Rozprawy doktorskie na temat „Cst Genes”

Proteus mirabilis PM13 is a well characterized chloramphenicol-sensitive isolate which spontaneously gives rise to resistant colonies on solid media containing chloramphenicol (50ug/ml) at a plating efficiency of between 10-4 and 10-5 per cell per generation. When a chloramphenicol resistant colony is grown in liquid medium in the absence of the antibiotic for I50 generations a population of predominantly sensitive cells arises. The cat gene responsible for the phenomenon is chromosomal, and has been cloned from P.mirabilis PMI3 with DNA prepared from cells grown in the absence or the presence of chloramphenicol. Recombinant plasmids which confer resistance to chloramphenicol carry an 8.5-kb PstI fragment irrespective of the source of host DNA. The location of The cat gene within the PstI fragment was determined by Southern blotting with a cat consensus 'active - site' oligonucleotide (5'-CCATCACAGACGGCATGATG-3') corresponding to the expected amino acid sequence of the active site region of chloramphenicol acetyltransferase. DNA sequence analysis has revealed a high degree of homology between the P. mirabllls cat -gene and the type I ca-t variant (Tn9), 76% at the amino acid level and 73% when nucleotides in the coding sequence are compared. The mechanism for the appearance and disappearance of chloramphenicol resistance in P. mirabilis appears to be associated with a host-specific trans-acting element which controls cat gene expression. A precedent for such a control network is given by phase variation in Salmonella typhimurium, where an invertible DNA segment controls the transcription of a trans-acting regulatory element. A comparison of the 5' regions of the S.typhimurium flagellin genes in and H2, which are alternately expressed by a flip-flop control mechanism with the 5' region of P.mirabilis cat show blocks of homology. Whether or not this homology is significant in the regulation of cat gene expression has not been determined.

Osteoclast formation is a complex process requiring the temporal activation of a yet unknown number of transcription factors. Osteoclast differentiation is dependent on two cytokines: macrophage colony stimulating factor (M-CSF) and receptor activator of NF-kB ligand (RANKL). These agents induce gene expression changes during the differentiation process, presumably by inducing transcription factors. A search for genes that are regulated in the developing osteoclast was performed using both differential display and gene arrays. Differential display revealed a novel member of the krüppel-associated box (KRAB) containing transcription repressor, KROCS, which was shown to be down regulated during osteoclast formation. The potential targets for this gene remain unknown, as do the targets of the majority of the other members of the krüppel associated box (KRAB) containing family of transcription repressors. In addition to KROCS, three other genes were also identified including ADO21, PRO1859 and an endogenous retrovirus like gene and the regulation of vitamin D up-regulated protein (VDUP) was also confirmed. Array analysis identified a number of other transcription factors regulated during osteoclast formation including the up-regulated NFATc1, GABP?, FBP, EGR1 and the repressed RelB and KOX31, a KRAB containing transcription repressor. The array also identified calmodulin 1 a member of the NFAT activation pathways as up-regulated by RANKL. The expression of NFATc1 to 4 in human osteoclasts was investigated showing NFATc1 to be the most expressed NFATc in osteoclasts. The transcription variants of NFATc1 were tested for expression differences showing that the mRNAs encoding the protein isoforms B and C were most expressed. The involvement of calmodulin, calcineurin and NFATc1 involvement in osteoclast formation was further studied by the use of inhibitors. BAPTA-AM is an intracellular chelator of calcium that prevents changes in calcium concentration. Phenoxybenzamine irreversibly binds calmodulin in the presence of calcium, inhibiting the action of calmodulin. Cyclosporin A (CsA) is an inhibitor of calcineurin. Use of both BAPTA-AM and phenoxybenzamine resulted in inhibition of osteoclast formation, decreasing the percentage of multinucleated cells from 54% in control cultures to 7.9% and 7.1% respectively. Both BAPTA-AM and phenoxybenzamine treated cells showed a marked reduction in TRAP activity with only 14.5% and 16.8% respectively staining positive for TRAP. This represents an approximate 60% reduction in TRAP positive cells compared to control osteoclasts. Both BAPTA-AM treated and phenoxybenzamine treated cells were negative for bone resorption. Addition of increasing doses of cyclosporin A (CsA) to M-CSF and RANKL treated cells resulted in the inhibition of multinucleated osteoclast formation. At 1000ng/mL CsA the formation of TRAP positive cells with more than one nucleus had reduced to less than 5% from 54% without the presence of CsA. Cells treated with 1000ng/mL CsA were unable to resorb bone, however the percentage of cells that were TRAP positive remained unchanged with CsA treatment. No significant decrease in expression of cathepsin K or TRAP transcripts were observed by real-time quantitative PCR (Q-PCR) in cells treated with CsA. Although all three agents inhibited the formation of multinuclear giant cells, both BAPTA-AM and phenoxybenzamine resulted in TRAP negative cells, whereas CsA resulted in TRAP positive cells. These results implicate the intracellular calcium increase caused by RANKL and calmodulin activation as a regulator of TRAP but place the calcineurin activation of NFATc1 downstream of TRAP induction. The regulation of a series of other genes was tested to determine if some RANKL mediated regulation of osteoclast genes were 'sensitive to CsA while others were 'resistant'. Of 28 genes tested, 13 were significantly affected by CsA and were considered 'sensitive' while the RANKL mediated regulation of 15 genes was unaffected by CsA and these were considered 'resistant'. This is strong evidence for two pathways of gene activation in osteoclasts, a CsA 'sensitive' pathway involving calcineurin, NFAT and possibly other transcription factors and a CsA 'resistant' pathway of gene activation, not dependent on calcineurin. Surprisingly, the RANKL mediated induction of NFATc1 was not inhibited by CsA, suggesting that NFATc1 induction is dependent on the resistant pathway. The identity of the second pathway (or pathways) is yet to be established, however the data indicate that this pathway mediate the RANKL sensitive regulation of at least one half of genes in human osteoclasts. The corollary if that only one half of osteoclast genes are dependent on calcineurin and presumably NFATc1 activation. There was no unifying principle that separated the CsA resistant from sensitive pathways of RANKL regulation. Cell surface markers, chemokines and transcription factors were among those affected by CsA. Even classical osteoclast markers fell neatly into two categories. The RANKL mediated induction of calcitonin receptor (CalcR) was inhibited by more than 100 fold in the presence of CsA implicating NFAT/calcineurin in the regulation of CalcR expression in osteoclasts. In contrast, the RANKL mediated induction of TRAP or cathepsin K, two prominent osteoclast markers, was totally unaffected by CsA. The expression of a series of chemokines and receptors was investigated. MCP-1 and RANTES were RANKL induced, and this induction was sensitive to CsA. The CC chemokines MCP-1 and RANTES were down regulated by around 10 fold in the presence of CsA. In contrast the RANKL mediated induction of MCP-1 receptor was resistant to CsA. The existence of chemokine and receptor in the same cell provides for a RANKL inducible autocrine loop, suggesting that MCP-1 should act directly on osteoclasts. The fact that the RANKL induction of the MCP-1 receptor, CCR2B, is unaffected by CsA suggests that exogenous MCP-1 should still signal in CsA treated osteoclasts. Addition of either MCP-1 or RANTES to CsA treated cultures resulted in a recovery of 70-80% of the multinuclear TRAP positive phenotype. The MCP-1 and RANTES induced multinuclear cell could not overcome the CsA induced inhibition of bone resorption. Surprisingly, MCP-1 and RANTES induced multinucleation in the absence of RANKL (M-CSF and chemokine treated cells) resulting in 50% of the normal multinucleation present in cells treated with RANKL. The data suggest that chemokines produced by osteoclasts are involved in promoting a multinuclear phenotype. When inhibited by CsA, osteoclasts fail to produce both MCP-1 and RANTES, although their respective receptors are present. This failure to produce MCP-1 and RANTES prevents the formation of an autocrine loop. When provided with MCP-1 or RANTES the CsA inhibited osteoclasts are subsequently able to pass through to the stage of a multinucleated giant cell. Similarly, in the absence of RANKL, chemokines promote the formation of TRAP positive osteoclast-like giant cells visually indistinguishable from osteoclasts. However, the multinuclear cells formed by chemokines in the absence of RANKL were also incapable of bone resorption. In order to determine if chemokines were capable of stimulating bone resorption, after osteoclasts had formed, pre-differentiated mature osteoclasts were plated onto bone and treated with a range of cytokines. The results showed that bone resorption occurred only in cultures that were exposed continuously to RANKL. These data indicate that chemokine induction by RANKL is required for multinucleation but that RANKL is required for bone resorption. The functional testing of genes detected by array analysis proved crucial involvement of both the NFAT pathway and CC chemokines in osteoclast formation knd function. Other genes identified such as GABP and FBP, are likely to be key factors in the development of a functional osteoclast. Future works investigating human osteoclast formation should take into strong consideration the genes identified in this thesis as targets for further functional studies.
Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
School of Medical Science
Full Text

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The granulocyte-macrophage colony-stimulating factor (GM-CSF) is a cytokine that belongs to a group of glycoprotein that regulates the proliferation and differentiation of hematopoietic cells, more specifically granulocytes and macrophages. The human GM-CSF is a 14. 4 kDa protein consisting of 127 amino acid polypeptide chain and shares 52% of similarities with murine protein. The human protein has 4 cysteine residues that forms two disulphide bonds; only the Cysteine 54 and 96 are required for the biologic activity of it. This biopharmaceutical has been widely used in neutropenic patients who receive high-dose chemotherapy or were transplanted. Therefore, GM-CSF is used to restore hematopoietic dysfunctions, to stimulate the hyper-production of functionally primed effectors cells and to augment host defense against infection and malignant diseases. Its use is associated with significant decreases in chemotherapy-associated infections, antibiotic use, length of hospital day and mortality. The international patent of the biopharmaceutical Molgramostim (generic name) expired in 2006, and thus became an interesting product to pharmaceutical industries, including those settled in Brazil. Presently, Molgramostim is sold in Brazil as an imported biopharmaceutical, which, in turn becomes very costly to the Brazilian government. Therefore, the aim of this work is to develop a methodology for subsequent production of a national Molgramostim. In this work the granulocyte-macrophage colony-stimulating factor gene was assembled by PCR. It was cloned into pET30a(+) expression vector and the best condition for expression of the protein was in the BL21(DE3) strain from Escherichia coli. To the isolation of inclusion bodies an efficient protocol was developed using multi step washing procedure and purification method of the recombinant protein from inclusion bodies using only a cationic and then an anionic exchange column. The immunoassay and N-terminal sequencing confirmed the identity of rhGM-CSF. The result of the biological activity assay, in vitro, showed that the rhGM-CSF produced has an equivalent biological potential to the standard reference. The protein rhGM-CSF was produced through simple, cost effective and economically feasible process and is extremely important to the industrial procedure and healthcare community.
O fator estimulador de colônias de granulócitos e macrófagos (GM-CSF) é uma citocina pertencente a um grupo de glicoproteínas que regula a proliferação e a diferenciação de células hematopoiéticas, mais especificamente macrófagos e granulócitos. O GM-CSF humano é uma proteína de 14,5 kDa constituída de 127 aminoácidos e possui 52% de similaridade com a proteína de rato. A proteína humana possui 4 resíduos de cisteína formando duas pontes dissulfeto, porém apenas as cisteínas 54 e 96 são requeridas para a atividade biológica da mesma. Este biofármaco tem sido usado em pacientes neutropênicos que receberam altas doses de quimioterapia ou transplantados. Além disso, GM-CSF é usado para restabelecer disfunções hematopoiéticas, estimular a hiper-produção de células efetoras pré-induzidas (“primed”) funcionalmente e promover a defesa do hospedeiro contra doenças infecciosas e malignas. O uso dos mesmos está relacionado à redução no número de infecções associadas à quimioterapia, no uso de antibióticos e no tempo total de internação do paciente bem como no número de mortes. A patente internacional do biofármaco Molgramostima (nome genérico) expirou em 2006 e, além disso, tornou-se um interessante produto para indústrias farmacêuticas, inclusive para aquelas estabelecidas no Brasil. Molgramostima é vendida no Brasil como um biofármaco importado, o qual, desta forma, torna-se muito custoso para o governo brasileiro. Contudo, o objetivo deste trabalho é desenvolver uma metodologia para a posterior produção industrial de uma molgramostima a nível nacional. Neste trabalho, o gene para o hGM-CSF foi construído por PCR, clonado no vetor de expressão pET30a(+) e expresso na cepa BL21(DE3) de Escherichia coli na sua forma insolúvel. Para o isolamento e solubilização dos corpos de inclusão um eficiente protocolo foi desenvolvido utilizando múltiplos passos de lavagem e um método de purificação usando somente duas colunas cromatográficas de troca catiônica e aniônica, respectivamente. O teste de atividade biológica in vitro demonstrou que o rhGM-CSF produzido tem potencial equivalente ao padrão internacional utilizado. A proteína foi obtida por meio de um processo simples e econômico, sendo de extrema importância em procedimento industrial e para saúde da população.

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Campylobacter is a bacteria related to foodborne illnesses. It is one of the most common causes of diarrhea in humans in the world. It might cause Guillain-Barre syndrome, which attacks the cells of the peripheral nervous system causing muscle paralysis. Some strains of this bacterium can produce a cytolethal distending toxin (CDT), which can exacerbate diarrheal diseases. Birds are the main reservoir of this micro-organism, of which they are asymptomatic hosts. During the slaughter of broilers, contamination of meat and its products may occur. They are the main responsible for infections in humans. The objective of this study was to verify the presence of C. jejuni and C. coli in poultry meat, chicken and human feces and investigate the presence of cdtA, cdtB and cdtC genes in the isolates. A hundred chicken fecal samples, a hundred samples of retail poultry products and a hundred samples of human feces were collected. The poultry products were washed with Brucella broth and spread onto plates of Columbia agar. The feces samples were directly spread onto plates containing this medium. Confirmation of isolates and species identification were performed by PCR. PCR was also used to investigate the presence of cdt genes. Campylobacter was found in 61% of the chicken fecal samples, in 20% of the poultry products and in 3% of the human feces. C. jejuni was the predominant species and 93,5% of them exhibited the cdt genes. Despite the fact that the prevalence of Campylobacter found in human feces was low, the occurrence of Campylobacter in broilers and poultry products sold in southern Rio Grande do Sul was high. Besides, it has been observed that most of the isolates were highly likely to produce CDT. These results suggest there is a need for preventive measures in the production system and good manufacturing practices in the industry so as to minimize contamination of products and reduce the risk to consumers.
Campylobacter é uma bactéria relacionada a doenças transmitidas por alimentos. É uma das causas mais comuns de diarreia em humanos em todo o mundo. Raramente, pode causar a Síndrome de Guillain-Barré, que ataca as células do sistema nervoso periférico, causando paralisia muscular. Algumas cepas desta bactéria podem produzir uma toxina citoletal distensiva (CDT) capaz de agravar os quadros diarreicos. As aves são o principal reservatório do micro-organismo, do qual são portadoras assintomáticas. Durante o abate de frangos de corte pode ocorrer a contaminação da carne e seus produtos, que são os principais responsáveis pelas infecções em humanos. O objetivo do trabalho foi verificar a presença de C. jejuni e C. coli em carne de frango, fezes de frango e humanas e pesquisar a presença dos genes cdtA, cdtB e cdtC nos isolados. Foram coletadas 100 amostras de conteúdo fecal de aves de corte, 100 de produtos de frango no comércio varejista e 100 de fezes de humanos. Os produtos de frango foram lavados com Caldo Brucella e semeados em placas de Agar Columbia. As amostras de fezes foram diretamente semeadas nas placas com este meio. A confirmação dos isolados e a identificação das espécies foram realizadas através da técnica de PCR. Também foi utilizada a PCR para pesquisar a presença dos genes cdt. Obteve-se 61% de amostras de fezes de frango positivas para Campylobacter, 20% de produtos de frango e 3% de fezes de humanos. A espécie C.jejuni foi predominante e 93,5% dos isolados desta espécie apresentaram os genes para a toxina CDT. Apesar da prevalência de Campylobacter observada em fezes de humanos ter sido baixa, a ocorrência em fezes de frangos de corte e produtos de frango comercializados na região Sul do Rio Grande do Sul foi elevada e a maioria dos isolados apresentou potencial para a produção da toxina CDT. Esses resultados são indicativos da necessidade de medidas preventivas no sistema de produção e de boas práticas de fabricação na indústria, de forma a minimizar a contaminação dos produtos e diminuir o risco para os consumidores.

Ctenocephalides felis is a major pest of companion animals worldwide. This project aimed to generate novel genetic resources for C. felis and develop tools to aid drug-target identification and validation. Sample handling methods were assessed and candidate reference genes validated, to ensure quality of RNA samples and reliable gene expression normalisation. Piercing C. felis samples prior to storage in RNAlater ensured RNA integrity was maintained over time. Glyceraldehyde 3-phosphate dehydrogenase , 60S ribosomal protein L19 and elongation factor-1α were demonstrated as stable reference genes across all comparisons tested. A C. felis transcriptome encompassing multiple developmental stages, sexes and tissues was sequenced and de novo assemblies produced with two assemblers, Trinity and Oases. Each assembly contained >100000 contigs. Annotation of the assemblies generated functional insight, such as top BLAST hits, GO annotations and signal peptide predictions. The Trinity assembly was deemed the highest quality and searched for genes of interest, involved in development. Expression analysis of selected transcripts across stadia gave insight into developmental processes, and demonstrated the utility of the transcriptome. This study was the first to demonstrate that C. felis can mount an RNAi response upon exposure to dsRNA. Knockdown of glutathione S-transferase σ (GSTσ), was demonstrated in adult C. felis: ≈80 % knockdown following microinjection of dsGSTσ; ≈64 % knockdown after soaking in dsGSTσ; ≈96 % knockdown after continuous feeding on dsGSTσ. RNAi machinery was identified in C. felis. siRNAi pathway components, Dicer 2 and Argonaute 2, were upregulated following dsRNA exposure. Dicer 2 was knocked-down by soaking in dsDicer2, although results of an “RNAi of RNAi” experiment were inconclusive. Transcripts encoding machinery putatively involved in dsRNA uptake and breakdown were also identified. Through these studies, this project has generated novel insights into C. felis biology and opened up new avenues for research.

Notre premier travail a concerne l'isolement et la caracterisation d'un mutant resistant a un herbicide montrant l'implication du residu gly 192 de la sous-unite l du centre reactionnel dans la liaison avec cet herbicide. Ensuite nous avons mis au point deux modes de transfert genetique puis construit une souche deletee de l'operon puf codant pour les sous-unites du centre reactionnel et de l'antenne lhi. L'implication du residu gly 192 dans la liaison a l'herbicide a ete confirmee par complementation. Par ailleurs, la caracterisation de la souche deletee et des souches d'insertions a permis de montrer que (i) le promoteur de puf est reprime par l'oxygene et que cet operon est exprime en aerobiose a partir d'un autre promoteur en amont, (ii) les genes carotenoides crtd et crtc sont localises en aval de puf et cotranscrits avec cet operon. Nous avons egalement montre l'implication des genes crt dans les deux voies de biosynthese des carotenoides chez cette souche. Un troisieme gene crtb a ete clone. Contrairement aux autres bacteries pourpres etudiees jusqu'a maintenant, r. Gelatinosus est la seule souche ayant une localisation des genes crt en aval de puf. Disposant de mutants de carotenoides, nous avons etudie le comportement des cellules vis a vis du stress photooxydatif. Nos resultats montrent que les intermediaires de biosyntheses accumules dans les mutants sont capables de proteger les cellules contre le stress, alors que l'absence des carotenoides resulte en un taux de mutations eleves chez la souche crtb#-. Des mutants resistant au stress photooxydatif ont ete isoles et caracterises. La caracterisation moleculaire de certains mutants indique que le stress photooxydatif induit soit des mutations ponctuelles soit des recombinaisons illegitimes.

Thesis: S.M., Massachusetts Institute of Technology, Department of Chemical Engineering, 2016. In conjunction with the Leaders for Global Operations Program at MIT.
Thesis: M.B.A., Massachusetts Institute of Technology, Sloan School of Management, 2016. In conjunction with the Leaders for Global Operations Program at MIT.
Cataloged from PDF version of thesis.
Includes bibliographical references (pages 51-56).
Gene therapy is a promising modality for the potential treatment of rare Mendelian diseases. To date a number of high profile proof-of-concept studies within the industry have demonstrated the significant disease-correcting promise of this therapeutic strategy. One of the major hurdles that remains for the commercialization of gene therapies is the lack of efficient manufacturing capabilities for the production of clinical-grade drug substance/drug product. The primary goals for this project were to decrease the biological contamination and cross-contamination risk associated with the biologic manufacturing process for viral gene therapy vectors and to adjust the process in order to optimize commercial profit. The project also included documenting the different existing processes for AAV production and developing a competitive analysis using information from ongoing clinical trials in the industry pipeline. The following process design steps were followed in order to fulfill the project objectives: (1) Define product specifications, analytical needs and market size, (2) Select production platform/process, (3) Collect data and create process flow diagram, (4) Perform material and energy balances, (5) Calculate costs: equipment and consumables, (6) Model the process in a spreadsheet, (7) Carry out sensitivity analyses, (8) Assess cost-effectiveness and risk, and (9) Develop recommendations. Five different AAV production platforms were identified and an AAV gene therapy landscape was generated. Also, the current process that Pfizer is planning to use was documented and an initial market sizing was performed. Finally, all the data necessary to model the process was collected and the cost-effectiveness and biological contamination and cross-contamination risk assessment were completed. This project confirmed that the use of a scalable line of single-use high cell density bioreactors for the production of AAV is cost-effective. This implies that sufficient AAV quantities can be manufactured for preclinical and clinical trials, using the process developed by Pfizer.
by Diego Rodríguez Pinhao Miessner.
S.M.
M.B.A.

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Epigenetics can be defined as the study of heritable changes in phenotype without the occurrence of changes in nucleotide sequence. Epigenetic modifications occur by the chemical changes in DNA and their associated proteins, such as DNA methylation and histone acetylation, respectively. Meat tenderness is a trait of great interest worldwide, resulting in the development of the beef livestock sector to produce meat of quality. It is worth to highlight the role of the calpain/calpastatin system on tenderness. Calpain encoded by the CAPN1 gene plays a role in proteolysis posmortem by cleaving proteins from muscle fiber. The calpastatin encoded by the CAST gene, on the other hand, acts controlling this cleavage by blocking the action of calpain. In addition, this system is also involved in myoblast differentiation into myotubes during embryogenesis. This system controls the proteolysis of proteins that constitute the cytoskeleton and the plasma membrane. To mimic the myotube formation during embryogenesis and to study the epigenetic control of CAPN1 and CAST gene expression, satellite cell cultures established from bovine muscle were kept undifferentiated (negative control) or were induced to differentiate by incubation with culture medium containing 2% fetal bovine serum in the absence (positive control) or after treatment with epigenetic modifiers like 5-Aza- 2'-deoxycytidine (Aza, DNA demethylating) for 48 h at 10 μM, and Trichostatin A (TSA, histone acetylating) for 24 h at 50 nM. The results showed no differences (p>0.05) in myoblast rate fusion between Aza, TSA and positive control groups, but there were differences (p>0.05) when these groups were compared to the negative control, which showed lower fusion rates. There was no difference (p>0.05) in cell viability among the four groups, showing that Aza and TSA were not cytotoxic at the used concentrations. Concerning the gene expression, the gene CAST was more expressed (p<0,05) in the positive control group than the negative one; but no differences were seen in the expression (p>0,05) between positive control, 5-Aza-2 - deoxycytidine and Trichostatin A groups. For the CAPN1 gene, no difference was seen in the expression (p>0,05) between negative and positive control groups, but the CAPN1 gene was more expressed (p<0,05) in the 5-Aza-2 -deoxycytidine and Trichostatin A treatments relative to the positive control group. When the expression ratio of CAPN1/CAST were compared between treatments, was seen more expression (p<0,05) in the positive control group both comparing with negative control group and with 5-Aza-2 -deoxycytidine and Trichostatin A treatments. We may conclude that the treatments with the epigenetic modifier agents didn't affect both the bovine myoblast differentiation into myotubes and the CAST gene expression, but did in the CAPN1 gene expression and so did in the expression ratio of CAPN1/CAST.
Epigenetics can be defined as the study of heritable changes in phenotype without the occurrence of changes in nucleotide sequence. Epigenetic modifications occur by the chemical changes in DNA and their associated proteins, such as DNA methylation and histone acetylation, respectively. Meat tenderness is a trait of great interest worldwide, resulting in the development of the beef livestock sector to produce meat of quality. It is worth to highlight the role of the calpain/calpastatin system on tenderness. Calpain encoded by the CAPN1 gene plays a role in proteolysis posmortem by cleaving proteins from muscle fiber. The calpastatin encoded by the CAST gene, on the other hand, acts controlling this cleavage by blocking the action of calpain. In addition, this system is also involved in myoblast differentiation into myotubes during embryogenesis. This system controls the proteolysis of proteins that constitute the cytoskeleton and the plasma membrane. To mimic the myotube formation during embryogenesis and to study the epigenetic control of CAPN1 and CAST gene expression, satellite cell cultures established from bovine muscle were kept undifferentiated (negative control) or were induced to differentiate by incubation with culture medium containing 2% fetal bovine serum in the absence (positive control) or after treatment with epigenetic modifiers like 5-Aza- 2'-deoxycytidine (Aza, DNA demethylating) for 48 h at 10 μM, and Trichostatin A (TSA, histone acetylating) for 24 h at 50 nM. The results showed no differences (p>0.05) in myoblast rate fusion between Aza, TSA and positive control groups, but there were differences (p>0.05) when these groups were compared to the negative control, which showed lower fusion rates. There was no difference (p>0.05) in cell viability among the four groups, showing that Aza and TSA were not cytotoxic at the used concentrations. Concerning the gene expression, the gene CAST was more expressed (p<0,05) in the positive control group than the negative one; but no differences were seen in the expression (p>0,05) between positive control, 5-Aza-2 - deoxycytidine and Trichostatin A groups. For the CAPN1 gene, no difference was seen in the expression (p>0,05) between negative and positive control groups, but the CAPN1 gene was more expressed (p<0,05) in the 5-Aza-2 -deoxycytidine and Trichostatin A treatments relative to the positive control group. When the expression ratio of CAPN1/CAST were compared between treatments, was seen more expression (p<0,05) in the positive control group both comparing with negative control group and with 5-Aza-2 -deoxycytidine and Trichostatin A treatments. We may conclude that the treatments with the epigenetic modifier agents didn't affect both the bovine myoblast differentiation into myotubes and the CAST gene expression, but did in the CAPN1 gene expression and so did in the expression ratio of CAPN1/CAST.
Epigenetics can be defined as the study of heritable changes in phenotype without the occurrence of changes in nucleotide sequence. Epigenetic modifications occur by the chemical changes in DNA and their associated proteins, such as DNA methylation and histone acetylation, respectively. Meat tenderness is a trait of great interest worldwide, resulting in the development of the beef livestock sector to produce meat of quality. It is worth to highlight the role of the calpain/calpastatin system on tenderness. Calpain encoded by the CAPN1 gene plays a role in proteolysis posmortem by cleaving proteins from muscle fiber. The calpastatin encoded by the CAST gene, on the other hand, acts controlling this cleavage by blocking the action of calpain. In addition, this system is also involved in myoblast differentiation into myotubes during embryogenesis. This system controls the proteolysis of proteins that constitute the cytoskeleton and the plasma membrane. To mimic the myotube formation during embryogenesis and to study the epigenetic control of CAPN1 and CAST gene expression, satellite cell cultures established from bovine muscle were kept undifferentiated (negative control) or were induced to differentiate by incubation with culture medium containing 2% fetal bovine serum in the absence (positive control) or after treatment with epigenetic modifiers like 5-Aza- 2'-deoxycytidine (Aza, DNA demethylating) for 48 h at 10 μM, and Trichostatin A (TSA, histone acetylating) for 24 h at 50 nM. The results showed no differences (p>0.05) in myoblast rate fusion between Aza, TSA and positive control groups, but there were differences (p>0.05) when these groups were compared to the negative control, which showed lower fusion rates. There was no difference (p>0.05) in cell viability among the four groups, showing that Aza and TSA were not cytotoxic at the used concentrations. Concerning the gene expression, the gene CAST was more expressed (p<0,05) in the positive control group than the negative one; but no differences were seen in the expression (p>0,05) between positive control, 5-Aza-2 - deoxycytidine and Trichostatin A groups. For the CAPN1 gene, no difference was seen in the expression (p>0,05) between negative and positive control groups, but the CAPN1 gene was more expressed (p<0,05) in the 5-Aza-2 -deoxycytidine and Trichostatin A treatments relative to the positive control group. When the expression ratio of CAPN1/CAST were compared between treatments, was seen more expression (p<0,05) in the positive control group both comparing with negative control group and with 5-Aza-2 -deoxycytidine and Trichostatin A treatments. We may conclude that the treatments with the epigenetic modifier agents didn't affect both the bovine myoblast differentiation into myotubes and the CAST gene expression, but did in the CAPN1 gene expression and so did in the expression ratio of CAPN1/CAST.
A epigenética pode ser definida como o estudo de mudanças herdáveis no fenótipo sem a ocorrência de mudanças na sequência de nucleotídeos. As modificações epigenéticas caracterizam-se por alterações químicas no DNA e em suas proteínas associadas, como a metilação no DNA e a acetilação nas proteínas histonas, respectivamente. A maciez da carne bovina tem ganhado interesse por todo mundo, e o setor pecuário tem se desenvolvido para produzir carne de qualidade que satisfaça a essa demanda. Vale destacar os papéis do sistema calpaína/calpastatina. A calpaína, codificada pelo gene CAPN1, desempenha um papel fundamental na proteólise posmortem pela clivagem de proteínas que constituem a fibra muscular. A calpastatina, codificado pelo gene CAST, por outro lado, age controlando essa clivagem pelo bloqueio da ação da calpaína. Além disso, esse sistema também está envolvido na diferenciação dos mioblastos em miotubos na embriogênese. A ação desse sistema ocorre pela proteólise controlada de proteínas que constituem a membrana plasmática e o citoesqueleto. Para reproduzir a formação de miotubos durante a embriogênese e estudar o controle epigenético na expressão dos genes CAPN1 e CAST, foram estabelecidas culturas de células satélites de músculo bovino, que foram mantidas sem diferenciação (controle negativo) ou foram induzidas à diferenciação, por meio da incubação com meio de cultivo com 2% de soro fetal bovino, na ausência (controle positivo) e após o tratamento com os agentes modificadores epigenéticos como o 5-Aza-2 - desoxicitidina (Aza; desmetilante de DNA), por um período de 48 h á concentração de 10 μM, e Tricostatina A (TSA; acetilante de histona), por um período de 24 h á concentração de 50 nM. Os resultados mostraram que não houve diferenças (p>0,05) no índice de fusão dos mioblastos entre os grupos Aza, TSA e controle positivo, mas que houve diferença (p<0,05) desses grupos em comparação ao controle negativo, que apresentou menor índice de fusão. Também não houve diferença (p>0,05) nas taxas de viabilidade das células entre os grupos, mostrando que o Aza e TSA não foram citotóxicos nas concentrações usadas Em relação à expressão gênica, o gene CAST foi mais expresso (p<0,05) no grupo controle positivo em comparação ao controle negativo; mas não foram observadas diferenças de expressão (p>0,05) entre os grupos controle positivo, 5-Aza-2 -desoxicitidina e Tricostatina A. Para o gene CAPN1, não foi observada diferença (p>0,05) de expressão entre os grupos controle negativo e positivo, mas o gene CAPN1 foi mais expresso (p<0,05) nos tratamentos 5-Aza-2 -desoxicitidina e Tricostatina A em comparação ao grupo controle positivo. Quando a razão de expressão CAST/CAPN1 foi comparada entre os tratamentos, foi observada maior expressão (p<0,05) no grupo controle positivo, tanto em comparação ao grupo controle negativo, quanto aos tratamentos 5-Aza-2 -desoxicitidina e Tricostatina A. Podemos concluir que os tratamentos com agentes modificadores epigenéticos não afetaram a diferenciação de mioblastos bovinos em miotubos e nem a expressão do gene CAST, mas afetaram a expressão do gene CAPN1 e a razão de expressão CAST/CAPN1.
A epigenética pode ser definida como o estudo de mudanças herdáveis no fenótipo sem a ocorrência de mudanças na sequência de nucleotídeos. As modificações epigenéticas caracterizam-se por alterações químicas no DNA e em suas proteínas associadas, como a metilação no DNA e a acetilação nas proteínas histonas, respectivamente. A maciez da carne bovina tem ganhado interesse por todo mundo, e o setor pecuário tem se desenvolvido para produzir carne de qualidade que satisfaça a essa demanda. Vale destacar os papéis do sistema calpaína/calpastatina. A calpaína, codificada pelo gene CAPN1, desempenha um papel fundamental na proteólise posmortem pela clivagem de proteínas que constituem a fibra muscular. A calpastatina, codificado pelo gene CAST, por outro lado, age controlando essa clivagem pelo bloqueio da ação da calpaína. Além disso, esse sistema também está envolvido na diferenciação dos mioblastos em miotubos na embriogênese. A ação desse sistema ocorre pela proteólise controlada de proteínas que constituem a membrana plasmática e o citoesqueleto. Para reproduzir a formação de miotubos durante a embriogênese e estudar o controle epigenético na expressão dos genes CAPN1 e CAST, foram estabelecidas culturas de células satélites de músculo bovino, que foram mantidas sem diferenciação (controle negativo) ou foram induzidas à diferenciação, por meio da incubação com meio de cultivo com 2% de soro fetal bovino, na ausência (controle positivo) e após o tratamento com os agentes modificadores epigenéticos como o 5-Aza-2 - desoxicitidina (Aza; desmetilante de DNA), por um período de 48 h á concentração de 10 μM, e Tricostatina A (TSA; acetilante de histona), por um período de 24 h á concentração de 50 nM. Os resultados mostraram que não houve diferenças (p>0,05) no índice de fusão dos mioblastos entre os grupos Aza, TSA e controle positivo, mas que houve diferença (p<0,05) desses grupos em comparação ao controle negativo, que apresentou menor índice de fusão. Também não houve diferença (p>0,05) nas taxas de viabilidade das células entre os grupos, mostrando que o Aza e TSA não foram citotóxicos nas concentrações usadas Em relação à expressão gênica, o gene CAST foi mais expresso (p<0,05) no grupo controle positivo em comparação ao controle negativo; mas não foram observadas diferenças de expressão (p>0,05) entre os grupos controle positivo, 5-Aza-2 -desoxicitidina e Tricostatina A. Para o gene CAPN1, não foi observada diferença (p>0,05) de expressão entre os grupos controle negativo e positivo, mas o gene CAPN1 foi mais expresso (p<0,05) nos tratamentos 5-Aza-2 -desoxicitidina e Tricostatina A em comparação ao grupo controle positivo. Quando a razão de expressão CAST/CAPN1 foi comparada entre os tratamentos, foi observada maior expressão (p<0,05) no grupo controle positivo, tanto em comparação ao grupo controle negativo, quanto aos tratamentos 5-Aza-2 -desoxicitidina e Tricostatina A. Podemos concluir que os tratamentos com agentes modificadores epigenéticos não afetaram a diferenciação de mioblastos bovinos em miotubos e nem a expressão do gene CAST, mas afetaram a expressão do gene CAPN1 e a razão de expressão CAST/CAPN1.
A epigenética pode ser definida como o estudo de mudanças herdáveis no fenótipo sem a ocorrência de mudanças na sequência de nucleotídeos. As modificações epigenéticas caracterizam-se por alterações químicas no DNA e em suas proteínas associadas, como a metilação no DNA e a acetilação nas proteínas histonas, respectivamente. A maciez da carne bovina tem ganhado interesse por todo mundo, e o setor pecuário tem se desenvolvido para produzir carne de qualidade que satisfaça a essa demanda. Vale destacar os papéis do sistema calpaína/calpastatina. A calpaína, codificada pelo gene CAPN1, desempenha um papel fundamental na proteólise posmortem pela clivagem de proteínas que constituem a fibra muscular. A calpastatina, codificado pelo gene CAST, por outro lado, age controlando essa clivagem pelo bloqueio da ação da calpaína. Além disso, esse sistema também está envolvido na diferenciação dos mioblastos em miotubos na embriogênese. A ação desse sistema ocorre pela proteólise controlada de proteínas que constituem a membrana plasmática e o citoesqueleto. Para reproduzir a formação de miotubos durante a embriogênese e estudar o controle epigenético na expressão dos genes CAPN1 e CAST, foram estabelecidas culturas de células satélites de músculo bovino, que foram mantidas sem diferenciação (controle negativo) ou foram induzidas à diferenciação, por meio da incubação com meio de cultivo com 2% de soro fetal bovino, na ausência (controle positivo) e após o tratamento com os agentes modificadores epigenéticos como o 5-Aza-2 - desoxicitidina (Aza; desmetilante de DNA), por um período de 48 h á concentração de 10 μM, e Tricostatina A (TSA; acetilante de histona), por um período de 24 h á concentração de 50 nM. Os resultados mostraram que não houve diferenças (p>0,05) no índice de fusão dos mioblastos entre os grupos Aza, TSA e controle positivo, mas que houve diferença (p<0,05) desses grupos em comparação ao controle negativo, que apresentou menor índice de fusão. Também não houve diferença (p>0,05) nas taxas de viabilidade das células entre os grupos, mostrando que o Aza e TSA não foram citotóxicos nas concentrações usadas Em relação à expressão gênica, o gene CAST foi mais expresso (p<0,05) no grupo controle positivo em comparação ao controle negativo; mas não foram observadas diferenças de expressão (p>0,05) entre os grupos controle positivo, 5-Aza-2 -desoxicitidina e Tricostatina A. Para o gene CAPN1, não foi observada diferença (p>0,05) de expressão entre os grupos controle negativo e positivo, mas o gene CAPN1 foi mais expresso (p<0,05) nos tratamentos 5-Aza-2 -desoxicitidina e Tricostatina A em comparação ao grupo controle positivo. Quando a razão de expressão CAST/CAPN1 foi comparada entre os tratamentos, foi observada maior expressão (p<0,05) no grupo controle positivo, tanto em comparação ao grupo controle negativo, quanto aos tratamentos 5-Aza-2 -desoxicitidina e Tricostatina A. Podemos concluir que os tratamentos com agentes modificadores epigenéticos não afetaram a diferenciação de mioblastos bovinos em miotubos e nem a expressão do gene CAST, mas afetaram a expressão do gene CAPN1 e a razão de expressão CAST/CAPN1.

Thesis advisor: Thomas N. Seyfried
Sandhoff Disease (SD) is an autosomal recessive neurodegenerative disease caused by a mutation in the Hexb gene for the β-subunit of β-hexosaminidase A, resulting in the inability to catabolize ganglioside GM2 within the lysosomes. SD presents with an accumulation of GM2 and its asialo derivative GA2 primarily in the CNS. Myelin-enriched glycolipids, cerebrosides and sulfatides, are also decreased in SD corresponding with dysmyelination. At present, no treatment exists for SD. Previous studies have shown the therapeutic benefit of using adeno-associated virus (AAV) vector-mediated gene therapy in the treatment of SD in murine and feline models. In this study, CNS tissue was evaluated from SD cats (4-6 week old) treated with bilateral injections of AAVrh8 expressing feline β-hexosaminidase α and β into the thalamus and deep cerebellar nuclei (Thal/DCN) or into the thalamus combined with intracerebroventricular injections (Thal/ICV). Both groups of treated animals had previously shown improved quality of life and absence of whole-body tremors. The activity of β-hexosaminidase was significantly elevated whereas the content of GM2 and GA2 was significantly decreased in tissue samples taken from the cerebral cortex, cerebellum, thalamus, and cervical intumescence. Treatment also increased levels of myelin-enriched cerebrosides and sulfatides in the cortex and thalamus. This study demonstrates the therapeutic benefits of AAV treatment for feline SD and suggests a similar potential for human SD patients
Thesis (MS) — Boston College, 2013
Submitted to: Boston College. Graduate School of Arts and Sciences
Discipline: Biology

Diabetic embryopathy is a major complication of pregnant women with type I diabetes. Immune defects in the pathogenesis of diabetic embryopathy have been suggested. We hypothesized that activated immune system can counteract diabetic effect and result in prevention of diabetic embryopathy. Diabetes was induced in pregnant ICR mice by streptozocin injection. Three different techniques of maternal immune stimulation, complete Freundâ s adjuvant (CFA), granulocyte-macrophage colony-stimulating factor (GM-CSF), or interferon-gamma (IFN-g), were used to stimulate the maternal immune system. Approximately 50% of fetuses from hyperglycemic (>27 mM/L) dams were malformed, with neural tube defects predominating. Maternal immune stimulation during the time of normoglycemia, i.e. prior to onset of hyperglycemia, was necessary for reducing teratogenic effects associated with hyperglycemia. The immune-stimulated diabetic mice then produced significantly lower numbers of malformed fetuses: CFA 20.9%, GM-CSF 23.3%, IFN-g 13.9%. A gene microarray was then used to examine a selected panel of placental and splenic genes. We hypothesized that a shared profile of placental or splenic gene expression changes may correlate to the reduced birth defect outcome induced by the different immune stimulation procedures. Diabetes did not cause significant changes in placenta or spleen gene expression profile. In placenta, CFA and GM-CSF changed placental gene expression relative to control or diabetes, but differentially affected such genes relative to each other; further, IFN-g did not affect gene expression relative to control or diabetes. Thus no common pattern of improved placental cytokine, cell-cycle, apoptotic, transcription factor, or other gene expression was identified in the immune-stimulated mice. In spleen, all 3 immune activators produced a common altered gene expression profile. The overall gene expression profile after all immune stimulation procedures suggested increased splenocyte activity and cytokine production. The cytokine GM-CSF, in particular, was up-regulated in splenic leukocytes. This cytokine has previously been associated with reduced cleft palate in urethane-exposed mice after immune stimulation, and with reduced limb malformations in cyclophosphamide-treated mice after intra-uterine administration. In contrast, the TGF-beta3 gene was down-regulated in immune-stimulated diabetic mice. This gene was up-regulated in urethane-exposed mice, an effect that may be associated with reduced cleft palate. Thus unlike urethane, TGF-beta3 gene expression did not show a relationship with reduced diabetes-induced birth defects. Taken together, these data prove our hypotheses and suggest that mechanistically diverse forms of immune activation result in protection against diabetes-related teratogenesis, but only if given prior to onset of hyperglycemia. Such immune stimulation in mice may act through systemic immune organs, i.e. spleen, over-riding adverse effects of diabetes on development.
Ph. D.

The technologies that enable writing and editing of DNA form the foundation of modern molecular biology and biotechnology. However, a number of methodological barriers have limited the widespread adoption of both high-throughput de novo gene synthesis and large-scale genome alteration. Increasingly, work in the fields of synthetic biology, protein design, and gene therapy has been hindered by shortcomings in current DNA writing and editing technologies. The goal of this dissertation has been to improve both the throughput of chemical gene synthesis and the accuracy of genome editing tools. The scale of gene synthesis is most acutely limited by the high cost of using column-synthesized oligonucleotides as the base material. It has been clear for some time that using the much cheaper microarray-synthesized DNA instead would significantly decrease costs of making long, double-stranded DNA. Unfortunately, microarrays’ high chemical complexity, high error rates, and low synthesis yield has prevented their adoption into gene synthesis workflows. We have used selective nucleotide pool amplification and enzymatic error removal to develop a synthesis pipeline that uses Agilent’s Oligonucleotide Library Synthesis microarrays to build 500-850 base pair-long double-stranded constructs. At the time of initial publication the size of the total pool (13,000 oligonucleotides encoded ~2.5 megabases of DNA) was at least one order of magnitude larger than previously reported attempts. Following our initial progress on increasing the throughput of gene synthesis, it became apparent that using applying synthetic DNA in vivo is bottlenecked by the low efficiencies and unpredictable accuracies of existing genome engineering techniques. In an effort to build tools that can be used in a large variety of organisms we focused our efforts on engineering site-specific recombinases, many of which can function without using host-encoded proteins. Unfortunately, many groups have reported that site-specific recombinases can cause toxicity possibly due to off-target binding and recombination activities. To address this problem, we proposed that the accuracy of DNA-binding proteins can be altered through mutations in the of protein-protein interaction domains. To test this idea we obtained single-residue mutants of Cre recombinases that exhibited improved site discrimination in in vivo and in vitro recombination experiments. We have also been interested in developing rapid and reproducible assay of protein binding assays. Towards this goal, we conducted proof-of-concepts experiments that demonstrated that gel shift assays could be used to generate binding curves in a multiplexed fashion. We propose that the slope of the information content as a function of binding affinity can be used to compare binding accuracy of dissimilar proteins.

A partir de 280 isolados fúngicos de cana-de-açúcar, 18 cepas foram avaliadas quanto á presença de genes da policetídeo sintase por meio da técnica do PCR. Estes fungos foram identificados taxonomicamente por uma abordagem polifásica, classificando-os dentro de quatro ordens e nove gêneros. A avaliação da atividade biológica demonstrou a presença de metabolitos com propriedades antibióticas quando enfrentados a micro-organismos patogênicos. Segundo a análise de correspondência múltipla, esta atividade poderia estar associada com a local de isolamento dos fungos. Foram detectadas 36 seqüências similares a genes PKS a partir de 17 destes fungos. A análise filogenética do domínio KS, conduzida pelo método de neighbor-joining, indicou que 16 seqüências se acomodaram dentro do grupo monofilético dos PKS envolvidos na produção de policetídeos não reduzidos e as outras 10 seqüências se acomodaram dentro do grupo monofilético dos PKS envolvidos na produção de policetídeos reduzidos. A análise do domínio CMT também apontou que as seqüências podiam se acomodaram em grupos de PKS dependendo do grau de redução do policetídeo, todas as seqüências CMT se relacionaram com PKS envolvidos na produção de policetídeos reduzidos. As análises dos modelos estruturais também demonstraram que as seqüências estavam altamente relacionadas com estruturas protéicas da família das enzimas de condensação, destacando a presença de uma hélice característica que carrega o resíduo de cisteína, responsável pela atividade de condensação. Extratos orgânicos obtidos de cultivos dos fungos foram avaliados parar detectar a presença de compostos tipo lovastatina. Por meio de cromatografia CCDS, detectaram-se bandas de 10 extratos com o mesmo deslocamento que a lovastatina padrão, mas apenas 6 destas foram confirmados por CLAE. O isolado A. flavus CBMAI 1023, foi selecionado para a realização de experimentos de produção a maior escala onde foi possível isolar e caracterizar um novo policetídeo.
From a group of 280 sugarcane-derived fungi 18 strains were assessed for the presence of polyketide synthase genes by PCR approaches. These fungi were identified taxonomically by a polyphasic approach classifying into four orders and nine genres. Biological activity tests showed the presence of antibiotic metabolites against pathogenic microorganisms and the relationship of this activity might be linked with the fungal isolate location by multiple correspondence analyses. 36 sequences similar to PKS genes fragments were detected from 17 of these fungi. A neighbor-joining phylogenetic analysis of the KS domain showed that 16 sequences fit on the monophyletic group of PKS evolved with production of non reduced polyketides, and the other 10 sequences fit on the monophyletic group of PKS evolved with the production of reduced polyketides. CMT domain analysis also pointed that the sequences fit with groups of PKS depending on polyketide reduction grade, all ten related to PKS evolved with the synthesis of reduced polyketides. Protein structural analysis also pointed out that these sequences are closely related with proteins from condensing enzyme family, highlighting the presence of a characteristic helix elbow that bears the cysteine residue responsible for the condensation activity. The fungi were also tested for their capacity of producing lovastatin compounds where chromatographic TLC detected bands from 10 extracts with the same dislocation compared to a lovastatin, but only 6 were confirmed by HPLC. The A. flavus CBMAI (1023) were selected for upscale production experiments, from where it was possible isolate and characterize a new polyketide compound.

La myéline est une gaine formée par l’enroulement de la membrane plasmique de la cellule de Schwann autour de l’axone dans le nerf périphérique. Lorsque cette gaine est détruite, on parle de démyélinisation, cela provoque de nombreuses maladies, dont les maladies de Charcot Marie Tooth (CMT) de type 1. Les maladies CMT sont héréditaires et atteignent le système nerveux périphérique. Les symptômes communs incluent : une faiblesse musculaire, une démarche maladroite, des troubles de l’équilibre et des pieds très cambrés ou très plats. Le type le plus fréquent est la forme autosomique dominante CMT1A.Une duplication du bras court du chromosome 17 contenant le gène PMP22 (Peripheral Myelin Protein 22) induit la CMT1A. La PMP22, une petite protéine exprimée par les cellules de Schwann, est donc en excès et entraine une démyélinisation. Il existe un modèle de rats transgéniques PMP22 (ou rats CMT1A) mimant cette pathologie humaine. Les rats CMT1A surexpriment la pmp22 de souris de façon hétérozygote. Jusqu’à présent, aucun remède n’existe pour les maladies CMT. Un des traitements envisageables est la thérapie génique. Le but de mon projet de thèse était d’étudier la validité et l'efficacité de la thérapie génique chez les rats CMT1A. La stratégie consiste à réduire la surexpression de la protéine PMP22 chez le rat CMT1A à l’aide d’ARNsh anti-PMP22. Pour ne pas être détruits par l’organisme et maintenir une expression longue, ces ARN sh-PMP22 sont transférés chez le rat grâce à des vecteurs viraux dérivés de virus adéno-associés, ou AAV (pour adeno-associated virus). Nous avons donc injecté un des différents sérotypes d'AAV,l'AAV9 exprimant les ARN sh-PMP22 de souris ainsi que la GFP comme marqueur des cellules infectées dans les nerfs sciatiques de rats CMT1A à l’âge de 6 jours ou 7 jours.Nous avons d’abord confirmé que les virus thérapeutiques infectaient une très large proportion de cellules de Schwann dans le nerf sciatique de rat CMT1A et ensuite que l’infection de ces cellules par les virus exprimant les ARN sh-PMP22 induisait une diminution significative de l’expression de la protéine PMP22. L'analyse du phénotype moteur des rats CMT1A traités avec les AAV9 exprimant les ARN sh-PMP22 montre que les rats CMT1A traités ne développent pas la maladie observée dans les contrôles. Également, les rats CMT1A présentent une hypoalgésie, un phénotype qui n’apparait pas dans les CMT1A traités avec les vecteurs thérapeutiques. Le traitement par thérapie génique empêche la réduction de la vitesse de conduction nerveuse observé dans les rats malades. Concernant la biodistribution des virus, 2,5 mois après le traitement, en dehors des nerfs sciatiques ou les virus ont été injectés, le virus était présent dans les muscles qui entourent le nerf et aussi dans quelques ganglion dorsaux. Pour la réponse immunitaire,les rats injectés, à seulement 2 exceptions près, n’ont pas développé de facteurs neutralisants anti-AAV9. Cette thérapie génique pourrait être utilisée dans les essais cliniques.Avant de passer aux études cliniques pour le traitement de la maladie CMT1A à l’aide d’AAV9 exprimant des ARN sh-PMP22 humain, la dose d’expression de ce ARN sh-PMP22 doit être très soigneusement déterminée car si la PMP22 est trop réduite, une autre maladie peut se développer, la neuropathie héréditaire avec hypersensibilité à la pression. Il est aussi important d’avoir un outil bien adapté qui permet d’évaluer l’efficacité du traitement. Aucun existant n’est assez fiable pour mesurer la myéline du nerf périphérique. Pour remédier à ce manque, nous avons testé la technique d'imagerie Coherent Anti-stokes Raman Scattering (CARS) en caractérisant avec succès les défauts de la myéline. Par conséquent, le CARS est une technique prometteuse permettant d’évaluer l’avancement des maladies de la myéline et l’efficacité de nouvelles thérapies pour les neuropathies périphériques démyélinisantes
Myelin, a tissue synthesized by Schwann cells, covers and protects nerves. If damaged, it causes many demyelinating diseases such as the inherited peripheral nervous system disorder Charcot Marie Tooth or CMT type 1. CMT neuropathies display a large variability from one patient to another. Nevertheless, the most common symptoms include muscle weakness, an awkward way of walking (gait), equilibrium problem and highly arched or very flat feet. The most common subtype of CMT is an autosomal dominant disorder known as CMT1A. CMT1A is caused by the duplication of the peripheral myelin protein 22 (PMP22) gene on the short arm of chromosome 17 (17p11.2) resulting in an excess of PMP22. This leads to demyelination. PMP22 is a small protein expressed by Schwann cells. There is still no cure for CMT diseases. One approach for a treatment is gene therapy. The aim of my thesis project was to deliver proof of principle for a gene therapy approach on a CMT1A rat model characterized by extra copies of mouse pmp22 gene (CMT1A rat). The treatment strategy consisted in reducing PMP22 overexpression in CMT1A rats with shRNA against PMP22. Viral vectors like adeno-associated virus (AAV having serotypes from1-10) are used to deliver shRNA in vivo so that they won’t be destroyed by the organism and for them to be long-lasting. Thus, we injected sciatic nerves of 6-7-day-old CMT1A rats with AAV9 expressing shRNA PMP22 with a GFP marker. We first confirmed that the virus highly transduced Schwann cells and that AAV9 shRNA PMP22 decreased PMP22 protein expression in CMT1A rats’ sciatic nerves. CMT1A rats treated with AAV9 shRNA PMP22 showed that they didn’t develop the motor phenotype seen in controls. Moreover, hypoalgesia observed in CMT1A rats was alleviated by treatment. In addition, gene therapy increased the reduced nerve conduction velocity found in CMT1A rats. Concerning safety, no viral off-targets were detected except in muscles close to the injection site (sciatic nerve) and in the dorsal root ganglions. Except for 2 rats, there was no immune response against AAV; no anti-AAV9 neutralizing factors. Consequently, this gene therapy could be used in clinical trials. Before moving to clinical studies, the minimal effective dosage should be very carefully defined because if PMP22 is completely deleted, another disease is caused: Hereditary Neuropathy with Pressure Palsies. It is also crucial to have a strong readout to evaluate the outcome of a treatment. However, no tool consistent enough exists for examining the peripheral nerve. Thus, we tested the label-free imaging technique Coherent Anti-stokes Raman Scattering (CARS) and successfully characterized myelination defects. Consequently, CARS could be used as a consistent outcome measure for developing new therapies for demyelinating peripheral neuropathies

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O fator estimulador de col?nias de granul?citos e macr?fagos (GM-CSF) ? uma citocina pertencente a um grupo de glicoprote?nas que regula a prolifera??o e a diferencia??o de c?lulas hematopoi?ticas, mais especificamente macr?fagos e granul?citos. O GM-CSF humano ? uma prote?na de 14,5 kDa constitu?da de 127 amino?cidos e possui 52% de similaridade com a prote?na de rato. A prote?na humana possui 4 res?duos de ciste?na formando duas pontes dissulfeto, por?m apenas as ciste?nas 54 e 96 s?o requeridas para a atividade biol?gica da mesma. Este biof?rmaco tem sido usado em pacientes neutrop?nicos que receberam altas doses de quimioterapia ou transplantados. Al?m disso, GM-CSF ? usado para restabelecer disfun??es hematopoi?ticas, estimular a hiper-produ??o de c?lulas efetoras pr?-induzidas ( primed ) funcionalmente e promover a defesa do hospedeiro contra doen?as infecciosas e malignas. O uso dos mesmos est? relacionado ? redu??o no n?mero de infec??es associadas ? quimioterapia, no uso de antibi?ticos e no tempo total de interna??o do paciente bem como no n?mero de mortes. A patente internacional do biof?rmaco Molgramostima (nome gen?rico) expirou em 2006 e, al?m disso, tornou-se um interessante produto para ind?strias farmac?uticas, inclusive para aquelas estabelecidas no Brasil. Molgramostima ? vendida no Brasil como um biof?rmaco importado, o qual, desta forma, torna-se muito custoso para o governo brasileiro. Contudo, o objetivo deste trabalho ? desenvolver uma metodologia para a posterior produ??o industrial de uma molgramostima a n?vel nacional. Neste trabalho, o gene para o hGM-CSF foi constru?do por PCR, clonado no vetor de express?o pET30a(+) e expresso na cepa BL21(DE3) de Escherichia coli na sua forma insol?vel. Para o isolamento e solubiliza??o dos corpos de inclus?o um eficiente protocolo foi desenvolvido utilizando m?ltiplos passos de lavagem e um m?todo de purifica??o usando somente duas colunas cromatogr?ficas de troca cati?nica e ani?nica, respectivamente. O teste de atividade biol?gica in vitro demonstrou que o rhGM-CSF produzido tem potencial equivalente ao padr?o internacional utilizado. A prote?na foi obtida por meio de um processo simples e econ?mico, sendo de extrema import?ncia em procedimento industrial e para sa?de da popula??o

INTRODUÇÃO: Diversas sociedades profissionais recomendam a realização de testes genéticos para mulheres que desenvolveram câncer de ovário, a fim de identificar portadores de mutação germinativa em genes BRCA1/2 e oferecer terapia redutora de risco. OBJETIVO: O objetivo deste estudo foi realizar análise de custo-efetividade de programa para diagnóstico de mutação germinativa em genes BRCA1/2 e de estratégias preventivas para pacientes com o diagnóstico de câncer de ovário e seus familiares de primeiro grau. METODOLOGIA: O estudo realizou análise de custo-efetividade mediante desenvolvimento de modelo de decisão de Markov e perspectiva do Sistema Único de Saúde. As estratégias comparadas refletiram a adoção de teste genético e estratégias preventivas para pacientes e familiares ou o acompanhamento proposto atualmente. A razão de custo-efetividade incremental foi expressa em termos de custo por caso evitado de neoplasia maligna. A análise de sensibilidade foi realizada de forma determinística univariada. RESULTADOS: Demonstrou-se incremento em efetividade e em custos com a realização de testes genéticos e a adoção de medidas profiláticas para pacientes e familiares. A razão de custo-efetividade incremental foi calculada em R$ 14.224,40 e em R$ 908,58, respectivamente, por caso evitado em pacientes com o diagnóstico prévio de câncer de ovário e em seus familiares de primeiro grau. Estes valores foram considerados inferiores ao limiar de custo-efetividade selecionado no estudo (de R$ 7.543,50 a R$ 23.786,70). DISCUSSÃO: O programa analisado pode ser considerado como estratégia custo-efetiva para a realidade nacional, sobretudo no que tange aos familiares de primeiro grau de pacientes com o diagnóstico de câncer de ovário. Outras publicações demonstraram conclusões similares para o tema em diversos países. CONCLUSÃO: Um possível desdobramento deste trabalho poderia ser representado pela realização de uma análise de impacto orçamentário da incorporação do programa como política de saúde no país
INTRODUCTION: Several professional societies recommend performing genetic tests for women who have developed ovarian cancer in order to identify BRCA1/2 germline-mutation carriers and offer risk-reducing therapy. OBJECTIVE: The objective of this study was to perform a cost-effectiveness analysis of a BRCA1/2 germline mutation diagnosis program and preventive strategies for patients diagnosed with ovarian cancer and their first degree relatives. METHODS: The study performed a cost-effectiveness analysis through the development of a Markov decision model and the perspective of the Unified Health System. The compared strategies reflected the adoption of genetic testing and preventive strategies for patients and their relatives or the usual follow-up. The incremental cost-effectiveness ratio was expressed in terms of cost per avoided case of cancer. Sensitivity analysis was performed in a univariate and deterministic manner. RESULTS: There has been an increase in effectiveness and in costs with genetic testing and the adoption of prophylactic measures for patients and their relatives. The incremental cost-effectiveness ratio was calculated at R$ 14,224.40 and R$ 908.58, respectively, for avoided cases in patients with prior diagnosis of ovarian cancer and their first-degree relatives. These values were considered lower than the cost-effectiveness threshold selected in the study (from R$ 7,543.50 to R$ 23,786.70). DISCUSSION: The analyzed program can be considered as a cost-effective strategy for the national reality, especially in relation to the first-degree relatives of patients with ovarian cancer. Other publications have shown similar conclusions for the subject in several countries. CONCLUSION: A possible development of this work could be represented by a budget impact analysis of the incorporation of the program as health policy in Brazil

O inseticida spinosad tem sido um dos mais utilizados para o controle de Spodoptera frugiperda (J. E. Smith) no Brasil, devido à sua eficácia e ao seu mecanismo de ação único (modulador alostérico de receptores nicotínicos da acetilcolina). Para fornecer subsídios a um programa de manejo da resistência, foram realizados estudos para compreender as bases genéticas e moleculares da resistência de S. frugiperda a este inseticida. Inicialmente, foi selecionada uma linhagem de S. frugiperda resistente a spinosad (Spin-res) em laboratório por meio da técnica \"F2 screen\". A razão de resistência, baseada na CL50, foi de aproximadamente 890 vezes. A partir de cruzamentos recíprocos entre a linhagem suscetível (Sus) e Spin-res, constatou-se que o padrão de herança da resistência de S. frugiperda a spinosad é autossômica e incompletamente recessiva. Retrocruzamentos da progênie F1 de cruzamentos recíprocos com a linhagem Spin-res confirmaram a hipótese de herança poligênica da resistência, com número mínimo de segregações independentes variando de 1,86 a 2,45. Além disso, observou-se um elevado custo adaptativo associado à resistência de S. frugiperda a spinosad, baseado nos parâmetros da tabela de vida e fertilidade. A partir dos dados de seqüenciamento de quatro bibliotecas de cDNA de lagartas de quarto ínstar das linhagens Sus e Spin-res (expostas ou não a spinosad), utilizando a plataforma HiScan1000® (Illumina©), foi realizada a comparação do perfil de transcrição e expressão diferencial de genes entre as linhagens Sus e Spin-R. O transcritoma foi montado utilizando a estratégia de novo contendo cerca de 19 milhões de leituras single-end com qualidades de score acima de 30, gerando 42406 transcritos com o N50 de 598 pb. A busca por similaridade no banco de dados não-redundante (nr) do NCBI, possibilitou a anotação funcional de 24980 (59%) transcritos, alinhando-se a Bombyx mori L., Helicoverpa armigera (Hübner) e Spodoptera spp. com 22,5; 3,81 e 3,6% das sequências respectivamente. Foram identificados 2903 transcritos apresentando expressão diferencial (P <= 0,05, t-test; fold-change > 2) entre as linhagens Spin-res e Sus. Dentre os transcritos relacionados a enzimas do complexo metabólico, 23 P450 monooxigenases, 13 glutathiona S-transferases, uma carboxilesterase e uma esterase foram superexpressas na linhagem Spin-res. Além disso, foi observada a superexpressão de 15 genes relacionados à produção energética na linhagem Spin-res, o que pode estar relacionada ao elevado custo adaptativo associado à resistência. Análises de PCR quantitativo em tempo real confirmaram que os padrões de expressão foram consistentes com os resultados de RNA-seq. Bioensaios com os sinergistas PBO e DEM mostraram pouco envolvimento de enzimas P450 e nenhum envolvimento de glutationa S-transferases na resistência de S. frugiperda a spinosad. O sequenciamento da subunidade α6 do receptor nicotínico de acetilcolina de ambas linhagens demonstrou a existência de uma mutação sinônima entre as duas linhagens (G567A), indicando que a subunidade α6 não é a única relacionada à resistência de S. frugiperda a spinosad.
Spinosad has been one of the most used insecticides to manage Spodoptera frugiperda (J. E. Smith) in Brazil, due to its efficacy and unique mode of action (nicotinic acetylcholine receptor allosteric modulator). To support an insect resistance management program (IRM), we selected and characterized in laboratory a spinosad-resistant strain (Spin-res) of S. frugiperda using the F2 screen method. The resistance ratio, based on LC50, was ≈ 890-fold. Based on reciprocal crosses between susceptible (Sus) and Spin-res, the inheritance of spinosad resistance in S. frugiperda was autosomal incompletely recessive. Backcrosses between the F1 from reciprocal crosses and the parental Spin-res revealed a polygenic resistance, with an estimation of at least 1.86 to 2.45 genes related to spinosad resistance. Furthermore, it was observed a strong fitness cost associated to spinosad-resistance in Spin-res strain, based on the life table and fertility parameters. The characterization of the transcriptional profile and the differential gene expression comparison between susceptible and spinosad-resistant strains of Spodoptera frugiperda were obtained from the sequencing of cDNA libraries from fourth instar larvae of Sus and Spin-res strains (exposed or not to spinosad) using a HiScan1000® platform (Illumina©). The transcriptome was de novo assembled using nearly 19 million single-end reads with quality score over 30, yielding 42,406 transcripts with a N50 of 598 bp. Based on similarity search in the non-redundant (nr) nucleotide database, 24,980 (59%) transcripts were annotated. Most of the transcripts aligned to Bombyx mori L., Helicoverpa armigera (Hübner) and Spodoptera spp., with 22.5%, 3.81, and 3.6, respectively. We identified 2,032 differentially expressed transcripts (P <= 0.05, t-test; fold-change > 2) between the susceptible and spinosad-resistant strains. Among metabolic enzyme transcripts, 23 P450 monooxigenases, 13 glutathione S-transferases, one carboxylesterase and one esterase were up-regulated in the spinosad-resistant strain. In addition, it was observed 15 genes superexpressed in spinosad-resistant strain related to energy production, which can be related to the high fitness cost associated with resistance. Quantitative real-time PCR analysis showed that patterns of gene expression were consistent with RNA-seq results. Synergistic bioassays using PBO and DEM showed little involvement of P450s in spinosad-resistance and lack of involvement regarding the glutathione Stransferases. Furthermore, we sequenced and compared the subunit α6 from the nicotinic acetylcholine receptor of S. frugiperda Spin-res and Sus strains. Only one synonymous mutation within the two strains (G567A) was found, showing that the α6 is not the only subunit involved in S. frugiperda resistance to spinosad.

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The Meat tenderness, a trate of economic importance in animal production, is influenced by the intensity of the degradation of myofibrillar proteins in post-mortem. The μ-calpain is the main enzyme responsible for meat tenderness of skeletal muscle, and, conversely, the calpastatin, which is encoded by the CAST gene, acts as endogenous inhibitor of calpain and thus decreases the extent of proteolysis in skeletal muscle. Polymorphisms in CAST were associated with enzyme activity and shear force, indicating the great importance of the study of CAST gene regulation. It is known that the transcription of most genes is stably suppressed in most tissues and only remains active in their tissue of expression and in certain developmental stages, and that can be controlled by epigenetic events such as methylation of DNA cytosine that is identified by sequencing of bisulfite-treated DNA. The aim of this study was to evaluate if there was preferential expression, of tissue, genotype and stage of development for the CAST gene in liver, muscle and skin of fetuses and muscle and liver of homozygous and heterozygous adult cattle for the A> G exon 30/3'UTR polymorphism, evaluated by real-time PCR with SYBR ® fluorophore, and to verify if the differential expression is regulated by the methylation status of promoter region. Differential gene expression analyses were normalized to the reference gene RPS-9. When we analyzed the tissue-specific expression in fetuses, the CAST gene was 2 times more expressed in liver than in skin (p <0.05) and almost two times more expressed in liver than in muscle (p <0.05). It was also found that this gene was 1.83 x up regulated in adult muscle when compared to fetal muscle (p <0.05), showing differential expression in the developmental stage. Differences in expression between genotypes were also found, when comparing the homozygous genotype to the heterozygous genotype (used as calibrator). Fetal samples of muscle and skin of individuals with GG genotype presented higher expression (p <0.05) of CAST gene (2x and 1,74 x, respectively, compared to heterozygous) and muscle of animals with AA genotypes also presented higher expression (1.4x compared to AG). In adult animals, the gene was up regulated in liver and muscle of individuals with GG genotype (2x and 1.63x more than AG, respectively) and was less expressed in the liver of homozygote AA (0,32x less than AG) (p <0.05). The presence of a CpG island in the promoter region of the gene CAST was identified and the methylation status was studied after bisulfite treatment, cloning of the fragment and sequencing of clones. The CpG island was hypomethylated in different tissues: 0.63% of methylated CpG dinucleotides in fetal muscle, 0.43% in fetal liver and 0.61% in adult muscle. According to the different genotypes the island was methylated in 0.61%, 0 49%, 0.60% in animal with AA genotype, 0.81%, 0.35%, 0.34% in AG, 0.4%, 0.45% ,0.9% in GG in fetal muscle, fetal liver and adult muscle respectively. In our results we show that the CpG island is hypomethylated and can allow transcription of the gene but the methylation does not explain the differences in expression within tissues, developmental stage and genotypes of the CAST gene.
A maciez da carne, uma característica de grande interesse econômico, é influenciada pela intensidade da degradação de proteínas miofibrilares no período pós-mortem. A μ-calpaína é a principal enzima responsável pelo amaciamento do músculo esquelético, e de maneira oposta, a calpastatina que é codificada pelo gene CAST, atua como inibidor endógeno das calpaínas e, portanto, diminui a taxa e extensão da proteólise no músculo esquelético. Polimorfismos no gene CAST já foram associados à atividade da enzima e à força de cisalhamento, indicando a grande importância no estudo da regulação desse gene. Sabe-se que a transcrição da maior parte dos genes é reprimida estavelmente na maioria dos tecidos e só permanece ativa nos seus tecidos de expressão e em determinados estádios do desenvolvimento, e que isso pode ser controlado por eventos epigenéticos como a metilação de citosinas do DNA, passível de identificação por sequenciamento de DNA tratado com bissulfito. Os objetivos deste estudo foram avaliar se ocorre expressão preferencial de tecido, de genótipo e de estádio do desenvolvimento para o gene CAST em fígado, músculo e pele de fetos e músculo e fígado de animais adultos em bovinos homozigotos e heterozigotos para o polimorfismo A>G no éxon 30/3 UTR por meio de PCR em tempo real com o fluoróforo SYBR®. Além disso, foi verificado se a expressão diferencial do gene é regulada pelo status de metilação no seu promotor. Todas as expressões foram normalizadas para o gene referência RPS-9. Em fetos o gene CAST foi duas vezes mais expresso (p<0,05) em fígado do que em pele e quase duas vezes mais expresso (p<0,05) em fígado do que em músculo. Também foi encontrado aumento na expressão do gene de 1,83 x (p<0,05) em músculo adulto quando comparado a músculo fetal, evidenciando expressão diferencial de estádio de desenvolvimento. Quando analisadas as diferenças de expressão entre genótipos, comparando o genótipo homozigoto com o genótipo heterozigoto (usado como calibrador) foi encontrado, em amostras de fetos, um aumento de expressão (p<0,05) do gene CAST em músculo e pele de indivíduos GG (2x e 1,74x, respectivamente, em relação a heterozigotos) e músculo de indivíduos AA (1,4x em reação a AG). Em amostras de animais adultos, o gene foi mais expresso em fígado e músculo de indivíduos GG (2x e 1,63x mais que AG, respectivamente) e foi menos expresso (p<0,05) em fígado de indivíduos homozigotos AA (0,32x menos que AG). Foi identificada a presença de uma ilha CpG na região promotora do gene CAST e foi realizado tratamento do DNA com bissulfito, a clonagem do fragmento e o sequenciamento de clones. A ilha CpG mostrou-se hipometilada nos diferentes tecidos: 0,63% de dinucleotídeos CpG metilados em músculo fetal, 0,43% em fígado fetal e 0,61% em músculo adulto; e nos diferentes genótipos: 0,61%, 0,49% e 0,60% em AA, 0,81%, 0,35%, 0,34% em AG, 0,4%, 0,45% e 0,9% em GG em músculo fetal, fígado fetal e músculo adulto respectivamente. Assim a hipometilação da ilha CpG pode permitir a transcrição do gene, mas não explica as diferenças de expressão entre tecidos, estádio de desenvolvimento e genótipo para o genes CAST.

Introduction: Pathogenic mutations in the TP53-gene is present in about 50% of all somatic cancers. The TP53 gene’s function is to stop cancer cells from dividing, thus protect us from cancer. When this gene is not functioning properly, carriers face 70-100% risk of developing cancer in their lifetime. Early diagnosis of cancer improves survival and currently individuals with pathogenic hereditary mutations in this gene are entitled to an extensive surveillance program to increase early detection of cancer. A new study, the Swedish TP53 study (SWEP53), is investigating a surveillance program offering whole-body magnetic resonance imaging (WBMRI) of confirmed carriers. It is not known if the potential health effects of such surveillance programs justify the additional costs. The objective of this thesis was to determine whether any of the surveillance programs are cost-effective in Sweden. Methods: A novel decision analytic model was developed using a health care perspective covering the lifetime of carriers of mutations in TP53. Nine different cancers were modelled. All cancers carry a cost. an impact on health-related quality of life and survival. Three separate scenarios were investigated; no surveillance, surveillance by current standard of care and surveillance using WBMRI as proposed in the SWEP53-study. The total costs and total quality adjusted life years (QALY) of each scenario were used to calculate incremental cost-effectiveness ratios for the current standard of care and the SWEP53-protocol. Results: Surveillance of both male and female carriers of pathogenic mutations in TP53 carries an incremental cost-effectiveness ratio of 748 194 SEK. Surveillance using is WBMRI carries a cost of more than seven million SEK. If the annual probability of diagnosis is ca 40-50 percentage points higher than in the standard of care this may change to a level similar to SOC in the current analysis. The greatest uncertainty of the results lay in the estimation of the impact on survival from cancer diagnosis and annual probability of diagnosis. Conclusion: The incremental cost per QALY of the current surveillance program is likely acceptable in Sweden given the rarity and severity of being a carrier of a hereditary pathogenic mutation in TP53. Surveillance using WBMRI carries an incremental cost per QALY that is much higher than what is traditionally acceptable in Sweden. The clinical benefit of surveillance using WBMRI in relation to current surveillance is unclear and more data is needed. This analysis is made under great uncertainty but shows that when analyzing hereditary mutations, it is imperative to consider the whole spectrum of attributed disease as this greatly impacts the cost-effectiveness of e.g. surveillance. These estimates may be uncertain but as of today this is the only and the best estimate available.

This study conducts an ex-ante economic impact evaluation of developing low cost technologies for pyramiding useful genes from wild relatives into elite progenitors of cassava in Nigeria, Ghana and Uganda. More specifically, it estimates the change in economic surplus generated by introducing cassava varieties with tolerance to cassava mosaic disease, green mites, whiteflies, and delayed post-harvest deterioration. It compares the economic benefits of marker-assisted selection (MAS) to conventional breeding for these traits. Results indicate that varieties developed with marker-assisted breeding that incorporate all three traits are worth US$2.89 billion in Nigeria, $854 million in Ghana, and $280 million in Uganda over 20 years. If these varieties were to be developed with tolerance to CMD and Green mites alone they would be worth US$1.49 billion in Nigeria, $675 million in Ghana, and $52 million in Uganda if developed through MAS. If developed solely by conventional breeding they would be worth about US$676 million in Nigeria, $304 million in Ghana, and $18 million in Uganda. The difference is mostly due to the faster timing of release for the varieties developed with MAS and the higher probability of success. Several sensitivity analyses were conducted and benefits for MAS range from US$1.7 billion to US$4.3 billion for all three traits depending on assumptions. In all cases, the research investment is highly profitable from a societal standpoint.
Master of Science

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Coordenação de Aperfeiçoamento de Pessoal de Nível Superior
Neste trabalho foi construída uma biblioteca metagenômica a partir de um consórcio microbiano termofílico com aproximadamente 135.000 clones, abrigando cerca de 3,5 Gpb de DNA metagenômico. Essa biblioteca foi construída com o objetivo de identificar genes que codificam enzimas lignocelulolíticas para serem expressos na levedura Kluyveromyces marxianus CCT 7735 (UFV-3). De 6.720 clones analisados (5 % do total), foram obtidos 182 hits positivos para atividades de celulases, xilanases e β-glicosidases, com seleção e sequenciamento de 30 fosmídeos que deram origem à identificação de 34 ORFs codificando para enzimas glicosil hidrolases, relacionadas com a hidrólise de celulose e hemicelulose. Paralelo à construção da biblioteca, foi obtido uma linhagem de K. marxianus CCT 7735 (UFV- 3) mutante (ura3 ̄ ). Pela primeira vez nesta levedura a deleção deste gene foi realizada utilizando-se a técnica split-marker, com seleção dos mutantes primeiramente em placas contendo geneticina e, posteriormente, associados à seleção em placas contendo ácido 5-fluorótico (5-FOA). Os resultados apresentados mostram que esta técnica de deleção pode ser eficientemente empregada para K. marxianus CCT 7735 (UFV-3), mesmo levando-se em conta a diploidia desta linhagem. A partir da obtenção do mutante ura3 ̄ , deu-se a construção do vetor pKmLPG para ser usado como sistema de expressão para essa levedura, uma vez que a marca de seleção contida neste vetor é o gene URA3. A característica diferencial e promissora deste sistema de expressão é o uso da sequência do promotor do gene que codifica a enzima endo-polygalacturonase endógena de K. marxianus CCT 7735 (UFV-3). A confirmação do vetor pKmLPG será realizada por sequenciamento. Sem essa confirmação, utilizou-se então o vetor de expressão pKMCL para clonagem de três genes de β-glicosidase isolados a partir da biblioteca fosmidial na levedura K. marxianus CCT 7735 (UFV-3). O vetor pKMCL é derivado do vetor de expressão pKLAC2 de K. lactis e utiliza a marca de seleção que confere resistência ao antibiótico geneticina. Por realização de teste enzimático dos transformantes em meio sólido, observou-se a presença de atividade extracelular de β-glicosidase endógena de K. marxianus CCT 7735 (UFV- 3). Com o genoma desta levedura anotado, foi possível identificar o gene, e juntamente com os demais genes de β-glicosidase (P3Gli, P8Gli e P9Gli), foram preditas as estruturas tri-dimensionais dessas proteínas. A confirmação dos transformantes para os genes P3Gli, P8Gli e P9Gli foi realizada por PCR, e atividade de β-glicosidase foi detectada tanto no sobrenadante extracelular quanto na região do periplasma em oito das nove cepas transformantes analisadas. Os resultados de expressão heteróloga de β-glicosidades em K. marxianus CCT 7735 (UFV-3) mostram que esta linhagem pode ser usada como hospedeira na expressão de diferentes genes lignocelulolíticos, com expectativa de uso das linhagens recombinantes capazes de secretar celulases visando a produção de etanol celulósico.
A metagenomic library harboring around 3,5 Gpb was constructed from a thermophilic microbial consortium. The aim of this library was to identify genes coding lignocellulolytic enzymes that could be expressed in the yeast Kluyveromyces marxianus CCT 7735 (UFV-3). In total, 6,720 clones (5% of all clones) were analysed and 182 positive hits were found for cellulases, xylanases and β-glucosidases. The sequencing of 30 selected fosmids resulted in the identification of 34 putative open reading frames (ORFs) coding glycoside hydrolases involved with cellulose and hemicellulose degradation. Simultaneously, a defective mutant strain of K. marxianus CCT 7735 (UFV-3) for gene ura3 was obtained. The gene was deleted by using, for the first time in this yeast, the split- marker technique that consisted in a first selection of mutants in solid medium with the antibiotic geneticin followed by a second selection in the presence of 5- Fluoroorotic Acid. The results presented here demonstrated the efficiency of the split-marker technique in K. marxianus CCT 7735 (UFV-3), even though this is a diploid strain. Once the ura3 - was obtained, the vector pKmLPG was constructed using the URA3 as a marker gene in order to have an expression system for the ura3 - mutant strain. The differential and promising feature of this vector lies in the presence of the promoter sequence of the gene coding an endo-polygalacturonase enzyme from K. marxianus CCT 7735 (UFV-3). The confirmation of the correct vector construction will be performed by sequencing. In order to express genes isolated from the metagenomic library in the yeast K. marxianus CCT 7735 (UFV-3) three genes coding β-glucosidase were cloned onto the vector pKMCL. This vector is derived from pKLAC2 of Kluyveromyces lactis and it uses the resistance gene for the antibiotic geneticin as a marker. Extracellular activity of endogenous β- glucosidase from K. marxianus CCT 7735 (UFV-3) was detected by enzymatic assay in solid medium during the analyses of transformants, and based in the annotated genome of this yeast, was possible to identify the β-glucosidase gene. The three dimensional structure of the endogenous protein as well from those codified by the β-glucosidase genes (P3Gli, P8Gli and P9Gli) were predicted. The confirmation of transformants for the cloned genes P3Gli, P8Gli and P9Gli was done by PCR, and the β-glucosidase activity was detected in both extracelllular supernatant and periplasm region in eight of nine transformants analysed. Results of heterologous expression of β-glucosidase in K. marxianus CCT 7735 (UFV-3) demonstrated that this strain can be used as a host for expression of various lignocellulolytic genes, with the expectation to use recombinant yeast strains capable to secret celulases targeting the production of cellulosic etanol.
Tese liberada do Sigilo pelo departamento em 04-04-2017, ver arquivo

O grande grupo heterogêneo de neuropatias periféricas hereditárias estão entre os casos mais comuns de perda sensitiva e fraqueza muscular em crianças e adolescentes. Pelo menos 84 genes estão envolvidos com neuropatias sensitivo-motoras hereditárias (NSMH), sendo suas formas de herança mais comuns as autossômico-dominantes desmielinizante e axonal e as neuropatias ligadas ao cromossomo X, e as mais raras as autossômicorecessivas desmielinizante e axonal e as formas ainda não classificadas. O gene HINT1, possuinte de 3 exons e localizado no cromossomo 5, codifica a proteína Histidine triad nucleotide binding protein 1, uma variante transcricional (mRNA) regulatória que hidroliza substratos. Recentemente mutações em HINT1 foram também relacionadas à neuropatias axonais com neuromiotonia (ARCMT2-NM), e portanto à CMT. O objetivo deste trabalho foi realizar o screening mutacional do gene HINT1 em uma amostra da população brasileira com quadro clínico de CMT recessivo (CMT2-AR), e foram encontradas 1 mutação silenciosa já previamente descrita, 1 polimorfismo exônico e 1 polimorfismo intrônico, também já conhecidos. Concluiu-se que mutações no gene HINT1 não são portanto responsáveis pela CMT-AR nesta amostra da população brasileira.
The large heterogeneous group of inherited peripheral neuropathies are among the most common causes of sensory loss and muscle weakness in children and adolescents. At least 84 genes are involved in inherited sensorymotor neuropathies (NSMH), being the demyelinating and axonal autosomaldominant and the X-linked neuropathies their most common forms of inheritance, and the demyelinating and axonal autosomal-recessive and not yet classified forms the most rare ones. The HINT1 gene, with 3 exons and located on chromosome 5, encodes the protein Histidine triad nucleotide binding protein 1, a regulatory transcriptional variant (mRNA) that hydrolyzes substrates. Recently, mutations in HINT1 were also related to axonal neuropathy with neuromyotonia (ARCMT2-NM), and therefore to CMT. The objective of this study was the mutational screening of the HINT1 gene in a sample of the Brazilian population with clinical recessive CMT (CMT2-AR), and 1 silent mutation previously described, 1 intronic polymorphism and 1 exonic polymorphism, both also known, were founded. It was then concluded that mutations in the HINT1 gene are not responsible for CMT2-AR in this particular sample of the Brazilian population.

Le controle de l'initiation de la traduction est une etape importante de l'expression des genes chloroplastiques et fait intervenir, chez e. Coli, la proteine ribosomique (proteine-r) s1. Afin d'etudier l'etape d'initiation de la traduction chez le chloroplaste, nous avons caracterise chez spinacia oleracea une proteine (cs1) apparentee a la proteine s1. Nous avons isole un adnc codant pour le precurseur de la proteine-r cs1. Cs1 est considerablement plus courte que sa contrepartie bacterienne. Un noyau central homologue se compose de trois repetitions degenerees qui presentent de l'homologie principalement avec le domaine de liaison a l'arn de la proteine s1 d'e. Coli. Cs1 a ete surproduite dans e. Coli et purifiee. Nous avons etudie les proprietes de liaison a l'arn de la proteine cs1 au sein de la sous-unite ribosomique 30s et de la proteine isolee. Nous montrons que cs1 joue un role actif dans la liaison des arnm durant l'initiation de la traduction. Les implications de ces resultats pour la comprehension du systeme traductionnel du chloroplaste sont discutees. Dans la seconde partie de ce travail, nous avons montre que l'arnm codant pour la proteine-r cs1 est synthetise tres precocement durant les premieres etapes du developpement des plantes et est accumule meme en absence de lumiere. Nous avons clone et sequence la totalite de la region codante ainsi que la region 5 regulatrice du gene nucleaire unique (rps1) codant pour cs1. Nous avons observe la presence de deux departs de transcription. L'arnm le plus long code par le gene rps1 est specifiquement transcrit dans les feuilles. Ces resultats sont a relier a une accumulation differentielle de l'arnm cs1 dans les racines et dans les feuilles. Ces observations nous amenent a conclure que le gene de menage rps1 est regule transcriptionnellement de maniere tissu-specifique

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Conselho Nacional de Pesquisa e Desenvolvimento Científico e Tecnológico - CNPq
Campylobacter termofílicos são, atualmente, as principais bactérias causadoras de doenças gastrointestinais em todo o mundo. Esse grupo é assim denominado devido a sua temperatura ótima de multiplicação oscilar entre 42 °C e 43 °C, sendo Campylobacter jejuni, C. coli, C. lari e C. upsaliensis, as principais espécies envolvidas nos casos de campilobacteriose em humanos. Dentre essas espécies, a mais relacionada à essa doença é C. jejuni, seguida por C. coli. O principal reservatório desses micro-organismos são as aves, principalmente os frangos, possivelmente pela temperatura corporal desses animais ser similar à temperatura ótima para Campylobacter termofílicos. Com isso, o objetivo desse estudo foi avaliar a ocorrência, a diversidade genética, o perfil de resistência a antimicrobianos e a presença de genes associados à virulência em isolados de Campylobacter termofílicos provenientes de frangos de corte e na cama de aviário em granjas aviárias da região sul do Rio Grande do Sul, Brasil. Um total de 48 amostras foram coletadas em três diferentes granjas (A, B e C), incluindo uma amostra de swab de arrasto da cama do aviário e 15 pools de amostras de swab de cloaca em cada granja. Das três granjas amostradas, apenas a granja C apresentou contaminação por Campylobacter termofílicos, sendo todos os isolados identificados por técnicas fenotípicas e moleculares como C. jejuni. Dessas 16 amostras positivas, obtiveram-se 28 isolados, sendo 16 pelo isolamento em ágar Preston e 12 do ágar mCCD. A diversidade genética entre os isolados foi avaliada por PFGE, verificando-se que todos os isolados apresentaram um único padrão de macrorestrição, sugerindo clonalidade entre os isolados e a presença de apenas uma fonte de infecção por Campylobacter nessa granja. O perfil de resistência a antimicrobianos foi avaliado pelo teste de disco difusão em ágar, utilizando-se oito antimicrobianos distintos, de três classes diferentes: tetraciclina, quinolonas e macrolídeos. Os isolados apresentaram perfil similar de resistência a antimicrobianos, sendo resistentes às quinolonas e tetraciclinas e sensíveis aos macrolídeos. Devido a relação clonal e ao perfil de resistência similar, um isolado representativo foi selecionado para detecção dos genes de virulência. A técnica de PCR foi utilizada para detectar a presença dos genes ciaB, cadF, cdtA, cdtB e cdtC, sendo o isolado selecionado positivo todos os genes pesquisados. Dessa forma, a presença de C. jejuni resistente a antimicrobianos e com potencial de virulência em frangos de corte prontos para o abate e na cama de aviário durante o período de produção é um risco à saúde pública, pois esses micro-organismos podem ser introduzidos no ambiente do abatedouro e contaminar as carcaças durante o abate.
Thermophilic Campylobacter are currently the leading bacteria causing of gastrointestinal diseases worldwide. This group is so named because its optimal multiplication temperature oscillates between 42 °C and 43 °C, being Campylobacter jejuni, C. coli, C. lari and C. upsaliensis, the main species involved in cases of human campylobacteriosis. Among these species, the most related to this disease is C. jejuni, followed by C. coli. The main reservoir of these microorganisms are birds, especially chickens, possibly because the body temperature of these animals coincides with the optimal temperature for thermophilic Campylobacter. Therefore, the aim of this study was to verify the occurrence, genetic relationship, antimicrobial susceptibility, and the presence of virulence genes in thermophilic Campylobacter from broilers and broiler bedding from the southern region of Rio Grande do Sul, Brazil. A total of 48 samples were collected in three different farms (A, B and C), which comprising one sample of drag swab and 15 pools of cloacal swabs in each farm. From the three farms sampled, only the farm C showed thermophilic Campylobacter contamination. All isolates were identified by phenotypic and molecular techniques such as C. jejuni. Of these 16 positive samples, 28 isolates were obtained, 16 being isolated by Preston agar and 12 by mCCD agar. The genetic diversity among the isolates was evaluated by PFGE, and it was observed that all the isolates belonged to the same macrorestriction pattern, suggesting clonality among the isolates and the presence of only one source of Campylobacter infection in this farm. The antimicrobial resistance profile was evaluated by the agar disc diffusion test using eight distinct antimicrobial agents from three different classes: tetracyclines, quinolones and macrolides. The isolates presented a similar antimicrobial resistance profile, being resistant to quinolones and tetracyclines and susceptible to macrolides. As the isolates shared the same PFGE pattern and similar resistance profile, a representative isolate was chosed for investigation of virulence genes. A PCR assay was carried out aiming to identify the presence of ciaB, cadF, cdtA, cdtB and cdtC virulence genes and all the genes evaluated were found. Thus, the presence of C. jejuni resistant to antimicrobial agents and harboring virulence genes in broilers and broiler farm during the broiler production period may represents a potential risk to public health, because these microorganisms can be introduced into the abattoir environment and may contaminate the carcasses during slaughter.

The emergence of extended spectrum β-lactamase (ESBL) producing Enterobacteriaceae worldwide has led to an increased use of carbapenems and may drive the development of carbapenem resistance. Existing mechanisms are mainly due to acquired carbapenemases or the combination of ESBL-production and reduced outer membrane permeability. The focus of this thesis was to study the development of carbapenem resistance in Escherichia coli in the presence and absence of acquired β-lactamases. To this end we used the resistance plasmid pUUH239.2 that caused the first major outbreak of ESBL-producing Enterobacteriaceae in Scandinavia. Spontaneous carbapenem resistance was strongly favoured by the presence of the ESBL-encoding plasmid and different mutational spectra and resistance levels arose for different carbapenems. Mainly, loss of function mutations in the regulators of porin expression caused reduced influx of antibiotic into the cell and in combination with amplification of β-lactamase genes on the plasmid this led to high resistance levels. We further used a pharmacokinetic model, mimicking antibiotic concentrations found in patients during treatment, to test whether ertapenem resistant populations could be selected even at these concentrations. We found that resistant mutants only arose for the ESBL-producing strain and that an increased dosage of ertapenem could not prevent selection of these resistant subpopulations. In another study we saw that carbapenem resistance can even develop in the absence of ESBL-production. We found mutants in export pumps and the antibiotic targets to give high level resistance albeit with high fitness costs in the absence of antibiotics. In the last study, we used selective amplification of β-lactamases on the pUUH239.2 plasmid by carbapenems to determine the cost and stability of gene amplifications. Using mathematical modelling we determined the likelihood of evolution of new gene functions in this region. The high cost and instability of the amplified state makes de novo evolution very improbable, but constant selection of the amplified state may balance these factors until rare mutations can establish a new function. In my studies I observed the influence of β-lactamases on carbapenem resistance and saw that amplification of these genes would further contribute to resistance. The rapid disappearance of amplified arrays of resistance genes in the absence of antibiotic selection may lead to the underestimation of gene amplification as clinical resistance mechanism. Amplification of β-lactamase genes is an important stepping-stone and might lead to the evolution of new resistance genes.

Cancer can develop through a series of genetic events in combination with external influential factors that alter the progression of the disease. Gene expression studies are designed to provide an enhanced understanding of the progression of cancer and to develop clinically relevant biomarkers of disease, prognosis and response to treatment. One of the main aims of microarray gene expression analyses is to develop signatures that are highly predictive of specific biological states, such as the molecular stage of cancer. This dissertation analyzes the classification complexity inherent in gene expression studies, proposing both techniques for measuring complexity and algorithms for reducing this complexity. Classifier algorithms that generate predictive signatures of cancer models must generalize to independent datasets for successful translation to clinical practice. The predictive performance of classifier models is shown to be dependent on the inherent complexity of the gene expression data. Three specific quantitative measures of classification complexity are proposed and one measure ( f) is shown to correlate highly (R 2=0.82) with classifier accuracy in experimental data. Three quantization methods are proposed to enhance contrast in gene expression data and reduce classification complexity. The accuracy for cancer prognosis prediction is shown to improve using quantization in two datasets studied: from 67% to 90% in lung cancer and from 56% to 68% in colorectal cancer. A corresponding reduction in classification complexity is also observed. A random subspace based multivariable feature selection approach using costsensitive analysis is proposed to model the underlying heterogeneous cancer biology and address complexity due to multiple molecular pathways and unbalanced distribution of samples into classes. The technique is shown to be more accurate than the univariate ttest method. The classifier accuracy improves from 56% to 68% for colorectal cancer prognosis prediction.  A published gene expression signature to predict radiosensitivity of tumor cells is augmented with clinical indicators to enhance modeling of the data and represent the underlying biology more closely. Statistical tests and experiments indicate that the improvement in the model fit is a result of modeling the underlying biology rather than statistical over-fitting of the data, thereby accommodating classification complexity through the use of additional variables.

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Introdução: Estudos e revisões da literatura científica internacional têm reunido dados de suporte para o papel da farmacogenômica na medicina clínica, especificadamente o genótipo UGT1A1*28 e UGT1A1*6, como preditores de toxicidade associada à terapia com CPT-11 (irinotecano), devido uma inserção de timina-adenina na região promotora TATAbox do gene UGT1A1 ou um polimorfismo de nucleotídeo único no éxon 1 do mesmo gene, causando menor expressão da enzima UGT1A1 e consequentemente menor glucuronidação do fármaco. Objetivo: Verificar a ocorrência de polimorfismos na região promotora do gene UGT1A1 e associar a presença destes com a manifestação de toxicidades ao fármaco CPT-11 em pacientes com câncer atendidos em dois Hospitais públicos especializados em oncologia em Belém/PA. Método: Os pacientes oncológicos em tratamento à base de CPT-11 foram acompanhados pelo método de acompanhamento farmacoterapêutico quanto a ocorrência de toxicidades. As reações adversas foram avaliadas de acordo com o National Cancer Institute Common Toxicity Criteria for Adverse Events, Version 4.0. O estudo também analisou o material genético dos pacientes, quanto à freqüência e distribuição do polimorfismo no gene UGT1A1 por reação em cadeia de Polimerase e sequenciamento. Assim como também puderam ser avaliados os dados clínicos e epidemiológicos dos sujeitos. Resultados: Um total de 31 pacientes foram recrutados, a maioria (80,6%) tratados com regime IFL modificado (120mg/m² de irinotecano), o gênero mais freqüente foi o feminino (54,8%) e o sítio primário do tumor, predominante, foi o reto (41,9%). Dentre os 27 pacientes que puderam ser genotipados nenhum apresentou polimorfismo no éxon 1 (UGT1A1*6), mas foram detectados os seguintes alelos quanto ao polimorfismo no promotor TATA do gene, TA5/6 (3,7%), TA6/6 (44,4%), TA6/7 (37%) e TA7/7 (14,8%). Um total de 71 toxicidades foram observados em 25 pacientes. A população estudada encontra-se em equilíbrio de Hardy-Weinberg (p=0,135). Nosso estudo não encontrou relação significante entre as diferentes toxicidades ou RAM’s (reações adversas ao medicamento) manifestadas nos pacientes com diferentes números de alelos variantes, porém foi observado que pacientes que tinham dois alelos ou um único alelo variante teve mais intervenções médicas (redução de dose, atraso ou interrupção do tratamento) devido toxicidades, do que pacientes do alelo tipo selvagem (p=0,016). Conclusão: Os achados deste estudo demonstraram alta frequência de reações adversas ao uso de CPT-11 nos pacientes estudados, mesmo em protocolos de baixa dose, em relação a outros estudos, apesar de não terem apresentado diferença significante, sugerem a continuidade do mesmo a fim de obter maior tamanho amostral, haja vista que quando a população foi estratificada por freqüência de intervenções médicas motivadas por toxicidade, o grupo portador da mutação, heterozigota ou homozigota, apresentou maior taxa de intervenção durante o tratamento, ou seja, esses pacientes podem apresentar toxicidades mais severas que comprometam a continuidade do tratamento.
Introduction: Studies and reviews the international scientific literature have gathered data to support the role of pharmacogenomics in clinical medicine, specifically genotype UGT1A1*28 and UGT1A1*6 as predictors of toxicity associated with therapy with CPT-11 (irinotecan), because an insert thymine-adenine in the promoter region of the UGT1A1 gene TATAbox or a single nucleotide polymorphism in exon 1 of the same gene, causing lesser extent UGT1A1 enzyme and hence lower glucuronidation of the drug. Objective: To investigate the occurrence of polymorphisms in the promoter region of the UGT1A1 gene and associate their presence with the toxicities of manifestation to CPT-11 drug in cancer patients treated at two public hospitals specialized in oncology in Belém /PA. Method: Patients in cancer treatment to CPT-11 base were accompanied by pharmacotherapeutic monitoring method as the occurrence of toxicities. Adverse reactions were assessed according to the National Cancer Institute Common Toxicity Criteria for Adverse Events, Version 4.0. The study also analyzed the genetic material of patients, the frequency and distribution of the polymorphism in the UGT1A1 gene by polymerase chain reaction and sequencing. As they could also be evaluated clinical and epidemiological data of the subjects. Results: A total of 31 patients were recruited, the majority (80.6%) treated with modified IFL regimen (120 mg /m² CPT-11), the most frequent gender was female (54.8%) and the primary site of the tumor , predominantly, it was the rectum (41.9%). Among the 27 patients could be genotyped none showed polymorphism in exon 1 (UGT1A1 * 6), but the following alleles were detected as the TATA promoter polymorphism in the gene, TA5/6 (3.7%), TA6/6 (44 , 4%), TA6/7 (37%) and TA7/7 (14.8%). A total of 71 toxicities were observed in 25 patients. The study population is in Hardy-Weinberg equilibrium (P = 0.135). Our study found no significant relationship between the different toxicities manifested in patients with different numbers of variant alleles, but it was observed that patients who had two alleles or a single variant allele had more medical interventions (dose reduction, delay or discontinuation of treatment) due to toxicity than patients in the wild-type allele (p = 0.016). Conclusion: The findings of this study showed a high frequency of adverse reactions to CPT-11 use in the studied patients, even low-dose protocols in relation to other studies, although they have not shown significant differences suggest the continuity of the same order to get larger sample size, considering that when the population was stratified by frequency of medical interventions motivated by toxicity, the carrier of the mutation group, heterozygous or homozygous, had higher intervention rate during treatment. Those patients can present toxicities more severe than compromise the continuity of care.

The study of bacterial evolution is fundamental for addressing current problems of antibiotic resistance and emerging infectious diseases and lays a solid foundation for successful and rational design in biotechnology and synthetic biology. The main aim of this thesis is to test evolutionary hypotheses, largely based on theoretical considerations and sequence analysis, by designing scenarios in a laboratory setting to obtain experimental data. Paper I examines how genomic GC-content can be reduced following a change in mutation rate and spectrum. Transcription-related biases in mutation location were found, but no replicative bias was detected. Paper II explores the distribution of fitness effects of random substitutions in two ribosomal protein genes using a highly sensitive fitness assay. The substitutions had a weakly deleterious effect, with low frequencies of both neutral and inactivating mutations. The surprising finding that synonymous and non-synonymous substitutions have very similar distribution of fitness effects suggests that, at least for these genes, fitness constraints are present mainly on the level of mRNA instead of protein. Paper III examines selective barriers to inter-species gene transfer by constructing mutants with a native gene replaced by an orthologue from another species. Results suggest that the fitness costs of these gene replacements are large enough to provide a barrier to this kind of horizontal gene transfer in nature. The paper also examines possible compensatory mechanisms that can reduce the cost of the poorly functioning alien genes and found that gene amplification acts as a first step to improve the selective contribution after transfer. Paper IV investigates the fitness constraints on horizontal gene transfer by inserting DNA from other species into the Salmonella chromosome. Results suggest that insertion of foreign DNA often is neutral and the manuscript provides new experimental data for theoretical analysis of interspecies genome variation and horizontal gene transfer between species.

Amaciamento natural devido proteólise miofibrilar pelas enzimas calpaínas (cálcio-dependentes) e descoloração devido oxidação do pigmento mioglobina podem ocorrer em carne maturada. Em bovinos, o tipo biológico Bos indicus apresenta maior atividade de calpastatina (CAST, inibidora das calpaínas) no músculo e concentração de melanina (modulador de vitamina D3) na pele do que Bos taurus. Maior concentração de melanina na pele reduz fotossíntese de vitamina D3 e, subsequentemente, poderia reduzir as concentrações de seus metabólitos 25-hidróxivitamina D3 (25-D) e 1,25-di-hidróxi-vitamina D3 (1,25-D; modulador de cálcio) no plasma de Bos indicus. Nos casos de maiores concentrações de 1,25-D plasmático, uma melhor absorção de cálcio da dieta com aumento de suas concentrações no plasma e músculo poderia resultar em atividade melhorada das calpaínas. Além disso, maiores concentrações de 1,25-D plasmático poderiam colaborar para minimizar oxidação de carne devido sua propriedade antioxidante. Então, além da maior atividade de CAST no músculo, os Bos indicus poderiam ter mais duas desvantagens para produzir carne mais macia e menos oxidada: concentrações maiores de melanina na pele e menores de 1,25-D no plasma. Desta forma, o objetivo deste trabalho foi estudar as relações entre as concentrações de melanina total (MELT) e suas frações [faeumelanina (FAE) e eumelanina (EUM)] na pele, metabólitos da vitamina D3 (25-D e 1,25-D) no plasma, cálcio plasmático e muscular e maciez [Índice de Fragmentação Miofibrilar (MFI) e força de cisalhamento (FC)] e cor (valores de L*, a* e b*) em carne maturada (1, 7 e 14 dias) e suas associações com polimorfismos de um único nucleotídeo (SNPs) nos genes candidatos receptor da melanocortina-1 [MC1R; rs109688013 (C/T) e rs110710422 (G/-)], proteína ligante à vitamina D3 [DBP; rs136359868 (T/C) e rs135330728 (T/C)] e CAST [rs109384915 (T/C)]. Bovinos Nelore (n=86), abatidos com 516 ± 39 kg aos 24 ± 1 meses, foram usados para determinação dos genótipos e mensuração das características. Na pele, a fração EUM foi positivamente correlacionada com MELT, mais do que a fração FAE. As frações de melanina na pele foram correlacionadas negativamente. A fração FAE foi correlacionada negativamente com 1,25-D plasmático, mas não foi correlacionada com 25-D plasmático. Melanina e suas frações na pele e metabólitos da vitamina D3 no plasma não foram correlacionadas com cálcio plasmático e muscular. Todavia, cálcio no plasma e músculo foram correlacionados positivamente com MFI e valores de L* e b* e negativamente com FC e valores de a*. A EUM e MELT na pele foram correlacionadas negativamente com FC e valores de a* e b* e positivamente com valores de L*, enquanto que 25-D no plasma foi correlacionada positivamente com MFI e valores de a* e b* e negativamente com valores de L*. A FAE foi correlacionada positivamente com MFI e negativamente com os valores de L*, a* e b*. No gene MC1R, o alelo T do SNP rs109688013 apresentou-se fixado (100%) na população, enquanto que o alelo G e sua deleção (-) do SNP rs110710422 tiveram frequência de 97,7 e 2,3%, respectivamente. SNPs do gene MC1R resultaram nos genótipos do loco Extension (E/E = T/T + G/G e E/e = T/T + G/-), que foi associado com 1,25-D plasmático e valores de b* no dia 1. No gene DBP, o alelo C do SNP rs136359868 foi menos frequente (3,5%) do que o alelo T, enquanto que os alelos C e T do SNP rs135330728 tiveram uma frequência de 73,8 e 26,2%, respectivamente. SNPs do gene DBP foram associados com MELT na pele e valores de L* e a* em diferentes dias. No gene CAST, os alelos C e T do SNP rs109384915 tiveram a mesma frequência. O SNP rs109384915 foi associado com MFI ao dia 7 e a substituição do alelo T por C reduziu os valores de MFI e a* no dia 7 e os valores de b* no dia 1. Ao final, maiores concentrações de FAE na pele e 25-D no plasma melhoraram proteólise miofibrilar e cor de carne, enquanto as maiores concentrações de EUM e MELT na pele resultaram em uma carne mais macia com uma pior cor. Associações do loco Extension e dos SNPs no gene DBP com cor de carne parecem consequência das diferenças em 1,25-D no plasma e melanina na pele. SNP do CAST associou-se com proteólise miofibrilar e cor de carne maturada, mas não com FC.
Natural tenderization by myofibrillar proteolysis through the calpains enzymes (calcium-dependent) and discoloration by oxidation of myoglobin pigment may occur in aged meat. In cattle, the Bos indicus biological type has higher calpastatin activity (CAST, inhibitor of calpains) in muscle and melanin concentration (modulator of vitam in D3) in skin than Bos taurus. Higher melanin concentration in skin reduces photosynthesis of vitamin D3 and, subsequently, could reduce the concentrations of its metabolites 25-hydroxy-vitamin D3 (25-D) and 1,25-di-hydroxy-vitamin D3 (1,25-D; modulator of calcium) in plasma from Bos indicus cattle. In cases of higher plasma 1,25-D concentrations, an improved absorption of calcium from the diet followed by increased plasma calcium concentrations could result in enhanced activity of calpains. Furthermore, higher plasma 1,25-D concentrations could collaborate to minimize meat oxidation due to its antioxidant propriety. Then, in addition to higher CAST activity in muscle, the Bos indicus cattle could have two more disadvantages to produce tender and less oxidized meat: higher melanin concentrations in skin and lower 1,25-D concentrations in plasma. Hence, the objective of this work was to study the relationships between the concentrations of total melanin (MELT) and its fractions [pheomelanin (PHEO) and eumelanin (EUM)] in skin, vitamin D3 metabolites (25-D and 1,25-D) in plasma, plasma and muscle calcium, and tenderness [Myofibrillar Fragmentation Index (MFI) and shear force (SF)] and color (L*, a*, and b* values) in aged meat (1, 7, and 14 days) and their associations with single nucleotide polymorphisms (SNPs) in candidate genes as melanocortin-1 receptor [MC1R; rs109688013 (C/T) and rs110710422 (G/-)], vitamin D3-binding protein [DBP; rs136359868 (T/C) and rs135330728 (T/C)], and CAST [rs109384915 (T/C)]. Nellore cattle (n=86), slaughtered with 516 ± 39 kg at 24 ± 1 months, were used for genotyping and traits measurements. In skin, the EUM fraction was positively correlated with MELT than the PHEO fraction. The melanin fractions in skin were negatively correla ted. The PHEO fraction was negatively correlated with plasma 1,25-D, but not with plasma 25-D. Melanin and its fractions in skin and vitamin D3 metabolites in plasma were not correlated with plasma and muscle calcium. Nevertheless, plasma and muscle calcium were positively correlated with MFI, and L* and b* values and negatively correlated with SF and a* values. The EUM and MELT in skin were negatively correlated with SF, and a* and b* values and positively correlated with L* values, while 25-D in plasma was positively correlated with MFI, and a* and b* values and negatively correlated with L* values. The PHEO was positively correlated with MFI and negatively correlated with L*, a*, and b* values. In MC1R gene, the rs109688013 SNP allele T was fixed (100%) in the population, while the rs110710422 SNP allele G and its deletion (-) had a frequency of 97.7 and 2.3%, respectively. MC1R SNPs resulted in genotypes of the Extension locus (E/E = T/T + G/G and E/e = T/T + G/-), which was associated with plasma 1,25-D and b* values at the day 1. In DBP gene, the rs136359868 SNP allele C was less frequent (3.5%) than allele T, while rs135330728 SNP alleles C and T had a frequency of 73.8 and 26.2%, respectively. DBP SNPs were associated with MELT in skin, and L* and a* values at different days. In CAST gene, the rs109384915 SNP alleles C and T had a similar frequency. The rs109384915 SNP was associated with MFI at the day 7 and the substitution from allele T to C reduced the MFI and a* values at the day 7 and the b* values at the day 1. At last, higher skin PHEO and plasma 25-D concentrations improved the myofibrillar proteolysis and meat color, while higher skin EUM and MELT concentrations resulted in a meat with improved tenderness and worsened color. Associations of the Extension locus and polymorphisms in DBP gene with the meat color seem to be a consequence of the differences in plasma 1,25-D and skin melanin. CAST SNP is associated with myofibrillar proteolysis and meat color, but not with SF.

Memoria para optar al Título Profesional de Médico Veterinario
En la producción de carne para consumo humano, una de las características más importantes del producto para los consumidores es la terneza de la carne, la cual posee un componente genético asociado, genes que codifican las enzimas que participan en el proceso de degradación de la carne en el postmortem y que pueden sufrir cambios en sus secuencias, del tipo polimorfismo de un solo nucleótido (SNP), que generan cambios en estas enzimas y por ende cambios en la característica del producto. Este hecho, hace muy importante el tener una herramienta de detección eficiente y rápida de estas variaciones genéticas. Muestras de semen de toros procedentes del catálogo de inseminación artificial de INDAP, 2007 y muestras de tejido de novillos híbridos de Wagyu, fueron sometidas a extracción de DNA, comprobando la efectividad de ésta mediante medición de concentración de DNA en espectrofotómetro. Se implementó una técnica de reacción de polimerasa en cadena alelo específica (AS – PCR), la cual fue aplicada a las muestras con alta concentración de DNA extraído, utilizando partidores sintetizados para los SNP CAPN1 – 316, CAPN1 – 530 y CAST – 2959. Los resultados del AS – PCR fueron confirmados con secuenciación de varias muestras. La extracción de DNA fue más efectiva en las muestras de tejido de novillos Wagyu que en las muestras de semen, probablemente por el estado de conservación de la muestra, el grado de condensación del DNA en los espermatozoides y la presencia de inhibidores en el semen. La implementación y ajuste de parámetros en el PCR se hizo de la misma forma que lo observado en la literatura, obteniendo resultados similares en frecuencias genotípicas y su asociación con el rasgo fenotípico, a estudios previos en el tema. La secuenciación de las muestras dejó en evidencia la eficiencia de la Taq polimerasa en la fase de extensión y además, identificó la presencia de una secuencia extra en el alelo C de CAPN – 316, compatible con los “directos repetidos” y con el proceso de arrastre de exones que ocurren durante la recombinación genética y la evolución de los genes. Todos los datos nos permiten concluir que la técnica de AS – PCR es una herramienta efectiva para determinar variaciones del tipo polimorfismo de un solo nucleótido en genes relacionados con características de importancia productiva.
Proyecto Bicentenario PSD23