Browsing by Author "Patterton, Hugh"

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    RNA-seq based transcriptional analysis of Saccharomyces cerevisiae and Lachancea thermotolerans in mixed-culture fermentations under anaerobic conditions
    (BMC (part of Springer Nature), 2019) Shekhawat, Kirti; Patterton, Hugh; Bauer, Florian; Setati, Mathabatha E.
    Background: In wine fermentation starter cultures, the blending of non-Saccharomyces yeast with Saccharomyces cerevisiae to improve the complexity of wine has become common practice, but data regarding the impact of co-cultivation on yeast physiology and on genetic and metabolic regulation remain limited. Here we describe a transcriptomic analysis of mixed fermentations of Saccharomyces cerevisiae and Lachancea thermotolerans. The fermentations were carried out in carefully controlled environmental conditions in a bioreactor to reduce transcriptomic responses that would be due to factors other than the presence of the second species. Results: The transcriptomic data revealed that both yeast species showed a clear response to the presence of the other. Affected genes primarily belonged to two groups: genes whose expression can be linked to the competition for certain trace elements such as copper and iron, as well as genes required for cell wall structure and integrity. Furthermore, the data revealed divergent transcriptional responses with regard to carbon metabolism in response to anoxic conditions. Conclusions: The results suggest that the mixed fermentation created a more competitive and stressful environment for the two species than single strain fermentations independently from total biomass, i.e. competition between cells of the same species is less stressful, or may present a different set of challenges, than interspecies competition. The changes in cell wall and adhesion properties encoding genes suggest that the adjustment of physical contact between cells may play a direct role in the response to the presence of competing species.
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    Strategies and opportunities for promoting bioinformatics in Zimbabwe
    (Public Library of Science, 2018-11-29) Shoko, Ryman; Manasa, Justen; Maphosa, Mcebisi; Mbanga, Joshua; Mudziwapasi, Reagan; Nembaware, Victoria; Sanyika, Walter T.; Tinago, Tawanda; Chikwambi, Zedias; Mawere, Cephas; Matimba, Alice; Mugumbate, Grace; Mufandaedza, Jonathan; Mulder, Nicola; Patterton, Hugh; Ouzounis, Christos A.
    Introduction: The increasing applications of advanced technologies in life sciences are fueling the growth of data from genome sequencing, functional genomics experiments, and macromolecular structure determination. Bioinformatics (sometimes interchangeably used with the term “computational biology”) permits researchers to collect, manage, and sift through these massive data sets and derive scientific insight from them [1,2]. Bioinformatics holds a big promise in addressing many of the problems that are facing humanity today, including human health, agriculture, and the environment [3–8]. Consequently, the demand for skilled scientists with the ability to use information technology to solve life science problems has been rising steadily globally. Similar to other developing countries in Africa, bioinformatics is slowly gaining popularity among Zimbabwean scientists. In this paper, we review the progress made by Zimbabwean scientists in bioinformatics and propose strategies for boosting bioinformatics capacity in the country. To our knowledge, this work is the first attempt to give a comprehensive report of bioinformatics activities in the country. As such, it is inevitable that our review may not be exhaustive and may fall short of mentioning or acknowledging groups or scientists who have contributed or presented their work on other platforms.