Coarse-graining and renormalisation group methods for the elucidation of the kinetics of complex nucleation and growth processes

We review our work on generalisations of the Becker-Doring model of cluster-formation as applied to nucleation theory, polymer growth kinetics, and the formation of upramolecular structures in colloidal chemistry. One valuable tool in analysing mathematical models of these systems has been the coarse-graining approximation which enables macroscopic models for observable quantities to be derived from microscopic ones. This permits assumptions about the detailed molecular mechanisms to be tested, and their influence on the large-scale kinetics of surfactant self-assembly to be elucidated. We also summarise our more recent results on Becker-Doring systems, notably demonstrating that cross-inhibition and autocatalysis can destabilise a uniform solution and lead to a competitive environment in which some species flourish at the expense of others, phenomena relevant in models of the origins of life.

ATTACHMENT, GROWTH AND PERSISTENCE OF CRONOBACTER ON GRANULAR ACTIVATED CARBON FILTERS

Several Cronobacter outbreaks have implicated contaminated drinking water. This study assessed the impact of granular activated carbon (GAC) on the microbial quality of the water produced. A simulated water filter system was installed by filling plastic columns with sterile GAC, followed by sterile water with a dilute nutrient flowing through the column at a steady rate. Carbon columns were inoculated with Cronobacter on the surface, and the effluent monitored for Cronobacter levels. During a second phase, commercial faucet filters were distributed to households for 4-month use. Used filters were backwashed with sterile peptone water, and analyzed for Cronobacter, total aerobic plate count, coliform bacteria and Enterobacteriaceae. Cronobacter colonized the simulated GAC and grew when provided minimal levels of nutrients. Backwashed used filters used in home settings yielded presumptive Escherichia coli, Pseudomonas and other waterborne bacteria. Presumptive Cronobacter strains were identified as negative through biochemical and genetic test.

Usefulness of the Hepatocyte Growth Factor as a Predictor of Mortality in Patients Hospitalized With Acute Heart Failure Regardless of Ejection Fraction

Hepatocyte growth factor (HGF) plays a role in the improvement of cardiac function and remodeling. Their serum levels are strongly related with mortality in chronic systolic heart failure (HF). The aim of this study was to study prognostic value of HGF in acute HF, interaction with ejection fraction, renal function, and natriuretic peptides. We included 373 patients (age 76 ± 10 years, left ventricular ejection fraction [LVEF] 46 ± 14%, 48% men) consecutively admitted for acute HF. Blood samples were obtained at admission. All patients were followed up until death or close of study (>1 year, median 371 days). HGF concentrations were determined using a commercial enzyme-linked immunosorbent assay (human HGF immunoassay). The predictive power of HGF was estimated by Cox regression with calculation of Harrell C-statistic. HGF had a median of 1,942 pg/ml (interquartile rank 1,354). According to HGF quartiles, mortality rates (per 1,000 patients/year) were 98, 183, 375, and 393, respectively (p <0.001). In Cox regression analysis, HGF (hazard ratio1SD = 1.5, 95% confidence interval 1.1 to 2.1, p = 0.002) and N-terminal pro b-type natriuretic peptide (NT-proBNP; hazard ratio1SD = 1.8, 95% confidence interval 1.2 to 2.6, p = 0.002) were independent predictors of mortality. Interaction between HGF and LVEF, origin, and renal function was nonsignificant. The addition of HGF improved the predictive ability of the models (C-statistic 0.768 vs 0.741, p = 0.016). HGF showed a complementary value over NT-proBNP (p = 0.001): mortality rate was 490 with both above the median versus 72 with both below. In conclusion, in patients with acute HF, serum HGF concentrations are elevated and identify patients at higher risk of mortality, regardless of LVEF, ischemic origin, or renal function. HGF had independent and additive information over NT-proBNP.

Demand and supply oriented input-output models: a linkage analysis for Portugal.

Doutoramento em Economia.

Understanding Co-translational Protein Targeting and Lithium Dendrite Formation through Free Energy Simulations and Coarse-Grained Models

We describe the application of alchemical free energy methods and coarse-grained models to study two key problems: (i) co-translational protein targeting and insertion to direct membrane proteins to the endoplasmic reticulum for proper localization and folding, (ii) lithium dendrite formation during recharging of lithium metal batteries. We show that conformational changes in the signal recognition particle, a central component of the protein targeting machinery, confer additional specificity during the the recognition of signal sequences. We then develop a three-dimensional coarse-grained model to study the long-timescale dynamics of membrane protein integration at the translocon and a framework for the calculation of binding free energies between the ribosome and translocon. Finally, we develop a coarse-grained model to capture the dynamics of lithium deposition and dissolution at the electrode interface with time-dependent voltages to show that pulse plating and reverse pulse plating methods can mitigate dendrite growth.

Quorum Sensing and Microbial Interactions in Coral Black Band Disease and Coral-Associated Bacteria

The black band disease (BBD) microbial consortium often causes mortality of reef-building corals. Microbial chemical interactions (i.e., quorum sensing (QS) and antimicrobial production) may be involved in the BBD disease process. Culture filtrates (CFs) from over 150 bacterial isolates from BBD and the surface mucopolysaccharide layer (SML) of healthy and diseased corals were screened for acyl homoserine lactone (AHL) and Autoinducer-2 (AI-2) QS signals using bacterial reporter strains. AHLs were detected in all BBD mat samples and nine CFs. More than half of the CFs (~55%) tested positive for AI-2. Approximately 27% of growth challenges conducted among 19 isolates showed significant growth inhibition. These findings demonstrate that QS is actively occurring within the BBD microbial mat and that culturable bacteria from BBD and the coral SML are able to produce QS signals and antimicrobial compounds. This is the first study to identify AHL production in association with active coral disease.

Improving Resource Management in Virtualized Data Centers using Application Performance Models

The rapid growth of virtualized data centers and cloud hosting services is making the management of physical resources such as CPU, memory, and I/O bandwidth in data center servers increasingly important. Server management now involves dealing with multiple dissimilar applications with varying Service-Level-Agreements (SLAs) and multiple resource dimensions. The multiplicity and diversity of resources and applications are rendering administrative tasks more complex and challenging. This thesis aimed to develop a framework and techniques that would help substantially reduce data center management complexity. We specifically addressed two crucial data center operations. First, we precisely estimated capacity requirements of client virtual machines (VMs) while renting server space in cloud environment. Second, we proposed a systematic process to efficiently allocate physical resources to hosted VMs in a data center. To realize these dual objectives, accurately capturing the effects of resource allocations on application performance is vital. The benefits of accurate application performance modeling are multifold. Cloud users can size their VMs appropriately and pay only for the resources that they need; service providers can also offer a new charging model based on the VMs performance instead of their configured sizes. As a result, clients will pay exactly for the performance they are actually experiencing; on the other hand, administrators will be able to maximize their total revenue by utilizing application performance models and SLAs. This thesis made the following contributions. First, we identified resource control parameters crucial for distributing physical resources and characterizing contention for virtualized applications in a shared hosting environment. Second, we explored several modeling techniques and confirmed the suitability of two machine learning tools, Artificial Neural Network and Support Vector Machine, to accurately model the performance of virtualized applications. Moreover, we suggested and evaluated modeling optimizations necessary to improve prediction accuracy when using these modeling tools. Third, we presented an approach to optimal VM sizing by employing the performance models we created. Finally, we proposed a revenue-driven resource allocation algorithm which maximizes the SLA-generated revenue for a data center.

Productivity growth and the structure of production

In this study, interactions between potential hierarchical value chains existing in the production structure and industry-wise productivity growths are sought. We applied generalized Chenery-Watanabe heuristics for matrix linearity maximization to triangulate the input-output incidence matrix for both Japan and the Republic of Korea, finding the potential directed flow of values spanning the industrial sectors of the basic (disaggregated) industry classifications for both countries. Sector specific productivity growths were measured by way of the Trönquvist index, using the 2000-2005 linked input-output tables for both Japan and Korea.

Effects of charcoal-enriched goat manure on soil fertility parameters and growth of pearl millet (Pennisetum glaucum L.) in a sandy soil from northern Oman

The effect of charcoal feeding on manure quality and its subsequent application to enhance soil productivity has received little attention. The objectives of the present study therefore were to investigate the effects of (i) charcoal feeding on manure composition, and (ii) charcoal-enriched manure application on soil fertility parameters and growth of millet (Pennisetum glaucum L.). To this end, two experiments were conducted: First, a goat feeding trial where goats were fed increasing levels of activated charcoal (AC; 0, 3, 5, 7, and 9% of total ration); second, a greenhouse pot experiment using the manure from the feeding trial as an amendment for a sandy soil from northern Oman. We measured manure C, N, P, and K concentrations, soil fertility parameters and microbial biomass indices, as well as plant yield and nutrient concentrations. Manure C concentration increased significantly (P<0.001) from 45.2% (0% AC) to 60.2% (9% AC) with increasing dietary AC, whereas manure N, P, and K concentrations decreased (P<0.001) from 0% AC (N: 2.5%, P: 1.5%, K: 0.8%) to 9% AC (N: 1.7%, P: 0.8%, K: 0.4%). Soil organic carbon, pH, and microbial biomass N showed a response to AC-enriched manure. Yield of millet decreased slightly with AC enrichment, whereas K uptake was improved with increasing AC. We conclude that AC effects on manure quality and soil productivity depend on dosage of manure and AC, properties of AC, trial duration, and soil type.

Age and growth of the bigeye thresher shark, Alopias superciliosus, from the pelagic longline fisheries in the tropical northeastern Atlantic Ocean, determined by vertebral band counts

The bigeye thresher, Alopias supercilious, is commonly caught as bycatch in pelagic longline fisheries targeting swordfish. Little information is yet available on the biology of this species, however. As part of an ongoing study, observers sent aboard fishing vessels have been collecting set of information that includes samples of vertebrae, with the aim of investigating age and growth of A. supercilious. A total of 117 specimens were sampled between September 2008 and October 2009 in the tropical northeastern Atlantic, with specimens ranging from 101 to 242 cm fork length (FL) (176 to 407 cm total length). The A. supercilious vertebrae were generally difficult to read, mainly because they were poorly calcified, which is typical of Lamniformes sharks. Preliminary trials were carried out to determine the most efficient band enhancement technique for this species, in which crystal violet section staining was found to be the best methodology. Estimated ages in this sample ranged from 2 to 22 years for females and 1 to 17 years for males. A version of the von Bertalanffy growth model (VBGF) re-parameterised to estimate L(0), and a modified VBGF using a fixed L(0) were fitted to the data. The Akaike information criterion (AIC) was used to compare these models. The VBGF produced the best results, with the following parameters: L(inf) = 293 cm FL, k = 0.06 y(-1) and L(0) = 111 cm FL for females; L(inf) = 206 cm FL, k = 0.18 y(-1) and L(0) = 93 cm FL for males. The estimated growth coefficients confirm that A. supercilious is a slow-growing species, highlighting its vulnerability to fishing pressure. It is therefore urgent to carry out more biological research to inform fishery managers more adequately and address conservation issues.

Influence of Baculovirus anticarsia on the growth rate and survival of some nontarget aquatic organisms.

Recently, microbial pest control agents (MPCAs) have been worldwide used to reduce chemical pesticide use and to diminish the high risk of those compounds in the environment. Among various MPCAs, the nuclear polyhedrosis virus Baculovirus anticarsia is widely used in Brazil in the biological control of the velvet bean caterpillar. Although literature data do not show adverse effects of baculoviruses to nontarget organisms, it is necessary to evaluate their toxicity or patogenicity in order to study th environmental risk of those products and to register the formulations in the Brazilian Environmental Regularory Agency - IBAMA. In the presente work, the influence of a Baculovirus anticarsia formulation was evaluted to measure the consequences in the growth rateof the green algae Selenastrum capricornutum, the duckweed Lemna valdiviana and the microcrustacean Daphnia similis. The survival of the fish Hyphessobrycon scholzei exposed during 28 days was also evaluated. No significative adverse effects (P > 0.05) were observed in the test organisms which were exposed to 1-1000 times the maximum calculated pesticide concentration following a direct application to 15 cm layer of water.

Development of 3D Cancer Cell Models to Test Metabolic Interventions as an Anticancer Strategy

In recent years, it has become evident that the role of mitochondria in the metabolic rewiring is essential for cancer development and progression. The metabolic profile during tumorigenesis has been performed mainly in traditional 2D cell models, including cell lines of various lineages and phenotypes. Although useful in many ways, their relevance can be often debatable, as they lack the interactions between different cells of the tumour microenvironment and/or interaction with the extracellular matrix 1,2. Improved models are now being developed using 3D cell culture technology, contributing with increased physiological relevance 3,4. In this work, we improved a method for the generation of 3D models from healthy and tumour colon tissue, based on organoid technology, and performed their molecular and biochemical characterization and validation. Further, in-plate cryopreservation was applied to these models, and optimal results were obtained in terms of cell viability and functionality of the cryopreserved models. We also cryopreserved colon fibroblasts with the aim to introduce them in a co-culture cryopreserved model with organoids. This technology allows the conversion of cell models into “plug and play” formats. Therefore, cryopreservation in-plate facilitates the accessibility of specialized cell models to cell-based research and application, in cases where otherwise such specialized models would be out of reach. Finally, we briefly explored the field of bioprinting, by testing a new matrix to support the growth of colon tumour organoids, which revealed promising preliminary results. To facilitate the reader, we organized this thesis into chapters, divided by the main points of work which include development, characterization and validation of the model, commercial output, and associated applications. Each chapter has a brief introduction, followed by results and discussion and a final conclusion. The thesis has also a general discussion and conclusion section in the end, which covers the main results obtained during this work.

Comprehensive characterization of SDH-deficient GIST using NGS data and iPSC models

Gastrointestinal stromal tumors (GIST) are the most common di tumors of the gastrointestinal tract, arising from the interstitial cells of Cajal (ICCs) or their precursors. The vast majority of GISTs (75–85% of GIST) harbor KIT or PDGFRA mutations. A small percentage of GIST (about 10‐15%) do not harbor any of these driver mutations and have historically been called wild-type (WT). Among them, from 20% to 40% show loss of function of the succinate dehydrogenase complex (SDH), also defined as SDH‐deficient GIST. SDH-deficient GISTs display distinctive clinical and pathological features, and can be sporadic or associated with Carney triad or Carney-Stratakis syndrome. These tumors arise most frequently in the stomach with predilection to distal stomach and antrum, have a multi-nodular growth, display a histological epithelioid phenotype, and present frequent lympho-vascular invasion. Occurrence of lymph node metastases and indolent course are representative features of SDH-deficient GISTs. This subset of GIST is known for the immunohistochemical loss of succinate dehydrogenase subunit B (SDHB), which signals the loss of function of the entire SDH-complex. The overall aim of my PhD project consists of the comprehensive characterization of SDH deficient GIST. Throughout the project, clinical, molecular and cellular characterizations were performed using next-generation sequencing technologies (NGS), that has the potential to allow the identification of molecular patterns useful for the diagnosis and development of novel treatments. Moreover, while there are many different cell lines and preclinical models of KIT/PDGFRA mutant GIST, no reliable cell model of SDH-deficient GIST has currently been developed, which could be used for studies on tumor evolution and in vitro assessments of drug response. Therefore, another aim of this project was to develop a pre-clinical model of SDH deficient GIST using the novel technology of induced pluripotent stem cells (iPSC).