Temperature regulation of a pilot-scale batch reaction system via explicit model predictive control

In this paper, the temperature of a pilot-scale batch reaction system is modeled towards the design of a controller based on the explicit model predictive control (EMPC) strategy -- Some mathematical models are developed from experimental data to describe the system behavior -- The simplest, yet reliable, model obtained is a (1,1,1)-order ARX polynomial model for which the mentioned EMPC controller has been designed -- The resultant controller has a reduced mathematical complexity and, according to the successful results obtained in simulations, will be used directly on the real control system in a next stage of the entire experimental framework

Role of membrane lipids in the regulation of erythrocytic oxygen-transport function in cardiovascular diseases

The composition and condition of membrane lipids, the morphology of erythrocytes, and hemoglobin distribution were explored with the help of laser interference microscopy (LIM) and Raman spectroscopy. It is shown that patients with cardiovascular diseases (CVD) have significant changes in the composition of their phospholipids and the fatty acids of membrane lipids. Furthermore, the microviscosity of the membranes and morphology of the erythrocytes are altered causing disordered oxygen transport by hemoglobin. Basic therapy carried out with the use of antiaggregants, statins, antianginals, beta-blockers, and calcium antagonists does not help to recover themorphofunctional properties of erythrocytes. Based on the results the authors assume that, for the relief of the ischemic crisis and further therapeutic treatment, it is necessary to include, in addition to cardiovascular disease medicines, medication that increases the ability of erythrocytes’ hemoglobin to transport oxygen to the tissues. We assume that the use of LIM and Raman spectroscopy is advisable for early diagnosis of changes in the structure and functional state of erythrocytes when cardiovascular diseases develop.

Expression-based and co-localization detection of arabinogalactan protein 6 and arabinogalactan protein 11 interactors in Arabidopsis pollen and pollen tubes

Arabinogalactan proteins (AGPs) are cell wall proteoglycans that have been shown to be important for pollen development. An Arabidopsis double null mutant for two pollen-specific AGPs (agp6 agp11) showed reduced pollen tube growth and compromised response to germination cues in vivo. A microarray experiment was performed on agp6 agp11 pollen tubes to search for genetic interactions in the context of pollen tube growth. A yeast two-hybrid experiment for AGP6 and AGP11 was also designed.

The regulation of cancer cell invasive behaviour by Chloride Interacellular Channel 3 (CLIC3) and Transglutaminasae 2

A study into the role of secreted CLIC3 in tumour cell invasion. The initiation and progression of cancers is thought to be linked to their relationship with a population of activated fibroblasts, which are associated with tumours. I have used an organotypic approach, in which plugs of collagen I are preconditioned with fibroblastic cells, to characterise the mechanisms through which carcinoma-associated fibroblasts (CAFs) influence the invasive behaviour of tumour cells. I have found that immortalised cancer-associated fibroblasts (iCAFs) support increased invasiveness of cancer cells, and that this is associated with the ability of CAFs to increase the fibrillar collagen content of the extracellular matrix (ECM). To gain mechanistic insight into this phenomenon, an in-depth SILAC-based mass proteomic analysis was conducted, which allowed quantitative comparison of the proteomes of iCAFs and immortalised normal fibroblast (iNFs) controls. Chloride Intracellular Channel Protein 3 (CLIC3) was one of the most significantly upregulated components of the iCAF proteome. Knockdown of CLIC3 in iCAFs reduced the ability of these cells to remodel the ECM and to support tumour cell invasion through organotypic plugs. A series of experiments, including proteomic analysis of cell culture medium that had been preconditioned by iCAFs, indicated that CLIC3 itself was a component of the iCAF secretome that was responsible for the ability of iCAFs to drive tumour cell invasiveness. Moreover, addition of soluble recombinant CLIC3 (rCLIC3) was sufficient to drive the extension of invasive pseudopods in cancer cell lines, and to promote disruption of the basement membrane in a 3D in vitro model of the ductal carcinoma in situ (DCIS) to invasive ductal carcinoma (IDC) transition. My investigation into the mechanism through which extracellular CLIC3 drives tumour cell invasiveness led me to focus on the relationship between CLIC3 and the ECM modifying enzyme, transglutaminase-2 (TG2). Through this, I have found that TG2 physically associates with CLIC3 and that TG2 is necessary for CLIC3 to drive tumour cell invasiveness. These data identifying CLIC3 as a key pro-invasive factor, which is secreted by CAFs, provides an unprecedented mechanism through which the stroma may drive cancer progression.

An alternative benchmarking approach for electricity utility regulation using maximum entropy

The main purpose of this study is to present an alternative benchmarking approach that can be used by national regulators of utilities. It is widely known that the lack of sizeable data sets limits the choice of the benchmarking method and the specification of the model to set price controls within incentive-based regulation. Ill-posed frontier models are the problem that some national regulators have been facing. Maximum entropy estimators are useful in the estimation of such ill-posed models, in particular in models exhibiting small sample sizes, collinearity and non-normal errors, as well as in models where the number of parameters to be estimated exceeds the number of observations available. The empirical study involves a sample data used by the Portuguese regulator of the electricity sector to set the parameters for the electricity distribution companies in the regulatory period of 2012-2014. DEA and maximum entropy methods are applied and the efficiency results are compared.

Adaptive Mechanisms of an Estuarine Synechococcus based on Genomics, Transcriptomics, and Proteomics

Picocyanobacteria are important phytoplankton and primary producers in the ocean. Although extensive work has been conducted for picocyanobacteria (i.e. Synechococcus and Prochlorococcus) in coastal and oceanic waters, little is known about those found in estuaries like the Chesapeake Bay. Synechococcus CB0101, an estuarine isolate, is more tolerant to shifts in temperature, salinity, and metal toxicity than coastal and oceanic Synechococcus strains, WH7803 and WH7805. Further, CB0101 has a greater sensitivity to high light intensity, likely due to its adaptation to low light environments. A complete and annotated genome sequence of CB0101 was completed to explore its genetic capacity and to serve as a basis for further molecular analysis. Comparative genomics between CB0101, WH7803, and WH7805 show that CB0101 contains more genes involved in regulation, sensing, and stress response. At the transcript and protein level, CB0101 regulates its metabolic pathways, transport systems, and sensing mechanisms when nitrate and phosphate are limited. Zinc toxicity led to oxidative stress and a global down regulation of photosystems and the translation machinery. From the stress response studies seven chromosomal toxin-antitoxin (TA) genes, were identified in CB0101, which led to the discovery of TA genes in several marine Synechococcus strains. The activation of the relB2/relE1 TA system allows CB0101 to arrest its growth under stressful conditions, but the growth arrest is reversible, once the stressful environment dissipates. The genome of CB0101 contains a relatively large number of genomic island (GI) genes compared to known marine Synechococcus genomes. Interestingly, a massive shutdown (255 out of 343) of GI genes occurred after CB0101 was infected by a lytic phage. On the other hand, phage-encoded host-like proteins (hli, psbA, ThyX) were highly expressed upon phage infection. This research provides new evidence that estuarine Synechococcus like CB0101 have inherited unique genetic machinery, which allows them to be versatile in the estuarine environment.

Synthetic regulation of eukaryotic gene expression by noncoding RNA

Synthetic biological systems promise to combine the spectacular diversity of biological functionality with engineering principles to design new life to address many pressing needs. As these engineered systems advance in sophistication, there is ever-greater need for customizable, situation-specific expression of desired genes. However, existing gene control platforms are generally not modular, or do not display performance requirements required for robust phenotypic responses to input signals. This work expands the capabilities of eukaryotic gene control in two important directions.

For development of greater modularity, we extend the use of synthetic self-cleaving ribozyme switches to detect changes in input protein levels and convey that information into programmed gene expression in eukaryotic cells. We demonstrate both up- and down-regulation of levels of an output transgene by more than 4-fold in response to rising input protein levels, with maximal output gene expression approaching the highest levels observed in yeast. In vitro experiments demonstrate protein-dependent ribozyme activity modulation. We further demonstrate the platform in mammalian cells. Our switch devices do not depend on special input protein activity, and can be tailored to respond to any input protein to which a suitable RNA aptamer can be developed. This platform can potentially be employed to regulate the expression of any transgene or any endogenous gene by 3’ UTR replacement, allowing for more complex cell state-specific reprogramming.

We also address an important concern with ribozyme switches, and riboswitch performance in general, their dynamic range. While riboswitches have generally allowed for versatile and modular regulation, so far their dynamic ranges of output gene modulation have been modest, generally at most 10-fold. We address this shortcoming by developing a modular genetic amplifier for near-digital control of eukaryotic gene expression. We combine ribozyme switch-mediated regulation of a synthetic TF with TF-mediated regulation of an output gene. The amplifier platform allows for as much as 20-fold regulation of output gene expression in response to input signal, with maximal expression approaching the highest levels observed in yeast, yet being tunable to intermediate and lower expression levels. EC50 values are more than 4 times lower than in previously best-performing non-amplifier ribozyme switches. The system design retains the modular-input architecture of the ribozyme switch platform, and the near-digital dynamic ranges of TF-based gene control.

Together, these developments suggest great potential for the wide applicability of these platforms for better-performing eukaryotic gene regulation, and more sophisticated, customizable reprogramming of cellular activity.

REGULATION OF SHAPE DYNAMICS AND ACTIN POLYMERIZATION DURING COLLECTIVE CELL MIGRATION

This thesis aims to understand how cells coordinate their motion during collective migration. As previously shown, the motion of individually migrating cells is governed by wave-like cell shape dynamics. The mechanisms that regulate these dynamic behaviors in response to extracellular environment remain largely unclear. I applied shape dynamics analysis to Dictyostelium cells migrating in pairs and in multicellular streams and found that wave-like membrane protrusions are highly coupled between touching cells. I further characterized cell motion by using principle component analysis (PCA) to decompose complex cell shape changes into a serial shape change modes, from which I found that streaming cells exhibit localized anterior protrusion, termed front narrowing, to facilitate cell-cell coupling. I next explored cytoskeleton-based mechanisms of cell-cell coupling by measuring the dynamics of actin polymerization. Actin polymerization waves observed in individual cells were significantly suppressed in multicellular streams. Streaming cells exclusively produced F-actin at cell-cell contact regions, especially at cell fronts. I demonstrated that such restricted actin polymerization is associated with cell-cell coupling, as reducing actin polymerization with Latrunculin A leads to the assembly of F-actin at the side of streams, the decrease of front narrowing, and the decoupling of protrusion waves. My studies also suggest that collective migration is guided by cell-surface interactions. I examined the aggregation of Dictyostelim cells under distinct conditions and found that both chemical compositions of surfaces and surface-adhesion defects in cells result in altered collective migration patterns. I also investigated the shape dynamics of cells suspended on PEG-coated surfaces, which showed that coupling of protrusion waves disappears on touching suspended cells. These observations indicate that collective migration requires a balance between cell-cell and cell-surface adhesions. I hypothesized such a balance is reached via the regulation of cytoskeleton. Indeed, I found cells actively regulate cytoskeleton to retain optimal cell-surface adhesions on varying surfaces, and cells lacking the link between actin and surfaces (talin A) could not retain the optimal adhesions. On the other hand, suspended cells exhibited enhanced actin filament assembly on the periphery of cell groups instead of in cell-cell contact regions, which facilitates their aggregation in a clumping fashion.

Multibiomarker assessment of cadmium-based quantum dots effects in the marine mussel Mytilus galloprovincialis

Tese de Doutoramento, Ciências do Mar, da Terra e do Ambiente, Ramo: Ciências e Tecnologias do Ambiente, Especialização em Ecotoxicologia, Faculdade de Ciências e Tecnologia, Universidade do Algarve, 2016

Hormone-Mediated Gene-Specific Translation Regulation

The central role of translation regulation in the control of critical cellular processes has long been recognized. Yet the systematic exploration of quantitative changes in translation at a genome-wide scale in response to specific stimuli has only recently become technically feasible. Using a genetic approach, we have identified new Arabidopsis weak-ethylene insensitive mutants that also display defects in translation, which suggested the existence of a previously unknown molecular module involved in ethylene-mediated translation regulation of components of this signaling pathway. To explore this link in detail, we implemented for Arabidopsis the ribosome-footprinting technology, which enables the study of translation at a whole-genome level at single codon resolution[1]. Using ribosome-footprinting we examined the effects of short exposure to ethylene on the Arabidopsis translatome looking for ethylene-triggered changes in translation rates that could not be explained by changes in transcript levels. The results of this research, in combination with the characterization of a subset of the aforementioned weak-ethylene insensitive mutants that are defective in the UPF genes (core-components of the nonsense-mediated mRNA decay machinery), uncovered a translation-based branch of the ethylene signaling pathway[2]. In the presence of ethylene, translation of a negative regulator of ethylene signaling EBF2 is repressed, despite induced transcription of this gene. These translational effects of ethylene require the long 3´UTR of EBF2 (3´EBF2), which is recognized by the C-terminal end of the key ethylene-signaling protein EIN2 (EIN2C) in the cytoplasm once EIN2C is released from the ER-membrane by proteolytic cleavage. EIN2C binds the 3´EBF2, recruits the UPF proteins and moves to P-bodies, where the translation of EBF2 in inhibited despite its mRNA accumulation. Once the ethylene signal is withdrawn, the translation of the stored EBF2 mRNAs is resumed, thus rapidly dampening the ethylene response. These findings represent a mechanistic paradigm of gene-specific regulation of translation in response to a key growth regulator. Translation regulatory elements can be located in both 3′ and 5′ UTRs. We are now focusing on the ead1 and ead2 mutants, another set of ethylene-signaling mutants defective in translational regulation. Ribosome-footprinting on the ead1 mutant revealed an accumulation of translating ribosomes in the 5´UTRs of uORF-containing genes and reduction in the levels of ribosomes in the main ORF. The mutant is also impaired in the translation of GFP when this reporter is fused to WT 5´UTR of potential EAD1 targets but not when GFP is fused to the uORF-less versions of the same 5´UTRs. Our hypothesis is that EAD1/2 work as a complex that is required for the efficient translation of mRNAs that have common structural (complex 5´UTR with uORFs) and functional (regulation of key cellular processes) features. We are working towards the identification of the conditions where the EAD1 regulation of translation is required. [1] Ingolia, N. et al. (2009) Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling. Science, 324; 218-222 [2] Merchante, C. et al. (2015) Gene-Specific Translation Regulation Mediated by the Hormone-Signaling Molecule EIN2. Cell, 163(3): 684-697

NAC-MYB basedtranscriptional networkinvolved in the regulation of phenylalanine biosynthesis in P. pinaster

P2-2 NAC-MYB-BASED TRANSCRIPCIONAL NETWORK INVOLVED IN THE REGULATION OF PHENYLALANINE BIOSYNTHESIS IN P. PINASTER Mª Belén Pascual, Rafael A. Cañas, Blanca Craven-Bartle, Francisco M. Cánovas and Concepción Ávila Departamento de Biología Molecular y Bioquímica. Facultad de Ciencias. Universidad de Málaga. Campus de teatinos s/n, Málaga, Spain Email: cavila@uma.es Conifer trees divert large quantities of carbon into the biosynthesis of phenylpropanoids, particularly to generate lignin, an important constituent of wood. Since phenylalanine is the precursor for phenylpropanoid biosynthesis, the precise regulation of phenylalanine synthesis and use should occur simultaneously. This crucial pathway is finely regulated primarily at the transcriptional level. Transcriptome analyses indicate that the transcription factors (TFs) preferentially expressed during wood formation in plants belong to the MYB and NAC families. Craven-Bartle et al. (2013) have shown that Myb8 is a candidate regulator of key genes in phenylalanine biosynthesis involved in the supply of the phenylpropane carbon skeleton necessary for lignin biosynthesis. This TF is able to bind AC elements present in the promoter regions of these genes to activate transcription. In Arabidopsis, the transcriptional network controlling secondary cell wall involves NAC-domain regulators operating upstream Myb transcription factors. We have identified in the P. pinaster genome three NAC proteins as potential candidates to be involved in vascular development. One of them, PpNAC1 is expressed both in xylem and compression wood from adult trees and has been thoroughly characterized. Its role upstream the transcriptional network involving Myb8 will be discussed. The understanding of the transcriptional regulatory network associated to phenylpropanoids and lignin biosynthesis in conifers is crucial for future applications in tree improvement and sustainable forest management.

A Pb2+-ion electrochemical biosensor based on single-stranded DNAzyme catalytic beacon

A novel strategy for selective and sensitive electrochemical lead ion (Pb²⁺) biosensor was developed based on the single-stranded DNAzyme catalytic beacon. A DNAzyme that requires Pb²⁺ for activation was selected and labeled with redox-active ferrocene (Fc) for signal transducer. The Fc-labeled single-stranded DNAzyme (Fc-ssDNAzyme) was self-assembled through SAu bonding on a gold electrode surface. In the presence of Pb²⁺, the ssDNAzyme was activated and catalyzed the hydrolytic cleavage of the substrate strand, resulting in the removal of the substrate strand along with the Fc from the Au electrode surface. The dissociation of Fc caused a decrease of electrochemical signal ("signal-off"). Under the optimal conditions, the electrochemical signal of Fc decreased directly with the increasing Pb²⁺ concentration, exhibiting a linear response in the range of 0.5nM to 5μM with a detection limit of 0.25nM. This strategy is simple, sensitive and selective with the minimal reagents and working steps, thereby holds great potential for Pb²⁺ detection in real environmental sample analysis.

Enhanced thermal energy harvesting performance of a cobalt redox couple in ionic liquid-solvent mixtures

Thermoelectrochemical cells are increasingly promising devices for harvesting waste heat, offering an alternative to the traditional semiconductor-based design. Advancement of these devices relies on new redox couple/electrolyte systems and an understanding of the interplay between the different factors that dictate device performance. The Seebeck coefficient (Se) of the redox couple in the electrolyte gives the potential difference achievable for a given temperature gradient across the device. Prior work has shown that a cobalt bipyridyl redox couple in ionic liquids (ILs) displays high Seebeck coefficients, but the thermoelectrochemical cell performance was limited by mass transport. Here we present the Se and thermoelectrochemical power generation performance of the cobalt couple in novel mixed IL/molecular solvent electrolyte systems. The highest power density of 880 mW m-2, at a ΔT of 70 °C, was achieved with a 31 (v/v) MPN-[C2mim][B(CN)4] electrolyte combination. The significant power enhancement compared to the single solvent or IL systems results from a combination of superior ionic conductivity and higher diffusion coefficients, shown by electrochemical analysis of the different electrolytes. This is the highest power output achieved to-date for a thermoelectrochemical cell utilising a high boiling point redox electrolyte.

Sad music as a means for acceptance-based coping

Self-identified sad music (SISM) is often listened to when experiencing sad life situations. Research indicatesthat the most common reason people give for listening to SISM is “to be in touch with or express feelings ofsadness”. But why might this be the case? We suggest that one reason people choose to listen to sad musicwhen feeling sad is to accept aversive situations. We tested if SISM is associated with acceptance copingand consolation. We hypothesized that SISM relates to acceptance-based coping via the recognitionand identification of emotional states, and that people will report more acceptance from SISM than selfidentifiedhappy music when seeking consolation. In Study 1, participants recalled how happy or sadthe music sounds that they normally listen to for consolation, and if they listen to this music to gainacceptance of negative moods and situations. In Study 2, participants reported their goals when listeningto sad music during a recalled time in which they experienced an adverse life situation and whether thislead to acceptance. Study 1: People reported that they were more likely to listen to sad music than happymusic when seeking consolation, though they preferred happy music in general. Listening to SISM (butnot self-identified happy music) when seeking consolation was associated with acceptance of both anegative situation and the associated negative emotions. Additionally, seeking to deal with emotions wasassociated with both SISM listening (for consolation) and acceptance. Study 2: Listening to SISM to get intouch with and express affect was the most important self-regulatory strategy (of six examined) throughwhich acceptance was recalled to be achieved. Experiencing adverse situations or seeking consolation,people report that listening to SISM is associated with acceptance coping (through the re-experiencing ofaffect). Implications for music therapy and theories of emotional coping are discussed.

The non-advertising effects of screen-based sedentary activities on acute eating behaviours in children, adolescents, and young adults. A systematic review.

Sedentary screen time may be an important determinant of childhood obesity. A number of potential mechanisms to explain the link between screen time and increased bodyweight have been proposed; however, the relationship appears to be best explained by the effects on dietary intake, which is attributed to either food advertising or effects independent of food advertising. Technological advances have allowed for greater accessibility and exposure to advertisement-free screen-based media. This review was conducted to systematically synthesise the evidence from laboratory based studies which have investigated the non-advertising effects of screen time (TV viewing, sedentary video games, and computer use) on dietary intake in children, adolescents, and young adults. MEDLINE, PubMed, PsychInfo, CINAHL, and Embase were searched from inception through 5 July 2013. Ten trials met the inclusion criteria and were included in the review. Risk of study bias was judged to range from low to high. Screen time in the absence of food advertising was consistently found to be associated with increased dietary intake compared with non-screen behaviours. Suggested explanations for this relationship included: distraction, interruption of physiologic food regulation, screen time as a conditioned cue to eat, disruption of memory formation, and the effects of the stress-induced reward system. Due to the limited number of high-quality studies available for this review, our findings are preliminary. More work is required to better establish the link between dietary intake and advertisement-free screen time and assess whether differences exist between the different screen-based activities.