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1
Fortino, Vittorio. "Sequence analysis in bioinformatics: methodological and practical aspects." Doctoral thesis, Universita degli studi di Salerno, 2013. http://hdl.handle.net/10556/985.
Full textAbstract:
2011 - 2012My PhD research activities has focused on the development of new computational methods for biological sequence analyses. To overcome an intrinsic problem to protein sequence analysis, whose aim was to infer homologies in large biological protein databases with short queries, I developed a statistical framework BLAST-based to detect distant homologies conserved in transmembrane domains of different bacterial membrane proteins. Using this framework, transmembrane protein domains of all Salmonella spp. have been screened and more than five thousands of significant homologies have been identified. My results show that the proposed framework detects distant homologies that, because of their conservation in distinct bacterial membrane proteins, could represent ancient signatures about the existence of primeval genetic elements (or mini-genes) coding for short polypeptides that formed, through a primitive assembly process, more complex genes. Further, my statistical framework lays the foundation for new bioinformatics tools to detect homologies domain-oriented, or in other words, the ability to find statistically significant homologies in specific target-domains. The second problem that I faced deals with the analysis of transcripts obtained with RNA-Seq data. I developed a novel computational method that combines transcript borders, obtained from mapped RNA-Seq reads, with sequence features based operon predictions to accurately infer operons in prokaryotic genomes. Since the transcriptome of an organism is dynamic and condition dependent, the RNA-Seq mapped reads are used to determine a set of confirmed or predicted operons and from it specific transcriptomic features are extracted and combined with standard genomic features to train and validate three operon classification models (Random Forests - RFs, Neural Networks – NNs, and Support Vector Machines - SVMs). These classifiers have been exploited to refine the operon map annotated by DOOR, one of the most used database of prokaryotic operons. This method proved that the integration of genomic and transcriptomic features improve the accuracy of operon predictions, and that it is possible to predict the existence of potential new operons. An inherent limitation of using RNA-Seq to improve operon structure predictions is that it can be not applied to genes not expressed under the condition studied. I evaluated my approach on different RNA-Seq based transcriptome profiles of Histophilus somni and Porphyromonas gingivalis. These transcriptome profiles were obtained using the standard RNA-Seq or the strand-specific RNA-Seq method. My experimental results demonstrate that the three classifiers achieved accurate operon maps including reliable predictions of new operons. [edited by author]
XI n.s.
2
Dimitrovska, Valentina Metodi <1978>. "Study of two novel streptococcus pneumoniae operons: pilus islet 2 and the lantibiotic operon." Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2010. http://amsdottorato.unibo.it/2615/1/Dimitrovska_Valentina_PhD_thesis.pdf.
Full textAbstract:
Analysis of publicly available genomes of Streptococcus pneumoniae has led to the
identification of a new genomic element resembling gram-positive pilus islets (PIs). Here, we
demonstrate that this genomic region, herein referred to as PI-2 (containing the genes pitA,
sipA, pitB, srtG1, and srtG2) codes for a novel functional pilus in pneumococcus. Therefore,
there are two pilus islets identified so far in this pathogen (PI-1 and PI-2). Polymerization of
the PI-2 pilus requires the backbone protein PitB as well as the sortase SrtG1 and the signal
peptidase-like protein SipA. PI-2 is associated with serotypes 1, 2, 7F, 19A, and 19F,
considered to be emerging in both industrialized and developing countries. Interestingly,
strains belonging to clonal complex 271 (CC271) contain both PI-1 and PI-2, as revealed by
genome analyses. In these strains both pili are surface exposed and independently assembled.
Furthermore, in vitro experiments provide evidence that the pilus encoded by PI-2 of S.
pneumoniae is involved in adherence. Thus, pneumococci encode at least two types of pili
that may play a role in the initial host cell contact to the respiratory tract. In addition, the
pilus proteins are potential antigens for inclusion in a new generation of pneumococcal
vaccines.
Adherence by pili could represent important factor in bacterial community formation, since it
has been demonstrated that bacterial community formation plays an important role in
pneumococcal otitis media. In vitro quantification of bacterial community formation by S.
pneumoniae was performed in order to investigate the possible role of pneumococcal pili to
form communities. By using different growth media we were not able to see clear association
between pili and community formation. But our findings revealed that strains belonging to
MLST clonal complex CC15 efficiently form bacterial communities in vitro in a glucose
dependent manner.
We compared the genome of forty-four pneumococcal isolates discovering four open reading
frames specifically associated with CC15. These four genes are annotated as members of an
operon responsible for the biosynthesis of a putative lanctibiotic peptide, described to be
involved in bacterial community formation. Our experiments show that the lanctibiotic
operon deletion affects glucose mediated community formation in CC 15 strain INV200.
Moreover, since glucose consumption during bacterial growth produce an acidic
environment, we tested bacterial community formation at different pH and we showed that
the lanctibiotic operon deletion affected pH mediated community formation in CC 15 strain
INV200. In conclusion, these data demonstrate that the putative lanctibiotic operon is
associated with pneumococcal CC 15 strains in vitro bacterial community formation.
3
Dimitrovska, Valentina Metodi <1978>. "Study of two novel streptococcus pneumoniae operons: pilus islet 2 and the lantibiotic operon." Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2010. http://amsdottorato.unibo.it/2615/.
Full textAbstract:
Analysis of publicly available genomes of Streptococcus pneumoniae has led to the
identification of a new genomic element resembling gram-positive pilus islets (PIs). Here, we
demonstrate that this genomic region, herein referred to as PI-2 (containing the genes pitA,
sipA, pitB, srtG1, and srtG2) codes for a novel functional pilus in pneumococcus. Therefore,
there are two pilus islets identified so far in this pathogen (PI-1 and PI-2). Polymerization of
the PI-2 pilus requires the backbone protein PitB as well as the sortase SrtG1 and the signal
peptidase-like protein SipA. PI-2 is associated with serotypes 1, 2, 7F, 19A, and 19F,
considered to be emerging in both industrialized and developing countries. Interestingly,
strains belonging to clonal complex 271 (CC271) contain both PI-1 and PI-2, as revealed by
genome analyses. In these strains both pili are surface exposed and independently assembled.
Furthermore, in vitro experiments provide evidence that the pilus encoded by PI-2 of S.
pneumoniae is involved in adherence. Thus, pneumococci encode at least two types of pili
that may play a role in the initial host cell contact to the respiratory tract. In addition, the
pilus proteins are potential antigens for inclusion in a new generation of pneumococcal
vaccines.
Adherence by pili could represent important factor in bacterial community formation, since it
has been demonstrated that bacterial community formation plays an important role in
pneumococcal otitis media. In vitro quantification of bacterial community formation by S.
pneumoniae was performed in order to investigate the possible role of pneumococcal pili to
form communities. By using different growth media we were not able to see clear association
between pili and community formation. But our findings revealed that strains belonging to
MLST clonal complex CC15 efficiently form bacterial communities in vitro in a glucose
dependent manner.
We compared the genome of forty-four pneumococcal isolates discovering four open reading
frames specifically associated with CC15. These four genes are annotated as members of an
operon responsible for the biosynthesis of a putative lanctibiotic peptide, described to be
involved in bacterial community formation. Our experiments show that the lanctibiotic
operon deletion affects glucose mediated community formation in CC 15 strain INV200.
Moreover, since glucose consumption during bacterial growth produce an acidic
environment, we tested bacterial community formation at different pH and we showed that
the lanctibiotic operon deletion affected pH mediated community formation in CC 15 strain
INV200. In conclusion, these data demonstrate that the putative lanctibiotic operon is
associated with pneumococcal CC 15 strains in vitro bacterial community formation.
4
Carmichael, C. S. J. "Decomposition of the lactose operon." Thesis, University of Edinburgh, 1992. http://hdl.handle.net/1842/13315.
Full textAbstract:
The immediate aims of the project, as set out in the introduction, were 1) to separate the lacZ and lacY genes of the lactose operon such that they could be controlled/induced independently 2) to maintain the expression construct in the E.coli chromosome. The lacY gene was subcloned into plasmid PBN372 downstream of the S.marsescens trp promoter. The flanking E.coli trp genes were exploited to integrate the construct into the E.coli chromosome at the trpB locus via homologous recombination. Homologous recombinants should be trp{-}. Two approaches were employed to achieve integration: 1) transformation of a recD strain (which was also a lacY deletion) 2) transduction with phage lambda. The first method was unsuccessful, only spontaneous trp- mutations were isolated. The second method yielded several integrants, one of which was used in subsequent growth experiments. Since the constructed strain was rendered trp-, the internal tryptophan concentration could be influenced by the concentration of tryptophan in the medium and the level of induction could be set by the addition of differing amounts of the antirepressor, IAA. The growth rate of the constructed strain in minimal lactose media was comparable with that of wild type E.coli. The permease activity of the constructed strain was seen to vary when assayed in the presence of varying amounts of IAA. The expression of permease was also demonstrated to be independent of galactosidase activity. The constructed strain therefore met all the initial requirements for the experimental system set out in this thesis. Difficulties were encountered during the analysis of permease induction in batch culture. This was due to the competition between antirepressor (IAA) and corepressor (tryptophan). These difficulties would have been minimal had the analysis been carried out in chemostat experiments. It would then have been possible to maintain a constant, low level of tryptophan throughout the experiment. In batch culture, the tryptophan level is constantly changing, initially being relatively high and becoming depleted as the experiment progresses.
5
Upadhyay, Manisha. "The flp operons of Lactococcus lactis." Thesis, University of Sheffield, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.274956.
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6
Flick, Jeremy Joseph. "Modus Operandi." College Park, Md.: University of Maryland, 2009. http://hdl.handle.net/1903/9372.
Full textAbstract:
Thesis (M.F.A.) -- University of Maryland, College Park, 2009.Thesis research directed by: Dept. of Art. Title from t.p. of PDF. Includes bibliographical references. Published by UMI Dissertation Services, Ann Arbor, Mich. Also available in paper.
7
Patterson, Kathryn Grace. "Gene regulation in the lac operon." Thesis, Montana State University, 2009. http://etd.lib.montana.edu/etd/2009/patterson/PattersonK0809.pdf.
Full textAbstract:
The lac operon, a jointly controlled series of genes in the bacteria E. coli, has been studied extensively since the 1940's. The lac operon genes are transcribed and then translated into proteins necessary for transport and digestion of lactose. The operon is activated in the presence of lactose after glucose, the preferred carbon source, has been expended. In this thesis, we introduce a biophysical model using the Shea-Ackers framework for modeling promoter dynamics. The model spans two scales: the inputs are biophysical parameters of molecular interactions and the result is a level of gene expression - a macroscopic behavior of the cell. We include all experimentally suggested control mechanisms into the model, even though the experimental evidence is stronger for some of these mechanisms than others. We compare our model to experimental data and explore the individual contribution of the proposed mechanisms by removing them one by one and testing the reduced model's fit to the data. Finally, we find a minimal model which faithfully represents the available data, yet includes only the minimal number of control mechanisms.
8
Uhlmann, Mareike. "Mutagenese des nuo-Operons von Escherichia coli." [S.l.] : [s.n.], 2005. http://deposit.ddb.de/cgi-bin/dokserv?idn=975459414.
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9
Curtis, Mark Douglas. "An investigation of the E9 colicin 'operon'." Thesis, University of East Anglia, 1991. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.304985.
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10
Pandey, Sundar. "Novel Role of Pseudomonas Aeruginosa LptD Operon." FIU Digital Commons, 2018. https://digitalcommons.fiu.edu/etd/3734.
Full textAbstract:
Pseudomonas aeruginosais an opportunistic pathogen that infects cystic fibrosis (CF) patients contributing to their high morbidity and mortality. P. aeruginosaundergoes a phenotypic conversion in the CF lung, from nonmucoid to mucoid, by constitutively producing a polysaccharide called alginate. These mucoid strains often revert to nonmucoid in vitrodue to second-site suppressor mutations. We hypothesized that mapping these mutations would lead to the identification of novel genes involved in alginate production. In a previous study, a mucoid strain, PDO300 (PAOmucA22), was used to isolate suppressors of alginate phenotype (sap). One of the uncharacterized nonmucoid revertants, sap27, is the subject of this study. The mucoid phenotype in sap27was restored by pMO012217 from a minimal tiling path cosmid library. The cosmid pMO012217 harbors 18 P. aeruginosaopen reading frames (ORF). The cosmid was mutagenized with a transposon to map the contributing gene. It was mapped tolptD(PA0595) encoding lipopolysaccharide transport protein. E. coliLptD transports lipopolysaccharide to the outer leaflet of the outer membrane. The Alg+phenotype was restored upon complementation with P. aeruginosa lptDalone, suggesting that sap27likely harbor a chromosomal mutation inlptD. Sequencing analysis of sap27showed the presence of a mutation not in lptDbut in algO, which encodes a periplasmic protease protein. This suggests LptD is able to bypass analgO mutation by positively regulating alginate production. The lptD is a part of a three-gene operon lptD-surA-pdxA. SurA is an essential protein for survival in starvation and a major chaperone protein for all outer membrane proteins and PdxA is a NAD-dependent dehydrogenase and is involved in the vitamin B6biosynthetic pathway. Pyridoxal 5’-phosphate (PLP) is the active form of vitamin B6.P. aeruginosagrown in a media supplemented with PLP increased production of pyocyanin, a virulence factor. The PLP and aromatic amino acids are synthesized from a common precursor chorismic acid. We demonstrated an increase in pyocyanin production when the bacteria were cultured supplemented by the aromatic amino acids phenylalanine. We concluded that the lptDoperon plays a role in the P. aeruginosavirulence by regulating alginate and pyocyanin production.
11
Warren, Anna Victoria. "Analysis of the chemosensory operons of Rhodobacter sphaeroides." Thesis, University of Oxford, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.275380.
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12
Khalil, Meriam, and Isabella Faruque. "Operans tillgänglighet för allmänheten." Thesis, Södertörns högskola, Institutionen för samhällsvetenskaper, 2013. http://urn.kb.se/resolve?urn=urn:nbn:se:sh:diva-19196.
Full textAbstract:
Bakgrund: Eftersom att operakonsten är präglad av en viss grupp människor kommer denna uppsats att grunda sig på analys kring hur Sveriges operahus marknadsförs samt vilka kundgrupper de lyckas nå ut till. Syfte: Syftet med studien är att analysera och kartlägga operakonst. Genom Pierre Bourdieus centrala teorier om de olika kapitalen ska vi förklara varför konsumentföreteelser är kopplade till vissa etablerade grupper. Metod: Studien innefattar både kvalitativ och kvantitativ undersökning. Den kvalitativa undersökningen består av sju intervjuer och den kvantitativa undersökningen består av en enkätundersökning som består av 100 respondenter. För att kunna besvara syftet och våra frågeställningar kommer befintliga teorier att användas. Teorier: Pierre Bourdieus centrala begrepp, GAP-modellen och POP- & POD. Slutsats: Operahusen når inte ut till ett bredare markndassegment då vanföreställningar existerar om att operakonsten är urgammal samt för främmande. Detta avskräcker potentiella konsumenter att besöka operan. Dessutom krävs det mer pengar till marknadsföring för att nå de potentiella kunderna.
13
Bishop, Michele R. "Resurgence of operant variability /." abstract and full text PDF (UNR users only), 2008. http://0-gateway.proquest.com.innopac.library.unr.edu/openurl?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&res_dat=xri:pqdiss&rft_dat=xri:pqdiss:3329717.
Full textAbstract:
Thesis (Ph. D.)--University of Nevada, Reno, 2008."August, 2008." Includes bibliographical references (leaves 92-100). Library also has microfilm. Ann Arbor, Mich. : ProQuest Information and Learning Company, [2009]. 1 microfilm reel ; 35 mm. Online version available on the World Wide Web.
14
Balfagón, Martín Aranzazu. "lux operon transformation of plastids in higher plants." Doctoral thesis, Universitat Internacional de Catalunya, 2013. http://hdl.handle.net/10803/125374.
Full textAbstract:
Este trabajo es parte de la investigación del Grupo de investigación de Arquitecturas Genéticas (2009 SGR 862). El objetivo global del grupo es investigar sobre las nuevas formas arquitectónicas y materiales para tratar de aportar soluciones eco-sostenibles de algunas de las necesidades humanas más importantes, como la luz, el calor y el hábitat, para reducir, al mismo tiempo, el impacto humano sobre el medio ambiente natural.
Esta investigación cubre el área de la biotecnología y presenta un primer estudio de la expresión del operón lux de origen bacteriano en los cloroplastos de las plantas superiores, con el fin de hacerlos capaces de emitir luz visible de manera autónoma, sin necesidad de ningún estímulos externos o suministro de la energía.
En este mismo campo se obtiene un sistema adecuado para expresar operón lux de cloroplasto en plantas superiores y un protocolo sencillo para obtener la organogénesis de las hojas de algunas plantas ornamentales con el fin de obtener nuevos objetivos de la planta a ser transformada.
15
Davis, Kevin. "An analysis of models of the tryptophan operon." Thesis, McGill University, 2008. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=19269.
Full textAbstract:
Though the tryptophan operon has received a fair amount of experimental study over recent decades, modeling e?orts have been relatively few and disparate in some of their conclusions regarding the behavior of the operon. We consider a selection of existing models of the tryptophan operon and analyze them from the standpoints of stability, response to periodic signals in the biochemistry, and existence of attracting invariant manifolds in the model state space. We ?nd that the stability properties of these models may depend greatly upon small changes in parameters that are in keeping with updated experimental data. Further, we show the ability of the tryptophan operon to act as a classical band-pass ?lter to periodic ?uctuations ostensibly caused by the periodic nature of the cell cycle. Finally, a functional iteration technique for the approximate computation of attracting invariant manifolds is presented and the manifold for one of the models is computed.Bien que l'opéron de tryptophane ait fait l'objet d'un nombre d'essais expérimentaux considérables dans les dernières décennies, les e?orts dans la modélisation ont été rel- ativement peu et disparates quant à leurs conclusions concernant le comportement de l'opéron. Nous considérons un choix de modèles existants de l'opéron de tryptophane et les analysons des points de vue de leur stabilité, de leur réponse aux signaux périodiques en biochimie, et de l'existence d'attractions de variétés invariantes dans l'espace d'états du modèle. Nous constatons que les propriétés de stabilité de ces modèles peuvent dépendre considérablement de petits changements des paramètres qui sont en accord avec des données expérimentales mises à jour. De plus, nous montrons la capacité de l'opéron de tryptophane à agir comme ?ltre passe-bande classique aux ?uctuations périodiques en apparence provoquées par la nature périodique du cycle cellulaire. En conclusion, une technique fonctionnelle d'itération pour le calcul approximatif de l'attraction de variété invariante est présentée et la variété pour un des modèles est calculée. fr
16
Clarke, Simon Richard. "Regulation of the bla operon in Staphylococcus aureus." Thesis, University of Oxford, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.326077.
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Min, Kyung-Tai. "Regulation of the spoIIA operon in Bacillus subtilis." Thesis, University of Oxford, 1993. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.333440.
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Low, Yuen Li. "Metal regulation of the E. faecalis efaCBA operon." Thesis, University of Bath, 2002. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.760823.
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Aguena, Meire. "Análise transcricional do operon pst de Escherichia coli." Universidade de São Paulo, 2007. http://www.teses.usp.br/teses/disponiveis/42/42132/tde-30012008-094907/.
Full textAbstract:
O operon pst de Escherichia coli é formado pelos genes pstS, pstC, pstA, pstB e phoU. Os quatro primeiros genes codificam proteínas que compõem um sistema de transporte do tipo ABC denominado Pst. O sistema Pst, junto com a proteína PhoU participa da repressão dos genes do regulon PHO. A transcrição dos genes do operon pst é induzida pela carência de fosfato inorgânico (Pi). Neste trabalho, o padrão de transcrição do operon pst foi analisado. A existência de um transcrito primário instável foi comprovada através de uma nova técnica de RT-PCR. O papel da RNase E na degradação do mRNA de pst foi demonstrado. A análise das seqüências intergênicas do operon revelou a importância da seqüência REP (Repetitive Extragenic Palindrome) localizada na região intergênica entre pstS e pstC na estabilização da mensagem de pstS. As seqüências localizadas a 5\' dos genes pstC, pstB e phoU também foram analisadas e demonstraram uma atividade promotora fraca, que resulta na síntese de transcritos dos genes distais de pst.The pst operon of Escherichia coli consists of the genes pstS, pstC, pstA, pstB and phoU. The four proximal genes of the operon encode the proteins of the ABC-type Pi phosphate (Pi) transporter Pst.The Pst system, together with the PhoU protein, also acts as a negative regulator of the PHO regulon. Transcription of the pst genes is induced by Pi starvation. The present study describes the transcription pattern of the pst operon. The existence of an unstable primary transcript was confirmed by using an improved RT-PCR protocol. The role of RNase E in pst transcript decay was demonstrated.Analysis of the operon intergenic regions revealed the role of a REP sequence (Repetitive Extragenic Palindrome) located between pstS and pstC in pst mRNA stability. The regions upstream of pstC, pstB and phoU displayed promoter activity. Transcription from these internal promoters resulted in a small amount of mRNAs corresponding to the pst distal genes.
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Sarkar, Debjani. "Spliced leader trans-splicing and operons in Dorylaimida (Nematoda)." Thesis, University of Aberdeen, 2014. http://digitool.abdn.ac.uk:80/webclient/DeliveryManager?pid=214855.
Full textAbstract:
Nematodes are an important animal group that have shown remarkable adaptability, leading to their ubiquitous global distribution. Many are also major parasites of humans, plants and animals; therefore an understanding of nematode biology is of great importance both medically and agriculturally. The phylum is divided into three main taxa: the Chromadoria; the Dorylaimia and the Enoplia. Most studies on nematode biology tend to focus on the nematode model, Caenorhabditis elegans or other nematodes within the Chromadorea (clades III, IV and V). To date the Dorylaimia and the Enoplia (nematodes that occupy clades I and II respectively) have been poorly studied, but recent work on the Dorylaim parasite, Trichinella spiralis, is providing valuable data to help understand the evolution of the Nematoda. The recent publication of the T. spiralis genome has revealed nematode-specific features and has allowed for in depth comparative genomic analyses. These analyses have revealed that in some respects – such as highly conserved signalling pathways, T. spiralis seems to more closely resemble the arthropod outgroup than it does to other nematodes within the Chromadorea. I decided to see whether attributes seen in T. spiralis were conserved in other Dorylaimian nematodes, and extended this study to include two additional Dorylaim nematodes, the free-living Prionchulus punctatus and the parasitic Trichuris muris. T. muris was chosen as it shares a relatively recent ancestor with the lineage leading to the Trichinellidae, whereas P. punctatus, whilst still a Dorylaimian, exists outside of this group. We used transcriptome data from P. punctatus, to further our analysis and characterisation of the Wnt, Hedgehog and TGF-β signalling pathways and show that like T. spiralis, this nematode also has a much less derived set of signaling pathways compared to C. elegans and other members of the Chromadoria. Spliced Leader (SL) trans-splicing is a phenomenon that occurs throughout the nematode phylum; as such it is a trait that was most likely present in the ancestral nematode. Nematodes in the Chromadorea have been shown to use two types of SLs, first characterized in C. elegans; SL1 and SL2. Previous studies have shown that the Dorylaim T. spiralis uses a range of highly polymorphic SL sequences that have only limited similarity to C. elegans SL1 and SL2. In contrast, initial searches for SLs in P. punctatus have shown that it possesses clear SL2-like sequences. I IV investigated the nature of SL trans-splicing within the Dorylaimia. In this study I identified the SL sequences present in T. muris and showed that they are similar to the SLs found in P. punctatus, which is unexpected given that T. muris is more closely related to T. spiralis. This indicates that the complement of SLs found in T. spiralis is derived relative to other nematodes. In C. elegans, it was found that SL trans-splicing is involved in the processing of polycistronic transcription units known as operons, into monocistronic mRNAs. To date, operons have only been seen within Chromadorean nematodes, but the presence of SL trans-splicing in the Dorylaimia implies that they may be present in these nematodes also. This thesis presents, for the first time, evidence for the presence of operons in the two Dorylaimian nematodes; T. spiralis and T. muris. We show that operons are likely to be an ancient feature of the Nematoda, with evidence for a conserved operon that spans throughout different nematode species within the phylum.
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Vichivanives, Padungsri. "Transcriptional regulation of the Rhodobacter Capsulatus CO? fixation operons /." The Ohio State University, 2001. http://rave.ohiolink.edu/etdc/view?acc_num=osu1488205318510482.
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Nold, Niklas. "Untersuchungen zur Regulation des sol-Operons in Clostridium acetobutylicum." [S.l. : s.n.], 2008. http://nbn-resolving.de/urn:nbn:de:bsz:289-vts-65443.
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Dole, Sudhanshu. "Multiple level regulation of the Escherichia coli bgl operon." [S.l. : s.n.], 2001. http://deposit.ddb.de/cgi-bin/dokserv?idn=963645978.
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Stephen, Robert John. "A study of the proU operon of Salmonella typhimurium." Thesis, University of Oxford, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.318587.
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Lack, Nathan. "Characterization of an operon involved in mycobacterial cholesterol metabolism." Thesis, University of Oxford, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.509971.
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Massam-Wu, Teresa. "Characterisation of the Vibrio cholerae antibiotic resistance var operon." Thesis, Durham University, 2007. http://etheses.dur.ac.uk/2562/.
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The discovery and use of antibiotics in the chemotherapy of bacterial infections has revolutionised medicine as it is today. Unfortunately, the progressive use of antibiotics has promoted the evolution of bacterial defences against these mediators and thus the emergence of antibiotic resistance. Multidrug resistance (MDR) in bacterial pathogens has grown with such rapid progression that it now threatens to compromise the effective chemotherapy of a plethora of diseases. This thesis aspires to elucidate the molecular resistance mechanisms adopted by these bacteria, in order to expand our knowledge and to assist in the development of new therapeutic approaches to circumvent these mechanisms. On this basis, this thesis presents insights into a novel Vibrio cholerae antibiotic resistance, var, operon that encodes a metallo- β -lactamase (Mßl), VarG, and a tripartite ATP-binding cassette-type (ABC-type) transport system, VarACDEF that has substrate specificities for antimicrobial peptides and macrolide antibiotics. Mßls are fast emerging as a primary resistance mechanism, possibly as a consequence of the introduction of newer ß-lactam antibiotics such as the carbapenems in response to increasing Gram-negative bacterial resistance. Fascinatingly, the ABC transporter, through secondary structure predictions, has been envisaged to adopt a tripartite structure similar to the MDR transporter, AcrAB-TolC, from the resistance nodulation and cell division (RND) family. The structural characterisation of this system would be the first such tripartite system to be elucidated and may bring new insights into how Gram-negative bacteria may have evolved to tackle the issue that threatens its existence. The resistance mechanisms in the var Operon are believed to be under the control of a LysR-type transcriptional regulatory protein (LTTR), VarR. LTTR proteins form one of the largest transcriptional regulatory families with extremely diverse functions ranging from amino acid biosynthesis to CO(_2) fixation. VarR binds to three distinct promoter regions, varRG, varGA and varBC located upstream and adjacent to VarG, VarA an AcrA-like membrane fusion protein and VarC a TolC-like outer membrane protein, respectively. VarR has also been shown to act as a repressor at the varRG promoter region in the absence of its substrate. Interestingly, the mechanism of regulation by VarR is strikingly similar to the well documented LTTR, AmpR and serine ß-lactamase AmpC system that are found in many pathogenic bacteria. It could be that V. cholerae has evolved from this regular system and developed a ß-lactamase that would prove more beneficial in light of current selective pressures. Contrary to LTTRs being notoriously recalcitrant to purification due to their low solubility, this thesis reports the successful purification and crystallisation of full-length VarR in the presence and absence of its cognate promoter DNA. Elucidating the structural characteristics of VarR would be the first such regulator associated with MDR in the LTTR family. This would advance the knowledge on the only currently existing full-length crystal structure of a LTTR, CbnR, and will provide further insights into how structural conformations may lead to dissociation from the promoter and induction of gene expression. Understanding the mechanism by which VarR induces expression of these resistance mechanisms is paramount for future strategies to prevent the emergence of MDR microorganisms. Although these mechanisms of MDR maybe elucidated in V. cholerae, the evolutionary relatedness and conservation of structure and function in all families will enable this information to be related to similar systems in alternative bacterial species.
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Matos, Jose Antonio Dos Santos Pereira De. "Studies on the operon of urease of Pseudomonas aeruginosa." Thesis, King's College London (University of London), 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.272115.
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Davies, Ian J. "Transcriptional regulation of the qua operon of Escherichia coli." Thesis, University of Southampton, 1989. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.314696.
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Pickett, M. A. "Regulatory aspects of the gua operon of Escherichia coli." Thesis, University of Southampton, 1987. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.381272.
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Webb, Isabel. "Characterisation of the fixABCX operon in symbiotic nitrogen fixation." Thesis, University of East Anglia, 2016. https://ueaeprints.uea.ac.uk/63286/.
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The fixABCX genes are essential for nitrogen fixation in R. leguminosarum bv. viciae 3841. Comparison of FixABCX to homologous proteins across the Kingdoms of Life suggests a role in electron transport to nitrogenase, which requires eight electrons per molecule of dinitrogen fixed. Mutation of this operon leads to bacteroids unable to fix nitrogen in symbiosis with P. sativum (pea). Electron microscopy revealed a drastically altered bacteroid morphology in fixAB mutants, revealing insights into the developmental response of both plant and bacteria to a lack of nitrogen fixation. Observations from electron microscopy were coupled to data obtained using single-cell Raman microscopy in order to understand metabolite production in nitrogen fixing and non-fixing bacteroids. The promoter controlling fixA has been characterised to a minimal region consisting of binding sites for NifA, the general transcriptional activator of nitrogen fixation, and RpoN (σ54), its cognate sigma factor. Mutation analysis reveals that fixABCX is part of a larger operon including the nifA gene. Promoter analysis of the downstream genes has identified a set of basal promoters found within the fixCX region, which control expression of the nifA gene. Control of nitrogen fixation occurs at the post-transcriptional level, whereby NifA is able to activate nitrogen fixation genes, including the fixABCXnifA operon, autoregulating its own expression under nitrogen-fixing conditions. Pull-down assays have revealed protein-protein interactions between FixAB and nitrogenase, as well as an interaction with both pyruvate dehydrogenase and 2-oxoglutarate dehydrogenase. FixAB may interact with these dehydrogenases and via electron bifurcation couple the exergonic reduction of the quinone pool to the endergonic reduction of ferredoxin and subsequently nitrogenase. Furthermore, FixAB, nitrogenase and pyruvate dehydrogenase and 2-oxoglutarate dehydrogenase may form a supra-molecular complex within nitrogen fixing bacteroids.
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Vail, Kimberly Gail. "Musical Priming and Operant Selection." Thesis, University of North Texas, 2017. https://digital.library.unt.edu/ark:/67531/metadc1062812/.
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Language is a cultural construct, and the relationship between words is taught. Priming research has long investigated the relationship between related and unrelated words. Similar research has been seen in music relationships, but most of these investigate harmonic relations despite the melodic relationship being the one listeners are mostly likely to describe. Further, these studies typically measure existing relationships and do not attempt to teach a new relationship, nothing that most adults are experienced musical listeners. This study seeks to establish a new melodic relationship (the enigmatic Scale) in addition to a familiar one (the major Scale) while measuring response time to the musical sequences. A baseline was conducted in which participants listened to a musical sequence and selected via response box if the final note is consonant (major Scale) or dissonant (enigmatic Scale). Following baseline a training section occurred in which participants heard sequences ranging from 2-7 notes and were provided feedback for correct and incorrect responses. Following completion of the training participants completed a post-test identical to baseline. Behavioral results are discussed in relation to Palmer's (2009) concept of the repertoire.
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Kaluza, Klaus. "Strukturanalyse des NIFDK Operons und repetitiver Sequenzen von Rhizobium japonicum /." [S.l.] : [s.n.], 1985. http://e-collection.ethbib.ethz.ch/show?type=diss&nr=7831.
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Vaňáč, David. "Leoš Janáček -operní dílo." Master's thesis, Akademie múzických umění v Praze. Hudební fakulta AMU. Knihovna, 2011. http://www.nusl.cz/ntk/nusl-96825.
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This master´s thesis refers about life and work of Leoš Janáček and also on the other hand about his music works. Janáček´s whole life is also mentioned for better understanding of him, his personality and his own music. Leoš janáček´s opera performances are viewed there in three ways - in the view of circumstancesof its origin, in the view of its content and in the view of enumeration of scenic cast of singers during the appearance of his performances in Brno and Prague.
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Kamenická, Kristýna. "Operní koprodukce jako projekt." Master's thesis, Akademie múzických umění v Praze.Divadelní fakulta. Knihovna, 2015. http://www.nusl.cz/ntk/nusl-202468.
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The thesis Coproducing in Opera discusses opera productions and opera joint projects that are based on the cooperation between theatres or festivals. While the thesis provides an insight into various issues of contemporary Czech opera scene, it comments on positive impact of the coproduction.
For the respective theatres, the coproduction decreases the costs of the production, as well as it broadens the repertory. Yet, the coproduction shows are still quite rare.
The thesis describes a process of a creation of such a project in the theatre operated by more than one theatre company; it discusses it's specific management and contractual relationships. The thesis also mentions other types of cooperation, e.g. purchase of the production or lease of the production.
The opera coproduction is the future of the Czech opera theatre.
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Kyovská, Šerých Mlada. "Leoš Janáček - operní tvorba." Master's thesis, Akademie múzických umění v Praze.Hudební a taneční fakulta. Knihovna, 2017. http://www.nusl.cz/ntk/nusl-358375.
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This thesis addresses two principal operas by composer, Leoš Janáček. These are Jenůfa (1903) and The Cunning Little Vixen (1923). The author’s inspiration sources and the method of processing the selected subject are introduced herein. In both operas, L. Janáček is also the author of the libretto, which forms a link between these pieces. The information is drawn from ample Janáček literature and, of course, from music papers. The direction’s point of view is based upon the gained information regarding the pieces and upon the examination of some performance interpretations. With this thesis, I have verified that a thorough familiarity with the work is an absolute necessity for one’s own direction intention. It leads to realize the fact that one can create various interpretations of one piece when having a deep and stable understanding of it.
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Bailey, Marc J. A. "HlyT, a transcriptional regulator of the Escherichai coli hemolysin operon." Thesis, University of Cambridge, 1992. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.259542.
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Coleman, Struan Howard. "The regulation of the rpmB,G operon of Escherichia coli." Thesis, University of Oxford, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.260156.
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Shevtsov, Mikhail Borisovich. "Structural studies of the trp operon regulation in Bacillus subtilis." Thesis, University of York, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.507488.
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Harighi, Behrouz. "Investigating the role of chemotaxis operon genes in Agrobacterium tumefaciens." Thesis, Durham University, 2003. http://etheses.dur.ac.uk/4083/.
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A 1.7 Kb chromosomal DNA of A. tumefaciens C58C1 downstream of chemotaxis operon was sequenced completely in both directions. The comparison of this sequence with sequence databases revealed one open reading frame with strong sequence identity to MCP gene in other bacteria. The sequencing of chromosomal DNA of A. tumefaciens C58 confirmed that this open reading frame has similarity with cytoplasmic domain of McpA. Four mutants of A. tumefaciens C58C1 (Cl/delYl, Cl/delY2, Cl/delB and Cl/delR) were created by in-frame deletion mutagenesis in cheYl, cheY2, cheB and cheR using pKlSmobsacB. Some phenotypic properties of mutants were studied. The cheY2, cheR and cheB mutants showed impaired chemotactic capabilities in both swarming and chemotaxis assays. Deletion of cheY1 appeared to have no significant effect on chemotaxis, under the conditions studied.
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Behravan, Javad. "Characterisation of the gerP spore germination operon of Bacillus cereus." Thesis, University of Sheffield, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.284763.
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Ben, Halim Asma. "Development and analysis of dynamic models of the lac operon." Thesis, Northumbria University, 2013. http://nrl.northumbria.ac.uk/29920/.
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In this work, the mathematical models describing the dynamics of the gene regulatory network of the lac operon are considered. The lac operon is one of the simplest biological systems which involves the regulation network of three genes. The mathematical models of the regulatory mechanisms of the lac system, developed in the literature are based on deterministic or fully stochastic approach to the problem. The aim of the thesis is the development of two stochastic models (reduced and full) based on extension of existing deterministic models with noise terms. The two models reflect different level of complexity of the regulatory processes. The advantage of this approach is based on the realistic description of protein concentrations, protein kinetics and time delays. The research considers first order stochastic delayed differential equations (SDDEs) and their solutions. Stability properties of the stochastic models are investigated by linearization of the systems of SDDEs. New sufficient conditions of mean square stability are obtained analytically for these models using Lyapunov function. Additionally, the threshold values for SDDEs are derived. These conditions and threshold values are applied to nd analytical solutions of the two models of nonlinear SDDE. Further, numerical solutions of these equations are obtained using Euler Maruyama method. A detailed analysis of the stability regions of the models is performed, analytically and numerically. A specific attention is given to the bistable region as it reflects important biological features of the system linked to the positive regulatory mechanism. It is concluded that the stochasticity can change the boundaries of the bistable region which cannot be obtained in the case of the deterministic model of the lac operon. This thesis provides a thorough investigation of the stochastic stability of two lac operon models and demonstrates that the system behaviour is very sensitive to protein concentrations. It also provides a novel way for estimating such concentrations.
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Zenzen, Ivan Luis. "Genômica comparativa do operon e regulon nod em Bradyrhizobium elkanii." reponame:Biblioteca Digital de Teses e Dissertações da UFRGS, 2015. http://hdl.handle.net/10183/142530.
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A Fixação Biológica de Nitrogênio (FBN), processo no qual o nitrogênio atmosférico é convertido à amonia, é muito bem estabelecida entre bactérias diazotróficas coletivamente chamadas de rizóbios e espécies leguminosas. No Brasil, esse tipo de associação (simbiótica) supre totalmente a necessidade de nitrogênio na cultura da soja. Para que a infecção seja efetiva e possa resultar na formação de um nódulo capaz de sustentar o processo de FBN conduzido pelo bacterioide, o rizóbio necessita, previamente, reconhecer e responder à presença das raízes da planta compatível. As associações simbióticas entre rizóbios e plantas leguminosas são altamente específicas, de forma que cada espécie, ou até mesmo estirpe de rizóbio, possui uma gama definida de plantas às quais está apto a se associar, e vice-versa. A principal função dos produtos dos genes de nodulação (nod) é garantir a troca de sinais entre os dois organismos envolvidos na relação simbiótica, onde os produtos dos genes nod regulatórios atuam no controle da expressão de genes nod estruturais. A expressão de genes nod estruturais, via de regra, não ocorre de forma autônoma nos micro-organismos simbiontes do gênero Bradyrhizobium, requerendo assim a presença de moléculas sinalizadoras secretadas pelas raízes das plantas (predominantemente flavonoides) e ativadores transcricionais do tipo-LysR – as proteínas NodD regulatórias. Neste contexto, motivos específicos das proteínas NodD ligam-se a sequências conservadas na região promotora do operon nod, conhecidas como nod boxes, mediando a transcrição dos genes nod. Aparentemente, este sistema regulatório envolvendo as proteínas NodD está presente na maioria das estirpes de Rhizobium, Bradyrhizobium e Azorhizobium, sugerindo um mecanismo geral de controle da nodulação. Em B. diazoefficiens, duas proteínas NodD foram identificadas, com funções e padrões de expressão distintos: NodD1, ativador da transcrição dos genes nod responsivo aos flavonoides liberados pelas raízes das plantas, e NodD2, com ação contrária, atuando como repressor da transcrição desses genes. Enquanto existe uma quantidade relativamente grande de conhecimento em relação à genética e aos mecanismos moleculares que regulam a expressão dos genes envolvidos na nodulação de B. diazoefficiens, incluindo a sequência completa de seu genoma, informações sobre a genética de B. elkanii ainda são relativamente escassas, mesmo que existam alguns dados genômicos disponíveis. Neste trabalho, sequências genômicas de seis linhagens de B. elkanii foram comparadas com o genoma da linhagem de referência B. diazoefficiens USDA 110 com o objetivo de elucidar mecanismos envolvidos na expressão dos genes nod, especialmente aqueles relacionados ao operon e ao regulon nod. Os resultados obtidos permitiram acrescentar aspectos importantes no modelo de regulação apresentado para a linhagem de referência e que pode ser estendido para linhagens de B. elkanii.The Biological Nitrogen Fixation (BNF), process in which atmospheric nitrogen is converted to ammonia, is well established among diazotrophs collectively called rhizobia and legume species. In Brazil, this type of symbiotic association fully meets the need for nitrogen in soybean crop. To infection be effective and result in the formation of a nodule able to sustain the BNF process lead by the bacterioid, the rhizobia need previously to recognize and respond to the presence of the root of a compatible plant. The symbiotic associations between rhizobia and leguminous plants are highly specific, so that each species or even strain of rhizobia has a defined range of plants to which it is able to associate, and vice-versa. The main function of the products of nodulation (nod) genes is to guarantee the exchange of signals between the two organisms involved in the symbiotic relationship, where the products of regulatory nod genes act to control the expression of structural nod genes. The expression of structural nod genes usually does not occur independently in the symbiotic microorganisms of the Bradyrhizobium genus, thus requiring the presence of signalling molecules secreted by plant roots (predominantly flavonoids) and transcriptional activators – the LysR-type regulatory NodD proteins. In this context, NodD proteins bind to specific motifs of conserved sequences in the promoter region of the nod operon, known as nod boxes, mediating transcription of the nod genes. Apparently, this regulatory system involving NodD proteins is present in most strains of Rhizobium, Bradyrhizobium and Azorhizobium, suggesting a general mechanism of nodulation control. In B. diazoefficiens two NodD proteins were identified with distinct functions and expression patterns: NodD1, a flavonoid responsive transcriptional activator of nod genes, and NodD2 with counteraction, acting as a transcriptional repressor of these genes. While there is a relatively large amount of knowledge about the genetics and molecular mechanisms that regulate the expression of genes involved in B. diazoefficiens nodulation, including the complete sequence of its genome, genetic information concerning B. elkanii is still relatively sparse, even if there are some available genomic data. In this study, genomic sequences of six strains of B. elkanii were compared with the genome of the reference strain B. diazoefficiens USDA 110 in order to elucidate mechanisms involved in the expression of nod genes, especially those related to the nod operon and the nod regulon. The results obtained allowed to add important aspects in the regulatory model presented to the reference strain and that could be extended to strains of B. elkanii.
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Zeng, Gang. "Charaterization of the glpEGR operon of Escherichia coli K-12." Diss., Virginia Tech, 1996. http://hdl.handle.net/10919/40227.
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Cho, SungAe. "Lac Operon Expression in Steady State Cells of Escherichia coli." W&M ScholarWorks, 1985. https://scholarworks.wm.edu/etd/1539625294.
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Zeuner, Yvonne Nicole. "Transkriptionskontrolle des nuoA-N-Operons (NADH-Dehydrogenase-I) von Escherichia coli." [S.l. : s.n.], 2002. http://ArchiMeD.uni-mainz.de/pub/2002/0163/diss.pdf.
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Lindberg, Stina. "Molecular analysis of transcription factors in uropathogenic E. coli adhesin operons." Doctoral thesis, Umeå universitet, Institutionen för molekylärbiologi (Medicinska fakulteten), 2009. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-27757.
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The main causative agent of human urinary tract infections is the uropathogenic Escherichia coli (UPEC) pathotype. It may cause disease due to its ability to express a number of bacterial virulence factors. Fimbrial adhesins are particularly important for the initial establishment of infection in the urinary tract. The fimbriae are hair-like structures protruding from the bacterial cell and by attaching to specific receptors in the urinary tract they mediate adherence to different cell types, allowing the bacteria to resist the shear forces from urine flow. The UPEC strains generally carry multiple determinants for fimbrial adhesins. Previous studies have indicated that there is a co-regulation between different fimbrial genes and one factor that has been implicated in this is the PapB protein, acting as a transcriptional regulator of P-fimbrial expression. The PapB protein can be regarded as the prototype of a family of fimbrial regulators that show high homology between different fimbrial operons. One homolog is FocB, regulator of F1C fimbriae. In this study, the role of the FocB protein in the regulation of F1C fimbriae as well as in the co-regulation with other fimbrial genes was investigated. It was observed that FocB binds to DNA, similarly to PapB, in an oligomeric fashion and that PapB and FocB can form hetero-oligomeric complexes, which appear to have a repressive role in the regulation of the F1C fimbriae. In addition, the FocB protein also had a repressive effect on transcription of the fim operon, which encodes theType 1 fimbriae. For further analysis of FocB in vitro, we developed efficient procedures for purification of the protein and established conditions for its crystal formation with the aim to conduct X-ray diffraction studies. By the hanging-drop vapour-diffusion method, we obtained crystals that in the X-ray analysis diffracted sufficiently well to allow modelling of a high resolution structure of FocB. The structural model was considered in relation to the DNA binding properties of the protein. The FocB analysis represents the first structural model of this family of transcriptional factors. This model should aid in further understanding of the roles and functions of these proteins in the regulation of the UPEC fimbrial operons. The complexity of the system, with multiple factors involved in the regulation of fimbrial operons, was revealed in earlier studies of the PapI protein showing that PapI activates transcription of the pap operon as a part of a complex with the global regulator Lrp. However, PapI itself did not appear to bind to DNA and its mode of action has remained unclear. By genetic analyses and in vitro studies we show that PapI may interact also with the α subunit of the RNA polymerase. This finding indicates that PapI might directly interact with the transcriptional apparatus and thus aid in the activation of pap expression. Bacteria are frequently releasing outer membrane vesicles (OMVs) from their surface. We studied the release of the haemolysin toxin from E. coli in connection with formation of OMVs and found that the toxin was tightly associated with the vesicles in an active form. By overproduction of the PapB or PapI regulators in order to maximise the population of bacteria expressing fimbriae, we could detect P fimbriae proteins associated with OMVs that displayed specific adhesion to receptor-coated beads. This suggests a possible scenario in which the vesicles canfunction as directed vehicles of bacterial virulence factors.
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Gould, Phillip Spencer. "Regulation and role of the three chaperonin operons of Rhizobium leguminosarum." Thesis, University of Birmingham, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.273921.
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Li, Jay-Shake. "Nonlinear dynamical analysis of operant behavior." [S.l. : s.n.], 2003. http://deposit.ddb.de/cgi-bin/dokserv?idn=96853032X.
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Kito, Nobutaka, and Naofumi Takagi. "Level-Testability of Multi-operand Adders." IEEE, 2008. http://hdl.handle.net/2237/12025.
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Kenzer, Amy L. "Dishabituation of operant responding in humans /." abstract and full text PDF (free order & download UNR users only), 2007. http://0-gateway.proquest.com.innopac.library.unr.edu/openurl?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&res_dat=xri:pqdiss&rft_dat=xri:pqdiss:3276957.
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Thesis (Ph. D.)--University of Nevada, Reno, 2007."May, 2007." Includes bibliographical references (leaves 61-64). Online version available on the World Wide Web. Library also has microfilm. Ann Arbor, Mich. : ProQuest Information and Learning Company, [2007]. 1 microfilm reel ; 35 mm.