Evolutionary Sequence Modeling for Discovery of Peptide Hormones

There are currently a large number of “orphan” G-protein-coupled receptors (GPCRs) whose endogenous ligands (peptide hormones) are unknown. Identification of these peptide hormones is a difficult and important problem. We describe a computational framework that models spatial structure along the genomic sequence simultaneously with the temporal evolutionary path structure across species and show how such models can be used to discover new functional molecules, in particular peptide hormones, via cross-genomic sequence comparisons. The computational framework incorporates a priori high-level knowledge of structural and evolutionary constraints into a hierarchical grammar of evolutionary probabilistic models. This computational method was used for identifying novel prohormones and the processed peptide sites by producing sequence alignments across many species at the functional-element level. Experimental results with an initial implementation of the algorithm were used to identify potential prohormones by comparing the human and non-human proteins in the Swiss-Prot database of known annotated proteins. In this proof of concept, we identified 45 out of 54 prohormones with only 44 false positives. The comparison of known and hypothetical human and mouse proteins resulted in the identification of a novel putative prohormone with at least four potential neuropeptides. Finally, in order to validate the computational methodology, we present the basic molecular biological characterization of the novel putative peptide hormone, including its identification and regional localization in the brain. This species comparison, HMM-based computational approach succeeded in identifying a previously undiscovered neuropeptide from whole genome protein sequences. This novel putative peptide hormone is found in discreet brain regions as well as other organs. The success of this approach will have a great impact on our understanding of GPCRs and associated pathways and help to identify new targets for drug development

Preconditioning-induced ischemic tolerance: a window into endogenous gearing for cerebroprotection

Ischemic tolerance defines transient resistance to lethal ischemia gained by a prior sublethal noxious stimulus (i.e., preconditioning). This adaptive response is thought to be an evolutionarily conserved defense mechanism, observed in a wide variety of species. Preconditioning confers ischemic tolerance if not in all, in most organ systems, including the heart, kidney, liver, and small intestine. Since the first landmark experimental demonstration of ischemic tolerance in the gerbil brain in early 1990's, basic scientific knowledge on the mechanisms of cerebral ischemic tolerance increased substantially. Various noxious stimuli can precondition the brain, presumably through a common mechanism, genomic reprogramming. Ischemic tolerance occurs in two temporally distinct windows. Early tolerance can be achieved within minutes, but wanes also rapidly, within hours. Delayed tolerance develops in hours and lasts for days. The main mechanism involved in early tolerance is adaptation of membrane receptors, whereas gene activation with subsequent de novo protein synthesis dominates delayed tolerance. Ischemic preconditioning is associated with robust cerebroprotection in animals. In humans, transient ischemic attacks may be the clinical correlate of preconditioning leading to ischemic tolerance. Mimicking the mechanisms of this unique endogenous protection process is therefore a potential strategy for stroke prevention. Perhaps new remedies for stroke are very close, right in our cells

Not all flavor expertise is equal : The language of wine and coffee experts

People in Western cultures are poor at naming smells and flavors. However, for wine and coffee experts, describing smells and flavors is part of their daily routine. So are experts better than lay people at conveying smells and flavors in language? If smells and flavors are more easily linguistically expressed by experts, or more "codable", then experts should be better than novices at describing smells and flavors. If experts are indeed better, we can also ask how general this advantage is: do experts show higher codability only for smells and flavors they are expert in (i.e., wine experts for wine and coffee experts for coffee) or is their linguistic dexterity more general? To address these questions, wine experts, coffee experts, and novices were asked to describe the smell and flavor of wines, coffees, everyday odors, and basic tastes. The resulting descriptions were compared on a number of measures. We found expertise endows a modest advantage in smell and flavor naming. Wine experts showed more consistency in how they described wine smells and flavors than coffee experts, and novices; but coffee experts were not more consistent for coffee descriptions. Neither expert group was any more accurate at identifying everyday smells or tastes. Interestingly, both wine and coffee experts tended to use more source-based terms (e.g., vanilla) in descriptions of their own area of expertise whereas novices tended to use more evaluative terms (e.g., nice). However, the overall linguistic strategies for both groups were en par. To conclude, experts only have a limited, domain-specific advantage when communicating about smells and flavors. The ability to communicate about smells and flavors is a matter not only of perceptual training, but specific linguistic training too

Distribuição da hipovitaminose A no Brasil nas últimas quatro décadas: ingestão alimentar, sinais clínicos e dados bioquímicos Distribution of hipovitaminosis A in Brazil in the last four decades: dietary intake, clinical signs and biochemical data

O presente estudo teve como objetivo o registro e a apresentação de trabalhos realizados no Brasil nos últimos 40 anos, relacionados com a investigação sobre a deficiência de vitamina A. Esta deficiência tem sido diagnosticada por um ou mais dos seguintes critérios: ingestão deficiente de alimentos fontes de vitamina A, exame clínico, níveis séricos de retinol abaixo dos aceitos como normais, concentração hepática de retinol, teste de adaptação ao escuro e corante de Rosa Bengala. A deficiência foi diagnosticada em grupos populacionais de vários Estados e capitais brasileiras em cidades grandes e pequenas e em zonas rurais. A maioria dos trabalhos foi desenvolvida em grupos populacionais de baixa renda. Quanto às conseqüências clínicas, relataram-se achados de sinais oculares leves, como cegueira noturna, manchas de Bitot e xerose conjuntival, encontrados principalmente na Região Nordeste. Alguns autores observaram, em menor número de casos, lesões graves, como lesões corneanas e ceratomalácia. Trabalhos da última década indicaram associação entre a hipovitaminose A e o aumento da morbidade e mortalidade, principalmente em crianças pré-escolares.<br>This work presents a review of investigations carried out in Brazil in the last 40 years, concerning the diagnosis of hypovitaminosis A. Vitamin A deficiency has been established by means of dietary intake, clinical signs, low serum and hepatic retinol concentrations, and by the rose bengal staining test and rapid dark-adaptation test. The vitamin deficiency has been found in many Brazilian, in many states capitals, in big and small cities and also in rural areas. Most of the research work has been undertaken with samples of populations of low socioeconomic level. As far as clinical signs are concerned, eye signs indicative of xerophtalmia were found mainly in the Northeastern Region. They included night blindness and conjunctival xerosis with or without Bitot's spots. More severe lesions such as irreversible changes or keratomalacia were rarely observed. Recent papers have shown the relationship between vitamin A deficiency and the increase in morbidity and mortality, mainly in pre-school children