An enhanced workflow for variant interpretation in UniProtKB/Swiss-Prot improves consistency and reuse in ClinVar.

Personalized genomic medicine depends on integrated analyses that combine genetic and phenotypic data from individual patients with reference knowledge of the functional and clinical significance of sequence variants. Sources of this reference knowledge include the ClinVar repository of human genetic variants, a community resource that accepts submissions from external groups, and UniProtKB/Swiss-Prot, an expert-curated resource of protein sequences and functional annotation. UniProtKB/Swiss-Prot provides knowledge on the functional impact and clinical significance of over 30 000 human protein-coding sequence variants, curated from peer-reviewed literature reports. Here we present a pilot study that lays the groundwork for the integration of curated knowledge of protein sequence variation from UniProtKB/Swiss-Prot with ClinVar. We show that existing interpretations of variant pathogenicity in UniProtKB/Swiss-Prot and ClinVar are highly concordant, with 88% of variants that are common to the two resources having interpretations of clinical significance that agree. Re-curation of a subset of UniProtKB/Swiss-Prot variants according to American College of Medical Genetics and Genomics (ACMG) guidelines using ClinGen tools further increases this level of agreement, mainly due to the reclassification of supposedly pathogenic variants as benign, based on newly available population frequency data. We have now incorporated ACMG guidelines and ClinGen tools into the UniProt Knowledgebase (UniProtKB) curation workflow and routinely submit variant data from UniProtKB/Swiss-Prot to ClinVar. These efforts will increase the usability and utilization of UniProtKB variant data and will facilitate the continuing (re-)evaluation of clinical variant interpretations as data sets and knowledge evolve.

Gene Ontology annotations and resources.

The Gene Ontology (GO) Consortium (GOC, http://www.geneontology.org) is a community-based bioinformatics resource that classifies gene product function through the use of structured, controlled vocabularies. Over the past year, the GOC has implemented several processes to increase the quantity, quality and specificity of GO annotations. First, the number of manual, literature-based annotations has grown at an increasing rate. Second, as a result of a new 'phylogenetic annotation' process, manually reviewed, homology-based annotations are becoming available for a broad range of species. Third, the quality of GO annotations has been improved through a streamlined process for, and automated quality checks of, GO annotations deposited by different annotation groups. Fourth, the consistency and correctness of the ontology itself has increased by using automated reasoning tools. Finally, the GO has been expanded not only to cover new areas of biology through focused interaction with experts, but also to capture greater specificity in all areas of the ontology using tools for adding new combinatorial terms. The GOC works closely with other ontology developers to support integrated use of terminologies. The GOC supports its user community through the use of e-mail lists, social media and web-based resources.

The IntAct molecular interaction database in 2010.

IntAct is an open-source, open data molecular interaction database and toolkit. Data is abstracted from the literature or from direct data depositions by expert curators following a deep annotation model providing a high level of detail. As of September 2009, IntAct contains over 200.000 curated binary interaction evidences. In response to the growing data volume and user requests, IntAct now provides a two-tiered view of the interaction data. The search interface allows the user to iteratively develop complex queries, exploiting the detailed annotation with hierarchical controlled vocabularies. Results are provided at any stage in a simplified, tabular view. Specialized views then allows 'zooming in' on the full annotation of interactions, interactors and their properties. IntAct source code and data are freely available at http://www.ebi.ac.uk/intact.

Collaborative annotation of genes and proteins between UniProtKB/Swiss-Prot and dictyBase.

UniProtKB/Swiss-Prot, a curated protein database, and dictyBase, the Model Organism Database for Dictyostelium discoideum, have established a collaboration to improve data sharing. One of the major steps in this effort was the 'Dicty annotation marathon', a week-long exercise with 30 annotators aimed at achieving a major increase in the number of D. discoideum proteins represented in UniProtKB/Swiss-Prot. The marathon led to the annotation of over 1000 D. discoideum proteins in UniProtKB/Swiss-Prot. Concomitantly, there were a large number of updates in dictyBase concerning gene symbols, protein names and gene models. This exercise demonstrates how UniProtKB/Swiss-Prot can work in very close cooperation with model organism databases and how the annotation of proteins can be accelerated through those collaborations.

IntAct--open source resource for molecular interaction data.

IntAct is an open source database and software suite for modeling, storing and analyzing molecular interaction data. The data available in the database originates entirely from published literature and is manually annotated by expert biologists to a high level of detail, including experimental methods, conditions and interacting domains. The database features over 126,000 binary interactions extracted from over 2100 scientific publications and makes extensive use of controlled vocabularies. The web site provides tools allowing users to search, visualize and download data from the repository. IntAct supports and encourages local installations as well as direct data submission and curation collaborations. IntAct source code and data are freely available from http://www.ebi.ac.uk/intact.

Nutritional status and food consumption patterns of young children living in Western Uganda.

OBJECTIVES: The aim of this pilot study was to compare the nutritional status and food consumption patterns of children under five years. DESIGN: Quantitative, exploratory, cross sectional study. SETTING: Kabarole district, western Uganda. Kabarole district is a rural district with subsistence farming as the main income. SUBJECTS: Two hundred and five children between 12 and 72 months of age living in AIDS affected homes versus children living in non-AIDS affected homes were examined. RESULTS: Fifty-five percent of all children were stunted and 20.5% were underweight. There was no difference in the prevalence of malnutrition between children living in AIDS affected homes versus non-AIDS affected homes. Only children between 12-35 months suffered from a daily deficit in caloric intake. The older children consumed the basic recommended daily intake (RDI) for protein, fat, iron and vitamin A. Due to frequent disease episodes and limitations in the estimations of individual total energy expenditure, the results are likely underestimations of the children's true nutritional requirements. The type of foods given to children in AIDS affected homes and controls were quite similar. CONCLUSION: Young children in Kabarole district suffer from severe chronic malnutrition rates, but rates and feeding patterns are not different in AIDS affected versus non AIDS affected homes.

Preferential inhibition by (-)-epigallocatechin-3-gallate of the cell surface NADH oxidase and growth of transformed cells in culture.

A drug-responsive and cancer-specific NADH oxidase of the mammalian plasma membrane, constitutively activated in transformed cells, was inhibited preferentially in HeLa and human mammary adenocarcinoma by the naturally-occurring catechin of green tea, (-)-epigallocatechin-3-gallate (EGCg). With cells in culture, EGCg preferentially inhibited growth of HeLa and mammary adenocarcinoma cells compared with growth of mammary epithelial cells. Inhibited cells became smaller, and cell death was accompanied by a condensed and fragmented appearance of the nuclear DNA as revealed by fluorescence microscopy with 4',6-diamidino-2-phenylindole, suggestive of apoptosis. Mammary epithelial cells recovered from EGCg treatment even at 50 microM, whereas growth of HeLa and mammary adenocarcinoma cells was inhibited by EGCg at concentrations as low as 1 microM with repeated twice-daily additions and did not recover from treatment with 50 microM EGCg. The findings correlate inhibition of cell surface NADH oxidase activity and inhibition of growth with EGCg-induced apoptosis.

Imperfect assessment and limited information preclude optimal strategies in male-male fights in the orb-weaving spider Metellina mengei.

Agonistic behaviour between male orb-web spiders Metellina mengei competing for access to female webs was examined in field experiments to test the major predictions of game theory. Winners of fights were significantly larger than losers, particularly with respect to the length of the first pair of legs, which are sexually dimorphic in this species and used extensively in agonistic encounters. The size of the winning male had no influence on contest intensity or duration, and neither did relative size. However, fight intensity and duration were both positively correlated with the size of the losing male. Resident males won significantly more contests than intruders. Winning intruders were significantly larger than winning residents and it was these winning intruders that tended to produce the longer fights. Female weight and hence reproductive value had a marked influence on fight intensity and duration of fights won by the intruder but not those won by the resident. This indicates that only the resident obtains information about the female. These data are discussed with reference to the discrepancy with theory and a failure of some contestants to obtain information on resource value and relative contestant size necessary to optimize fight strategy.

The plasma membrane NADH oxidase of soybean has vitamin K(1) hydroquinone oxidase activity.

Isolated plasma membrane vesicles and the plasma membrane NADH oxidase partially purified from soybean plasma membrane vesicles exhibited a cyanide-insensitive vitamin K(1) hydroquinone oxidase activity with isolated plasma membrane vesicles. Reduced vitamin K(1) (phylloquinol) was oxidized at a rate of about 10 nmol/min/mg protein as determined by reduced vitamin K(1) reduction or oxygen consumption. The K(m) for reduced K(1) was 350 microM. With the partially purified enzyme, reduced vitamin K(1) was oxidized at a rate of about 600 nmol/min/mg protein and the K(m) was 400 microM. When assayed in the presence of 1 mM KCN, activities of both plasma membrane vesicles and of the purified protein were stimulated (0.1 microM) or inhibited (0.1 mM) by the synthetic auxin growth factor 2, 4-dichlorophenoxyacetic acid. The findings suggest the potential participation of the plasma membrane NADH oxidase as a terminal oxidase of plasma membrane electron transport from cytosolic NAD(P)H via reduced vitamin K(1) to acceptors (molecular oxygen or protein disulfides) at the cell surface.

The fission yeast SPB component Cut12 links bipolar spindle formation to mitotic control.

During fission yeast mitosis, the duplicated spindle pole bodies (SPBs) nucleate microtubule arrays that interdigitate to form the mitotic spindle. cut12.1 mutants form a monopolar mitotic spindle, chromosome segregation fails, and the mutant undergoes a lethal cytokinesis. The cut12(+) gene encodes a novel 62-kD protein with two predicted coiled coil regions, and one consensus phosphorylation site for p34(cdc2) and two for MAP kinase. Cut12 is localized to the SPB throughout the cell cycle, predominantly around the inner face of the interphase SPB, adjacent to the nucleus. cut12(+) is allelic to stf1(+); stf1.1 is a gain-of-function mutation bypassing the requirement for the Cdc25 tyrosine phosphatase, which normally dephosphorylates and activates the p34(cdc2)/cyclin B kinase to promote the onset of mitosis. Expressing a cut12(+) cDNA carrying the stf1.1 mutation also suppressed cdc25.22. The spindle defect in cut12.1 is exacerbated by the cdc25.22 mutation, and stf1.1 cells formed defective spindles in a cdc25.22 background at high temperatures. We propose that Cut12 may be a regulator or substrate of the p34(cdc2) mitotic kinase.

Immunoreactive gonadotropin-releasing hormone (GnRH) is detected only in the form of chicken GnRH-II within the brain of the green anole, Anolis carolinensis.

The presence of multiple forms of gonadotropin-releasing hormone (GnRH) within a single brain is common among vertebrate species. In previous studies of reptiles, two forms of GnRH were isolated from the brain of alligators and the primary structure was determined to be that of chicken (c)GnRH-I and cGnRH-II. GnRH has also been detected by indirect methods in other reptiles including turtles, lizards, and snakes. We used a combination of high-performance liquid chromatography (HPLC) and radioimmunoassay to determine the number and molecular form(s) of GnRH in the brain of a lizard, Anolis carolinensis, that was reported to lack GnRH cells in the forebrain. Immunoreactivity was detected in the same HPLC elution position in which synthetic cGnRH-II elutes, but not in any other position. Detection was based on five antisera that among them detect the 12 known forms of GnRH; these antisera include ones that are specific to cGnRH-I and cGnRH-II. We conclude that the lizard A. carolinensis contains cGnRH-II, but not cGnRH-I or another known form of GnRH. These data, coupled with our earlier immunocytochemical study, suggest that the lizard studied here lacks cGnRH-I, the form that is found in the terminal nerve, olfactory bulb, and forebrain in nonsquamate reptiles and in birds. Our hypothesis is that the presence of both cGnRH-I and cGnRH-II in the brain is ancestral in the reptilian lineage and retained in the orders that include turtles (Chelonia) or alligators (Crocodilia). However, the pattern in the order Squamata varies: in A. carolinensis, only cGnRH-II is present in the brain and cGnRH-I is absent, whereas in the snake Thamnophilis sirtalis, cGnRH-I is retained and cGnRH-II is absent in the brain, as recently reported. This raises the question of how reproduction is controlled in reptiles that lack one form of GnRH.

Acyl-CoA:Cholesterol O-acyltransferase (ACAT) inhibitors. 2. 2-(1,3-Dioxan-2-yl)-4,5-diphenyl-1H-imidazoles as potent inhibitors of ACAT.

The second in this series of papers concerns our further investigations into the search for a potent bioavailable acyl-CoA:cholesterol O-acyltransferase (ACAT) inhibitor suitable for the treatment of atherosclerosis. The design, synthesis, and structure-activity relationship for a series of ACAT inhibitors based on the 2-(1,3-dioxan-2-yl)-4,5-diphenyl-1H-imidazole pharmacophore are described. Compounds such as 13a bearing simple alkyl or hydroxymethyl substituents at the 5-position of the 1,3-dioxane ring are potent bioavailable inhibitors of the rat hepatic microsomal enzyme in vitro (IC50 < 100 nM) but are only weak inhibitors of the human hepatic enzyme. We have found however that 1,3-dioxanes substituted at the 5-cis position with pyrazolylalkyl or aminoalkyl groups are potent inhibitors in vitro of human macrophage ACAT, the potency depending on the nature of the terminal heterocycle and the length of the alkyl chain. An ex vivo bioassay herein demonstrates that potent inhibitors such as 13t (IC50 = 10 nM) which contain lipophilic terminal heterocycles do not appear to be systematically available. Less potent but more water soluble compounds such as 13h (IC50 = 60 nM) and 13n (IC50 = 70 nM) are absorbed following oral dosing and achieve plasma levels significantly in excess of their IC50 for ACAT inhibition. These compounds are therefore possible candidates for further investigation as oral antiatherosclerotic agents.

Acyl-CoA:cholesterol O-acyl transferase (ACAT) inhibitors. 1. 2-(Alkylthio)-4,5-diphenyl-1H-imidazoles as potent inhibitors of ACAT.

A potent, bioavailable ACAT inhibitor may have beneficial effects in the treatment of atherosclerosis by (i) reducing the absorption of dietary cholesterol, (ii) reducing the secretion of very low density lipoproteins into plasma from the liver, and (iii) preventing the transformation of arterial macrophages into foam cells. We have found that a mevalonate derivative 2, which contains a 4,5-diphenyl-1H-imidazol-2-yl moiety, inhibits rat hepatic microsomal ACAT in vitro and produces a significant hypocholesterolemic effect in the cholesterol-fed rat. Structure-activity relationships for analogues of 2 demonstrate that the 4,5-diphenyl-1H-imidazole moiety is a pharmacophore for inhibition of rat microsomal ACAT.

The regulation of porcine theca cell proliferation in vitro: synergistic actions of epidermal growth factor and platelet-derived growth factor.

An important but poorly understood aspect of mammalian follicle development involves the regulation of theca cell proliferation. To investigate the premise that growth factors regulate theca cell proliferation, porcine theca cells were prepared by collagenase/DN'ase digestion of follicle linings after the removal of the granulosa cells and allowed to attach for 24 h. This method provided a monolayer of theca cells that had little if any granulosa cell contamination and which secreted high levels of androstenedione relative to granulosa cells during moderate-term culture (33-fold difference, P less than 0.01). In medium containing fetal calf serum (10%), theca cells were significantly more responsive to platelet-derived growth factor (PDGF) than epidermal growth factor (EGF) in terms of proliferation (13.4 +/- 0.2-vs. 7.0 +/- 0.1-fold increases relative to the initial cell count, P less than 0.05). This is in contrast to granulosa cells which were significantly more responsive to EGF than PDGF (7.1 +/- 0.1 vs. 4.0 +/- 0.2 fold-increases, P less than 0.05). Since serum has been shown to contain both EGF and PDGF, proliferation studies were performed using plasma-derived serum (PDS) which is growth factor restricted to examine more closely the direct effects of growth factors. In medium containing 0.25% PDS and within experiments, PDGF (1-25 ng/ml) stimulated theca cell proliferation in a dose-dependent manner (2.3-fold increase relative to controls, P less than 0.05) whereas EGF did not. EGF, however, markedly enhanced the proliferative action of PDGF (6.4-fold increase relative to controls, P less than 0.05). Insulin-like growth factor I and low density lipoprotein, factors which enhance markedly the proliferative effects of EGF and PDGF in terms of granulosa cell proliferation, exhibited only a modest synergistic effect with respect to EGF and PDGF upon theca cells (9.5-fold increase vs. a 6.4-fold increase above controls, P less than 0.05). Temporal studies in vitro indicate that theca cell proliferation is low during the first 3-day exposure to growth factors irrespective of treatment (a 2-fold increase over the seeding density). During the second 3-day exposure, however, theca cell proliferation increases 4- to 5-fold. The temporal pattern of theca cell proliferation stimulated by fetal calf serum supplemented with EGF or PDGF and PDS-containing medium supplemented with PDGF, EGF, insulin-like growth factor I, and low density lipoprotein is similar. These results suggest that PDGF is a major mitogen toward porcine theca cells and that EGF greatly enhances its activity.(ABSTRACT TRUNCATED AT 400 WORDS)

Regulation of granulosa cell proliferation: facilitative roles of platelet-derived growth factor and low density lipoprotein.

Recent studies suggest that epidermal growth factor (EGF) and/or transforming growth factor-alpha (TGF-alpha) and insulin-like growth factor-I (IGF-I) act synergistically to promote granulosa cell proliferation in vitro suggesting a similar role in vivo. Using a serum-restricted, monolayer culture system containing very low levels of platelet-poor plasma-derived serum (PPPDS), the facilitative roles of platelet-derived growth factor (PDGF) and low density lipoprotein (LDL) with respect to growth factor-stimulated granulosa cell proliferation were investigated. In nutrient medium containing only 0.1% PPPDS, PDGF (1-25 ng/ml) had no effect upon granulosa cell proliferation. When combined with EGF, which alone does not stimulate granulosa cell proliferation, PDGF dose-dependently increased cell proliferation to levels obtained with 10% fetal calf serum (2.4-fold increase relative to controls, P less than 0.05). When combined with EGF and IGF-I, a combination which does stimulate mitosis in granulosa cells, PDGF again dose-dependently enhanced proliferation (P less than 0.05). The extent of proliferation obtained with EGF + IGF-I + PDGF was consistently greater than that obtained with 10% fetal calf serum (P less than 0.05) but significantly less than that obtained with EGF + fetal calf serum, a treatment which stimulates rapid granulosa cell proliferation. LDL has been shown to greatly enhance granulosa cell steroidogenesis by providing exogenous cholesterol. However, cholesterol is also required for plasma membrane biosynthesis and cell growth. LDL alone, had no effect upon porcine granulosa cell proliferation relative to media controls (0.1% PPPDS) nor did it synergize with any single growth factor to induce mitosis. When combined with EGF + IGF-I, and EGF + PDGF, but not PDGF + IGF-I, LDL dose-dependently (1-25 micrograms/ml) enhanced proliferation (P less than 0.05) to levels equivalent to that obtained with 10% fetal calf serum. When combined with EGF, IGF-I, and PDGF, LDL at 10 micrograms/ml enhanced proliferation to an extent equivalent with EGF + fetal calf serum (a 5.4-fold increase relative to media controls). High density lipoprotein did not itself stimulate proliferation nor did it facilitate proliferation mediated by growth factors. When maintained in medium alone (0.1% PPPDS), the cell population doubling time was 8.0 +/- 0.5 days. In the presence of EGF, IGF-I, PDGF, and LDL (10, 10, and 5 ng/ml, and 10 micrograms/ml, respectively) the doubling time was reduced to 2.0 +/- 0.1 days.(ABSTRACT TRUNCATED AT 400 WORDS)

Carta federal del agua; proyecto (revisión literal)

Señala los lineamientos para la estructuración de una política hídrica federal. Considera normas de jurisdicción hídrica. Estipula: la administración hídrica federal, principios constitucionales aplicables al manejo de los recursos hídricos, principios y criterios del derecho substantivo que regulan el régimen de dominio de los recursos hídricos. Incluye artículos que tocan los recursos hídricos en particular

Carta federal del agua; proyecto (revisión literal)

Señala los lineamientos para la estructuración de una política hídrica federal. Considera normas de jurisdicción hídrica. Estipula: la administración hídrica federal, principios constitucionales aplicables al manejo de los recursos hídricos, principios y criterios del derecho substantivo que regulan el régimen de dominio de los recursos hídricos. Incluye artículos que tocan los recursos hídricos en particular

Implicancias jurídicas de la aplicación de nuevas tecnologías

Efectua una regulación legal de la modificación artificial del clima en el derecho comparado, analizando las áreas de acción y las técnicas empleadas para modificar el clima. Revisa las implicancias legales de la modificación del clima en los Estados Unidos de Norte América, entre otros aspectos. Distingue el régimen jurídico de los recursos geotérmicos, la ley de energía y facetas de los mencionados recursos