lck is involved in the maturation of T-cells from double negative (DN) into double positive (DP) T-cells. The objective of this experiment was to determine changes in the levels of thymic and splenic T-cell p56lck using Western immunoblotting, along with the proportion and number of T-cell subsets in thymus, spleen and blood using flow cytometry in growing Sprague-Dawley rats. Thymic p56lck levels were negatively correlated with age (r=-0.42, p=0.04) and positively correlated with age in the spleen (r=0.50, p=0.01). Nine-week-old rats had a higher percentage of thymic DN and CD8 cells with fewer DP cells compared to younger rats. There were minor differences in the proportions of T-cell subsets in the spleen and blood. T-cell numbers remained proportional to body weight in the lymphoid organs; however, the lower absolute number of T-cells in the younger rats might indicate that they are less able to respond to antigens.
Open Access
Integration of Solexa sequences on an ultradense genetic map in Brassica rapa L.
(2011-05-19) Li, Wei; Zhang, Jiefu; Mou, Yanglong; Geng, Jianfeng; McVetty, Peter B; Hu, Shengwu; Li, Genyi
Abstract Background Sequence related amplified polymorphism (SRAP) is commonly used to construct high density genetic maps, map genes and QTL of important agronomic traits in crops and perform genetic diversity analysis without knowing sequence information. To combine next generation sequencing technology with SRAP, Illumina's Solexa sequencing was used to sequence tagged SRAP PCR products. Results Three sets of SRAP primers and three sets of tagging primers were used in 77,568 SRAP PCR reactions and the same number of tagging PCR reactions respectively to produce a pooled sample for Illumina's Solexa sequencing. After sequencing, 1.28 GB of sequence with over 13 million paired-end sequences was obtained and used to match Solexa sequences with their corresponding SRAP markers and to integrate Solexa sequences on an ultradense genetic map. The ultradense genetic bin map with 465 bins was constructed using a recombinant inbred (RI) line mapping population in B. rapa. For this ultradense genetic bin map, 9,177 SRAP markers, 1,737 integrated unique Solexa paired-end sequences and 46 SSR markers representing 10,960 independent genetic loci were assembled and 141 unique Solexa paired-end sequences were matched with their corresponding SRAP markers. The genetic map in B. rapa was aligned with the previous ultradense genetic map in B. napus through common SRAP markers in these two species. Additionally, SSR markers were used to perform alignment of the current genetic map with other five genetic maps in B. rapa and B. napus. Conclusion We used SRAP to construct an ultradense genetic map with 10,960 independent genetic loci in B. rapa that is the most saturated genetic map ever constructed in this species. Using next generation sequencing, we integrated 1,878 Solexa sequences on the genetic map. These integrated sequences will be used to assemble the scaffolds in the B. rapa genome. Additionally, this genetic map may be used for gene cloning and marker development in B. rapa and B. napus.
Open Access
Versatile surface biofunctionalization of poly(ethylene terephthalate) by interpenetrating polymerization of a butynyl monomer followed by “Click Chemistry”
(Elsevier, 2011-11-27) Li, Lingdong; Zhao, Nan; Liu, Song
Biofunctionalization of poly(ethylene terephthalate) (PET) is crucial to its medical and biomedical applications such as surgical drapes, vascular grafts and ligament prostheses. To furnish PET with an alkynyl handle, N-(2-methylbut-3-yn-2-yl)acrylamide (MBAA) underwent photo-initiated copolymerization with N,N0-methylenebisacrylamide (MBA) in methanol-swollen PET surface to form a 3- dimensional interpenetrating network (IPN). The alkynyl handle terminated surface was denoted as PMBAA-PET. A region-selective modification could be achieved using an engraved mask during the photo-initiated copolymerization. Several functional azides including dansyl-azide 1, azido-5,5- dimethyl-hydantoin analog 2, per-azido-b-cyclodextrin (per-azido-b-CD) and azido-Bovine Serum Albumin (BSA-N3), were successfully bonded onto PMBAA-PET surface via Huisgen 1,3-dipolar cycloaddition. Kinetic study of the heterogeneous “click” reaction between PMBAA-PET and 1 was investigated using X-ray photoelectron spectroscopy (XPS) and elemental analysis. PMBAA-PET was rendered with effective biocidal activity against a healthcare-associated methicilin-resistant Staphylococcus aureus (HAMRSA) and a multi-drug-resistant Escherichia coli (MDR-E. coli) after 2 was conferred. Meanwhile, accessible CD cavity was determined and the amount of covalently immobilized BSA protein was also quantified after the respective “click” linkages of per-azido-b-CD and BSA-N3 on PMBAA-PET surface were established.
Open Access
Structural and Biochemical Changes in Salicylic-Acid-Treated Date Palm Roots Challenged with Fusarium oxysporum f. sp. albedinis
(2011-12-7) Dihazi, Abdelhi; Serghini, Mohammed Amine; Jaiti, Fatima; Daayf, Fouad; Driouich, Azeddine; Dihazi, Hassan; El Hadrami, Ismail
Histochemical and ultrastructural analyses were carried out to assess structural and biochemical changes in date palm roots pretreated with salicylic acid (SA) then inoculated with Fusarium oxysporum f. sp. albedinis (Foa). Flavonoids, induced proteins, and peroxidase activity were revealed in root tissues of SA-treated plants after challenge by Foa. These reactions were closely associated with plant resistance to Foa. Host reactions induced after inoculation of SA-treated plants with Foa included the plugging of intercellular spaces, the deposition of electron-dense materials at the sites of pathogen penetration, and several damages to fungal cells. On the other hand, untreated inoculated plants showed marked cell wall degradation and total cytoplasm disorganization, indicating the protective effects provided by salicylic acid in treated plants.
Open Access
Surface Engineering of Poly(ethylene terephthalate) for Durable Hemocompatibility via a Surface Interpenetrating Network Technique
(Wiley, 2012-05-08) Li, Jiang; Lin, Francis; Li, Lingdong; Li, Jing; Liu, Song
Heparin was covalently bonded on chemically inert PET substrate using a surface modifi cation technique–surface interpenetrating network with the purpose of fabricating long-lasting biocompatible materials as vascular grafts. FTIR and XPS spectra confi rmed the successful heparinization of PET (PET-Hep). The density of surface-immobilized heparin as quantifi ed by a colorimetric method could reach 2.4 μ g cm − 2 (in the reported optimal range: 1.5–3.0 μ g cm − 2 ). The hemocompatibility of the heparin-immobilized PET was improved as evidenced by a platelet adhesion test: signifi cantly less platelet adhesion on PET-Hep (11.60%) than on untreated PET (48.91%). An MTT assay indicated PET-Hep was nontoxic to human dermal fi broblast cells. After an initial 5.24% loss of heparin from PETHep in the fi rst 14 h immersion in PBS buffer solution, no further leaching of heparin was found.
Open Access
Menhaden oil, but not safflower or soybean oil, aids in restoring the polyunsaturated fatty acid profile in the novel [increment]-6-desaturase null mouse
(2012-05-29) Monteiro, Jessica; Li, Feng-Jun; MacLennan, Mira; Rabalski, Alexandra; Moghadasian, Mohammed H; Nakamura, Manabu T; Ma, David WL
AbstractBackgroundPolyunsaturated fatty acids (PUFA) have diverse biological effects, from promoting inflammation to preventing cancer and heart disease. Growing evidence suggests that individual PUFA may have independent effects in health and disease. The individual roles of the two essential PUFA, linoleic acid (LA) and α-linolenic acid (ALA), have been difficult to discern from the actions of their highly unsaturated fatty acid (HUFA) downstream metabolites. This issue has recently been addressed through the development of the Δ-6 desaturase knock out (D6KO) mouse, which lacks the rate limiting Δ-6 desaturase enzyme and therefore cannot metabolize LA or ALA. However, a potential confounder in this model is the production of novel Δ-5 desaturase (D5D) derived fatty acids when D6KO mice are fed diets containing LA and ALA, but void of arachidonic acid.ObjectiveThe aim of the present study was to characterize how the D6KO model differentially responds to diets containing the essential n-6 and n-3 PUFA, and whether the direct provision of downstream HUFA can rescue the phenotype and prevent the production of D5D fatty acids.MethodologyLiver and serum phospholipid (PL) fatty acid composition was examined in D6KO and wild type mice fed i) 10% safflower oil diet (SF, LA rich) ii) 10% soy diet (SO, LA+ALA) or iii) 3% menhaden oil +7% SF diet (MD, HUFA rich) for 28 days (n = 3-7/group).ResultsNovel D5D fatty acids were found in liver PL of D6KO fed SF or SO-fed mice, but differed in the type of D5D fatty acid depending on diet. Conversely, MD-fed D6KO mice had a liver PL fatty acid profile similar to wild-type mice.ConclusionsThrough careful consideration of the dietary fatty acid composition, and especially the HUFA content in order to prevent the synthesis of D5D fatty acids, the D6KO model has the potential to elucidate the independent biological and health effects of the parent n-6 and n-3 fatty acids, LA and ALA.
Open Access
Durability of amide N-chloramine biocides to ethylene oxide sterilization
(Oxford University Press, 2012-07-01) Zhao, Nan; Logsetty, Sarvesh; Liu, Song
The objective of this work is to study the stability of three novel topical antimicrobial dressings consisting of amide N-chloramine structures against ethylene oxide sterilization. Cotton gauze samples bonded with one of three amide N-chloramine structures were subjected to standard ethylene oxide (EtO) sterilization. The amounts of amide N-chloramine structures before and after the sterilization were quantified to indicate the stabilities of these amide N-chloramine structures to the sterilization. The samples after sterilization were challenged with a clinical isolate of healthcare-associated multidrug-resistant Escherichia coli. N-Chloramine structure converted from polymethacrylamide (dressing 2) had the highest durability (89.7% retained active chlorine) toward EtO sterilization; that from hydantoin (dressing 3; 86.3% retained active chlorine) followed; and poly(N-chloroacrylamide) (dressing 1) had the lowest (64.0% retained active chlorine). After EtO sterilization, all the samples still reduced E. coli presence at 5 minutes of contact, with dressing 2 retaining a log 6 reduction. The three tested amide N-chloramine structures could all survive EtO sterilization while retaining percentages of active chlorine ranging from 64.0 to 89.7%. Dressing 2 showed the best durability, whereas dressing 1 had the poorest durability. With the remaining amounts of amide N-chloramine structures after EtO sterilization, all the dressings could still reduce E. coli numbers within 5 minutes of contact, and dressing 2 resulted in a log 6 reduction in colony count.
Open Access
New Biocide with Both N -Chloramine and Quaternary Ammonium Moieties Exerts Enhanced Bactericidal Activity
(Wiley, 2012-07-03) Li, Lingdong; Pu, Tianyun; Zhanel, George; Zhao, Nan; Ens, Werner; Liu, Song
Considering the rise of antibiotic resistance, the development of new antibacterial agents with improved biocidal functions is urgently required. In this study, ionic 5,5-dimethylhydantoin (DMH) analogues containing either a quaternary ammonium moiety (2)–4) or a phosphonate functional group (5),–6), were designed and synthesized to investigate the possible enhancing effect of quaternary ammonium moieties on the antibacterial performance of N -chloramines. These ionic DMH analogues were converted to their N- chloramine counterparts either in free form or after being covalently immobilized on a polymer surface via the “click” chemistry method. In the subsequent antimicrobial assessment against multi-drug-resistant Escherichia coli (MDRE. coli ) and methicillin-resistant Staphylococcus aureus (MRSA), chlorinated 2 and 3, the cyclic N -chloramines with a structural cation, exhibited distinctly enhanced biocidal functions in solution and after immobilization on surfaces.
Open Access
Normative Data for Bone Mass in Healthy Term Infants from Birth to 1 Year of Age
(2012-10-2) Gallo, Sina; Vanstone, Catherine A.; Weiler, Hope A.
For over 2 decades, dual-energy X-ray absorptiometry (DXA) has been the gold standard for estimating bone mineral density (BMD) and facture risk in adults. More recently DXA has been used to evaluate BMD in pediatrics. However, BMD is usually assessed against reference data for which none currently exists in infancy. A prospective study was conducted to assess bone mass of term infants (37 to 42 weeks of gestation), weight appropriate for gestational age, and born to healthy mothers. The group consisted of 33 boys and 26 girls recruited from the Winnipeg Health Sciences Center (Manitoba, Canada). Whole body (WB) as well as regional sites of the lumbar spine (LS 1–4) and femur was measured using DXA (QDR 4500A, Hologic Inc.) providing bone mineral content (BMC) for all sites and BMD for spine. During the year, WB BMC increased by 200% ( versus g), spine BMC by 130% ( versus g), and femur BMC by 190% ( versus g). Spine BMD increased by 14% ( versus g/cm2) during the year. This data, representing the accretion of bone mass during the first year of life, is based on a representative sample of infants and will aid in the interpretation of diagnostic DXA scans by researchers and health professionals.
Open Access
SNP Discovery through Next-Generation Sequencing and Its Applications
(2012-11-22) Kumar, Santosh; Banks, Travis W.; Cloutier, Sylvie
The decreasing cost along with rapid progress in next-generation sequencing and related bioinformatics computing resources has facilitated large-scale discovery of SNPs in various model and nonmodel plant species. Large numbers and genome-wide availability of SNPs make them the marker of choice in partially or completely sequenced genomes. Although excellent reviews have been published on next-generation sequencing, its associated bioinformatics challenges, and the applications of SNPs in genetic studies, a comprehensive review connecting these three intertwined research areas is needed. This paper touches upon various aspects of SNP discovery, highlighting key points in availability and selection of appropriate sequencing platforms, bioinformatics pipelines, SNP filtering criteria, and applications of SNPs in genetic analyses. The use of next-generation sequencing methodologies in many non-model crops leading to discovery and implementation of SNPs in various genetic studies is discussed. Development and improvement of bioinformatics software that are open source and freely available have accelerated the SNP discovery while reducing the associated cost. Key considerations for SNP filtering and associated pipelines are discussed in specific topics. A list of commonly used software and their sources is compiled for easy access and reference.
Open Access
DNA barcoding of Northern Nearctic Muscidae (Diptera) reveals high correspondence between morphological and molecular species limits
(2012-11-23) Renaud, Anais K; Savage, Jade; Adamowicz, Sarah J
Abstract Background Various methods have been proposed to assign unknown specimens to known species using their DNA barcodes, while others have focused on using genetic divergence thresholds to estimate “species” diversity for a taxon, without a well-developed taxonomy and/or an extensive reference library of DNA barcodes. The major goals of the present work were to: a) conduct the largest species-level barcoding study of the Muscidae to date and characterize the range of genetic divergence values in the northern Nearctic fauna; b) evaluate the correspondence between morphospecies and barcode groupings defined using both clustering-based and threshold-based approaches; and c) use the reference library produced to address taxonomic issues. Results Our data set included 1114 individuals and their COI sequences (951 from Churchill, Manitoba), representing 160 morphologically-determined species from 25 genera, covering 89% of the known fauna of Churchill and 23% of the Nearctic fauna. Following an iterative process through which all specimens belonging to taxa with anomalous divergence values and/or monophyly issues were re-examined, identity was modified for 9 taxa, including the reinstatement of Phaonia luteva (Walker) stat. nov. as a species distinct from Phaonia errans (Meigen). In the post-reassessment data set, no distinct gap was found between maximum pairwise intraspecific distances (range 0.00-3.01%) and minimum interspecific distances (range: 0.77-11.33%). Nevertheless, using a clustering-based approach, all individuals within 98% of species grouped with their conspecifics with high (>95%) bootstrap support; in contrast, a maximum species discrimination rate of 90% was obtained at the optimal threshold of 1.2%. DNA barcoding enabled the determination of females from 5 ambiguous species pairs and confirmed that 16 morphospecies were genetically distinct from named taxa. There were morphological differences among all distinct genetic clusters; thus, no cases of cryptic species were detected. Conclusions Our findings reveal the great utility of building a well-populated, species-level reference barcode database against which to compare unknowns. When such a library is unavailable, it is still possible to obtain a fairly accurate (within ~10%) rapid assessment of species richness based upon a barcode divergence threshold alone, but this approach is most accurate when the threshold is tuned to a particular taxon.
Open Access
Genome wide SNP discovery in flax through next generation sequencing of reduced representation libraries
(2012-12-06) Kumar, Santosh; You, Frank M; Cloutier, Sylvie
Abstract Background Flax (Linum usitatissimum L.) is a significant fibre and oilseed crop. Current flax molecular markers, including isozymes, RAPDs, AFLPs and SSRs are of limited use in the construction of high density linkage maps and for association mapping applications due to factors such as low reproducibility, intense labour requirements and/or limited numbers. We report here on the use of a reduced representation library strategy combined with next generation Illumina sequencing for rapid and large scale discovery of SNPs in eight flax genotypes. SNP discovery was performed through in silico analysis of the sequencing data against the whole genome shotgun sequence assembly of flax genotype CDC Bethune. Genotyping-by-sequencing of an F6-derived recombinant inbred line population provided validation of the SNPs. Results Reduced representation libraries of eight flax genotypes were sequenced on the Illumina sequencing platform resulting in sequence coverage ranging from 4.33 to 15.64X (genome equivalents). Depending on the relatedness of the genotypes and the number and length of the reads, between 78% and 93% of the reads mapped onto the CDC Bethune whole genome shotgun sequence assembly. A total of 55,465 SNPs were discovered with the largest number of SNPs belonging to the genotypes with the highest mapping coverage percentage. Approximately 84% of the SNPs discovered were identified in a single genotype, 13% were shared between any two genotypes and the remaining 3% in three or more. Nearly a quarter of the SNPs were found in genic regions. A total of 4,706 out of 4,863 SNPs discovered in Macbeth were validated using genotyping-by-sequencing of 96 F6 individuals from a recombinant inbred line population derived from a cross between CDC Bethune and Macbeth, corresponding to a validation rate of 96.8%. Conclusions Next generation sequencing of reduced representation libraries was successfully implemented for genome-wide SNP discovery from flax. The genotyping-by-sequencing approach proved to be efficient for validation. The SNP resources generated in this work will assist in generating high density maps of flax and facilitate QTL discovery, marker-assisted selection, phylogenetic analyses, association mapping and anchoring of the whole genome shotgun sequence.
Open Access
Global Gene Expression Profiling in PPAR-γ Agonist-Treated Kidneys in an Orthologous Rat Model of Human Autosomal Recessive Polycystic Kidney Disease
(2012-5-13) Yoshihara, Daisuke; Kugita, Masanori; Yamaguchi, Tamio; Aukema, Harold M.; Kurahashi, Hiroki; Morita, Miwa; Hiki, Yoshiyuki; Calvet, James P.; Wallace, Darren P.; Toyohara, Takafumi; Abe, Takaaki; Nagao, Shizuko
Kidneys are enlarged by aberrant proliferation of tubule epithelial cells leading to the formation of numerous cysts, nephron loss, and interstitial fibrosis in polycystic kidney disease (PKD). Pioglitazone (PIO), a PPAR-γ agonist, decreased cell proliferation, interstitial fibrosis, and inflammation, and ameliorated PKD progression in PCK rats (Am. J. Physiol.-Renal, 2011). To explore genetic mechanisms involved, changes in global gene expression were analyzed. By Gene Set Enrichment Analysis of 30655 genes, 13 of the top 20 downregulated gene ontology biological process gene sets and six of the top 20 curated gene set canonical pathways identified to be downregulated by PIOtreatment were related to cell cycle and proliferation, including EGF, PDGF and JNK pathways. Their relevant pathways were identified using the Kyoto Encyclopedia of Gene and Genomes database. Stearoyl-coenzyme A desaturase 1 is a key enzyme in fatty acid metabolism found in the top 5 genes downregulated by PIO treatment. Immunohistochemical analysis revealed that the gene product of this enzyme was highly expressed in PCK kidneys and decreased by PIO. These data show that PIO alters the expression of genes involved in cell cycle progression, cell proliferation, and fatty acid metabolism.
Open Access
Modelling Soil Water Retention for Weed Seed Germination Sensitivity to Water Potential
(2012-5-6) Bullied, W. John; Bullock, Paul R.; Van Acker, Rene C.
Soil water retention is important for the study of water availability to germinating weed seeds. Six soil water retention models (Campbell, Brooks-Corey, four- and five-parameter van Genuchten, Tani, and Russo) with residual soil water parameter derivations were evaluated to describe water retention for weed seed germination at minimum threshold soil water potential for three hillslope positions. The Campbell, Brooks-Corey, and four-parameter van Genuchten model with modified or estimated forms of the residual parameter had superior but similar data fit. The Campbell model underestimated water retention at a potential less than −0.5 MPa for the upper hillslope that could result in underestimating seed germination. The Tani and Russo models overestimated water retention at a potential less than −0.1 MPa for all hillslope positions. Model selection and residual parameter specification are important for weed seed germination by representing water retention at the level of minimum threshold water potential for germination. Weed seed germination models driven by the hydrothermal soil environment rely on the best-fitting soil water retention model to produce dynamic predictions of seed germination.
Open Access
Consumption of low-fat dairy foods for 6 months improves insulin resistance without adversely affecting lipids or bodyweight in healthy adults: a randomized free-living cross-over study
(2013-05-02) Rideout, Todd C; Marinangeli, Christopher P F; Martin, Heather; Browne, Richard W; Rempel, Curtis B
Abstract Background Given the highly debated role of dairy food consumption in modulating biomarkers of metabolic syndrome, this study was conducted to examine the influence of long-term (6 month) dairy consumption on metabolic parameters in healthy volunteers under free-living conditions without energy restriction. Methods Twenty-three healthy subjects completed a randomized, crossover trial of 12 months. Participants consumed their habitual diets and were randomly assigned to one of two treatment groups: a high dairy supplemented group instructed to consume 4 servings of dairy per day (HD); or a low dairy supplemented group limited to no more than 2 servings of dairy per day (LD). Baseline, midpoint, and endpoint metabolic responses were examined. Results Endpoint measurements of body weight and composition, energy expenditure, blood pressure, blood glucose, and blood lipid and lipoprotein responses did not differ (p > 0.05) between the LD and HD groups. HD consumption improved (p < 0.05) plasma insulin (-9%) and insulin resistance (-11%, p = 0.03) as estimated by HOMA-IR compared with the LD group. Conclusions Study results suggest that high dairy consumption (4 servings/d) may improve insulin resistance without negatively impacting bodyweight or lipid status under free-living conditions. Trial registration Trial registration: NCT01761955
Open Access
Genetic characterization of a core collection of flax (Linum usitatissimum L.) suitable for association mapping studies and evidence of divergent selection between fiber and linseed types
(2013-05-06) Soto-Cerda, Braulio J; Diederichsen, Axel; Ragupathy, Raja; Cloutier, Sylvie
Abstract Background Flax is valued for its fiber, seed oil and nutraceuticals. Recently, the fiber industry has invested in the development of products made from linseed stems, making it a dual purpose crop. Simultaneous targeting of genomic regions controlling stem fiber and seed quality traits could enable the development of dual purpose cultivars. However, the genetic diversity, population structure and linkage disequilibrium (LD) patterns necessary for association mapping (AM) have not yet been assessed in flax because genomic resources have only recently been developed. We characterized 407 globally distributed flax accessions using 448 microsatellite markers. The data was analyzed to assess the suitability of this core collection for AM. Genomic scans to identify candidate genes selected during the divergent breeding process of fiber flax and linseed were conducted using the whole genome shotgun sequence of flax. Results Combined genetic structure analysis assigned all accessions to two major groups with six sub-groups. Population differentiation was weak between the major groups (FST = 0.094) and for most of the pairwise comparisons among sub-groups. The molecular coancestry analysis indicated weak relatedness (mean = 0.287) for most individual pairs. Abundant genetic diversity was observed in the total panel (5.32 alleles per locus), and some sub-groups showed a high proportion of private alleles. The average genome-wide LD (r 2) was 0.036, with a relatively fast decay of 1.5 cM. Genomic scans between fiber flax and linseed identified candidate genes involved in cell-wall biogenesis/modification, xylem identity and fatty acid biosynthesis congruent with genes previously identified in flax and other plant species. Conclusions Based on the abundant genetic diversity, weak population structure and relatedness and relatively fast LD decay, we concluded that this core collection is suitable for AM studies targeting multiple agronomic and quality traits aiming at the improvement of flax as a true dual purpose crop. Our genomic scans provide the first insights into candidate regions affected by divergent selection in flax. In combination with AM, genomic scans have the ability to increase the power to detect loci influencing complex traits.
Open Access
Effect of dietary sphingomyelin on absorption and fractional synthetic rate of cholesterol and serum lipid profile in humans
(2013-08-19) Ramprasath, Vanu R; Jones, Peter JH; Buckley, Donna D; Woollett, Laura A; Heubi, James E
Abstract Background Diets enriched with sphingolipids may improve blood lipid profiles. Studies in animals have shown reductions in cholesterol absorption and alterations in blood lipids after treatment with sphingomyelin (SM). However, minimal information exists on effect of SM on cholesterol absorption and metabolism in humans. The objective was to assess the effect of SM consumption on serum lipid concentrations and cholesterol metabolism in healthy humans. Methods Ten healthy adult males and females completed a randomized crossover study. Subjects consumed controlled diets with or without 1 g/day SM for 14 days separated by at least 4 week washout period. Serum lipid profile and markers of cholesterol metabolism including cholesterol absorption and synthesis were analyzed. Results Serum triglycerides, total, LDL- and VLDL- cholesterol were not affected while HDL cholesterol concentrations were increased (p = 0.043) by SM diet consumption. No change in cholesterol absorption and cholesterol fractional synthesis rate was observed with supplementation of SM compared to control. Intraluminal cholesterol solubilization was also not affected by consumption of SM enriched diet. Conclusions In humans, 1 g/day of dietary SM does not alter the blood lipid profile except for an increased HDL-cholesterol concentration and has no effect on cholesterol absorption, synthesis and intraluminal solubilization compared to control. Trial registration Clinicaltrials.gov # NCT00328211
Open Access
The diversity and biogeography of the Coleoptera of Churchill: insights from DNA barcoding
(2013-10-29) Woodcock, Thomas S; Boyle, Elizabeth E; Roughley, Robert E; Kevan, Peter G; Labbee, Renee N; Smith, Andrew B T; Goulet, Henri; Steinke, Dirk; Adamowicz, Sarah J
Abstract Background Coleoptera is the most diverse order of insects (>300,000 described species), but its richness diminishes at increasing latitudes (e.g., ca. 7400 species recorded in Canada), particularly of phytophagous and detritivorous species. However, incomplete sampling of northern habitats and a lack of taxonomic study of some families limits our understanding of biodiversity patterns in the Coleoptera. We conducted an intensive biodiversity survey from 2006–2010 at Churchill, Manitoba, Canada in order to quantify beetle species diversity in this model region, and to prepare a barcode library of beetles for sub-arctic biodiversity and ecological research. We employed DNA barcoding to provide estimates of provisional species diversity, including for families currently lacking taxonomic expertise, and to examine the guild structure, habitat distribution, and biogeography of beetles in the Churchill region. Results We obtained DNA barcodes from 3203 specimens representing 302 species or provisional species (the latter quantitatively defined on the basis of Molecular Operational Taxonomic Units, MOTUs) in 31 families of Coleoptera. Of the 184 taxa identified to the level of a Linnaean species name, 170 (92.4%) corresponded to a single MOTU, four (2.2%) represented closely related sibling species pairs within a single MOTU, and ten (5.4%) were divided into two or more MOTUs suggestive of cryptic species. The most diverse families were the Dytiscidae (63 spp.), Staphylinidae (54 spp.), and Carabidae (52 spp.), although the accumulation curve for Staphylinidae suggests that considerable additional diversity remains to be sampled in this family. Most of the species present are predatory, with phytophagous, mycophagous, and saprophagous guilds being represented by fewer species. Most named species of Carabidae and Dytiscidae showed a significant bias toward open habitats (wet or dry). Forest habitats, particularly dry boreal forest, although limited in extent in the region, were undersampled. Conclusions We present an updated species list for this region as well as a species-level DNA barcode reference library. This resource will facilitate future work, such as biomonitoring and the study of the ecology and distribution of larvae.
Open Access
Identification and characterization of the three homeologues of a new sucrose transporter in hexaploid wheat (Triticum aestivum L.)
(2013-11-16) Deol, Kirandeep K; Mukherjee, Shalini; Gao, Feng; Brûlé-Babel, Anita; Stasolla, Claudio; Ayele, Belay T
Abstract Background Sucrose transporters (SUTs) play important roles in regulating the translocation of assimilates from source to sink tissues. Identification and characterization of new SUTs in economically important crops such as wheat provide insights into their role in determining seed yield. To date, however, only one SUT of wheat has been reported and functionally characterized. The present study reports the isolation and characterization of a new SUT, designated as TaSUT2, and its homeologues (TaSUT2A, TaSUT2B and TaSUT2D) in hexaploid wheat (Triticum aestivum L.). Results TaSUT2A and TaSUT2B genes each encode a protein with 506 amino acids, whereas TaSUT2D encodes a protein of 508 amino acids. The molecular mass of these proteins is predicted to be ~ 54 kDA. Topological analysis of the amino acid sequences of the three homeologues revealed that they contain 12 transmembrane spanning helices, which are described as distinct characteristic features of glycoside-pentoside-hexuronide cation symporter family that includes all known plant SUTs, and a histidine residue that appears to be localized at and associated conformationally with the sucrose binding site. Yeast SUSY7/ura3 strain cells transformed with TaSUT2A, TaSUT2B and TaSUT2D were able to uptake sucrose and grow on a medium containing sucrose as a sole source of carbon; however, our subcellular localization study with plant cells revealed that TaSUT2 is localized to the tonoplast. The expression of TaSUT2 was detected in the source, including flag leaf blade, flag leaf sheath, peduncle, glumes, palea and lemma, and sink (seed) tissues. The relative contributions of the three genomes of wheat to the total expression of TaSUT2 appear to differ with tissues and developmental stages. At the cellular level, TaSUT2 is expressed mainly in the vein of developing seeds and subepidermal mesophyll cells of the leaf blade. Conclusion This study demonstrated that TaSUT2 is a new wheat SUT protein. Given that TaSUT2 is localized to the tonoplast and sucrose is temporarily stored in the vacuoles of both source and sink tissues, our data imply that TaSUT2 is involved in the intracellular partitioning of sucrose, particularly between the vacuole and cytoplasm.