Introdução. As Repetições Palindrômicas Curtas Agrupadas e Regularmente Interespaçadas (CRISPRs) são DNAs que consistem de repetições de nucleotídeos. Existem 3 tipos: CRISPR1-CAS, CRISPR3-CAS e CRISPR2. Os bacteriófagos são partículas virais que infectam bactérias. Os bacteriófagos SAP6, IME-EF1, BC-611, VD-13 e F4 são encontrados em E. faecalis assim como FL1ABC, FL2AB, FL3AB e FL4A. Objetivo. Identificar e caracterizar as classes de CRISPRs e bacteriófagos de E. faecalis e E. faecium isoaldos de amostras alimentares, clínicas e fezes de animais. Materiais e métodos. Foram usadas DNA de 153 isolados, sendo 98 de E. faecalis e 55 de E. faecium. A técnica de detecção foi a PCR utilizando iniciadores para os genes CRISPR1-Cas, CRISPR2, CRISPR3-cas e bacteriófagos, seguido por electroforese em gel de agarose. Resultados. Para E. faecalis foram detectadas 58 isolados que amplifacaram para o gene CRISPR1-Cas; 87 para CRISPR2 e 13 para CRISPR3-Cas. Para E. faecium foram detectadas 4 isolados positivos para o gene CRISPR1-Cas; 18 para CRISPR2 e 1 para CRISPR3-CAS. O bacteriófago FL2ABfoi detectado em 13 isolados de E. faecalis; o bacteriófago FL3AB em 13 isolados de E. faecalis e o FL4A em 28 isolados de E. faecalis. Conclusão. Neste estudo nos encontramos diferentes proporções e distribuições dos genes CRISPRs em E. faecalis e E. faecium. O bacteriófago FL4A apresentou-se como o mais frequente entre os bacteriófagos avalados. / Introduction. The CRISPR are small portions of DNA consisting of nucleotide repeats. There are three types of CRISPRs recognized: CRISPR-associated genes cas: CRISPR1-CAS and CRISPR3-CAS and a orphan locus lacking cas genes: CRISPR2. Bacteriophages are viral particles that infect bacterial. The bacteriophages SAP6, IME-EF1, BC-611 and F4 are found in E. faecalis as well as FL1ABC, FL2AB, FL3AB, FL4A. Objectivy: To Identify and to characterize CRISPRs genes and bacteriophage genes in E. faecalis and E. faecium isolated from food, clinical and animal fecal samples. Materials and methods. A total of 153 DNA samples were used, 98 from E. faecalis and 55 from E. faecium. The PCR technique using primers was used to detect the genes CRISPR1-Cas, CRISPR2, CRISPR3-cas and bacteriophages, followed the agarose gel electrophoresis. Results. To E. faecalis was detected 58 isolates that amplified the CRISPR1-Cas genes, 87 to CRISPR2 and 13 to CRISPR3-Cas. To E. faecium was detected 4 isolates positive to CRISPR1-Cas gene, 18 to CRISPR2 e 1 to CRISPR3-CAS. The FL2AB bacteriophage was detected in 13 isolates of E. faecalis; the FL3AB bacteriophage in 13 isolates of E. faecalis and the FL4A in 28 isolates of E. faecalis. Conclusion. In this work, we found out different proportions and distributions of CRISPRs genes in E. faecalis e E. faecium. The FL4A bacteriophage showed a high frequency among the bacteriophages tested.

Conselho Nacional de Desenvolvimento CientÃfico e TecnolÃgico / FundaÃÃo de Amparo à Pesquisa do Estado do Cearà / Este trabalho descreve algumas das pesquisas multidisciplinares realizadas pelo Departamento de FÃsica da Universidade Federal do Cearà (UFC), envolvendo o aproveitamento de resÃduos e a utilizaÃÃo da microscopia de forÃa atÃmica (AFM) na caracterizaÃÃo de estruturas biolÃgicas. TrÃs resÃduos foram estudados: o bagaÃo do caju, as cinzas de carvÃo mineral e as conchas de mexilhÃo Perna perna. No primeiro, foi feita a caracterizaÃÃo das cinzas originadas da queima do pedÃnculo do caju, destacando os compostos gerados neste processo: KHCO3 e K2SO4. Ambos sÃo importantes na indÃstria farmacÃutica e na produÃÃo de adubos fosfatados. No segundo, foi demonstrado o uso das cerÃmicas produzidas a partir das cinzas volantes de carvÃo mineral originadas da termelÃtrica Presidente MÃdici (RS), como substratos para a imobilizaÃÃo da invertase responsÃvel pela produÃÃo de aÃÃcar invertido. Esta aplicaÃÃo tem uso direto na produÃÃo de bebidas, medicamentos e cosmÃticos. Finalmente no terceiro, foram estudadas as alteraÃÃes na composiÃÃo, topografia da superfÃcie e dureza das conchas de mexilhÃo Perna perna tratadas termicamente. O nÃcar (ou superfÃcie perolada) de mexilhÃes tem sido usado como biomaterial na regeneraÃÃo Ãssea, tendo que sofrer processos de esterelizaÃÃo (normalmente tÃrmicos). Por isso, a importÃncia do estabelecimento de regiÃes de estabilidade mecÃnica, estrutural e composicional durante estes processos. No uso do microscÃpio de forÃa atÃmica para estudar estruturas biolÃgicas, destacou-se a importÃncia desta tÃcnica na caracterizaÃÃo do desenvolvimento de biofilmes de Enterococcus faecalis, freqÃentemente encontrada em casos clÃnicos; e a anÃlise nanoestrutural da esporopolinina de grÃos de pÃlen de Ilex Paraguarinsis St. Hill. A esporopolinina à um dos biopolÃmeros mais resistente que existe, sendo do interesse crescente dos cientistas e engenheiros de materiais.

Next Generation Sequencing (NGS) is a new technology that has revolutionized the way we study living organisms. Where previously only a few genes could be studied at a time through targeted direct probing, NGS offers the possibility to perform measurements for a whole genome at once. The drawback is that the amount of data generated in the process is large and extracting useful information from it requires new methods to process and analyze it. The main contribution of this thesis is the development of a novel experimental method coined tagRNA-seq, combining 5’tagRACE, a previously developed technique, with RNA-sequencing technology. Briefly, tagRNA-seq makes it possible to identify the 5’ ends of RNAs in bacteria and directly probe for their type, primary or processed, by ligating short RNA sequences, the tags, to the beginnings of RNA molecules. We used the method to directly probe for transcription start and processing sites in two bacterial species, Escherichiacoli and Enterococcus faecalis. It was also used to study polyadenylation in E. coli, where the ability to identify processed RNA molecules proved to be useful to separate direct and indirect regulatory effects of this mechanism. We also demonstrate how data from tagRNA-seq experiments can be used to increase confidence on the discovery of anti-sense transcripts in bacteria. Analyses of RNA-seq data obtained in the context of these experiments revealed subtle artifacts in the coverage signal towards gene ends, that we were able to explain and quantify based Kolmogorov’s broken stick model. We also discovered evidences for circularization of a few RNA transcripts, both in our own data sets and publicly available data. Designing the tags used in tagRNA-seq led us to the problem of words absent from a text. We focus on a particular subset of these, the minimal absent words (MAWs), and develop a theory providing a complete description of their size distribution in random text. We also show that MAWs in genomes from viruses and living organisms almost always exhibit a behavior different from random texts in the tail of the distribution, and that MAWs from this tail are closely related to sequences present in the genome that preferentially appear in regions with important regulatory functions. Finally, and independently from tagRNA-seq, we propose a new approach to the problem of bacterial community reconstruction in metagenomic, based on techniques from compressed sensing. We provide a novel algorithm competing with state-of-the-art techniques in the field. / <p>QC 20150930</p>

SANTOS, Ricardo Pires dos. Aproveitamento de resíduos e microscopia de força atômica em materiais biológicos. 2007. 308 f. Tese (Doutorado em Física) - Programa de Pós-Graduação em Física, Departamento de Física, Centro de Ciências, Universidade Federal do Ceará, Fortaleza, 2007. / Submitted by Edvander Pires (edvanderpires@gmail.com) on 2015-05-25T21:29:16Z No. of bitstreams: 1 2007_tese_rpsantos.pdf: 5997888 bytes, checksum: d6004e303ddc73c35d5f9a89c5c3c2a7 (MD5) / Approved for entry into archive by Edvander Pires(edvanderpires@gmail.com) on 2015-05-27T18:56:00Z (GMT) No. of bitstreams: 1 2007_tese_rpsantos.pdf: 5997888 bytes, checksum: d6004e303ddc73c35d5f9a89c5c3c2a7 (MD5) / Made available in DSpace on 2015-05-27T18:56:00Z (GMT). No. of bitstreams: 1 2007_tese_rpsantos.pdf: 5997888 bytes, checksum: d6004e303ddc73c35d5f9a89c5c3c2a7 (MD5) Previous issue date: 2007 / Este trabalho descreve algumas das pesquisas multidisciplinares realizadas pelo Departamento de Física da Universidade Federal do Ceará (UFC), envolvendo o aproveitamento de resíduos e a utilização da microscopia de força atômica (AFM) na caracterização de estruturas biológicas. Três resíduos foram estudados: o bagaço do caju, as cinzas de carvão mineral e as conchas de mexilhão Perna perna. No primeiro, foi feita a caracterização das cinzas originadas da queima do pedúnculo do caju, destacando os compostos gerados neste processo: KHCO3 e K2SO4. Ambos são importantes na indústria farmacêutica e na produção de adubos fosfatados. No segundo, foi demonstrado o uso das cerâmicas produzidas a partir das cinzas volantes de carvão mineral originadas da termelétrica Presidente Médici (RS), como substratos para a imobilização da invertase responsável pela produção de açúcar invertido. Esta aplicação tem uso direto na produção de bebidas, medicamentos e cosméticos. Finalmente no terceiro, foram estudadas as alterações na composição, topografia da superfície e dureza das conchas de mexilhão Perna perna tratadas termicamente. O nácar (ou superfície perolada) de mexilhões tem sido usado como biomaterial na regeneração óssea, tendo que sofrer processos de esterelização (normalmente térmicos). Por isso, a importância do estabelecimento de regiões de estabilidade mecânica, estrutural e composicional durante estes processos. No uso do microscópio de força atômica para estudar estruturas biológicas, destacou-se a importância desta técnica na caracterização do desenvolvimento de biofilmes de Enterococcus faecalis, freqüentemente encontrada em casos clínicos; e a análise nanoestrutural da esporopolinina de grãos de pólen de Ilex Paraguarinsis St. Hill. A esporopolinina é um dos biopolímeros mais resistente que existe, sendo do interesse crescente dos cientistas e engenheiros de materiais.

Introdução. As Repetições Palindrômicas Curtas Agrupadas e Regularmente Interespaçadas (CRISPRs) são DNAs que consistem de repetições de nucleotídeos. Existem 3 tipos: CRISPR1-CAS, CRISPR3-CAS e CRISPR2. Os bacteriófagos são partículas virais que infectam bactérias. Os bacteriófagos SAP6, IME-EF1, BC-611, VD-13 e F4 são encontrados em E. faecalis assim como FL1ABC, FL2AB, FL3AB e FL4A. Objetivo. Identificar e caracterizar as classes de CRISPRs e bacteriófagos de E. faecalis e E. faecium isoaldos de amostras alimentares, clínicas e fezes de animais. Materiais e métodos. Foram usadas DNA de 153 isolados, sendo 98 de E. faecalis e 55 de E. faecium. A técnica de detecção foi a PCR utilizando iniciadores para os genes CRISPR1-Cas, CRISPR2, CRISPR3-cas e bacteriófagos, seguido por electroforese em gel de agarose. Resultados. Para E. faecalis foram detectadas 58 isolados que amplifacaram para o gene CRISPR1-Cas; 87 para CRISPR2 e 13 para CRISPR3-Cas. Para E. faecium foram detectadas 4 isolados positivos para o gene CRISPR1-Cas; 18 para CRISPR2 e 1 para CRISPR3-CAS. O bacteriófago FL2ABfoi detectado em 13 isolados de E. faecalis; o bacteriófago FL3AB em 13 isolados de E. faecalis e o FL4A em 28 isolados de E. faecalis. Conclusão. Neste estudo nos encontramos diferentes proporções e distribuições dos genes CRISPRs em E. faecalis e E. faecium. O bacteriófago FL4A apresentou-se como o mais frequente entre os bacteriófagos avalados. / Introduction. The CRISPR are small portions of DNA consisting of nucleotide repeats. There are three types of CRISPRs recognized: CRISPR-associated genes cas: CRISPR1-CAS and CRISPR3-CAS and a orphan locus lacking cas genes: CRISPR2. Bacteriophages are viral particles that infect bacterial. The bacteriophages SAP6, IME-EF1, BC-611 and F4 are found in E. faecalis as well as FL1ABC, FL2AB, FL3AB, FL4A. Objectivy: To Identify and to characterize CRISPRs genes and bacteriophage genes in E. faecalis and E. faecium isolated from food, clinical and animal fecal samples. Materials and methods. A total of 153 DNA samples were used, 98 from E. faecalis and 55 from E. faecium. The PCR technique using primers was used to detect the genes CRISPR1-Cas, CRISPR2, CRISPR3-cas and bacteriophages, followed the agarose gel electrophoresis. Results. To E. faecalis was detected 58 isolates that amplified the CRISPR1-Cas genes, 87 to CRISPR2 and 13 to CRISPR3-Cas. To E. faecium was detected 4 isolates positive to CRISPR1-Cas gene, 18 to CRISPR2 e 1 to CRISPR3-CAS. The FL2AB bacteriophage was detected in 13 isolates of E. faecalis; the FL3AB bacteriophage in 13 isolates of E. faecalis and the FL4A in 28 isolates of E. faecalis. Conclusion. In this work, we found out different proportions and distributions of CRISPRs genes in E. faecalis e E. faecium. The FL4A bacteriophage showed a high frequency among the bacteriophages tested.

Introdução. As Repetições Palindrômicas Curtas Agrupadas e Regularmente Interespaçadas (CRISPRs) são DNAs que consistem de repetições de nucleotídeos. Existem 3 tipos: CRISPR1-CAS, CRISPR3-CAS e CRISPR2. Os bacteriófagos são partículas virais que infectam bactérias. Os bacteriófagos SAP6, IME-EF1, BC-611, VD-13 e F4 são encontrados em E. faecalis assim como FL1ABC, FL2AB, FL3AB e FL4A. Objetivo. Identificar e caracterizar as classes de CRISPRs e bacteriófagos de E. faecalis e E. faecium isoaldos de amostras alimentares, clínicas e fezes de animais. Materiais e métodos. Foram usadas DNA de 153 isolados, sendo 98 de E. faecalis e 55 de E. faecium. A técnica de detecção foi a PCR utilizando iniciadores para os genes CRISPR1-Cas, CRISPR2, CRISPR3-cas e bacteriófagos, seguido por electroforese em gel de agarose. Resultados. Para E. faecalis foram detectadas 58 isolados que amplifacaram para o gene CRISPR1-Cas; 87 para CRISPR2 e 13 para CRISPR3-Cas. Para E. faecium foram detectadas 4 isolados positivos para o gene CRISPR1-Cas; 18 para CRISPR2 e 1 para CRISPR3-CAS. O bacteriófago FL2ABfoi detectado em 13 isolados de E. faecalis; o bacteriófago FL3AB em 13 isolados de E. faecalis e o FL4A em 28 isolados de E. faecalis. Conclusão. Neste estudo nos encontramos diferentes proporções e distribuições dos genes CRISPRs em E. faecalis e E. faecium. O bacteriófago FL4A apresentou-se como o mais frequente entre os bacteriófagos avalados. / Introduction. The CRISPR are small portions of DNA consisting of nucleotide repeats. There are three types of CRISPRs recognized: CRISPR-associated genes cas: CRISPR1-CAS and CRISPR3-CAS and a orphan locus lacking cas genes: CRISPR2. Bacteriophages are viral particles that infect bacterial. The bacteriophages SAP6, IME-EF1, BC-611 and F4 are found in E. faecalis as well as FL1ABC, FL2AB, FL3AB, FL4A. Objectivy: To Identify and to characterize CRISPRs genes and bacteriophage genes in E. faecalis and E. faecium isolated from food, clinical and animal fecal samples. Materials and methods. A total of 153 DNA samples were used, 98 from E. faecalis and 55 from E. faecium. The PCR technique using primers was used to detect the genes CRISPR1-Cas, CRISPR2, CRISPR3-cas and bacteriophages, followed the agarose gel electrophoresis. Results. To E. faecalis was detected 58 isolates that amplified the CRISPR1-Cas genes, 87 to CRISPR2 and 13 to CRISPR3-Cas. To E. faecium was detected 4 isolates positive to CRISPR1-Cas gene, 18 to CRISPR2 e 1 to CRISPR3-CAS. The FL2AB bacteriophage was detected in 13 isolates of E. faecalis; the FL3AB bacteriophage in 13 isolates of E. faecalis and the FL4A in 28 isolates of E. faecalis. Conclusion. In this work, we found out different proportions and distributions of CRISPRs genes in E. faecalis e E. faecium. The FL4A bacteriophage showed a high frequency among the bacteriophages tested.

No description available.

No description available.

Magister Chirurgiae Dentium - MChD / When faced with a failing or failed root treatment, the dentist must decide whether the tooth can be retreated and saved or extracted. The dentist's decision to retreat is often based on the x-ray presenting a failing root treatment. The dentist must be aware that there might be a number of factors that have contributed to the failure and which may preclude, following retreatment, a successful long term clinical function. The current study has been made to determine those factors that may influence the prognosis in order to assist the clinician in advising the patient of the best course of treatment. A literature review was made to determine and identify these factors and explain their relevance and influence on the healing process. The current study included identifying the factors described in the literature review and noting their influence on the prognosis following non-surgical retreatment. Retreatment of failed root treated teeth requires special knowledge and skill from the clinician in order to correct and manage the case. The current study was made in a clinical setting and compared results of retreatment with two types of rotary files on the market: progressive or variable taper (Pro Taper) with constant non-ISO 06 taper (K3). Clinical signs and symptoms were noted at the patient's presentation and following recalls at 1, 4 months and 1 year. The results were recorded and statistically analysed and the results were discussed. The results showed that out of 81 patients 10cases of retreatment were considered to have failed and 68 cases were considered to have been successful. Three patients did not return for their assessments and were therefore not considered in further results. There was a statistically significant (p<0.1 0) recording of deep periodontal pockets associated with teeth with failing root treatments (40%) and (13%) in the "Success" group. The two estimated proportions of "Sinus" present (60%) in the "Failure" group and 10% in the 'Success' group were significantly different (p<0.01). "Sinus present" in the "Success group" means in the initial clinical assessment before retreatment was initiated. The presence of a sinus at the One Year follow up signified a failure of the root retreatment (p<0.001). The two estimated proportions of "Occlusion" present (80% and 99%) in the "Failure" and "Success" group were significantly different (p<0.05). Therefore, teeth in "occlusion" were more within the "Success" group. 70% of those teeth that failed had pretreatment apical rarefactions of greater than 6mm diameter; whereas 76.5% of successful retreatments had areas less than 6mm diameter. The differences were significant according to Fisher's Exact Test (p<0.01). 44% of failed cases had areas of rarefaction described as "diffuse"; and 56% of failed cases had areas that were described as "well-defined". 95% of cases that were successful had areas described as "diffuse" and the rest were "welldefined". The differences between the success and failure categories were statistically significant (p<0.0 1). The two estimated proportions of "Post present" (0% and 31%) in the "Failure" and "Success" groups were significantly different (p<0.1 0). Therefore, the "Post was present" in many more cases within the "Success" group than in the "Failure" group. There was no difference between the Median "Crown/Root" ratios of the "Failure" (Median = 0.595) or "Success" groups (Median = 0.662) (Wilcoxon Test, p>O.10). Teeth with longer roots tend to lead to failure, however there was a considerable overlap between the distributions. Therefore the finding is that the Median length of the roots of the "Failures" is longer than that of the "Successes". (Wilcoxon Rank Sum Test, p-value = 0.0628). The results also indicated that previous short root filling preparation contributes to the final success of retreatment (Fisher Exact Test, p<0.05). There was a significant difference between the distribution of the "Failure" and "Success" (88.2%) groups (Fisher Exact Test, p<O.OI) in those cases with initial short obturated fillings. When comparing the outcome following the use of the two types of rotary files it was found that the "Successes" with K3 File (35 out of 41) was 85%; and with Protaper File (32 out of 36) 89%. The "Success" rate certainly was not different between the two file types. The conclusions drawn from the current study was not significantly different from those in the literature review and the overall results were of a similar nature with some minor changes. However it is clear that non-surgical root retreatment offers a good prognosis and should be included as an option for failed or failing root treatment.

Diss. (sammanfattning) Linköping : Linköpings universitet, 2005. / Härtill 5 uppsatser.