A systems biology approach for the characterization of metabolic bottlenecks in recombinant protein production processes

The purpose of this project is to derive strategies for increasing the productivity of recombinant protein production processes by applying a systems biology perspective to the phenomena occurring in the recombinant cell. This will specifically involve the use of genome-scale analysis of the transcriptome, proteome and fluxome. Escherichia coli have been the organism of choice for the production of many recombinant proteins with high therapeutic value. However, there are still some associated phenomena that decrease the process performance, like the stringent response that usually occurs when very high levels of heterologous protein production. In this work, the high-cell density fed-batch recombinant protein production process in E. coli will be studied, giving particular relevance to stringent response. The approach is intended to be systematic, by first compiling the existing knowledge about this phenomenon, extending existing genome-scale models to accommodate that knowledge, and derive hypothesis in silico that will then be tested by using genome-scale analysis of the transcriptome

A new adaptive scheme for the adaptive linearizing control of bioprocesses

This work deals with the development of model-based adaptive control algorithms for bioprocess operation. Non-linear adaptive control laws are proposed for single input single output regulation. Parameters are continuously adapted following a new adaptive scheme which ensures second-order dynamics of the parameter error system. A computational study is presented of the application of this theory to baker’s yeast fermentation. Results put in evidence the efficient performance both of the adaptive scheme and of the related control laws.Instituto de Sistemas e Robótica, Pólo do Porto

Effects ofWolbachiaon Transposable Element Expression Vary BetweenDrosophila melanogasterHost Genotypes

Transposable elements (TEs) are repetitive DNA sequences capable of changing position in host genomes, thereby causing mutations. TE insertions typically have deleterious effects but they can also be beneficial. Increasing evidence of the contribution of TEs to adaptive evolution further raises interest in understanding what factors impact TE activity. Based on previous studies associating the bacterial endosymbiont Wolbachia with changes in the abundance of piRNAs, a mechanism for TE repression, and to transposition of specific TEs, we hypothesized that Wolbachia infection would interfere with TE activity. We tested this hypothesis by studying the expression of 14 TEs in a panel of 25 Drosophila melanogaster host genotypes, naturally infected with Wolbachia and annotated for TE insertions. The host genotypes differed significantly in Wolbachia titers inside individual flies, with broad-sense heritability around 20%, and in the number of TE insertions, which depended greatly on TE identity. By removing Wolbachia from the target host genotypes, we generated a panel of 25 pairs of Wolbachia-positive and Wolbachia-negative lines in which we quantified transcription levels for our target TEs. We found variation in TE expression that was dependent on Wolbachia status, TE identity, and host genotype. Comparing between pairs of Wolbachia-positive and Wolbachia-negative flies, we found that Wolbachia removal affected TE expression in 21.1% of the TE-genotype combinations tested, with up to 2.3 times differences in the median level of transcript. Our data show that Wolbachia can impact TE activity in host genomes, underscoring the importance this endosymbiont can have in the generation of genetic novelty in hosts.info:eu-repo/semantics/publishedVersio

Towards an electroless deposition of gold on metallic substrates using ionic liquids as electrolytes

Recent research has suggested a number of applications for gold in fuel cells and related hydrogen fuel processing, which include light weight corrosion resistance bipolar plates and the incorporation of gold as catalyst to provide improvements in electrode conductivity, among others. This paper reports on the electroless deposition of gold on copper substrates from a HAuCl4.3H2O solution in 1-butyl-1- methylpyrrolidinium dicyanamide (BMP-DCA), in laboratory atmospheric conditions. The electrochemical behaviour of the plating solution was studied by potential sweep techniques. Results suggest that gold ions are reduced and deposited on copper without the aid of external polarization, probably by displacement deposition involving copper dissolution, since no other oxidation reaction was identified. Preliminary studies using SEM/EDX showed that compact gold thin films, deposited on copper substrates at 333 K, present a granular nanostructured morphology

Electrodeposition of black chromium thin films from trivalent chromium-ionic liquid solution

Abstract -In the present study, black chromium thin films were electrodeposited from a solution of 1-butyl-3-methylimidazolium tetrafluoroborate ([BMIm][BF4] ionic liquid containing trivalent chromium (Cr(III)). Homogeneous and well adherent coatings have been obtained on nickel, copper and stainless steel substrates. The nucleation and growth of the films were investigated by cyclic voltammetry and current-density/time transient techniques. SEM/EDS, XPS and XRD were used to study the morphology, chemical composition and structure of the films. The coatings consist of a mixture of metallic chromium and chromium oxides (black chromium) and present a sub-micrometric granular structure. Black chromium is an important coating material used in solar thermal systems as a spectrally selective surface and is usually produced by electrodeposition from hexavalent chromium (Cr(VI)) aqueous solutions. However, these electrolytes raise serious health and environmental concerns, and their replacement has been long pursued. Developments in green chemistry have shown that ionic liquids can be used as electrolytes, due to their wide electrochemical window and enhanced chemical stability when compared to water In the present study, black chromium thin films were electrodeposited from solutions of 1-butyl-3-methylimidazolium tetrafluoroborate ([BMIm][BF 4 ]) containing trivalent chromium (Cr(III)). Cyclic voltammetry and current-density/time transient techniques were used to study the nucleation and growth of the films. Electrodeposition was carried out on copper, nickel and austenitic stainless steel substrates, by a potentiostatic method. The coatings were characterized by SEM/EDS, XPS and XRD. Cyclic voltammetry allows the identification of the potential range at which the reduction reaction corresponding to the formation of black chromium occurs. Current-density/time transients were recorded on stainless steel substrates and fitted the Scharifker-Hills model equations. This analysis indicates that the formation of black chromium on this substrate occurs by an instantaneous nucleation process with diffusion controlled three-dimensional growth. Homogeneous and well adherent black chromium coatings were obtained on all substrate materials. The films present a sub-micrometric granular structur

Long-term stability of a non-adapted aerobic granular sludge process treating fish canning wastewater associated to EPS producers in the core microbiome

The tolerance of aerobic granular sludge (AGS) to variable wastewater composition is perceived as one of its greatest advantages compared to other aerobic processes. However, research studies select optimal operational conditions for evaluating AGS performance, such as the use of pre-adapted biomass and the control of wastewater composition. In this study, non-adapted granular sludge was used to treat fish canning wastewater presenting highly variable organic, nutrient and salt levels over a period of ca. 8 months. Despite salt levels up to 14 g NaCl L−1, the organic loading rate (OLR) was found to be the main factor driving AGS performance. Throughout the first months of operation, the OLR was generally lower than 1.2 kg COD m−3 day−1, resulting in stable nitrification and low COD and phosphorous levels at the outlet. An increase in OLR up to 2.3 kg COD m−3 day−1 disturbed nitrification and COD and phosphate removal, but a decrease to average values between 1 and 1.6 kg COD m−3 day−1 led to resuming of those processes. Most of the bacteria present in the AGS core microbiome were associated to extracellular polymeric substances (EPS) production, such as Thauera and Paracoccus, which increased during the higher OLR period. Ammonium-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) species were detected in AGS biomass; while AOB were identified throughout the operation, NOB were no further identified after the period of increased OLR. Different polyphosphate-accumulating organisms (PAOs) were detected along the process: Candidatus Accumulibacter, Tetrasphaera and Gemmatimonas. A non-adapted granular sludge was able to treat the fish canning wastewater and to tolerate salinity fluctuations up to 14 g L−1. Overall, a high microbial diversity associated to EPS producers allowed to preserve bacterial groups responsible for nutrients removal, contributing to the adaptation and long-term stability of the AGS system.info:eu-repo/semantics/publishedVersio