While nocturnal basal snakes have rod-dominant retinae, diurnal garter snakes have all-cone retinae. Previous work from the Chang lab identified three visual pigments expressed in the photoreceptors of Thamnophis proximus: SWS1, LWS and RH1. I further characterized T. proximus photoreceptors using electron microscopy, immunohistochemistry, and in vitro protein expression. T. proximus have four types of morphological cones: double cones, large single cones, small single cones, and very small single cones. Some small single cones have rod-like features, such as rod-like outer-segment membranes and a lack of micro-droplets. Immunohistochemistry showed that rod-specific transducin is expressed in some T. proximus photoreceptors. In vitro expression of T. proximus RH1 produced a functional rhodopsin with λmax at 485nm, which corresponds to microspectrophotometry measurement from some small single cones. Current results suggest that small single cones of T. proximus may have evolved from ancestral rods, and secondarily acquired a cone-like morphology as adaptation to diurnality.

While nocturnal basal snakes have rod-dominant retinae, diurnal garter snakes have all-cone retinae. Previous work from the Chang lab identified three visual pigments expressed in the photoreceptors of Thamnophis proximus: SWS1, LWS and RH1. I further characterized T. proximus photoreceptors using electron microscopy, immunohistochemistry, and in vitro protein expression. T. proximus have four types of morphological cones: double cones, large single cones, small single cones, and very small single cones. Some small single cones have rod-like features, such as rod-like outer-segment membranes and a lack of micro-droplets. Immunohistochemistry showed that rod-specific transducin is expressed in some T. proximus photoreceptors. In vitro expression of T. proximus RH1 produced a functional rhodopsin with λmax at 485nm, which corresponds to microspectrophotometry measurement from some small single cones. Current results suggest that small single cones of T. proximus may have evolved from ancestral rods, and secondarily acquired a cone-like morphology as adaptation to diurnality.

Universidade Federal do Cearà / A busca por novas bactÃrias com propriedades funcionais tem sido foco de intensa pesquisa nas Ãltimas dÃcadas. Diversas espÃcies do gÃnero Lactobacillus jà sÃo conhecidas como probiÃticas e sÃo adicionadas em alimentos. Para uma cultura bactÃriana ser selecionada como probiÃtica à preciso apresentar determinadas caracterÃsticas, como a capacidade de sobreviver Ãs condiÃÃes gastrointestinais e ser livre de patogenicidade. O objetivo desse estudo foi isolar, selecionar e identificar cepas de lactobacilos a partir de leite e queijo de cabra, e avaliar seu potencial probiÃtico e sua inocuidade atravÃs da identificaÃÃo de genes relacionados Ãs caracterÃsticas benÃficas e de riscos para o consumo humano, verificando sua expressÃo in vitro. Foram identificados vinte e trÃs cepas diferentes de Lactobacillus plantarum e adicionadas ao estudo outras quatro cepas de L. plantarum e trÃs Lactobacillus mucosae previamente isoladas. As vinte e nove cepas foram avaliadas quanto à presenÃa de genes relacionados a propriedades probiÃticas como o gene bsh, codificante para a enzima hidrolase de sais biliares, msa, relacionado à capacidade de adesÃo ao epitÃlio intestinal induzido por manose e outros trÃs genes, map, mub e ef-tu associados Ãs propriedades de adesÃo ao muco. Os genes bsh e msa tiveram sua expressÃo avaliada in vitro, por meio de testes bioquÃmicos de desconjugaÃÃo de sais biliares e agregaÃÃo de leveduras, respectivamente. Os resultados mostraram que 80% das cepas testadas foram capazes de sobreviver em presenÃa dos sais biliares e 76% foram capazes de desconjugar pelo menos um dos quatro sais testados. Quanto à capacidade de adesÃo, quatro cepas apresentaram resultado positivo, sendo para trÃs delas confirmada interaÃÃo via manose. Ainda com relaÃÃo Ãs propriedades de adesÃo, apenas duas cepas apresentaram um alto valor de hidrofobicidade da superfÃcie celular, propriedade que tem sido associada indiretamente a essa capacidade, e 90% das cepas estudadas mostraram um perfil genÃtico favorÃvel à ligaÃÃo à mucosa intestinal, apresentando trÃs dos quatro genes de adesÃo avaliados. A inocuidade desses microrganismos tambÃm foi avaliada quanto à presenÃa e expressÃo de doze genes relacionados a fatores de virulÃncia, incluindo a resistÃncia a antimicrobianos e produÃÃo de aminas biogÃnicas. A expressÃo de genes associados à produÃÃo de gelatinase (gelE), e das aminas tirosina (tdc) e histamina (hdc1 e hdc2), bem como à resistÃncia à vancomicina (vanA e vanB) foi investigada por meio de testes bioquÃmicos. Apesar de algumas cepas amplificarem o gene gelE, este nÃo apresentou expressÃo in vitro. Foi constatada in vitro resistÃncia à vancomicina, muito comum entre lactobacilos, sendo observado tambÃm em cepas que nÃo amplificaram os genes vanA e vanB. Com relaÃÃo à produÃÃo de aminas biogÃnicas, apenas o gene tdc para tirosina foi detectado nas cepas, sendo um dos genes com maior frequÃncia de amplificaÃÃo entre as cepas. No entanto, apenas uma cepa que apresentou o gene teve sua expressÃo confirmada no teste in vitro utilizando meio de descarboxilaÃÃo, enquanto que algumas cepas que nÃo amplificaram o gene obtiveram resultado positivo in vitro. Quatorze isolados nÃo amplificaram genes relacionados à virulÃncia. Destas, apenas a cepa Lactobacillus plantarum Q24 nÃo apresentou expressÃo in vitro relacionada a fator de virulÃncia, alÃm de amplificar trÃs dos genes relacionados à adesÃo ao muco, e de ter sobrevivido e desconjugado dois dos sais biliares avaliados, mostrando ser a mais promissora para se prosseguir com os estudos de investigaÃÃo do potencial probiÃtico. / The search for new bacteria with functional properties has been the focus of intense research in recent decades. Several species of Lactobacillus gender are known as probiotic and are added in foods. To be selected as a probiotic bacteria, it need to present certain characteristics, as capacity to survive the gastrointestinal conditions and be free of pathogenic. The aim of this study was to isolate, identify and select strains of Lactobacillus from goat milk and cheese, and evaluate its potential probiotic and its safety through the identification of related genes with beneficial characteristics and risks for human consumption, checking its in vitro expression. Were identified twenty-three different strains of Lactobacillus plantarum and added to study other four strains of L. plantarum and three Lactobacillus mucosae. The thirty strains were evaluated for the presence of genes related to probiotic properties as bsh gene, coding for the enzyme bile salt hydrolase, the msa, related to capacity of adhesion to intestinal epithelium induced by mannose, three other genes map, mub and ef-tu associated the mucus adhesion properties. The bsh and msa gene had their expression evaluated in vitro, by means of biochemical tests deconjugation of bile salts and addition of yeast, respectively. The results show that 80% of the strains were able to survive in the presence of bile salts and 76% were able to deconjugate at least one of the four salts tested. As for the adhesion capacity, four strains show a positive result, and three of them confirmed interactinon via mannose. Still evaluating adhesion properties, only two strains have a high hydrophobicity value in the cell suface, property that has been linked indirectly to the ability to adhere to the intestinal mucosa, and 90% from these strains have a genetic profile favorable for binding to the intestinal mucosa, with three of the four genes adherence evaluated. The safety of the microorganisms was also evaluated for the presence and expression of the thirteen genes related to virulence factors, including resistance to antibiotics and production of biogenic amines. The expression of genes associated with the production of gelatinase (gelE), and tyrosine amines (TDC) and histamine (hdc1 and hdc2) and resistance to vancomycin (vanA and vanB) was investigated by means of biochemical tests. Although some strains amplify the gelE gene it did not show in vitro expression. Was verified in vitro resistance to vancomycin, very common among lactobacilli, also observed in strains that did not amplify the genes vanA and vanB. With respect to production of biogenic amines, only the tdc gene for tyrosine was detected in strains, one of the genes with the greatest percentage of amplification. However, only one strain that presented the gene had its expression confirmed in vitro test using descarboxilaÃÃo medium, while some strains that do not amplify the gene had positive results in vitro. Fourteen isolated did not amplified genes related to virulence. Of these, only the Lactobacillus plantarum Q24 strain showed no expression in vitro related to virulence factor, in addition to amplify three of the genes related to adherence to mucus, and have survived and disconjugate two of bile salts evaluated, showing be the most promising to pursue studies potential of probiotic research.

La porphyrie aiguë intermittente (PAI) est la plus fréquente des porphyries hépatiques aiguës. Elle est décrite comme une maladie autosomique dominante dont le trait génétique est estimé à 1/1675 en France avec une pénétrance faible et variable allant de 10% à 50% dans les familles connues de PAI. La PAI est due à des mutations réduisant le niveau d’activité de l’hydroxyméthylbilane-synthase (HMBS). Son déficit entraîne l’accumulation de précurseurs neurotoxiques responsables de la symptomatologie clinique. Dans le foie, la synthèse d’hème est contrôlée par l’enzyme ALA-Synthétase 1 (ALAS1) dont l’activité est régulée par un rétrocontrôle négatif par le produit final : l’hème. Le traitement consiste à freiner l’induction d’ALAS1 induit par la carence en hème, par l’administration d’hème exogène. Ce traitement de la crise aiguë est très efficace mais génère rapidement une dépendance physique avec apparition de crises récurrentes nécessitant l’administration chronique d’hème exogène. L’objectif principal de ce projet a été d’étudier les mécanismes physiopathologiques et génétiques liés à cette pathologie afin de traiter et conseiller au mieux les patients. Une partie du projet a consisté à explorer les facteurs génétiques modulateurs de la pénétrance de la maladie. Tout d’abord, une prévalence minimale du trait génétique dans la population générale a été estimée à 1/1299 permettant d’en déduire une pénétrance de l’ordre de 1% alors que celle dans les familles PAI suivies par le CFP est estimée à 22,9 %. Ensuite, concernant les facteurs pouvant expliquer cette différence, la présence d’une mutation type non-sens est plus fréquemment associée aux formes sévères et à une pénétrance plus élevée. De plus, les études de corrélation et d’héritabilité suggèrent plutôt une transmission de type oligogénique associée à des facteurs épigénétiques modulateurs de la pénétrance dont le facteur environnemental. Une autre partie a consisté à explorer les effets de l’administration d’hème exogène sur les patients et un modèle murin de PAI créé génétiquement. Chez l’homme, le traitement est associé à une augmentation des formes chroniques (1,7 % avant vs 7,5 % après l’introduction du celui-ci). Dans le modèle murin de PAI, les injections intrapéritonéales répétées induisent une augmentation paradoxale d’ALAS1 (3 fois), une augmentation de l’hème oxygénase 1 qui catabolise l’hème (HMOX1, 9 fois) ainsi que des voies de l’inflammation (analyse transcriptomique et protéomique hépatique) et une surcharge en fer. De plus, cette administration induit une altération des complexes de la chaine respiratoire mitochondriale responsable d’anomalies du métabolisme énergétique au niveau hépatique, cérébral et musculaire pouvant expliquer la symptomatologie neuroviscérale. En conclusion, ce travail a permis d’explorer les caractéristiques génétiques de la maladie (prévalence, pénétrance) en remettant en cause le mode de transmission autosomique dominant jusqu’ici admis, et d’explorer les mécanismes physiopathologiques associées à l’administration d’hème exogène faisant de cette thérapeutique un pharmakon / The biosynthesis of porphyrins is one of the most conserved pathways known. By associating different metals, porphyrins give rise to the "pigments of life". The formation of haem is accomplished by a sequence of eight dedicated enzymes encoded by different genes, some being active in ubiquitous as well as in erythroid isoforms. In humans, the genes for each of the haem synthetic enzymes may become the target of mutations that give rise to an impaired cellular enzyme activity called porphyrias. The acute porphyrias are characterized by attacks of neuropsychiatric symptoms, which may be due to a toxic surplus of the porphyrin precursor 5-aminolevulinic acid, or a consequence of a deficit of vital hemoproteins. Mutations of the gene encoding the third enzyme: hydroxymethylbilane synthase, are associated with the most frequent type of acute hepatic porphyria, acute intermittent porphyria. AIP is thought to display autosomal dominant inheritance with incomplete penetrance. In the classical form of AIP, HMBS activity is about 50% lower than normal in all tissues. These levels of activity in basal conditions are not sufficiently low to cause symptoms. However, factors increasing hepatic heme demand, resulting in an upregulation of hepatic aminolevulinate synthase (ALAS1, the first enzyme of the heme biosynthesis pathway), precipitate acute attacks. The treatment of the attack of AIP consists to repress ALAS1 and restores metabolic equilibrium. But this treatment leads side effects and dependency. The pathophysiological mechanism of the disease is partially known and difficult to explore because there is not an AIP model or prediction model of porphyrogenicity. We aimed to obtain further insight into the pathophysiological mechanism of AIP and into the genetic (prevalence and penetrance) of AIP, and the contribution of genetic factors to the variable clinical expression of HMBS mutations.We first calculated the penetrance of HMBS mutations in AIP patients seen at the French reference center for porphyria: 22.9%. We then used the Exome Variant Server (EVS) to estimate the prevalence of deleterious HMBS mutations in the general population: 1/1299; and the penetrance of the AIP genetic trait in France: 1%. Finally, we investigated further the genetic factors underlying the penetrance of AIP by analyzing genotype/phenotype correlations, and the pattern of familial correlations for the symptoms of the acute crises of AIP. Intrafamily correlation studies showed correlations to be strong overall and modulated by kinship and the era in which the person was living, demonstrating strong influences of genetic and environmental modifiers on inheritance suggesting that AIP inheritance does not follow the classical autosomal dominant model. Null alleles were associated with a more severe phenotype and a higher penetrance than for other mutant alleles.On the other hand, we explored the effect of heme administration. In human, the introduction of hemin into the pharmacopeia has coincided with a 4.4-fold increase in the prevalence of chronic patients. We show that repeated hemin infusions in mice trigger a high level heme oxygenase 1 response, induce a pro-oxidative iron accumulation, a complex pattern of liver inflammation with macrophage infiltration and an alteration of oxidative phosphorylation

Auf der Basis von Fossilien wird angenommen, dass die ersten Säugetiere nachtaktiv waren. Diese Arbeit untersucht diese Hypothese mit bioinformatischen und molekularbiologischen Techniken. Der Fokus liegt auf dem Rhodopsin, ein Sehpigment im Wirbeltierauge, das für Sehen unter schlechten Lichtverhältnissen verantwortlich ist. Zunächst wurde das Rhodopsin der monotrematen Echidna, einem basalen Säugetier, sequenziert und mit zwei Mutanten mit Mutationen an Positionen 158 und 169 in vitro exprimiert. Die biochemische und funktionelle Charakterisierung ergab, dass das Echidna-Rhodopsin farbpigment-typische Charakteristika aufweist, was auf eine Expression auch in Zapfen hindeutet. Dies ist die erste Charakterisierung eines Rhodopsins eines nachtaktiven Tieres. Dann wurden anzestrale Rhodopsinsequenzen für die Knotenpunkte Amniota, Mammalia und Theria mithilfe der Maximum-Likelihood-Methode berechnet. Die in vitro Expression und biochemische und funktionelle Charakterisierung zeigt funktionale und rhodopsin-typische Sehpigmente. Das Mammalia- und Theria-Rhodopsin zeigen eine hohe Meta II Halbwertszeit. Dieses Ergebnis wird als eventuelle Anpassung an Sehen unter schlechten Lichtverhältnissen interpretiert, wobei, aufgrund von Unstimmigkeiten in der Literatur, Schlussfolgerungen auf ökologisch-bedingte Anpassungen basierend auf einzelnen Funktionstests problematisch sind, da die visuelle Signalkaskade ein sehr komplexes und durch viele Proteine vernetztes System darstellt. Zuletzt zeigen Selektionsanalysen, dass das Rhodopsin entlang der Theria-Linie positive Selektion auf nicht-synonyme Substitutionen erfahren hat, was zu Anpassungen in einem Protein führt. Der Fossilbericht belegt entlang dieser Linie mehrere Einnischungsevents in neue Lebensräume. Entlang der Mammalia-Linie wurde positive Selektion auf synonyme Substitutionen gemessen, was zu einer Zunahme an Rhodopsin-Molekülen führt und damit eine Anpassung an Sehen unter schlechten Lichtverhältnissen darstellt. / Based on information from the fossil record, the first mammals are thought to have been nocturnal. This thesis investigates this popular hypothesis using bioinformatic and molecular techniques, focusing on the rhodopsin, a visual pigment in the vertebrate eye that is responsible for vision at low-light levels. First, the rhodopsin gene of the monotreme echidna, a basal mammal, was sequenced and successfully expressed in vitro, together with two mutants with substitutions at sites 158 and 169. Biochemical and functional analyses revealed that the echidna rhodopsin displays cone-like characteristics, likely due to being also expressed in cones. With the echidna being nocturnal, this thesis comprises the first characterisation of a rhodopsin of a nocturnal animal. Second, ancestral rhodopsin sequences for the tetrapod nodes Amniota, Mammalia, and Theria were inferred using Maximum likelihood estimates. All expressed pigments were successfully expressed in vitro, functional and rod-like. Mammalia and Theria rhodopsins display a high meta II half life time, a pattern that is usually interpreted to facilitate better vision at low-light levels. However, due to inconsistency in the available data, the result also suggests that, with the visual signaling cascade being a complex and interconnected system, erecting ecological interpretations based on single biochemical and functional reactions is problematic. Third, selective constraint analyses performed on a set of tetrapod rhodopsin sequences indicate that positive selection on non-synonymous sites, was acting along the branch leading to Theria. This result reflects the rapid diversification into modern ecological habitats during the Triassic and Jurassic, as indicated by the fossil record. In addition, positive selection on synonymous sites, leading to an increase of rhodopsin molecules, was found along the branch leading to Mammalia and suggests adaptations to vision at low-light levels.

CHEK2 gene codes for serin/threonine kinase Chk2 (Checkpoint kinase 2). In response to genomic DNA damage, Chk2 phosphorylates its substrates (proteins Cdc25C, BRCA1 or p53), whose activation leads either to cell cycle arrest, DNA damage repair or induction of apoptosis. Germline mutations in CHEK2 gene increase risk of cancer development. Analysis of high risk breast cancer patients in Czech Republic reveals rare CHEK2 mutations (mainly missense) with yet unknown clinical significance. This work focuses on functional impact of these variants and analysis of kinase activity of variant isoforms of Chk2 kinase. For this purpose, recombinant constructs were expressed in bacterial cells of E. coli. Enzymatic activity of Chk2 kinase isoforms in crude cell lysates was measured by the phosphorylation of Chk2 arteficial substrate spectrophotometrically. Results of in vitro kinase assay were correlated to the results of in silico prediction software. The results show that from 15 analyzed mutations (together with one in frame deletion), kinase activity was abrogated in all variants affecting the kinase domain of Chk2, in concordance with in silico predictions. The same result has been found for a FHA domain variant p.R145Q. No significant changes in kinase activity were observed in case of two FHA domain variants...

L’ingénierie des protéines fonctionnelles est un processus d’amélioration des propriétés physiques ou catalytiques d’enzyme au travers d’approches rationnelles et d'évolution dirigée, aussi bien que la combinaison des deux méthodes. Malgré le progrès de la modélisation moléculaire des protéines, les méthodes de prédiction restent aléatoires et un grand nombre de variantes restent à tester. De ce fait, le développement et l’utilisation d’un système de criblage d’activité de protéines à très haut débit, comme la microfluidique en gouttes, est indispensable. Cette thèse de doctorat présente trois projets d’évolution dirigée de protéines en trois approches différentes avec expression d’enzyme in vitro et in vivo. Les plateformes microfluidiques ont été développées et validées pour chaque projet. De plus, plusieurs banques de variants ont été criblées avec, dans certains cas, isolement de molécules 5-10 fois que le clone parental. / This work describes the development of high-throughput droplet microfluidic platforms fine-tuned for protein of interest and their employment in directed evolution experiments. When not available, fluorogenic assay for monitoring desired enzyme activity (-ies) in droplets was developed. Moreover, the in vivo expression allowed the successive integration of microfluidic modules on the same chip. After a couple of evolution rounds the initial retro-aldolase variant was significantly improved. In other project, to meet industrial requirements a high-throughput screening platform for protease evolution in detergent has been assembled and validated. Two evolution rounds showed the accumulation of a certain pool of beneficial mutations over the selection rounds. The research described in this work highlighted that in vitro expression systems are sensitive to the amount of supplied DNA and reaction conditions. This observation led to the development of a multistep completely in vitro microfluidic platform.

Synthesizing proteins for use in therapeutics is restrained by, in part, contaminants in in vivo expression systems and limited production capacity of in vitro systems. Cell free expression (CFE) systems have emerged as a potential alternative for protein expression because of the inherently lower contents of contaminants, and their flexible modular design that allows the addition of factors that aid in synthesis of complex products. Here, we investigate and establish an in-house Escherichia coli-based cell free protein synthesis (CFPS) system, explore different CFPS commercial kits, develop assays to test performance of these systems and identify potential rules that dictate expression levels. Using CFE, we were able to test different vectors and conditions of system, as well as scale-up protein synthesis reactions. In conclusion, this work shows that CFPS is a functional and easy-to-use platform and can potentially meet the requirements for the synthesis of therapeutics.