Dissertations / Theses on the topic 'DSBF'
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Urban, Andreas. "Die Rolle der Thiol-Disulfid-Oxidoreduktasen DsbA und DsbC bei der Proteinsekretion in Pseudomonas aeruginosa." [S.l. : s.n.], 2000. http://deposit.ddb.de/cgi-bin/dokserv?idn=959986855.
Full textFrank, Lisa Lucie [Verfasser]. "Die Bedeutung der Proteine BamC, HlpA, DsbB, DsbH und DsbA1 für die Integrität der Außenmembran von Pseudomonas aeruginosa / Lisa Lucie Frank." Tübingen : Universitätsbibliothek Tübingen, 2020. http://d-nb.info/122345116X/34.
Full textBhandari, Murari. "Investigating the role of DsbA enzymes in growth and virulence of uropathogenic Escherichia coli." Thesis, Queensland University of Technology, 2018. https://eprints.qut.edu.au/120696/2/Murari_Bhandari_Thesis.pdf.
Full textMitta, Ever. "Consulting report – DSB Mobile." Master's thesis, Pontificia Universidad Católica del Perú, 2017. http://tesis.pucp.edu.pe/repositorio/handle/123456789/9409.
Full textDSB Mobile es una pequeña empresa peruana de desarrollo de software con sede en Lima. DSB Mobile se especializa en el desarrollo de aplicaciones móviles y web y ha trabajado con grandes empresas como Samsung, Claro y Entel. La compañía está compuesta por el Gerente General, Zico Herrera, un gerente de ventas, un gerente de operaciones y desarrolladores de software a tiempo completo y algunos que se contratan en base a la demanda actual de servicio. DSB Mobile ha establecido una fuerte reputación y marca en Perú y ahora está buscando expandirse fuera de Perú donde puedan introducir sus productos de software en los mercados internacionales. En su aspiración de internacionalización, DSB Mobile está tratando de descubrir no sólo los mercados más rentables para su empresa, sino también los mercados que mejor se alinean con la misión DSB Mobile. La solución a su problema de expansión fue determinar los mejores mercados utilizando una variedad de factores tanto cuantitativos como cualitativos. Al utilizar un informe de competitividad de TI que fue realizado por la British Software Alliance, se utilizó como punto de referencia para determinar los países mejor clasificados para la competitividad de TI y los mejores países para llevar a cabo negocios en base de importantes indicadores asociados a estos. Combinado con estadísticas de datos de software en términos de gastos por proyecto y coste de consultores en TI, esto permitió reducir aún más el alcance para obtener un mercado más atractivo, rentable y mutuamente beneficioso. El plan de implementación propuesto involucró dos líneas de mercado, a saber, la línea del mercado norteamericano y la línea del mercado europeo. La solución propuesta posee diferentes escenarios; por ejemplo, el escenario con trabajo moderado consta de 1 proyecto por mes y tiene un costo total de $391,065 por año obteniendo así una rentabilidad de $180,736. El gráfico de Gantt esbozado pretende guiar a la compañía con la implementación paso a paso de esta expansión internacional y prepararlos para ejecutar este plan de la manera más eficiente y efectiva
Tesis
Sinha, Sunita. "Functional characterisation of three DsbA proteins of Neisseria meningitidis." Thesis, Imperial College London, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.417906.
Full textAnderson, Taylah. "Investigating the repertoire of DsbA enzymes in Klebsiella pneumoniae." Thesis, Queensland University of Technology, 2022. https://eprints.qut.edu.au/235382/1/Taylah%2BAnderson%2BThesis%2BIF80%281%29.pdf.
Full textPonnampalam, Thilaka Vadhanaa. "Phenotypic characterization of a Salmonella typhimurium dsbA null mutant and identification of factors that regulate the expression of the disulfide oxidoreductase DsbA (Salmonella typhimurium)." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1999. http://www.collectionscanada.ca/obj/s4/f2/dsk1/tape7/PQDD_0005/MQ42679.pdf.
Full textMa, Yue. "Double-strand breaks (DSBs) and structure transition on genome-sized DNA." Thesis, https://doors.doshisha.ac.jp/opac/opac_link/bibid/BB13097333/?lang=0, 2018. https://doors.doshisha.ac.jp/opac/opac_link/bibid/BB13097333/?lang=0.
Full textThe protective effect of ascorbic acid (AA) and DMSO against double-strand breaks (DSBs) in DNA was evaluated by single-molecule observation of giant DNA (T4 DNA; 166kbp) through fluorescence microscopy. Samples were exposed to three different forms of radiation: visible light, γ-ray, and ultrasound or freeze/thawing. The change of the higher-order structure of genomic DNA molecules in the presence of alcohols by use of single DNA observation with fluorescence microscopy, by focusing our attention to unveil the different effect between 1-propanol and 2-propanol.
博士(工学)
Doctor of Philosophy in Engineering
同志社大学
Doshisha University
Turcot, Isabelle. "Identification and characterization of the Salmonella enterica serovar Typhimurium disulfide oxidoreductase DsbA." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1997. http://www.collectionscanada.ca/obj/s4/f2/dsk2/ftp04/mq22410.pdf.
Full textCOUPRIE, JOEL. "Etude structurale et dynamique de l'oxydoreductase de dithiol-disulfure dsba d'escherichia coli." Paris 11, 2001. http://www.theses.fr/2001PA112051.
Full textLiuski, T. (Teemu). "AM- ja DSB modulaatioiden toteuttaminen Simulink-ohjelmistolla USRP-ohjelmistoradioalustalle." Bachelor's thesis, University of Oulu, 2019. http://jultika.oulu.fi/Record/nbnfioulu-201902271248.
Full textMavridou, Despoina A. I. "Elucidation of the structure-function relationships in the bacterial transmembrane disulfide oxidoreductase DsbD." Thesis, University of Oxford, 2008. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.497048.
Full textGirardi, Cristina. "Human cell response to ionizing radiation in ground gravity and microgravity condition." Doctoral thesis, Università degli studi di Padova, 2011. http://hdl.handle.net/11577/3427434.
Full textLe radiazioni ionizzanti (IR), colpendo le cellule degli organismi eucarioti è in grado di provocare danni a proteine, lipidi e molecole di DNA, in modo diretto o indiretto come risultato della formazione di radicali liberi. Tra i numerosi tipi di danno al DNA, le rotture a doppio filamento o double-strand breaks (DSBs) rappresentano il tipo di lesione più grave, dal momento che una riparazione inefficiente o non accurata può portare a morte cellulare o instabilità genomica. La presenza di DSBs induce una complessa risposta al danno al DNA che vede coinvolti una serie di eventi cellulari quali: la rilevazione del danno, la trasduzione del segnale agli effettori della riparazione, l’arresto del ciclo cellulare e l’induzione di apoptosi. Nei mammiferi, una delle risposte cellulari più precoci dopo l’induzione di una doppia rottura è la fosforilazione dell’istone H2AX (γ-H2AX) in corrispondenza del sito di danno, che avviene per opera delle fosfatidilinositolol-3-OH-chinasi (ATM, DNA-PK and ATR). Questo evento sembra essere importante nel reclutamento di fattori di segnalazione del danno e di proteine coinvolte nella riparazione delle DSBs nei siti danneggiati (i.e 53BP1, Mre11, Rad50, Nbs1), dando origine a ionizing radiation-induced foci (IRIF), che possono essere costituiti da migliaia di queste molecole proteiche. Monitorando la cinetica di formazione e scomparsa degli IRIF, che si accumulano nei siti danneggiati, è possibile analizzare il danno al DNA e la sua riparazione; in particolare, è stato osservato che la diminuzione dei foci di γ-H2AX correla con la progressione della riparazione delle DSBs. Gli eventi di segnalazione attivati in risposta alle radiazioni ionizzanti dipendono, oltre che dalle caratteristiche genetiche e fisiologiche del sistema biologico osservato, anche dalle condizioni ambientali presenti durante la riparazione del DNA. Per questa ragione abbiamo analizzato e confrontato la risposta cellulare umana alle IR in condizioni diverse di gravità, normale come sulla Terra (1g) e ridotta come nell’ambiente spaziale; in quest’ultimo l’esposizione ai raggi cosmici a cui l’uomo è soggetto durante le missioni spaziali e associata alla riduzione della forza di gravità. L’ambiente spaziale è caratterizzato dalla presenza di radiazioni ionizzanti, nella forma di particelle atomiche cariche che rappresentano il più importante fattore limitante la lunga permanenza dell’uomo nello spazio, ma anche dalla condizione di assenza di peso, che prende il nome di microgravità (10-4–10-6g). In letteratura sono stati riportati alcuni effetti della microgravità osservati in astronauti di ritorno dai voli spaziali, questi riguardano: la soppressione del sistema immunitario, l’atrofia muscolare, problemi cardiovascolari e la demineralizzazione e decalcificazione ossea. Cellule mantenute in coltura durante le missione spaziali e modelli a terra della microgravità mostrano inibizione della proliferazione dei linfociti, soppressione o alterazione della secrezione di citochine, modificazioni del citoscheletro e anche incremento delle aberrazioni cromosomiche e apoptosi. Pertanto, capire se gli effetti della radiazione ionizzante possano essere influenzati dalla microgravità rimane un punto di rilevante importanza nella valutazione dei rischi durante le missioni spaziali. In questo lavoro, la microgravità è stata simulata in laboratorio usando il bioreattore “Rotating Wall Vessel” (Synthecon) messo a punto nei laboratori della NASA a Houston; questo strumento permette di riprodurre un aspetto dei voli spaziali che è l’assenza di peso, condizione che prende il nome di “modeled microgravity” (MMG). Nella prima parte di questo progetto è stata studiata la riparazione delle DSBs in linfociti umani irradiati con raggi gamma e mantenuti durante il tempo di riparazione in 1g o MMG. La formazione e la scomparsa dei foci dell’istone γ-H2AX è stata monitorata a diversi tempi dall’irradiazione mediante immunofluorescenza; nei medesimi campioni è stato anche analizzato l’indice apoptotico e la frammentazione del DNA, quest’ultimo con la tecnica della pulsed-field gel electrophoresis (PFGE) in cui la frazione di DNA rilasciata nel gel (FR) è considerata una misura delle DSBs. I risultati ottenuti confermano che l’incubazione in MMG durante il tempo di riparazione influenza la sopravvivenza cellulare, l’apoptosi e ritarda la riparazione delle DSBs, incrementando l’effetto genotossico delle radiazioni ionizzanti. Sulla base delle osservazioni fatte, si è passati a studiare se la IR e la MMG possono avere un’azione sinergica sulle cellule analizzando i profili di espressione dei microRNAs: regolatori negativi dell’espressione genica. I microRNAs (miRNAs) sono una classe di corti RNA (~22nt) endogeni, che svolgono un ruolo chiave in molti processi cellulari poiché reprimono l’espressione dei mRNA target. Nelle cellule animali, queste molecole vanno a reprimere la traduzione dei geni codificanti proteine legandosi a sequenze complementari nelle regioni non tradotte al 3’ terminale (3’UTR) dei mRNA. Per questo motivo i miRNAs sono coinvolti in numerosi processi biologici come: lo sviluppo, la proliferazione cellulare, l’apoptosi, la funzionalità delle cellule staminali e la tumorigenesi. Scopo: Questo progetto si proponeva di: i) analizzare l’efficienza di riparazione del DNA in condizione di microgravità simulata (MMG), puntando l’attenzione alla cinetica di riparazione delle DSBs; ii) capire se la radiazione ionizzante e la microgravità simulata possono avere un’azione sinergica in cellule umane, confrontando i miRNA radio-responsivi nelle due condizioni di gravità (1g e MMG) Attività svolta: La presenza di foci nucleari dell’istone γ-H2AX e l’indice apoptotico sono stati monitorati in linfociti umani irradiati con raggi γ e non, incubati in 1g e MMG. Negli stessi campioni è stata studiata la riparazione delle DSBs analizzando la frazione di DNA rilasciata (FR) dopo Pulsed-field gel electrophoresis (PFGE). In seguito, usando l’approccio dei microarray con “Human miRNA microarray Kit V2” (Agilent) e della real-time qPCR, sono stati analizzati i profili di espressione dei miRNAs in linfociti umani irradiati con raggi γ e incubati in 1g e MMG. Impiegando poi i microarrays “Whole Human Genome Oligo Microarray” (Agilent) per gli stessi campioni di cellule, è stato possibile determinare i profili di espressione genica; allo scopo di identificare i probabili mRNA target dei miRNA radio-responsivi i dati di espressione dei miRNA e dei mRNA sono stati integrati in un’analisi di anticorrelazione. Infine, per studiare i processi biologici maggiormente coinvolti nella risposta cellulare alle radiazioni ionizzanti è stata eseguita una Gene Ontology analysis (GO) applicata ai miRNA-mRNA target significativamente anti-correlati. Risultati e conclusioni: I risultati ottenuti dallo studio dei foci dell’istone γ-H2AX in PBL irradiati mostrano che il numero medio di foci/nucleo a tempi brevi di riparazione nelle due condizioni di gravità è comparabile. Al contrario, per tempi lunghi, la diminuzione del numero di foci è significativamente differente; infatti, a 24h dall’irradiazione i PBL incubati in 1g presentano 2 foci/nucleo, mentre quelli in MMG 6.4 foci/nucleo. Per verificare che la scomparsa dei foci di γ-H2AX fosse correlata con la riparazione delle DSBs è stata utilizzata la tecnica della PFGE. La cinetica di riparazione delle DSBs è stata analizzata in PBL irradiati e incubati in 1g e MMG; nelle cellule incubate in MMG il contenuto di DNA frammentato era maggiore rispetto alla 1g (FR 77% vs. 33% a 2 h e FR 50% vs. 17% a 6 h, rispettivamente). Probabilmente la MMG influisce sulle modificazioni strutturali della cromatina che avvengono in risposta alla DSBs, diminuendo l’efficienza di riparazione; pertanto, la riparazione delle DSBs che in 1g avviene in poche ore, richiede più tempo in MMG. Nella seconda parte del progetto sono stati analizzati i profili di espressione di miRNA in PBL irradiati con raggi γ e incubati in 1g e MMG. Dai risultati ottenuti è emerso che la radiazione altera i profili di espressione dei miRNA in modo dose e tempo dipendente, in entrambe le condizioni di gravità. L’esposizione ai raggi gamma in 1g altera i profili di espressione dei miRNA, sia a tempi brevi che lunghi, con maggior numero di miRNA radio-responsivi a 24h dopo esposizione alla dose maggiore (2Gy). Dal confronto dei profili di espressione di miRNA in PBL irradiati e mantenuti 24h nelle due condizioni di gravità vengono individuati miRNAs espressi in modo specifico durante l’incubazione in MMG; questi miRNAs vengono probabilmente alterati dall’azione combinata della IR con la MMG con effetto dose-dipendente. Anche le cellule non irradiate ma mantenute 24h in MMG presentano 42 miRNA deregolati rispetto alla 1g. Per far luce sul meccanismo col quale i miRNAs possono modulare alcuni processi biologici in risposta alle radiazioni ionizzanti, sono stati analizzati i profili di espressione di mRNAs negli stessi campioni per i quali sono stati ricavati i profili dei miRNAs. L’analisi di anti-correlazione tra i miRNA e i mRNA differenzialmente espressi e l’analisi computazionale con PITA hanno permesso di predire geni target dei miRNA. Infine, è stata eseguita la Gene Ontology analisi su geni target significativamente anti-correlati, allo scopo di identificare le categorie biologiche di appartenenza. Dai nostri risultati è emerso che alcuni geni sono attivati in PBL irradiati e incubati 24h sia in 1g che MMG, molti di loro sono gravità-specifici. In cellule irradiate con 2Gy e incubate in 1g un grande numero di mRNAs alterati appartiene alle categorie della risposta al danno al DNA (DDR): apoptosi, risposta allo stress, risposta al danno al DNA. Queste categorie non sono risultanti dall’analisi dei PBL irradiati e mantenuti in MMG, dove invece sono alterati processi coinvolti nel differenziamento e attivazione cellulare, sistema immunitario, produzione di citochine ed emopoiesi; tutte caratterizzate da una sostanziale down-regolazione genica. Questo studio fornisce prove che la MMG associata alla radiazione ionizzante porta ad una non appropriata risposta al danno al DNA in linfociti umani, dovuta probabilmente alla perdita di miRNAs radio-responsivi coinvolti nella DDR. Per meglio studiare le funzioni biologiche dei miRNAs in condizione di microgravità simulata è stato necessario puntare l’attenzione sulla validazione dei messageri target predetti e sull’analisi funzionale. Per questa ragione il programma finale di dottorato è stato svolto presso il laboratorio del Prof. Riccardo Dalla-Favera all’“Institute for Cancer Genetics” (Columbia University, New York, USA), per un periodo di sette mesi, allo scopo di acquisire competenze di biologia molecolare che vengono applicate allo studio dei microRNAs.
Findlay, Gordon. "Biogenesis of virulence factors in Vibrio cholerae." Thesis, University of Kent, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.294636.
Full textGattamorta, Karina Alvarez. "A Comparison of Adjacent Categories and Cumulative DSF Effect Estimators." Scholarly Repository, 2009. http://scholarlyrepository.miami.edu/oa_dissertations/343.
Full textSaab, Lahouaria Maria. "Experimental and numerical investigations of soil reinforced with DSF fabrics." Thesis, University of Manchester, 1991. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.261965.
Full textGoecke, Michelle Elisa. "A study of the regulation of expression of dsbA from Salmonella enterica serovar Typhimurium." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1998. http://www.collectionscanada.ca/obj/s4/f2/dsk2/ftp01/MQ28200.pdf.
Full textMedhi, Darpan K. "The repair of DSBs catalyzed by VMA1 derived endonuclease by homologous recombination during meiosis." Thesis, University of Sheffield, 2013. http://etheses.whiterose.ac.uk/5721/.
Full textSalimbeni, Simona. "Déficience en TDP1 et instabilité génomique dans les cellules non-réplicatives." Thesis, Toulouse 3, 2020. http://www.theses.fr/2020TOU30065.
Full textSpinocerebellar ataxia with axonal neuropathy (SCAN1) is a rare recessive neurodegenerative syndrome associated with cerebellar atrophy and peripheral neuropathy. It is caused by a homozygous missense mutation in the tyrosyl-DNA phosphodiesterase-1 (TDP1) gene (A1478G). This results in a substitution of histidine for arginine-493 (H493R) in the TDP1 catalytic site, leading to a reduced TDP1 activity. TDP1 hydrolyses the bond between a DNA 3’-end and a tyrosyl moiety within a trapped topoisomerase I cleavage complex (TOP1cc). TDP1 not only excises trapped TOP1ccs but also processes other 3’-end-blocking lesions, including 3’-phosphoglycolates that result from oxidation. Even so, how TDP1 H493R mutation promotes the SCAN1 phenotype, which is associated with the death of post-mitotic neurons, is unclear. DNA double-strand breaks (DSBs) are infrequent but among the most harmful genomic lesions. Their defective repair can induce cell death, and they have been implicated in the pathogenesis of several human diseases, including neurodegenerative syndromes. Hence, my Ph.D. objective was to investigate whether the SCAN1 phenotype could be related to an accumulation of DSBs in non-replicating cells harboring the H493R mutation of TDP1. The only available models to study the impact of TDP1 H493R mutation were lymphoblastoid cell lines derived from SCAN1 patients compared to those of healthy individuals. Hence, we have generated models of osteosarcoma U2OS cells homozygous for TDP1 H493R or TDP1 KO employing the CRISPR-Cas9 technique. We have also generated primary lung WI38 hTERT fibroblasts TDP1 KO. We found that both TDP1 H493R and TDP1 KO cells accumulate endogenous DSBs, primarily in the G1 phase of the cell cycle compared to S phase. A similar increase of DSBs was observed in quiescent WI38 hTERT cells following depletion of TDP1 with siRNA, suggesting the replication-independent nature of DSBs. Treatment of TDP1 H493R and TDP1 KO cells with camptothecin to induced trapped TOP1ccs, further suggests that accumulation of DSBs could be related to the defective removal of TOP1ccs. Next, we asked whether DSB accumulation in those cells could be related to an increase in DSB production and/or a defect in their repair. Notably, R-loop structures that form co-transcriptionally can induce DSBs in non-replicating cells. We found that TDP1 deficiency modulated R-loop levels at some gene loci, raising the possibility of their implication in DSB formation. Analysis of DSB repair following camptothecin treatment revealed that both TDP1 H493R and TDP1 KO cells were defective in the repair of DSBs in G1 but not in S, with TDP1 H493R having the most pronounced effect. These results suggest that DSBs would accumulate specifically in TDP1-deficient cells that do not undergo replication, due to a defective repair of those breaks. Together, our results provide insights on the etiology of the SCAN1 neurodegenerative syndrome. This work was supported by a PhD fellowship under the French-Italian University VINCI Program 2016
Tong, Xinlin. "Mechanisms of action of Dipeptidyl Peptidase 9 in liver cancer." Thesis, The University of Sydney, 2020. https://hdl.handle.net/2123/24732.
Full textKyryk, Anzhela. "DSB repair by illegitimate and homologous DNA recombination in Arabidopsis thaliana." [S.l. : s.n.], 2001. http://deposit.ddb.de/cgi-bin/dokserv?idn=96435859X.
Full textHulme, Lydia. "The roles of Tel1, Srs2 and Rad6 during meiotic DSB repair." Thesis, University of Sheffield, 2009. http://etheses.whiterose.ac.uk/14522/.
Full textRinaldi, Fabio Cupri. "Estudos estruturais e funcionais das oxidoredutases de pontes dissulfeto da familía DsbA de Xylella fastidiosa." [s.n.], 2008. http://repositorio.unicamp.br/jspui/handle/REPOSIP/277458.
Full textTese (doutorado) - Universidade Estadual de Campinas, Instituto de Fisica Gleb Wataghin
Made available in DSpace on 2018-09-27T18:06:10Z (GMT). No. of bitstreams: 1 Rinaldi_FabioCupri_D.pdf: 8466921 bytes, checksum: 8a88bf7cf4ccef10efbca8ec0412db74 (MD5) Previous issue date: 2008
Resumo: As oxidoredutases de pontes dissulfeto da família DsbA são responsáveis pela catálise da formação de pontes dissulfeto em proteínas secretadas para o periplasma, participando do processo de enovelamento de fatores de virulência de diversos organismos. É a proteína com maior potencial de oxidação atualmente caracterizada e tal propriedade é associada às interações eletrostáticas envolvendo resíduos de seu sítio ativo, que apresenta um arranjo Cys-Pro-His-Cys altamente conservado. A bactéria fitopatogênica Xylella fastidiosa possui dois genes adjacentes que codificam duas oxidoredutases pertencentes à família das DsbAs (XfDbsA e XfDbsA2). Embora a XfDbsA conserve o arranjo CPHC, a XfDbsA2 possui a substituição do resíduo histidina, descrito como essencial à atividade da enzima, por alanina (CPAC). Visando a caracterização estrutural e funcional destas proteínas, a estrutura cristalográfica da XfDsbA foi determinada a 1,9 Å de resolução e um modelo por homologia da XfDsbA2 foi construído. Além disso os potenciais de oxidação das enzimas foram determinados por medidas de fluorescência. A estrutura da XfDsbA revelou a presença de um peptídeo ligado próximo a região do sítio ativo em um dos monômeros mostrando, pela primeira vez em uma estrutura a alta resolução, o provável modo de interação da DsbA com um substrato. Os ensaios funcionais revelaram que as DsbAs de X. fastidiosa apresentam potenciais redox similares e ligeiramente superiores ao da homóloga de Escherichia coli. Embora trabalhos sobre a importância do arranjo CPHC têm associado o alto potencial redox das DsbAs à presença do resíduo histidina no sítio ativo, os resultados obtidos para a XfDsbA2 mostraram que a substituição do resíduo de histidina por alanina não afeta seu potencial redox. A análise das interações envolvendo resíduos do sítio ativo mostrou diferenças importantes entre XfDsbA, XfDsbA2 e suas homólogas de E. coli e Vibrio cholerae. Ensaios funcionais com mutantes foram realizados em busca da identificação dos resíduos que possam compensar a ausência da histidina em XfDsbA2. Os resultados obtidos fornecem novas informações sobre o mecanismo molecular dessa família de enzimas
Abstract: Disulfide oxidoreductase DsbA catalyzes disulfide-bond formation in proteins secreted to the periplasm and has been related to the folding process of virulence factors in many organisms. It is the most oxidizing of the thioredoxin-like proteins and DsbA redox power is understood in terms of the electrostatic interactions involving the active site motif CPHC. The plant pathogen Xylella fastidiosa has two chromosomal genes encoding two oxidoreductases belonging to the DsbA family and, in one of them, the canonical motif CPHC is replaced by CPAC. Aiming at the structural and functional characterization of X. fastidiosa DsbAs, the crystal structure of XfDsbA was solved at 1.9 Å resolution and the XfDsbA2 homology model was calculated. We also determined the redox potential of both enzymes by means of fluorescence experiments. The crystal structure of the XfDsbA revealed an electron density corresponding to an 8-mer peptide interacting with the hydrophobic groove on the surface of the monomer C next to the active site. This modeled peptide shows at first time in a high-resolution crystal structure the probable mode of interaction between DsbA and a substrate. Furthermore, the results presented in this work surprisingly show that, despite the absence of the active site histidine in XfDsbA2, both proteins have similar redox potentials. In addition, the structure of XfDsbA revealed critical differences in the interactions involving the active site residues. Biochemical assays with XfDsbA mutants were performed in order to investigate the residues which may be responsible for compensate for the lack of the conserved histidine in XfDsbA2. The results presented contribute to the understanding of DsbA molecular mechanism
Doutorado
Física da Matéria Condensada
Doutor em Ciências
Ishak, Layal. "Etude de la Poly(ADP-ribosyl)ation dans un contexte des cassures double-brins des ADN nucléaire et mitochondriaux chez Drosophila melanogaster." Thesis, Clermont-Ferrand 2, 2016. http://www.theses.fr/2016CLF22685.
Full textBoth nuclear and mitochondrial DNA alterationsarise following exposure to environmental and endogenous stresses. These genomic alterations are various, ranging from base oxidation to DNA strand breaks, single- and double-strand breaks. These damages are highly detrimental to the cell because they can lead to loss of genetic information and thus to cell death. However, cells have developed various mechanisms to counteract this biological issue and to lead up to a complex DNA damage response (DDR). The Poly (ADP- ribosyl) ation (PARylation) is among these DDR systems. This post-translational modification is mainly carried out by PARP and PARG proteins and is characterized by the incorporation of polymers of ADP-ribose on target proteins. The majority of the PARylationfunctions are related to cellular stress response, particulary in response to genomic damages where it is implicated in many DNA integrity pathways such as Base Excision Repair, Non Homologous End Joining and Homologous Recombination. In contrast to the nucleus, PARylation is also described in the mitochondria but its role in mtDNA integrityis still a heavily debate issue, particularly in case of mtDNA DSBs.To understand it, we used Drosophila model wherePARP-B isoform (human PARP-1 ortholog) is the only enzymatically active form in Drosophila PARP family. The aim of this thesis is to study the role of PARylation in response to DSBs induction in nucleus and mitochondrial DNAand then to understand the mechanisms involved in mtDNA integrity and to evaluate the role of PARylation in this process. Our results show that PARylation level remains stable during DSBs induction and also during repair process,contrary to what is shown in Human cells.However, PARP-I and PARP-II mRNA expression increase during repair period. In mitochondria compartment,our data show an increase of mtDNA copy number in presence of mtDNA DSBs. This increased level returns to normal during repair period and seems to be dependent on PARP. All these results suggest that DSBs repair is PARylation independent at the nuclear level but that the presence of PARP is important. In addition, PARP appears to have a role in the regulation of mtDNA replication in response to genotoxic stress
DI, LILLO ALESSIA. "CAN A PRECISELY-POSITIONED DNA DOUBLE-STRAND BREAK (DSB) ACTIVATE GENE EXPRESSION?" Doctoral thesis, Università degli Studi di Milano, 2021. http://hdl.handle.net/2434/884393.
Full textSantos, Clelton Aparecido dos 1984. "Estudos estruturais e funcionais de proteínas relacionadas à patogenicidade de Xylella fastidiosa." [s.n.], 2013. http://repositorio.unicamp.br/jspui/handle/REPOSIP/316504.
Full textTese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia
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Resumo: Xylella fastidiosa é uma bactéria responsável por inúmeras doenças de plantas em culturas economicamente importantes ao redor do mundo, incluindo a clorose variegada dos citros. Após a infecção de seu hospedeiro, as células de X. fastidiosa é apta a formarem uma estrutura de biofilme que bloqueia os vasos xilemáticos, levando a uma condição de estresse hídrico na planta hospedeira e desencadeando o desenvolvimento da doença. Tendo como estímulo a relevância econômica da citricultura para o Brasil e, visando reduzir os prejuízos provocados pelos problemas fitossanitários que acometem esta cultura, foi realizado um consórcio de pesquisa com o intuito de se conhecer completamente o genoma da linhagem 9a5c de X. fastidiosa. Inúmeras proteínas associadas com patogenicidade, adaptação e sobrevivência bacteriana foram identificadas, incluindo XfDsbC (proteína disulfeto isomerase), Xf5'-Nt (5'-nucelotidase), XfTolB (proteína de translocação B) e XfPal (lipoproteína associada ao peptidoglicano) que foram caracterizadas neste estudo. Empregando ferramentas de caracterização de proteínas, aspectos funcionais e estruturais destas quatro proteínas alvos foram avaliados. Dentre os resultados destaca-se a imunodetecção de XfDsbC, Xf5'-Nt, XfTolB e XfPal durante as diferentes fases de formação e desenvolvimento do biofilme de X. fastidiosa, que é tido como o principal mecanismo de patogenicidade deste fitopatógeno, confirmando a predição inicial de tais proteínas como associadas à patogenicidade bacteriana. Adicionalmente, resultados funcionais e estruturais revelaram detalhes finos do papel biológico desempenhado por cada uma das proteínas estudadas. Juntos, os resultados apresentados neste trabalho contribuem para o melhor entendimento de patogenicidade bacteriana, especialmente com respeito ao fitopatógeno X. fastidiosa
Abstract: Xylella fastidiosa is a plant pathogen bacterium responsible for numerous economically important crops diseases around the world, including the citrus variegated chlorosis. Following the host infection, the X. fastidiosa cells are able to form a biofilm structure which block the xylem vessels, leading to a hydric stress condition in the host plant and triggers the disease development. Given the economic relevance of citriculture for Brazil and in order to reduce the damage caused by phytosanitary problems that affect the citrus production, a research consortium was established with the aim to elucidate the complete genome sequence of the X. fastidiosa 9a5c strain. Numerous proteins associated with bacterial pathogenicity, adaptation and survival have been identified, including XfDsbC (protein disulfide isomerase), Xf5'-Nt (5'-nucleotidase), XfTolB (protein translocation B) and XfPal (peptidoglycan-associated lipoprotein) which were characterized in this study. Using tools for protein characterization, structural and functional aspects of these four protein targets were evaluated. Among the results, we highlight the immunodetection of XfDsbC, Xf5'-Nt, XfTolB and XfPal during the different stages of X. fastidiosa biofilm formation and development which is considered the primary mechanism of pathogenicity of this pathogen. These findings, confirming the initial prediction that relates such proteins as associated with bacterial pathogenicity. Additionally, structural and functional results revealed accurate details of the biological role played by each protein studied. Taken together, the findings presented in this study contribute to a better understanding of bacterial pathogenesis, especially with regard to the plant pathogen X. fastidiosa
Doutorado
Genetica de Microorganismos
Doutor em Genetica e Biologia Molecular
Takahashi, Yoh-Hei. "Biochemical analyses of the quinone-coupled enzyme, DsbB, of Escherichia coli involved in disulfide bond generation." 京都大学 (Kyoto University), 2007. http://hdl.handle.net/2433/136787.
Full textCESENA, DANIELE. "The RNA processing proteins Xrn1 and Rrp6 regulate DNA damage checkpoint activation and telomere metabolism." Doctoral thesis, Università degli Studi di Milano-Bicocca, 2017. http://hdl.handle.net/10281/158272.
Full textGenome instability is one of the most pervasive characteristics of cancer cells. It can be due to DNA repair defects, failure to arrest the cell cycle and loss of telomere-end protection that lead to end-to-end fusion and degradation. Among the many types of DNA damage, the DNA Double Strand Break (DSB) is one of the most severe, because it can cause mutations and chromosomal rearrangements. Eukaryotic cells respond to DSBs by activating a checkpoint that depends on the protein kinases Tel1/ATM and Mec1/ATR, in order to arrest the cell cycle until DSBs are repaired. Mec1/ATR is activated by RPA-coated single-stranded DNA (ssDNA) that arises upon nucleolytic degradation (resection) of the DSB. A similar checkpoint response is triggered when the natural ends of eukaryotic chromosomes lose their protection, resembling and being recognized as DSBs. This protection is provided by specialized nucleoprotein complexes called telomeres. Telomeric DNA consists of repetitive G-rich sequences that terminate with a 3’-ended single-stranded overhang (G-tail), which is important for telomere extension by telomerase. Several proteins, including the CST complex, are necessary to maintain telomere structure and length in both yeast and mammals. Emerging evidences indicate that RNA processing proteins play critical, yet poorly understood, roles in genomic stability and telomere metabolism. We provide evidence that the Saccharomyces cerevisiae RNA decay factors Xrn1, Rrp6 and Trf4 facilitate activation of Mec1/ATR by promoting the generation of RPA-coated ssDNA at intrachromosomal DSBs. Xrn1 and Rrp6 are also required to activate a Mec1/ATR-dependent checkpoint at uncapped telomeres due to loss of the CST component Cdc13. Xrn1 promotes checkpoint activation by facilitating the generation of ssDNA at both DSBs and uncapped telomeres. Xrn1 exerts this function at DSBs by promoting the loading of the MRX complex, whereas how it does at uncapped telomeres remains to be determined. By contrast, DSB resection is not affected by the absence of Rrp6 or Trf4, but their lack impairs the recruitment of RPA, and therefore of Mec1, to the DSB. Rrp6 and Trf4 inactivation affects neither Rad51/Rad52 association nor DSB repair by homologous recombination (HR), suggesting that full Mec1 activation requires higher amount of RPA-coated ssDNA than HR-mediated repair. Finally, we demonstrate that Xrn1 maintains telomere length by promoting the association of Cdc13 to telomeres independently of ssDNA generation and exerts this function by downregulating the RIF1 transcript. Our results provide novel links between RNA processing and genome stability.
VILLA, MATTEO. "Regulation of DNA-end resection at DNA double strand breaks and stalled replication forks." Doctoral thesis, Università degli Studi di Milano-Bicocca, 2018. http://hdl.handle.net/10281/198950.
Full textGenome instability is an hallmark of cancer cells and can be due to DNA damage or replication stress. DNA double strand breaks (DSBs) are the most dangerous type of damage that cells have to manage. In response to DSBs, cells activate an highly conserved mechanism known as DNA damage checkpoint (DDC), whose primary effect is to halt the cell cycle until the damage is repaired. DDC is activated by the apical kinases Tel1/ATM and Mec1/ATR, which phosphorylate and activate the effector kinases Rad53/CHK2 and Chk1/CHK1. The Homologous Recombination (HR)-mediated repair of a DSB starts with the nucleolytic degradation (resection) of the 5’ ends to create long ssDNA tails. In Saccharomyces cerevisiae, resection starts with an endonucleolytic cleavage catalyzed by the MRX complex together with Sae2. More extensive resection relies on two parallel pathways that involve the nucleases Exo1 and Dna2, together with the helicase Sgs1. Resection must be tightly controlled to avoid excessive ssDNA creation. The Ku complex and the checkpoint protein Rad9 negatively regulate resection. While Ku inhibits Exo1, Rad9 restrains nucleolytic degradation by an unknown mechanism. The absence of Sae2 impairs DSB resection and causes prolonged MRX binding at DSB that leads to persistent Tel1 and Rad53-dependent DNA damage checkpoint. SAE2 deleted strains are sensitive to DSBs inducing agents, like camptothecin (CPT). This sensitivity has been associated to the resection defect of sae2∆ cells, but what causes this resection defect and if the enhanced checkpoint signaling contributes to the DNA damage sensitivity of sae2∆ cells is unknown. For these reasons, we tried to identify other possible mechanisms regulating MRX/Sae2 requirement in DSB resection by searching extragenic mutations that suppressed the sensitivity to DNA damaging agents of sae2Δ cells. We identified three mutant alleles (SGS1-G1298R, rad53-Y88H and tel1-N2021D) that suppress both the DNA damage hypersensitivity and the resection defect of sae2∆ cells. We show that Sgs1-G1298R-mediated suppression depends on Dna2 but not on Exo1. Furthermore, not only Sgs1-G1298R suppresses the resection defect of sae2∆ cells but also increases resection efficiency even in a wild type context by escaping Rad9-mediated inhibition. In fact, Rad9 negatively regulates the binding/persistence of Sgs1 at the DSB ends. When inhibition by Rad9 is abolished by the Sgs1-G1298R mutant variant, the requirement for MRX/Sae2 in DSBs resection is reduced. Rad53-Y88H and Tel1-N2021 are loss of function mutant variants that suppress sae2∆ cells sensitivity in a Sgs1-Dna2 dependent manner. Furthermore, abolishing Rad53 and Tel1 kinase activity results in a similar suppression phenotype which does not involve the escape from the checkpoint mediated cell cycle arrest. Rather, defective Rad53 or Tel1 signaling bypasses Sae2 function in DSBs resection by decreasing the amount of Rad9 bound at DSBs. This increases the Sgs1-Dna2 activity that, in turn, can compensate for the lack of Sae2. We propose that persistent Tel1 and Rad53 checkpoint signaling in sae2∆ cells causes DNA damage hypersensitivity and defective DSB resection by increasing the amount of Rad9 that, in turn, inhibits Sgs1-Dna2. Replication stress can induce fork stalling and controlled resection can be a relevant mechanism to allow repair/restart of stalled replication forks. We show that loss of the inhibition that Rad9 exerts on resection exacerbates the sensitivity to replication stress of Mec1 defective yeast cells by exposing stalled replication forks to Dna2-dependent degradation. This Rad9 protective function is independent of checkpoint activation and relies mainly on Rad9-Dpb11 interaction. We propose that Rad9 not only regulates the action of Sgs1-Dna2 at DSBs but also at stalled replication forks, supporting cell viability when the S-phase checkpoint is not fully functional.
Saini, Natalie. "Understanding the mechanisms underlying DSB repair-induced mutagenesis at distant loci in yeast." Diss., Georgia Institute of Technology, 2014. http://hdl.handle.net/1853/51843.
Full textRiches, Lucy C. "Investigating DNA Double Strand Breaks (DSB) in mammalian cells by novel fluorescent reporters." Thesis, Imperial College London, 2008. http://hdl.handle.net/10044/1/1363.
Full textMurphy, Richard F. "Aza-analogues of distyrilbenzene (DSB) synthesis, structures, and properties of 1,4-phenylenediamine bisimines (PDABI)." Diss., Columbia, Mo. : University of Missouri-Columbia, 2006. http://hdl.handle.net/10355/5922.
Full textThe entire dissertation/thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file (which also appears in the research.pdf); a non-technical general description, or public abstract, appears in the public.pdf file. Title from title screen of research.pdf file (viewed on August 30, 2007) Includes bibliographical references.
Oliveira, André Guimarães de. "Análise de moléculas secretadas por populações celulares utilizando técnicas eletroanalíticas." Universidade de São Paulo, 2012. http://www.teses.usp.br/teses/disponiveis/46/46136/tde-02052013-140246/.
Full textCis-11-methyl-2-dodecenoic acid, also known as DSF (autoinducer of the Quorum Sensing system used by the bacteria Xanthomonas axonopodis pv. citri) was explored as a study model for the cell secreted molecules analysis by electroanalytical techniques. Cell cultures from three different cell lines of the bacteria Xanthomonas axonopodis pv. citri were used for this study. A wild type (WT), which produced DSF in naturally observed quantities and two genetically modified ones. One of the lines (ΔC) had a genetic modification that resulted in an elevated production of DSF, and the other (ΔF) had a modification that stopped DSF production. Main analytical techniques used were: cyclic voltammetry, capillary electrophoresis and liquid chromatography (with UV-Vis detection and coupled with mass spectrometry), this last one was used with comparison purposes. Liquid-liquid extractions with organic solvents were realized as sample pre-treatment steps aiming the reduction of interfering species and analyte pre-concentration. Three main methodologies were adopted. One based in the differentiation of cell cultures analyzing or the cell culture supernatants or the resulting extracts from the pre-treatment steps. The main focus was the identification of a differential signal between the cultures that corresponded to the DSF quantities, in other words, null for the ΔF line, high intensity for the ΔC line and a an intermediary intensity for the WT line. The second methodology was based in experiments with a model molecule to obtain some data such as physical-chemistry parameters. Lauric acid (dodecanoic acid) was chosen for its structural similarity and easily acquisition. Calibration curves and similar structure molecules separation experiments were realized using capillary electrophoresis. Third and last methodology was developed using standard cis-11-methyl-2-dodecenoic acid (DSF). Calibration curves were obtained with the isolated standard showing great linearities using both capillary electrophoresis and liquid chromatography with UV-Vis detection. Experiments of standard addiction to the samples were also realized. Experiments using the samples did not show the expected results. Problems found were mainly associated with high amount of interfering species and low analyte concentration at the cultures, extraction methods used were not enough to solve this. The failures with the cyclic voltammetric techniques were associated to electrode poisoning, due to the high amount of organic compounds present at the sample, and DSF lack of electroactivity. Difficulties found with capillary electrophoresis were associated with the samples high ionic strength, presence of interfering species and low analyte concentration. Even liquid chromatography coupled with mass spectrometry experiments didn\'t attended the expectations. Making it difficult to elucidate the problems and not allowing the development of a methodology that could achieve the proposed objectives.
Jayaram, Sumithra. "INVESTIGATING ADENOVIRUS INTERACTIONS WITH HOST DOUBLE-STRAND BREAK REPAIR DEFENSES." Miami University / OhioLINK, 2005. http://rave.ohiolink.edu/etdc/view?acc_num=miami1133983657.
Full textKartchner, Laurel Brianne. "Role of the Endoplasmic Reticulum Chaperone dsbA-L Gluthathione S-Transferase Activity in the Assembly of Adipocyte Hormone Adiponectin." Thesis, The University of Arizona, 2011. http://hdl.handle.net/10150/144537.
Full textLacerda, Fábio de, and Instituto de Engenharia Nuclear. "Conversor DSB-SSB a capacitores chaveados por transformador de Hilbert em tecnologia CMOS de 180nm." Instituto de Engenharia Nuclear, 2017. http://carpedien.ien.gov.br:8080/handle/ien/1870.
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Este trabalho trata da realização de um circuito integrado analógico para a conversão de sinais com modulação em amplitude de banda dupla (Double Sideband ou DSB) para modulação de banda simples (Single Sideband ou SSB). Implementado por circuitos de tempo discreto a capacitores chaveados, utiliza-se de um filtro com resposta infinita ao impulso (Infinite Input Response ou IIR) para compor um transformador de Hilbert como alternativa a implementações digitais, que se aproveitam da grande capacidade de processamento paralelo dos circuitos digitais para a obtenção do transformador de Hilbert por meio de filtros com resposta finita ao impulso (Finite Impulse Response ou FIR) de ordem elevada. Fabricado em tecnologia CMOS de 180 nm com capacitores do tipo metal-metal (MiM), a adoção de filtros estruturalmente passa-tudo reduz significativamente a sensibilidade do conversor ao descasamento de capacitores. Para alimentação de 1,8 V e sinais diferenciais de até 1 V, resultados experimentais mostram que o conversor atinge taxa de rejeição de imagem (Image Rejection Ratio ou IRR) maior que 39,5 dB para modulação Lower Sideband (LSB) e 38,0 dB para modulação Upper Sideband (USB) para sinais de entrada na faixa de 25% a 75% da frequência da portadora, valores estes superiores a propostas analógicas anteriores e comparáveis a propostas digitais do estado da arte em circuitos integrados. Com área de silício de 1,09 mm2, o conversor consome apenas 17,7 mW para frequência de amostragem de 1 MHz enquanto sua IRR apresentou desvio padrão de apenas 0,5 dB dentre 20 amostras avaliadas.
The realization of an analog integrated circuit for conversion of Double-Sideband (DSB) amplitude-modulated signals into Single-Sideband (SSB) is presented. Implemented by discrete-time switched-capacitor circuits, it adopts an Infinite Impulse Response (IIR) filter to realize a Hilbert transformer as alternative to digital implementations which take advantage of high processing capacity from parallel digital circuits to obtain the Hilbert transformer by means of high-order Finite Impulse Response (FIR) filters. Fabricated in a 180 nm CMOS technology with metal-metal (MiM) capacitors, the use of structurally all-pass filters greatly reduces the converter’s sensitivity to capacitor mismatch. For 1.8 V power supply and 1 V differential input/output signals, experimental results show the converter achieves Image Rejection Ratio (IRR) greater than 39.5 dB for Lower-Sideband (LSB) modulation and 38.0 dB for Upper-Sideband (USB) modulation for input signals ranging from 25% to 75% of the carrier frequency. These figures are higher than previous analog circuit proposals and comparable to digital implementations of state-of-the-art integrated circuits. Its silicon area is 1.09 mm2 and the converter consumes only 17.7 mW for 1 MHz sampling frequency while its IRR presents standard deviation of only 0.5 dB among 20 chip samples.
Mirza, Zainulabedeen Reda. "Control of Shigella sonnei and adhesive invasive Escherichia coli infections with a natural product which inhibits the bacterial oxidoreductase DsbA." Thesis, University of Strathclyde, 2017. http://digitool.lib.strath.ac.uk:80/R/?func=dbin-jump-full&object_id=28637.
Full textQin, Song. "Acetylation of histone n-terminal tails contributes to DNA double strand break repair." The Ohio State University, 2006. http://rave.ohiolink.edu/etdc/view?acc_num=osu1134575402.
Full textVasianovich, Yuliya. "Investigating the roles of the Srs2 and Pif1 helicases in DNA double-strand break repair in Saccharomyces cerevisiae." Thesis, University of Edinburgh, 2015. http://hdl.handle.net/1842/17984.
Full textLacerda, Fábio de, and Instituto de Engenharia Nuclear. "Conversor DSB-SSB a capacitores chaveados por Transformador de Hilbert em tecnologia CMOS de 180 nm/." Instituto de Engenharia Nuclear, 2017. http://carpedien.ien.gov.br:8080/handle/ien/1907.
Full textMade available in DSpace on 2017-09-11T18:04:32Z (GMT). No. of bitstreams: 1 FABIO DE LACERDA D.pdf: 4651972 bytes, checksum: 40eb0d71a79f39e524da9bb7fc917c63 (MD5) Previous issue date: 2017-03
Este trabalho trata da realização de um circuito integrado analógico para a conversão de sinais com modulação em amplitude de banda dupla (Double Sideband ou DSB) para modulação de banda simples (Single Sideband ou SSB). Implementado por circuitos de tempo discreto a capacitores chaveados, utiliza-se de um filtro com resposta infinita ao impulso (Infinite Input Response ou IIR) para compor um transformador de Hilbert como alternativa a implementações digitais, que se aproveitam da grande capacidade de processamento paralelo dos circuitos digitais para a obtenção do transformador de Hilbert por meio de filtros com resposta finita ao impulso (Finite Impulse Response ou FIR) de ordem elevada. Fabricado em tecnologia CMOS de 180 nm com capacitores do tipo metal-metal (MiM), a adoção de filtros estruturalmente passa-tudo reduz significativamente a sensibilidade do conversor ao descasamento de capacitores. Para alimentação de 1,8 V e sinais diferenciais de até 1 V, resultados experimentais mostram que o conversor atinge taxa de rejeição de imagem (Image Rejection Ratio ou IRR) maior que 39,5 dB para modulação Lower Sideband (LSB) e 38,0 dB para modulação Upper Sideband (USB) para sinais de entrada na faixa de 25% a 75% da frequência da portadora, valores estes superiores a propostas analógicas anteriores e comparáveis a propostas digitais do estado da arte em circuitos integrados. Com área de silício de 1,09 mm2, o conversor consome apenas 17,7 mW para frequência de amostragem de 1 MHz enquanto sua IRR apresentou desvio padrão de apenas 0,5 dB dentre 20 amostras avaliadas.
The realization of an analog integrated circuit for conversion of Double-Sideband (DSB) amplitude-modulated signals into Single-Sideband (SSB) is presented. Implemented by discrete-time switched-capacitor circuits, it adopts an Infinite Impulse Response (IIR) filter to realize a Hilbert transformer as alternative to digital implementations which take advantage of high processing capacity from parallel digital circuits to obtain the Hilbert transformer by means of high-order Finite Impulse Response (FIR) filters. Fabricated in a 180 nm CMOS technology with metal-metal (MiM) capacitors, the use of structurally all-pass filters greatly reduces the converter’s sensitivity to capacitor mismatch. For 1.8 V power supply and 1 V differential input/output signals, experimental results show the converter achieves Image Rejection Ratio (IRR) greater than 39.5 dB for Lower-Sideband (LSB) modulation and 38.0 dB for Upper-Sideband (USB) modulation for input signals ranging from 25% to 75% of the carrier frequency. These figures are higher than previous analog circuit proposals and comparable to digital implementations of state-of-the-art integrated circuits. Its silicon area is 1.09 mm2 and the converter consumes only 17.7 mW for 1 MHz sampling frequency while its IRR presents standard deviation of only 0.5 dB among 20 chip samples.
Lafaye, Céline. "Étude biochimique et structurale de DsbA1, DsbA2 et DsbA3 : les trois homologues à l'oxydoréductase de Thiol-disulfure DsbA chez Neisseria meningitidis." Grenoble 1, 2009. http://www.theses.fr/2009GRE10243.
Full textNeisseria meningitidis is an invasive bacterial pathogen causing life-threatening infection. Host-pathogen interactions depend on the correct folding of many surface-exposed proteins, which often requires disulfide bond formation. In Gram-negative bacteria, the synthesis of disulfide bonds is catalyzed by the thiol-disulfide oxidoreductase DsbA. N. Meningitidis possesses three genes encoding three active DsbA (DsbA1, DsbA2 and DsbA3). DsbA1 and DsbA2 are lipoproteins involved in the virulence while DsbA3 is a soluble periplasmic protein non related to the virulence. This work reports the biochemical characterisation of the three neisserial enzymes and the crystal structures of DsbA1 and DsbA3. DsbA1 and DsbA3 adopt the classical Escherichia coli DsbA fold. The most striking feature shared by all three proteins is their exceptional oxidizing power. With a redox potential of -80 mV, they are the most oxidizing thioredoxin-like enzymes known to date. For each of these enzymes, the threonine residue found within the active site region plays a key role in dictating this extraordinary oxidizing power. Consistent with these findings, thermal studies indicate that their reduced form is also extremely stable. This result highlights how residues located outside the CXXC motif may influence the redox potential of members of the thioredoxin family. In addition, this functional and structural study shows that the phenotype associated with DsbA3 in N. Meningitidis cannot be explained by a difference of redox activity
Reul, Christian [Verfasser], Markus [Akademischer Betreuer] Löbrich, and Bodo [Akademischer Betreuer] Laube. "Mechanisms and factors determining DSB repair pathway choice in G2 / Christian Reul. Betreuer: Markus Löbrich ; Bodo Laube." Darmstadt : Universitäts- und Landesbibliothek Darmstadt, 2014. http://d-nb.info/1110902247/34.
Full textQuinternet, Marc. "Analyse structurale et dynamique par RMN des domaines N-terminaux des protéines DsbD et PilB de Neisseria meningitidis et de leur interaction." Thesis, Vandoeuvre-les-Nancy, INPL, 2008. http://www.theses.fr/2008INPL102N/document.
Full textWe show, on one hand, that the NMR solution structure of DsbD N-terminal domain from Neisseria meningitidis (nDsbD) displays, in its reduced state, an immunoglobulin fold with a closed conformation of its active site. Nonetheless, our backbone dynamics study shows that the cap-loop region of the protein, which covers active residues in both oxidized and reduced forms, displays internal motions. This illustrates the inner structural adjustment capacities of nDsbD. On the other hand, we show that NMR solution structures of the oxidized and reduced forms of N. meningitidis NterPilB display a thioredoxin-like fold. These two structures appear to be very similar and globally rigid. Consequently, the NterPilB characteristic FLHE loop, which covers one edge of the active site, does not reveal new structural and/or dynamics properties for its involvement in the substrate specificity. Finally, we point out, from the structural and dynamics study of a complex between nDsbD and NterPilB from N. meningitidis, that nDsbD exhibits a powerful adaptability in its complex state. Its cap-loop region opens and comes over the a helix containing the NterPilB active cysteines. In contrast, the NterPilB FLHE loop does not seem to play a role in the complex stabilization. We propose that internal dynamics should facilitate, on one hand, the relative adaptability between the two partners of the complex and, on the other hand, their subsequent dissociation
Quinternet, Marc Cung Manh Thông. "Analyse structurale et dynamique par RMN des domaines N-terminaux des protéines DsbD et PilB de Neisseria meningitidis et de leur interaction." S. l. : S. n, 2008. http://www.scd.inpl-nancy.fr/theses/2008_QUINTERNET_M.pdf.
Full textAdrian, Andrew B. "Fine scale recombination variation in Drosophila melanogaster." Diss., University of Iowa, 2015. https://ir.uiowa.edu/etd/2175.
Full textRINALDI, CARLO. "Functions and regulation of the MRX and Ku protein complexes at DNA ends." Doctoral thesis, Università degli Studi di Milano-Bicocca, 2023. https://hdl.handle.net/10281/402372.
Full textGenome instability is one of the hallmarks of cancer cells and it can be caused by DNA repair defects. Among several types of DNA damage, DNA double-strand breaks (DSBs) are highly cytotoxic lesions that can form accidentally during DNA replication or upon exposure to genotoxic agents. DSBs must be repaired to avoid loss of genetic information and to ensure genomic stability. Eukaryotic cells repair DSBs by activating the DNA damage response (DDR) and by using two main mechanisms: non-homologous end joining (NHEJ) and homologous recombination (HR). The cellular response to DSBs is initiated by the recruitment of Ku (Ku70-Ku80) and MRX/N (Mre11-Rad50-Xrs2/Nbs1) complexes at the two DSB broken ends. MRX in turn recruits Tel1/ATM, a kinase involved in the DNA damage checkpoint, a surveillance mechanism that couples DSB repair and cell-cycle progression. Tel1 allows to promote and stabilize MRX association at both DSBs and telomeres in a positive feedback loop. Ku, MRX/MRN, and Tel1/ATM are also required to maintain the length of telomeres, specialized nucleoprotein complexes at the ends of eukaryotic chromosomes. Furthermore, telomeric DNA must be distinguished from intrachromosomal DSBs ends through different protein complexes, which are recruited to telomeres in order to prevent DDR activation. In S. cerevisiae, Rif2 and Rap1 are two of the main proteins that compose these complexes. Both Rif2 and Rap1 counteract Tel1 activation, nucleolytic degradation, and NHEJ at telomeres. Rif2 appears to exert all these functions by inhibiting MRX association with telomeric DNA, however how Rap1 negatively controls MRX activity at DNA ends remained to be determined. In the first part of my PhD, I contributed to show that Rif2 counteracts MRX association at both DSBs and telomeres in a Rap1-dependent manner. Rap1 in turn can inhibit MRX functions in a Rif2-dependent and -independent manner, and Rap1 functions at DNA ends are influenced by its DNA binding mode. An important issue in NHEJ is the maintenance of the DSB ends in close proximity to allow their correct re-ligation. This function is called end-tethering and some data in E.coli suggested an involvement of the Ku complex in this control mechanism. However, a Ku role in end-tethering remained to be determined. In the second part of my PhD, I investigated this issue by generating a Ku70 mutant variant that increases Ku persistence at DSBs. The characterization of the ku70-C85Y allele has allowed to show that the Ku complex promotes DSB end-tethering and the C85Y mutation enhances this bridging function by increasing Ku retention very close to the DSB ends. The function of Ku in DSB end-tethering is also regulated by Tel1/ATM, which antagonizes this Ku function by limiting Ku persistence at the DSB ends. As the presence of Ku at the DSB ends prevents the access of resection nucleases, the Tel1-mediated regulation of Ku association with the DSB ends provides an important layer of control in the choice between NHEJ and HR mechanism, suggesting a new function of Tel1 in the DNA damage response. All these findings contributed to elucidate the molecular mechanisms that modulate DNA repair and maintain genome stability in response to DSBs, with a specific focus on the functions and regulation of MRX and Ku complexes.
MARSELLA, ANTONIO. "Functions and regulation of the MRX complex at DNA double strand breaks." Doctoral thesis, Università degli Studi di Milano-Bicocca, 2021. http://hdl.handle.net/10281/310478.
Full textDNA double strand breaks (DSBs) are among the most severe DNA lesions. If not properly repaired, DSBs could lead to loss of genetic information and genome instability, which is one of the hallmarks of cancer cells. Eukaryotic cells repair DSBs by non-homologous end joining (NHEJ), which directly re-ligates the DNA broken ends, and homologous recombination (HR), which uses the intact homologous DNA sequence as a template to repair the DSB. HR requires a nucleolytic degradation of the broken DNA ends, in a process called resection. In Saccharomyces cerevisiae, the MRX (Mre11, Rad50 and Xrs2) complex, aided by Sae2, initiates resection of the DSB ends by performing an endonucleolytic cleavage on the 5’-ended strands. This cleavage, catalyzed by the Mre11 subunit, allows the access of Exo1 and Dna2 nucleases that elongate the ssDNA ends. In NHEJ, the two broken ends need to be physically connected to allow their correct religation. This function, called end tethering, depends on the Rad50 subunit, which binds and hydrolyses ATP. A transitions between an ATP-bound state to a post-hydrolysis cutting state regulates MRX DNA binding and processing activities. The MRX complex is also essential in DNA damage checkpoint activation because it recruits the checkpoint kinase Tel1 at the break site. In this thesis, we studied functions and regulation of the MRX complex in DSB repair. We found mre11 alleles that suppress the hypersensitivity of sae2Δ cells to genotoxic agents. The mutations in the Mre11 N-terminus suppress the resection defect of sae2Δ cells by lowering MRX and Tel1 association to DSBs. The diminished Tel1 persistence potentiates Dna2 resection activity by decreasing Rad9 association to DSBs. By contrast, the mre11 mutations localized at the C-terminus bypass Sae2 function in end-tethering but not in DSB resection, possibly by destabilizing the Mre11–Rad50 open conformation. These findings unmask the existence of structurally distinct Mre11 domains that support resistance to genotoxic agents by mediating different processes. In vitro Tel1 activation by MRX requires ATP binding to Rad50, suggesting a role for the MR subcomplex in Tel1 activation. In this thesis, we describe two separation-of-functions alleles, mre11-S499P and rad50-A78T, which we show to specifically affect Tel1 activation without impairing MRX functions in DSB repair. Both Mre11-S499P and Rad50-A78T reduce Tel1–MRX interaction leading to low Tel1 association at DSBs that reduces Tel1 activation. Molecular dynamics simulations show that the wild type MR subcomplex bound to ATP lingers in a tightly ‘closed’ conformation, while ADP presence leads to the destabilization of Rad50 dimer and of Mre11–Rad50 association, both events being required for MR conformational transition to an open state. By contrast, MRA78T undertakes complex opening even if Rad50 is bound to ATP, indicating that defective Tel1 activation caused by MRA78T results from destabilization of the ATP- bound conformational state. The lack of Sae2 increases MRX persistence at DSBs and checkpoint activation. In this thesis, we also show that the telomeric protein Rif2, which stimulates ATP hydrolysis by Rad50, inhibits the Mre11 endonuclease activity and is responsible for the increased MRX retention at DSBs in sae2Δ cells. We identified a Rad50 residue that is important for Rad50-Rif2 interaction and Rif2-mediated inhibition of Mre11 nuclease. This residue is located nearby a Rad50 surface that binds Sae2 and is important to stabilize the Mre11-Rad50 interaction in the cutting state. We propose that Sae2 stimulates MRX endonuclease activity by stabilizing the cutting state, whereas Rif2 inhibits it by antagonizing Sae2 binding to Rad50 and stabilizing a MR conformation that is not competent for DNA cleavage. The results described in this PhD thesis contribute to the understanding of the molecular mechanisms supporting functions and regulation of the MRX complex at DSBs.
Gomez-Paramio, Idoia. "Analysis of the role of Rad5 for the regulation of repair of DSB, small deletions and oxidative damage." Diss., lmu, 2007. http://nbn-resolving.de/urn:nbn:de:bvb:19-81936.
Full textRimsa, Vadim. "Targeting an E3 ubiquitin ligase Siah1 and a cysteine protease SENP1 using SPR and DSF-based fragment screening." Thesis, University of Dundee, 2013. https://discovery.dundee.ac.uk/en/studentTheses/0dfaa23f-8048-423a-b3c0-560ac40de2a4.
Full textGómez-Paramio, Idoia. "Analysis of the role of Rad5 for the regulation of repair of DSB, small deletions and oxidative damage." München Verl. Dr. Hut, 2007. http://d-nb.info/988228920/04.
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