No description available.

A monitoring effort that spanned across one and a half years was conducted to examine three types of produce-associated microbiota. Produce type was determined to be the predominant factor affecting the microbial communities. Other significant factors that resulted in differences in the microbial populations were the origin and sampling date. Specifically, produce-associated microbiota among lettuce and tomatoes clustered based on the sampling period. Through molecular and cultivation-based approaches, sporadic presence of extended spectrum beta-lactamase (ESBL)-positive Klebsiella pneumoniae and Acinetobacter baumannii was detected on lettuce and cucumbers during certain periods of sampling. Quantitative microbial risk assessment denoted varying levels of ingestion risks associated with different types of produce. In particular, the risks arising from ESBL-positive K. pneumoniae in the lettuce were higher than the acceptable annual risk of 10-4. Commonly used approaches to clean and wash the produce were insufficient in removing majority of the produce-associated microbiota. More invasive cleaning approaches or thorough cooking of the produce would be required to mitigate the associated risks. Most of the current reports of ESBL-positive bacterial isolates were identified in nosocomial environment. However, the carriage of such drug-resistant bacteria in food that is consumed daily

No description available.

A unique undosciribed gramnegative rod is extensively characterized in this study. The cells of this unusual water isolate measure 1.2 X 6.5 microns, The most distinguishing characteristic of the bacterium is a polar tuft of 35-40 flagella that aggregate to function as a single organelle which is visible under phase contrast. Aging cells deposit poly- -hydroxybutyric acid granules which are bound by an inclusion membrane made up of four distinct layers. It also possesses an unusual exterior membrane outside the cell wall which contains large fibrils of protein running at a slight angle to the longitudinal axis of the cell. The guanosine-cytosine ratio was found to be 62.2$. The organism's taxonomic position was further investigated by immunological, morphological, and biochemical methods. It was found to be most closely akin to members of the genus Pseudo onas, although somewhat divergent from other species classified in this genus. After careful evaluation of the findings obtained during this study, the new bacterium was subsequently named Pseudomonas multiflagella.

A porção paulista do Vale do Ribeira concentra a maior quantidade de comunidades remanescentes de quilombos do estado de São Paulo, abrangendo uma área de cerca de 10% de seu território. Por meio das análises de marcadores moleculares, de frequências de casais com mesmo sobrenome e de dados genealógicos, procuramos obter parâmetros globais de caracterização das comunidades: sistema de cruzamentos e medidas de subestruturação populacional. Utilizamos dados genealógicos de cerca de 2000 indivíduos e moleculares de cerca de 1000 indivíduos das comunidades de Maria Rosa, Pilões, Galvão, São Pedro, Pedro Cubas, Ivaporanduva, Sapatu, André Lopes, Nhunguara, Abobral (margens esquerda e direita), Poça e Reginaldo. A estimativa média de F obtida pela análise de genealogias apresentou valor 0,00134, o qual, embora subestimado devido à falta de informações genealógicas, é cerca de 1,5 vezes mais elevado do que a estimativa apresentada para a população total brasileira e duas vezes maior que a obtida para o estado de São Paulo, comparando-se a valores apresentados em outros isolados da literatura. A partir das análises de locos genômicos obtivemos, para as comunidades separadamente, os valores médios de F relativos aos 239 locos de todas as comunidades, dentre os quais 12 (5%) mostraram-se estatisticamente diferentes de zero ao nível de P <= 0,05/n, frequência esperada de desvios ocorrendo ao acaso. Quando analisada de forma conjunta, a população apresentou quatro dos 30 locos (13,33%) com desvios significativos de pan-mixia, valor acima do esperado ao acaso, o que indica um excesso de homozigose no isolado total. Obtivemos o valor médio total de F pela ponderação dos F de cada um dos locos pelos recíprocos de suas variâncias, estas calculadas por meio de uma metodologia inédita proposta neste trabalho, a qual é aplicável a casos de marcadores contendo mais de dois alelos. O valor médio de F que obtivemos é comparável aos obtidos de outros isolados da literatura. Os valores do índice Fst obtidos em uma análise de subestruturação populacional tiveram valores modestos geralmente bem menores que 5%, indicando a presença de níveis de subestruturação muito modestos. / Vale do Ribeira is a region located at the southern part of the state of São Paulo, corresponding to about 10% of its territory. Most of the quilombo remnants of the state are placed inside this region. Using both molecular markers and genealogical data analyses, we estimated population genetic parameters from the communities (breeding system and subestructure organization). Genealogical and molecular data (collected from 2000 and 1000 individuals respectively) were obtained from 13 quilombo communities: Maria Rosa, Pilões, Galvão, São Pedro, Pedro Cubas, Ivaporanduva, Sapatu, André Lopes, Nhunguara, Abobral (both left and right edges), Poça e Reginaldo. Genealogical analysis enabled us to obtain a mean F value of 0.00134, that represents an underestimate of the true value due to lack of reliable genealogical information. Even so, this value is almost 1.5 times higher than the value estimated for the total Brazilian population and almost twice as high than the same parameter estimated for the state of São Paulo. By means of genomic loci data analysis, we obtained mean nF/n value for the quilombo communities separately. Twelve (5%) out of a total of 239 loci from eight communities were in p2:2pq:q2 ratios, as expected by chance; and for the set of all quilombo communities, four (13.33%) out of 30 loci deviated significantly from Hardy-Weinberg ratios, indicating an excess of homozygosis. We also estimated the weighted mean value of F for the whole population by averaging the nF/n values obtained from each locus by the reciprocal of their corresponding variances. For calculating the variance of estimated nF/n values we developed a novel method that can be easily generalized to the case of any number of alleles segregating at an autosomal locus/ No significant levels of population subtructure were detected since the estimated Fst values among populations were in general quite modest. We present also, as attachment to this work, the listings of the main computer program codes we used in our calculations and a section on the evolution of the fixation index F under different systems of regular endogamy.

Thesis (M.Sc. (Agriculture Agronomy)) --University of Limpopo, 2017 / Among the fungal diseases infecting tomato crop, early blight caused by Alternaria solani (Ellis & G. Martin) is one of the most destructive fungal foliar diseases. The aim of this current study was to document the prevailing pathogenic diversity of A. solani populations in Limpopo based on morphological characteristics, fungicide sensitivity, and aggressiveness of A. solani isolates. The tested isolates were collected from four different areas across different tomato production sites in the Limpopo Province and pathogen isolations were carried-out under laboratory conditions. The the morphological variation of different A. solani isolates was evaluated. The results obtained in this study show that A. solani isolates exhibit high variations in mycelial pigmentation, number of septa, beak length and colony diameter. The current study also evaluated the sensitivity of A. solani isolates obtained from different areas in the Limpopo to commonly used fungicides. All the tested fungicides (chlorothalonil, copper oxychloride and mancozeb) reduced the mycelial growth of A. solani isolates, even at lower concentrations. However copper oxychloride fungicide provides better inhibition of mycelial growth as compared to other tested fungicides. Furthermore, the aggressiveness of the different isolates was investigated using Money-maker and Rodade tomato cultivars. The results obtained in our, study revealed that isolates from different areas differed in terms of their level of aggressiveness on both cultivars. However, all the tested isolates were aggressive in their ability to cause early blight in both cultivars. There was a difference on how both cultivars responded to isolates from different areas with the Money-maker being highly susceptible to all the tested isolates as than the Rodade Key words: Aggressiveness, Alternaria solani, Fungicide sensitivity, isolates, Limpopo Province, Morphological characterization, susceptible tomato cultivars. / NRF (National Research Foundation)

The overarching goal of this research was to investigate the differences in the physicochemical and functional properties of protein isolates produced from seven different faba bean genotypes (CDC Fatima, Taboar, SSNS-1, FB9-4, FB18-20, Snowbird and CDC Snowdrop) grown at different locations in Canada (Saskatchewan, Alberta and Manitoba) in 2011 and 2012. The protein isolates were prepared by alkaline extraction (pH 9.5) followed by isoelectric precipitation at pH 4.5. The isolates had an average protein content of ~94% and average protein and isolate yields of ~77% and ~25%, respectively. The physicochemical properties assessed in this study included surface charge/zeta potential (ZP), surface hydrophobicity (SH), and surface and interfacial tension (ST and IT). The functional properties tested included foaming capacity (FC) and foam stability (FS), emulsion capacity (EC) and creaming stability (CS), emulsion activity index (EAI) and emulsion stability index (ESI), oil holding capacity (OHC), and protein solubility. The findings indicated that all physicochemical properties for all isolates were independent of genotype. Overall, an average ZP of + 22.1 mV, SH of 47.2 arbitrary units, and ST and IT of 65.0 mN/m and 10.7 mN/m, respectively, were observed. However, with the exception of ZP considerable differences were observed due to the effect of environment. The ratio of the major globulin protein fractions [legumin:vicilin (L/V)] was found to shift during processing, from 3.8 (range: 3.4-4.6) in the flour to 4.5 (range 4.0-4.9) in the isolates. The L/V ratio for faba bean flour and isolate samples was also found to be independent of genotype. For all genotypes, with the exception of the zero-tannin varieties (Snowbird and CDC Snowdrop), the L/V ratio was affected by the environment. Similar to the physicochemical properties, all functional attributes were found to be independent of genotype. However, environmental effects were observed for all functional properties with the exception of EAI and ESI. Average values for FC of 162.0%, for FS of 65.0%, for EC of 184.0 g/g, for CS of 94.0%, for OHC of 5.7 g/g, for EAI of 13.0 m2/g, for ESI of 10.7 min and for solubility of 81.0% were reported. Zeta potential was observed to be positively correlated with CS (r = 0.46; p<0.05) and FS (r = 0.54; p<0.01), whereas SH and L/V ratio were not. The L/V ratio in the isolate, however, was correlated positively with SH (r = 0.40; p<0.05) and negatively with ZP (r = -0.39; p<0.05). Moreover, the solubility of faba bean isolates was found to be positively correlated with ZP (r = 0.44; p<0.05) and negatively correlated with both IT (r = -0.38; p<0.05) and OHC (r = -0.38; p<0.05). The functional properties of some commercial protein isolates (soy, pea, whey, egg and wheat) were evaluated for comparative purposes. The OHC of the faba bean isolate was found to be higher than that of any of the commercial isolates. With the exception of CS (soy and pea) and FC (egg), all of the emulsifying (EC, EAI and ESI) and foaming (FC and FS) properties of the faba bean protein isolates were comparable to those of soy, pea and egg isolates. In contrast, values for most of the other functional properties were greater for faba bean isolates than for the pea and wheat isolates, but lower than for the whey isolate. For example, the solubility of the protein isolates was observed to decrease in the following order: whey (89.0%) = egg (88.1%) > faba bean (81.0%) > soybean (30.5%) > pea (20.1%) > wheat (10.7%).

No description available.

The thesis describes algorithms for detecting regions of recent identity by descent (IBD) from human genetic data and its applications in optimising resequencing studies, genomic predictions and detecting Mendelian subtypes of diseases. Firstly, we describe the algorithm ANCHAP, which scans pairs of multi-point SNP genotypes for sharing IBD of long haplotypes. A comparison with other methods shows that ANCHAP outperforms them in terms of speed or accuracy. We demonstrate the algorithm on data from population isolates - from Orcades, Croatian islands, and from a population of unrelated individuals. We compare the abundance of IBD segments between cohorts, and identify genetic regions where IBD is most common. Secondly, we verify the IBD regions detected from array data against exome sequence data. We estimate that where sharing IBD between a pair of individuals is inferred, this is confirmed by exome data in 98% of cases. Correctness of IBD detection varies with settings of ANCHAP, length of IBD segments, and position with respect to segment endpoints. We find that with sample sizes of 1000 individuals from an isolated population genotyped using a dense SNP array, and with 20% of these individuals sequenced, 65% of sequences of the un-sequenced subjects can be partially inferred. Implementation of such resequencing strategies requires an IBD-based imputation algorithm, which is outlined. Thirdly, we use recent IBD to detect carriers of Mendelian subtypes of colon cancer. We show this with the example of Lynch syndrome, which accounts for about 3% of colon cancer patients. We detect IBD sharing between known and unknown carriers around DNA mismatch-repair genes. Using the IBD relationship, we build and evaluate a model that predicts presence of Lynch Syndrome mutations. Finally, we discuss whether regions of identity by descent can be used for genomic predictions. We conclude that the utility of the inferred IBD regions depends on accuracy of detection, time to most recent common ancestors and mutation rates since.

Magister Scientiae - MSc / South Africa