Em sentido geral, a quimiotaxia é o movimento dirigido que desenvolvem alguns seres vivos em resposta aos gradientes químicos presentes no seu ambiente. Uma bactéria é um organismo unicelular que usa a quimiotaxia como mecanismo de mobilização para encontrar os nutrientes de que precisa para sobreviver e para escapar de ambientes nocivos. Evoluída durante milhões de anos pela natureza, a quimiotaxia de bactérias é um processo altamente otimizado de busca e exploração em espaços desconhecidos. Graças aos avanços no campo da computação, as estratégias quimiotácticas das bactérias e sua excelente capacidade de busca podem ser modeladas, simuladas e emuladas para desenvolver métodos de otimização inspirados na natureza que sejam uma alternativa aos métodos já existentes. Neste trabalho, desenvolvem-se dois algoritmos baseados em estratégias quimiotácticas de bactérias: o BCBTOA (Bacterial Chemotaxis Based Topology Optimization Algorithm) e o BCMOA (Bacterial Chemotaxis Multiobjective Optimization Algorithm) os quais são um algoritmo de otimização topológica e um algoritmo de otimização multi-objetivo, respectivamente. O desempenho dos algoritmos é avaliado mediante a sua aplicação à solução de diversos problemas de prova e os resultados são comparados com os de outros algoritmos atualmente relevantes. O algoritmo de otimização multi-objetivo desenvolvido, também foi aplicado na solução de três problemas de otimização de projeto mecânico de eixos. Os resultados obtidos e os analise comparativos feitos, permitem concluir que os algoritmos desenvolvidos são altamente competitivos e demonstram o potencial do processo de quimiotaxia de bactérias como fonte de inspiração de algoritmos de otimização distribuída, contribuindo assim, a dar resposta à constante demanda por técnicas de otimização mais eficazes e robustas. / In general, chemotaxis is the biased movement developed by certain living organisms as a response to chemical gradients present in their environment. A bacterium is a unicellular organism that uses chemotaxis as a mechanism for mobilization that allows it to find nutrients needed to survive and to escape from harmful environments. Millions of years of natural evolution became bacterial chemotaxis a highly optimized process in searching and exploration of unknown spaces. Thanks to advances in the computing field, bacterial chemotactical strategies and its excellent ability in searching can be modeled, simulated and emulated developing bio-inspired optimization methods as alternatives to classical methods. Two algorithms based on bacterial chemotactical strategies were designed, developed and implemented in this work: i) the topology optimization algorithm, BCBTOA (Bacterial Chemotaxis Based Topology Optimization Algorithm) and ii) the multi-objective optimization algorithm, BCMOA (Bacterial Chemotaxis Multiobjective Optimization Algorithm). Algorithms performances were evaluated by their applications in the solution of benchmark problems and the results obtained were compared with other algorithms also relevant today. The BCMOA developed here was also applied in the solution of three mechanical design problems. The results obtained as well as the comparative analysis conducted lead to conclude that the algorithms developed were competitive. This also demonstrates the potential of bacterial chemotaxis as a process in which distributed optimization techniques can be inspired.

Cancer metastasis is the critical event leading to 90% of cancer related death. Although significant improvement in our understanding on cancer metastasis has been made through years of research, the fundamental mechanism behind this process is still not fully elucidated. For cancer researchers, the “gold standard” for metastasis studies has traditionally been the use of tissue culture and mouse models. Tissue culture offers the simplest system and ease of control but is not able to recapitulate many of the features found in an in vivo tumor microenvironment. On the other hand, mouse model systems offer the most sophisticated and physiologically relevant platforms for studying cancer. However, the lack of control over the in vivo environment in these mouse models and inherent discrepancies from human physiology make results from these models difficult to be translated to clinical trials. The advancement in microfabrication techniques and cancer models developed based on these techniques has shown potential in addressing the gap between in vitro tissue culture and mouse models. Microscopic tumor microenvironments could be built in these in vitro systems to study behavior of human cancer cells. However, the expertise involved in and extra instrumentation needed for implementing these systems have prevented their widespread use by general cancer researchers. In this dissertation, we developed two simple microfabricated systems and demonstrated their application in two aspects of cancer research. The first system is a microfabricated cell patterning stencil, where paracrine signaling can be established and its impact can be measured based on cell migration. Using this tool, we investigated the interaction between melanoma and microenvironmental cells from their common metastasis target organ. Through these simple patterning techniques, we observed significant effects that a given microenvironmental cell line had on the two different melanoma lines, as well as how melanoma affected different microenvironmental cell lines. The second system, a microfluidic device, is able to present individual soluble factors to cancer cells in order to test the response of cancer cells to these physiologically relevant factors. Through this stand-alone system, we found that breast cancer metastasis is influenced by the protein molecules secreted by themselves as well as the local glucose level. Through these findings we believe that our microfabricated systems can benefit the general cancer research community in which a complicated problem can be broken down into manageable pieces and studied on a simple platform in a controlled way. Observation made through these systems can inspire general cancer researchers to form new hypotheses and eventually lead to new findings. / 2017-02-17T00:00:00Z

Systemic Lupus Erythematosus (SLE) is an autoimmune disease affecting 20 to 250 individuals per 100,000 worldwide. Symptomology includes dermatological manifestations such as discoid lesions, acute cutaneous rashes, and oral and nasal ulcers, along with musculoskeletal, pulmonary, and renal complications. Abnormal T and B lymphocyte function and apoptosis, immune complex clearance, complement function, and nucleosome processing are typical of disease pathophysiology. SLE is the result of both environmental and genetic factors, which together create the conditions leading to disease onset and progression. Of these environmental factors, Epstein-Barr virus (EBV) infection is known to cause the genesis of cross-reactive antibodies in SLE prone individuals that can initiate disease activity. Viral infection and modulation of cellular genes is important in understanding the microenvironment that could lead to immune mis-regulation and the inception of lupus in those individuals at risk. During disease development, a variety of variables assist and detract from disease progression and the quality of life experienced by SLE patients. Research into EBV-infected naïve B lymphocytes revealed that EBV modulates the chemotactic receptor EBI2 during viral infection via the BRRF1 viral gene product Na. This likely changes B lymphocyte chemotaxis in secondary tissue in virally infected B cells. Current literature suggests this results in sequestration of cells to peripheral areas of the tissue and mis-regulation of the immune response. It is not uncommon for SLE patients to have neuropsychiatric disorders due to lupus disease activity. With SLE patients being up to 6 times more at risk for depression, recognition and treatment of depression and anxiety have been shown to improve quality of life, pain, and treatment outcomes. Two studies investigate both clinical laboratory and psychosocial assessment variables that we suspect to be correlated with depression in patients with SLE. Univariate and multivariate analysis from our first study identified an array of variables that show strong associations with depression, including: Body Mass Index, Pain, Total Complement, fatigue assessments, and SF-36 scores. The second study found similar associations, but further found that serum IL-10 levels demonstrated a strong correlation with depression in SLE patients. In this final study SLE patients are compared alongside healthy, clinically depressed, and rheumatoid arthritis patients to provide evidence that increased depression in SLE patients is due more to disease pathology than a result of chronic inflammation.

<p>Mast cells are very potent multifunctional effector cells of the immune system normally distributed throughout connective tissues. An accumulation of mast cells has been described in several pathological conditions such as allergic- and autoimmune inflammations and in certain tumours. This necessitates two different processes: 1) Recruitment of mast cell progenitors from peripheral blood; 2) Accretion of mature mast cells at sites of inflammation and tumour areas. Both processes are depending on the local production of chemotactic factors. The aim of this study was to investigate the role of chemokines and their corresponding receptors in mast cell chemotaxis. </p><p>By cloning and mRNA-screening of cord blood derived mast cells several chemokine receptors were found to be expressed. Functional expression was confirmed of chemokine receptors CXCR4, CCR1 and CCR4. CXCL12, the only known ligand for CXCR4, acted as a mast cell chemotaxin and induced migration of progenitor cells with capacity to differentiate into mast cells. Of several ligands known to bind CCR1 and CCR4, only CCL5 induced migration of mast cells. The migration to CCL5 was mediated through both CCR1 and CCR4. In contrast, the ligands to CCR4, CCL17 and CCL22, could inhibit CCL5-induced migration. Expression of CCR1 and CCR4 could also be confirmed on mast cells in lung from asthmatic patients. Furthermore, we could demonstrate that mast cells were attracted by CCL5 produced by tumour cells in Hodgkin´s lymphoma.</p><p>In conclusion, the work in this thesis has identified two chemokines that regulates mast cell migration. This knowledge helps us understand the mechanisms behind homing of mast cell progenitors from the blood into the tissue and the accumulation of mature mast cells at sites of inflammation and tumourigenesis.</p>

Mass spectrometry based proteomics has emerged as a powerful methodology for investigating protein expression. “Bottom up” techniques in which proteins are first digested, and resulting peptides separated via multi-dimensional chromatography then analyzed via mass spectrometry provide a wide depth of coverage of expressed proteomes. This technique has been successfully and extensively used to survey protein expression (expression proteomics) and also to investigate proteins and their associated interacting partners in order to ascertain function of unknown proteins (functional proteomics). Azospirillum brasilense is a free-living diazotrophic soil bacteria, with world-wide significance as a plant-growth promoting bacteria. Living within the rhizosphere of cereal grasses, its diverse metabolism is important for its survival in the competitive rhizospheric environment. The recently sequenced genome of strain Sp245 provided a basis for the proteome studies accomplished in this work. After initial mass spectrometer parameter optimization studies, the expressed proteomes of two strains of Azospirillum brasilense, Sp7 and Sp245, grown under both nitrogen fixing and optimal growth (non nitrogen fixing) conditions were analyzed using a bottom up proteomics methodology. Further proteome studies were conducted with A. brasilense strain Sp7 in order to ascertain the effect of one chemotaxis operon, termed Che1. In this study, proteomic surveys were conducted on two bacterial derivative strains, created earlier, which lacked either a forward signaling pathway or an adaptation pathway. The proteomic surveys conducted in this work provide a foundation for further biochemical investigations. In order to facilitate further investigation and a movement into functional proteomics, a set of destination vectors was created that contain a variety of tandem affinity tags. The addition of tandem affinity tags to a protein allow for generic purification schemes, and can facilitate future studies to investigate proteins of interest discovered in the first expression proteomic surveys of A. brasilense. Taken together, this dissertation provides a valuable data set for investigation into the physiology of A. brasilense and further provides biochemical tools for analysis of the functional protein interactions of A. brasilense cells.

Mastitis, or mammary gland inflammation, causes the greatest loss in profit for dairy producers. Mastitis susceptibility differs among cows due to environmental, physiological, and genetic factors. Prior research identified a genetic marker in a chemokine receptor, CXCR1, associated with mastitis susceptibility and decreased neutrophil migration. Current research seeks to identify reasons behind mastitis susceptibility by validating this model through in vivo challenge with Streptococcus uberis and studying specific mechanisms causing impaired neutrophil migration. Holstein cows with GG (n=19), GC (n=28), and CC (n=20) genotypes at CXCR1+777 were challenged intramammarily with S. uberis strain UT888. After challenge 68% of quarters from GG genotype, 74% from CC genotype and only 47% from GC genotype cows had ≥10 colony forming units/ml S. uberis for at least two sampling time points (P<0.05). However, among infected cows, number of S. uberis, somatic cell count, rectal temperature, milk scores and mammary scores were comparable among genotypes throughout infection. These findings suggest that cows with GC genotypes may be more resistant to S. uberis mastitis, but have similar responses if infected. To better understand the mechanisms associated with disease resistance, migration patterns in neutrophils from cows with different CXCR1+777 genotypes were evaluated. Neutrophils from cows with GG (n=11) and CC (n=11) genotypes were isolated and stimulated with zymosan activated sera (ZAS). Cells were fixed and stained for F-actin and evaluated for F-actin content, distribution, and cell morphology. Neutrophils from CC cows had significantly lower average F-actin polymerization than GG cows v (P=0.05). Directed migration of neutrophils from GG (n=10) and CC (n=10) genotypes was imaged and tracking data was analyzed for individual cells. Cells from GG genotype traveled further on an X axis and had higher X/Y movement towards IL8 compared to CC genotype, meaning they moved more directly towards IL8. Our findings suggest lower F-actin polymerization in combination with lower ability to directly move towards IL8 could impair neutrophil response to infection in cows with a CC genotype and may contribute to increased mastitis susceptibility. Finding what makes certain cows more susceptible to mastitis could lead to strategies aimed at improved prevention and treatment of mastitis.

Mast cells are very potent multifunctional effector cells of the immune system normally distributed throughout connective tissues. An accumulation of mast cells has been described in several pathological conditions such as allergic- and autoimmune inflammations and in certain tumours. This necessitates two different processes: 1) Recruitment of mast cell progenitors from peripheral blood; 2) Accretion of mature mast cells at sites of inflammation and tumour areas. Both processes are depending on the local production of chemotactic factors. The aim of this study was to investigate the role of chemokines and their corresponding receptors in mast cell chemotaxis. By cloning and mRNA-screening of cord blood derived mast cells several chemokine receptors were found to be expressed. Functional expression was confirmed of chemokine receptors CXCR4, CCR1 and CCR4. CXCL12, the only known ligand for CXCR4, acted as a mast cell chemotaxin and induced migration of progenitor cells with capacity to differentiate into mast cells. Of several ligands known to bind CCR1 and CCR4, only CCL5 induced migration of mast cells. The migration to CCL5 was mediated through both CCR1 and CCR4. In contrast, the ligands to CCR4, CCL17 and CCL22, could inhibit CCL5-induced migration. Expression of CCR1 and CCR4 could also be confirmed on mast cells in lung from asthmatic patients. Furthermore, we could demonstrate that mast cells were attracted by CCL5 produced by tumour cells in Hodgkin´s lymphoma. In conclusion, the work in this thesis has identified two chemokines that regulates mast cell migration. This knowledge helps us understand the mechanisms behind homing of mast cell progenitors from the blood into the tissue and the accumulation of mature mast cells at sites of inflammation and tumourigenesis.

Previous studies have shown that chemotaxis plays an important role in the colonization of the wheat roots surfaces by Azospirillum brasilense and a chemotaxis operon shown to control motility and chemotaxis in A. brasilense has been isolated. This study looked at the effects of mutations in individual genes coding for chemotaxis proteins from this operon on the ability of the cells to colonize the surface of sterile wheat roots. Using both quantitative and qualitative assays, the study shows differences in the colonization ability of the mutants relative to the wild type: the cheB, cheR, cheBR, and cheOp mutants were significantly impaired in wheat root colonization. Interestingly, the cheA mutant was not affected in its ability to colonize the wheat root surface relative to the wild type. Future studies will look for the factors that compensate for cheA impairment in the rhizosphere.

Angiogenesis is the formation of new blood vessels from pre-existing vasculature and is important during development as well as wound healing and tissue remodeling. Angiogenesis also occurs during pathological conditions such as diabetic retinopathy and cancer. This thesis is centered on the biology of endothelial cells, lining the blood vessels, and myofibroblasts, important for wound healing. We investigated an endothelial cell specific gene, ExoC3l2, and its role in VEGFR2 signaling and migration. EXOC3L2 co-localize with members of the exocyst complex, involved in vesicular transport, as well as VEGFR2. Reducing the level of EXOC3L2 in microvascular endothelial cells results in reduced VEGFR2 signaling and subsequently reduced chemotactic response to VEGF-A. MicroRNA (miRNA) have been shown to be regulators of gene transcription and cell type specific miRNAs have been identified. We investigated two miRNAs, miR-145 and miR-24. miR-145 is expressed in pericytes and fibroblasts but was shown to regulate fli1, an endothelial transcription factor. miR-145 overexpression reduced chemotaxis in both fibroblasts and endothelial cells, as did suppression of the endogenous miR-145 level in fibroblasts. miR-24 in contrast is expressed by endothelial cells and are able to target Ndst1, important for heparan sulfate (HS) sulfation. Sulfation of HS is important for many processes, amongst them growth factor signaling. Overexpression of miR-24 resulted in lower sulfation of HS chains, decreasing the ability of HS to interact with VEGF-A. Overexpressing miR-24 resulted in disturbed chemotaxis, similar to suppressing Ndst1 using siRNA. Myofibroblast recruitment is an important step in wound healing. The myofibroblasts contract the wound, synthesize new extracellular matrix and contribute to revascularization by looping angiogenesis. Maturation from resting fibroblast to myofibroblast is dependent on TGF-β. We found that fibrin fragment E (FnE), a degradation product of fibrin, potentiated the response of fibroblasts to TGF-β thus enhancing TGF-β-induced myofibroblast differentiation. FnE was also found to influence the migration of fibroblasts. These responses are dependent on integrins and toll-like receptors. These findings may serve to further increase the understanding of angiogenesis and wound healing to develop new therapies against pathological conditions.

The general goal of this project was to use computational biology to understand signal transduction mechanisms in prokaryotes. Its specific focus was to characterize the cytoplasmic domain of methyl-accepting chemotaxis proteins (MCP_CD), a protein domain central to the function of chemotaxis, the most complex signaling network in prokaryotes. Chemotaxis enables cells to sense and respond to multiple external and internal stimuli by actively navigating to an optimal environment. MCP_CD is a central part of this circuit, but its coiled coil structure is difficult to analyze using traditional tools of computational biology. In this project, a new method for analysis of the domain was developed and used to gain insight into its function and evolution. Research advance 1: Characterization of the MCP_CD protein domain. Before this work, MCP_CD was known to have two distinct functional regions: the signaling region that activates the histidine kinase CheA and the methylation region where adaptation enzymes CheB and CheR store information about recent stimuli. The result of this project is classification of ~2000 MCP_CDs into twelve subfamilies. The unique mechanism of evolution of the domain has been clarified and precise boundaries of the adaptation and signaling regions determined. A new functional region, the flexible bundle subdomain, was identified and its contribution to the signaling mechanism elucidated by analysis of conserved sequence features. Conserved and variable sequence features in the adaptation and signaling subdomains led to a better understanding of the evolutionary history of the adaptation mechanism and of alternative higher-order arrangements of receptors within the membrane. Research advance 2: Development of a sensor / kinase correlation algorithm to couple diverse MCP_CD and kinase subfamilies. The receptor diversity discovered in this work is complemented by diversity in the kinases with which they interact. In this work, an algorithm was developed to associate receptor / kinase pairs which facilitated understanding of the function and evolution of chemotaxis. Research advance 3: Development of Cheops, a database of chemotaxis pathways. The Cheops (Chemotaxis operons) database presents the results of the sensor / kinase correlation algorithm and the information about receptor and kinase diversity in an integrated and intuitive way.