Evolutionary Computation 2020

Intelligent optimization is based on the mechanism of computational intelligence to refine a suitable feature model, design an effective optimization algorithm, and then to obtain an optimal or satisfactory solution to a complex problem. Intelligent algorithms are key tools to ensure global optimization quality, fast optimization efficiency and robust optimization performance. Intelligent optimization algorithms have been studied by many researchers, leading to improvements in the performance of algorithms such as the evolutionary algorithm, whale optimization algorithm, differential evolution algorithm, and particle swarm optimization. Studies in this arena have also resulted in breakthroughs in solving complex problems including the green shop scheduling problem, the severe nonlinear problem in one-dimensional geodesic electromagnetic inversion, error and bug finding problem in software, the 0-1 backpack problem, traveler problem, and logistics distribution center siting problem. The editors are confident that this book can open a new avenue for further improvement and discoveries in the area of intelligent algorithms. The book is a valuable resource for researchers interested in understanding the principles and design of intelligent algorithms

Characterisation of high and low avidity peptide specific CD8+ T cells using immunologic, transcriptomic and proteomic tools

One of the hallmarks of successful immunotherapy is the generation of high avidity cytotoxic T cells which can recognise and respond to very low concentration of antigens. This sensitivity of T cells is usually determined by peptide titration ELISpot assays. Even though these assays are generally useful, they are laborious and sample demanding. The assays become even more difficult if the peptide(s) accountable for the generation of vaccine specific responses are unknown such as whole protein or cell vaccines. Therefore, there is a need to identify markers which can quickly and reliably identify a high avidity T cell response in cancer vaccination settings. To achieve this goal, this study utilised a C57Bl/6J mouse model which could efficiently generate high and low avidity T cell responses, when immunisation was undertaken with two form of vaccines to deliver the target antigens. The antigenic epitopes used for this study were derived from TRP-2 ‘self’ and ovalbumin (OVA) ‘foreign’ antigens. Immunisation of animals with these antigens in a DNA vaccine format induces a high avidity T cell response, in contrast to the response when these are administered in the peptide vaccine format. However, both the immunisations produced same number of peptide specific CD8+ T cells, which was assessed my multimer staining. When these cells were subjected to in vitro stimulations with the target peptides, the functionality of the low avidity T cells was restored whereas the high avidity T cells failed to respond to lower peptide concentrations. This showed the plasticity of antigen specific T cells and their ability to modulate their functionality according to the stimulation they have received

Expansion of and reclassification within the family Lachnospiraceae

Many of the taxa in the family Lachnospiraceae are currently misclassified as Clostridium spp. Here attempt to rectify many of these issues, beginning with an in-depth genomic and physiologic analysis of Clostridium methoxybenzovorans, culminating in the assertion that is a heterotype of Clostridium indolis, followed by reclassification of the broader group in which this organism resides. We propose two novel genera, Lacriformis and Enterocloster, to reclassify this clade, this includes reclassification of Clostridium sphenoides, Clostridium indolis, Clostridium saccharolyticum, Clostridium celerecrescens, Clostridium xylanolyticum, Clostridium algidixylanolyticum, Clostridium aerotolerans, Clostridium amygdalinum, and Desulfotomaculum guttoideum as Lacriformis sphenoides, comb. nov., Lacriformis indolis, comb. nov., Lacriformis saccharolyticum, comb. nov., Lacriformis celerecrescens, comb. nov., Lacriformis xylanolyticum, comb. nov., Lacriformis algidixylanolyticum, comb. nov., Lacriformis aerotolerans, comb. nov., Lacriformis amygdalinum, comb. nov., and Lacriformis guttoideum, comb. nov. A second genus, Enterocloster, includes Clostridium clostridioforme, Clostridium bolteae, Clostridium citroniae, Clostridium lavalense, Clostridium aldenense, and Clostridium asparagiforme, reclassified as Enterocloster clostridioforme, comb. nov., Enterocloster bolteae, comb. nov., Enterocloster citroniae, comb. nov., Enterocloster lavalense, comb. nov., Enterocloster aldenense, comb. nov., and Enterocloster asparagiforme, comb. nov. We then propose reclassification of another group of cellulolytic and hemicellulolytic Clostridium species. One genus, Cellulospecium, gen. nov., includes Cellulospecium herbivorans, comb. nov., Cellulospecium populeti, comb. nov., and Cellulospecium polysaccharolyticum, comb. nov., formerly Clostridium herbivorans, Clostridium populeti, and Clostridium polysachharolyticum. Another genus, Leschinia, houses Leschinia phytofermentans, comb. nov., formerly Clostridium phytofermentans. We also describe a novel species, Anaerocolumna spermata. We propose the classification of a novel genus and species, Kineothrix alysoides, a highly motile anaerobic spore-former with broad saccharolytic capabilities. It produces butyrate as a major fermentation product and appears to be able to fix nitrogen. We end with the microcosm from which the novel taxa were isolated. With the most abundant members isolated, we were able to approach the question of the rare biosphere through synthetic ecology. Rather than culling out diversity with toxins, we were able to remove diversity by leaving members out. These rare members had a significant positive effect on plant degradation, though nutrient limitation had a more pronounced effect. This approach is especially useful for comparative and perturbation studies

STRUCTURE AND DYNAMICS OF MICROBIAL COMMUNITIES IN ANAEROBIC DIGESTION PROCESSES

Nowadays world energy needs rely mostly on fossil fuels (oil, coal and natural gas) which accounts for more than 80% of global energy production. Fossil fuels reserves are estimated to deplete in the next future. In this context, it arises the need to establish new renewable energetic sources. A well-established technology for bioenergy production in the form of biogas is anaerobic digestion (AD). This process involves a complex consortium of different functional groups of microbes which, degrading the organic matter, produce biogas composed mainly of methane and carbon dioxide. In the latest 10 years there has been renewed interest for energy production from biomass through AD because of its versatility and potentiality. So far, the control and performance of AD process has typically been performed working on operational parameters (such as T, pH, COD, loading rate, etc.). However, recent studies concerning the microbial consortia involved in this complex process have been developing with the final aim to get an exhaustive knowledge of microbiology of the process and how it correlates to the operation of the reactor in order to improve the digester performance making preventive action possible. the general aim of this PhD thesis was to investigate the microbiology of both batch and continuous, single and two-stage anaerobic systems. The goals were (i) to elucidate the structure of the microbial communities, (ii) to investigate the dynamics, interactions and responses of the key metabolic groups responsible for the degradation of substrates and (iii) to give valuable information on the correlation between structure and function inside the microbial consortiums

Biochemical characterisation of unusual glycolytic enzymes from the human intestinal parasite Blastocystis hominis

Blastocystis is an important parasite that infects humans and a wide range of animals like rats, birds, reptiles, etc. infecting a sum of 60% of world population. It belongs to the Stramenopiles, a Heterologous group that includes for example the Phythophthora infestans the responsible for the Irish potato famine. Previous work had reported the presence of an unusual fusion protein that is composed of two of the main glycolytic enzymes; Triosephosphate isomerase-glyceraldehyde-3-phosphate dehydrogenase (TPI-GAPDH). Little is known about this protein. Blastocystis TPI-GAPDH and Blastocystis enolase were both characterized biochemically and biophysically in this project. The phylogenetic relationships of those two proteins among other members of either Stramenopiles, or other members of the kingdom of life were examined and found to be grouping within the chromalveolates. Our studies revealed that those two proteins, Blastocystis enolase and Blastocystis TPI-GAPDH, had a peptide signal targeting them to the mitochondria. This was an unusual finding knowing that text books always referred to the glycolytic pathway as a canonical cytoplasmic pathway. Structural studies had also been conducted to unravel the unknown structure of the fusion protein Blastocystis TPI-GAPDH. X-ray crystallography had been conducted to solve the protein structure and the protein was found to be a tetrameric protein composed of a central tetrameric GAPDH protein flanked with two dimmers of TPI protein. Solving its structure would be the starting point towards reviling the role that TPI-GAPDH might play in Blastocystis and other organisms that it was found in as well. Although a fusion protein, the individual components of the fusion were found to contain all features deemed essential for function for TPI and GAPDH and contain all expected protein motifs for these enzymes