Der Embryonale Stammzelltest (EST) ist ein validierter In-vitro-Embryotoxizitätstest, der zur Untersuchung embryotoxischer Wirkungen von Chemikalien eingesetzt werden kann. Während des zehntägigen Differenzierungsassays differenzieren sich die pluripotenten murinen embryonalen Stammzellen (ES-Zellen) der Linie D3 in vitro in spontan kontrahierende Herzmuskelzellen. Dabei rekapitulieren sie Prozesse der frühen Embryogenese in vivo. Ein Zytotoxizitätsassay mit D3-Zellen und ausdifferenzierten, adulten 3T3-Maus-Fibroblasten dient der Ermittlung allgemeiner zytotoxischer Effekte und unterschiedlicher Sensitivitäten beider Zelllinien. Somit basiert der EST auf den beiden wichtigsten Mechanismen pränataler Toxizität, der Störung der Differenzierung und der Zytotoxizität. Ziel dieser Arbeit war es, mit Hilfe des EST das embryotoxische Potential der vier Chemikalien Trichostatin A (TSA), Methylazoxymethanolacetat (MAMac), Natriumdodecylsulfat (SDS) und Benzoesäure (BA) abzuschätzen. Dazu wurde mikroskopisch ermittelt, bei welcher Testsubstanzkonzentration in 50 % der während der In-vitro-Differenzierung gebildeten Embryonalkörperchen die Kardiomyozytendifferenzierung inhibiert wird (ID50). Außerdem wurde die halbmaximale Hemmkonzentration des Zellwachstums auf die beiden Zelllinien bestimmt (IC50D3 bzw. IC503T3). Als Erweiterung dieses konventionellen EST wurden mittels quantitativer Real Time-PCR an den Tagen 5, 7 und 10 der Differenzierung zusätzlich Genexpressionsanalysen etablierter herzmuskelspezifischer Markergene (Mesoderm Posterior 1, Tag 5; Myosin light chain 1, Tag 7 und 10) durchgeführt. Deren Expression korreliert in den ES-Zellen mit der embryonalen Herzdifferenzierung in vivo und kann zur Ermittlung der von der Prüfsubstanz hervorgerufenen halbmaximalen Hemmung der Genexpression in den Kardiomyozyten (IC50 Exp) herangezogen werden. Um letztlich embryotoxische Effekte in vivo auf Grundlage der ermittelten In-vitro-Daten abschätzen zu können, wurden die ermittelten Parameter mittels eines für den EST empirisch abgeleiteten mathematischen Prädiktionsmodells (PM) zur Klassifizierung der Testsubstanzen als nicht, schwach oder stark embryotoxisch herangezogen. Für jede der Substanzen waren die ermittelten Halbhemmkonzentrationen in den überwiegenden Fällen vergleichbar und führten unter Verwendung des PMs im konventionellen und im molekularen EST zu deren identischer Klassifizierung. TSA wurde als „stark embryotoxisch“ klassifiziert und beeinflusste insbesondere das Differenzierungspotential der ES-Zellen. Das als „schwach embryotoxisch“ klassifizierte SDS wirkte auf die D3-Zellen stärker differenzierungsinhibierend als zytotoxisch, hemmte jedoch das Wachstum der 3T3-Zellen bereits in deutlich niedrigeren Konzentrationen. MAMac und BA wurden als „nicht embryotoxisch“ klassifiziert. Bei ihnen stand die zytotoxische Wirkung deutlich im Vordergrund. Diese Prädiktionen stimmten mit In-vivo-Befunden überein, was von der Stabilität und der Brauchbarkeit der im konventionellen und molekularen EST ermittelten Parameter zeugte. Einzige Ausnahme war das als Entwicklungsneurotoxin in vivo bekannte MAMac. Da der EST auf mesodermaler Differenzierung basiert, können spezifische Effekte auf neuronale Entwicklungsprozesse offenbar nicht vollständig erfasst werden. Substanzkonzentrationen, die sich als differenzierungsinhibierend auf die morphologische Kardiomyozytendifferenzierung erwiesen haben, führten auch zu einer messbaren Repression der herzmuskelspezifischen Genexpression. Dabei erwies sich die IC50 Exp als ebenso sensitiv wie die konventionellen Parameter und als nutzbringende Ergänzung zu diesen, da sie bereits nach 5 bzw. 7 Tagen der In-vitro-Differenzierung eine mit dem mikroskopischen Parameter übereinstimmende Einschätzung des embryotoxischen Potentials der Chemikalien in vivo ermöglichte. Genexpressionsanalysen weiterer differenzierungsspezifischer Gene können zusätzlich zur Aufklärung zu Grunde liegender Mechanismen der Embryotoxizität von Testsubstanzen dienen. Somit kann der EST durch die Vorteile der Stammzelltechnologie und der Genexpressionsanalyse als neues prädiktives Screening-Instrument zur frühzeitigen Detektion embryotoxischer Substanzeffekte in der pharmazeutischen und chemischen Industrie genutzt werden. / The embryonic stem cell test (EST) represents a validated in vitro embryotoxicity test that can be utilised for investigations of embryotoxic effects of chemical substances. During the 10-day differentiation assay the pluripotent murine embryonic stem cells (ES cells) of the D3 line differentiate in vitro into spontaneously beating cardiac muscle cells that can be observed microscopically. Thereby, ES cells recapitulate processes of early embryogenesis in vivo. A cytotoxicity assay with D3 cells as well as differentiated, adult 3T3 mouse fibroblasts is used to determine general cytotoxic effects and to consider differences in the sensitivity of both cell lines. Hence the EST is based on the two most important mechanisms of prenatal toxicity, such as inhibition of differentiation and cytotoxicity. The aim of the presented work consisted in the evaluation of the embryotoxic potential of the four chemicals trichostatin A (TSA), methylazoxymethanolacetate (MAMac), sodium dodecyl sulfate (SDS) and benzoic acid (BA) by means of the EST. For this purpose the concentration of the test substance that causes an inhibition of cardiomyocyte differentiation in 50 % of the embryoid bodies which are formed during the in vitro differentiation (ID50-value) and the halfmaximal inhibiting concentration of cell proliferation of D3 and 3T3 cell lines (IC50D3 and IC503T3) were determined. As extension of this conventional EST, the effect of test substances was investigated at the molecular level by gene expression analyses of cardiac specific genes (Mesoderm Posterior 1, day 5; Myosin light chain 1, day 7 and 10). Their expression in ES cells correlates with the embryonic heart differentiation in vivo. Quantitative Real Time-PCR gene expression analysis was used to determine the halfmaximal inhibition of the cardiomyocyte gene expression (IC50 Exp) caused by the test compound. To predict embryotoxic effects in vivo from the determined in vitro data, these parameters were used for the classification of the test chemicals as non, weak or strong embryotoxic via a mathematical prediction model (PM). In the majority of cases comparable halfmaximal inhibiting concentrations were calculated in the conventional and molecular EST that resulted in the identical classification of the tested chemicals concerning their embryotoxic potential. TSA was estimated as “strongly embryotoxic” and affected particularly the differentiation potential of the ES cells. SDS was classified as “weakly embryotoxic” and acted by inhibiting the differentiation of D3 cells at concentrations lower than cytotoxic concentrations but already repressed the growth of the 3T3 cells in significantly lower ranges. As to MAMac and BA that were classified as “non-embryotoxic” the cytotoxic effects on both cell lines predominated. These predictions were consistent with in vivo findings that testifies the stability and the usefulness of the parameters used in the conventional and molecular EST. MAMac, which is known as a developmental neurotoxin in vivo, represented the single exception. Its misclassification as compared to in vivo data may originate from the limitations of the model system that is based on mesodermal differentiation. Thus, specific effects on neuronal developmental processes obviously cannot be detected completely. Gene expression analysis showed that test substance concentrations which were proved to be inhibiting on the morphological differentiation of cardiomyocytes caused a repression of cardiac-specific marker gene expression as well. Thereby, IC50 Exp-values proved to be just as sensitive as the conventional parameters and can provide valuable and supportive data. They allowed a prediction of the embryotoxic potential of the chemicals in vivo already at day 5 and day 7 of in vitro differentiation. Moreover, gene expression analysis of appropriate differentiation specific genes could be used to investigate mechanisms that are responsible for embryotoxic properties of the test compounds. Thus, the EST is considered to represent a new, predictive screening test especially in the pharmaceutical industry to detect the embryotoxic potential of chemical compounds early in the process of compound development.

Made available in DSpace on 2015-03-26T13:42:23Z (GMT). No. of bitstreams: 1 texto completo.pdf: 636309 bytes, checksum: ca1e7c510537c62820f228b759c5a23d (MD5) Previous issue date: 2011-07-25 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / O suíno (Sus scrofa) é considerado um animal de grande importância para produção de carne, sendo seu potencial de crescimento muscular objeto de grande interesse e geralmente associado com características determinadas na fase pré-natal durante a miogênese. Para o estudo de genes responsáveis por estas características, as etiquetas de sequências expressas (Expressed Sequence Tags - EST) fornecem informações diretas sobre o transcriptoma e indiretas sobre a relação entre o genoma e diferentes fenótipos, proporcionando o conhecimento sobre genes diferencialmente expressos (GDE) bem como sequências genômicas transcritas para o controle da expressão gênica como, por exemplo, alguns RNAs não codificantes. Características de tecidos musculares em suínos podem ser influenciadas diretamente por genes, e estes sendo regulados como, por exemplo, através de miRNAs, em diferentes fases de desenvolvimento. O presente trabalho teve como objetivo a identificação e a anotação in sílico de GDE e sequências não codificantes, com enfoque aos miRNAs, de bibliotecas de cDNA construídas a partir do músculo esquelético semi-membranoso de três diferentes raças de suínos (Duroc, Large White e naturalizada brasileira Piau) bem como a análise dos níveis de expressão dos genes identificados e miRNAs em sete fases de desenvolvimento do Longissimus Dorsi (21, 40, 70 e 90 dias pré-natal e 107, 121 e 171 dias pós-natal) de animais de linha comercial. Foram identificados 34 GDE sendo 21 pertencentes a uma rede gênica musculo-específica. Destes, 13 genes tiveram seus perfis de expressão analisados com o uso do qRT-PCR durante os sete períodos citados, formando quatro grupos de expressão semelhantes, um com maior expressão na fase pós-natal e três na fase pré-natal. Nas análises das sequências não codificantes um resultado importante foi a identificação de dois novos miRNAs em suínos, os quais tiveram suas sequências maduras similares aos miRNAs hsa-miR-1207-5p e hsa-miR-665 foram classificadas como verdadeiras pelo programa MiPred e formaram estruturas secundárias. Destes, encontrou-se 289 e 214 genes regulados por eles respectivamente, dos quais quatro são músculo-específicos. Os novos miRNAs tiveram seus perfis de expressão analisados com o uso do PCR em tempo real durante os sete períodos citados juntamente com outros três já identificados em suínos. Seus níveis de expressão mostraram diferenças entre os estágios pré- e pós-natal. Estes estudos podem fornecer valiosas informações possibilitando um maior entendimento dos mecanismos moleculares envolvidos no desenvolvimento muscular. As análises de GDE em fases pré e pós-natal sugerem a presença de genes atuando especificamente em determinados estágios de desenvolvimento do músculo, contribuindo para melhor explicar suas funções. A identificação de dois novos miRNAs, somados a outros já identificados e postados nos bancos de dados em suínos, podem contribuir para um maior entendimento dos modos de regulação gênica, sendo de importância para os estudos de genética e melhoramento animal, permitindo o entendimento da fisiologia da deposição de músculo para produção de carne em suínos. / The pig (Sus scrofa) is considered an important animal for meat production. This interest revolves around the potential for muscle growth, which usually is associated with certain characteristics during prenatal myogenesis. To study the genes responsible for these characteristics, expressed sequence tags (EST) provide direct information about the transcriptome and indirectly on the relationship between the genome and different phenotypes, supplying knowledge about differentially expressed genes (DEG) as well as other transcribed genomic sequences for the control of gene expression, e.g., some non-coding RNAs. Characteristics of muscle tissue in pigs may have been directly influenced by genes, and those being regulated, for example, by miRNAs, in different stages of development. This study aimed to identify by in silico annotation, DEG and non-coding sequences, focusing on miRNAs, using cDNA libraries constructed from semi-membranous skeletal muscle of three different pig breeds (Duroc, Large White and naturalized Brazilian Piau ) as well as analysis of gene expression profiles of identified genes and miRNAs during seven stages of development (21, 40, 70 and 90 days prenatal and 107, 121 and 171 days postnatal) from commercial line animals Longissimus Dorsi muscle. Twenty-one identified genes out of 34 DEGs belongs to the muscle-specific path. From these, 13 genes had their expression profiles analyzed by qRT-PCR during the seven periods, forming four clusters of similar expression, with one having greater expression in the postnatal period and three in the prenatal. In the analysis of non-coding sequences, an important result was the identification of two new miRNAs in pigs, which had their sequences similar to mature miRNAs hsa-miR-1207- 5p and hsa-miR-665 which had their precursor sequences forming secondary structures and classified as real precursor sequence by MiPred program. From these, we found 289 genes and 214 respectively regulated by them, of which four are muscle-specific. The new miRNAs and other three which have been identified in previous studies in pigs had their expression levels analyzed by quantitative real time PCR during the mentioned seven periods. Their levels of expression differed between pre-and postnatal stages. These studies may provide valuable information allowing a better understanding of the molecular mechanisms involved in muscle development. Analyses of DEG in the pre-and postnatal periods suggest the presence of genes acting specifically on certain stages of muscle development, contributing to better explain their functions. The identification of two new miRNAs, together with other previously identified and posted on the databases in pigs, may contribute to a better understanding of gene regulation and is important for studies of genetics and animal breeding, allowing the understanding of the muscle deposition physiology to meat production in pigs.

The potential for environmental toxicants to cause genetic damage (genotoxicity) in organisms is a prominent concern because effects on DNA can compromise reproductive success and survival in organisms. Genotoxicity in male germ cells is of particular concern because damage to DNA in sperm may not be repaired and the consequences of damaged genetic material may be transgenerational (from parent to offspring). An integrated approach across multiple levels of biological organization is necessary to establish linkages between exposure to genotoxicants and subsequent effects at molecular and higher levels of biological organization. This thesis addresses the relation between toxicant-induced genotoxicity and reproductive success in zebrafish, and focuses on a model genotoxicant (hydrogen peroxide) and dissolved metals (radionuclide or non-radioactive forms) under controlled laboratory conditions. Uptake and depuration kinetics of a mixture of radionuclides (54Mn, 60Co, 65Zn, 75Se, 109Cd, 110mAg, 134Cs, and 241Am) were investigated, and radiation dose estimations were computed to link exposure and bioaccumulation with radiation dose. Cobalt (Co, non-radioactive) was selected as an environmentally relevant toxicant for investigation of genotoxicity and effects on reproductive success with a focus on male fish. Chronic exposure (12-d) to 0 – 25 mg l-1 Co resulted in reduced numbers of spawned eggs, lower fertilization success, and reduced survival of larvae to hatching. In male fish, DNA damage was detected in sperm and genes involved in DNA repair (xrcc5, xrcc6, and rad51) were induced in testes from some Co treatments, generally consistent with reduced reproductive success. No change in expression of repair genes in larvae spawned from parents exposed to Co was observed. Overall, results indicate that DNA damage and induction of DNA repair genes can occur rapidly after exposure to genotoxicants and that, if exposure levels are elevated, negative effects on reproduction can occur. Results are considered with particular focus on implications of male genotoxicity on reproductive success and the potential for transgenerational effects of toxicants.

This thesis provides evidence for the presence of multiple RNAs in the axons and growth cones of developing thalamic cells, particularly the mRNA for the cell adhesion and Wnt-signalling-related molecule b-catenin. After many decades of effort, mRNAs have been shown to be present in the axons of many different systems in recent years. Furthermore, these mRNAs have been shown to be locally translated at the growth cone, and this local translation is required for axons to turn in response to multiple guidance cues. As studies accumulate, it is becoming clear that different axonal systems contain different complements of mRNAs and have different requirements for local translation. One axonal system which has not been investigated to date is the thalamocortical tract. The nuclei of the thalamus are connected to the areas of the cortex via bundles of axons which travel from the thalamus to the cortex via the ventral telencephalon during embyronic development. These axons make a number of turns and are guided by many cues and other axonal tracts before innervating their cortical target. In this thesis, a quantitative real-time polymerase chain reaction (qRT-PCR) approach is developed to isolate multiple mRNAs from developing thalamic axons in vitro, including b-catenin mRNA, b-actin mRNA, 18S ribosomal RNA and ten other mRNAs. The method used should be suitable for use with other axonal systems and also for testing the effect of guidance cues on mRNA expression in axons. The qRT-PCR results for b-catenin, b-actin and 18S have been validated using in situ hybridisation. Analysis of in situ hybridisation results indicates that b-catenin and 18S, but not b-actin, are upregulated in the growth cone compared to the axon. As b-catenin has been shown to be involved in axon guidance via Slit and ephrin guidance cues in other axonal systems, and these guidance cues act upon thalamocortical axons, the identification of b-catenin mRNA in thalamic axons is an important step towards a full understanding of the thalamocortical system. The results presented here indicate that local protein synthesis is likely to occur in thalamic axons as it does in other axonal systems, and that local translation is likely to be important for thalamic axonal responses to guidance cues and other axonal tracts.

Acinetobacter baumannii is an important nosocomial pathogen characterized by the ability to acquire and develop complex resistance to antimicrobial agents. This capability is caused by eflux systems removing molecules of antibiotics from bacterial intracellular space. AdeABC is an RND-type chromosomal eflux system specific for A. baumannii which has a broad substrate spectrum. In this work, we focused on functional analysis of AdeABC to define its role in the resistance development to aminoglycosides in genetically different strains. We studied a set of 15 epidemiologically and genotypically well characterized strains of A. baumannii which were fully susceptible to aminoglycosides and other antibiotics primarily effective against this species. We determined genotyp of AdeABC for these strains and performed a selection for resistant variants in the presence of netilmicin. Using real-time qRT-PCR we compared the expression of the transporter gene adeB in originally sensitive strains and selected variants. The obtained results confirmed that the increased expression of AdeABC significantly reduces susceptibility to aminoglycosides and other antibiotics. The results also suggest that the efflux system provides a significant selective advantage for nosocomial strains of A. baumannii.

<p>The aim of this thesis was to investigate the cellular role of the mouse RBBP6 gene using the interference RNA (RNAi) gene targeting technology and also to understand the relevance of two promoters for the RBBP6 gene.</p>

Softwood is the predominant form of land plant biomass in the Northern hemisphere, and is among the most recalcitrant biomass resources to bioprocess technologies. The white rot fungus Phanerochaete carnosa has been isolated almost exclusively from softwoods, while most other known white-rot species, including Phanerochaete chrysosporium, were mainly isolated from hardwoods. Accordingly, it is anticipated that P. carnosa encodes a distinct set of enzymes and proteins that promote softwood decomposition. To elucidate the genetic basis of softwood bioconversion by P. carnosa, its genome was sequenced and transcriptomes were evaluated after growth on wood compared to liquid medium. Results indicate that P. carnosa differs from P. chrysosporium in the number and expression levels of genes that encode lignin peroxidase (LiP) and manganese peroxidase (MnP), two enzymes that modify lignin present in wood. P. carnosa has more genes for MnP with higher expression levels than LiP, while the reverse has been observed for P. chrysosporium. The abundances of transcripts predicted to encode lignocellulose-modifying enzymes were then measured over the course of P. carnosa cultivation on four wood species. Profiles were consistent with decay of lignin before carbohydrates. Transcripts encoding MnP were highly abundant, and those encoding MnP and LiP featured significant substrate-dependent response. Since differences in modes of lignin degradation catalyzed by MnP and LiP could affect the ability of each to degrade lignin from different types of wood, their activity on various hardwoods and softwoods were tested. Results suggest that MnP degrades softwood lignin more effectively than hardwood lignin, consistent with high levels of this enzyme in P. carnosa.

Clinical management of esophageal adenocarcinoma (EAC) relies on radiation therapy, yet radioresistance is a pervasive challenge in this disease. The mechanisms of EAC radioresistance remain largely unknown due to a paucity of validated preclinical models. The present studies report on the development of seven primary xenograft models established from patient tumours. These models are used to interrogate the range of radiosensitivities and mechanisms of radioresistance in EAC tumours. We found that radiation enriches the tumour-initiating cell population in two xenograft lines tested. Furthermore, three tested xenograft lines respond to irradiation by upregulating Hedgehog transcripts, a pathway involved in stem cell maintenance and proliferation. Upregulation occurs in autocrine and paracrine patterns simultaneously, suggesting that Hedgehog signalling may have a complex role in the radioresponse of EAC tumours. These findings suggest that inhibiting stem cell pathways in combination with radiotherapy may have an important role in the clinical management of EAC.

Grass family is most important family in plant kingdom due to intensive usage of crops in agriculture. To date, molecular biology researches on grass family have had limitations because of inappropriate characteristics of barley and wheat to conduct experiments on them. Brachypodium distachyon that belongs to grass family has recently emerged as a model organism for crops. It shares common characteristics for a model plant due to its small genome, small physical plant size, a short lifecycle, and less demanding growth requirements / as other model organisms / Arabidopsis thaliana, Oryza sativa, and Zea mays (Draper et al. 2001). Especially after appreciating, the genetic distance of O. sativa to grasses (Garvin et al. 2008), it become a key organism to understand complicated genomic organization of agriculturally valuable grasses. Virus-induced gene silencing (VIGS) is one of the revolutionary methods allowing a rapid and effective loss of a gene function through RNA interference (Holzberg et al. 2002 / Liu et al. 2008). Barley stripe mosaic virus (BSMV) is still the most effective vector used in monocot gene silencing. It has a tripartite RNA genome having a wide range of infection ability for monocots including barley, oat, wheat, and maize as host (Holzberg et al. 2002 / Scofield 2005). In this thesis, Phytoene desaturase (PDS) gene of Brachypodium distachyon was silenced via BSMV mediated VIGS. Additionally, with Green fluorescence protein (GFP) bearing BSMV transcripts, GFP expression was observed under fluorescent microscope. To our knowledge, this is the first report demonstrating a VIGS via BSMV in Brachypodium distachyon. The success of virus induced gene silencing method in Brachypodium distachyon, will be a new convenient tool for evaluating functions of crop genes in this model organism.

<p>The aim of this thesis was to investigate the cellular role of the mouse RBBP6 gene using the interference RNA (RNAi) gene targeting technology and also to understand the relevance of two promoters for the RBBP6 gene.</p>