The diploma thesis deals with the issue of a quality assessment of a bore of shotgun barrels. There are mentioned both definitions of a quality shotgun barrel and also a quality of shotgun barrel bore. In conclusion, there are presented particular proposals for evaluation of parameters of surface texture of forged shotgun barrel blanks.

La thèse aborde le problème de l’évolution de la forme à travers l’exemple d’une différence de forme de branches ventrales mâles liée à l’isolement reproducteur chez deux espèces soeurs : Drosophila yakuba et Drosophila santomea. L’objectif de ce travail est d’identifier les gènes impliqués dans l’évolution de cette différence de forme ainsi que les causes évolutives de cette différence entre espèces. Dans une première partie, la thèse interroge la notion de “gène” et sa recherche. Puis sont caractérisées, dans un cadre formel, les questions de type "comment" et "pourquoi" et leur lien avec la distinction causes prochaines/causes ultimes ou évolutives. Ces réflexions philosophiques sont ensuite reliées à l’Evo-Devo et au projet expérimental. Dans la deuxième partie, par morphométrie géométrique et une nouvelle méthode de génotypage à haut débit, le MSG, nous identifions un locus de 2.7 méga-bases situé sur le chromosome 3L comme étant impliqué dans l’évolution de la forme des branches ventrales entre D. yakuba et D. santomea. Ces résultats sont mis en perspective avec notre analyse quantitative de la variation de forme dans plusieurs souches naturelles, souches de laboratoire et souches élevées à différentes températures qui apportent des indices sur les causes évolutives de cette différence de forme / The thesis tackles the problem of the evolution of shape through the example of a shape difference in the male ventral branches linked to reproductive isolation in two sister species: Drosophila yakuba and Drosophila santomea. The goal is to identify the genes involved in the evolution of this shape difference and the evolutionary causes of such difference. In a first part, the thesis interrogates the concept of “gene” and its search. Then are scientifically characterized the “how” and “why” questions and their link with the distinction of proximal/ultimate, or evolutionary, causes; these philosophical grounds are then linked to Evo-Devo and the experimental work presented in the thesis. In a second part, through geometric morphometrics and a new high-throughput genotyping method, MSG, we identify a loci of 2.7 mega-bases located on chromosome 3L as involved in the evolution of the shape of ventral branches between D. yakuba and D. santomea. These results are linked to our quantitative analysis of shape variation in multiple natural and laboratory strains and strains reared at different temperatures which bring light into the evolutionary causes of this shape difference

Submitted by DHARA CARLESSO ZAMPIVA (dhara.zampiva@univates.br) on 2018-08-20T17:17:13Z No. of bitstreams: 3 license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) 2018EdinaAparecidadosReisBlasi.pdf: 4920714 bytes, checksum: 936b932d7a6e49e5bca50678cab5e1d9 (MD5) 2018Edina_artigo.pdf: 1100636 bytes, checksum: a4919dc64d214daf7c76333e0b77f3a0 (MD5) / Rejected by Ana Paula Lisboa Monteiro (monteiro@univates.br), reason: Inserir o Lattes do autor. on 2018-09-11T18:28:07Z (GMT) / Submitted by DHARA CARLESSO ZAMPIVA (dhara.zampiva@univates.br) on 2018-09-17T17:18:08Z No. of bitstreams: 3 license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) 2018EdinaAparecidadosReisBlasi.pdf: 4920714 bytes, checksum: 936b932d7a6e49e5bca50678cab5e1d9 (MD5) 2018Edina_artigo.pdf: 1100636 bytes, checksum: a4919dc64d214daf7c76333e0b77f3a0 (MD5) / Approved for entry into archive by Ana Paula Lisboa Monteiro (monteiro@univates.br) on 2018-10-03T16:31:01Z (GMT) No. of bitstreams: 3 license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) 2018EdinaAparecidadosReisBlasi.pdf: 4920714 bytes, checksum: 936b932d7a6e49e5bca50678cab5e1d9 (MD5) 2018Edina_artigo.pdf: 1100636 bytes, checksum: a4919dc64d214daf7c76333e0b77f3a0 (MD5) / Made available in DSpace on 2018-10-03T16:31:01Z (GMT). No. of bitstreams: 3 license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) 2018EdinaAparecidadosReisBlasi.pdf: 4920714 bytes, checksum: 936b932d7a6e49e5bca50678cab5e1d9 (MD5) 2018Edina_artigo.pdf: 1100636 bytes, checksum: a4919dc64d214daf7c76333e0b77f3a0 (MD5) Previous issue date: 2018-08-20 / High levels of Schizotetranychus oryzae phytophagous mite infestation on rice leaves can severely affect pro- ductivity. Physiological characterization showed that S. oryzae promotes a decrease in chlorophyll concentration and the establishment of a senescence process in rice leaves. Late-infested leaves also present high levels of superoxide radical and hydrogen peroxide accumulation, along with high levels of membrane integrity loss, which is indicative of cell death. To better understand the rice molecular responses to high levels of mite in-festation, we employed the Multidimensional Protein Identification Technology (MudPIT) approach to identify differentially expressed proteins. We identified 83 and 88 proteins uniquely present in control and late-infested leaves, respectively, along with 11 and one proteins more abundant in control and late-infested leaves, re-spectively. S. oryzae infestation induces a decreased abundance of proteins related to translation, protease in-hibition, and photosynthesis. On the other hand, infestation caused increased abundance of proteins involved in protein modification and degradation. Our results also suggest that S. oryzae infestation interferes with in-tracellular transport, DNA structure maintenance, and amino acid and lipid metabolism in rice leaves. Proteomic data were positively correlated with enzymatic assays and RT-qPCR analysis. Our findings describe the protein expression patterns of late-infested rice leaves and suggest several targets which could be tested in future bio-technological approaches aiming to avoid the population increase of phytophagous mite in rice plants.

The new field of ‘omics’ has spawned the development of metaproteomics, an approach that has the ability to identify and decipher the metabolic functions of a proteome derived from a microbial community that is largely uncultivable. With the development and availabilities of high throughput proteomics, high performance liquid chromatography coupled to mass spectrometry (MS) has been leading the field for metaproteomics. MS-based metaproteomics has been successful in its’ investigations of complex microbial communities from soils to the human body. Like the environment, the human body is host to a multitude of microorganisms that reside within the skin, oral cavity, vagina, and gastrointestinal tract, referred to as the human microbiome. The human microbiome is made up of trillions of bacteria that outnumber human genes by several orders of magnitude. These microbes are essential for human survival with a significant dependence on the microbes to encode and carryout metabolic functions that humans have not evolved on their own. Recently, metaproteomics has emerged as the primary technology to understand the metabolic functional signature of the human microbiome. Using a newly developed integrated approach that combines metagenomics and metaproteomics, we attempted to address the following questions: i) do humans share a core functional microbiome and ii) how do microbial communities change in response to disease. This resulted in a comprehensive identification and characterization of the metaproteome from two healthy human gut microbiomes. These analyses have resulted in an extended application to characterize how Crohn’s disease affects the functional signature of the microbiota. Contrary to measuring highly complex and representative gut metaproteomes is a less complex, controlled human-derived microbial community present in the gut of gnotobiotic mice. This human gut model system enhanced the capability to directly monitor fundamental interactions between two dominant phyla, Bacteroides and Firmicutes, in gut microbiomes colonized with two or more phylotypes. These analyses revealed membership abundance and functional differences between phylotypes when present in either a binary or 12-member consortia. This dissertation aims to characterize host microbial interactions and develop MS-based methods that can provide a better understanding of the human gut microbiota composition and function using both approaches.

Submitted by Automa??o e Estat?stica (sst@bczm.ufrn.br) on 2018-03-21T11:48:14Z No. of bitstreams: 1 JonathasDiegoLimaSantos_TESE.pdf: 8935214 bytes, checksum: 86433d89608ea11b99ac2a3911f14149 (MD5) / Approved for entry into archive by Arlan Eloi Leite Silva (eloihistoriador@yahoo.com.br) on 2018-03-23T11:23:51Z (GMT) No. of bitstreams: 1 JonathasDiegoLimaSantos_TESE.pdf: 8935214 bytes, checksum: 86433d89608ea11b99ac2a3911f14149 (MD5) / Made available in DSpace on 2018-03-23T11:23:51Z (GMT). No. of bitstreams: 1 JonathasDiegoLimaSantos_TESE.pdf: 8935214 bytes, checksum: 86433d89608ea11b99ac2a3911f14149 (MD5) Previous issue date: 2017-12-15 / Coordena??o de Aperfei?oamento de Pessoal de N?vel Superior (CAPES) / Chromobcterium violaceum (C. violaceum) ? uma bact?ria Gram-negativa, encontrada em regi?es tropicais e subtropicais, considerada organismo modelo de vida livre. Alguns estudos prote?micos realizados com esta bact?ria demonstraram sua capacidade de adapta??o a desafios ambientais, como alta concentra??o de ferro e exposi??o ao estresse oxidativo. No entanto, nenhum estudo foi feito com esta esp?cie submetida ? microgravidade simulada (MGS), ou seja, em condi??es em que a gravidade ? artificialmente reduzida para menos de 1xg. Estudos MGS podem ser importantes para entender as modula??es em n?vel molecular sofridas pelos organismos vivos. Portanto, o objetivo deste estudo foi caracterizar a resposta de C. violaceum, como organismo modelo de vida livre, cultivado em MGS, usando t?cnicas de prote?mica para entender como a bact?ria responde a esse estresse. A MGS foi conseguida por meio da rota??o do vessel ao redor do eixo horizontal perpendicular ao vetor gravitacional nos sistemas de cultura de c?lulas rotativas - Rotating Cell Culture Systems ? (RCCS4). MGS foi conduzido a uma velocidade de 40 rpm por um per?odo de 12 horas para obter a curva de crescimento a cada 2 horas. Prote?nas totais foram extra?das de amostras de cultura de c?lulas bacteriana coletada ?s 5 e 12 horas, correspondendo as fases exponenciais inicial (MG5) e tardia (MG12), respectivamente, tendo a curva de crescimento como refer?ncia. Ap?s a tripsiniza??o, as amostras foram analisadas em espectr?metro de massas Q-TOF. Como resultado um total de 212 prote?nas durante ?s 5h de crescimento e 192 ?s 12h foram detectadas, das quais 144 delas foram comuns em ambos os per?odos. No proteoma de C. violaceum obitido em 5h de crescimento 195 prote?nas foram identificadas em gravidade normal (GN5) e 155 prote?nas foram identificadas em MG5, sendo 18 upreguladas, 19 downreguladas e 17 expressas somente na condi??o de MG5. No proteoma obtido em 12h de crescimento, 165 prote?nas foram identificadas em gravidade normal (GN12) e 173 em MG12, das quais, 17 foram upreguladas, 22 downreguladas e 28 expressas somente na condi??o de MG12 Al?m disso, foi poss?vel identificar 25 prote?nas com fun??o desconhecida em MG5 e MG12. Utilizando ferramentas computacionais foi poss?vel construir redes de intera??es prote?na-prote?na (PPI) e as sub-redes contendo grupo de prote?nas com fun??es correlacionadas, analisar vias metab?licas, processos biol?gicos, contexto gen?mico e busca por dom?nios conservados e sequ?ncias hom?logas de prote?nas com fun??o desconhecida. Como resultado, identificamos sub-redes relacionadas com a bioss?ntese de prote?nas, regula??o da transcri??o e tradu??o, resposta ao estresse e metabolismo energ?tico, conclu?mos que as respostas celulares associadas ? express?o diferencial induzida pela MGS levaram ? diminui??o do crescimento de C. violaceum, acompanhado pela regula??o negativa de prote?nas relacionadas com processos transcricionais, traducionais e libera??o de energia por vias aer?bicas e pela regula??o positiva de prote?nas envolvidas no estresse oxidativo, na via anaer?bica e na sobreviv?ncia celular. / Chromobcterium violaceum (C.violaceum) is a Gram-negative bacteria, which has been found at tropical and subtropical regions, considered a free living model organism. Some proteomic studies performed with this bacterium have demonstrated its ability to adapt to environmental challenges such as high iron concentration and oxidative stress exposure. However, no study was made with this specie submitted to simulated microgravity (SMG), that is, under conditions in which the gravity is artificially reduced to less than 1xg. MGS studies may be important in understanding the molecular-level modulations undergone by living organisms. Therefore, the aim of this study was to characterize the response of C. violaceum, as free-living model organism, cultured at MGS, using proteomics techniques in order to understand how this bacterium response to this stress. The SMG was achieved by rotating the vessel around the horizontal axis perpendicular to the gravitational vector in Rotating Cell Culture Systems (RCCS4). SMG was conducted at a speed of 40 rpm for a period of 12 hours to obtain the growth curve every 2 hours. Total protein extraction was made in two times: 5 and 12 hours, corresponding to early (MG5) and late (MG12) exponential phase, respectively, taking the growth curve as a reference. After trypsinization, samples were analyzed with Q-TOF mass spectrometer. As a result a total of 212 proteins during 5h of growth and 192 at 12h were detected, of which 144 of them were common in both periods. We detected 155 proteins during MG5, from which 18 proteins were upregulated, 19 down-regulated and 17 proteins were exclusive when compared to GN5. In the proteome obtained in 12h of growth, 165 proteins were identified in normal gravity (GN12) and 173 in MG12, of which, 17 were upregulated, 22 were downregulated and 28 expressed only in MG12 condition. In addition, it was possible to identify 25 proteins with unknown function in MG5 and MG12. Using computational tools it was possible to construct networks of protein-protein interactions (PPI) and sub-networks containing group of proteins with correlated functions, to analyze metabolic pathways, biological processes, genomic context and search for conserved domains and homologous sequences of proteins with unknown function . As a result, we identified sub-networks related to protein biosynthesis, transcription regulation and translation, stress response and energetic metabolism, we conclude that the cellular responses associated with differential expression induced by MGS led to a decrease in the growth of C. violaceum, accompanied by the negative regulation of proteins related to transcriptional, translational and energy release by aerobic pathways and by the positive regulation of proteins involved in oxidative stress, anaerobic pathway and cell survival.

nÃo hà / O presente estudo avaliou os efeitos da inclusÃo de 13% de farelo de castanha de caju (CNM) na dieta de carneiros Morada Nova nos parÃmetros seminais e proteÃnas do plasma seminal. Vinte carneiros foram distribuÃdos em dois grupos iguais: grupo castanha de caju (CNG) e grupo controle (COG). O CNG e COG receberam 13% e 0% de CNM na dieta durante 90 dias. Os grupos foram comparados para peso corporal, circunferÃncia escrotal, parÃmetros seminais e proteÃnas do plasma seminal, utilizando o MÃtodo de Shotgun Proteomics. Peso corporal e circunferÃncia escrotal aumentaram durante os 90 dias do perÃodo experimental em ambos grupos, porÃm nÃo existiu diferenÃa significativa entre CNG e COG. Contudo, apÃs 60 dias, o consumo de matÃria seca foi inferior no CNG (2,9  0,1; aos 90 dias) em relaÃÃo ao COG (3,4  0,1; aos 90 dias). Os parÃmetros seminais nÃo diferiram entre CNG e COG. A anÃlise shotgun proteomics identificou isoaspartil peptidase L asparaginase, gliceraldeÃdo 3 fosfato desidrogenase e prostaglandina H2 D isomerase com alta expressÃo no CNG quando comparado COG. Ao mesmo tempo, 12 proteÃnas do plasma seminal apresentaram baixa expressÃo no CNG, identificadas como beta galactosidase, caltrina, beta mannosidase, glutationa peroxidase, sorbitol desidrogenase, clusterina, albumina and serotransferrina. AlÃm disso, 20 proteÃnas detectadas no plasma seminal do COG foram ausentes no CNG e cinco proteÃnas foram presentes somente nos carneiros que receberam dieta hiperlipÃdica. Em conclusÃo, o presente estudo descreveu, pela primeira vez, os efeitos de uma dieta hiperlipÃdica nos parÃmetros do sÃmen fresco e do plasma seminal de carneiros. Enquanto os critÃrios seminais nÃo foram afetados, proteÃnas especÃficas do fluido seminal foram alteradas em decorrÃncia da dieta com castanha de caju. Visto os aspectos multifuncionais dessas proteÃnas, nÃs sugerimos que certos aspectos da fertilidades de carneiros podem ser alteradas se a castanha de caju for fornecida. / The present study was carried out to evaluate the effects of 13% of cashew nut meal (CNM) inclusion in the diet of Morada Nova rams on semen parameters and seminal plasma proteins. Twenty rams were distributed in two equal groups: cashew nut group (CNG) and control group (COG). The CNG and COG received 13% and 0% of CNM in the diet for 90 days. The groups were compared for live weight, scrotal circumference, seminal parameters and seminal plasma proteins, using shotgun proteomics. Body weight and scrotal circumference increased during the 90-day experimental period in both cashew nut-fed and control groups but with no differences between CNG and COG. However, after 60 days until 90 days, percentage of dry matter intake (% live weight) was inferior in CNG (2,9  0,1; at 90 days) group than COG (3,4  0,1; at 90 days). The sperm quality parameters were not different between CNG and COG.The shotgun proteomics analysis identified isoaspartyl peptidase L asparaginase, glyceraldehyde 3 phosphate dehydrogenase and prostaglandin H2 D isomerase with higher expression in the cashew nut group as compared to animals receiving the control diet. Conversely, 12 seminal plasma proteins had lower expression in the cashew nut group, identified as beta galactosidase, caltrin, beta mannosidase, glutathione peroxidase, sorbitol dehydrogenase, clusterin, albumin and serotransferrin. Moreover, 20 proteins detected in the seminal plasma of the control animals were absent in the cashew nut fed animals and five were present only in the rams receiving the high fat diet. In conclusion, the present study describes, for the first time, the effects of a high fat diet on parameters of the fresh semen and seminal plasma proteins of rams. While sperm criteria were not affected, specific seminal fluid proteins did change as the result of cashew nut feeding. Given the multifunctional aspects of such proteins, we suggest that certain aspects of the ram fertility can be altered if cashew nut is provided.

Hajj, the annual Islamic pilgrimage to Makkah, Saudi Arabia, is a unique mass gathering event that brings more than 2 million individuals from around the world. Several public health considerations, such as the spread of infectious diseases, must be taken into account with this large temporary influx of people. Gastrointestinal diseases, such as diarrhea, are common at Hajj, yet little is known about the etiology. The human gut microbiome, collection of organisms residing within the intestinal tract, has been under intense study recently, since next generation DNA sequencing technologies allow for extensive surveying of genetic material found in complex biological samples, such as those containing many different organisms. Thus, using 16S rRNA and metagenomic shotgun sequencing, we have characterized the gut microbiome of over 612 pilgrims with and without diarrhea. Several metadata factors, such as hospitalization and different comorbidities, were found to have significant effects on the overall gut microbiome composition. Metagenomic shotgun sequencing efforts revealed the presence of antimicrobial resistance genes originating from disparate regions from around the world. This study provides a snapshot of information concerning the health status of the gut microbiome of Hajj pilgrims and provides more context to the investigation of how to best prepare for mass gathering events.

In shotgun proteomics, the liquid chromatography step is used to separate peptides in order to analyze as few as possible at the same time in the mass spectrometry step. Each peptide has a retention time, that is how long it takes to pass through the chromatography column. Prediction of the retention time can be used to gain increased identification of peptides or in order to create targeted proteomics experiments. Using machine learning methods such as support vector machines has given a high prediction accuracy, but such methods require known features that the retention time depends on. In this thesis we let a convolutional network, learn to rank the retention times instead of predicting the retention times themselves. We also tested how the prediction accuracy depends on the size of the training set. We found that pairwise ranking of peptides outperforms pointwise ranking and that adding more training data increased accuracy until the end without an increase in training time. This implies that accuracy can be further increased by training on even greater training sets.

Archaeological dental calculus represents a depositional environment that entraps oral microbes, and debris of dietary, environmental, and cultural material that entered the mouth throughout the host’s life. Hence, they represent valuable archives of information about the host’s lifestyle, health, and environment. The aim of this study was to identify if the farming transition and its’ associated change in diet composition, may have influenced species composition in the oral cavity. To shed some light into the evolution of ancient oral microbiomes from Africa, 3 novel Iron Age dental calculus metagenomes together with a comparative dataset of 18 archaeological dental calculus metagenomes from North African Upper Palaeolithic, Later Stone Age, Iron Age, and 18th-19th century populations where analysed. Shotgun sequencing data was used to reconstruct 21 oral metagenomes from the past 15,000 years. This study found an oral microbiome that has been maintained from the Upper Palaeolithic (North Africa) to the 19th Century. However, closer examination to the relative abundance of three keystone species of the subgingival plaque, portray a chronological evolution that reflects that of its host during the major dietary and cultural transition that occurred during the farming revolution in the Iron Age.

No description available.