A genetic and biochemical analysis of pre-mRNA splicing in Saccharomyces cerevisiae

Pre-mRNA splicing requires interaction of cis- acting intron sequences with trans -acting factors: proteins and small nuclear ribonucleoproteins (snRNPs). The assembly of these factors into a large complex, the spliceosome, is essential for the subsequent two step splicing reaction. First, the 5' splice site is cleaved and free exon 1 and a lariat intermediate (intron- exon2) form. In the second reaction the 3' splice site is cleaved the exons ligated and lariat intron released. A combination of genetic and biochemical techniques have been used here to study pre-mRNA splicing in yeast.

Yeast introns have three highly conserved elements. We made point mutations within these elements and found that most of them affect splicing efficiency in vivo and in vitro, usually by inhibiting spliceosome assembly.

To study trans -acting splicing factors we generated and screened a bank of temperature- sensitive (ts) mutants. Eleven new complementation groups (prp17 to prp27) were isolated. The four phenotypic classes obtained affect different steps in splicing and accumulate either: 1) pre-mRNA, 2) lariat intermediate, 3) excised intron or 4) both pre-mRNA and intron. The latter three classes represent novel phenotypes. The excised intron observed in one mutant: prp26 is stabilized due to protection in a snRNP containing particle. Extracts from another mutant: prpl8 are heat labile and accumulate lariat intermediate and exon 1. This is especially interesting as it allows analysis of the second splicing reaction. In vitro complementation of inactivated prp18 extracts does not require intact snRNPs. These studies have also shown the mutation to be in a previously unknown splicing protein. A specific requirement for A TP is also observed for the second step of splicing. The PRP 18 gene has been cloned and its polyadenylated transcript identified.

Molecular mechanism of sulfated carbohydrate recognition: structural and biochemical studies of the cysteine-rich domain of mannose receptor

Mannose receptor (MR) is widely expressed on macrophages, immature dendritic cells, and a variety of epithelial and endothelial cells. It is a 180 kD type I transmembrane receptor whose extracellular region consists of three parts: the amino-terminal cysteine-rich domain (Cys-MR); a fibronectin type II-like domain; and a series of eight tandem C-type lectin carbohydrate recognition domains (CRDs). Two portions of MR have distinct carbohydrate recognition properties: Cys-MR recognizes sulfated carbohydrates and the tandem CRD region binds terminal mannose, fucose, and N-acetyl-glucosamine (GlcNAc). The dual carbohydrate binding specificity allows MR to interact with sulfated and nonsulfated polysaccharide chains, and thereby facilitating the involvement of MR in immunological and physiological processes. The immunological functions of MR include antigen capturing (through binding non-sulfated carbohydrates) and antigen targeting (through binding sulfated carbohydrates), and the physiological roles include rapid clearance of circulatory luteinizing hormone (LH), which bears polysaccharide chains terminating with sulfated and non-sulfated carbohydrates.

We have crystallized and determined the X-ray structures of unliganded Cys-MR (2.0 Å) and Cys-MR complexed with different ligands, including Hepes (1.7 Å), 4SO_4-N-Acetylgalactosamine (4SO_4-GalNAc; 2.2 Å), 3SO_4-Lewis^x (2.2 Å), 3S04-Lewis^a (1.9 Å), and 6SO_4-GalNAc (2.5 Å). The overall structure of Cys-MR consists of 12 anti-parallel β-strands arranged in three lobes with approximate three fold internal symmetry. The structure contains three disulfide bonds, formed by the six cysteines in the Cys-MR sequence. The ligand-binding site is located in a neutral pocket within the third lobe, in which the sulfate group of ligand is buried. Our results show that optimal binding is achieved by a carbohydrate ligand with a sulfate group that anchors the ligand by forming numerous hydrogen bonds and a sugar ring that makes ring-stacking interactions with Trpll7 of CysMR. Using a fluorescence-based assay, we characterized the binding affinities between CysMR and its ligands, and rationalized the derived affinities based upon the crystal structures. These studies reveal the mechanism of sulfated carbohydrate recognition by Cys-MR and facilitate our understanding of the role of Cys-MR in MR recognition of its ligands.

The isolation and partial biochemical analysis of Sindbis virus proteins

Recently, the amino acid sequences have been reported for several proteins, including the envelope glycoproteins of Sindbis virus, which all probably span the plasma membrane with a common topology: a large N-terminal, extracellular portion, a short region buried in the bilayer, and a short C-terminal intracellular segment. The regions of these proteins buried in the bilayer correspond to portions of the protein sequences which contain a stretch of hydrophobic amino acids and which have other common characteristics, as discussed. Reasons are also described for uncertainty, in some proteins more than others, as to the precise location of some parts of the sequence relative to the membrane.

The signal hypothesis for the transmembrane translocation of proteins is briefly described and its general applicability is reviewed. There are many proteins whose translocation is accurately described by this hypothesis, but some proteins are translocated in a different manner.

The transmembraneous glycoproteins E1 and E2 of Sindbis virus, as well as the only other virion protein, the capsid protein, were purified in amounts sufficient for biochemical analysis using sensitive techniques. The amino acid composition of each protein was determined, and extensive N-terminal sequences were obtained for E1 and E2. By these techniques E1 and E2 are indistinguishable from most water soluble proteins, as they do not contain an obvious excess of hydrophobic amino acids in their N-terminal regions or in the intact molecule.

The capsid protein was found to be blocked, and so its N-terminus could not be sequenced by the usual methods. However, with the use of a special labeling technique, it was possible to incorporate tritiated acetate into the N-terminus of the protein with good specificity, which was useful in the purification of peptides from which the first amino acids in the N-terminal sequence could be identified.

Nanomole amounts of PE2, the intracellular precursor of E2, were purified by an immuno-affinity technique, and its N-terminus was analyzed. Together with other work, these results showed that PE2 is not synthesized with an N-terminal extension, and the signal sequence for translocation is probably the N-terminal amino acid sequence of the protein. This N-terminus was found to be 80-90% blocked, also by Nacetylation, and this acetylation did not affect its function as a signal sequence. The putative signal sequence was also found to contain a glycosylated asparagine residue, but the inhibition of this glycosylation did not lead to the cleavage of the sequence.

Radiobiological and biochemical investigations of polyoma virus-cell interactions

The cytolytic interaction of Polyoma virus with mouse embryo cells has been studied by radiobiological methods known to distinguish temperate from virulent bacteriophage. No evidence for "temperate" properties of Polyoma was found. During the course of these studies, it was observed that the curve of inactivation of Polyoma virus by ultraviolet light had two components - a more sensitive one at low doses, and a less sensitive one at higher doses. Virus which survives a low dose has an eclipse period similar to that of unirradiated virus, while virus surviving higher doses shows a significantly longer eclipse period. If Puromycin is present during the early part of the eclipse period, the survival curve becomes a single exponential with the sensitivity of the less sensitive component. These results suggest a repair mechanism in mouse cells which operates more effectively if virus development is delayed.

A comparison of the rates of inactivation of the cytolytic and transforming abilities of Polyoma by ultraviolet light, X-rays, nitrous acid treatment, or the decay of incorporated P³², showed that the transforming ability has a target size roughly 60% of that of the plaque-forming ability. It is thus concluded that only a fraction of the viral genes are necessary for causing transformation.

The appearance of virus-specific RNA in productively infected mouse kidney cells has been followed by means of hybridization between pulse-labelled RNA from the infected cells and the purified virus DNA. The results show a sharp increase in the amount of virus-specific RNA around the time of virus DNA synthesis. The presence of a small amount of virus-specific RNA in virus-free transformed cells has also been shown. This result offers strong evidence for the persistence of at least part of the viral genome in transformed cells.

Biochemical and Biophysical Characterization of Huntingtin

Huntington’s disease (HD) is a fatal autosomal dominant neurodegenerative disease. HD has no cure, and patients pass away 10-20 years after the onset of symptoms. The causal mutation for HD is a trinucleotide repeat expansion in exon 1 of the huntingtin gene that leads to a polyglutamine (polyQ) repeat expansion in the N-terminal region of the huntingtin protein. Interestingly, there is a threshold of 37 polyQ repeats under which little or no disease exists; and above which, patients invariably show symptoms of HD. The huntingtin protein is a 350 kDa protein with unclear function. As the polyQ stretch expands, its propensity to aggregate increases with polyQ length. Models for polyQ toxicity include formation of aggregates that recruit and sequester essential cellular proteins, or altered function producing improper interactions between mutant huntingtin and other proteins. In both models, soluble expanded polyQ may be an intermediate state that can be targeted by potential therapeutics.

In the first study described herein, the conformation of soluble, expanded polyQ was determined to be linear and extended using equilibrium gel filtration and small-angle X-ray scattering. While attempts to purify and crystallize domains of the huntingtin protein were unsuccessful, the aggregation of huntingtin exon 1 was investigated using other biochemical techniques including dynamic light scattering, turbidity analysis, Congo red staining, and thioflavin T fluorescence. Chapter 4 describes crystallization experiments sent to the International Space Station and determination of the X-ray crystal structure of the anti-polyQ Fab MW1. In the final study, multimeric fibronectin type III (FN3) domain proteins were engineered to bind with high avidity to expanded polyQ tracts in mutant huntingtin exon 1. Surface plasmon resonance was used to observe binding of monomeric and multimeric FN3 proteins with huntingtin.

Autophagic Marker MAP1LC3B Expression Levels Are Associated with Carotid Atherosclerosis Symptomatology

Objectives: The mechanism by which atheroma plaque becomes unstable is not completely understood to date but analysis of differentially expressed genes in stable versus unstable plaques may provide clues. This will be crucial toward disclosing the mechanistic basis of plaque instability, and may help to identify prognostic biomarkers for ischaemic events. The objective of our study was to identify differences in expression levels of 59 selected genes between symptomatic patients (unstable plaques) and asymptomatic patients (stable plaques). Methods: 80 carotid plaques obtained by carotid endarterectomy and classified as symptomatic (>70% stenosis) or asymptomatic (>80% stenosis) were used in this study. The expression levels of 59 genes were quantified by qPCR on RNA extracted from the carotid plaques obtained by endarterectomy and analyzed by means of various bioinformatic tools. Results: Several genes associated with autophagy pathways displayed differential expression levels between asymptomatic and symptomatic (i.e. MAP1LC3B, RAB24, EVA1A). In particular, mRNA levels of MAP1LC3B, an autophagic marker, showed a 5-fold decrease in symptomatic samples, which was confirmed in protein blots. Immune system-related factors and endoplasmic reticulum-associated markers (i.e. ERP27, ITPR1, ERO1LB, TIMP1, IL12B) emerged as differently expressed genes between asymptomatic and symptomatic patients. Conclusions: Carotid atherosclerotic plaques in which MAP1LC3B is underexpressed would not be able to benefit from MAP1LC3B-associated autophagy. This may lead to accumulation of dead cells at lesion site with subsequent plaque destabilization leading to cerebrovascular events. Identified biomarkers and network interactions may represent novel targets for development of treatments against plaque destabilization and thus for the prevention of cerebrovascular events.

A construção da síndrome pré-menstrual

Esta pesquisa visa problematizar a síndrome pré-menstrual (SPM) enquanto entidade biomédica a-histórica tornada evidente a partir do preenchimento de critérios diagnósticos. O ponto de partida é a hipótese de que o modelo biomédico de explicação da SPM incorpora e reproduz os padrões sociais vigentes que insistem em visões estereotipadas dos gêneros em função da diferenciação biológica dos sexos. A partir de uma reflexão sobre a construção do fato científico e da preponderância do discurso biomédico na compreensão dos corpos, emoções e comportamentos femininos, analisamos as mudanças históricas ocorridas nessa visão considerada reducionista. No final do século XVIII e início do XIX, a essência da feminilidade era localizada no útero; a partir de meados do século XIX, os ovários passaram a ser considerados a fonte das doenças das mulheres, inclusive as nervosas e mentais. No início do século XX começou a ocorrer uma mudança nos discursos biomédicos e a essência da feminilidade passou a ser localizada em substâncias químicas denominadas hormônios. Desde então o organismo feminino tornou-se cada vez mais representado como controlado pelos hormônios, reificando a crença de que as mulheres são cíclicas e em determinados períodos, instáveis, irracionais e, portanto, não confiáveis. Essa ênfase nos hormônios coincide com a primeira descrição, em 1931, do que era chamado tensão pré-menstrual. Na década de 1950, a terminologia mudou para síndrome pré-menstrual. Inicialmente foi compreendida como diretamente produzida pelos hormônios femininos, mas não há evidência empírica que comprove esta hipótese. Após 80 anos de pesquisas, não se encontrou um marcador biológico ou teste bioquímico que possa ser utilizado para o diagnóstico. Os próprios critérios diagnósticos não são consensuais entre os pesquisadores, pois foram descritos mais de 200 sintomas que incidem de forma variada e inconstante. Não se conhece ainda o mecanismo etiopatogênico e alguns autores questionam a própria existência da síndrome enquanto entidade biomédica e apresentam visões feministas e sócio-culturais para a compreensão do fenômeno. Muitas mulheres, entretanto, afirmam ter TPM (nomenclatura mais comum nos meios leigos). Para aprofundar esta questão e ampliar nossa compreensão, a análise de artigos biomédicos recentes (2000 a 2011) sobre a SPM foi confrontada com a experiência direta ou indireta da TPM em mulheres de camadas médias da população. Com este objetivo, foram analisados artigos científicos sobre a SPM selecionados a partir de um levantamento no PubMed, ferramenta de buscas online, e realizadas entrevistas individuais em profundidade, abertas, semi-estruturadas com mulheres em idade reprodutiva selecionadas através do sistema de amostragem conhecido como bola de neve (snow ball). Após a análise tanto dos artigos científicos quanto das entrevistas, concluímos que apesar de pressupostos comuns que a biologia determina diferenças de gênero naturais e universais entre homens e mulheres a SPM dos artigos biomédicos e a TPM das mulheres não coincidem. Sem desconsiderar as sensações desagradáveis, os problemas e o sofrimento das mulheres que afirmam ter TPM, os resultados deste estudo apontam para uma realidade complexa que enseja mais pesquisa em direção a descrições menos reducionistas destas experiências femininas

Genetic identification of four Malaysian mackerel species off Coast of Peninsular Malaysia based on molecular marker

Random Amplified Polymorphic DNA (RAPD) markers and cytochrome b (Cyt-b) gene sequences were utilized to fingerprint and construct phylogenetic relationships among four species of mackerel commonly found in the Straits of Malacca namely Rastrelliger kanagurta, R. brachysoma, Decapterus maruadsi and D. russelli. The UPGMA dendogram and genetic distance clearly showed that the individuals clustered into their own genus and species except for the Decapterus. These results were also supported by partial mtDNA cytochrome b gene sequences (279 bp) which found monotypic sequence for all Decapterus studied. Cytochrome b sequence phylogeny generated through Neighbor Joining (NJ) method was congruent with RAPD data. Results showed clear discrimination between both genera with average nucleotide divergence about 25.43%. This marker also demonstrated R. brachysoma and R. kanagurta as distinct species separated with average nucleotide divergence about 2.76%. However, based on BLAST analysis, this study indicated that the fish initially identified as D. maruadsi was actually D. russelli. The results highlighted the importance of genetic analysis for taxonomic validation, in addition to morphological traits.

Avaliação da função endotelial em mulheres jovens portadoras da síndrome dos ovários policísticos

A síndrome dos ovários policísticos é uma desordem frequente e complexa, com grande variabilidade fenotípica, predominando os sinais de disfunção ovariana. Alterações metabólicas, inflamatórias e vasculares vinculadas à resistência à insulina são muito prevalentes nessa desordem podendo manifestar-se precocemente. O objetivo principal deste estudo foi investigar a presença de alterações microvasculares em mulheres jovens e não obesas portadoras da síndrome dos ovários policísticos, através de videocapilaroscopia periungueal e dosagem dos níveis séricos de endotelina-1. O objetivo secundário foi verificar a existência de associações entre os achados vasculares, níveis séricos de androgênios, parâmetros clínicos, bioquímicos, metabólicos e inflamatórios relacionados ao risco cardiovascular. Em estudo observacional, transverso e controlado avaliamos 12 mulheres com diagnóstico de síndrome dos ovários policísticos, segundo os critérios estabelecidos pelo consenso de Rotterdam e nove voluntárias saudáveis. A idade (22,82,3 X 24,62,7), o índice de massa corporal (22,53,4 X 23,73,1) e a circunferência da cintura (7510,1 X 77,38,1) foram semelhantes nos dois grupos. As portadoras da síndrome apresentavam hiperandrogenismo clínico. Não foram observadas diferenças significativas entre os grupos quando analisados os níveis séricos de estradiol, testosterona total, androstenediona ou o índice de testosterona livre, entretanto a SHBG mostrou-se significativamente mais baixa no grupo de estudo (p=0,011). A glicemia de jejum, insulina, HOMA-IR e o perfil lipídico foram normais e sem diferença entre os grupos. A amostra com síndrome dos ovários policísticos não apresentava intolerância à glicose ou Diabetes Mellitus pelo teste oral de tolerância à glicose. Os níveis séricos dos marcadores inflamatórios (leucócitos, ácido úrico, adiponectina, leptina e proteína c reativa) e do marcador de função endotelial avaliado também foram similares nos dois grupos. A velocidade de deslocamento das hemácias no basal e após oclusão foram significativamente menores nas pacientes de estudo (p=0,02), mas o tempo para atingir a VDHmax e os parâmetros relativos à morfologia e densidade capilar foram semelhantes. Não observamos correlação entre a velocidade de deslocamento das hemácias e níveis plasmáticos de endotelina-1, androgênios ou parâmetros de resistência insulínica. A velocidade de deslocamento das hemácias associou-se positivamente aos níveis plasmáticos de estradiol (r= 0,45, p<0,05) e negativamente aos de colesterol total e LDL colesterol (r= -0,52, p<0,05; r=-0,47, p<0,05, respectivamente). Em conclusão nossos resultados fornecem evidência adicional de dano precoce à função microvascular em mulheres portadoras de síndrome dos ovários policísticos. Através da capilaroscopia periungueal dinâmica, demonstramos que mulheres jovens com moderado hiperandrogenismo, sem obesidade, RI, hipertensão ou dislipidemia, já apresentam disfunção microvascular nutritiva, caracterizada por redução na velocidade de fluxo das hemácias no basal e após oclusão. Estes achados micro-circulatórios não foram acompanhados de elevações nos níveis plasmáticos de endotelina-1.

A Bayesian method for identification of stock mixtures from molecular marker data

Molecular markers have been demonstrated to be useful for the estimation of stock mixture proportions where the origin of individuals is determined from baseline samples. Bayesian statistical methods are widely recognized as providing a preferable strategy for such analyses. In general, Bayesian estimation is based on standard latent class models using data augmentation through Markov chain Monte Carlo techniques. In this study, we introduce a novel approach based on recent developments in the estimation of genetic population structure. Our strategy combines analytical integration with stochastic optimization to identify stock mixtures. An important enhancement over previous methods is the possibility of appropriately handling data where only partial baseline sample information is available. We address the potential use of nonmolecular, auxiliary biological information in our Bayesian model.

Biochemical biomarkers in samples processed by different methods in Environmental Specimen Banks

In the last decades the creation of new Environmental Specimen Banks (ESB) is increasing due to the necessity of knowing the effects of pollutants in both the environment and human populations. ESBs analyze and store samples in order to understand the effects of chemicals, emerging substances and the environmental changes in biota. For a correct analysis of the effect induced by these variables, there is a need to add biological endpoints, such as biomarkers, to the endpoints based on chemical approaches which have being used until now. It is essential to adapt ESB´s sampling strategies in order to enable scientists to apply new biological methods. The present study was performed to obtain biochemical endpoints from samples stored in the BBEBB (Biscay Bay Environmental Biospecimen Bank) of the Marine Station of Plentzia (PIE - UPV/EHU). The main objective of the present work was to study the variability caused in biochemical biomarkers by different processing methods in mussels (Mytilus galloprovincialis) from two localities (Plentzia and Arriluze) with different pollution history. It can be concluded that the selected biomarkers (glutathione S-transferase and acetylcholinesterase) can be accurately measured in samples stored for years in the ESBs. The results also allowed the discrimination of both sampling sites. However, in a further step, the threshold levels and baseline values should be characterized for a correct interpretation of the results in relation to the assessment of the ecosystem health status.

Biochemical and morphometric approaches to characterize farmed tilapias

Biochemical (electrophoresis and mitochondrial DNA) and morphological analysis are important tools for the characterization of strains. Reference is made to studies conducted in the framework of the Genetic Improvement of Farmed Tilapias project to establish a new base tilapia population for culture purposes, describing the basic concepts of electrophoresis and morphometric analysis.