Dissertations / Theses on the topic 'Transcriptomic analysi'
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Jousset, Agnès. "analyse génomique et transcriptomique de bactéries productrices de carbapénèmases." Thesis, Université Paris-Saclay (ComUE), 2018. http://www.theses.fr/2018SACLS527.
Full textMultidrug resistant bacteria and in particular carbapenemase-producing Enterobacteriaceae remain a major health public challenge. Some successful clones are emerging globally, due to their high transmissibility and their ability to colonize and persist in patients over time. Genomic analyses revealed that the dissemination of KPC carbapenemase is closely related to the spread of Klebsiella pneumoniae of the sequence-type (ST) 258 and to few successful plasmids linked to IncFIIk family. However, the reasons of the association between K. pneumoniae ST258, IncFIIk plasmids and KPC that led to the rapid spread of this clone are currently unknown.Furthermore, there is no correlation between expression level of a carbapenemase-encoding gene, in vitro susceptibility to carbapenems and efficiency of a carbapenem-based treatment. Most of the time, KPC-producing K. pneumoniae exhibit a heteroresistant phenotype with carbapenems, but its clinical impact remains unknown. The mechanisms underlying the regulation of carbapenemases expression remain to be explored.The objectives of the thesis are to obtain deeper insights into genomic plasticity of carbapenemase–producing clones, and into the expression of their β-lactamases.The first part of this work was dedicated to the in vivo evolution of a single strain of KPC-producing K. pneumoniae ST258 that colonized a patient for almost 5 years. Genomic comparison of 17 isolates revealed a remarkable diversification with occurrence of several mutations with impact on bacterial virulence and susceptibility to antibiotics.Several studies extensively described the genetic structures of blaKPC-carrying plasmids, but information regarding gene expression at the whole plasmid level are lacking. Accordingly, we performed RNA-seq on Escherichia coli TOP10 transformed with an IncFIIk-IncFI blaKPC-2-carrying plasmid, with or without imipenem exposure. In both conditions, plasmid-encoded genes related to antimicrobial resistance and involved in plasmid replication were the most expressed. Imipenem exposure led to a more general response with overexpression of E. coli numerous chromosome-encoded genes involved in oxidative stress response. In addition, analysis of blaKPC-2 gene expression in several species using 5’RACE revealed the presence of several promoters whose strength depends on the bacterial genetic background. This could promote higher expression of blaKPC-2 gene and explain the association of some isoforms of Tn4401 in different species. The tools developed in the frame of this work were also applied to study a single Enterobacter kobei ST125 clone whose natural cephalosporinase (ACT-28) has increased hydrolytic activity towards imipenem. Finally, genomic analysis of the first ESBL-producing Shewanella sp. was performed. It revealed the presence of blaCTX-M-15 and blaSHV-2 genes carried on an IncA/C plasmid and a new chromosomally-encoded oxacillinase variant of OXA-48 with carbapenemase activity, called OXA-535. OXA-535 was found to be closely related to OXA-436, another carbapenemase which has recently spread in Enterobacteriaceae. Analysis of the genetic environment of both blaOXA-48-like genes confirmed the role of Shewanella spp. as progenitors of class D carbapenemases.Overall, this work contributes to a better comprehension of the diffusion of multi-drug resistant clones and of the mechanisms implicated in β-lactamase expression
Rodó, Morera Jordi. "Transcriptomic analysis of white and brown adipose tissue during non-shivering thermogenesis." Doctoral thesis, Universitat Autònoma de Barcelona, 2019. http://hdl.handle.net/10803/667915.
Full textObesity and type 2 diabetes (T2D) are two closely related diseases that represent a serious health, social and economic problem due to their high prevalence worldwide. Both diseases are also associated with other pathologies that present high mortality. The currently available therapies are not entirely effective. Thus, the development of new therapeutic strategies for obesity and T2D is crucial. Adipose tissue has been defined as an organ that plays a central role in the control of energy balance. The proved endocrine and thermogenic functions of adipocytes has renewed interest in the study of this tissue. Non-shivering thermogenesis has been described as occurring in brown adipose tissue of mice, but under certain stimuli, such as prolonged cold exposure, brown fat-like cells (beige adipocytes), appear in some white adipose tissue depots of rodents and humans. The activation of non-shivering thermogenesis in humans through cold-exposure increases resting energy expenditure, whole-body glucose disposal, insulin sensitivity, and ameliorates glucose metabolism independently of BMI. However, more gene expression studies to gain insight into the molecular mechanisms underlying the cold-induced enhancement of non-shivering thermogenesis, as well as to determine differences between BAT activation and browning of WAT, are needed. In this study, the transcriptomic response of epididymal and inguinal white adipose depots (eWAT and iWAT, respectively) as well as that of the interscapular brown adipose depot (iBAT) of mice either exposed to 22ºC or 4ºC for the period of 4 days were examined. Cold exposure increased the metabolic and thermogenic activity of iWAT. In this depot, genes related to glycolysis, tricarboxylic acid cycle, lipolysis, and the degradation of some amino acids presented a high upregulation to maintain the protonmotive power to generate heat. Moreover, the expression of thermogenic-related genes was also highly increased, demonstrating a cold-induced browning of iWAT. The eWAT depot has been reported to be resilient to browning. Thus, the observed metabolic activation of this depot was mild in comparison with that of iWAT, and no relevant enhancement of non-shivering thermogenesis was observed in this depot. Finally, iBAT already presented high expression levels of thermogenic genes because mice were not housed at thermoneutrality. The observation that genes related to thermogenesis and metabolism presented a similar expression pattern among samples endorsed the utilization of pattern matching analysis tools to unravel Atp4b and 1700040L02Rik as novel genes potentially involved in thermogenesis. The overexpression of Atp4b and 1700040L02Rik in adipose tissue by means of AAV vectors produced a body weight gain reduction, decreased eWAT, and liver weight, amelioration of white adipocytes hypertrophy, and reduced hepatic steatosis potentially as a result of the detected enhanced thermogenesis in iWAT. Overall, these results indicate a new potential anti-obesogenic role for these genes. The results from this thesis contributed to a better understanding of the induction of non-shivering thermogenesis in adipose tissue depots in mice. Among the different adipose depots, exploratory data analysis of the gene expression levels of mice exposed from 22ºC to 4ºC determined that iWAT was the depot that responded most significantly to cold exposure. Moreover, as observed in the pathway enrichment and gene ontology analysis, this response was highly coordinated, presenting a high number of genes related to metabolic pathways highly affected. The detailed study of the metabolic pathways led to the detection of a high induction of non-shivering thermogenesis, revealing that both energy production and energy consumption mechanisms were highly synchronized. This in detail study of the adipose tissue also allowed the identification of novel genes potentially involved in non-shivering thermogenesis.
Stranneheim, Henrik. "Enabling massive genomic and transcriptomic analysis." Doctoral thesis, KTH, Genteknologi, 2011. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-45957.
Full textQC 20111115
Braga, D. "TRANSCRIPTOMIC ANALYSIS IN SEPTIC SHOCK PATIENTS." Doctoral thesis, Università degli Studi di Milano, 2017. http://hdl.handle.net/2434/473670.
Full textLoe-mie, Yann. "Contribution bioinformatique à l' analyse du transcriptome humain." Thesis, Aix-Marseille, 2012. http://www.theses.fr/2012AIXM4002/document.
Full textIn first part of this thesis I have analysed small RNA-seq transcriptome data. I have noticed : - a large fraction of reads can't be aligned perfectly on reference genome - lot of reads are very short (15-18 nt) and don't match on previously known functionnal small RNAs. These experiments are designed for miRNA discovery and bioinformatics analysis of these data use alignments on genome or on known small RNA precursors sequences. I have eliminated the alignment and I have clustered these sequences. This clustering let me to observe these data with a new view in wich the genomic location is not central and open the gate to discover unconventional events. The second part is the analysis of deregulate genes by the silencing of the gene REST/NRSF in mouse N18 cell line. This gene is a transcription factor and it works as a repressor of neuronal genes in non neuronal cells. This deregulate genes repertoire potentially contains key genes in neuron biology. We found in this repertoire a network of genes centered on SWI/SNF complex including SMARCA2. This gene was associated to schizophrenia (SZ) in association studies and structural variation studies. In this network we found another genes associated to SZ. We show that these genes exhibit positive evolution in primate compare to rodents
Sidaway, Adam. "Transcriptomics analysis of differentiating erythroblasts." Thesis, University of Bristol, 2016. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.715794.
Full textBadawi, Sally. "Characterization of dynamic molecular networks in control ischemic-reperfused mouse heart." Thesis, Lyon, 2019. http://www.theses.fr/2019LYSE1158.
Full textCardiovascular diseases represent a major health burden worldwide. According to the World Health Organization, 17 million people are dying each year by heart diseases which account to 31% of total deaths globally. Among these diseases is myocardial infarction (MI). Several efforts have been made to decrease the associated mortality rates but unfortunately, only few has succeeded to date. This failure is contributed to several factors, among them is the misunderstanding of the mechanism responsible for the progression of the disease.Our understanding of the MI pathology has been greatly improved by the approaches that have been widely used in the previous decades, relying mainly on studying molecules/pathways separately. However, this knowledge was not enough to make a difference clinically. Therefore, deciphering the interconnections between molecules has become an urge for better understanding of the diseases’ progression. In this regard, the work in this doctoral thesis involves different aspects of the MI pathology. The general aim of this work is to improve the dynamic analytical approach using systems biology tools, where new mechanistic information is decoded. Firstly, in a 3D heart model, we propose a chain of methods using clarified mouse heart and fluorescence microscopy to molecularly characterize the area at risk in the myocardium of IR and cardioprotected mice based on its redox state. In addition, we aim to develop a new analytical approach using dynamical large-scale transcriptomic data for characterizing the dynamic transcripts expression. Applying this approach on a control mouse model (mice subjected to anesthesia and surgical interventions), we show that Il-6 is a major mediator of the activated inflammatory reaction. In conclusion, this analytical approach highlights the necessity of the sapatio-temporal analysis to characterize the molecular events occurring in response to MI
Schwalb, Björn. "Dynamic transcriptome analysis (DTA)." Diss., lmu, 2012. http://nbn-resolving.de/urn:nbn:de:bvb:19-147748.
Full textBERTOLAZZI, Giorgio. "MicroRNA Interaction Networks." Doctoral thesis, Università degli Studi di Palermo, 2021. http://hdl.handle.net/10447/498927.
Full textBertolazzi’s thesis focuses on developing and applying computational methods to predict microRNA binding sites located on messenger RNA molecules. MicroRNAs (miRNAs) regulate gene expression by binding target messenger RNA molecules (mRNAs). Therefore, the prediction of miRNA binding is important to investigate cellular processes. Moreover, alterations in miRNA activity have been associated with many human diseases, such as cancer. The thesis explores miRNA binding behavior and highlights fundamental information for miRNA target prediction. In particular, a machine learning approach is used to upgrade an existing target prediction algorithm named ComiR; the original version of ComiR considers miRNA binding sites located on mRNA 3’UTR region. The novel algorithm significantly improves the ComiR prediction capacity by including miRNA binding sites located on mRNA coding regions.
Crivelente, Horta Maria Augusta 1981. "Análise do transcriptoma de Trichoderma harzianum para a bioprospecção de enzimas hidrolíticas = Analysis of Trichoderma harzianum transcriptome for bioprospecting of hydrolytic enzymes." [s.n.], 2014. http://repositorio.unicamp.br/jspui/handle/REPOSIP/316510.
Full textTese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia
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Resumo: Buscando contribuir com o desenvolvimento da tecnologia de produção do etanol de segunda geração, o presente estudo analisa o transcriptoma de T. harzianum IOC-3844 utilizando técnicas de sequenciamento high-thoughput. O principal objetivo dessas análises foi identificar, caracterizar e catalogar os transcritos expressos por T. harzianum relacionados com a degradação de substratos complexos, como o bagaço de cana de açúcar, revelando o conjunto de genes envolvidos na degradação da biomassa. A análise do transcriptoma do fungo Trichoderma harzianum sob condições que induzem a degradação da biomassa permitiu a identificação de sequências de genes potencialmente eficazes no processo de biodegradação, uma etapa essencial à compreensão do processo de hidrólise enzimática. O sequenciamento resultou em 246 milhões de sequências com 72 pb, o que corresponde a 14,7 GPB analisados. Após a montagem , 32.494 contigs foram gerados, submetidos à identificação e classificados de acordo com sua identidade. Todas as sequências de contigs foram comparados com o banco de dados do NCBI, Gene Ontology (GO terms), Enciclopédia de Genes Kyoto (KEGG), Carbohydrate Active-Enzymes (CAZYmes). Foram identificados 487 CAZymes no transcriptoma, inclusive aquelas ligadas as reações químicas de despolimerização de celulose e hemicelulose. As sequências classificadas como atividade catalítica (6.975) e atividade reguladora (143) podem estar envolvidas com esse tipo de reação.A análise permitiu definir o principal conjunto de genes envolvidos na degradação da celulose e de hemicelulose do T. harzianum , e genes acessórios relativos à despolimerização de biomassa. Uma análise dos níveis de expressão permitiu determinar os conjuntos de genes diferencialmente expressos em diferentes condições de cultivo. Os resultados obtidos acrescentam conhecimento sobre a constituição do genoma, as atividades de expressão gênica do fungo Trichoderma harzianum e fornece informações importantes a respeito dos mecanismos genéticos de degradação de biomassa que o fungo utiliza. As informações obtidas poderão ser utilizadas para outras espécies de fungos filamentosos com potencial para a biodegradação
Abstract: In order to contribute to the development of second-generation ethanol technology, this study analyzes the transcriptome of T. harzianum IOC-3844 using high-thoughput sequencing techniques. The main objective of this analysis was to identify, characterize and catalog the transcripts expressed by T. harzianum related to the degradation of complex substrates such as sugar cane bagasse, revealing the set of genes involved in the degradation of biomass. The analysis of the transcriptome of the fungus Trichoderma harzianum under conditions that induce the degradation of biomass allowed the identification of genes potentially effective in the biodegradation process, an essential step for understanding the enzymatic process. Sequencing resulted in 246 million sequences with 72 bp, which corresponds to 14.7 GBP analyzed. After assembly, 32,494 contigs were generated, identified and classified according to their identity. All sequence contigs were compared with NCBI database, Gene Ontology (GO terms), Kyoto Encyclopedia of Genes (KEGG), Carbohydrate Active-Enzymes (CAZYmes). 487 CAZymes were identified in the transcriptome, including those related to reactions of cellulose and hemicellulose depolymerization. Sequences classified as catalytic activity (6,975) and regulatory activity (143) may be involved with this type of reaction. This analysis define the set of genes involved in the degradation of cellulose and hemicellulose of T. harzianum, and accessories genes related to depolymerization of the biomass. An analysis of expression levels was used to calculate the set of differentially expressed genes in different culture conditions. The results add to knowledge about the composition of the genome and gene expression activity of the fungus Trichoderma harzianum, and provides important information regarding the genetic mechanisms of biomass degradation that the fungus uses. The information obtained may be used for other species of filamentous fungi with potential for biodegradation
Doutorado
Genetica Vegetal e Melhoramento
Doutora em Genética e Biologia Molecular
Sjödin, Andreas. "Populus transcriptomics : from noise to biology /." Umeå : Department of Plant Physiology, Umeå University, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-1423.
Full textCardoso-Silva, Cláudio Benício 1982. "Análise do transcriptoma e de sequências genômicas de variedades comerciais de cana-de-açúcar = Transcriptome and genomic sequences analysis of commercial sugarcane varieties." [s.n.], 2015. http://repositorio.unicamp.br/jspui/handle/REPOSIP/316503.
Full textTese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia
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Resumo: A cana-de-açúcar é uma das espécies de maior importância econômica no mundo devido ao seu potencial bioenergético. No entanto, o seu alto nível de complexidade genética é um desafio para a aplicação de ferramentas moleculares no melhoramento. Os recentes avanços das tecnologias de sequenciamento e genotipagem indicam o potencial de aumentar o nosso entendimento sobre a genética e a biologia molecular desta espécie. As sequências genômicas e de transcriptomas são valiosa fonte de informação para o desenvolvimento de ferramentas moleculares que permitam a identificação de regiões no genoma que estejam relacionadas com características de interesse para o melhoramento. O uso das novas tecnologias de sequenciamento de alto desempenho tem grande potencial de impacto nestas pesquisas. A presente tese objetivou analisar o transcriptoma de seis variedades comerciais e dados genômico da variedade R570, com a finalidade de identificar genes potencialmente úteis para o desenvolvimento de marcadores moleculares. A partir do método RNA-Seq, foram geradas mais de 400 milhões de sequências, as quais permitiram obter um total de 72.269 transcritos representados por uma única isoforma montados com auxílio do programa Trinity. Estes transcritos foram alinhados com sequências de Viridiplantae, gramíneas, e exclusivamente contra proteínas de sorgo, arroz, milho e transcriptoma de cana-de-açúcar, depositados em banco de dados público. Esta análise permitiu identificar o conjunto de genes de cana-de-açúcar compartilhados com outras gramíneas, bem como levou à identificação de novos transcritos que não haviam sido catalogados para cana-de-açúcar, além de longos RNAs não codificantes. Os transcritos foram anotados no Cluster of Orthologous Groups (COG) e no Gene Ontology (GO), com posterior análise de enriquecimento dos termos GO, a partir da qual foram anotados os transcritos, possivelmente relacionados a genes que conferem características de importância agronômica. No transcriptoma foram identificados mais de 700 mil SNPs e aproximadamente cinco mil regiões microssatélites. Analisando um total de 32 Mbp de sequências genômicas da variedade R570 foram identificados 4.342 microssatélites, com frequência média de sete SSR/Kb. As sequências geradas e exploradas neste trabalho são valiosa fonte de informações para entender a arquitetura genética da cana-de-açúcar, principalmente para o desenvolvimento de marcadores moleculares, os quais podem ser utilizados no mapeamento genético
Abstract: The sugarcane is one of the most economically important species in the world, due to their energy potential. However, high level of genetic complexity has been a major challenge for the use of molecular tools applied to improvement of this crop. Recent advances in sequencing and genotyping technologies indicate the potential to increase our understanding of the genetics and molecular biology of this specie. The genomic and transcriptomic are valuable sources of information for the molecular tools development that allow identification of regions in the genome that are related to characteristics of interest for the improvement. The high-throughput sequencing technologies have great impact of this research. This thesis aimed to analyze the transcriptome of six commercial varieties and genomic sequencing from R570 variety, in order to identify genes potentially useful for the molecular markers development. From RNA-Seq method were generated over 400 million sequences, which allowed obtain a total of 72,268 transcripts representing a single isoform assembled by Trinity. These transcripts were aligned against Viridiplantae, grasses, and exclusively against sorghum, rice and maize proteins, and sugarcane transcriptome available in the public database. This analysis allowed identifying a set of shared genes with other grasses, new transcripts that had not yet been cataloged for sugarcane and long non-coding RNAs. The transcripts were also annotated using the COG (Cluster of Orthologous Groups) and GO (Gene Ontology) database, followed by enrichment analysis for GO terms, from which it was possible to identify genes that play roles, possibly related to traits of agronomic importance. In the transcriptome were identified over 700 thousands SNPs and five thousands microsatellites regions. In the genomic sequences from R570 variety, in a total of 32 Mbp were identified 4,342 microsatellites, with an average frequency of seven SSR / Kb. The sequences generated and explored in this work is a valuable source to understand the genetic architecture of the sugarcane, mainly for molecular markers development, which can be used in genetic mapping
Doutorado
Genetica Vegetal e Melhoramento
Doutor em Genetica e Biologia Molecular
Chevallier, Lucie. "Recherche de facteurs génétiques contrôlant la résistance de lignées de souris consanguines à une infection expérimentale par Yersinia pestis, l’agent de la peste." Thesis, Paris, AgroParisTech, 2012. http://www.theses.fr/2012AGPT0077/document.
Full textYersinia pestis, the agent of plague, is a deadly gram-negative bacterium classified as a re-emerging pathogen and class A biological weapon. The appearance of a multi-resistant strain highlights the need to better understand how this pathogen kills its host. To identify genetic factors of host susceptibility to plague, our laboratory is investigating the response of resistant versus susceptible mice to Y. pestis. Our strategy to decipher genetic determinants involved in resistance to plague combines Quantitative Trait Loci (QTL) mapping with gene expression analysis. We previously described the Mus spretus-derived SEG/Pas strain as the first to resist fully virulent Y. pestis, while most inbred strains, such as C57BL/6, are highly susceptible. Crosses between these two strains identified three QTLs (located on chromosome 3, 4 and 6) contributing to resistance. Two of the QTLs (on chromosome 4 and 6) were confirmed through creation of congenic mice. Up to 40% of the congenic mice heterozygous at these two QTLs, on a C57BL/6J background, survived the infection while all C57BL/6J mice died. Further dissection of these two QTLs, through the use of subcongenic strains, enabled us to refine the genetic architecture of resistance to plague in SEG/Pas mice. We concluded that a minimum of four genetic factors, within these two QTLs, are required to increased resistance to Y. pestis in mice. Despite production of numerous congenic strains, including triple congenic mice, we were not able to confirm the existence of the third QTL identified on chromosome 3. In parallel to genetic studies, we determined that SEG/Pas and C57BL/6J macrophages exhibit distinct characteristics upon in vitro exposure to Y. pestis. The underlying molecular differences were investigated by using microarrays. Our results show strong activation of cytokines in SEG/Pas macrophages in response to Y. pestis, which is not found in C57BL/6J macrophages. These results suggest that SEG/Pas mice are able to better activate innate immune response to Y. pestis than C57BL/6J mice.We further studied the expression of 44 genes in a kinetic study on macrophages in vitro of SEG/Pas, C57BL/6J and bicongenic mice (carrying QTLs on chromosome 4 and 6). This study confirmed that SEG/Pas mice are able to build a stronger inflammatory response at early time of infection. Nevertheless no significant differences were observed in the bicongenic strain compared to C57BL/6J. Further studies will be required to understand the mechanisms involved in the intermediate resistance of this strain. This combination of genetic dissection and gene expression analysis of resistant and susceptible mouse strains will enhance our ability to better understand the host response to plague
Weinberg, Kerry Rachel. "Streamlining and standardizing transcriptomic analysis in Amgen process development." Thesis, Massachusetts Institute of Technology, 2016. http://hdl.handle.net/1721.1/104314.
Full textThesis: S.M. in Engineering Systems, Massachusetts Institute of Technology, Department of Biological Engineering, 2016. In conjunction with the Leaders for Global Operations Program at MIT.
Cataloged from PDF version of thesis.
Includes bibliographical references (pages 71-75).
Building biological understanding of the Chinese Hamster Ovary (CHO) system used to manufacture therapeutic proteins is paramount to efficient CHO bioprocess optimization. This understanding can be built by analyzing and synthesizing biological data; such as transcriptomic (gene expression), proteomic (protein levels), or metabolomic (metabolite levels). This thesis describes a streamlined workflow for analyzing transcriptomic data. This streamlined workflow not only reduced the barrier to conducting the analysis but also reduced the analysis cycle time. With the use of this workflow, a number of historical Amgen microarray datasets were mined to identify gene expression signatures indicative of productivity. The result of this mining identified key biological pathways specific to a highly productive Amgen cell line. This work suggests that these pathways are critical to heightened levels of protein production. Using this information to engineer future cell lines could enable Amgen to improve cellular protein production by over 30%, impacting costs associated with drug substance manufacturing. More broadly, this example of streamlining and standardizing transcriptomic data provides a framework for how Amgen Process Development can leverage biological data to improve CHO systems understanding and achieve operational impacts.
by Kerry Rachel Weinberg.
M.B.A.
S.M. in Engineering Systems
Halbritter, Florian. "Genome-scale transcriptomic and epigenomic analysis of stem cells." Thesis, University of Edinburgh, 2012. http://hdl.handle.net/1842/9900.
Full textWeisheit, Sabine. "Transcriptomic and proteomic analysis of arbovirus-infected tick cells." Thesis, University of Edinburgh, 2014. http://hdl.handle.net/1842/10058.
Full textCaterino, Cinzia. "The aging synapse: an integrated proteomic and transcriptomic analysis." Doctoral thesis, Scuola Normale Superiore, 2019. http://hdl.handle.net/11384/86004.
Full textVidotto, Michele. "Transcriptomic analysis of the polyploid Adriatic sturgeon (Acipenser naccarii)." Doctoral thesis, Università degli studi di Padova, 2013. http://hdl.handle.net/11577/3422646.
Full textGli storioni sono un gruppo di pesci Condrostei, di elevato interesse evoluzionistico, economico e di conservazione. Le uova di questi fossili viventi costituiscono uno degli alimenti di origine animale più preziosi sul mercato. L'intenso sfruttamento delle popolazioni selvatiche per la raccolta del caviale ha causato, negli ultimi decenni, un calo drammatico della loro distribuzione ed abbondanza che ha portato, nel 2010, l'Unione Internazionale per la Conservazione della Natura ad indicarli come il gruppo di specie a maggior rischio di estinzione. Come diretta conseguenza, sono stati compiuti sforzi notevoli, in tutto il mondo, per sviluppare programmi finalizzati alla produzione di caviale via acquacoltura. In questo contesto, l'allevamento selettivo delle femmine aumenterebbe i profitti economici e la caratterizzazione dei geni coinvolti nella determinazione del sesso, diventa decisiva. Il sequenziamento 454 di quattro librerie di cDNA normalizzate, costruite a partire da gonadi e cervello di A naccarii e A. stellatus, un maschio ed una femmina (fratelli) per specie, ha prodotto 182,066 e 167,776 reads grezze rispettivamente per i due sessi di A naccarii, che dopo un severo controllo di qualità sono state assemblate insieme attraverso un processo iterativo, risultando in più di 55,000 Expressed Sequence Tags (ESTs) di qualità elevata. Per la specie A. stellatus, invece, sono state prodotte 184,374 reads per la libreria maschile e 169,286 per quella femminile, allineate in 63,606 ESTs dopo due giri di assemblaggio. E’ stato stimato che, l’assemblaggio di A. naccarii contenga i tag di circa l’80% dei trascritti totali espressi in gonadi e cervello, in questa specie, con una copertura media dei contigs pari a 4X. La copertura del trascrittoma di A. stellatus è stata stimata in circa l’86%, con 3.6X come media di copertura dei contigs. Il processo di annotazione multi-fase, ha portato ad annotare correttamente, con termini GO circa 16% ed il 15% delle sequenze, rispettivamente in A. naccarii ed A. stellatus. Entrambi i trascrittomi sono stati interrogati alla ricerca di 32 geni legati al sesso e sono stati evidenziati 5 geni potenzialmente espressi in modo specifico nel maschio e 2 nella femmina di A. naccarii, nel primo stadio di sviluppo, in cui il sesso è istologicamente identificabile. La ricerca nel trascrittoma di A. stellatus è attualmente preliminare e sono necessarie ulteriori fasi di filtraggio. Entrambi i trascrittomi sono stati confrontati con quelli di altre specie di pesci, per la quali erano disponibili rilevanti informazioni genomiche. Infine, 21.791 putativi Single Nucleotide Polymorphisms (SNPs) e 5.295 Single Sequence Repeats (SSR) EST-linked sono stati identificati in A. naccarii, mentre 15.449 e 5.696 sono stati rispettivamente classificati nell’assemblaggio di A. stellatus. Questo studio rappresenta la prima caratterizzazione dei trascrittomi di due specie di storione ad elevato rischio di estinzione. Gran parte delle informazioni acquisite per la specie A. naccarii sono state organizzati all’interno della banca dati pubblica AnaccariiBase, liberamente disponibile all’indirizzo http://compgen.bio.unipd.it/anaccariibase/, mentre le informazioni ottenute per A stellatus saranno rilasciate al più presto. Questa analisi rappresenta una preziosa fonte di informazioni per ulteriori studi più mirati, volti a caratterizzare o confrontare geni, a decifrare i meccanismi molecolari o le vie genetiche in questo gruppo di specie, o a scoprire centinaia di marcatori associati ad ESTs per diverse applicazioni nella conservazione dello storione.
Silveira, Willian Abraham da. "Genetic profile analysis of tumor stem cells in locally advanced breast cancer." Universidade de São Paulo, 2015. http://www.teses.usp.br/teses/disponiveis/17/17145/tde-05012016-144854/.
Full textINTRODUÇÃO: O cancer de mama é no mundo o câncer mais comum em mulheres e a disseminação metastática é o principal fator relacionado com a morte pela doença. Acreditasse que as células tronco do câncer de mama - bCSC, na sigla em inglês e definida neste trabalho com a população ALDH1high/LIN-/ESA+ - é responsável pela metástase e pela quimioresistência. O objetivo deste trabalho é encontrar genes que são essenciais para o controle do fenótipo das bCSC, em particular fatores de transcrição. MATERIAIS E MÉTODOS: Nesse trabalho nós utlizamos dois grupos de datasets com dados do transcriptoma, o grupo de datasets de descoberta contém um dataset gerado por nós com 3 amostras pareadas comparando as bCSC com o tumor total (My Data - bCSC/Bulk dataset), um dataset com 8 amostras pareadas comparando as bCSC com as células cancerígenas (Wicha - bCSC/CC dataset) e um dataset com 115 amostras de tecido de câncer de mama (Clinical Response dataset). O segundo grupo, grupo de validação, contém o dataset BRCA-TCGA com 621 amostras, as 4142 amostras de câncer de mama da ferramenta Kmplot, as 17 amostras humanas primárias do subtipo BasL e sua informação sobre a geração, ou não, de tumores em camundongos imunosuprimidos e a análise de linhagens celulares (MF10A e HMLE). Para a análise dos dataset utilizamos o test-t pareado no pacote Limma da liguagem R, o algoritmo ARACNE para a inferência de regulons no dataset Clinical Response, a análise MRA-FET para definir os Reguladores Mestres para o fenótipo das bCSC e a análise GSEA para identificar o significado biológico de nosso achados nos diferentes datasets. RESULTADOS E DISCUSSÃO: Nós identificamos 12 TFs como reguladores mestres, com 9 deles formando duas redes altamente conectadas, uma positivamente relacionada ao fenótipo bCSC formada por SNAI2, TWIST, PRRX1, BNC2 e TBX5 com seus regulons, e definida aqui como a rede de transcrição mesenquimal, e uma rede correlacionada negativamente, formada por SCML4, ZNF831, SP140 e IKZF3, definida aqui como a rede de transcrição da resposta imune e totalmente desconhecida da literatura no contexto do câncer de mama. Embora ainda com fraca evidencia, ZEB1 para controlar as duas redes e ser responsável pela expressão de ALDH1 e dos 3 TFs restantes: ID4, HOXA5 e TEAD1. Como mostram seus nomes, e independente do dataset, do subtipo molecular ou da plataforma utilizada, a rede de transcrição mesenquimal, parece ser responsável pela manutenção do fenótipo de células tronco cancerígenas e a rede de transcrição da resposta imune pela resposta imune adaptativa ao tumor e a um bom prognóstico para as pacientes. CONCLUSÃO: Nós encontramos e descrevemos duas redes de fatores de transcrição que parecem controlar o fenótipo das bCSC, uma delas totalmente desconhecida até agora e relacionada a um bom prognóstico. Nosso achados possuem um claro potencial para uso clínico.
Biton, Anne. "Analyse en composantes indépendantes du transcriptome de cancers." Thesis, Paris 11, 2011. http://www.theses.fr/2011PA11T028.
Full textPractice of gene expression data analysis shows that it is advantageous to analyze biologicalprocesses in terms of modules rather than simply consider gene one by one. In this project, we conducted anunsupervised analysis of the gene expression data of several cohorts of urothelial tumors, applying theIndependent Component Analysis method. Several studies demonstrated the outperformance of ICA overPCA and clustering-based methods in obtaining a more realistic decomposition of the expression data intoconsistent patterns of coexpressed genes associated with the studied phenotypes[1, 2, 3, 4].Urothelial tumors arise and evolve through two distinct pathways which radically differ on their probabilityof progression to muscle invasion. Except the mutation of FGFR3 in the less aggressive group, theunderlying molecular processes have not been completely identified. The first and main objective of the PhDthesis was dedicated to the biological interpretation of the different independent components to help toconfirm and extend the list of biological processes known to be involved in bladder cancer.Each independent component (IC) is characterized by a list of gene projections on the one hand and weightedcontributions of tumor samples on the other hand. By combining biological expertise and comparison of theassociated list of genes to known pathways, and jointly studying the association of the components tomolecular and clinical annotations, we have been able to differentiate components that were caused bytechnical factors, such as surgical sampling, from those having consistent biological interpretationin terms of tumor biology. Moreover, among the biologically meaningful signals, this analysis allowed us todifferentiate the signals from stroma of the tumor, like immune response mediated by B- and T-lymphocytes,from the signals produced by the tumors themselves, like signals related to proliferation, or differentiation.The clustering of the tumor samples according to their contributions on some ICs can be closely associated toanatomo-clinical annotations, and highlighted new potential subtypes of tumors which suggest existence ofadditional pathways of bladder cancer progression. Similarly, the study of the contributions of preestablishedgroups of tumors based on clinical or molecular criteria showed different levels of stromacontamination between FGFR3 non-mutated and mutated tumors. The reproducibility of the components wasinvestigated using correlation graphs. The major part of the interpreted ICs was validated on threeindependent bladder cancer datasets, and several of them were also identified in an urothelial cancer celllines data set.A second study about retinoblastoma gave us the occasion to show that we can take advantage ofICA in various contexts. Retinoblastoma is initiated by the loss of both alleles of the RB1 tumor suppressorgene. Although necessary for initiation, other genomic events, that remain to be identified, are needed for theprogression of the disease [5]. We observed, as it was previously described [6], an association between age ofthe patients and levels of genomic aberrations, the younger patients having fewer alterations than the olderpatients, which generally present gain of 1q and loss of 16q. We showed that this tendency of the tumors tobe clustered into two groups of age can also be observed on the expression data by applying ICA whose oneof the component was highly correlated to the age of the patients. These results suggest the existence of twopathways of progression in retinoblastoma.The analysis of high throughput data provides many lists of genes. To interpret them, a possibility isto study the latest related publications grouped by pre-defined group of topics (function, cellular location...).To that aim, in a third study, we introduced a web-based Java application tool named GeneValorization whichgives a clear and handful overview of the bibliography corresponding to one particular gene list [7]
Noguero, Mélanie. "Contribution de l'albumen au développement de la graine chez Medicago truncatula : caractérisation d'un facteur de transcription de type DOF exprimé dans l'albumen chalazal." Thesis, Dijon, 2014. http://www.theses.fr/2014DIJOS022/document.
Full textIn the current context, which necessitates a reduction in inputs in crop systems and boosting of production of plant proteins to reduce France’s dependency on feed imports,, growing legumes represents an alternative. Grain legumes are major sources of proteins for animal and human nutrition. In the UMR1347 Agroécologie, the objectives of the study group "déterminismes Génétiques et Environnementaux de l’Adaptation des Plantes à des Systèmes de culture Innovants" (GEAPSI) are to promote legume cultivation and adaptation to environmental stresses, via multidisciplinary approaches (genetics, ecophysiology, molecular physiology). This thesis project was carried out in the "Étude des Mécanismes Moléculaires" team, particularly interested in seed quality traits such as protein content or seed size and identification of genes implicated in variations of these trait s. Experiments were performed using Medicago truncatula as a model species for legumes with a view to transferring the information to the target crop species Pisum sativum.Legume seed size is determined by the embryo’s capacity to divide during embryogenesis and to accumulate reserves during seed filling. At early developmental stages, nutrient assimilation occurs predominantly in embryo-surrounding tissues: the endosperm and seed coat. This thesis project aims to evaluate the endosperm contribution to seed development in M. truncatula. We have shown several DOF (DNA-binding One Zinc Finger) genes to be expressed in this tissue. They belong to a large family of transcription factors implicated in numerous biological processes, but whose role remain to be elucidated. One of these genes, termed DASH for Dof Affecting Seed embryogenesis and Hormone metabolism, is expressed preferentially in the endosperm during embryogenesis. TILLING and TnT1 mutants isolated for this transcription factor are affected in seed development (abortion at 10 DAP). The cytology of development at early stages (6 to 10 DAP) revealed that the expression of this gene in the endosperm is required for the normal development of the embryo, demonstrating the role of the endosperm in the control of embryogenesis in legumes. A comparative transcriptomics study of dash vs wild-type pods allowed us to suggest hypothesis about the function of the DASH gene. Evidence for a deregulation of hormone metabolism, in particular for auxin, was obtained, and several potential target genes of this transcription factor were selected. A comparison of the transcriptome of the three tissues of the seed at 12 DAP was carried out for the reference wild-type line (Jemalong A17). This allowed the tissue localization of the target genes, to reveal metabolic pathways preferentially expressed in the endosperm, and to propose hypotheses about the role of this tissue during seed development
Wragg, Joseph. "Transcriptomic analysis of the tumour vasculature and its clinical relevance." Thesis, University of Birmingham, 2016. http://etheses.bham.ac.uk//id/eprint/6544/.
Full textMickus, Brian E. "Transcriptomic and proteomic analysis of lycopene-overproducing Escherichia coli strains." Thesis, Massachusetts Institute of Technology, 2009. http://hdl.handle.net/1721.1/51672.
Full textThis electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.
Includes bibliographical references.
Systems biology represents a powerful method to describe and manipulate phenotypes of interest by incorporating biological information from various levels of cellular organization. Such an approach is illustrated from a library of both rationally-directed and combinatorial gene knockout strains of E. coli recombinantly producing the small molecule lycopene. Global genomic and proteomic expression changes associated with increased lycopene production of mutant E. coli constructs were discovered using whole-genome DNA microarrays and a novel LC-MS technique, respectively. While most genes and proteins showed few expression changes, key differences were identified, including targets distal to the non-mevalonate and precursorsupplying pathways. Based upon the expression data sets, it was hypothesized that the following may be associated with lycopene overproduction: histidine biosynthesis (hisH); the quinone pool (wrbA); acid resistance (ydeO and gadE); the glyoxylate pathway (iclR); NADPH redox balance (pntB); growth rate reduction; and membrane composition. In the pre-engineered background strain, deleting pntB (~20-25%) and ydeO (~30%) each led to moderately increased production; overexpressing wrbA led to 50-100% more production at 8 hours and 5-15% more production at later time points; deleting iclR caused small production increases (~5-10%); and supplementing media with histidine caused the parental and mutant strains to have similar production.
(cont.) From these observations, several themes emerged. First, reduced cellular growth and energy conservation appear to be important tradeoffs for increasing lycopene production. Second, reducing overflow metabolism to acetate and corresponding acid stress as well as providing a gluconeogenic flux to increase lycopene precursors appeared beneficial. Next, NADPH availability and balance seemed to be critical production factors. The sS factor is known to affect lycopene accumulation, and it was observed to have far-reaching effects on both the transcriptomic and proteomic data sets. While expression changes were not strictly additive between the five mutant strains examined in comparison to the pre-engineered background strain, a number of these common factors appear to be responsible for the high lycopeneproduction phenotype. This work serves as an important example of incorporating multiple layers of complementary biological information to define a basis for an observed phenotype, demonstrating a powerful paradigm for realizing production increases via systems metabolic engineering.
by Brian E. Mickus.
Ph.D.
Xu, Huan. "Controlling false positive rate in network analysis of transcriptomic data." University of Cincinnati / OhioLINK, 2019. http://rave.ohiolink.edu/etdc/view?acc_num=ucin156267322069819.
Full textVermont, Sarah J. "Proteomic and transcriptomic analysis of the protozoan parasite Neospora caninum." Thesis, University of Liverpool, 2012. http://livrepository.liverpool.ac.uk/11637/.
Full textDAS, VIVEK. "LEVERAGING TRANSCRIPTOMIC ANALYSIS TO IDENTIFY TRANSCRIPTION FACTORS ORCHESTRATING CANCER PROGRESSION." Doctoral thesis, Università degli Studi di Milano, 2018. http://hdl.handle.net/2434/559711.
Full textHe, Liqun. "Analysis of kidney glomerular and microvascular transcriptomes /." Stockholm : Karolinska institutet, 2007. http://diss.kib.ki.se/2007/978-91-7357-300-9/.
Full textHernandez-Ferrer, Carles 1987. "Bioinformatic tools for exposome data analysis : application to human molecular signatures of ultraviolet light effects." Doctoral thesis, Universitat Pompeu Fabra, 2017. http://hdl.handle.net/10803/572046.
Full textMost common diseases are caused by a combination of genetic, environmental and lifestyle factors. These diseases are referred to as complex diseases. Examples of this type of diseases are obesity, asthma, hypertension or diabetes. Several empirical evidence suggest that exposures are necessary determinants of complex disease operating in a causal background of genetic diversity. Moreover, environmental factors have long been implicated as major contributors to the global disease burden. This leads to the formulation of the exposome, that contains any exposure to which an individual is subjected from conception to death. The study of the underlying mechanics that links the exposome with human health is an emerging research field with a strong potential to provide new insights into disease etiology. The first part of this thesis is focused on ultraviolet radiation (UVR) exposure. UVR exposure occurs from both natural and artificial sources. UVR includes three subtypes of radiation according to its wavelength (UVA 315-400 nm, UVB 315-295 nm, and UVC 295-200 nm). While the main natural source of UVR is the Sun, UVC radiation does not reach Earth's surface because of its absorption by the stratospheric ozone layer. Then, exposures to UVR typically consist of a mixture of UVA (95%) and UVB (5%). Effects of UVR on human can be both beneficial and detrimental, depending on the amount and form of UVR. Detrimental and acute effects of UVR include erythema, pigment darkening, delayed tanning and thickening of the epidermis. Repeated UVR-induced injury to the skin, may ultimately predispose one to the chronic effects photoaging, immunosuppression, and photocarcinogenesis. The beneficial effect of UVR is the cutaneous synthesis of vitamin D. Vitamin D is necessary to maintain physiologic calcium and phosphorous for normal bone mineralization and to prevent rickets, osteomalacia, and osteoporosis. But the exposome paradigm is to work with multiple exposures at a time and with one or more health outcomes rather focus in a single exposures analysis. This approach tends to be a more accurate snapshot of the reality that we live in complex environments. Then, the second part is focused on the tools to explore how to characterize and analyze the exposome and how to test its effects in multiple intermediate biological layers to provide insights into the underlying molecular mechanisms linking environmental exposures to health outcomes.
Agaton, Charlotta. "Transcriptome and Proteome Analysis using Signature Tags." Doctoral thesis, KTH, Biotechnology, 2003. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-3678.
Full textWith the full sequence of the human genome now available, anexciting era in biomedical research has started. The sequenceprovides information about all our genes and greatly increasesthe scope to compare genetic activities in different cells, toanalyze genetic variation between individuals and betweendifferent species and, most importantly, to investigatesystematically the whole genome in a gene-by-gene manner, andthus increase our understanding of gene function.
This thesis describes studies in which developments weremade in several areas of functional genomics. Messenger RNAlevels were analyzed by the use of an amplification procedure,in which the 3´-ends of the transcripts were selected inorder to amplify the mRNA population in an unbiased fashion. Bysonicating cDNA originating from expressed mRNA, uniformlysized representatives of the transcripts,signaturetags, were obtained. The mRNA levels in the original mRNApopulation correlated well with the levels in the amplifiedmaterial, as verified by microarray analysis and realtimequantitative PCR. The expressed transcripts can be identifiedusing pyrosequencing, by comparing the obtained sequenceinformation from the signature tags to information contained invarious sequence databases. In one of the articles, the use ofpyrosequencing is illustrated by efforts to find genes involvedin the disease progression of atherosclerosis.
More challenging than the study of mRNA levels is to analyzewhen, where and how proteins fulfill their wide-ranging rolesin all the various cellular processes. Proteins are morecomplex biomolecules than mRNA, each having unique properties.Current techniques for studying proteins need much improvement,and are often limited to investigations of a specific portionof the proteome. One approach for studying the whole proteomeis to systematically generate reagents with specific affinityfor the proteins encoded by the genome, one by one. Theaffinity reagents can be used as flags for their targets,providing a flag-specific detection system, so that the targetproteins can be sub-cellularly localized in the majority ofhuman tissues in an array format. One of the articles includedin the thesis presents a pilot project for large-scale affinityreagent production. The aim was to provide a sound basis forwhole proteome studies, but as a pilot study this investigationwas limited to the proteins encoded by human chromosome 21. Allputative genes on the chromosome were subjected to antibodygeneration in a systematic manner. Small, uniform, and easilyproduced representative portions of the full-length proteinswere expressed. These were denotedProtein EpitopeSignature Tagsand were designed to be unique for theirfull-length counterparts. The antibodies were produced inrabbits and two of the articles in the thesis discuss differentapproaches for affinity purification of the antibodies toachieve the highest possible specificity towards the targets.The resultingmono-specific, but stillmulti-epitope, antibodies can be used for a widerange of additional biochemical studies, such as protein arrayand protein pull-out analyses.
Keywords:functional genomics, 3´-end signaturetags, pyrosequencing, amplification, PrEST, chromosome 21,polyclonal antibodies, dual expression, affinitypurification.
Moertel, Luke Paul Frank, and mobileluke@hotmail com /. Luke Moertel@qimr edu au. "Microarray Analysis of the Schistosoma japonicum Transcriptome." Central Queensland University. Chemical and Biomedical Sciences, 2007. http://library-resources.cqu.edu.au./thesis/adt-QCQU/public/adt-QCQU20070705.120939.
Full textKostadima, Myrto Areti. "Analysis of the haematopoietic transcriptome in development." Thesis, University of Cambridge, 2015. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.708506.
Full textVickovic, Sanja. "Transcriptome-wide analysis in cells and tissues." Doctoral thesis, KTH, Genteknologi, 2017. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-199447.
Full textQC 20170109
Lima, Bruna de Araujo 1985. "Análise dos mecanismos da atividade antimicrobiana da violaceína sobre Staphylococcus aureus = Analysis of antimicrobial activity mechanisms of violacein against Staphylococcus aureus." [s.n.], 2013. http://repositorio.unicamp.br/jspui/handle/REPOSIP/317022.
Full textTese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia
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Resumo: A violaceína é um pigmento violeta produzido por algumas espécies bacterianas de origem ambiental, tais como Chromobacterium violaceum e Janthinobacterium lividum. Esta molécula apresenta várias propriedades biológicas incluindo antibacteriana, antifúngica, antiviral, antiprotozoária e antitumoral, apesar de sua função exata na fisiologia dos micro-organismos que a produz, ainda é desconhecido. No presente trabalho, a atividade antimicrobiana da violaceína produzida comercialmente, o extrato semi purificado e nanopartículas de vanadato de prata foram avaliados contra espécies de bacterianas gram-positivas e gram-negativas. A violaceína exibiu efeito antimicrobiano contra Staphylococcus aureus resistente à meticilina (MRSA) e Enterococcus resistente à vancomicina (VRE), que são micro-organismos frequentemente relacionados com infecções adquiridas em hospitais. Os valores de MIC (concentração inibitória mínima) e MBC (concentração bactericida mínima) da violaceína produzida comercialmente foram de 0,625 ?M e 1,25 ?M respectivamente e, análise de curvas de crescimento e tempo-morte revelaram um efeito antibacteriano durante 12 horas contra MRSA. A microscopia eletrônica de transmissão mostrou os efeitos da violaceína com alterações morfológicas e ultra estruturais, incluindo alterações na parede celular e formação de septos de divisão anormais. Nos resultados obtidos das análises de proteômica e transcriptoma a violaceína afetou a expressão de várias classes funcionais de proteínas e genes em MRSA, incluindo processos biológicos em biossíntese da parede celular e divisão celular que corroboram as alterações ultra estruturais visualizadas. Em conclusão, a violaceína produzida comercialmente demonstrou atividade antimicrobiana para S. aureus MRSA e pela primeira vez, os efeitos da violaceína sobre o metabolismo de S. aureus foram descritos, indicando possíveis alvos e vias metabólicas afetadas por esta droga. No seu conjunto, estes dados indicam a violaceína como uma droga potencial para o tratamento de infecções provocadas por MRSA
Abstract: Violacein is a violet pigment produced by some bacterial species of environmental source, such as Chromobacterium violaceum and Janthinobacterium lividum. This molecule has numerous biological properties including antibacterial, antifungal, antiviral, antiprotozoal and antitumor activity, although the exact role in the physiology of producing microorganisms is still unknown. In this study, the antimicrobial activity of violacein produced commercially, semi purified extract and silver vanadate nanoparticles were evaluated against several species of gram-positive and gram-negative bacteria. Violacein exhibited antimicrobial activity against methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococcus (VRE), microorganisms that are often related to hospital-acquired infections. MIC (minimum inhibitory concentration) and MBC (minimum bactericidal concentration) values of violacein produced commercially were 1.25 ?M mM and 0.625 ?M respectively, and analysis of growth and time-kill curves showed an antibacterial effect against MRSA for 12 hours. The transmission electron microscopy showed the effects of violacein with morphological and ultra-structural changes, including changes in cell wall formation and abnormal division septum. The results obtained from the analysis of proteomic and transcriptomic revealed that violacein affects the expression of several functional classes of proteins and genes in MRSA, including biological processes in cell wall biosynthesis and cell division, supporting ultra-structural changes. In conclusion, violacein produced commercially demonstrated antimicrobial activity against S. aureus MRSA and the effects on the metabolism of S. aureus have been described, indicating possible targets and pathways affected by this drug. These data indicate violacein as a potential drug for the treatment of infections caused by MRSA
Doutorado
Microbiologia
Doutora em Genética e Biologia Molecular
Owen, Anne M. "Widescale analysis of transcriptomics data using cloud computing methods." Thesis, University of Essex, 2016. http://repository.essex.ac.uk/16125/.
Full textMartini, Paolo. "Dissecting the transcriptome complexity with bioinformatics tools." Doctoral thesis, Università degli studi di Padova, 2012. http://hdl.handle.net/11577/3422923.
Full textCon l’avvento degli approcci genomici la bioinformatica ha acquisito un importanza sempre maggiore nello studio della biologia. Infatti, gli approcci “omici” permettono di produrre un enorme quantitativo di dati che deve essere archiviato in corrette strutture (database). L’archiviazione del dato comporta la necessità di permettere l’accesso e la manipolazione dello stesso al fine di svolgere gli studi appropriati. Sono quindi richiesti strumenti appropriati che consentano l’ispezione e la manipolazione dei database fine di formulare delle ipotesi coerenti con la problematica biologica che si sta studiando. Il trascrittoma è definito come l’insieme delle molecole di RNA che sono prodotte da una cellula e rappresentano un passaggio necessario nel processo che dal gene porta alla produzione della proteina. Le molecole di RNA possono essere suddivise in due grandi gruppi: gli RNA codificanti o messaggeri e gli RNA non codificanti. Mentre la prima classe è stata oggetto di ampi studi negli ultimi decenni, gli RNA non codificanti sono stati scoperti solo di recente e associati a funzioni puramente regolative. La classe più importante coinvolta nel processo regolativo degli RNA messaggeri è quella dei micro RNA (miRNA) che sono stati oggetto di un studio intenso che li ha messi in relazione con lo sviluppo di patologie come il cancro in quanto coinvolti nella regolazione fine dell’espressione genica di oncogeni, oncosoppressori o geni del ciclo cellulare. In questa tesi presento una serie di soluzioni bioinformatiche mirate a fornire le strutture appropriate per condurre gli esperimenti e le analisi dei dati di trascrittomica. Nel corso del periodo di dottorato, ho sviluppato un metodo che consente l’integrazione dei livelli di espressione genica ottenuti da esperimenti di microarray con informazioni riguardanti la localizzazione degli stessi nei cromosomi o la loro organizzazione in processi biologici. Questo metodo è stato messo a punto e raffinato nel suo funzionamento usando due gruppi di dati disponibili nei database pubblici: il primo riguarda dati di espressione genica ottenuti da esperimenti di microarray su leucemia mieloide acuta; il secondo riguarda l’espressione genica di distrofie muscolari derivanti sempre da dati di microarray. I risultati di questo nuovo metodo si sono dimostrati molto promettenti, in particolare nell’applicazione della meta-analisi che consiste nell’integrare dati provenienti da differenti laboratori. Forte di questo primo risultato, ho applicato questo metodo di analisi anche all’ispezione dei processi sregolati nelle miopatie infiammatorie affiancando ai dati disponibili prodotti nel laboratorio di Genomica Funzionale diretto dal Prof. G. Lanfranchi quelli depositati nei database pubblici. La meta-analisi da me implementata ha permesso di studiare questa serie di dati sfruttando, per la prima volta, la localizzazione dei geni e raggruppandoli per la funzione permettendo di generare ipotesi sui meccanismi patologici. Grazie a questa tipologia di analisi ho ipotizzato il coinvolgimento nelle miopatie infiammatorie delle vie di segnale che fanno capo a JAK/STAT e agli interferoni. Le ipotesi generate analizzando i dati sono state confermate andando a validare i geni coinvolti nelle vie di segnale appena menzionate usando la qRT-PCR. Inoltre, usando approcci di proteomica, in collaborazione con la Prof. C. Gelfi (Università di Milano) e la tecnica ELISA, è stata anche validata la presenza delle proteine coinvolte in queste vie di segnale nei pazienti affetti da miopatie infiammatorie. Nella parte conclusiva del mio dottorato, mi sono occupato di completare ed estendere la conoscenza della fisiologia muscolare. Per far questo mi sono spostato sul maiale, un organismo modello molto importante per lo studio di patologie umane e per la produzione di componenti biologiche che possono essere utilizzate per sostituire quelle degradate nell’uomo (valvole aortiche per esempio). Usando il maiale ho sviluppato un sistema per integrare l’espressione dei miRNA e la regolazione che questi esercitano nei messaggeri target. Come prima cosa ho sviluppato le piattaforme di microarray per eseguire l’analisi dell’espressione genica di 14 tessuti di maiale. In particolare ho sviluppato due tipi di piattaforme per eseguire l’analisi dell’espressione dei trascritti e dei miRNA purificati dallo stesso campione. Con questi dati di espressione ho condotto analisi per delucidare alcuni aspetti inerenti la biogenesi dei miRNA. Infine, la completezza dei dati prodotti mi ha permesso di costruire delle reti di regolazione specifiche per ogni tessuto analizzato. Per confermare la validità del nostro approccio ho analizzato il grado di sovrapposizione tra le sequenze derivate dal nostro studio e le sequenze prodotte dai vari esperimenti di RNA-seq. Con questa analisi ho confermato la validità del mio approccio in quanto è stato rivelato una sovrapposizione importante tra le nostre sequenze e quelle derivate da RNA-seq
Akhbari, Pouria. "Analysis of cellular transcriptomic changes induced by Merkel cell polyomavirus miRNA." Thesis, University of Bradford, 2017. http://hdl.handle.net/10454/15902.
Full textBecht, Etienne. "Transcriptomic analysis of the immune microenvironment of non-hematopoietic human tumors." Thesis, Sorbonne Paris Cité, 2015. http://www.theses.fr/2015PA05T029/document.
Full textTumors grow within a complex microenvironment composed of immune cells, fibroblasts, endothelial cells and other non-malignant cells. The study of the composition of tumor microenvironments has led to classifications with prognostic and theranostic values, as well as the discovery of treatments modulating the composition and the functional orientation of the microenvironment. Concurrently, molecular classifications of tumors have proposed taxonomies within cancers that define groups of patients with different prognoses and are associated with response to treatments. Recent evidence suggest that the phenotype of the malignant cell is a critical determinant in the shaping of its microenvironment, suggesting potential correlations between immune and molecular classifications. The goal of this PhD project was therefore to analyze the microenvironment of molecularly-classified human tumors. Colorectal cancer represents a paradigm for tumor immunology, as it is the humancancer in which it was exemplified that an adaptive immune response can control tumor Growth and metastasis. Conversely, clear-cell renal cell carcinoma represents an exception in tumor immunology, as an extensive adaptive immune response is associated with more aggressive diseases. Molecular transcriptomic classifications were recently proposed for both of these apparently immunologically contrasted cancers. In this work, I propose a methodology that enables the characterization of the tumor microenvironment using transcriptomic data, and apply it to describe the immune contexture of molecular subgroups of colorectal and clear-cell renal cell carcinomas. These analyses argue in favor of the unification of molecular and immune classifications of human cancers, challenge our current views of the relationship between the composition of the tumor microenvironment and patient’s prognosis, and suggest immunotherapeutic approaches that could benefit subgroups of patients in these two cancers
Sears, Connor R. "Transcriptomic analysis of the effect of dark-rearing on Astyanax mexicanus." University of Cincinnati / OhioLINK, 2019. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1553613296760282.
Full textAlasvand, Zarasvand Azita. "Comparative Analysis of Zinc Oxide Nanoparticles Induced Transcriptomic Responses in Arabidopsis." Thesis, North Dakota State University, 2019. https://hdl.handle.net/10365/31694.
Full textSun, Mai. "Global analysis of mRNA metabolism by comparative dynamic transcriptome analysis." Diss., Ludwig-Maximilians-Universität München, 2013. http://nbn-resolving.de/urn:nbn:de:bvb:19-173316.
Full textFerreira, Natalia Cristina Verza. "Analise, classificação, anotação e perfil de expressão de fatores de transcrição no endosperma de milho (Zea mays L.)." [s.n.], 2006. http://repositorio.unicamp.br/jspui/handle/REPOSIP/317205.
Full textTese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia
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Resumo: O seqüenciamento de ESTs (etiquetas de seqüências expressas) e a sua organização em bancos de dados constituem poderosas ferramentas para identificar genes de interesse expressos em determinados tecidos e/ou tipos celulares. Neste trabalho criou-se um banco de seqüências expressas chamado MAIZESTdb, que contém ESTs de diversos tecidos de milho, porém enriquecido com seqüências provenientes do endosperma de milho em desenvolvimento. O MAIZESTdb contém 227.431 ESTs vindos de mais de 30 órgãos e tecidos de milho diferentes, 30.531 seqüenciados em nosso laboratório a partir de bibliotecas construídas com RNA mensageiro de endosperma. Estas seqüências representam uma grande contribuição na identificação de novos genes expressos no endosperma. A análise deste banco de ESTs possibilitou a identificação de 4.032 transcritos preferencialmente expressos no endosperma, e a sua anotação revelou uma ampla variedade de prováveis genes novos envolvidos no desenvolvimento e no metabolismo do endosperma. O banco MAIZESTdb foi utilizado neste trabalho para a identificação de fatores de transcrição (TFs) expressos no endosperma de milho, e, especialmente, na identificação de fatores preferencialmente expressos no endosperma, que podem desempenhar papéis regulatórios importantes durante a formação da semente. Foram identificados 1.233 TFs expressos em milho, 414 dos quais expressos no endosperma em desenvolvimento. Foram identificados ainda, através de análises in silico, 113 TFs preferencialmente expressos no endosperma, conjunto este que representa 9.2% dos TFs expressos identificados em milho, e que possivelmente contém reguladores importantes dos processos de especificação celular e desenvolvimento do endosperma de milho. Esta é a maior coleção de fatores de transcrição já descrita para este tecido, e representa uma fonte de dados importante para identificação de reguladores dos principais processos relacionados ao desenvolvimento do endosperma, como metabolismo de nitrogênio e carboidratos e controle da massa da semente. Uma das famílias mais representadas entre os TFs preferencialmente expressos no endosperma foi a família NAC de fatores de transcrição. Esta família apresentou 12 membros preferencialmente expressos no endosperma de milho. Um novo membro da família NAC, chamado de EPN-1 (Endosperm Specific NAM 1), teve seu perfil de expressão caracterizado. Sua expressão pode ser detectada desde os 5 DAPs, embora o pico de expressão ocorra entre 20 e 25 DAP, e ele apresenta expressão preferencial no endosperma. O promotor do gene EPN-1 foi clonado, seqüenciado e analisado quanto aos seus possíveis elementos CIS regulatórios; foram encontrados elementos conservados relacionados à endosperma-especificidade, elementos relacionados à regulação por ácido abscísico e giberelinas, e elementos conservados presentes nos promotores de a-amilases, indicando uma possível relação deste gene com o processo de transição entre a maturação e a germinação da semente. Ensaios de expressão transitória com o promotor do gene EPN-1 revelaram que sua expressão está dirigida à camada de aleurona do endosperma de milho, o que constitui mais uma evidência de sua possível função na regulação de genes relacionados aos processos de maturação e germinação da semente
Abstract: The sequencing of ESTs (expressed sequence tags) and its organization in databases constitute powerful tools to identify genes of interest in certain tissues and/or cell types. In this work we have created MAIZESTdb, a database of ESTs expressed in diverse maize tissues. The importance of this database, however, is that it is enriched with sequences from developing maize endosperm. The MAIZESTdb contains 227,431 ESTs coming from more than 30 different maize tissues and organs, 30,531 of which sequenced from endosperm cDNA libraries constructed in our laboratory. These sequences represent a great contribution for the identification of novel genes expressed in endosperm. The analysis of this ESTs database led to the identification of 4,032 transcripts preferentially expressed in the endosperm, and its annotation revealed a great variety of new genes involved in endosperm metabolism and development. The MAIZESTdb was then used to identify transcription factors (TFs) expressed in maize endosperm, and, mainly, in the identification of TFs preferentially expressed in the endosperm. We identified 1,233 TFs expressed in diverse maize tissues, 414 of which expressed in developing endosperm. We also identified, through in silico comparison of transcript abundance and library source, 113 TFs with preferential expression in endosperm, representing 9,2% of the TFs identified in this work. This dataset probably contains important regulators of cellular specification of the endosperm development. This is the biggest TFs collection reported for this tissue, and represents an important source of data for identification of regulators for main processes related to the endosperm development such as nitrogen and carbohydrate metabolism and control of seed mass. One of the most represented families among the TFs preferentially expressed in endosperm was the NAC family of transcription factors. This family presented 12 members with preferential expression in the endosperm. A new member of the NAC family, called EPN-1 (Endosperm Specific NAM 1), was characterized. Its expression
Doutorado
Genetica Vegetal e Melhoramento
Doutor em Genetica e Biologia Molecular
Ferreira, Susana Duarte Barros Lopes. "In silico analysis of regenerating spinal cord transcriptomes." Master's thesis, Universidade de Aveiro, 2016. http://hdl.handle.net/10773/19034.
Full textAs lesões na medula espinal são uma desordem neurológica comum com um impacto significativo na sociedade moderna do ponto de visto físico, psicosocial e socioeconómico. Apesar de vários vertebrados serem capazes de regenerar lesões do sistema nervoso central, nomeadamente da medula espinal (ex. Rã, Peixe-zebra, Salamandra), está bem estabelecido que os seres humanos, e outros mamíferos adultos, não o conseguem fazer. Como tal, em consequência de lesões traumáticas no cérebro ou medula espinal, há incapacidade dos axónios crescerem extensivamente no tecido lesado. No entanto, um estudo importante realizado no virar do século por Ramón y Cajal, comprovou que a incapacidade das fibras nervosas regenerarem “deriva de condições externas, da presença ou ausência de fatores auxiliares que são indispensáveis para o processo regenerativo”, trazendo assim esperança que a neuroregeneração possa ser alcançada por modulação de condições celulares e moleculares. Esta dissertação tem como objetivo adquirir uma melhor e mais extensa compreensão dos genes e processos fisiológicos que são cruciais durante a regeneração da medula espinal, usando estudos de expressão genómica de modelos regenerativos, tais como Xenopus laevis, Xenopus tropicalis e Danio rerio, estabelecendo-se simultaneamente um paralelismo com os respetivos ortólogos humanos com o objetivo de encontrar genes candidatos no genoma humano passíveis de serem modulados com vista a alterar o estatuto não-regenerativo dos mamíferos adultos.
Spinal cord injuries are a common neurologic disorder that have devastating impacts on modern society, be it from physical, psychosocial, or socioeconomic point of view. Although many small vertebrates are capable of regenerating lesions to the central nervous system, namely the spinal cord, (e.g. frog, zebrafish, salamander) it is well established that humans and other adult mammals cannot. As so, failure of axons to grow extensively through damaged central nervous system (CNS) tissues is a common consequence of injury to the brain and spinal cord on adult mammals. However, an important study made at the turn of the century by Ramón y Cajal, proved that the failure of central fibers to regrow “derives from external conditions, the presence or absence of auxiliary factors that are indispensable to the regenerative process”, thus bringing hope that neuroregeneration can be achieved by modulating cellular and molecular conditions. Through this dissertation, we aim to get a better understanding of the involvement of the genes and physiological processes that are crucial during regeneration of the spinal cord, using genome wide expression studies of regenerative models such as Xenopus laevis, Xenopus tropicalis, and Danio rerio, while drawing parallel to its human orthologues. Being our goal to find perfect gene candidates in the human genome that are predictably capable of being modulated so we can alter the non-regenerative status of the adult mammals.
Östman, Josephine. "The fertile ovary transcriptome and proteome." Thesis, Uppsala universitet, Institutionen för kvinnors och barns hälsa, 2021. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-447785.
Full textGräns, Hanna. "Transcriptome analysis of patients with chronic fatigue syndrome /." Stockholm, 2005. http://diss.kib.ki.se/2005/91-7140-448-1/.
Full textChappell, Lia Victoria Louise. "Novel approaches for transcriptome analysis in Plasmodium parasites." Thesis, University of Cambridge, 2014. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.648817.
Full textPascoal, Sónia Cristina Marques. "Nucella lapillus: imposex transcriptome analysis and phenotypic plasticity." Doctoral thesis, Universidade de Aveiro, 2011. http://hdl.handle.net/10773/4267.
Full textO conhecimento de mecanismos de genómica funcional tem sido maioritariamente adquirido pela utilização de organismos modelo que são mantidos em condições laboratoriais. Contudo, estes organismos não reflectem as respostas a alterações ambientais. Por outro lado, várias espécies, ecologicamente bem estudadas, reflectem bem as interacções entre genes e ambiente mas que, das quais não existem recursos genéticos disponíveis. O imposex, caracterizado pela superimposição de caracteres sexuais masculinos em fêmeas, é induzido pelo tributilestanho (TBT) e trifenilestanho (TPT) e representa um dos melhores exemplos de disrupção endócrina com causas antropogénicas no ambiente aquático. Com o intuito de elucidar as bases moleculares deste fenómeno, procedeu-se à combinação das metodologias de pirosequenciação (sequenciação 454 da Roche) e microarrays (Agilent 4*180K) de forma a contribuir para um melhor conhecimento desta interacção gene-ambiente no gastrópode Nucella lapillus, uma espécie sentinela para imposex. O trancriptoma de N. lapillus foi sequenciado, reconstruído e anotado e posteriormente utilizado para a produção de um “array” de nucleótidos. Este array foi então utilizado para explorar níveis de expressão génica em resposta à contaminação por TBT. Os resultados obtidos confirmaram as hipóteses anteriormente propostas (esteróidica, neuroendócrina, retinóica) e adicionalmente revelou a existência de potenciais novos mecanismos envolvidos no fenómeno imposex. Evidência para alvos moleculares de disrupção endócrina não relacionados com funções reprodutoras, tais como, sistema imunitário, apoptose e supressores de tumores, foram identificados. Apesar disso, tendo em conta a forte componente reprodutiva do imposex, esta componente funcional foi a mais explorada. Assim, factores de transcrição e receptores nucleares lipofílicos, funções mitocondriais e actividade de transporte celular envolvidos na diferenciação de géneros estão na base de potenciais novos mecanismos associados ao imposex em N. lapillus. Em particular, foi identificado como estando sobre-expresso, um possível homólogo do receptor nuclear “peroxisome proliferator-activated receptor gamma” (PPARγ), cuja função na indução de imposex foi confirmada experimentalmente in vivo após injecção dos animais com Rosiglitazone, um conhecido ligando de PPARγ em vertebrados. De uma forma geral, os resultados obtidos mostram que o fenómeno imposex é um mecanismo complexo, que possivelmente envolve a cascata de sinalização envolvendo o receptor retinoid X (RXR):PPARγ “heterodimer” que, até à data não foi descrito em invertebrados. Adicionalmente, os resultados obtidos apontam para alguma conservação de mecanismos de acção envolvidos na disrupção endócrina em invertebrados e vertebrados. Finalmente, a informação molecular produzida e as ferramentas moleculares desenvolvidas contribuem de forma significativa para um melhor conhecimento do fenómeno imposex e constituem importantes recursos para a continuação da investigação deste fenómeno e, adicionalmente, poderão vir a ser aplicadas no estudo de outras respostas a alterações ambientais usando N. lapillus como organismo modelo. Neste sentido, N. lapillus foi também utilizada para explorar a adaptação na morfologia da concha em resposta a alterações naturais induzidas por acção das ondas e pelo risco de predação por caranguejos. O contributo da componente genética, plástica e da sua interacção para a expressão fenotípica é crucial para compreender a evolução de caracteres adaptativos a ambientes heterogéneos. A contribuição destes factores na morfologia da concha de N. lapillus foi explorada recorrendo a transplantes recíprocos e experiências laboratoriais em ambiente comum (com e sem influência de predação) e complementada com análises genéticas, utilizando juvenis provenientes de locais representativos de costas expostas e abrigadas da acção das ondas. As populações estudadas são diferentes geneticamente mas possuem o mesmo cariótipo. Adicionalmente, análises morfométricas revelaram plasticidade da morfologia da concha em ambas as direcções dos transplantes recíprocos e também a retenção parcial, em ambiente comum, da forma da concha nos indivíduos da F2, indicando uma correlação positiva (co-gradiente) entre heritabilidade e plasticidade. A presença de estímulos de predação por caranguejos estimulou a produção de conchas com labros mais grossos, de forma mais evidente em animais recolhidos de costas expostas e também provocou alterações na forma da concha em animais desta proveniência. Estes dados sugerem contra-gradiente em alterações provocadas por predação na morfologia da concha, na produção de labros mais grossos e em níveis de crescimento. O estudo das interacções gene-ambiente descritas acima demonstram a actual possibilidade de produzir recursos e conhecimento genómico numa espécie bem caracterizada ecologicamente mas com limitada informação genómica. Estes recursos permitem um maior conhecimento biológico desta espécie e abrirão novas oportunidades de investigação, que até aqui seriam impossíveis de abordar.
Our understanding of functional genomic mechanisms is largely acquired from model organisms through laboratory conditions of exposure. Yet, these laboratory models typically have little environmental relevance. Conversely, there are numerous “ecological” model species that present important geneenvironment interactions, but lack genomic resources. Imposex, the superimposition of male sexual characteristics in females, is caused by tributyltin (TBT) and triphenyltin (TPT) and provides among the most widely cited ecological examples of anthropogenically-induced endocrine disruption in aquatic ecosystems. To further elucidate the functional genomic basis of imposex, combinations of 454 Roche pyrosequencing and microarray technologies (Agilent 4*180K) were employed to elucidate the nature and extent of gene-environment interactions in the prosobranch gastropod, Nucella lapillus, a recognized sentinel for TBT-induced imposex. Following transcriptome characterization (de novo sequencing, assembly and annotation), microarray fabrication and competitive hybridizations, differential gene expression analyses provided support for previously suggested hypotheses underpinning imposex (steroid, neuroendocrine, retinoid), but also revealed potential new mechanisms. Evidence for endocrine disruption (ED) targets such as the immune system, apoptosis and tumour suppressors other than reproduction-related functions were found; however, given the ED nature of imposex, primary focus was on gender-differentiation pathways. Among these, transcription factors and lipophilic nuclear receptors as transducers of TBT toxicity along with mitochondrial functions and deregulation in transport activity suggested new putative mechanisms for the TBT-induced imposex in N. lapillus. Particularly, up-regulation of a putative nuclear receptor peroxisome proliferator-activated receptor gamma (PPARγ) homolog was evident, and its role was further confirmed by inducing imposex in vivo using Rosiglizatone, a well-known vertebrate PPARγ ligand. Our analyses show that TBT-induced imposex is a complex mechanism, but is likely to act through the retinoid X receptor (RXR):PPARγ heterodimer signalling pathway, hitherto not described in invertebrates. Moreover, collectively, our findings support a commonality of signalling between invertebrate and vertebrate species that has previously been overlooked in the study of endocrine disruption. The genomic resources generated here largely contribute to the molecular understanding of imposex, yielding valuable insights for further examination of responses to TBT contamination exposure. Additionally, we anticipate that the new genomic resources described herein will contribute to the further exploration of adaptive responses of dogwhelks to environmental variation. N. lapillus was also used to explore adaptive shell shape morphology in response to natural variation in wave-action and crab predation. Knowledge of the contributions of genotype, plasticity and their interaction to phenotypic expression is crucial for understanding the evolution of adaptive character traits in heterogeneous environments. We assessed contributions of the above factors by reciprocal transplantation of snails between two shores differing in exposure to wave action and predation, and rearing snails of the same provenance in a laboratory common garden experiment with crab-predation odour, complemented by genetic analysis. The two target populations are genetically different but maintain the same karyotype. Truss-length and morphometric analyses revealed plasticity of shell shape in reciprocal transplants, but also the partial retention of parental shape by F2 snails in common garden controls, indicating co-gradient variation between heritable and plasticity components. Crab-predation odour influenced shell shape of snails from exposed-site origin and stimulated the production of thicker shell lips with greater response in snails of exposed-site ancestry. We interpret these data as countergradient variation on predator-induced changes in shell shape and increased thickening of the shell lip as well as on growth rates. The above exploration of gene-environment interactions demonstrates the feasibility, insights and novel opportunities that can now be addressed in a species that is well characterised ecologically, but hitherto constrained by the general lack of genomic tools and archived resources. Notably, a greater focus on detailed responses of a single species facilitates the comparative approach, as illustrated by the apparent commonality in regulation of endocrine disruption processes in invertebrates and vertebrates.
FCT; FSE - SFRH/BD/27711/2006
Rambani, Aditi. "Transcriptome and Methylation Analysis of Gossypium Petal Tissue." BYU ScholarsArchive, 2012. https://scholarsarchive.byu.edu/etd/3910.
Full textMok, Bobo. "Genomic and transcriptomic variation in blood stage Plasmodium falciparum /." Stockholm : Karolinska institutet, 2007. http://diss.kib.ki.se/2007/978-91-7357-291-0/.
Full textLim, Chee Yee. "Understanding transcriptional regulation through computational analysis of single-cell transcriptomics." Thesis, University of Cambridge, 2017. https://www.repository.cam.ac.uk/handle/1810/267786.
Full textAb-Ghaffer, Mohamad Bahagia. "Transcriptomics analysis of phloem-feeding insect resistance in rice germplasm." Thesis, University of Birmingham, 2012. http://etheses.bham.ac.uk//id/eprint/3403/.
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