Dissertations / Theses on the topic 'Promoter Recognition'
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Li, Xiaomeng. "Human Promoter Recognition Based on Principal Component Analysis." Thesis, The University of Sydney, 2008. http://hdl.handle.net/2123/3656.
Full textLi, Xiaomeng. "Human Promoter Recognition Based on Principal Component Analysis." University of Sydney, 2008. http://hdl.handle.net/2123/3656.
Full textThis thesis presents an innovative human promoter recognition model HPR-PCA. Principal component analysis (PCA) is applied on context feature selection DNA sequences and the prediction network is built with the artificial neural network (ANN). A thorough literature review of all the relevant topics in the promoter prediction field is also provided. As the main technique of HPR-PCA, the application of PCA on feature selection is firstly developed. In order to find informative and discriminative features for effective classification, PCA is applied on the different n-mer promoter and exon combined frequency matrices, and principal components (PCs) of each matrix are generated to construct the new feature space. ANN built classifiers are used to test the discriminability of each feature space. Finally, the 3 and 5-mer feature matrix is selected as the context feature in this model. Two proposed schemes of HPR-PCA model are discussed and the implementations of sub-modules in each scheme are introduced. The context features selected by PCA are III used to build three promoter and non-promoter classifiers. CpG-island modules are embedded into models in different ways. In the comparison, Scheme I obtains better prediction results on two test sets so it is adopted as the model for HPR-PCA for further evaluation. Three existing promoter prediction systems are used to compare to HPR-PCA on three test sets including the chromosome 22 sequence. The performance of HPR-PCA is outstanding compared to the other four systems.
Pieretti, Simone. "ToxT promoter recognition by ToxR transcription factor, a co-activator within the Vibrio cholerae virulence cascade." Doctoral thesis, Universitat de Barcelona, 2016. http://hdl.handle.net/10803/396666.
Full textEl cólera es una infección diarreica aguda causada por la bacteria Vibrio cholerae. La producción de la toxina colérica se controla a través del regulador maestro de virulencia ToxT, cuya activación se lleva a cabo por las proteínas de membrana ToxR y TcpP. Este proyecto de tesis tiene como objetivo el estudio de los complejos formados por ToxR junto con el ADN, dado que se conoce que ToxR se une al promotor toxT para reclutar TcpP y consecuentemente la ARN polimerasa, produciendo la activación de la transcripción. Mediante cristalografía de rayos X hemos resuelto la estructura de tres complejos del dominio de unión a ADN de ToxR con oligonucleótidos de 20, 40 y 25 pares de bases a resoluciones de 2.0 A, 2.6 A y 3.2 A, respectivamente. De acuerdo con las tres estructuras, ToxR es capaz de unirse a una amplia región del promotor toxT que se expande desde la posición -97 hasta la posición -45. Teniendo en cuenta el modelo integrado de las tres estructuras, cuatro moléculas de ToxR se unen al promotor toxT en tándem e invertidas. En las tres estructuras, ToxR muestra un tipo de plegamiento winged helix-turn-helix (w-HTH). El ala (wing) interactúa con el surco menor del ADN, mientras que la hélice de reconocimiento penetra en el surco mayor. Comparando ToxR con el resto de proteínas de la familia w-HTH, hemos encontrado un nuevo elemento estructural, el ala secundaria (secondary wing), que interacciona con el ADN. La determinación de la estructura de los tres complejos es importante para definir con mayor precisión el sitio de unión de ToxR en el promotor toxT. Este sitio se caracteriza por once bases con una secuencia rica en A-T seguida de una caja CATA/CATG/TGTA, donde las dos últimas bases contactan directamente y específicamente con la proteína. Proponemos que ToxR actuaría como co-activador de la transcripción de toxT a diferentes niveles: (i) podría ser responsable de capturar el ADN y mantenerlo cerca de la membrana citoplasmática, (ii) podría jugar un papel clave en el desplazamiento de H-NS, (iii) podría reclutar TcpP y estabilizar su interacción con el promotor.
Sanderson, Andrew. "Recognition of 'extended-10' elements of bacterial promoters." Thesis, University of Birmingham, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.275668.
Full textZhang, Da Jiang. "Involvement of the Polypyrimidine Tract-Binding Protein-Associated Splicing Factor (PSF) in the Hepatitis Delta Virus (HDV) RNA-Templated Transcription." Thèse, Université d'Ottawa / University of Ottawa, 2014. http://hdl.handle.net/10393/31095.
Full textMiroslavova, Nora Svetoslavova. "Studies on the recognition of Escherichia coli promoters and their elements." Thesis, University of Birmingham, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.422293.
Full textUgolini, Matteo. "Recognition of microbial viability via TLR8 promotes innate and adaptive immunity." Doctoral thesis, Humboldt-Universität zu Berlin, 2019. http://dx.doi.org/10.18452/20035.
Full textThe detection of the so-called vitality-associated molecular patterns (vita-PAMPs) signals to the immune system the presence of living microorganisms and triggers an increased immune response. The present study investigated the detection of bacterial vitality by human antigen-presenting cells (APC), as well as the effects of this recognition events on adaptive immunity. Transcriptome analysis of human monocytes showed a selective transcriptional response to live versus heat-killed bacteria. Among others, the inflammatory cytokines IL-12 and TNF were expressed almost exclusively in response to live bacteria. Moreover, the detection of bacterial vitality is conserved in humans, pigs, mice and fish. In mice, bacterial RNA was identified as a bacterial vita-PAMP. In human monocytes, supplementation of dead bacteria with bacterial RNA or with synthetic ligands of toll-like receptor (TLR) 7 and TLR8, but not with other TLR ligands, resulted in the reconstitution of the TNF and IL-12 responses. Conversely, silencing of TLR8 inhibited vita-PAMP-dependent cytokine production. T-follicular helper cells (TFH) play a central role in the initiation of humoral immune responses. Here, the recognition of living bacteria, bacterial RNA or synthetic TLR8 ligands by APCs was identified as a stimulus for robust TFH cell differentiation. TFH differentiation is dependent on the recognition of bacterial RNA via TLR8 and the production of IL-12. Immunization of pigs with a live bacterial vaccine elicited significantly more robust TFH cell and antibody responses than immunization with the heat-killed version of the same vaccine. In summary, we identified TLR8 as the first known vita-PAMP receptor in human and demonstrated its pivotal role in TLR8-mediated “viability recognition” for the induction of TFH cells and vaccine reactions.
Hedemalm, Emil. "Online Transportation Mode Recognition and an Application to Promote Greener Transportation." Thesis, Luleå tekniska universitet, Institutionen för system- och rymdteknik, 2017. http://urn.kb.se/resolve?urn=urn:nbn:se:ltu:diva-65348.
Full textDel av Erasmus Mundus PERCCOM. Redovisning skedde på anordnad summer school av partner-universitet där hela konsortiet närvarade.
Keselowsky, Benjamin George. "Engineering surgaces to direct integrin binding and signaling to promote osteoblast differentiation." Available online, Georgia Institute of Technology, 2004, 2004. http://etd.gatech.edu/theses/available/etd-03152004-111413/.
Full textDavid Collard, Committee Member ; Robert Guldberg, Committee Member ; Cheng Zhu, Committee Member ; Elliot Chaikoff, Committee Member ; Harish Radhakrishna, Committee Member ; Andres J. Garcia, Committee Chair. Includes bibliographical references.
Brown, Maria D. "Does Retrieval Practice Among Medical Trainees Promote Recognition, Diagnosis and Treatment of Eating Disorders?" The Ohio State University, 2020. http://rave.ohiolink.edu/etdc/view?acc_num=osu1606914020488199.
Full textUgolini, Matteo [Verfasser], Leif Erik [Gutachter] Sander, Kai [Gutachter] Matuschewski, and Benedikt [Gutachter] Beckmann. "Recognition of microbial viability via TLR8 promotes innate and adaptive immunity / Matteo Ugolini ; Gutachter: Leif Erik Sander, Kai Matuschewski, Benedikt Beckmann." Berlin : Humboldt-Universität zu Berlin, 2019. http://d-nb.info/1189213370/34.
Full textReis, Adriana Neves dos. "Reconhecimento e predição de promotores procarióticos: investigação de uma metodologia in silico baseada em HMMs." Universidade do Vale do Rio do Sinos, 2005. http://www.repositorio.jesuita.org.br/handle/UNISINOS/2210.
Full textUniversidade do Vale do Rio dos Sinos
A expressão dos genes em procariotos é desencadeada quando a enzima RNApolimerase interage com uma região adjacente ao gene, chamada de promotor, onde se encontram os principais elementos regulatórios do processo de transcrição. Apesar do crescente avanço das técnicas experimentais em biologia molecular, caracterizar e identificar um número significante de promotores, presentes em um dado genoma, continua sendo uma tarefa demorada e cara. Abordagens in silico são bastante utilizadas para reconhecer essas regiões em procariotos. Entretanto, além do alto número de falsos positivos obtidos, elas enfrentam a inexistência de um número adequado de promotores conhecidos para identificar padrões conservados entre as espécies. Logo, um método criterioso e confiável para predizêlos em qualquer organismo procariótico ainda é um desafio. Esta dissertação propõe um protocolo de uso de hidden Markov models (HMMs) que emprega Estimação de Limiar de Decisão (ELD) e Análise de Discriminação (AD) neste problema. Quatro espécie
Gene expression on prokaryotes initiates when the RNA-polymerase enzyme interacts with DNA regions called promoters. In these regions are located the main regulatory elements of the transcription process. Despite the improvement of in vitro techniques for molecular biology analysis, characterizing and identifying a great number of promoters on a genome is a complex task. In silico approaches are usually employed to recognize theses regions on prokaryotes. Nevertheless, the main drawback is the absence of a large set of promoters to identify conserved patterns among the species. Hence, a in silico method to predict them on any species is a challenge. This work proposes a protocol to use hidden Markov models (HMMs) methodology with Decision Threshold Estimation and Discrimination Analysis on this problem. Four prokaryotic species are investigated (Escherichia coli, Bacillus subtilis, Helicobacter pylori e Helicobacter hepaticus). The influence of different aspects in the recognition and prediction are examined:
Perez, Martell Raul Ivan. "Deep learning for promoter recognition: a robust testing methodology." Thesis, 2020. http://hdl.handle.net/1828/11701.
Full textGraduate
Siegele, Deborah Anne. "Identification of two regions of the [sigma]⁷⁰ subunit of Escherichia coli RNA polymerase that are involved in promoter recognition." 1989. http://catalog.hathitrust.org/api/volumes/oclc/22377216.html.
Full textTypescript. Vita. eContent provider-neutral record in process. Description based on print version record. Includes bibliographical references.
Kranthi, Balla Venkata. "Identification Of Key DNA Elements Involved In promoter Recognition By Mxr1p , A key Regulator Of Methanol Utilisation Pathway In Pichia Pastoris." Thesis, 2009. http://hdl.handle.net/2005/671.
Full textYi-Gong, Ma, and 馬宜恭. "Recognition of Xanthomonas campestris RNA polymerase with sigma 70 and sigma 32 type promoters." Thesis, 1999. http://ndltd.ncl.edu.tw/handle/74982837799263043125.
Full text國立中興大學
分子生物學研究所
87
The events that some of the X. campestris (Xc) promoters, studied by promoter probing vector in vivo, are recognized very poorly by E. coli RNA polymerase (RNAP), lead us to define the characteristic of promoters recognition by Xc RNA polymerase. In order to achieve this study, purification of Xc RNAP was done firstly. Using a step salt gradient of KCl, RNAP holoenzyme (Es70) and core enzyme (E) were partially purified through Heparin-Sepharose CL-6B chromatographic steps. The holoenzyme, which was preliminary isolated at 0.3 M of KCl, was then purified by DEAE A25. Whereas, the core enzyme isolated at 0.4 M was then purified by Bio-Rex 70. The transcriptional activities of these purified RNAPs, as well as the reconstituted Es32 , had been examined by run-off in vitro transcription system using T7A1 and dnaK promoter as template, respectively. With respect to a fixed amount of core polymerase (1 pmol), the amount of sigma 32 required for reconstitution was roughly 3 pmol. Taken together, the results indicated that purified Es70 and Es32 are capable to direct transcription in vitro. In vitro transcription studies using T7A1 and rpoD promoters and that of Xc and E. coli RNAP under various reaction conditions were performed. Neither Xc nor E. coli RNAP showed differences under different RNAP concentrations and preincubation time factors with T7A1 promoter. In contrast to E. coli enzyme, Xc RNAP was demonstrated to have different behavior under different DNA and NaCl concentrations, and temperature factors. RNAP from Xc11 gave a best fit of transcription under 300 mM of NaCl, 32°C and 2 pmol of DNA template (1:20, RNAP:DNA). Conversely, the conditions for E. coli RNAP is 50 mM of NaCl, 37°C and 2 pmol of DNA template. When Xc11 rpoD promoter was applied as template, the NaCl concentration for Xc RNAP was 100mM and 200 mM for E. coli enzyme. These results revealed that Xc and E. coli RNAP are somewhat different in promoter selectivity. The promoter specific binding site of Xc RNAP to the rpoD promoter at 28°C was demonstrated by DNase I footprint analysis. The protected region in the non-template strand was from base +18 to -40, which is suggested to be binding site of Xc RNAP open complex. The DNaseI hypersensitive sites were -26 and -36, and sensitive sites -22 and -31 nt upstream of the transcription start site. The TATAAT and TTCCGG sequences recognized by Xc RNAP were proposed to be the -10 and -35 region, respectively. The spacing between these two regions is 20 bp, which is not well consistent with the E. coli sigma 70 consensus. Taken together, the results showed that the promoter structure recognized by purified Xc RNAP are similar, but not identical to those recognized by E. coli Es70.
YANG, CHIA-LI, and 楊佳莉. "Using the TRIZ Innovation System to Promote the Ability of Recognitions Words for Junior Students of Elementary School." Thesis, 2016. http://ndltd.ncl.edu.tw/handle/27650702579982640959.
Full text中華大學
土木工程學系
104
Word recognition is the core language education for junior classes in elementary schools. Given that course plans are usually tight, most teachers have little options but teaching in rather conventional ways, which features one-way give-and-take patterns and demanding repetitive character printing practice. The insipidity fails to draw attention of the students, thus, students’ learning performance compromises. If teachers develop interesting strategies which meet cognitive development of the juniors, instead of the said pattern, it’s believed that students will be more interested in word recognition learning and furthermore their autonomous learning capabilities can be as well promoted. Once students have established adequate vocabulary, they will be able to set up firmer base to learn reading and writing. Therefore aims to discuss ways to improve junior students’ motivation and interest in word recognition education. The research surveys a junior class with 28 pupils in an elementary school in Hsinchu County by analyzing their problems of learning and providing appropriate suggestion based on the TRIZ theory. Conclusions are drawn as following: 1. Group competition and games help promote students’ interest of learning; 2. Multiple materials such as riddles and nursery rhymes motivate students to learn and help develop concept of categorization of characters and their radicals.
Assante, Perrotta Katherine Anne. "More than a Feeling: A Study on Conditions that Promote Historical Empathy in Middle and Secondary Social Studies Classes with "The Elizabeth Jennings Project"." 2016. http://scholarworks.gsu.edu/mse_diss/41.
Full textHU, CHIH-HUI, and 胡智惠. "A Study on the Activities of Tourism Industry to Promote Brand Recognition and Tourists' Willingness to Purchase - A Case Study of Guo Yuan-yang Cake Museum." Thesis, 2017. http://ndltd.ncl.edu.tw/handle/5z2x35.
Full text開南大學
觀光運輸學院碩士在職專班
105
In recent years, the government has encouraged the transformation of traditional industries into a tourist factory with manufacturing, history, culture and recreation. It is an emerging tourist attraction, providing visitors with leisure and entertainment, industry knowledge and local culture. It is fascinated by its experience. , Such as DIY courses, game activities, so that consumers can operate in a safe space, personally experience or feel the production and life-related things, enjoy the fun of exploration. In this study, we will use the five facets proposed by Schmitt (1999): sensory experience, emotional experience, thinking experience, action experience and association experience. Based on the domestic sightseeing factory, the scale is made from June to July in 2017, A total of 398 valid questionnaires were collected and the effective recovery rate was 99.5%. The results were analyzed by descriptive statistics, independent sample t test, single factor mutation analysis, correlation analysis (P <0.05). The questionnaire was collected from the visitors of Guo Yuan-yang Cake Museum. And the results of the study show that: experience activities and enhance brand awareness and visitors to buy a significant positive relationship, that through the visitors' Experience, can give brand awareness to enhance the positive, enhance the purchase intention.
Ramkrishnan, Gayatri. "Recognition of Structures, Functions and Interactions of Proteins of Pathogens : Implications in Drug Discovery." Thesis, 2016. http://etd.iisc.ernet.in/2005/3818.
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