2017 Summer Research Symposium Abstract Book

2017 Summer volume of abstracts for science research projects conducted by students at Trinity College

ANISERP: a new serpin from the parasite Anisakis simplex

Background: Serine proteinase inhibitors (serpins) finely regulate serine proteinase activity via a suicide substrate-like inhibitory mechanism. In parasitic nematodes, some serpins interact with host physiological processes; however, little is known about these essential molecules in Anisakis. This article reports the gene sequencing, cloning, expression and preliminary biochemical and bioinformatically-based structural characterization of a new Anisakis serpin (ANISERP). Methods: The full AniSerp gene was cloned by specific RACE-PCR after screening an Anisakis simplex (L3) cDNA library. For biochemical assays, the AniSerp gene was subcloned into both prokaryotic and eukaryotic vectors, and the recombinant proteins were purified. The inhibitory properties of the proteins were tested in classical biochemical assays using human serine peptidases and AMC substrates. Immunolocalization of ANISERP, theoretical structural analysis and bioinformatically-based structural modelling of the ANISERP protein were also conducted. Results: The AniSerp gene was found to have 1194 nucleotides, coding for a protein of 397 amino acid residues plus a putative N-terminal signal peptide. It showed significant similarity to other nematode, arthropod and mammalian serpins. The recombinant ANISERP expressed in the prokaryotic and eukaryotic systems inhibited the human serine proteases thrombin, trypsin and cathepsin G in a concentration-dependent manner. No inhibitory activity against Factor Xa, Factor XIa, Factor XIIa, elastase, plasmin or chymotrypsin was observed. ANISERP also acted on the cysteine protease cathepsin L. ANISERP was mainly localized in the nematode pseudocoelomic fluid, somatic muscle cell bodies and intestinal cells. The findings of molecular dynamics studies suggest that ANISERP inhibits thrombin via a suicide substrate-like inhibitory mechanism, similar to the mechanism of action of mammalian coagulation inhibitors. In contrast to findings concerning human antithrombin III, heparin had no effect on ANISERP anticoagulant inhibitory activity. Conclusions: Our findings suggest that ANISERP is an internal Anisakis regulatory serpin and that the inhibitory activity against thrombin depends on a suicide substrate-like inhibitory mechanism, similar to that described for human antithrombin (AT)-III. The fact that heparin does not modulate the anticoagulant activity of ANISERP might be explained by the absence in the latter of five of the six positively charged residues usually seen at the AT-III-heparin binding site.We thank Biomol-Informatics SL (http://www.biomol-informatics.com/) for bioinformatic consultation. We also thank Juan Francisco Alcaide and Julia Medrano for their invaluable help in the ANISERP patenting process. We thank Dr Raúl Iglesias (Laboratorio de Parasitología, Facultad de Biología, Universidad de Vigo) for his helpful comments on the interpretation of the IHQ studies

ESR, ENDOR and TRIPLE resonance studies of the primary donor radical cation P960+ in the photosynthetic bacterium Rhodopseudomonas viridis

The light-induced radical cation of the primary electron donor P960+• in photosynthetic reaction centers from Rhodopseudomonas viridis has been investigated by ESR, ENDOR and TRIPLE techniques. Both the comparison with the cation radical of monomeric bacteriochlorophyll b (BChl b) and with molecular-orbital calculations performed on P960+• using the results of an X-ray structure analysis, consistently show an asymmetric distribution of the unpaired electron over the two BChl b molecules which constitute P960+•. The possible relevance of this result for the primary electron transfer step in the reaction center is briefly discussed

ПРОИЗВОДСТВО ЭТАНОЛА ИЗ КОЛОКАЗИИ (Xanthosoma sagittifolium): ПРИМЕНЕНИЕ ТЕРМОДИНАМИКО-ТОПОЛОГИЧЕСКОГО АНАЛИЗА

Cocoyam (Xanthosoma sagittifolium (L.) Schott) is a tropical plant of the family of Araceas. Nigeria, China and Ghana are the countries that currently own most of the world production of this plant. In Colombia, there are not extensive crops of this plant, but it is used for animal feeding mainly. The plant has an aerial part with a high content of protein (leaves) and a tuber with an average starch content about 25% w/w. Compared to others starchy raw materials, this is a high value. Due to this fact this first-generation starchy material could be considered as a possible feedstock for the production of ethanol. Process design must ensure that the most advanced concepts are applied at the design and processing stage for every raw material to ensure efficient and more sustainable processes. For this reason, thermodynamic-topological analysis was used for the design of the stage of the produced ethanol purification. This work presents the process of ethanol production using cocoyam tuber. The software Aspen Plus v8.6 (Aspen Technology, Inc., USA) was used for the techno-economic assessment, and the Waste Reduction Algorithm (WAR) of the Environmental Protection Agency of the EE.UU. (EPA) was used to measure the environmental performance. The obtained production cost was 1,6 USD per kilogram, and the environmental impact was very low. This is an excellent incentive to promote the application of this feedstock to obtain a feasible alternative for the production of ethanol. Additionally, the use of thermodynamic-topological analysis in the design stage of the purification stage of the process proved to be very useful and easily applied.Колоказия (Xanthosoma sagittifolium (L.) Schott) является тропическим растением семейства Araceas. Нигерия, Китай и Гана представляют собой страны, которые в настоящее время являются лидерами мирового производства этого растения. Колумбия не культивирует колоказию в промышленных масштабах, внутри страны данное растение применяют главным образом в качестве корма для животных. Растение имеет надземную часть с высоким содержанием белка в листьях, при этом содержание крахмала в клубнях составляет в среднем около 25% мас. По сравнению с другим сырьем колоказия содержит крахмала намного больше, что позволяет рассматривать ее как первоочередного кандидата в качестве сырья для промышленного производства этанола. При проектировании промышленного процесса следует учесть наиболее передовые технологические решения, которые позволят увеличить его эффективность и устойчивость. По этой причине на этапе разработки стадии очистки этанола использован термодинамико-топологический анализ. В статье представлен технологический процесс производства этанола с использованием клубней колоказии в качестве сырья. Технико-экономическая оценка процесса и измерение его экологических характеристик проведено с использованием современного программного обеспечения: Aspen Plus v8.6 (Aspen Technology, Inc., США) и Алгоритма сокращения отходов (WAR) Агентства по охране окружающей среды EE.UU. (EPA). Стоимость производства этанола составила 1,6 долл. США за килограмм при низком воздействии на окружающую среду. Это отличный стимул для продвижения данного вида сырья в качестве приемлемой альтернативы при производстве этанола. Использование термодинамико-топологического анализа на стадии проектирования этапа очистки процесса оказалось простым очень полезным средством

The light requirements for growth and photosynthesis in seagrasses with emphasis on Texas estuaries : a literature survey

During the last 20 years, seagrass communities throughout the world have experienced decreased productivity and distribution. These declines have often been attributed to decreased water transparency as a result of turbidity or shading by epiphytic algae. Epiphytic shading is often an indication of nutrient enrichment caused by anthropogenic inputs. Although both epiphytes and turbidity occur as natural phenomena, human activities can exacerbate existing natural conditions with adverse effects on seagrass communities. The objectives of this study were (a) to review the existing literature and data available on the effect of natural and anthropogenic factors on the underwater light environment; (b) to examine the relationship between light and seagrass distribution and productivity; and (c) to make recommendations on how to protect seagrass habitats in Texas bays and estuaries. To meet these goals, we have examined the available literature, emphasizing the physiological response of seagrasses to light and temperature. By using data and observations collected on a variety of species from around the world we may be better able to define the light requirements of Texas seagrasses. A knowledge of the minimum annual light requirements for seagrass growth is necessary to maintain the current distribution of Texas species. This information will also be required in the development of a management plan that permits the expansion and establishment of new seagrass habitat.Submitted to United States Environmental Protection Agency, Region 6 ... Dallas, Tx31 July 1993Marine Scienc

Production planning of biopharmaceutical manufacture.

Multiproduct manufacturing facilities running on a campaign basis are increasingly becoming the norm for biopharmaceuticals, owing to high risks of clinical failure, regulatory pressures and the increasing number of therapeutics in clinical evaluation. The need for such flexible plants and cost-effective manufacture pose significant challenges for planning and scheduling, which are compounded by long production lead times, intermediate product stability issues and the high cost - low volume nature of biopharmaceutical manufacture. Scheduling and planning decisions are often made in the presence of variable product titres, campaign durations, contamination rates and product demands. Hence this thesis applies mathematical programming techniques to the planning of biopharmaceutical manufacture in order to identify more optimal production plans under different manufacturing scenarios. A deterministic mixed integer linear programming (MILP) medium term planning model which explicitly accounts for upstream and downstream processing is presented. A multiscenario MILP model for the medium term planning of biopharmaceutical manufacture under uncertainty is presented and solved using an iterative solution procedure. An alternative stochastic formulation for the medium term planning of biomanufacture under uncertainty based on the principles of chance constrained programming is also presented. To help manage the risks of long term capacity planning in the biopharmaceutical industry, a goal programming extension is presented which accounts for multiple objectives including cost, risk and customer service level satisfaction. The model is applied to long term capacity analysis of a mix of contractors and owned biopharmaceutical manufacturing facilities. In the final sections of this thesis an example of a commercial application of this work is presented, followed by a discussion on related validation issues in the biopharmaceutical industry. The work in this thesis highlighted the benefits of applying mathematical programming techniques for production planning of biopharmaceutical manufacturing facilities, so as to enhance the biopharmaceutical industry's strategic and operational decision-making towards achieving more cost-effective manufacture

On the Conflicting Estimations of Pigment Site Energies in Photosynthetic Complexes: A Case Study of the CP47 Complex

Citation: Reinot, T., Chen, J. H., Kell, A., Jassas, M., Robben, K. C., Zazubovich, V., & Jankowiak, R. (2016). On the Conflicting Estimations of Pigment Site Energies in Photosynthetic Complexes: A Case Study of the CP47 Complex. Analytical Chemistry Insights, 11, 35-48. doi:10.4137/aci.s32151We focus on problems with elucidation of site energies (E-0(n)) for photosynthetic complexes (PSCs) in order to raise some genuine concern regarding the conflicting estimations propagating in the literature. As an example, we provide a stern assessment of the site energies extracted from fits to optical spectra of the widely studied CP47 antenna complex of photosystem II from spinach, though many general comments apply to other PSCs as well. Correct values of E-0(n) for chlorophyll (Chl) a in CP47 are essential for understanding its excitonic structure, population dynamics, and excitation energy pathway(s). To demonstrate this, we present a case study where simultaneous fits of multiple spectra (absorption, emission, circular dichroism, and nonresonant hole-burned spectra) show that several sets of parameters can fit the spectra very well. Importantly, we show that variable emission maxima (690-695 nm) and sample-dependent bleaching in nonresonant hole-burning spectra reported in literature could be explained, assuming that many previously studied CP47 samples were a mixture of intact and destabilized proteins. It appears that the destabilized subpopulation of CP47 complexes could feature a weakened hydrogen bond between the 13(1)-keto group of Chl29 and the PsbH protein subunit, though other possibilities cannot be entirely excluded, as discussed in this work. Possible implications of our findings are briefly discussed