O principal objetivo deste trabalho foi avaliar a presença de polimorfismos e de possíveis associações com características relacionadas com a resistência às parasitoses gastrintestinais e a prolificidade em ovinos da raça Santa Inês. Para avaliação da resistência às parasitoses gastrintestinais, amostras de fezes e de sangue de aproximadamente 700 animais, infectados naturalmente e oriundos de quatro propriedades diferentes, foram coletadas entre os meses de outubro e novembro de 2011, para avaliação das características condição corporal, grau de anemia avaliado pelo cartão FAMACHA, as características dos pelos dos animais, consistência das fezes, contagem de ovos por grama de fezes, hematócrito, contagem de células brancas, contagem de células vermelhas, hemoglobina e plaquetas. Para a avaliação da prolificidade, 340 ovelhas foram avaliadas quanto ao número total de cordeiros nascidos, divididos pelo número de partos de cada ovelha, assim como a correlação dessa característica com o peso médio ao nascimento de seus cordeiros e a eficiência produtiva da mãe ao parto. Foram selecionados 28 polimorfismos de base única (SNP) para o desenvolvimento deste estudo os quais foram genotipados por meio da plataforma Sequenom MassARRAY iPLEX. Foram analisadas as freqüências alélicas e genotípicas, o equilíbrio de Hardy-Weinberg, os efeitos de substituição alélica, de aditividade e de desvio de dominância. Os resultados obtidos demonstraram variabilidade considerável das características avaliadas na população e da maioria dos polimorfismos estudados. Foi verificado também efeito significativo (p≤0,05) ou sugestivo (0,05>p≤0,10) de substituição alélica de pelo menos um SNP para cada uma das características avaliadas, indicando que esses polimorfismos podem auxiliar nos processos de seleção das características relacionadas com a resistência às parasitoses gastrintestinais e com a prolificidade. / The aim of this work was to evaluate the presence of polymorphisms and possible associations with characteristics associated with resistance to gastrointestinal parasites and prolificacy in Santa Ines sheep. To evaluate the resistance to gastrointestinal parasites, feces and blood samples of approximately 700 animals infected naturally and from four different properties, were collected between the months of October and November, 2011 to assess characteristics body condition, degree of anemia measured by FAMACHA card, the characteristics of the hair of sheep, feces consistency, egg counts per gram of feces, hematocrit, white blood cell count, red blood cell count, hemoglobin and platelets count. For the evaluation of prolificacy, 340 sheep were evaluated for the total number of lambs born, divided by the number of births from each dam, as well as the correlation of this feature with the average birth weight of their lambs and productive efficiency of dam. 28 single nucleotide polymorphisms (SNPs) were selected for the development of this study and were genotyped by Sequenom MassARRAY iPLEX platform. Allele and genotype frequencies, the Hardy-Weinberg equilibrium, the effects of allelic substitution, additivity and dominance deviation were analyzed. The results showed considerable variability of the characteristics evaluated in the population in study and in most of the polymorphisms. Significant effect was observed (p ≤ 0.05) or suggestive (0.05> p ≤ 0.10) for allelic substitution of at least one SNP for each of the evaluated traits, indicating that these polymorphisms may help in the selection processes of characteristics related to resistance to gastrointestinal parasites and prolificacy.

Prediction of outcome in colorectal cancer (CRC) is currently based on the TNM staging classification; however, histopathological classification alone is insufficient for accurately predicting survival in stage II and III patients. Studies indicate that microarray gene expression profiles can predict survival in CRC. We hypothesize that tumor gene expression in combination with clinical parameters, is a better predictor of outcome in stage II and III colorectal cancers than the TNM stage classification alone. Clinical records and follow-up data were retrospectively reviewed for 58 Stage II and Stage III patients with primary colorectal cancer, who did not receive any neoadjuvant therapy preoperatively and whose samples had been previously analyzed for gene expression profiles using the Affymetrix U 133a Gene chip. For molecular classification of patients as being at high or low risk for poor survival, samples were divided into two clusters by hierarchical cluster analysis of genes selected by SAM. Univariate and multivariate analyses using Cox proportional hazard models were done to identify significant prognostic factors. The 3-year and 5-year survival estimates were 72.41% (SE=5.8%) and 55.17% (SE=6.7%), respectively, for all 58 patients. Univariate analysis showed that advanced stage, older age, high-risk molecular classification, positive lymph nodes were the statistically significant prognostic factors of poor survival (p<0.05), while gender, preoperative CEA level, and family history of CRC in first degree relatives were not statistically significant. In multivariate analysis molecular classification, age and body mass index were independent significant prognostic factors. In Cox proportional hazard model, the estimated hazard ratios for Stage III vs II was 2.45 (95%CI: 0.85-7.04), for high vs low molecular risk was 3.83 (95%CI: 1.22-12.06) and old vs young age was 3.72 (95%CI: 1.2-11.49). Model containing clinical stage in conjunction with molecular risk, body mass index, and age was a stronger indicator of clinical outcome (p= 0.0056) than model with clinical stage alone. Gene expression profiles predict survival independent of clinical parameters, and the addition of gene expression profiles to stage is more predictive of survival than stage alone. Further analysis needs to be done to validate the molecular classification on an independent dataset.

Because American black bears (Ursus americanus) are an important game species in Arizona and are endangered in México, an understanding of the population structure, gene flow, and connectivity are important for effective management. Black bears inhabit coniferous and broadleaf deciduous woodlands in southern Arizona and northern México, usually in sky islands (sky islands are mountains that rise from the desert and are isolated from each other). Because a single sky island is too small to support a viable bear population, black bears move through desert lowlands to reach other sky islands. My objective was to assess genetic structure, connectivity, and conservation implications for sky island black bears in southern Arizona and northern México. I addresses 4 components of bear ecology and genetics: a literature review of genetic information available for black bears in North America; the use of 2 mitochondrial DNA genes (Control Region and ATP synthase protein 8) to study the phylogenetic relationship of black bears from the sky islands of southern Arizona and northern México relative to all North America; the use of 10 microsatellite loci to detect the current genetic structure of black bears in the sky islands in Arizona and northern México; and the use of noninvasive samples collected from the field to determine bear density and population size for black bear in Sierra San Luis, Sonora, México. These studies provide information that can be used by biologists, land managers, and others to assist in the conservation of black bears and their habitat.

Up till now ecology and biodiversity of Sarcocystis species in game fauna in Lithuania has been investigated using traditional morphological methods. In the period of 2005-2011, muscle samples of 384 birds and 177 mammals were examined for Sarcocystis sarcocysts. Cysts of Sarcocystis spp. were investigated using light microscopy, transmission electron microscopy and DNA analysis (18S rDNA, 28S rDNA, ITS–1 region). Statistically significant higher Sarcocystis infection prevalence and intensity rates (p< 0.05) were determined in mammals as compared to the birds. Macrocysts were detected only in the mallard, they were identified as S. rileyi and this is the first evidence of S. rileyi infection in Europe. Based on results of cyst wall ultrastructure and DNA analysis four new bird Sarcocystis species were described: S. albifronsi, S. wobeseri, S. anasi, S. cornixi. Eight Sarcocystis species were identified in the examined mammals using morphological and DNA analysis: S. miescheriana from wild boar; S. gracilis, S. capreolicanis, S. oviformis, S. silva and S. hofmanni-like from roe deer; S. hjorti, S. hofmanni-like and Sarcocystis sp. ex Cervus elaphus from red deer; S. hjorti from moose. S. columbae, S. oviformis, S. hjorti and S. silva were found in Lithuania for the first time. Using molecular investigation it was proved that some analyzed Sarcocystis species (S. wobeseri, S. hjorti, S. silva and S. hofmanni-like) are not rigidly specific to the intermediate host. Sarcocystis... [to full text] / Lietuvoje medžiojamosios faunos Sarcocystis rūšių ekologija ir bioįvairovė iki šiol tirta naudojant tradicinius morfologinius metodus. 2005-2011 metais ieškant Sarcocystis sarkocistų Lietuvos medžiojamoje faunoje analizuoti 384 paukščių ir 177 žinduolių raumenų pavyzdžiai. Sarcocystis cistos tirtos naudojant šviesinės ir elektroninės mikroskopijos metodus bei DNR žymenis (18S rDNR, 28S rDNR, ITS–1 regionas). Lyginant paukščių ir žinduolių sistematines grupes, žinduoliuose nustatyti patikimai (p< 0,05) didesni Sarcocystis infekcijos ekstensyvumo bei intensyvumo rodikliai. Makrocistos aptiktos tik didžiojoje antyje ir buvo priskirtos S. rileyi rūšiai – tai pirmas svarus S. rileyi infekcijos įrodymas Europoje. Remiantis cistų sienelės ultrastruktūros ir DNR tyrimo duomenimis aprašytos keturios naujos mokslui paukščių sarkosporidijų rūšys: S. albifronsi, S. wobeseri, S. anasi, S. cornixi. Naudojant morfologinius ir DNR tyrimo metodus tirtuose žinduoliuose identifikuotos aštuonios Sarcocystis rūšys: šernuose S. miescheriana; stirnose S. gracilis, S. capreolicanis, S. oviformis, S. silva, S. hofmanni-like; tauriuosiuose elniuose S. hjorti, S. hofmanni-like, Sarcocystis sp. ex Cervus elaphus ir briedžiuose S. hjorti. Šio darbo metu pirmą kartą Lietuvoje aptiktos S. columbae, S. oviformis, S. hjorti, S. silva rūšys. Molekuliniais tyrimais įrodyta, kad kai kurios tirtos Sarcocystis rūšys (S. wobeseri, S. hjorti, S. silva, S. hofmanni-like) nėra griežtai specifinės tarpiniam... [toliau žr. visą tekstą]

Lietuvoje medžiojamosios faunos Sarcocystis rūšių ekologija ir bioįvairovė iki šiol tirta naudojant tradicinius morfologinius metodus. 2005-2011 metais ieškant Sarcocystis sarkocistų Lietuvos medžiojamoje faunoje analizuoti 384 paukščių ir 177 žinduolių raumenų pavyzdžiai. Sarcocystis cistos tirtos naudojant šviesinės ir elektroninės mikroskopijos metodus bei DNR žymenis (18S rDNR, 28S rDNR, ITS–1 regionas). Lyginant paukščių ir žinduolių sistematines grupes, žinduoliuose nustatyti patikimai (p< 0,05) didesni Sarcocystis infekcijos ekstensyvumo bei intensyvumo rodikliai. Makrocistos aptiktos tik didžiojoje antyje ir buvo priskirtos S. rileyi rūšiai – tai pirmas svarus S. rileyi infekcijos įrodymas Europoje. Remiantis cistų sienelės ultrastruktūros ir DNR tyrimo duomenimis aprašytos keturios naujos mokslui paukščių sarkosporidijų rūšys: S. albifronsi, S. wobeseri, S. anasi, S. cornixi. Naudojant morfologinius ir DNR tyrimo metodus tirtuose žinduoliuose identifikuotos aštuonios Sarcocystis rūšys: šernuose S. miescheriana; stirnose S. gracilis, S. capreolicanis, S. oviformis, S. silva, S. hofmanni-like; tauriuosiuose elniuose S. hjorti, S. hofmanni-like, Sarcocystis sp. ex Cervus elaphus ir briedžiuose S. hjorti. Šio darbo metu pirmą kartą Lietuvoje aptiktos S. columbae, S. oviformis, S. hjorti, S. silva rūšys. Molekuliniais tyrimais įrodyta, kad kai kurios tirtos Sarcocystis rūšys (S. wobeseri, S. hjorti, S. silva, S. hofmanni-like) nėra griežtai specifinės tarpiniam... [toliau žr. visą tekstą] / Up till now ecology and biodiversity of Sarcocystis species in game fauna in Lithuania has been investigated using traditional morphological methods. In the period of 2005-2011, muscle samples of 384 birds and 177 mammals were examined for Sarcocystis sarcocysts. Cysts of Sarcocystis spp. were investigated using light microscopy, transmission electron microscopy and DNA analysis (18S rDNA, 28S rDNA, ITS–1 region). Statistically significant higher Sarcocystis infection prevalence and intensity rates (p< 0.05) were determined in mammals as compared to the birds. Macrocysts were detected only in the mallard, they were identified as S. rileyi and this is the first evidence of S. rileyi infection in Europe. Based on results of cyst wall ultrastructure and DNA analysis four new bird Sarcocystis species were described: S. albifronsi, S. wobeseri, S. anasi, S. cornixi. Eight Sarcocystis species were identified in the examined mammals using morphological and DNA analysis: S. miescheriana from wild boar; S. gracilis, S. capreolicanis, S. oviformis, S. silva and S. hofmanni-like from roe deer; S. hjorti, S. hofmanni-like and Sarcocystis sp. ex Cervus elaphus from red deer; S. hjorti from moose. S. columbae, S. oviformis, S. hjorti and S. silva were found in Lithuania for the first time. Using molecular investigation it was proved that some analyzed Sarcocystis species (S. wobeseri, S. hjorti, S. silva and S. hofmanni-like) are not rigidly specific to the intermediate host. Sarcocystis... [to full text]

High linoleic acid soybeans facilitate maximum production of soy-based polyurethane. The objectives of this study were to: 1) Evaluate environmental influence on yield and seed composition traits; 2) Estimate correlation coefficients between linoleic acid with agronomic traits; 3) Validate SSR markers associated with fatty acid QTL in multiple environments and across diverse genotypes; and 4) Evaluate the influence of fertilizers differing in P and K concentrations on seed fatty acids. RG25 was identified as the best genotype to be commercialized for polyurethane production. Strong marker-trait associations across environments included Satt_335, Satt389, Satt556 associated with palmitic and stearic, Satt389 with oleic, Satt389 and Satt537 with linoleic acid. A significant increase in linoleic acid content was observed when plants received modified Hoagland’s solution with 2×K compared to without K. Development of a high linoleic acid soybean line for polyurethane production is feasible using validated SSR markers and high K fertility. / Ontario Ministry of Agriculture, Food and Rural Affairs

Brassica napus is grown as an edible oil (canola) and an industrial oil (HEAR). Its fatty acid profile and chlorophyll concentration affect the quality. It is important to develop accurate and efficient methods to evaluate these traits. The first objective of this study was to improve the single nucleotide polymorphism (SNP) and sequence characterized amplified region (SCAR) molecular markers for erucic acid genotypes in the Bn-FAE1.1 and Bn-FAE1.2 genes in the A and C genomes in Brassica napus originally developed by Rahman et al. (2008). When put into practice, the error rate was unacceptably high. With the modifications that were made to the protocols, the overall accuracy remained relatively consistent indicating that further improvements are still required. The second objective was to develop a near infrared reflectance (NIR) based calibration equation for chlorophyll concentration in whole Brassica napus seeds. In this case, an equation was successfully created.

Brassica carinata is being actively pursued as a new industrial oil crop platform for the Canadian Prairies. A genetic assessment of B. carinata was performed to elucidate its evolutionary origins and create a genetic map to assist in locating genes and traits of interest that would help in marker-assisted breeding. First, genetic analysis using simple sequence repeat (SSR) markers, previously tested on B. juncea and B. napus, was performed, to examine the genetic diversity of 37 B. carinata lines. SSR analysis revealed world accessions were more diverse than lines conditioned to grow in the prairies. Diversity analysis revealed that the parental lines of a double haploid (DH) population, 179 and 345, obtained from the John Innes Centre (JIC), were among the more genetically diverse lines, supporting the use of this population for linkage mapping. Genetic markers created from 3’ targeted SNP discovery between 179 and 345, were tested on the DH population resulting in the generation of a B. carinata genetic linkage map essentially with no prior sequence data knowledge. This genetic map contained 341 SNP and 86 SSR loci identifying eight linkage groups belonging to the B genome, nine belonging to the C genome and two unidentified groups spanning 2041 cM. Comparative mapping of polymorphic markers identified in the amphidiploid B. carinata indicated the orientation of B and C genomes coincide with that of other Brassica species, and the two genomes have remained essentially unaltered, with no major chromosomal rearrangements since the formation of B. carinata. A lesser number of polymorphic markers were detected in the C genome, which suggested the B genome is more genetically diverse in B. carinata. Limited field trials of the 179 x 345 DH population were performed during the 2011 and 2012 growing seasons. Preliminary quantitative trait loci (QTLs) for agronomic traits including flowering time (FT), plant height (PH), and seed quality were identified.

The larger grain borer (LGB) Prostephanus truncatus (Horn) is the most important pest of farm stored maize and cassava in Africa. This alien invasive species was introduced into the continent from Mesoamerica in the late 1970s and by 2008 had spread to at least 18 countries. In contrast to indigenous primary storage pests, LGB exists as on-farm and as wild populations, hence, sustainable control must target both environments. Biological control is especially attractive for wild populations to reduce early season grain store infestation, while cultural and chemical methods are useful to protect stored produce directly. Two populations of the predator Teretrius nigrescens Lewis were introduced into several African countries' as a biocontrol agent. It has shown long-term success and cost effective control in warm-humid areas. Control has however not been successful in cool and hot-dry zones. The aim of this study was to investigate the possible underlying genetic and ecological explanations for these observations and the possibility of joint use of molecular markers and ecological parameters in the development of sustainable control strategies. A 28-month baseline monitoring and recovery activity was done in from 2004 in five regions in Kenya along an east-westerly transect. Monitoring and live sample collection was also done in the original outbreak area in eastern Kenya. There was greater LGB flight activity in western Kenya (high potential maize production area) than the low potential areas. Very few T. nigrescens were recovered, solely in the eastern regions. LGB flight activity followed a seasonal pattern mostly related to changes in the relative humidity at 12:00, rainfall and dew point temperature but with a 3 - 4 week lag. A linear predictive model based on these factors predicted 27 % of the observed flight activity. The survival and predation of five strains of T. nigrescens were compared at eight temperature levels between 15 °C and 36 °C at low and high humidity. All the strains of T. nigrescens exerted a significant reduction of LGB population build-up between 21 °C and 33 °C with generally better performance under humid conditions. There was no evidence of T. nigrescens development at 15 °C. At 18 °C, T. nigrescens oviposition and development was observed but the effect on LGB did not differ significantly from the control. The KARI population was the least effective in preventing grain damage at lower temperatures, but performed better than other strains above 30 °C at low humidity conditions. There was no control at 18 °C and 36 °C under both high and low humidity conditions. Since the extent of genetic differentiation in T. nigrescens was unclear from prior studies, several molecular marker techniques were progressively used. The RAPD-PCR did not reveal any genetic diversity between geographical populations. A 1000bp region of the mitochondrial mtCOI gene revealed two distinct clades differing consistently at 26 segregating sites. The two clades can be identified by simple PCR-RFLP procedure using single or double sequential restriction with EcoR1, HincII, RsaI and DdeI digestion. However, the two lineages co-exist among the mid-altitude Central American populations. The internal transcribed spacer regions ITS1 and ITS2 with some neighbouring coding sequences of the ribosomal DNA were cloned and sequenced. The spacer regions were so variable in length and sequence between T. nigrescens and related Histeridae species that direct sequence alignment was not meaningful. Within T. nigrescens, there was intragenomic variability of the spacer regions mostly involving insertions and deletions of variable tandem repeat units predominantly within the ITS regions. The short flanking coding (18S, 5.8S and 21S) regions were conserved across populations and six other Histeridae species. There was no significant secondary structure variation of the ITS regions among populations of T. nigrescens. Twenty-four novel variable microsatellite markers were developed and tested on the Honduras populations. Alleles per locus ranged between two and twelve with observed heterozygosity between 0.048 and 0.646. Six loci deviated significantly from Hardy Weinberg Equilibrium and possibly had null alleles. The success of microsatellite amplification in outgroup species and variability of markers declined with an increase in the phylogenetic distance between the test species and T. nigrescens. Genotyping 432 individuals from 13 geographic populations revealed a comparatively higher genetic diversity in field populations. Partial isolation by distance and time was observed. Population bottlenecks were not detected, but recent expansion was evident in laboratory populations. Although five dominant genetic clusters were identified by Bayesian methods, meaningful hierarchical population structure was observed at between two and nine population groups (p < 0.01; 10,000 iterations). Biological control of the larger grain borer using T. nigrescens seems an important aspect of the sustainable integrated control approach of the pest. Ecological adaptations, appropriate release strategies and genetic diversity are all essential considerations in these efforts and could be responsible for the variable success already observed. There is some genetic differentiation between populations of T. nigrescens but, further studies would be necessary to ascertain the contribution of such diversity to its predatory performance. The effect of laboratory culturing in aggravating genetic drift should be accommodated to avoid loss of diversity during sampling, quarantine, rearing and release of the predator. / Thesis (Ph.D. (Environmental Science))--North-West University, Potchefstroom Campus, 2009.

Brassica napus is grown as an edible oil (canola) and an industrial oil (HEAR). Its fatty acid profile and chlorophyll concentration affect the quality. It is important to develop accurate and efficient methods to evaluate these traits. The first objective of this study was to improve the single nucleotide polymorphism (SNP) and sequence characterized amplified region (SCAR) molecular markers for erucic acid genotypes in the Bn-FAE1.1 and Bn-FAE1.2 genes in the A and C genomes in Brassica napus originally developed by Rahman et al. (2008). When put into practice, the error rate was unacceptably high. With the modifications that were made to the protocols, the overall accuracy remained relatively consistent indicating that further improvements are still required. The second objective was to develop a near infrared reflectance (NIR) based calibration equation for chlorophyll concentration in whole Brassica napus seeds. In this case, an equation was successfully created.