Made available in DSpace on 2017-05-12T14:48:37Z (GMT). No. of bitstreams: 1 isamara.pdf: 1125655 bytes, checksum: 8f7b2f7606310b4ddb2713e9e4043ec0 (MD5) Previous issue date: 2012-02-13 / Chemical contamination removal in soil and water depends on microbiological community that is able to degrade these compounds. There is a great evolutionary interest on studying microorganisms that metabolize the xenobiotic ones, since they have relatively been seen as new in the last five decades. Little is known about structure variation of microbiological community of soil due do the absence and presence of s-triazine herbicides.Unlike crop dependent methods that require time to detect bacteria, molecular techniques have been developed to identify individual species in mixed populations under natural enviromments. Fluorescence in situ Hibiridization (FISH) technique overcomes some difficulties that are found out in other molecular techniques, as it does not need DNA isolation and amplification steps and allows the identification of specific genes in intact cells. Thus, this study aimed at comparing the absence/presence of atrazine effect on bacteriological community structure in soil according to the phylogenetic aspect. Target probes were used on subdivisions of alpha, beta and gamma Proteobacteria, gram-positive bacteria with high G+C content, ammonia oxidizing bacteria, nitrite oxidizing bacteria and Planctomycetes. It was also used an AtzB1 specific probe to check the atzB gene presence, which makes part of s-triazine degradation. Bacteriological amount was determined by direct counting on epifluorescence microscopy, while the corresponding values to each probe were expressed in percentages of the total count with DAPI for each sample. According to this study, positive cells were found out for all probes used in both soils, but the abundance of all groups was lower in soil contaminated with atrazine herbicide, thereby demonstrating its negative influence. Planctomycetes was the most affected group with 57% lower abundance in contaminated soil. The nitrite oxidizing bacteria was the second most affected group followed by β-Proteobacteria. It was also detected the gene atzB presence, so, it can be inferred that there are potentially degrading s-triazine bacteria in both soils. / A remoção da contaminação química no solo e água é dependente principalmente da presença de uma comunidade microbiana capaz de degradar tais compostos. A existência de microorganismos capazes de metabolizar xenobióticos é de um considerável interesse evolucionário, uma vez que estes compostos são relativamente novos no planeta nas últimas cinco décadas. Pouco se sabe sobre a variação da estrutura da comunidade microbiana do solo em função da ausência e presença dos herbicidas s-triazínicos. Diferentemente dos métodos dependentes de cultivo, que requerem tempo para a detecção de bactérias, técnicas moleculares vem sendo desenvolvidas para o reconhecimento de espécies individuais em populações mistas em ambientes naturais. A técnica de Hibridização Fluorescente in situ (FISH) supera algumas dificuldades encontradas com outras técnicas moleculares, pois dispensa as etapas de isolamento e amplificação de DNA e permite a identificação de genes específicos em células intactas. Em virtude disso, o presente trabalho teve como objetivo comparar o efeito da ausência/presença de atrazina na estrutura da comunidade bacteriana do solo no aspecto filogenético. Foram utilizadas sondas alvo para as subdivisões de Proteobactéria alfa, beta e gama, bactérias Gram-positivas com alto teor de G + C e Betaproteobactérias oxidantes de amônia, Bactérias oxidantes de Nitrito e Planctomicetos. Também foi utilizada uma sonda específica AtzB1 para verificar a presença do gene atzB que está envolvido na degradação das s-triazínas. A abundância bacteriana foi determinada através de contagem direta em microscopia de epifluorescência, e os valores correspondentes a cada sonda foram expressos em porcentagem da contagem total com DAPI para cada amostra. No presente estudo células positivas para todas as sondas utilizadas foram encontradas em ambos os solos, porém a abundância de todos os grupos foi menor no solo contaminado com o herbicida atrazina, demonstrando dessa forma a influência negativa do mesmo, sendo o grupo mais afetado o dos Planctomicetos com uma abundância 57% menor em solo contaminado. O segundo grupo mais afetado foi o das bactérias oxidantes de nitrito seguido pelo grupo das β-Proteobactérias. Foi também detectado no presente estudo a presença do gene atzB demonstrando que em ambos os solos existem bactérias potencialmente degradadoras de s-triazinas.

Thesis (M.S.)--West Virginia University, 2002. / Title from document title page. Document formatted into pages; contains viii, 100 p. : ill. (some col.). Vita. Includes abstract. Includes bibliographical references (p. 80-96).

Activity-induced immediate-early gene (IEG) transcription foci can be labelled with fluorescent probes, permitting high temporal and spatial resolution in mapping neuronal circuits. Previous quantification approaches have assumed a Boolean function of transcription foci, assuming that cells are either active or inactive. Due to multiple amplification steps in the in situ hybridization process, it was thought that information relating to magnitudes of firing rates was lost. However, the current data suggest that transcription foci actually exhibit non-Boolean intensity and size values which vary according to behavioural condition. Systematic characterization of transcription foci intensity and size revealed incremental variations such that: home-cage < one-environment exposure < five-environment exposure < maximal electroconvulsive shock. Visual differences in transcription foci may result from a quantifiable relationship between spiking patterns and transcription rates. The exact stoichiometry between neuronal spiking and transcription is not yet clear, but these results suggest that Boolean applications of IEG imaging may neglect accurate neuronal activation properties. / xvi, 125 leaves : ill. ; 29 cm

Submitted by VICTOR BERNARDES BARROSO DA COSTA null (victorbernardes_@hotmail.com) on 2016-03-16T04:08:27Z No. of bitstreams: 1 Dissertação - VICTOR (Versão Final).pdf: 20193346 bytes, checksum: f7da64e79358575f01cf61a5054c4587 (MD5) / Approved for entry into archive by Juliano Benedito Ferreira (julianoferreira@reitoria.unesp.br) on 2016-03-18T12:52:04Z (GMT) No. of bitstreams: 1 costa_vbb_me_sjc.pdf: 20193346 bytes, checksum: f7da64e79358575f01cf61a5054c4587 (MD5) / Made available in DSpace on 2016-03-18T12:52:04Z (GMT). No. of bitstreams: 1 costa_vbb_me_sjc.pdf: 20193346 bytes, checksum: f7da64e79358575f01cf61a5054c4587 (MD5) Previous issue date: 2016-01-21 / Submitted by VICTOR BERNARDES BARROSO DA COSTA null (victorbernardes_@hotmail.com) on 2016-01-26T01:08:29Z No. of bitstreams: 1 Dissertação - VICTOR (Versão Final).pdf: 20193437 bytes, checksum: c041b8e5fa02ed4f74d445c5838128fd (MD5) / Approved for entry into archive by Sandra Manzano de Almeida (smanzano@marilia.unesp.br) on 2016-01-26T13:39:40Z (GMT) No. of bitstreams: 1 costa_vbb_me_sjc.pdf: 20193437 bytes, checksum: c041b8e5fa02ed4f74d445c5838128fd (MD5) / Made available in DSpace on 2016-01-26T13:39:40Z (GMT). No. of bitstreams: 1 costa_vbb_me_sjc.pdf: 20193437 bytes, checksum: c041b8e5fa02ed4f74d445c5838128fd (MD5) Previous issue date: 2016-01-21 / Item merged in doublecheck by Felipe Augusto Arakaki (arakaki@reitoria.unesp.br) on 2016-03-21T13:12:44Z Item was identical to item(s): 135509, 132061 at handle(s): http://hdl.handle.net/11449/136305, http://hdl.handle.net/11449/132945 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Fundação de Amparo à Pesquisa do Estado do Amazonas (FAPEAM) / O carcinoma de células escamosas (CEC) de boca é uma neoplasia incomum em pacientes jovens. Na literatura de língua inglesa não há relatos de estudos que investiguem a amplificação do EGFR e a expressão desta proteína neste grupo etário. O objetivo deste estudo foi investigar a amplificação do EGFR através da técnica de hibridização por fluorescência in situ (FISH) e correlacionar os resultados obtidos através da imunomarcação da proteína EGFR com a epidemiologia e com o prognóstico dos pacientes avaliados. Ao final dos testes de FISH e imuno- histoquímicos, 21 amostras do grupo teste (pacientes ≤ 40 anos) e 39 amostras do grupo controle (pacientes ≥ 50 anos) foram consideradas adequadas para avaliação. As variáveis clínicas e anatomopatológicas foram comparadas pelos testes Qui-Quadrado ou exato de Fisher. A expressão do marcador EGFR e do método de FISH foi comparada entre os grupos por meio do teste não paramétrico de Mann-Whitney. As curvas de sobrevida foram calculadas utilizando o método de Kaplan-Meier e suas curvas foram comparadas através do teste de log-rank. Houve maior número de pacientes do sexo masculino, leucodermas, tabagistas e etilistas. A amplificação do EGFR foi maior no grupo teste (p = 0,018). A amplificação do EGFR associou-se estatisticamente com a variável estadiamento clínico avançado (p = 0,013), independente do grupo. A expressão da proteína EGFR correlacionou-se com tumores bem diferenciados (p = 0,011) e a presença de metástase (p = 0,035), independente da idade. A presença de amplificação foi mais frequente no grupo tese. Alguns casos de pacientes ≥40 anos de idade podem ser adequados ao emprego da terapia anti-EGFR, devido à amplificação do EGFR. / Oral squamous cell carcinoma (OSCC) is uncommon neoplasia in young patients. In the English literature, there are no reports of studies that investigate the amplification of EGFR and expression of this protein in this age group. The aim of this study was to investigate the amplification of EGFR by fluorescence in situ hybridization (FISH) and to correlate the results by immunostaining of EGFR protein with clinicopathological features and prognosis. After FISH and immunohistochemistry, 21 samples of the test group (≤ 40 years) and 39 samples of control group (≥ 50 years) were suitable for evaluating. Categorical variables were compared by the Pearson chi-square test or Fisher's exact test. Associations between protein levels and FISH results with clinicopathological characteristics of the patients were analyzed by Mann-Whitney U test. Survival rates were calculated using the Kaplan-Meier method and the curves were compared by the log-rank test. There was predominance for male patients, leucoderma, smoking and alcohol consumption. The EGFR amplification was higher in the test group (p = 0.018) and it was associated statistically with advanced clinical stage (p = 0.013), independent of the group. The expression of EGFR protein was correlated to well differentiated tumors (p = 0.011) and presence of metastasis (p = 0.035), regardless of age. Presence of EGFR amplification and/or expression. Some cases of patients ≥40 years old might be suitable for anti-EGFR therapy because of EGFR amplification. / FAPEAM: 254/2014

La présence de Wolbachia dans les ovogonies assure la transmission verticale de la bactérie à la descendance de l'hôte. Cependant, nous montrons que chez l'hôte Armadillidium vulgare, l'efficacité de l'infection des descendants tient à un enrichissement en Wolbachia au cours de la maturation des ovaires et des ovocytes dû à une sélection en faveur des ovocytes infectés et/ou à l'entrée secondaire de Wolbachia dans les ovocytes en cours de maturation via l'infection des tissus somatiques. Dans ces tissus, nous avons précisé la localisation de Wolbachia au niveau cellulaire et révélé des morphotypes typiques de chaque tissu. Nous avons également observé Wolbachia chez des hôtes très inattendus; des nématodes non filaires infectant les cloportes, posant la question d'une transmission horizontale, et les A. vulgare mâles, sans qu'ils soient féminisés. Etonnamment, nous avons observé l'infection des gonades mâles dans des lignées d'hôtes chez lesquelles les femelles sont infectées de manière cryptique mais sans que leurs ovocytes ne soient infectés. Le maintien de l'infection entre les générations d'hôtes pourrait alors être dû à une transmission paternelle, inédite pour Wolbachia, ou à une capacité de transmission horizontale très efficace de la bactérie. Par immersion de tissus directement dans des broyats d'organes infectés nous avons en effet démontré que Wolbachia infecte très rapidement des cellules de novo. Les mécanismes d'entrée de Wolbachia dans les cellules sont inconnus mais en monitorant des voies métaboliques clefs de l'hôte nos résultats montrent que l'infection entraine une réponse globale des tissus et implique notamment un détournement de la voie autophagique chez l'hôte. / Wolbachia presence in oogonia ensures bacteria to be vertically transmitted to host offspring. However, in Armadillidium vulgare, we show that the proportion of infected oocytes increases in the course of both ovary and oocyte maturation to reach the transmission rate at the end of ovary maturation. This enrichment can be explained by a preferential selection of oocytes infected with Wolbachia and/or by a secondary acquisition of the bacteria by oocytes. We suspect an acquisition through infected somatic tissues. We localize Wolbachia at the cell level in these tissues and showed particular morphotypes for each tissue. We also observe Wolbachia in unexpected hosts; non filarial nematodes infecting woodlice (suggesting horizontal transmission), and in A. vulgare males (without a feminizing effect of the bacteria). We also observe lineages in which females are cryptically infected. Surprisingly, we observe infected male gonads in these lineages for which female oocytes are uninfected. The infection maintenance across host generations could be due to a paternal transmission of the bacteria (a transmission never described for Wolbachia), or due to an astonishing ability of horizontal transmission. Nevertheless, immersion of uninfected tissues in a solution of crushed infected tissues proves that Wolbachia can quickly infect new tissues. Cellular mechanisms that allow Wolbachia internalization into the cell are still unknown. Thus, we monitor key host metabolic pathways in ovaries and we denote that infection enhances a global response of the entire tissue. Additionally, Wolbachia infection especially implicates a high-jacking of the autophagic pathway.

京都大学 / 0048 / 新制・課程博士 / 博士(理学) / 甲第20953号 / 理博第4405号 / 新制||理||1633(附属図書館) / 京都大学大学院理学研究科生物科学専攻 / (主査)教授 中野 伸一, 教授 木庭 啓介, 教授 中川 尚史 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DFAM

Dissertation submitted in fulfilment with the requirements for the Masters Degree: Biotechnology, Durban University of Technology, 2011. / Untreated vegetable oil effluents (VOEs) are known for creating shock-loading problems for the receiving wastewater treatment installations, resulting in poor quality final effluents being produced which do not satisfy municipal discharge standards. Onsite activated sludge treatment as an alternative has not been fully investigated. Hence, in this investigation biological treatment using the activated sludge process was chosen as the method for the treatment of VOE. The effect of VOE on measured process parameters was also determined. Novel molecular techniques such as fluorescent in situ hybridisation (FISH) and dot-blot hybridization have become powerful tools for the analysis of complex microbial communities that exist within activated sludge. The aim of this investigation was to evaluate biological treatment, optimize and apply FISH and dot-blot hybridization in order to analyze the microbial community implicated the biological treatment of VOE using probes EUBmix, ALF1b, BET42a, GAM42a and HGC69a. A laboratory-scale modified Ludzack-Ettinger (MLE) process setup and fed VOE with a COD (chemical oxygen demand) of ± 1000 mg/L. Daily monitoring of the process involved COD and TKN (total kjeldahl nitrogen) analysis of the influent and effluent as well as direct OUR (oxygen utilization rate) measurement and monitoring of the MLVSS (mixed liquor volatile suspended solids) concentration of the aerobic mixed liquor. The process exhibited overall COD and TKN removal capacities of 84% and 90% respectively. The aerobic mixed liquor had an OUR of 19 mgO/L.h and an average MLVSS concentration of 3000 mg/L. FISH results revealed that 72% of cells stained with 4‟, 6-diamidino-2-phenylindole (DAPI) within the aerobic mixed liquor bound to probe EUBmix, indicating a substantial Bacterial population within the laboratory-scale biological process. The alpha-Proteobacteria was identified as the dominant bacterial community comprising 31% of Bacterial cells, followed by the beta-Proteobacteria (17% of EUBmix), gamma-Proteobacteria (8% of EUBmix) and Actinobacteria (4% of EUBmix). Results of dot-blot hybridization were in agreement with FISH Adrian Phillip Degenaar| CHAPTER 1: General Introduction - v - results reiterating dominance of the alpha-Proteobacteria. This indicated that the class alpha-Proteobacteria could play a primary role in the biological degradation of VOE. This research will therefore aid in process design and retrofitting of biological processes treating VOE.

Made available in DSpace on 2014-06-11T19:30:55Z (GMT). No. of bitstreams: 0 Previous issue date: 2007-04-27Bitstream added on 2014-06-13T21:01:36Z : No. of bitstreams: 1 araujo_d_dr_rcla.pdf: 1858376 bytes, checksum: dbeb43d42be45d0e0d9524437faa5d74 (MD5) / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Dentre todas as ordens de aracnideos conhecidas taxonomicamente, Araneae e a segunda mais diversa, com numero de especies menor somente em relacao a Acari. Atualmente, 39.725 especies ja foram descritas, sendo que centenas de novas descricoes sao feitas a cada ano em diversas familias de aranhas. O conhecimento citogenetico sobre a ordem restringe-se a analise de 638 especies (ca 2%) do total descrito do ponto de vista taxonomico. Este trabalho tem como objetivos fornecer uma compilacao dos dados citogeneticos existentes para a ordem na literatura ate a presente data, bem como caracterizar e estabelecer as estrategias de diferenciacao cromossomica em 13 especies de aranhas pertencentes ao grupo das haploginas, clado que corresponde a somente 3.257 especies (ca 8%) do total da ordem e a apenas 41 especies (ca 6%) do total cariotipado ate os dias atuais. Aliado a baixa representatividade dos dados cariologicos, outros pontos que fazem das haploginas um grupo interessante para estudos sao a predominancia de cromossomos meta/submetacentricos e de sistemas cromossomicos de determinacao sexual simples e multiplos, muitas vezes incluindo um cromossomo Y, ambas caracteristicas raras entre os outros clados de Araneae. As especies analisadas pertencem a tres familias de haploginas, Pholcidae (Mesabolivar luteus e Micropholcus fauroti), Sicariidae (Loxosceles amazonica, Loxosceles gaucho, Loxosceles hirsuta, Loxosceles intermedia, Loxosceles laeta, Loxosceles puortoi, Loxosceles similis e Sicarius tropicus) e Scytodidae (Scytodes fusca, Scytodes globula e Scytodes itapevi). Em Pholcidae, os resultados ineditos para os dois generos mostraram... / Mesabolivar luteus (Keyserling 1891) and Micropholcus fauroti (Simon 1887) specimens were collected in Ubatuba and Rio Claro, both in the state of São Paulo, Brazil. Mesabolivar luteus showed 2n(.) = 15 = 14 + X and 2n(.) = 16 = 14 + XX in mitotic metaphases and 7II + X in diplotenic cells. During late prophase I, all bivalents presented a ring shape, evidencing two chiasmata per bivalent. In this species, some diplotenic cells appear in pairs, maybe due to specific characteristics of the intercellular bridges. The metaphases II showed n = 7 or n = 8 = 7 + X chromosomes. Micropholcus fauroti evidenced 2n(.) = 17 = 16 + X in spermatogonial metaphases and 8II+X in diplotenic cells, with only one chiasma per bivalent, contrasting with M. luteus. In both species, all chromosomes were metacentrics. The X sexual chromosome was the largest element and appeared as a univalent during meiosis I. These are the first cytogenetical data for the genera Mesabolivar and Micropholcus. Additionally, M. luteus is the first chromosomally analyzed species of the New World clade and the observed diploid number for M. fauroti had not yet been recorded in Pholcidae.

<p>The telomeres are specialized structures at the end of the chromosomes composed of the repeated DNA sequence (TTAGGG)n and specific proteins bound to the DNA. The telomeres protect the chromosomes from degradation and end to end fusions. Due to the end-replication problem, the telomeric DNA shortens every cell division, forcing the cells into senescence at a critical telomere length. This process can be counteracted by activating a specialized enzyme, telomerase, which adds telomeric repeats to the chromosome ends leading to an extended or infinite cellular life span. Telomerase activity is absent in most somatic tissues but is found in germ cells, stem cells, activated lymphocytes and the vast majority of tumor cells and permanent cell lines. Hence, telomerase has been suggested as a target for cancer treatment as malignant cells almost exclusively express the enzyme and in that context telomere length measurements will be of great importance.</p><p>Telomere length is traditionally measured with a Southern blot based technique. A new method for telomere analysis of cells in suspension, called flow-FISH, was developed based on fluorescence in situ hybridization using a telomeric peptide nucleic acid (PNA) probe,</p><p>DNA staining with propidium iodide and quantification by flow cytometry. Flow-FISH had high reproducibility and the telomere length measurements showed good correlation with Southern blotting results. The flow-FISH technique also allows studies of cells in specific phases of the cell cycle and the replication timing of telomeric, centromeric and other repetitive sequences were analyzed in a number of cells. Like previous studies, centromeres were shown to replicate late in S phase while the telomere repeats were found to replicate early in S phase or concomitant with the bulk DNA, which is opposite to the patterns described in yeast.</p><p>In benign immunopurified lymphocytes from tonsils, high telomerase activity was found in germinal center (GC) B cells. This population also had high hTERT mRNA levels and displayed a telomere elongation as shown by flow-FISH and Southern blotting. Combined immunophenotyping and flow-FISH on unpurified tonsil cells confirmed the results.</p><p>Chronic lymphocytic leukemia (CLL), the most common leukemia in adults, can be divided into pre-GC CLL, characterized by unmutated immunoglobulin VH genes and worse prognosis, and post-GC CLL, with mutated VH genes and better prognosis. In 61 cases of CLL, telomere length was measured with Southern blotting and VH gene mutation status was analyzed. A new association was found between VH mutation status and telomere length, where cases with longer telomeres and mutated VH genes (post-GC CLL) had better prognosis</p><p>than CLL with short telomeres and unmutated VH genes (pre-GC CLL). A larger study of 112 CLL cases was performed using flow-FISH. The same correlation between telomere length and VH mutation status was found but gender seemed to be of importance as telomere length was a significant prognostic factor for the male CLL patients but not in the female group. Age of the patients and spread of disease seemed to affect the prognostic value of VH gene mutation status.</p>

The telomeres are specialized structures at the end of the chromosomes composed of the repeated DNA sequence (TTAGGG)n and specific proteins bound to the DNA. The telomeres protect the chromosomes from degradation and end to end fusions. Due to the end-replication problem, the telomeric DNA shortens every cell division, forcing the cells into senescence at a critical telomere length. This process can be counteracted by activating a specialized enzyme, telomerase, which adds telomeric repeats to the chromosome ends leading to an extended or infinite cellular life span. Telomerase activity is absent in most somatic tissues but is found in germ cells, stem cells, activated lymphocytes and the vast majority of tumor cells and permanent cell lines. Hence, telomerase has been suggested as a target for cancer treatment as malignant cells almost exclusively express the enzyme and in that context telomere length measurements will be of great importance. Telomere length is traditionally measured with a Southern blot based technique. A new method for telomere analysis of cells in suspension, called flow-FISH, was developed based on fluorescence in situ hybridization using a telomeric peptide nucleic acid (PNA) probe, DNA staining with propidium iodide and quantification by flow cytometry. Flow-FISH had high reproducibility and the telomere length measurements showed good correlation with Southern blotting results. The flow-FISH technique also allows studies of cells in specific phases of the cell cycle and the replication timing of telomeric, centromeric and other repetitive sequences were analyzed in a number of cells. Like previous studies, centromeres were shown to replicate late in S phase while the telomere repeats were found to replicate early in S phase or concomitant with the bulk DNA, which is opposite to the patterns described in yeast. In benign immunopurified lymphocytes from tonsils, high telomerase activity was found in germinal center (GC) B cells. This population also had high hTERT mRNA levels and displayed a telomere elongation as shown by flow-FISH and Southern blotting. Combined immunophenotyping and flow-FISH on unpurified tonsil cells confirmed the results. Chronic lymphocytic leukemia (CLL), the most common leukemia in adults, can be divided into pre-GC CLL, characterized by unmutated immunoglobulin VH genes and worse prognosis, and post-GC CLL, with mutated VH genes and better prognosis. In 61 cases of CLL, telomere length was measured with Southern blotting and VH gene mutation status was analyzed. A new association was found between VH mutation status and telomere length, where cases with longer telomeres and mutated VH genes (post-GC CLL) had better prognosis than CLL with short telomeres and unmutated VH genes (pre-GC CLL). A larger study of 112 CLL cases was performed using flow-FISH. The same correlation between telomere length and VH mutation status was found but gender seemed to be of importance as telomere length was a significant prognostic factor for the male CLL patients but not in the female group. Age of the patients and spread of disease seemed to affect the prognostic value of VH gene mutation status.