In silico generation and analysis of “green” mono-ethylene glycol synthesis routes from synthesis gas [Abstract]

Conference abstract

A comparison between analytical and numerical solution of the Krogh's tissue cylinder model for human bone marrow

The Danish physiologist, August Krogh is the founder of the theory of oxygen transport to tissues. It was his famous tissue cylinder model developed for skeletal muscle, together with his colleague mathematician Erlang that laid down the foundation of the mathematical modeling of oxygen transport to tissues. Here an analytical solution of the Krogh’s model has been presented based on justifiable assumptions in order to validate the numerical approach used to solve more realistic oxygen transport models. The numerical solution of Krogh’s model is performed using computational fluid dynamics (CFD) software CFX 4.4. From the analytical solution, it is demonstrated that variation from the numerical result is less than 0.2% which in turn justifies the use of computer software in developing mathematical model for such physiological systems like BM

Designing novel biochemical pathways to commodity chemicals

Commodity chemicals are high-value chemicals used by industries to synthesise countless consumer products of daily use. For example, it was estimated that the global demand for benzene in 2015 was 46 million tonnes [1]. Many of these chemicals are mainly derived from petroleum feedstocks. With these feedstocks depleting and global pressure to reduce CO2 emissions, there is an urgent need to turn to sustainable bio-based methods to produce these chemicals [2]. Computational software can provide insight and be used to design novel biochemical pathways to produce commodity chemicals. The advantage being that these tools help engineer routes and suggest enzymes capable of catalysing these reactions [3]. In this study, the software ReactPRED and RetroPath 2.0 was used to design pathways to a few bulk chemicals, including benzene, phenol and 1,2-propanediol. These chemicals were chosen due to their high demands and current pathway knowledge

Systems-level metabolic modelling of a denitrifying bacterium important for mitigating fixed nitrogen pollution

Anaerobic ammonium oxidation (Anammox) is a novel biological process by which a group of strictly anaerobic bacteria convert ammonia together with nitrite into nitrogen gas. 4+ + 2− → 2 + 22 Due to the slow growth rate of these bacteria, as indicated by the doubling time of 2 to 11, the denitrification process can hardly be utilized in an industrial scale for the removal of excess fixed nitrogen compounds from the environment. The Anammox bacterium selected in the project is Candidatus Kuenenia stuttgartiensis (CKS), an Anammox bacterium that was discovered by Strous and his colleagues in 1999. A genome-scale metabolic model is generated to reveal the metabolic network within the Anammox bacteria

Computational design of a biosensor

Research poster presented at AACME Summer Bursary Student Poster Competition

Characterizing the metabolism of Dehalococcoides with a constraint-based model

Dehalococcoides strains respire a wide variety of chloro-organic compounds and are important for the bioremediation of toxic, persistent, carcinogenic, and ubiquitous ground water pollutants. In order to better understand metabolism and optimize their application, we have developed a pan-genome-scale metabolic network and constraint-based metabolic model of Dehalococcoides. The pan-genome was constructed from publicly available complete genome sequences of Dehalococcoides sp. strain CBDB1, strain 195, strain BAV1, and strain VS. We found that Dehalococcoides pan-genome consisted of 1118 core genes (shared by all), 457 dispensable genes (shared by some), and 486 unique genes (found in only one genome). The model included 549 metabolic genes that encoded 356 proteins catalyzing 497 gene-associated model reactions. Of these 497 reactions, 477 were associated with core metabolic genes, 18 with dispensable genes, and 2 with unique genes. This study, in addition to analyzing the metabolism of an environmentally important phylogenetic group on a pan-genome scale, provides valuable insights into Dehalococcoides metabolic limitations, low growth yields, and energy conservation. The model also provides a framework to anchor and compare disparate experimental data, as well as to give insights on the physiological impact of "incomplete" pathways, such as the TCA-cycle, CO 2 fixation, and cobalamin biosynthesis pathways. The model, referred to as iAI549, highlights the specialized and highly conserved nature of Dehalococcoides metabolism, and suggests that evolution of Dehalococcoides species is driven by the electron acceptor availability

Synthetic biology strategies for improving microbial synthesis of "green" biopolymers

Polysaccharide-based biopolymers have many material properties relevant to industrial and medical uses, including as drug delivery agents, wound-healing adhesives, and food additives and stabilizers. Traditionally, polysaccharides are obtained from natural sources. Microbial synthesis offers an attractive alternative for sustainable production of tailored biopolymers. Here, we review synthetic biology strategies for select “green” biopolymers: cellulose, alginate, chitin, chitosan, and hyaluronan. Microbial production pathways, opportunities for pathway yield improvements, and advances in microbial engineering of biopolymers in various hosts are discussed. Taken together, microbial engineering has expanded the repertoire of green biological chemistry by increasing the diversity of biobased materials

Commodity chemicals production in Moorella thermoacetica

The thermophilic acetogen Moorella thermoacetica produces acetate from C1 gases during gas fermentation, making it an interesting chassis organism for bio-based chemical production

Moorella thermoacetica: a chassis organism for biochemicals production?

Microbial chassis organisms are crucial for chemicals bioproduction

Commodity chemicals production from C1 gases in Moorella thermoacetica

Microbial chassis organisms are crucial for chemicals bioproduction