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At least 523 records · Page 29Linked to original sources
PubMed2002

Suggestive linkage on chromosome 1 for a quantitative alcohol-related phenotype.

BACKGROUND: Alcohol dependence is a clinically and etiologically heterogeneous disorder. Accordingly, a variety of subtypes of alcohol-dependent individuals have been proposed, and multiple operational definitions of alcohol use, abuse, and dependence have been used in linkage analyses directed toward detecting genes involved in alcohol use and problems. Here, we develop quantitative phenotypes that characterize drinking patterns among both alcoholic and nonalcoholic subjects, and use these phenotypes in subsequent linkage analyses. METHODS: More than 9000 individuals from alcoholic and control families were administered a semistructured interview and personality questionnaire as part of the initial stage of the Collaborative Study on the Genetics of Alcoholism (COGA). A principal component analysis was conducted on items that captured many of the dimensions of drinking and related behaviors, including aspects of alcohol use, antisocial behavior and affective disturbance when drinking, and personality. Factor scores were computed for all individuals. Nonparametric linkage analyses were conducted on these factor scores, in the initial COGA sample consisting of 987 individuals from 105 extended families, and in a replication sample consisting of 1295 individuals from 157 extended families. RESULTS: Three factors were identified, accounting for 68% of the total variance. The most promising regions of linkage appeared for factor 2, on which higher scores indicate a later age of onset of regular drinking and higher harm avoidance. Chromosome 1 yielded consistent evidence of linkage in both samples, with a maximum lod score of 3.3 when the samples were combined for analysis. Consistent suggestion of linkage also was found to chromosome 15. CONCLUSIONS: Developing novel phenotypes that more accurately model the effect of influential genes may help efforts to detect genes involved in complex disorders. Applying principal component analysis in the COGA sample provided support for some regions of linkage previously reported in COGA, and identified other new, promising regions of linkage.

Alcoholism↗
PubMed2006

Thrombin inhibitors with novel P1 binding pocket functionality: free energy of binding analysis.

The high incidence of thrombembolic diseases justifies the development of new antithrombotics. The search for a direct inhibitor has resulted in the synthesis of a considerable number of low molecular weight molecules that inhibit human alpha-thrombin potently. However, efforts to develop an orally active drug remain in progress as the most active inhibitors with a highly basic P1 moiety exhibit an unsatisfactory bioavailability profile. In our previous work we solved several X-ray structures of human alpha-thrombin in complexes with (1) novel bicyclic arginine mimetics attached to the glycylproline amide and pyridinone acetamide scaffold and (2) inhibitors with a novel aza scaffold and with charged or neutral P1 moieties. In the present contribution, we correlate the structures of the complex between these inhibitors and the protein with the calculated free energy of binding. The energy of solvation was calculated using the Poisson-Boltzmann approach. In particular, the requirements for successful recognition of an inhibitor at the protein's active site pocket S1 are discussed.

Antithrombins↗
PubMed2006

Undiagnosed coronary fistula causing low cardiac output syndrome after pediatric heart surgery.

A patient with preoperative pulmonary hypertension and a large left to right intracardiac shunt underwent surgical correction of a complex cardiac anomaly and required extracorporeal life support for unexplained ventricular dysfunction following the procedure. Following recovery, a fistulous connection between the right coronary artery and main pulmonary artery was demonstrated. Implications and management strategies of unsuspected coronary fistula in pediatric heart surgery are discussed.

Arterio-Arterial Fistula↗
PubMed2002

Structure of the mammalian ribosome-channel complex at 17A resolution.

The co-translational translocation of proteins into the endoplasmic reticulum (ER) lumen and the biogenesis of membrane proteins require ribosome binding to a membrane channel formed by the Sec61p complex. We now report the 17A structure of a mammalian ribosome-channel complex derived from ER membranes. Atomic models of the ribosomal subunits were aligned to the programmed ribosome from Thermus thermophilus, to provide a common reference frame. The T.thermophilus ribosome, and by extension all known high resolution subunit models, were then docked within our map of the ribosome-channel complex. The structure shows that the ribosome contains a putative tRNA in the exit site, and a comparison with a non-programmed, yeast ribosome suggests that the L1 stalk may function as a gate in the tRNA exit path. We have localized six major expansion segments in the large subunit of the vertebrate ribosome including ES27, and suggest a function for ES30. The large ribosomal subunit is linked to the channel by four connections. We identified regions in the large subunit rRNA and four proteins that may help form the connections. These regions of the ribosome probably serve as a template to guide the assembly of the asymmetric translocation channel. Three of the connections form a picket fence that separates the putative translocation pore from the attachment site of an additional membrane component. The ribosome-channel connections also create an open junction that would allow egress of a nascent chain into the cytosol. At a threshold that is appropriate for the entire complex, the channel is rather solid and the lumenal half of the putative translocation pore is closed. These data suggest that the flow of small molecules across the membrane may be impeded by the channel itself, rather than the ribosome-channel junction.

Animals↗
PubMed2006

Swimming pool drownings among US residents aged 5-24 years: understanding racial/ethnic disparities.

OBJECTIVE: We examined circumstances surrounding swimming pool drownings among US residents aged 5 to 24 years to understand why Black males and other racial/ethnic groups have high drowning rates. METHODS: We obtained data about drowning deaths in the United States (1995-1998) from death certificates, medical examiner reports, and newspaper clippings collected by the US Consumer Product Safety Commission. RESULTS: During the study period, 678 US residents aged 5 to 24 years drowned in pools. Seventy-five percent were male, 47% were Black, 33% were White, and 12% were Hispanic. Drowning rates were highest among Black males, and this increased risk persisted after we controlled for income. The majority of Black victims (51%) drowned in public pools, the majority of White victims (55%) drowned in residential pools, and the majority of Hispanic victims (35%) drowned in neighborhood pools (e.g., an apartment complex pool). Foreign-born males also had an increased risk for drowning compared with American-born males. CONCLUSIONS: Targeted interventions are needed to reduce the incidence of swimming pool drownings across racial/ethnic groups, particularly adult supervision at public pools.

Adolescent↗
PubMed2002

Hepatitis C virus particles of different density in the blood of chronically infected immunocompetent and immunodeficient patients: Implications for virus clearance by antibody.

The purpose of this study was to analyse the influence of the humoral immune response on the generation and clearance of hepatitis C virus (HCV) RNA containing particles in the blood of chronically infected patients. Blood samples were fractionated by sequential flotation ultracentrifugation and HCV RNA was recovered in three fractions: low density of < 1.063 g/ml, intermediate density of 1.063-1.21 g/ml, and high density of > 1.21 g/ml. Serum low-density lipoproteins co-fractionated with the low-density particles, and high-density lipoproteins co-fractionated with the intermediate-density particles. Immunoglobulins were found exclusively in the high-density fractions. In patients with congenital immunodeficiencies, with no or low serum antibodies to the virus, mean HCV RNA titres were equal in each fraction, at approximately 10(5) IU/ml. In antibody-positive, immunocompetent patients, however, virus titres in the low-density fraction and those in the high-density fraction were reduced or absent in most patients, suggesting that virus particles in these fractions are subject to antibody-mediated clearance. Particles of intermediate density were approximately equal in titre in both patient groups, suggesting that these particles are neither generated by, nor cleared, as a result of the humoral immune response. Immunoprecipitation experiments indicated that particles of intermediate density were not complexed with either high-density lipoprotein or immunoglobulins. Elucidation of the mechanisms by which these particles are generated and maintained in the blood may provide valuable insight into the mechanism of virus persistence.

Adolescent↗
PubMed2003

Explicit water near the catalytic I helix Thr in the predicted solution structure of CYP2A4.

The solution structure of mouse cytochrome P450 2A4 (CYP2A4), a monooxygenase of deoxysteroids, was obtained using homology modeling and molecular dynamics. The solvent-equilibrated CYP2A4 preserves the essential features of CYP450s. A comparison of the models CYP2A4 and CYP2A4 with testosterone bound CYP2A4/T illustrates the changes induced by the binding of the substrate. Experimental evidence links four amino acid residues to the catalytic activity, substrate specificity, and regioselectivity of this enzyme. Three of the four amino acids are found within contact distance of the testosterone substrate, and therefore may control the binding of the substrate through direct interaction. Remarkably, a water complex previously observed in x-ray crystal structure forms near the bulge in the central I helix that contains a conserved Thr. The properties of the I helix are computed in the context of the presence or absence of ligand.

Amino Acid Sequence↗
PubMed2003

Structure of the coiled-coil dimerization motif of Sir4 and its interaction with Sir3.

The yeast silent information regulators Sir2, Sir3, and Sir4 physically interact with one another to establish a transcriptionally silent state by forming repressive chromatin structures. The Sir4 protein contains binding sites for both Sir2 and Sir3, and these protein-protein interactions are required for gene silencing. Here, we report the X-ray structure of the coiled-coil dimerization motif within the C-terminus of Sir4 and show that it forms a stable 1:1 complex with a dimeric fragment of Sir3 (residues 464-978). We have identified a cluster of residues on the surface of the Sir4 coiled coil required for specific interactions with Sir3. The histone deacetylase Sir2 can also bind to this complex, forming a ternary complex with the truncated Sir3 and Sir4 proteins. The dual interactions of Sir4 with Sir3 and Sir2 suggest a physical basis for recruiting Sir3 to chromatin by virtue of its interactions with Sir4 and with deacetylated histones in chromatin.

Amino Acid Sequence↗
PubMed2004

Kinetic and thermodynamic preferences in aryl vs benzylic C-H bond activation with cationic Pt(II) complexes.

Anhydrous cationic Pt(II) complexes [(NN)Pt(CH3)(CF3CD2OD)]+ (1, NN = ArN=C(Me)-C(Me)=NAr), which are obtained by reaction of (NN)Pt(CH3)2 with B(C6F5)3 in CF3CD2OD, activate C-H bonds of benzene and methylbenzenes, with enhanced reactivity compared to the previously prepared equilibrium mixtures with the (thermodynamically favored) aquo complexes. For methylbenzenes (toluene, p-xylene, mesitylene), activation at the aromatic and benzylic positions are kinetically competitive, but the product of the latter is strongly favored thermodynamically. This unusual trend is attributed to formation of eta3-benzyl structures, which can be observed spectroscopically for 1,4-diethylbenzene activation.

Benzyl Compounds↗
PubMed2006

Structural biology and bioinformatics in drug design: opportunities and challenges for target identification and lead discovery.

Impressive progress in genome sequencing, protein expression and high-throughput crystallography and NMR has radically transformed the opportunities to use protein three-dimensional structures to accelerate drug discovery, but the quantity and complexity of the data have ensured a central place for informatics. Structural biology and bioinformatics have assisted in lead optimization and target identification where they have well established roles; they can now contribute to lead discovery, exploiting high-throughput methods of structure determination that provide powerful approaches to screening of fragment binding.

Computational Biology↗
PubMed2005

Subcellular localization of ALMS1 supports involvement of centrosome and basal body dysfunction in the pathogenesis of obesity, insulin resistance, and type 2 diabetes.

Alström syndrome is a rare autosomal recessive disorder caused by mutations in a novel gene of unknown function, ALMS1. Central features of Alström syndrome include obesity, insulin resistance, and type 2 diabetes, and therefore investigating ALMS1 function stands to offer new insights into the pathogenesis of these common conditions. To begin this process, we have analyzed the subcellular localization and tissue distribution of ALMS1 by immunofluorescence. We show that ALMS1 is widely expressed and localizes to centrosomes and to the base of cilia. Fibroblasts with disrupted ALMS1 assemble primary cilia and microtubule cytoskeletons that appear normal, suggesting that the Alström syndrome phenotype results from impaired function rather than abnormal development. Coupled with recent data on the complex phenotype of Bardet-Biedl syndrome, our findings imply an unexpected central role for basal body and centrosome dysfunction in the pathogenesis of obesity, insulin resistance, and type 2 diabetes. Unraveling the molecular mechanisms underlying the Alström syndrome phenotype will be important in the search for new therapeutic targets for these conditions.

Amino Acid Sequence↗
PubMed2003

Voltage-dependent anion channel localises to the plasma membrane and peripheral but not perinuclear mitochondria.

Activity of the antioestrogen-activated maxi-Cl(-) channel has been recorded in different cell types, including fibroblasts, vascular smooth muscle, endothelial and neuroblastoma cells. Its electrophysiological properties resemble those of the voltage-dependent anion channel (VDAC) of the outer mitochondrial membrane, a channel of particular relevance to the physiology and pathophysiology of mitochondria. The hypothesis that VDAC could be the molecular correlate of the plasma membrane maxi-Cl(-) channel has been debated over the last few years, with the lack of clear evidence for the presence of VDAC in the plasma membrane constituting the main argument of the detractors. In the present study, we investigated the cellular localisation of VDAC in NIH3T3 fibroblasts. The presence of a plasma membrane VDAC was demonstrated by immunoblotting of membrane fractions with monoclonal antibodies against the VDAC and by RT-PCR using primers that hybridise to a VDAC sequence coding for a N-terminal leader peptide required for its plasma membrane sorting. In addition, confocal microscopy studies showed the colocalisation of VDAC with caveolin-1. As expected, VDAC also localised to mitochondria. Colocalisation studies with TOM-20, a protein also present in the outer mitochondrial membrane, showed that VDAC proteins localised only to peripheral and not to perinuclear mitochondria.

3T3 Cells↗
PubMed2005

A lysine residue in the fingers subdomain of T7 DNA polymerase modulates the miscoding potential of 8-oxo-7,8-dihydroguanosine.

8-oxo-7,8-dihydroguanosine (8oG) is a highly mutagenic DNA lesion that stably pairs with adenosine, forming 8oG(syn).dA(anti) Hoogsteen base pairs. DNA polymerases show different propensities to insert dCMP or dAMP opposite 8oG, but the molecular mechanisms that determine faithful or mutagenic bypass are poorly understood. Here, we report kinetic and structural data providing evidence that, in T7 DNA polymerase, residue Lys536 is responsible for attenuating the miscoding potential of 8oG. The Lys536Ala polymerase shows a significant increase in mutagenic 8oG bypass versus wild-type polymerase, and a crystal structure of the Lys536Ala mutant reveals a closed complex with an 8oG(syn).dATP mismatch in the polymerase active site, in contrast to the unproductive, open complex previously obtained by using wild-type polymerase. We propose that Lys536 acts as a steric and/or electrostatic filter that attenuates the miscoding potential of 8oG by normally interfering with the binding of 8oG in a syn conformation that pairs with dATP.

Bacteriophage T7↗
PubMed2006

"Dormant" secondary metal-alkyl complexes are not omnipresent.

This theoretical study was inspired by the perpetual debate over the so-called "dormancy" of the active sites in propylene polymerization, i.e., a drop in their activity after a regioerror (2,1-insertion), which was reported to occur in many (although not all) catalytic systems. To explore the range of possible situations, we have selected two homogeneous systems of fundamentally different structure: an octahedral system of C2 symmetry with a tetradentate -O-N-N-O- ligand and a bridged indenyl catalyst. This choice was not accidental; it is in these two systems where the experimentalists cannot reach a consensus about dormancy. Our density-functional theory calculations explain why in certain catalytic systems both primary and secondary alkyl complexes can be equally reactive toward propylene polymerization, despite the intuitive concept of dormancy. To understand such a behavior, it was imperative to build an extensive model, including the counteranion and solvent effects. The discussion is also supplemented by our latest calculations on the classical second-generation Ziegler-Natta system.

Journal Article↗
PubMed2003

Cooperation of transmembrane segments during the integration of a double-spanning protein into the ER membrane.

While membrane insertion of single-spanning membrane proteins into the endoplasmic reticulum (ER) is relatively well understood, it is unclear how multi-spanning proteins integrate. We have investigated the cotranslational ER integration of a double-spanning protein that is derived from leader peptidase. Both transmembrane (TM) segments are inserted into the membrane by the Sec61 channel. While the first, long and hydrophobic TM segment (TM1) inserts into the lipid bilayer on its own, the second, shorter TM anchor (TM2) collaborates with TM1 during its integration. TM1 diffuses away from the Sec61 complex in the absence of TM2, but is close to Sec61 when TM2 arrives inside the channel. These data suggest that the exit of a weak TM segment from the Sec61 channel into the lipid phase can be facilitated by its interaction with a previously integrated strong and stabilizing TM anchor.

Amino Acid Sequence↗
PubMed2001

Biogenesis of the dicarboxylate carrier (DIC): translocation across the mitochondrial outer membrane and subsequent release from the TOM channel are membrane potential-independent.

The mitochondrial inner membrane of Saccharomyces cerevisiae contains a group of homologous carrier proteins that mediate the exchange of several metabolites. The members of this protein family are synthesized in the cytosol and reach their final topology after translocation across the mitochondrial outer membrane. Using the ADP/ATP carrier (AAC) as a model protein, previous studies have established four distinct steps of the import pathway (stages I-IV). In the absence of the mitochondrial membrane potential (deltapsi), the AAC accumulates at the inner surface of the outer membrane (stage IIIa) and remains bound to the outer membrane import channel. Only in the presence of the membrane potential, can a complex of small Tim proteins mediate transfer of the AAC to the inner membrane. In this study, we characterized the import pathway of the dicarboxylate carrier (DIC). Different from the AAC, the DIC showed complete deltapsi-independent translocation across the outer membrane, release from the import pore, and mainly accumulated in a soluble state in the intermembrane space, thus defining a new translocation intermediate (stage III*). The DIC should be a suitable model protein for the characterization of deltapsi-independent functions of the intermembrane space Tim proteins.

Carrier Proteins↗
PubMed2002

Performance reassessment of a real-time seizure-detection algorithm on long ECoG series.

PURPOSE: Automated seizure detection and blockage requires highly sensitive and specific algorithms. This study reassessed the performance of an algorithm by using a more extensive database than that of a previous study and its suitability for safety/efficacy closed-loop studies to block seizures in humans. METHODS: Up to eight electrocorticography (EcoG) channels from 15 subjects were analyzed off-line. Visual and computerized analyses of the data were performed by different (blinded) investigators. Independent visual analysis also was performed for clinical seizures and for detections identified only by the algorithm. The following were computed: FP rate, number of FNs, latency to automated detection, warning rate for clinical onset and warning times, seizure duration/intensity, and interrater agreement. Adaptations to improve performance were performed when indicated. RESULTS: Fourteen subjects met inclusion criteria. Generic algorithm "relative sensitivity" for clinical seizures was 100%; two undetected subclinical seizures and two unclassified seizures were captured after adaptation. FPs/day were zero in seven and fewer than one in an additional three subjects. Adaptations for four subjects with greater than 1 FP/day (7.7-66.6/day) reduced the rate to 0 in one subject and to fewer than five FP/day (1.7-4.2/day) in the remainder. Generic latency to automated detection was <5 s in eight of 13 subjects, and in 12 of 13 after adaptation. Detections provided warning of clinical onset in three of four subjects in whom it always followed electrographic onset, and in four of four after adaptation. Interrater agreement was low for FPs and EDs. CONCLUSIONS: The generic algorithm demonstrated high sensitivity, specificity, and speed, characteristics further enhanced by adaptation. This algorithm is well suited for seizure detection/warning and use in safety/efficacy closed-loop therapy studies.

Adolescent↗
PubMed2004

The AMP-activated protein kinase AAK-2 links energy levels and insulin-like signals to lifespan in C. elegans.

Although limiting energy availability extends lifespan in many organisms, it is not understood how lifespan is coupled to energy levels. We find that the AMP:ATP ratio, a measure of energy levels, increases with age in Caenorhabditis elegans and can be used to predict life expectancy. The C. elegans AMP-activated protein kinase alpha subunit AAK-2 is activated by AMP and functions to extend lifespan. In addition, either an environmental stressor that increases the AMP:ATP ratio or mutations that lower insulin-like signaling extend lifespan in an aak-2-dependent manner. Thus, AAK-2 is a sensor that couples lifespan to information about energy levels and insulin-like signals.

AMP-Activated Protein Kinases↗