Exploring the transcriptome of non-model oleaginous microalga Dunaliella tertiolecta through high-throughput sequencing and high performance computing

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GENERATION OF LIPID-RICH MUTANTS AND CHARACTERIZATIONS IN GREEN ALGA MICROALGA DUNALIELLA TERTIOLECTA

Ph.DDOCTOR OF PHILOSOPH

Genome Mining and Synthetic Biology in Marine Natural Products Discovery

In recent years, marine genomics has become a growning rapidly field, helped by the large amount of information that is becoming available to the international scientific community. Taking into account the current excitement in the field of marine biotechnology, this Special Issue entitled “Genome Mining and Synthetic Biology in Marine Natural Product Discovery” aims to to assess the impact of these molecular approaches on the discovery of bioactive compounds from marine organisms. The term “genome mining” is used to identify all bioinformatic investigations aimed at detecting the biosynthetic pathways of bioactive natural products and their possible functional and chemical interactions. Several studies are now reporting on marine organisms. Oceans cover nearly 70% of the Earth’s surface and host a huge ecological, chemical, and biological diversity. The natural conditions of the sea favor, in marine organisms, the production of a large variety of novel molecules with great pharmaceutical potential. Marine organisms are unique in their structural and functional features compared to terrestrial ones. Innovation in this field is very rapid, as revealed by the funding of several Seventh Framework Programme (FP7) and Horizon 2020 projects under the topic “Blue Growth”, with the urgent goal of discovering new drugs

Intelligent Energy-Savings and Process Improvement Strategies in Energy-Intensive Industries

S tím, jak se neustále vyvíjejí nové technologie pro energeticky náročná průmyslová odvětví, stávající zařízení postupně zaostávají v efektivitě a produktivitě. Tvrdá konkurence na trhu a legislativa v oblasti životního prostředí nutí tato tradiční zařízení k ukončení provozu a k odstavení. Zlepšování procesu a projekty modernizace jsou zásadní v udržování provozních výkonů těchto zařízení. Současné přístupy pro zlepšování procesů jsou hlavně: integrace procesů, optimalizace procesů a intenzifikace procesů. Obecně se v těchto oblastech využívá matematické optimalizace, zkušeností řešitele a provozní heuristiky. Tyto přístupy slouží jako základ pro zlepšování procesů. Avšak, jejich výkon lze dále zlepšit pomocí moderní výpočtové inteligence. Účelem této práce je tudíž aplikace pokročilých technik umělé inteligence a strojového učení za účelem zlepšování procesů v energeticky náročných průmyslových procesech. V této práci je využit přístup, který řeší tento problém simulací průmyslových systémů a přispívá následujícím: (i)Aplikace techniky strojového učení, která zahrnuje jednorázové učení a neuro-evoluci pro modelování a optimalizaci jednotlivých jednotek na základě dat. (ii) Aplikace redukce dimenze (např. Analýza hlavních komponent, autoendkodér) pro vícekriteriální optimalizaci procesu s více jednotkami. (iii) Návrh nového nástroje pro analýzu problematických částí systému za účelem jejich odstranění (bottleneck tree analysis – BOTA). Bylo také navrženo rozšíření nástroje, které umožňuje řešit vícerozměrné problémy pomocí přístupu založeného na datech. (iv) Prokázání účinnosti simulací Monte-Carlo, neuronové sítě a rozhodovacích stromů pro rozhodování při integraci nové technologie procesu do stávajících procesů. (v) Porovnání techniky HTM (Hierarchical Temporal Memory) a duální optimalizace s několika prediktivními nástroji pro podporu managementu provozu v reálném čase. (vi) Implementace umělé neuronové sítě v rámci rozhraní pro konvenční procesní graf (P-graf). (vii) Zdůraznění budoucnosti umělé inteligence a procesního inženýrství v biosystémech prostřednictvím komerčně založeného paradigmatu multi-omics.Zlepšení průmyslových procesů, Model založený na datech, Optimalizace procesu, Strojové učení, Průmyslové systémy, Energeticky náročná průmyslová odvětví, Umělá inteligence.

Bioprospecting marine thraustochytrids highly producers of polyunsaturated fatty acids : environmental microbiomes, high-throughput screening and bioreactor lipid production

Orientador: Prof. Dr. Carlos Ricardo SoccolCoorientador: Prof. Dr. Gilberto Vinícius de Melo PereiraTese (doutorado) - Universidade Federal do Paraná, Setor de Tecnologia, Programa de Pós-Graduação em Engenharia de Bioprocessos e Biotecnologia. Defesa : Curitiba, 16/06/2021Inclui referências: p. 126-156Resumo: O Brasil apresenta potencial biotecnológico para a desenvolvimento de novos produtos para atender a grande demanda da indústria de alimentos e farmacêutica, os quais aportem benefícios à saúde humana e animal. O consumo de alimentos ricos em lipídeos de alto valor como os ácidos graxos essenciais ômega-3 tem ganho grande destaque, tendo como principal fonte a extração a partir do óleo de pescados. Porém, alguns problemas relacionados à produção de ácidos graxos a partir de pescados incluem (i) a diminuição dos estoques de peixes devido à pesca predatória extrativista, (ii) a poluição dos mares tem causado graves problemas ambientais e (ii) a baixa disponibilidade de fontes alternativas para consumidores alérgicos ou com dieta vegana. Para tal se faz necessário a busca de alternativas biotecnológicas para produção desses biocompostos. Desta forma, os traustoquitrídeos aparecem como uma solução sustentável, eco-amigável e renovável de fontes microbianas de lipídeos de alto valor como o ômega-3, principalmente o DHA (ácido docosahexaenóico). Traustoquitrídeos são protistas ou microalgas heterotróficas que habitam o ecossistema de mangues e águas costeiras oceânicas. Nesta tese, um estudo sobre o uso de traustoquitrídeos e microalgas como fontes de lipídeos microbianos foi realizado. Diferentes abordagens sobre técnicas de isolamento, manutenção e cultivo celular foram discutidas. Uma análise do desenvolvimento destes protistas em biorreatores, estratégias para promover o acúmulo de lipídeos, técnicas de moleculares de melhoramento e inovações visando a produção em larga escala foram estudadas. Da mesma forma, uma revisão aprofundada sobre os traustoquitrídeos como fonte sustentável de ômega- 3, tendencias, avanços tecnológicos e mapeamento de patentes foi realizado. Seguidamente, uma abordagem integrando metagenômica e cultivo em microescala junto com espectroscopia de fluorescência foi usada na bioprospecção de traustoquitrídeos acumuladores de lipídeos a partir de amostras de manguezal e água do mar costeira no sul do Brasil. Estas estratégias permitiram isolar eficientemente traustoquitrídeos, dos quais vinte isolados foram cultivados em fermentação submersa e seus perfis lipídicos foram caracterizados. O isolado B36 foi identificado como Aurantiochytrium sp. pelo sequenciamento do rRNA 18s e obteve uma alta produção de biomassa (25.60 g/l) e lipídeos (17.12 g/l) com 44.37% de AGPI-CL e 34.6% de DHA. Paralelamente, estudos de melhoramento do traustoquitrídeo Aurantiochytrium limacinum SR21 por técnicas de mutação UV e otimização de bioprocessos utilizando subprodutos agroindustriais de baixo custo foram realizados. Assim, modelos de regressão matemáticos e superfícies de resposta foram gerados a fim de obter as melhores condições de cultivo. O traustoquitrídeo otimizado foi escalonado em biorreator de tanque agitado de 10L utilizando melaço de cana, milhocina e creme de levedura. Estudos cinéticos fermentativos foram realizados nos cultivos em shaker e biorreator. A maior produção obtida no biorreator em batelada foi 39.29 g/l de biomassa e 14.98 g/l de lipídeos com um rendimento (YP/X) de 0.45 g de lipídeos/g de biomassa. Os resultados obtidos tanto dos isolados como da cepa SR21 otimizada foram promissórios visando ao aumento em escala de bancada e piloto. Portanto, a biomassa de traustoquitrídeos rica em lipídeos de alto valor poderia ser usada como uma alternativa sustentável na alimentação humana e animal.Abstract: Brazil has biotechnological potential for the development of new products to meet the great demand of the food and pharmaceutical industry, which bring benefits to human and animal health. The consumption of foods rich in high-value lipids such as omega-3 essential fatty acids has gained great prominence, where the main source is fish oil. However, some problems related to the production of fatty acids from fish include (i) the decrease in fish stocks due to overfishing, (ii) the pollution of the seas has caused serious environmental problems and (ii) the low availability of alternative sources for allergic or vegan consumers. Thus, the search for biotechnological alternatives for the production of these biocompounds is necessary. Thus, thraustochytrids appear as a sustainable, eco-friendly and renewable solution of high-value microbial sources of lipids such as omega-3, mainly DHA (docosahexaenoic acid). Thraustochytrids are protists or heterotrophic microalgae that inhabit the ecosystem of mangroves and oceanic coastal waters. In this thesis, a study on the use of thraustochytrids and microalgae as sources of microbial lipids was carried out. Different approaches to cell isolation, maintenance and culture techniques were discussed. An analysis of the development of these protists in bioreactors, strategies to promote lipid accumulation, molecular improvement techniques and innovations aimed at large-scale production were studied. Likewise, an in-depth review of thraustochytrid as a sustainable source of omega-3, trends, technological advances and patent mapping was performed. Next, an approach integrating metagenetics and microscale cultivation with fluorescence spectroscopy was used in the bioprospection of lipid accumulating thraustochytrid from mangrove and coastal seawater samples in southern Brazil. These strategies allowed the efficient isolation of thraustochytrids, where twenty isolates were cultivated in submerged fermentation and their lipid profiles were characterized. Isolate B36 was identified as Aurantiochytrium sp. by sequencing 18s rRNA and obtained a high production of biomass (25.60 g/l) and lipids (17.12 g/l) with 44.37% LC-PUFAs and 34.6% DHA. In parallel, studies on the improvement of the thraustochytrid Aurantiochytrium limacinum SR21 by UV mutation techniques and optimization of bioprocesses using low-cost agro-industrial byproducts were carried out. Thus, mathematical regression models and response surfaces were generated in order to obtain the best growing conditions. The optimized thraustochytrid was scale-up in a 10L stirred tank bioreactor using sugarcane molasses, corn steep liquor and residual yeast cream. Fermentation kinetic studies were carried out in shaker and bioreactor cultures. The highest production obtained in the batch bioreactor was 39.29 g/l of biomass and 14.98 g/l of lipids with a yield (YP/X) of 0.45 g of lipids/g of biomass. The results obtained from the isolates and the optimized SR21 strain were promising, aiming at increasing bench and pilot scale. Therefore, high-value lipid-rich thraustochytrid biomass could be used as a sustainable alternative in human and animal feed

Exploring the transcriptome of non-model oleaginous microalga Dunaliella tertiolecta through high-throughput sequencing and high performance computing

10.1186/s12859-017-1551-xBMC Bioinformatics18112