Microbial fuel cells (MFCs) are electrochemical devices that exploit the ability of certain microorganisms to anaerobically respire using an insoluble terminal electron acceptor and therefore generate an electrical current. These bacteria are called electrogens or electrogenic bacteria. Two species of Arcobacter, Arcobacter butzleri ED-1 and Arcobacter L were isolated from the anodic chamber of an acetate fed MFC, and A. butzleri ED-1 was found to be the more electrogenic of the two bacteria. Arcobacter spp. are  proteobacteria and A. butzleri ED-1 and Arcobacter L were the first example of electrogenically active e proteobacteria. It was decided to study their interactions with the anode by fluorescent microscopy and study their electrogenic mechanisms by comparative proteomics using the iTRAQ method as it would allow for simultaneous identification and quantification of peptides in multiple samples. Fluorescent imaging over a period of 120 h in a half MFC showed that both A. butzleri ED-1 and Arcobacter L formed a thin anodic biofilm of a few cells thick and that A. butzleri ED-1 maintained a more stable anodic biofilm than Arcobacter L. iTRAQ analysis showed that the flagellin FlaA was up-regulated 2.4 fold at the anode but no other electron transport proteins or adhesins were upregulated. These results were distinct from those observed for other electrogenic bacteria (Geobacter sulfurreducens and Shewanella oneidensis MR-1) in previous studies which exhibited up-regulated electron transport proteins at the anode as well as forming an anodic biofilm of 50 μm thick. Therefore based on these results it was concluded that FlaA was most likely playing an important role A. butzleri ED-1 anode biofilm formation and that the mechanisms of electrogenesis in A. butzleri ED- 1 and Arcobacter L may be novel compared to those previously characterised. It was also concluded that one possible reason for A. butzleri ED-1 being more electrogenic than Arcobacter L was its ability to form a more stable anodic biofilm. It must be noted that both of these conclusions are highly speculative and further study is needed to elucidate the electrogenic mechanisms of A. butzleri ED-1 and to further compare biofilm formation between the two species.

As toxinas de veneno de serpentes têm como principal função alterar a homeostase das presas para fins de alimentação ou defesa. O estudo aprofundado da composição do veneno de serpentes é importante para a produção de soros antiofídicos mais eficientes, para a descoberta de novos fármacos e na compreensão de processos biológicos, ecológicos e evolutivos. As pesquisas com toxinas têm mostrado uma versatilidade natural, refinada pela evolução, na diversificação de funções em famílias de proteínas recrutadas de suas funções endógenas, por meio de sucessivas duplicações e acumulo de mutações levando a uma evolução acelerada. A miríade de toxinas disponíveis e sua diversidade de funções ainda não foram completamente descritas. A combinação das análises em larga escala do transcriptoma de novo da glândula de veneno e do proteoma do veneno permite elaborar um perfil mais completo do toxinoma do veneno, permitindo inclusive um aumento na sensibilidade da detecção de toxinas pouco representadas e inesperadas nos venenos. O objetivo geral deste estudo foi analisar o toxinoma do veneno de uma das mais perigosas espécies australianas, a Pseudonaja textilis (Elapidae). Foi possível identificar no veneno as toxinas: fatores de coagulação de veneno do complexo protrombinase, subunidades de fosfolipases A2 (PLA2) da neurotoxina textilotoxin e PLA2 de atividade procoagulante, neurotoxinas tipo three-finger toxin (3FTx), inibidores de protease do tipo-kunitz textilinin, e pela primeira vez, uma nova variante de 3FTx, lectinas tipo C, CRiSP além de indícios de toxinas de lagarto Heloderma e outras proteínas candidatas a toxinas como calreticulin e dipeptidase 2. Metaloproteinases, pouco estudadas em Elapidae, foram clonadas e detectadas no veneno por ensaios de fracionamento e imunoreatividade. A análise do transcriptoma identificou novas isoformas e variantes de toxinas, principalmente das 3FTx e dos inibidores de serinoproteases, assim como transcritos de toxinas que não foram detectadas no veneno e que merecem mais investigações. O quadro de sintomas com acidentes em humanos é bem explicado pelas toxinas identificadas, porém, em seu habitat natural, as toxinas pouco conhecidas e até então não descritas devem ter funções importantes e específicas na predação. Identificar esta diversidade de variantes é importante para entender o modo de ação das toxinas. / Snake venom toxins alter prey homeostasis for feeding or defense. In depth studies of venom composition are important for better antivenom production, for new drugs lead and discovery and for better understanding of biological, ecological and evolutionary processes. Research on toxins have shown the natures way of innovating, refined by evolution, diversifying functions of protein families recruited from their endogenous function to the venom gland by successive gene duplication and mutation accumulation, leading to an accelerated evolution. A myriad of available toxins and diversity of functions is still available for discovery. Combining high throughput techniques such as venom gland de novo transcriptomics and venom proteomics, one can assess and observe a more complete profile of the snake toxinome, additionally allowing an upscale in low represented and unexpected toxin detection. The aim of this project was to investigate the venom toxinome of one of the most dangerous Australian species, Pseudonaja textilis (Elapidae). The toxins identified in it venom was: protrombinase complex coagulation factors, neurotoxic textilotoxin phospholipase A2 (PLA2) subunits and procoagulant PLA2, neurotoxic three-finger toxins (3FTx), Kunitz-type protease inhibitor textilinin, and for the first time, a new long 3FTx, C-type lectins, CRiSPs, as well as evidences of lizard toxins from Heloderma genus and other toxin candidates calreticulin and dipeptidase 2. Metalloproteinases, little investigated in Elapidae, was cloned and detected in the venom after fractionation and immunoassay. The transcriptome revealed new toxin variants and isoforms, specially 3FTx and serine protease inhibitors, as well as transcripts from toxins not detected in the venom that deserves further investigation. Human accident symptoms are well explained by the identified toxins, however, in its natural environment, little known and undescribed toxins must have specific and important role in predation. Identifying this diversity is important to better understand toxins ways of action.

O chumbo (Pb) é um metal pesado que pode ocasionar alterações em todos os sistemas. Porém os maiores danos à saúde ocorrem quando este acomete o sistema nervoso central (SNC). Muitos estudos demonstram as alterações clinicas/comportamentais causadas pela ação do Pb no SNC. Entretanto, ainda são necessários estudos que demonstrem as alterações bioquímicas causadas pelo Pb neste sistema. Por outro lado, tem sido relatado que o ferro (Fe) parece ter um efeito protetor na toxicidade cerebral causada pelo Pb. Assim, o objetivo deste estudo foi analisar a concentração de Pb no tecido cerebral, bem como realizar análise proteômica em cérebro de ratos intoxicados por Pb, submetidos à suplementação com Fe ou não. O experimento foi realizado com 30 ratos recém-desmamados (Rattus norvegicus, variedade Wistar) divididos em 6 grupos (n=5/grupo), de acordo com o tratamento recebido por 6 semanas, a saber: Controle (não exposto ao Pb ou Fe), Controle Fe (exposto à administração de 20 mg/Kg p.c. de FeSO4 a cada 2 dias, por gavagem gástrica), Pb 100 (exposto à água contendo 100 mg/L de Pb), Pb 400 (exposto à água contendo 400 mg/L de Pb) Pb100 + Fe (exposto à água contendo 100 mg/L de Pb e à gavagem com FeSO4) e Pb400 + Fe (exposto à água contendo 400 mg/L de Pb e à gavagem com FeSO4). Decorrido o período experimental, os animais foram eutanasiados e o cérebro dos animais foi removido, sendo descartados o cerebelo e o tronco encefálico. O restante foi submetido à concentração de Pb e à análise proteômica. Foi observada uma dose-resposta em relação à concentração de Pb no cérebro. A administração de FeSO4 reduziu os níveis de Pb no cérebro, embora sem significância estatística. A análise dos géis com os spots proteicos demonstrou uma redução na quantidade destes de acordo com o tratamento recebido pelos grupos. O grupo controle mostrou a maior quantidade de spots, ao passo que os grupos que receberam a maior concentração de Pb (400 mg/L) apresentaram as menores quantidade de spots. Também houve uma diminuição na quantidade de spots detectados quando administrado FeSO4. Dos spots que apresentaram diferença de expressão nas comparações entre o grupo controle e os grupos experimentais e os grupos experimentais comparados aos seus pares suplementados ou não com FeSO4, 75 proteínas foram identificadas por espectrometria de massas, sendo 20 proteínas (26,0%) relacionadas à função de metabolismo, 21 proteínas (28,0%) relacionadas a estrutura e organização das estruturas, 22 proteínas (30,0%) relacionadas à função de processos celulares, nove proteínas (12,0%) relacionadas às vias de informação e três proteínas (4,0%) pertencentes à categoria miscelânea. A expressão das proteínas dimunuiu na maioria das vezes, para todas as classificações funcionais. O presente estudo, associado a achados anteriores, aponta para um papel deletério do Pb no córtex cerebral dos animais expostos a este metal, independente da concentração utilizada, não sendo possível observar um efeito protetor do FeSO4. Este processo parece ser mediado por proteínas como Gamma-enolase, Alpha-internexin, várias isoformas de 14-3-3 e Homer protein homolog 1. / Lead (Pb) is a heavy metal that may yield changes in all body systems, yet the greatest health damages occur when it affects the central nervous system (CNS). Many studies demonstrate the clinical/behavioral changes caused by the action of Pb on the CNS. However, studies are necessary to demonstrate the biochemical changes caused by Pb in this system. Conversely, it has been reported that iron (Fe) seems to play a protective role on the brain toxicity caused by Pb. Therefore, this study analyzed the concentration of Pb in the brain tissue, and conducted proteomic analysis in the brain of rats intoxicated by Pb, submitted or not to Fe supplementation. The study was conducted on 30 weaning rats (Rattus norvegicus, Wistar type) divided in 6 groups (n=5/group), according to the treatment established for 6 weeks, as follows: Control (not exposed to Pb or Fe), Control Fe (exposed to administration of 20 mg/Kg p.c. of FeSO4 at every 2 days, by gastric gavage), Pb 100 exposed to water containing 100 mg/L of Pb), Pb 400 (exposed to water containing 400 mg/L of Pb) Pb100 + Fe (exposed to water containing 100 mg/L of Pb and gavage with FeSO4) and Pb400 + Fe (exposed to water containing 400 mg/L of Pb and gavage with FeSO4). After the experimental period, the animals were killed and the brains of animals were removed, discarding the cerebellum and brainstem. The remaining structure was submitted to analysis of Pb concentration and proteomic analysis. A dose-response relationship was observed in Pb concentration in the brain. The administration of FeSO4 reduced the levels of Pb in the brain, though without statistical significance. The analysis of gels with proteic spots demonstrated reduction in their quantity according to the treatment performed in the groups. The control group exhibited greater concentration of spots, while groups receiving higher Pb concentration (400 mg/L) presented the lowest quantity of spots. There was also reduction in the quantity of spots detected when FeSO4 was administered. Among the spots presented different expression in the comparisons between the control group and experimental groups and between the experimental groups and their counterparts supplemented or not with FeSO4, 75 proteins were identified by mass spectrometry, being 20 proteins (26.0%) related to metabolic functions, 21 proteins (28.0%) related to structure and organization of structures, 22 proteins (30.0%) related to cell functions and processes, nine proteins (12.0%) related to information pathways and three proteins (4.0%) from the miscellaneous category. The expression of proteins was reduced in most cases, for all functional classifications. The present study, combined to previous findings, indicates a harmful effect of Pb in the cerebral cortex of animals exposed to this metal, regardless of the concentration employed, without observation of a protective effect of FeSO4. This process seems to be mediated by proteins as Gamma-enolase, Alpha-internexin, several isoforms of 14-3-3 and Homer protein homolog 1.

A produção in vitro de embriões (PIVE) vem se destacado como biotecnologia reprodutiva nos rebanhos bovinos, porém ainda com algumas limitações. A diferença de fertilidade entre touros é uma delas e dentre os atributos espermáticos que podem impactar na PIVE, pouco se sabe sobre a composição do núcleo espermático. Sendo assim, este trabalho teve como objetivo principal identificar quais aspectos nucleares do espermatozoide caracterizam a diferença nos índices de PIVE. Para tanto, o estudo foi dividido em 3 experimentos nos quais foi utilizado o banco de dados da empresa In Vitro Brasil para seleção de touros de alta (AF) e baixa (BF) taxa de desenvolvimento embrionário (taxa de blastocisto/taxa de clivados; n=5 touros/grupo). No primeiro experimento, foi realizado a avaliação da cromatina para susceptibilidade ao desafio ácido (SCSA modificado), deficiência de protaminação (CMA3) e fragmentação do DNA (COMETA). Apenas a deficiência de protaminação apresentou diferença entre os grupos, entretanto a porcentagem de células positivas para o CMA3 foi baixa, não sendo possível atribuir a esta alteração as diferenças de fertilidade encontradas. No segundo experimento, foi realizada a avaliação de proteômica do núcleo espermático destes touros. Para tanto, as amostras foram incubadas com detergente CTAB para remoção de parte da membrana e cauda, extração das proteínas, digestão com tripsina e análise por espectrometria de massas. A quantificação das proteínas foi avaliada pelo índice iBAQ obtido após a identificação dos peptídeos e a média deste índice comparado entre os grupos para identificação das proteínas diferencialmente expressas. Foram identificadas 196 proteínas, 21 diferencialmente expressas, sendo 17 hiperexpressas no grupo AF e 4 hiperexpressas no grupo BF. Dentre elas, proteínas relacionadas ao processo de espermatogênese, fecundação e motilidade. No terceiro experimento, com objetivo de identificar as marcações epigenéticas relacionadas com a diferença de fertilidade in vitro, foi realizado a avaliação das estruturas de nucleossomos utilizando a enzima MNase para posteriormente utilização na técnica de imunoprecipitação das marcações de histona. Entretanto, não foi identificado a presença de nucleossomos no DNA espermático bovino, inviabilizando análises posteriores. Sendo assim, a avalição da metilação de DNA foi escolhida como marcação epigenética para ser estudada. Neste caso, foi utilizada a técnica de RRBS (reduced representation of bisulfite sequencing) para identificar as citosinas diferencialmente metiladas (CDM) entre os grupos AF e BF. Foram identificadas 440 CDM, sendo 327 hipometiladas e 113 hipermetiladas no grupo AF. Além disto, 184 genes contendo estas CDM foram identificados, entretanto nenhum processo biológico foi enriquecido por estes genes. Foi possível concluir com este trabalho que a fertilidade in vitro pode ser considerada de caráter multifatorial, sendo que alterações pequenas de integridade de cromatina não afetam diretamente, já proteínas relacionadas a espermatogênese, motilidade e fecundação podem ter relação com o fenótipo fertilidade estudado. Dentre as marcações epigenética estudadas, as estruturas de nucleossomo pareceram estar ausentes no espermatozoide bovino, e a metilação de DNA não apresenta impacto significativo no perfil de fertilidade. / In vitro embryo production (IVP) has been highlighted as reproductive biotechnique in bovine herds, but still with some limitations. The fertility difference between bulls is one of them and among the sperm attributes that can impact on IVP, little is known about the composition of the bovine sperm nucleus. Therefore, this work had as main goal to identify which sperm nuclear aspects characterize the difference in the IVP index. Then, the study was divided in 3 experiments in which the database of the company In Vitro Brasil was used for selection of bulls with high (HF) and low (LF) embryo development rate (blastocyst rate/cleavage rate; n=5 bulls/group). In the first experiment, chromatin analysis of susceptibility to acid denaturation (modified SCSA), protamine deficiency (CMA3) and DNA fragmentation (COMET assay) were performed. Only protamine deficiency presented difference between groups, however the percentage of CMA3 positive cells was low and it was not possible to attribute to this alteration the fertility difference between groups. In the second experiment, proteomic analysis of the sperm nucleus of these bulls was performed. For that, samples were incubated with CTAB detergent to remove part of the membrane and tail, submitted to protein extraction, trypsin digestion and mass spectrometry analysis. The amount of the proteins was evaluated by the iBAQ index obtained after the identification of peptides and the average of this index compared to identify the differentially expressed proteins. In this experiment, 196 proteins were identified, 21 differentially expressed, being 17 overexpressed in the HF and 4 overexpressed in LF group. Among them, proteins related to the spermatogenesis, fertilization and motility. In the third experiment, in order to identify the epigenetic marks related to in vitro fertility differences it was performed the evaluation of the nucleosome structures using the MNase enzyme to later utilization of immunoprecipitation of the histone marks technique. However, the presence of nucleosomes in bovine sperm DNA was not identified, unfeasible further analysis. Thus, the evaluation of DNA methylation was chosen as epigenetic mark to be studied. In this case, the RRBS (reduced representation of bisulfite sequencing) technique was used to identify the differentially methylated cytosines (DMC) between the two groups. In this experiment, it was identified 440 DMC, being 327 hypomethylated and 113 hypermethylated in HF group. In addition, 184 genes containing these DMCs were identified, however no biological process enrichment was identified with these genes. In conclusion, this study indicated that in vitro fertility characterization can be multifactorial; small changes in chromatin integrity do not directly affect, but proteins related to spermatogenesis, motility and fertilization may be related to the fertility phenotype studied. Among the epigenetic marks studied, nucleosome structures were absent in bovine spermatozoa, and DNA methylation did not have a significant impact on the fertility profile.

Chronic consumption of, and acute intoxication from, alcohol can have profound effects on the functional integrity of the central nervous system (CNS). The resident immunomodulatory cells of the CNS, microglia, provide signaling factors with both pro- and anti-inflammatory effects for protection. Microglial activation ranges through a multiplex of phases, of which have yet to be defined when induced by exposure to alcohol, and how the activation impacts surrounding cells. Exposure of alcohol has been revealed to induce an immune response in microglia, which can exhibit characteristics unique to a pro-inflammatory response depending on dose and time of alcohol exposure. To define the activation state produced by microglia in response to alcohol, ethanol-induced microglial protein and microRNA (miRNA) global profile expression changes were obtained in vitro, using the BV2 murine microglial cells, using mass spectrometry (MS)-based proteomics and microarray-based transcriptomic approaches, respectively, revealing potential regulatory miRNAs for inflammation mediation. The 2,277 protein groups identified through mass spectrometry and 3,195 miRNA genes identified using microarray analysis provided a strong foundation to determine miRNA-mRNA regulators and the pathways in which they are involved, that potentially play a role in microglial activation. The comparison of the miRNA expressed in microglia after lipopolysaccharide (LPS) and ethanol (EtOH) exposure, indicate that EtOH influenced miRNA does not signify having a pro-inflammatory activation phenotype, but the miRNA expressed under the influence of LPS does support this phenotype. The global pathway regulation evidence and defined proteins and miRNA-mRNA interactions upon microglial activation have the possibility to unite the pathways described in previous studies and further our understanding of EtOH-induced microglial activation, and their role in neuroinflammation and neurodegeneration. Further research to determine and validate the extent of gene regulation by miRNAs and subsequent impact on specific protein levels should be employed to define the miRNA transcriptome influence on pathways relevant to microglial function.

<p>This review article presents the splicing process during messenger RNA maturation and how it is regulated by different <em>Cis</em>-regulatory RNA-sequence elements and splicing factors. A more detailed description of the process alternative splicing and its importance to the function of genes from the model organism <em>Arabidopsis thaliana</em> is also given. A single eukaryotic gene can by the process alternative splicing (AS) give rise to a number of functionally mature mRNA-molecules, which in turn encodes for structurally and/or functionally different proteins. During the course of evolution, the process alternative splicing has thus shown to be effective in increasing transcriptome and proteome diversity of most eukaryotic organisms. This suggests therefore that the dominant theory in molecular biology, a gene encodes for a protein, needs to be corrected. A future challenge is to determine the function of the proteins obtained from a given gene by alternative splicing.</p>

Protein prefractionation is a popular and effective strategy for improved MS analysis of complex proteome mixtures. A challenge of prefractionation is the even partitioning with high recovery of all components of the mixture, particularly hydrophobic proteins. This thesis assesses various proteome prefractionation platforms, with a goal of comprehensive proteome analysis. A more reliable dataset of 1136 S. cerevisiae transmembrane proteins was computationally generated, and used to assess two gel-based platforms (GeLC/MS and GELFrEE/MS). These platforms were determined to be comparable for proteome analysis. The requirement for high-throughput, automated fractionation demands a gel-free separation workflow. Here, a LC-based workflow was optimized, relying on SDS-assisted yeast extraction, organic solvent protein precipitation, and reversed phase separation in a formic acid/isopropanol solvent system. Though this workflow afforded improvements over conventional LC strategies to proteome fractionation, the gel-based platforms were demonstrated to be superior, in terms of their unbiased separation of hydrophobic vs hydrophilic proteins.

Membrane proteins are found in all kingdoms of life and are essential for cellular interactions with the environment. Although a large research effort have been put into this group many membrane proteins remains uncharacterized, both in terms of function and evolutionary history. We have estimated the component of α-helical membrane proteins within the human proteome; the membrane proteome. We found that the human membrane proteome make up 27% of all protein, which we could classify the majority of into 234 families and further into three major functional groups: receptors, transporters or enzymes. We extended this analysis by determining the membrane proteome of 24 organisms that covers all major groups of eukaryotes. This comprehensive membrane protein catalog of over 100,000 proteins was utilized to determine the evolutionary history of all membrane protein families throughout eukaryotes.  We also investigated the evolutionary history across eukaryotes of the antiviral Interferon induced transmembrane proteins (IFITM) and the G protein-coupled receptor (GPCR) superfamily in detail.  We identified ten novel human homologs to the IFITM proteins, which together with the known IFITMs forms a family that we call the Dispanins. Using phylogenetic analysis we show that the Dispanins first emerged in eukaryotes in a common ancestor of choanoflagellates and animals, and that the family later expanded in vertebrates into four subfamilies. The GPCR superfamily was mined across eukaryotic species and we present evidence for a common origin for four of the five main human GPCR families; Rhodopsin, Frizzled, Adhesion and Secretin in the cAMP receptor family that was found in non-metazoans and invertebrates, but has been lost in vertebrates. Here we present the first accurate estimation of the human proteome together with comprehensive functional and evolutionary classification and extend it to organisms that represents all major eukaryotic groups. Moreover, we identify a novel protein family, the Dispanins, which has an evolutionary history that has been formed by horizontal gene transfer from bacteria followed by expansions in the animal lineage. We also study the evolution of the GPCR superfamily throughout eukaryotic evolution and provide a comprehensive model of the evolution and relationship of these receptors.

Very little is known about the hydrophobic proteins of psychrophiles and their roles in cold adaptation. In light of this situation, methods were developed to analyse the hydrophobic proteome (HPP) of the model psychrophilic archaeon Methanococcoides burtonii. Central to this analysis was a novel differential solubility fractionation procedure, which resulted in a significant increase in the efficiency of resolving the HPP. Over 50% of the detected proteins were not identified in previous whole cell extract analyses, and these underwent an intensive manual annotation process producing high quality functional assignments. Utilising the functional assignments, biological context analysis of the HPP was performed, revealing novel and often unique biology. The analysis acted as a platform for differential proteomics of the organism???s response to both temperature and substrate using stable isotope labelling. The results of which revealed that low temperature growth was associated with an increase in the abundance of surface and secreted proteins, and translation apparatus. Conversely, growth at a higher temperature was associated with an increase in the abundance of general protein folding machinery and indications of an oxidative stress response, emphasising that the temperature for maximum growth rate is stressful. Through investigation of the response of M. burtonii to substrate it was found that growth on methanol was stressful, and its low energy yield resulted in an increase in the abundance of energy conserving systems. The extracellular polymeric substance (EPS) and morphology of M. burtonii was also investigated with respect to both temperature and substrate, using a number of techniques in microscopy. It was found that the EPS was comprised of proteins, sugars and RNA, and that growth at different temperatures resulted in the production of EPS that displayed significantly different properties on dehydration, thus indicating compositional variation. When cells were grown on methanol they took on highly irregular shapes and had electron transparent inclusions. The observations from the ultrastructural analysis were contemplated with respect to the proteomic findings, revealing novel avenues of research. This study has highlighted the roles of hydrophobic proteins in cold adaptation biology, and the value of comprehensive proteomics for the examination of adaptation in microorganisms

Diss. (sammanfattning) Stockholm : Karol. inst., 2004. / Härtill 6 uppsatser.