GWAS for executive function and processing speed suggests involvement of the CADM2 gene

To identify common variants contributing to normal variation in two specific domains of cognitive functioning, we conducted a genome-wide association study (GWAS) of executive functioning and information processing speed in non-demented older adults from the CHARGE (Cohorts for Heart and Aging Research in Genomic Epidemiology) consortium. Neuropsychological testing was available for 5429-32,070 subjects of European ancestry aged 45 years or older, free of dementia and clinical stroke at the time of cognitive testing from 20 cohorts in the discovery phase. We analyzed performance on the Trail Making Test parts A and B, the Letter Digit Substitution Test (LDST), the Digit Symbol Substitution Task (DSST), semantic and phonemic fluency tests, and the Stroop Color and Word Test. Replication was sought in 1311-21860 subjects from 20 independent cohorts. A significant association was observed in the discovery cohorts for the single-nucleotide polymorphism (SNP) rs17518584 (discovery P-value=3.12 × 10(-8)) and in the joint discovery and replication meta-analysis (P-value=3.28 × 10(-9) after adjustment for age, gender and education) in an intron of the gene cell adhesion molecule 2 (CADM2) for performance on the LDST/DSST. Rs17518584 is located about 170 kb upstream of the transcription start site of the major transcript for the CADM2 gene, but is within an intron of a variant transcript that includes an alternative first exon. The variant is associated with expression of CADM2 in the cingulate cortex (P-value=4 × 10(-4)). The protein encoded by CADM2 is involved in glutamate signaling (P-value=7.22 × 10(-15)), gamma-aminobutyric acid (GABA) transport (P-value=1.36 × 10(-11)) and neuron cell-cell adhesion (P-value=1.48 × 10(-13)). Our findings suggest that genetic variation in the CADM2 gene is associated with individual differences in information processing speed.

Association analysis of SNPs in the IL4R locus with type I diabetes

The Type I Diabetes Genetics Consortium (T1DGC) has collected thousands of multiplex and simplex families with type I diabetes (T1D) with the goal of identifying genes involved in T1D susceptibility. These families have all been genotyped for the HLA class I and class II loci and a subset of samples has been typed for an major histocompatibility complex (MHC) single-nucleotide polymorphism (SNP) panel. In addition, the T1DGC has genotyped SNPs in candidate genes to evaluate earlier reported T1D associations. Individual SNPs and SNP haplotypes in IL4R, which encodes the alpha-chain of the IL4 and IL13 receptors, have been associated with T1D in some reports, but not in others. In this study, 38 SNPs in IL4R were genotyped using the Sequenom iPLEX Gold MassARRAY technology in 2042 multiplex families from nine cohorts. Association analyses (transmission-disequilibrium test and parental-disequilibrium test) were performed on individual SNPs and on three-SNP haplotypes. Analyses were also stratified on the high-risk HLA DR3/DR4-DQB1*0302 genotype. A modest T1D association in HBDI families (n=282) was confirmed in this larger collection of HBDI families (n=424). The variant alleles at the non-synonymous SNPs (rs1805011 (E400A), rs1805012 (C431R), and rs1801275 (Q576R)), which are in strong linkage disequilibrium, were negatively associated with T1D risk. These SNPs were more associated with T1D among non-DR3/DR4-DQB1*0302 genotypes than DR3/DR4-DQB1*0302 genotypes. This association was stronger, both in terms of odds ratio and P-values, than the initial report of the smaller collection of HBDI families. However, the IL4R SNPs and the three-SNP haplotype containing the variant alleles were not associated with T1D in the total data. Thus, in the overall families, these results do not show evidence for an association of SNPs in IL4R with T1D.

Overview of the Rapid Response data

The Type I Diabetes Genetics Consortium (T1DGC) Rapid Response Workshop was established to evaluate published candidate gene associations in a large collection of affected sib-pair (ASP) families. We report on our quality control (QC) and preliminary family-based association analyses. A random sample of blind duplicates was analyzed for QC. Quality checks, including examination of plate-panel yield, marker yield, Hardy-Weinberg equilibrium, mismatch error rate, Mendelian error rate, and allele distribution across plates, were performed. Genotypes from 2324 families within nine cohorts were obtained from a panel of 21 candidate genes, including 384 single-nucleotide polymorphisms on two genotyping platforms performed at the Broad Institute Center for Genotyping and Analysis (Cambridge, MA, USA). The T1DGC Rapid Response project, following rigorous QC procedures, resulted in a 2297 family, 9688 genotyped individual database on a single-candidate gene panel. The available data include 9005 individuals with genotype data from both platforms and 683 individuals genotyped (276 in Illumina; 407 in Sequenom) on only one platform.

Overview of the MHC fine mapping data

AIM

The aim of this study was to perform quality control (QC) and initial family-based association analyses on the major histocompatibility complex (MHC) single nucleotide polymorphism (SNP) and microsatellite marker data for the MHC Fine Mapping Workshop through the Type 1 Diabetes Genetics Consortium (T1DGC).

METHODS

A random sample of blind duplicates was sent for analysis of QC. DNA samples collected from participants were shipped to the genotyping laboratory from several T1DGC DNA Repository sites. Quality checks including examination of plate-panel yield, marker yield, Hardy-Weinberg equilibrium, mismatch error rate, Mendelian error rate and allele distribution across plates were performed.

RESULTS

Genotypes from 2325 families within nine cohorts were obtained and subjected to QC procedures. The MHC project consisted of three marker panels - two 1536 SNP sets (Illumina Golden Gate platform performed at the Wellcome Trust Sanger Institute, Cambridge, UK) and one 66 microsatellite marker panel (performed at deCODE). In the raw SNP data, the overall concordance rate was 99.1% (+/-0.02).

CONCLUSIONS

The T1DGC MHC Fine Mapping project resulted in a 2300 family, 9992 genotyped individuals database comprising of two 1536 SNP panels and a 66 microsatellite panel to densely cover the 4 Mb MHC core region for use in statistical genetic analyses.

Hormone replacement therapy is associated with increased C-reactive protein in women with Type 2 diabetes in the Diabetes Heart Study

AIMS

Increased levels of inflammatory biomarkers, especially C-reactive protein (CRP), are associated with increased risk for cardiovascular disease (CVD) events, such as myocardial infarction, stroke, peripheral vascular disease, and sudden cardiac death. Medical interventions that increase CRP levels, such as hormone replacement therapy (HRT) in post-menopausal women, are under increasing scrutiny. The effect of HRT on CRP levels in women with Type 2 diabetes (T2DM) is not well documented, and conflicting conclusions have been reported. The aim of this study was to determine the influence of HRT on women with diabetes in a large cross-sectional study.

METHODS

Three hundred and twenty-seven post-menopausal women with T2DM from the Diabetes Heart Study participated. Current use of HRT was determined and serum CRP levels were measured using a high-sensitivity ELISA kit. Generalized estimating equation methods were used to assess the relationship of multiple clinical and lifestyle (e.g. smoking) measures on CRP levels including differences between women taking HRT (HRT+) and not taking HRT (HRT-).

RESULTS

Overall serum CRP levels were strongly associated with body mass index (P < 0.0001) and age (P < 0.0001). Of the women, 243 were not using HRT and 84 were using HRT. HRT+ and HRT- women did not differ significantly in measures of clinical traits, with the exception of higher mean low-density lipoprotein cholesterol in HRT- women (P = 0.004). In all models tested, HRT+ women had significantly higher circulating CRP levels, with P-values ranging from 0.0045 to 0.010.

CONCLUSIONS

In this study of serum CRP concentration as a function of HRT in women with Type 2 diabetes, there was consistent evidence for increased circulating CRP levels in women receiving oestrogen-containing HRT. Whether HRT-induced increases in CRP can account for the adverse cardiovascular effects of HRT remains to be established; however, based on these data, there is little reason to believe that diabetic women would be spared from such an effect.

Development of real-time RT-PCR for the detection of avian influenza virus

A real-time reverse transcriptase/polymerase chain reaction (RRT-PCR) assay was developed using hydrolysis probes for the detection of avian influenza virus (AIV) and the H5 and H7 subtypes. The AIV specific primers and probes were directed to regions of the AIV matrix gene that are conserved among most type A influenza viruses. The H5 and H7 primers and probes are directed to H5 and H7 hemagglutinin gene regions that are conserved among North American avian influenza viruses. The sensitivity and specificity of this RRT-PCR assay was compared to virus isolation (VI) in chicken embryos with 1550 clinical swab samples from 109 live-bird markets (LBMs) in New York and New Jersey. RRT-PCR detected influenza in samples from 61 of 65 (93.8%) of the LBMs that were the sources of VI positive samples. Of the 58 markets that were positive for H7 influenza by hemagglutination inhibition assay, RRT-PCR detected H7 influenza in 56 markets (96.5%). Too few H5 positive samples were obtained to validate the H5 RRT-PCR assay in this study. Although RRT-PCR was less sensitive than VI on an individual sample basis, this study demonstrated that the AIV and H7 RRT-PCR assays are good tools for the rapid screening of flocks and LBMs.

Adiponectin as a novel determinant of bone mineral density and visceral fat

Growing evidence suggests that positive associations between fat mass (FM) and bone mineral density (BMD) are mediated by not only biomechanical but also biochemical factors. Adiponectin is a novel adipocyte-derived hormone that regulates energy homeostasis and has anti-inflammatory and anti-atherogenic effects. Unlike other adipokines such as leptin, adiponectin levels decrease in obesity and type 2 diabetes. The purpose of our study was to investigate associations of serum adiponectin with BMD (DXA and QCT), FM (DXA and QCT), and serum leptin and soluble leptin receptor levels in 38 women and 42 men (age 39-81, BMI 17-55, 86% with type 2 diabetes). After adjusting for age, gender, race, smoking, and diabetes status, serum adiponectin was inversely associated with areal BMD (r = -0.20 to -0.3, all P < 0.01), volumetric BMD (r = -0.35 to -0.44, all P < 0.01), and visceral fat volume (r = -0.30, P < 0.01). These associations remained significant after adjusting for whole body fat mass. The associations of adiponectin with subcutaneous fat volume, whole body FM, and serum leptin level were not significant (all P > 0.1). These data suggest that adiponectin may play a role in the protective effects of visceral fat on BMD.

Atmospheric fate and transport of dioxins: local impacts

We conducted model simulations of the atmospheric fate and transport of PCDD/F to assess the fraction of emitted PCDD/F that would deposit within 100 km from the source. We considered eight major categories of PCDD/F emission sources and six different locations, to cover a wide range of source characteristics, PCDD/F congener profiles and particle size distributions, meteorological conditions and terrain configurations. These results suggest that for sources that have tall stacks and/or high plume rise (e.g., copper smelters, cement kilns, sinter plants), only a small fraction of PCDD/F emissions is deposited locally (typically, less than 10% within 100 km). Other source categories such as municipal solid waste incinerators, medical waste incinerators and diesel trucks lead to a greater fraction of PCDD/F being deposited locally; nevertheless, the majority of their PCDD/F emissions tends to be transported beyond 100 km. Although local impacts may need to be addressed for these latter source categories, it appears that the long-range potential impacts of PCDD/F need to be addressed for all source categories. Sensitivity studies were conducted to investigate the effect of various key model inputs on simulation results. These studies suggest that an advanced atmospheric dispersion model should be used for cases where PCDD/F emissions may present some local concerns because the results are very sensitive to the treatment of dispersion. Also, it is essential to obtain accurate characterizations of the particle size distribution of particulate PCDD/F because the dry deposition flux is very sensitive to the particle size distribution.

High-density lipoprotein cholesterol and vascular stiffness at baseline in the activity counseling trial

In a middle-aged patient population, age was associated with stiffer vessels and high-density lipoprotein cholesterol with more elastic vessels. High-density lipoprotein cholesterol may be an indirect indicator of aerobic capacity or of less atherosclerosis, suggesting mechanisms for preserving vascular integrity.

Phylogeography of the tailed frog (Ascaphus truei): implications for the biogeography of the Pacific Northwest

Tailed frogs are distributed in high-gradient streams within the disjunct mesic forests of the Pacific Northwest and represent the basal lineage of the anurans. We sequenced 1,530 nucleotides of the mitochondrial cytochrome b and NADH dehydrogenase subunit two genes from 23 populations and used parsimony, maximum-likelihood, and nested-clade analyses to estimate relationships among populations and infer evolutionary processes. We found two divergent haplotype clades corresponding with inland Rocky Mountain populations and coastal populations and separated by up to 0.133 substitutions per site. Within the coastal assemblage, haplotypes formed clades by mountain range with 0.010-0.024 substitutions per site divergence among populations. Inland haplotypes exhibited minimal genetic structure, with the exception of 0.021 substitutions per site distance between populations from the East Fork of the South Fork of the Salmon River and all other inland haplotypes. The magnitude of divergence between inland and coastal populations, as well as the paleobotanical record, suggest isolation of these lineages occurred during the late Miocene to early Pliocene, probably in response to the rise of the Cascade Mountains. Genetic structure within coastal and inland populations is consistent with isolation in refugia during the late Pliocene and early Pleistocene. Closely related inland haplotypes reflect range expansion following glaciation. The depth of divergence between inland and coastal populations supports the persistence of mesic forests within the inland Pacific Northwest throughout the Pleistocene and is congruent with patterns found in several other mesic forest species. Based on mitochondrial divergence and previous allozyme and morphological data, we recommend recognition of inland populations as a distinct species, Ascaphus montanus.

Sensitivity analysis of mercury human exposure

We present a comprehensive analysis of the sensitivity of mercury (Hg) human exposure to environmental variables using a multimedia model of the fate and transport of Hg in the environment. The results of the analysis show that the Hg dose is most sensitive to the lake pH, the burial rate of Hg adsorbed to sediments, and the chemical speciation of Hg emissions to the atmosphere. The lake pH has a strong non-linear effect on the methylation rate and bioaccumulation of Hg in fish. The burial of sediments is a major pathway for removing Hg from the lake cycling. The speciation of Hg emissions is important because Hg(II) is deposited much more rapidly than Hg(0). These results highlight the importance of key variables that should be investigated through well-designed field programs, so that we can minimize the overall uncertainties associated with the modeling of mercury fate and transport.

The Department of Defense laboratory-based global influenza surveillance system

Military global influenza surveillance began in 1976 as an Air Force program. In 1997, the Department of Defense (DoD) Global Emerging Infections Surveillance and Response System expanded the program to include all services. Also included were local residents in areas where DoD overseas research activities operated. This new, worldwide DoD surveillance infrastructure provides valuable information and can respond quickly to outbreaks. This was demonstrated during the current influenza season when a suspected outbreak was reported in Panama. In less than 3 weeks, specimens were collected, transported, and cultured, and isolates were subtyped and sent to the Centers for Disease Control and Prevention for further studies. This influenza surveillance initiative combines viral isolation, antigenic characterization, and molecular sequencing with clinical and public health management of information. The information obtained is shared with the Centers for Disease Control and Prevention and the World Health Organization and has contributed to important decisions in influenza vaccine composition.

Homogeneous Cell- and Bead-Based Assays for High Throughput Screening Using Fluorometric Microvolume Assay Technology

High throughput drug screening has become a critical component of the drug discovery process. The screening of libraries containing hundreds of thousands of compounds has resulted in a requirement for assays and instrumentation that are amenable to nonradioactive formats and that can be miniaturized. Homogeneous assays that minimize upstream automation of the individual assays are also preferable. Fluorometric microvolume assay technology (FMAT) is a fluorescence-based platform for the development of nonradioactive cell- and bead-based assays for HTS. This technology is plate format-independent, and while it was designed specifically for homogeneous ligand binding and immunological assays, it is amenable to any assay utilizing a fluorescent cell or bead. The instrument fits on a standard laboratory bench and consists of a laser scanner that generates a 1 mm(2) digitized image of a 100-µmm deep section of the bottom of a microwell plate. The instrument is directly compatible with a Zymark Twistertrade mark (Zymark Corp., Hopkinton, MA) for robotic loading of the scanner and unattended operation in HTS mode. Fluorescent cells or beads at the bottom of the well are detected as localized areas of concentrated fluorescence using data processing. Unbound flurophore comprising the background signal is ignored, allowing for the development of a wide variety of homogeneous assays. The use of FMAT for peptide ligand binding assays, immunofluorescence, apoptosis and cytotoxicity, and bead-based immunocapture assays is described here, along with a general overview of the instrument and software.

Identification of three genes expressed primarily during development in Physarum polycephalum

During the life cycle of Physarum polycephalum, uninucleate amoebae develop into multinucleate syncytial plasmodia. These two cell types differ greatly in cellular organisation, behaviour and gene expression. Classical genetic analysis has identified the mating-type gene, matA, as the key gene controlling the initiation of plasmodium development, but nothing is known about the molecular events controlled by matA. In order to identify genes involved in regulating plasmodium formation, we constructed a subtracted cDNA library from cells undergoing development. Three genes that have their highest levels of expression during plasmodium development were identified: redA, redB (regulated in development) and mynD (myosin). Both redA and redB are single-copy genes and are not members of gene families. Although redA has no significant sequence similarities to known genes, redB has sequence similarity to invertebrate sarcoplasmic calcium-binding proteins. The mynD gene is closely related to type II myosin heavy-chain genes from many organisms and is one of a family of type II myosin genes in P. polycephalum. Our results indicate that many more red genes remain to be identified, some of which may play key roles in controlling plasmodium formation.

Direct quantitation of HIV by flow cytometry using branched DNA signal amplification

Adaptation of the branched DNA signal amplification technology to flow cytometry has resulted in a quantitative nuclei-acid assay with significant advantages over the microwell-based format. In this assay, microbeads, rather than microwell plates, are derivatized with nucleic-acid capture probes and the derivatized beads are used to capture single nucleic-acid targets, which then capture fluorescent reporter probes via branched DNA. The assay detects DNA or RNA targets, has a current lower sensitivity limit of 500 human immunodeficiency virus (HIV) RNA molecules and responds linearly to target level from 500 to at least 50,000 molecules. Since microbeads can easily interrogate large volumes, viral lysis and genomic RNA capture can proceed in one step from comparatively large volumes, and sample preparation is greatly simplified compared to the microwell-format bDNA assay.

A novel, rapid in cell RNA amplification technique for the detection of low copy mRNA transcripts

Growing interest now focuses on improvements of in situ polymerase chain reaction (PCR) technology for the detection of DNA and RNA cellular sequences. In this study, reverse transcription PCR in situ hybridisation (RT PCR-ISH) was developed and used to determine gene expression of pyruvate dehydrogenase in a cell model system, using human peripheral blood lymphocytes (PBLs). The success of in cell RNA amplification depends on the type of cell/tissue fixation, cell permeabilisation, and the efficiency of reverse transcription and cDNA amplification. This paper presents new approaches to overcome the critical aspects of fixation, permeabilisation, and reverse transcription when performing in cell RNA amplification. A novel fixative, "Permeafix", possessing fixative and permeabilisation properties, was used for cell fixation procedures. "Permeafix" obviated the need for pre-amplification proteolysis, facilitating entry of PCR reagents to target sequences within the cell. In addition, a simple on step RNA in cell amplification protocol using recombinant Thermus thermophilus (rTth) DNA polymerase, which reverse transcribes mRNA efficiently to cDNA and then catalyses cDNA amplification, was used. The value of a semi-junctional primer system for in cell gene expression studies, without the need to perform DNase digestion, is demonstrated.

Active site mutants of Escherichia coli dethiobiotin synthetase: effects of mutations on enzyme catalytic and structural properties

Five active site residues, Thr11, Glu12, Lys15, Lys37, and Ser41, implicated by the protein crystal structure studies of Escherichia coli DTBS, were mutated to determine their function in catalysis and substrate binding. Nine mutant enzymes, T11V, E12A, E12D, K15Q, K37L, K37Q, K37R, S41A, and S41C, were overproduced in an E. coli strain lacking a functional endogenous DTBS gene and purified to homogeneity. Replacement of Thr11 with valine resulted in a 24,000-fold increase in the Km(ATP) with little or no change in the Kd(ATP), KM(DAPA) and DTBS k(cat), suggesting an essential role for this residue in the steady-state affinity for ATP. The two Glu12 mutants showed essentially wild-type DTBS activity (slightly elevated k(cat)'s). Unlike wild-type DTBS, E12A had the same apparent KM(DAPA) at subsaturating and saturating ATP concentrations, indicating a possible role for Glu12 in the binding synergy between DAPA and ATP. The mutations in Lys15 and Lys37 resulted in loss of catalytic activity (0.01% and <0.9% of wild-type DTBS k(cat) for K15Q and the Lys37 mutant enzymes, respectively) and higher KM's for both DAPA (40-fold and >100-fold higher than wild-type for the K15Q and Lys37 mutant enzymes, respectively) and ATP (1800-fold and >10-fold higher than wild-type for K15Q and the K37 mutant enzymes, respectively). These results strongly suggest that Lys15 and Lys37 are crucial to both catalysis and substrate binding. S41A and S41C had essentially the same k(cat) as wild-type and had moderate increases in the DAPA and ATP KM and Kd (ATP) values. Replacement of Ser41 with cysteine resulted in larger effects than replacement with alanine. These data suggest that the H-bond between N7 of DAPA and the Ser41 side chain is not very important for catalysis. The catalytic behavior of these mutant enzymes was also studied by pulse-chase experiments which produced results consistent with the steady-state kinetic analyses. X-ray crystallographic studies of four mutant enzymes, S41A, S41C, K37Q, and K37L, showed that the crystals were essentially isomorphous to that of the wild-type DTBS. The models of these mutant enzymes were well refined (1.9 -2.6 A) and showed good similarity to the wild-type enzyme (rmsd of C alpha atoms: 0.16-0.24 A). The crystal structure of S41C complexed with DAPA, Mn2+/Mg2+, and AMPPCP revealed a localized conformational change (rotations of side chains of Cys41 and Thr11) which can account for the changes in the kinetic parameters observed for S41C. The crystal structures of the Lys37 mutant enzymes showed that the positive charge of the side chain of Lys37 is indispensable. Mutations of Lys37 to either glutamine or leucine resulted in a shift of the metal ion (up to 0.5 A) together with side chains of other active site residues which could disrupt the subtle balance between the positive and negative charges in the active site. The conformational change of the phosphate binding loop (Gly8-X-X-X-X-X-Gly14-Lys15-Thr16) upon nucleotide binding observed previously [Huang, W., Jia, J., Gibson, K. J., Taylor, W. S., Rendina, A. R., Schneider, G., & Lindqvist, Y. (1995) Biochemistry 34, 10985] appears to be important to attain the proper active site scaffold.

Cellular and molecular analysis of plasmodium development in Physarum

The development of an amoeba into a plasmodium involves extensive changes in cellular organisation and gene expression. The genetic basis of a number of recessive mutations that block plasmodium development has been elucidated. The stage at which development becomes abnormal has been determined for all the mutants, as has the terminal phenotype. In order to investigate the changes in gene expression that accompany plasmodium development, a cDNA library has been made using RNA isolated from cell populations in which development was occurring.

Rhizobium meliloti mutants unable to synthesize anthranilate display a novel symbiotic phenotype

Analyses of Rhizobium meliloti trp auxotrophs suggest that anthranilate biosynthesis by the R. meliloti trpE(G) gene product is necessary during nodule development for establishment of an effective symbiosis. trpE(G) mutants, as well as mutants blocked earlier along this pathway in aromatic amino acid biosynthesis, form nodules on alfalfa that have novel defects. In contrast, R. meliloti trp mutants blocked later in the tryptophan-biosynthetic pathway form normal, pink, nitrogen-fixing nodules. trpE(G) mutants form two types of elongated, defective nodules containing unusually extended invasion zones on alfalfa. One type contains bacteroids in its base and is capable of nitrogen fixation, while the other lacks bacteroids and cannot fix nitrogen. The trpE(G) gene is expressed in normal nodules. Models are discussed to account for these observations, including one in which anthranilate is postulated to act as an in planta siderophore.

A directional, high-frequency chromosomal mobilization system for genetic mapping of Rhizobium meliloti

A system for mapping of the Rhizobium meliloti chromosome that utilizes transposon Tn5-Mob, which carries the mobilization site of IncP plasmid RP4 (R. Simon, Mol. Gen. Genet. 196:413-420, 1984), was developed. Insertions of Tn5-Mob that were located at particular sites on the R. meliloti chromosome were isolated and served as origins of high-frequency chromosomal transfer when IncP tra functions were provided in trans. This approach is, in principle, applicable to any gram-negative bacterium in which Tn5 can transpose and into which IncP plasmids can conjugate.