bluuebunny/crossref_metadata_2025 huggingface dataset:
atxAControlsBacillus anthracisCapsule Synthesis viaacpAand a Newly Discovered Regulator,acpB
Authors: Drysdale Melissa , Bourgogne Agathe , Hilsenbeck Susan G. , Koehler Theresa M.
Published: December 2003

Two regulatory genes,acpAandatxA, have been reported to control expression of theBacillus anthraciscapsule biosynthesis operoncapBCAD. TheatxAgene is located on the virulence plasmid pXO1, while pXO2 carriesacpAand thecapgenes.acpAhas been viewed as the major regulator of thecapoperon because it is essential for capsule gene expression in a pXO1−pXO2+strain.atxAis essential for toxin gene transcription but has also been implicated in control of thecapgenes. The molecular functions of the regulatory proteins are unknown. We examinedcapgene expression in a genetically complete pXO1+pXO2+strain. Our results indicate that another pXO2 gene,acpB(previously called pXO2-53; accession no.NC002146.1:49418-50866), has a role incapexpression. The predicted amino acid sequence of AcpB is 62% similar to that of AcpA and 50% similar to that of AtxA. Assessment ofcapgene transcription revealed thatcapexpression was not affected in a pXO1+pXO2+acpB-null mutant and was slightly reduced in an isogenicacpAmutant. However,capgene expression was abolished in anacpA acpBdouble mutant. Microscopic examination of capsule synthesis by the mutants corroborated these findings.acpAandacpBexpression is controlled byatxA; capsule synthesis and transcription ofacpAandacpBwere markedly reduced in anatxAmutant. The data suggest that, in a strain containing both virulence plasmids,atxAis the major regulator of capsule synthesis and controlscapBCADexpression indirectly, via positive regulation ofacpAandacpB.
The Alternative Sigma Factor σBofBacillus cereus: Response to Stress and Role in Heat Adaptation
Authors: van Schaik Willem , Tempelaars Marcel H. , Wouters Jeroen A. , de Vos Willem M. , Abee Tjakko
Published: December 2003

A gene cluster encoding the alternative sigma factor σB, three predicted regulators of σB(RsbV, RsbW, and RsbY), and one protein whose function is not known (Orf4) was identified in the genome sequence of the food pathogenBacillus cereusATCC 14579. Western blotting with polyclonal antibodies raised against σBrevealed that there was 20.1-fold activation of σBafter a heat shock from 30 to 42°C. Osmotic upshock and ethanol exposure also upregulated σB, albeit less than a heat shock. When the intracellular ATP concentration was decreased by exposure to carbonyl cyanidem-chlorophenylhydrazone (CCCP), only limited increases in σBlevels were observed, revealing that stress due to ATP depletion is not an important factor in σBactivation inB. cereus. Analysis of transcription of thesigBoperon by Northern blotting and primer extension revealed the presence of a σB-dependent promoter upstream of the first open reading frame (rsbV) of thesigBoperon, indicating that transcription ofsigBis autoregulated. A second σB-dependent promoter was identified upstream of the last open reading frame (orf4) of thesigBoperon. Production of virulence factors and the nonhemolytic enterotoxin Nhe in asigBnull mutant was the same as in the parent strain. However, σBwas found to play a role in the protective heat shock response ofB. cereus. ThesigBnull mutant was less protected against the lethal temperature of 50°C by a preadaptation to 42°C than the parent strain was, resulting in a more-than-100-fold-reduced survival of the mutant after 40 min at 50°C.
Dihydropteridine Reductase as an Alternative to Dihydrofolate Reductase for Synthesis of Tetrahydrofolate in
Thermus thermophilus
Authors: Wilquet Valérie , Van de Casteele Mark , Gigot Daniel , Legrain Christianne , Glansdorff Nicolas
Published: December 2003

A strategy devised to isolate a gene coding for a dihydrofolate reductase from
Thermus thermophilus
DNA delivered only clones harboring instead a gene (the
T. thermophilus
dehydrogenase [DH

Tt

] gene) coding for a dihydropteridine reductase which displays considerable dihydrofolate reductase activity (about 20% of the activity detected with 6,7-dimethyl-7,8-dihydropterine in the quinonoid form as a substrate). DH

Tt

appears to account for the synthesis of tetrahydrofolate in this bacterium, since a classical dihydrofolate reductase gene could not be found in the recently determined genome nucleotide sequence (A. Henne, personal communication). The derived amino acid sequence displays most of the highly conserved cofactor and active-site residues present in enzymes of the short-chain dehydrogenase/reductase family. The enzyme has no pteridine-independent oxidoreductase activity, in contrast to
Escherichia coli
dihydropteridine reductase, and thus appears more similar to mammalian dihydropteridine reductases, which do not contain a flavin prosthetic group. We suggest that bifunctional dihydropteridine reductases may be responsible for the synthesis of tetrahydrofolate in other bacteria, as well as archaea, that have been reported to lack a classical dihydrofolate reductase but for which possible substitutes have not yet been identified.
Helicobacter acinonychis
: Genetic and Rodent Infection Studies of a
Helicobacter pylori
-Like Gastric Pathogen of Cheetahs and Other Big Cats
Authors: Dailidiene Daiva , Dailide Giedrius , Ogura Keiji , Zhang Maojun , Mukhopadhyay Asish K. , Eaton Kathryn A. , Cattoli Giovanni , Kusters Johannes G. , Berg Douglas E.
Published: December 2003

Insights into bacterium-host interactions and genome evolution can emerge from comparisons among related species. Here we studied
Helicobacter acinonychis
(formerly
H. acinonyx
), a species closely related to the human gastric pathogen
Helicobacter pylori
. Two groups of strains were identified by randomly amplified polymorphic DNA fingerprinting and gene sequencing: one group from six cheetahs in a U.S. zoo and two lions in a European circus, and the other group from a tiger and a lion-tiger hybrid in the same circus. PCR and DNA sequencing showed that each strain lacked the
cag
pathogenicity island and contained a degenerate vacuolating cytotoxin (
vacA
) gene. Analyses of nine other genes (
glmM
,
recA
,
hp519
,
glr
,
cysS
,
ppa
,
flaB
,
flaA
, and
atpA
) revealed a ∼2% base substitution difference, on average, between the two
H. acinonychis
groups and a ∼8% difference between these genes and their homologs in
H. pylori
reference strains such as 26695.
H. acinonychis
derivatives that could chronically infect mice were selected and were found to be capable of persistent mixed infection with certain
H. pylori
strains. Several variants, due variously to recombination or new mutation, were found after 2 months of mixed infection.
H. acinonychis
' modest genetic distance from
H. pylori
, its ability to infect mice, and its ability to coexist and recombine with certain
H. pylori
strains in vivo should be useful in studies of
Helicobacter
infection and virulence mechanisms and studies of genome evolution.
Phage Shock Protein PspA of
Escherichia coli
Relieves Saturation of Protein Export via the Tat Pathway
Authors: DeLisa Matthew P. , Lee Philip , Palmer Tracy , Georgiou George
Published: December 2003

Overexpression of either heterologous or homologous proteins that are routed to the periplasm via the twin-arginine translocation (Tat) pathway results in a block of export and concomitant accumulation of the respective protein precursor in the cytoplasm. Screening of a plasmid-encoded genomic library for mutants that confer enhanced export of a TorA signal sequence (ssTorA)-GFP-SsrA fusion protein, and thus result in higher cell fluorescence, yielded the
pspA
gene encoding phage shock protein A. Coexpression of
pspA
relieved the secretion block observed with ssTorA-GFP-SsrA or upon overexpression of the native Tat proteins SufI and CueO. A similar effect was observed with the
Synechocystis
sp. strain PCC6803 PspA homologue, VIPP1, indicating that the role of PspA in Tat export may be phylogenetically conserved. Mutations in Tat components that completely abolish export result in a marked induction of PspA protein synthesis, consistent with its proposed role in enhancing protein translocation via Tat.
Identification of NAD+Synthetase fromStreptococcus sobrinusas a B-Cell-Stimulatory Protein
Authors: Veiga-Malta Isabel , Duarte Margarida , Dinis Márcia , Madureira Pedro , Ferreira Paula , Videira Arnaldo
Published: December 2003

Streptococcus sobrinus, one agent of dental caries, secretes a protein that induces lymphocyte polyclonal activation of the host as a mechanism of immune evasion. We have isolated from culture supernatants of this bacterium a protein with murine B-cell-stimulatory properties and subsequently cloned the relevant gene. It contains an open reading frame of 825 bp encoding a polypeptide with 275 amino acid residues and a molecular mass of 30 kDa. The protein displays high sequence homology with NAD+synthetases from several organisms, including a conserved fingerprint sequence (SGGXD) characteristic of ATP pyrophosphatases. The polypeptide was expressed inEscherichia colias a hexahistidine-tagged protein and purified in an enzymatically active form. The recombinant NAD+synthetase stimulates murine B cells after in vitro treatment of spleen cell cultures, as demonstrated by its ability to induce up-regulation of the expression of CD69, an early marker of lymphocyte activation. Stimulation with the recombinant NAD+synthetase was also observed with other B-cell markers, such as CD19+, B220+, and CD21+. Cell proliferation follows the activation induced by the recombinant NAD+synthetase.
Occurrence and Characterization of Mercury Resistance in the Hyperthermophilic Archaeon
Sulfolobus solfataricus
by Use of Gene Disruption
Authors: Schelert James , Dixit Vidula , Hoang Viet , Simbahan Jessica , Drozda Melissa , Blum Paul
Published: December 2003

Mercury resistance mediated by mercuric reductase (MerA) is widespread among bacteria and operates under the control of MerR. MerR represents a unique class of transcription factors that exert both positive and negative regulation on gene expression. Archaea and bacteria are prokaryotes, yet little is known about the biological role of mercury in archaea or whether a resistance mechanism occurs in these organisms. The archaeon
Sulfolobus solfataricus
was sensitive to mercuric chloride, and low-level adaptive resistance could be induced by metal preconditioning. Protein phylogenetic analysis of open reading frames SSO2689 and SSO2688 clarified their identity as orthologs of MerA and MerR. Northern analysis established that
merA
transcription responded to mercury challenge, since mRNA levels were transiently induced and, when normalized to 7S RNA, approximated values for other highly expressed transcripts. Primer extension analysis of
merA
mRNA predicted a noncanonical TATA box with nonstandard transcription start site spacing. The functional roles of
merA
and
merR
were clarified further by gene disruption. The
merA
mutant exhibited mercury sensitivity relative to wild type and was defective in elemental mercury volatilization, while the
merR
mutant was mercury resistant. Northern analysis of the
merR
mutant revealed
merA
transcription was constitutive and that transcript abundance was at maximum levels. These findings constitute the first report of an archaeal heavy metal resistance system; however, unlike bacteria the level of resistance is much lower. The archaeal system employs a divergent MerR protein that acts only as a negative transcriptional regulator of
merA
expression.
The Sorbitol Phosphotransferase System Is Responsible for Transport of 2-
C
-Methyl-
d
-Erythritol into
Salmonella enterica
Serovar Typhimurium
Authors: Testa Charles A. , Cornish Rita M. , Poulter C. Dale
Published: December 2003

2-
C
-methyl-
d
-erythritol 4-phosphate is the first committed intermediate in the biosynthesis of the isoprenoid precursors isopentenyl diphosphate and dimethylallyl diphosphate. Supplementation of the growth medium with 2-
C
-methyl
-d-
erythritol has been shown to complement disruptions in the
Escherichia coli
gene for 1-deoxy
-d-
xylulose 5-phosphate synthase, the enzyme that synthesizes the immediate precursor of 2-
C
-methyl
-d-
erythritol 4-phosphate. In order to be utilized in isoprenoid biosynthesis, 2-
C
-methyl
-d-
erythritol must be phosphorylated. We describe the construction of
Salmonella enterica
serovar Typhimurium strain RMC26, in which the essential gene encoding 1-deoxy
-d-
xylulose 5-phosphate synthase has been disrupted by insertion of a synthetic mevalonate operon consisting of the yeast
ERG8
,
ERG12
, and
ERG19
genes, responsible for converting mevalonate to isopentenyl diphosphate under the control of an arabinose-inducible promoter. Random mutagenesis of RMC26 produced defects in the sorbitol phosphotransferase system that prevented the transport of 2-
C
-methyl
-d-
erythritol into the cell. RMC26 and mutant strains of RMC26 unable to grow on 2-C-methyl
-d-
erythritol were incubated in buffer containing mevalonate and deuterium-labeled 2-
C
-methyl
-d-
erythritol. Ubiquinone-8 was isolated from these cells and analyzed for deuterium content. Efficient incorporation of deuterium was observed for RMC26. However, there was no evidence of deuterium incorporation into the isoprenoid side chain of ubiquinone Q8 in the RMC26 mutants.
An Evolutionary Hot Spot: the pNGR234
b
Replicon of
Rhizobium
sp. Strain NGR234
Authors: Streit W. R. , Schmitz R. A. , Perret X. , Staehelin C. , Deakin W. J. , Raasch C. , Liesegang H. , Broughton W. J.
Published: December 2003

Rhizobium
sp. strain NGR234 has an exceptionally broad host range and is able to nodulate more than 112 genera of legumes. Since the overall organization of the NGR234 genome is strikingly similar to that of the narrow-host-range symbiont
Rhizobium meliloti
strain 1021 (also known as
Sinorhizobium meliloti
), the obvious question is why are the spectra of hosts so different? Study of the early symbiotic genes of both bacteria (carried by the SymA plasmids) did not provide obvious answers. Yet, both rhizobia also possess second megaplasmids that bear, among many other genes, those that are involved in the synthesis of extracellular polysaccharides (EPSs). EPSs are involved in fine-tuning symbiotic interactions and thus may help answer the broad- versus narrow-host-range question. Accordingly, we sequenced two fragments (total, 594 kb) that encode 575 open reading frames (ORFs). Comparisons revealed 19 conserved gene clusters with high similarity to
R. meliloti
, suggesting that a minimum of 28% (158 ORFs) of the genetic information may have been acquired from a common ancestor. The largest conserved cluster carried the
exo
and
exs
genes and contained 31 ORFs. In addition, nine highly conserved regions with high similarity to
Agrobacterium tumefaciens
C58,
Bradyrhizobium japonicum
USDA110, and
Mesorhizobium loti
strain MAFF303099, as well as two conserved clusters that are highly homologous to similar regions in the plant pathogen
Erwinia carotovora
, were identified. Altogether, these findings suggest that ≥40% of the pNGR234
b
genes are not strain specific and were probably acquired from a wide variety of other microbes. The presence of 26 ORFs coding for transposases and site-specific integrases supports this contention. Surprisingly, several genes involved in the degradation of aromatic carbon sources and genes coding for a type IV pilus were also found.
PmrAB, a Two-Component Regulatory System of
Pseudomonas aeruginosa
That Modulates Resistance to Cationic Antimicrobial Peptides and Addition of Aminoarabinose to Lipid A
Authors: Moskowitz Samuel M. , Ernst Robert K. , Miller Samuel I.
Published: December 2003

Spontaneous polymyxin-resistant mutants of
Pseudomonas aeruginosa
were isolated. The mutations responsible for this phenotype were mapped to a two-component signal transduction system similar to PmrAB of
Salmonella enterica
serovar Typhimurium. Lipid A of these mutants contained aminoarabinose, an inducible modification that is associated with polymyxin resistance. Thus,
P. aeruginosa
possesses a mechanism that induces resistance to cationic antimicrobial peptides in response to environmental conditions.
Biphasic Excitation by Leucine in
Escherichia coli
Chemotaxis
Authors: Khan Shahid , Trentham David R.
Published: December 2003

Leucine concentration jumps (applied by photolysis of inert derivatives) triggered swim or tumble responses in
Escherichia coli
mutants lacking Tsr or Tar, respectively. Wild-type
E. coli
bacteria were attracted in spatial assays when the initial leucine concentration difference was 5 to 120 μM but were repulsed when it was over 0.5 mM. Their responses to concentration jumps confirmed earlier deductions regarding biphasic excitation.
Pharmacokinetics of Etoricoxib in Patients with Renal Impairment
Authors: Agrawal Nancy G. B. , Matthews Catherine Z. , Mazenko Ralph S. , Kline Walter F. , Woolf Eric J. , Porras Arturo G. , Geer Leslie A. , Wong Peggy H. , Cho Meehung , Cote Josee , Marbury Thomas C. , Moncrief Jack W. , Alcorn Harry , Swan Suzanne , Sack Marshall R. , Robson Richard A. , Petty Kevin J. , Schwartz Jules I. , Gottesdiener Keith M.
Published: December 2003

The effect of renal insufficiency on the pharmacokinetics of etoricoxib, a selective inhibitor of cyclooxygenase‐2, was examined in 23 patients with varying degrees of renal impairment (12 moderate [creatinine clearance between 30 and 50 mL/min/1.73 m2], 5 severe [creatinine clearance below 30 mL/min/1.73 m2], and 6 with end‐stage renal disease requiring hemodialysis) following administration of single 120‐mg oral doses of etoricoxib. Even the most severe renal impairment was found to have little effect on etoricoxib pharmacokinetics. The low recovery of etoricoxib in dialysate (less than 6% of the dose) supports that hemodialysis also has little effect on etoricoxib pharmacokinetics, and binding of etoricoxib to plasma proteins was generally unaffected by renal disease. Single doses of etoricoxib were generally well tolerated by patients with renal impairment. Based on pharmacokinetic considerations, dosing adjustments are not necessary for patients with any degree of renal impairment. However, because patients with advanced renal disease (creatinine clearance below 30 mL/min/1.73 m2) are likely to be very sensitive to any further compromise of renal function, and there is no long‐term clinical experience in these patients, the use of etoricoxib is not recommended in patients with advanced renal disease.
Pharmacokinetics and Pharmacodynamics of the ETA‐Selective Endothelin Receptor Antagonist SPP301 in Healthy Human Subjects
Authors: Dieterle Walter , Mann Jessica , Kutz Klaus
Published: December 2003

SPP301 is a competitive antagonist of ET‐1 with a high selectivity for the ETA receptor. A double‐blind, placebocontrolled study was performed to investigate the tolerability, pharmacokinetics, and pharmacodynamics of SPP301 after single oral doses in male healthy subjects; doses of 5, 20, 50, 100, and 200 mg were given to different groups of 4 or 8 subjects each. The effect of food on the pharmacokinetics of SPP301 was assessed for the 50‐mg dose according to a sequential design in the same subjects. At regular intervals, blood pressure and pulse rate, plasma levels of ET‐1 and of SPP301 and its hydroxymethyl metabolite, and urinary excretion of the parent drug and its metabolite were determined. SPP301 was generally well tolerated. At doses > 20 mg, adverse events that are typical for vasodilating agents—namely, headache, nausea and vomiting, dizziness, and postural hypotension—were observed. Maximum plasma levels of SPP301 were reached within 4.5 hours. Cmax and AUC values increased linearly with doses up to 100 mg. The apparent terminal half‐life was quite constant over the whole dose range and ranged from 7.5 to 15.2 hours. Urinary excretion of SPP301 was below 0.1% of any dose. Cmax and AUC of the metabolite amounted only to about 5% of the values for SPP301. Concomitant food intake had no effect on the overall exposure but increased average peak plasma concentrations of SPP301 by around 50%. Plasma ET‐1 increased nearly twofold at the 5‐mg SPP301 dose, with no further relevant increase at higher doses. In conclusion, SPP301 is an active ET‐1 antagonist and is well tolerated. The pharmacokinetics of the drug and its metabolite are linear up to 100 mg. Food does not affect overall exposure of SPP301 but increases Cmax. Urinary excretion of SPP301 is below 0.1% of the dose administered.
Using simultaneous equation modeling for defining complex phenotypes
Authors: King Terri M
Published: December 2003

Background

Interactions between multiple biological phenotypes are difficult to model. Simultaneous equation modelling (SEM), as used in econometric modelling, may prove an effective tool for this problem. Generalized linear models were used to derive the structural equations defining the interactions between cholesterol, glucose, triglycerides and high-density lipoprotein cholesterol (HDL-C). These structural equations were then applied, using SEM, to Cohort 2 data (replicates 1–100) to estimate the phenotypic structure underlying the simulation. The goal was to determine if this empiric method of deriving structural equations for use in SEM was able to recover the simulation model better than generalized linear models.

Results

First, the underlying structural equations were estimated using generalized linear model techniques, which found strong a relationship between glucose, triglycerides and HDL-C. Using these structural equations, I used SEM to evaluate these relationships jointly. I found that a combination of the empiric structural equations and the SEM method was better at recovering the underlying simulated relationship between biologic measures than generalized linear modelling.

Conclusion

The empiric SEM procedure presented here estimated different relationships between dependent variables than generalized linear modelling. The SEM procedure using empirically developed structural equations was able to recover the underlying simulation relationship partially and thus holds promise as a technique for complex phenotype analysis. Robust methods for determining the structural equations must be developed for application of SEM to population data.
Search for genetic factors predisposing to atherogenic dyslipidemia
Authors: Yip Agustin G , Ma Qianli , Wilcox Marsha , Panhuysen Carolien I , Farrell John , Farrer Lindsay A , Wyszynski Diego F
Published: December 2003

Background

Atherogenic dyslipidemia (AD) is a common feature in persons with premature coronary heart disease. While several linkage studies have been carried out to dissect the genetic etiology of lipid levels, few have investigated the AD lipid triad comprising elevated serum triglyceride, small low density lipoprotein (LDL) particles, and reduced high density lipoprotein (HDL) cholesterol levels. Here we report the results of a whole-genome screen for AD using the Framingham Heart Study population.

Results

Our analyses provide some evidence for linkage to AD on chromosomes 1q31, 3q29, 10q26, 14p12, 14q13, 16q24, 18p11, and 19q13.

Conclusion

AD susceptibility is modulated by multiple genes in different chromosomes. Our study confirms results from other populations and suggests new areas of potential importance.
Genome-wide linkage analysis of systolic blood pressure: a comparison of two approaches to phenotype definition
Authors: Slager Susan L , Iturria Stephen J
Published: December 2003

Problem 1 of the Genetic Analysis Workshop 13(GAW13) contains longitudinal data of cardiovascular measurements from 330 pedigrees. The longitudinal data complicates the phenotype definition because multiple measurements are taken on each individual. To address this complication, we propose an approach that uses generalized estimating equations to obtain residuals for each time point for each person. The mean residual is then taken as the new phenotype with which to use in a variance components linkage analysis. We compare our phenotype definition approach to an approach that first reduces the multiple measurements to a single measurement and then models these summary statistics as regression terms in a variance components analysis. For each approach, multipoint linkage analysis was performed using the residuals and the SOLAR computer program. Our results show little difference between the methods based on the LOD scores.
Longitudinal variance-components analysis of the Framingham Heart Study data
Authors: Macgregor Stuart , Knott Sara A , White Ian , Visscher Peter M
Published: December 2003

The Framingham Heart Study offspring cohort, a complex data set with irregularly spaced longitudinal phenotype data, was made available as part of Genetic Analysis Workshop 13. To allow an analysis of all of the data simultaneously, a mixed-model- based random-regression (RR) approach was used. The RR accounted for the variation in genetic effects (including marker-specific quantitative trait locus (QTL) effects) across time by fitting polynomials of age. The use of a mixed model allowed both fixed (such as sex) and random (such as familial environment) effects to be accounted for appropriately. Using this method we performed a QTL analysis of all of the available adult phenotype data (26,106 phenotypic records).

In addition to RR, conventional univariate variance component techniques were applied. The traits of interest were BMI, HDLC, total cholesterol, and height. The longitudinal method allowed the characterization of the change in QTL effects with aging. A QTL affecting BMI was shown to act mainly at early ages.
Genetic linkage analysis of longitudinal hypertension phenotypes using three summary measures
Authors: Rao Shaoqi , Li Lin , Li Xia , Moser Kathy L , Guo Zheng , Shen Gongqing , Cannata Ruth , Zirzow Erich , Topol Eric J , Wang Qing
Published: December 2003

Background

Longitudinal data often have multiple (repeated) measures recorded along a time trajectory. For example, the two cohorts from the Framingham Heart Study (GAW13 Problem 1) contain 21 and 5 repeated measures for hypertension phenotypes as well as epidemiological risk factors, respectively. Direct modelling of a large number of serially and biologically correlated traits in the context of linkage analysis can be prohibitively complex. Alternatively, we may consider using univariate transformation for linkage analysis of longitudinal repeated measures.

Results

We evaluated the utility of three conventional summary measures (mean, slope, and principal components) for genetic linkage analysis of longitudinal phenotypes by analyzing the chromosome 10 data of the Framingham Heart Study. Except for the temporal slope, all of the summary methods and the multivariate analysis identified the previously reported region, marker GATA64A09, for systolic blood pressure or high blood pressure. Further analysis revealed that this region may harbor gene(s) affecting human blood pressure at multiple stages of life.

Conclusion

We conclude that mean and principal components are feasible alternatives for genetic linkage analysis of longitudinal phenotypes, but the slope might have a separate genetic basis from that of the original longitudinal phenotypes.
Longitudinal variance components models for systolic blood pressure, fitted using Gibbs sampling
Authors: Scurrah Katrina J , Tobin Martin D , Burton Paul R
Published: December 2003

This paper describes an analysis of systolic blood pressure (SBP) in the Genetic Analysis Workshop 13 (GAW13) simulated data. The main aim was to assess evidence for both general and specific genetic effects on the baseline blood pressure and on the rate of change (slope) of blood pressure with time. Generalized linear mixed models were fitted using Gibbs sampling in WinBUGS, and the additive polygenic random effects estimated using these models were then used as continuous phenotypes in a variance components linkage analysis. The first-stage analysis provided evidence for general genetic effects on both the baseline and slope of blood pressure, and the linkage analysis found evidence of several genes, again for both baseline and slope.
Power of linkage analysis using traits generated from simulated longitudinal data of the Framingham Heart Study
Authors: Wang Dai , Li Xiaohui , Lin Ying-Chao , Yang Kai , Guo Xiuqing , Yang Huiying
Published: December 2003

The Framingham Heart Study is a very successful longitudinal research for cardiovascular diseases. The completion of a 10-cM genome scan in Framingham families provided an opportunity to evaluate linkage using longitudinal data. Several descriptive traits based on simulated longitudinal data from the Genetic Analysis Workshop 13 (GAW13) were generated, and linkage analyses were performed for these traits. We compared the power of detecting linkage for baseline and slope genes in the simulated data of GAW13 using these traits. We found that using longitudinal traits based on multiple follow-ups may not be more powerful than using cross-sectional traits for genetic linkage analysis.
Genetic analyses of longitudinal phenotype data: a comparison of univariate methods and a multivariate approach
Authors: Yang Qiong , Chazaro Irmarie , Cui Jing , Guo Chao-Yu , Demissie Serkalem , Larson Martin , Atwood Larry D , Cupples L Adrienne , DeStefano Anita L
Published: December 2003

Background

We explored three approaches to heritability and linkage analyses of longitudinal total cholesterol levels (CHOL) in the Genetic Analysis Workshop 13 simulated data without knowing the answers. The first two were univariate approaches and used 1) baseline measure at exam one or 2) summary measures such as mean and slope from multiple exams. The third method was a multivariate approach that directly models multiple measurements on a subject. A variance components model (SOLAR) was employed in the univariate approaches. A mixed regression model with polynomials was employed in the multivariate approach and implemented in SAS/IML.

Results

Using the baseline measure at exam 1, we detected all baseline or slope genes contributing a substantial amount (0.08) of variance (LOD > 3). Compared to the baseline measure, the mean measures yielded slightly higher LOD at the slope genes, and a lower LOD at the baseline genes. The slope measure produced a somewhat lower LOD for the slope gene than did the mean measure. Descriptive information on the pattern of changes in gene effects with age was estimated for three linked loci by the third approach.

Conclusion

We found simple univariate methods may be effective to detect genes affecting longitudinal phenotypes but may not fully reveal temporal trends in gene effects. The relative efficiency of the univariate methods to detect genes depends heavily on the underlying model. Compared with the univariate approaches, the multivariate approach provided more information on temporal trends in gene effects at the cost of more complicated modelling and more intense computations.
Consistency of linkage results across exams and methods in the Framingham Heart Study
Authors: Atwood Larry D , Heard-Costa Nancy L , Cupples L Adrienne , Levy Daniel
Published: December 2003

Background

The repeated measures in the Framingham Heart Study in the Genetic Analysis Workshop 13 data set allow us to test for consistency of linkage results within a study across time. We compared regression-based linkage to variance components linkage across time for six quantitative traits in the real data.

Results

The variance components approach found 11 significant linkages, the regression-based approach found 4. There was only one region that overlapped. Consistency between exams generally decreased as the time interval between exams increased. The regression-based approach showed higher consistency in linkage results across exams.

Conclusion

The low consistency between exams and between methods may help explain the lack of replication between studies in this field.
Age-stratified heritability estimation in the Framingham Heart Study families
Authors: Brown W Mark , Beck Stephanie R , Lange Ethan M , Davis Cralen C , Kay Christine M , Langefeld Carl D , Rich Stephen S
Published: December 2003

The Framingham Heart Study provides a unique source of longitudinal family data related to CVD risk factors. Age-stratified heritability estimates were obtained over three age groups (31–49 years, 50–60 years, and 61–79 years), reflecting the longitudinal nature of the data, for four quantitative traits. Age-adjusted heritability estimates were obtained at a single common time point for the same four quantitative traits. The importance of these groups is that they consist of the same individuals. The highest age-stratified heritability estimate (h2 = 0.88 (± 0.06)) was for height in the model adjusting for gender over all three age groups. SBP gave the lowest heritability estimate (h2 = 0.15 (± 0.11)) for the 70 age group in the model adjusting for gender, height, BMI, smoker, and drinker. BMI had slightly higher estimates (h2 = 0.64 (± 0.11)) in the 40 age group than previously published. The highest age-adjusted heritability estimate (h2 = 0.90 (± 0.06)) was for height in the model adjusting for gender. SBP gave the lowest heritability estimate (h2 = 0.38 (± 0.09)) for unadjusted model. These results indicate that some common, complex traits may vary little in their genetic architecture over time and suggest that a common set of genes may be contributing to observed variation for these longitudinally collected phenotypes.
Bootstrap calibration of TRANSMIT for informative missingness of parental genotype data
Authors: Allen Andrew S , Collins Julianne S , Rathouz Paul J , Selander Craig L , Satten Glen A
Published: December 2003

Informative missingness of parental genotype data occurs when the genotype of a parent influences the probability of the parent's genotype data being observed. Informative missingness can occur in a number of plausible ways and can affect both the validity and power of procedures that assume the data are missing at random (MAR). We propose a bootstrap calibration of MAR procedures to account for informative missingness and apply our methodology to refine the approach implemented in the TRANSMIT program. We illustrate this approach by applying it to data on hypertensive probands and their parents who participated in the Framingham Heart Study.
Comparison of missing data approaches in linkage analysis
Authors: Xing Chao , Schumacher Fredrick R , Conti David V , Witte John S
Published: December 2003

Background

Observational cohort studies have been little used in linkage analyses due to their general lack of large, disease-specific pedigrees. Nevertheless, the longitudinal nature of such studies makes them potentially valuable for assessing the linkage between genotypes and temporal trends in phenotypes. The repeated phenotype measures in cohort studies (i.e., across time), however, can have extensive missing information. Existing methods for handling missing data in observational studies may decrease efficiency, introduce biases, and give spurious results. The impact of such methods when undertaking linkage analysis of cohort studies is unclear. Therefore, we compare here six methods of imputing missing repeated phenotypes on results from genome-wide linkage analyses of four quantitative traits from the Framingham Heart Study cohort.

Results

We found that simply deleting observations with missing values gave many more nominally statistically significant linkages than the other five approaches. Among the latter, those with similar underlying methodology (i.e., imputation- versus model-based) gave the most consistent results, although some discrepancies remained.

Conclusion

Different methods for addressing missing values in linkage analyses of cohort studies can give substantially diverse results, and must be carefully considered to protect against biases and spurious findings.
Interaction of gender and body mass index (BMI) reveals evidence of linkage for hypertension in the Framingham Heart Study
Authors: Daley Denise , Edwards Shannon R , Song Yeunjoo , Baechle Dan , Puppala Sobha , Schick JH , Olson Jane M , Goddard Katrina AB
Published: December 2003

Background

Genetic heterogeneity and complex biologic mechanisms of blood pressure regulation pose significant challenges to the identification of susceptibility loci influencing hypertension. Previous linkage studies have reported regions of interest, but lack consistency across studies. Incorporation of covariates, in particular the interaction between two independent risk factors (gender and BMI) greatly improved our ability to detect linkage.

Results

We report a highly significant signal for linkage to chromosome 2p, a region that has been implicated in previous linkage studies, along with several suggestive linkage regions.

Conclusion

We demonstrate the importance of including covariates in the linkage analysis when the phenotype is complex.
Transmission ratio distortion in families from the Framingham Heart Study
Authors: Paterson Andrew D , Sun Lei , Liu Xiao-Qing
Published: December 2003

Background

One implicit assumption in most linkage analysis is that live-born siblings unselected for a phenotype do not share alleles greater than the Mendelian expectation at any particular locus. However, since most families are recruited for genetic studies because of the presence of disease, there is little data available to confirm that this is the case. We hypothesized that loci that behave in a non-Mendelian fashion could be identified using genotype data from the Framingham Heart Study families. We tested the hypothesis that live-born sibs, either stratified by or irrespective of gender, demonstrate excess sharing of alleles on the autosomes, i.e., transmission ratio distortion. Multipoint linkage analysis of siblings either according to gender or not was performed using an allele-sharing method. Such observations may have implications for the mapping of loci for complex disease and quantitative traits in human pedigrees.

Results

No results that reached genome-wide significance were observed. However, four regions demonstrated excess sharing of alleles at p < 0.002 when sibships were stratified by gender-three of which were present in males. Of note, a female-specific locus co-localized with region that is linked to mean systolic blood pressure in the same families. In addition, three other regions demonstrated excess sharing of alleles in sibships irrespective of gender, including a region on chromosome 10p14-p15 (p = 7.5 × 10-4).

Conclusion

Although no loci meeting genome-wide significance were detected to demonstrate transmission ratio distortion, loci with suggestive evidence for linkage were detected. These may have implications for the mapping of susceptibility loci for complex disease in human pedigrees.
Susceptibility scoring in family-based association testing
Authors: Poisson Laila M , Rybicki Benjamin A , Coon Steven W , Barnholtz-Sloan Jill S , Chase Gary A
Published: December 2003

Background

Family-based association testing is an important part of genetic epidemiology. Tests are available to include multiple siblings, unaffected offspring, and to adjust for environmental covariates. We explore a susceptibility residual method of adjustment for covariates.

Results

Through simulation, we show that environmental adjustments that down-weight persons who are "destined" to be affected decrease the power to detect genetic association. We used the residual adjusted method on the Framingham Heart Study offspring data, provided for Genetic Analysis Workshop 13, and got mixed results.

Conclusion

When the genetic effect and environmental effects are independent, a susceptibility residual method of adjustment for environmental covariates reduces the power of the association test. Further study is necessary to determine if residual adjustment is appropriate in more complex disease models.
A statistical method for adjusting covariates in linkage analysis with sib pairs
Authors: Wu Colin O , Zheng Gang , Leifer Eric , Follmann Dean , Lin Jing-Ping
Published: December 2003

Background

We propose a statistical method that includes the use of longitudinal regression models and estimation procedures for adjusting for covariate effects in applying the Haseman-Elston (HE) method for linkage analysis. Our methodology, which uses the covariate adjusted trait, contains three steps: a) modelling the covariate-adjusted population means of quantitative traits through regression; b) estimating the value of covariate-adjusted quantitative traits; and c) evaluating the linkage between the adjusted trait values and the markers based on alleles shared identically by descent.

Results

We applied our adjusted HE method and the standard HE method in S.A.G.E. to the sib-pair subset of the Framingham Heart Study distributed by Genetic Analysis Workshop 13 with systolic blood pressure as the quantitative trait. Both methods gave similar patterns for the LOD scores, and exhibited highest multipoint LOD scores near location 70 cM of chromosome 12.

Conclusion

The adjusted HE method has two major advantages over the standard HE method used in S.A.G.E.: a) it has the capability to handle longitudinal data; b) it provides a more natural approach for adjusting the repeatedly measured covariates from each subject.
Multivariate variance-components analysis of longitudinal blood pressure measurements from the Framingham Heart Study
Authors: Kraft Peter , Bauman Lara , Yuan Jin Ying , Horvath Steve
Published: December 2003

Multivariate variance-components analysis provides several advantages over univariate analysis when studying correlated traits. It can test for pleiotropy or (in the longitudinal context) gene × age interaction. It can also have more power than univariate analyses to detect a quantitative trait locus influencing several traits. We apply multivariate variance components to longitudinal systolic blood pressure data from the Framingham Heart Study. We find evidence for a polygenic influence on blood pressure (heritabilities at different ages range from 27% to 38%). Tests based on a factor-analytic parameterization of the polygenic variance find significant (p < 2 × 10-3) evidence that different genes affect blood pressure at different ages. Still, estimates for the proportion of polygenic variance due to shared genes ran as high as 85% for some trait pairs. Univariate and multivariate linkage analyses replicate previous linkage results on chromosome 17 (maximum LOD scores of 2.2 and 2.4, respectively). In this study, multivariate analysis provides no increase in power; this is likely due to the strong positive correlation in systolic blood pressure measured at different ages.
Similarity by state/descent and genetic vector spaces: analysis of a longitudinal family study
Authors: Stassen Hans H , Hoffman Katrin , Scharfetter Christian
Published: December 2003

Using the genome-wide screening data of the Framingham Heart Study (394 nuclear families, 1328 genotyped subjects, 397 marker loci) we have quantified the underlying genetic diversity through high-dimensional genetic feature vectors and constructed a genetic vector space for the analysis of population substructure. Adaptive clustering procedures led to three major subgroups that were regarded as being related to "biological" ethnicity and that included more than 70% of the subjects. Based on these subgroups we addressed the question of ethnicity-related and ethnicity-independent risk factors for coronary heart disease (CHD). To this end, we relied upon hypertension as an endophenotype of CHD and applied a multivariate sib-pair method in order to search for oligogenic marker configurations for which the sib-sib similarities deviated from the parent-offspring similarities. Indeed, the latter similarities are always "0.5" irrespective of the affection status of parents and offspring. Loci with significant contributions to the oligogenic marker configuration constituted a CHD-specific genetic vector space. We found several ethnicity-independent signals. One signal on chromosome 8 may relate to the CYP11B1/CYP11B2 genes.
Bivariate linkage analysis of cholesterol and triglyceride levels in the Framingham Heart Study
Authors: Zhang Xuyang , Wang Kai
Published: December 2003

We performed a bivariate analysis on cholesterol and triglyceride levels on data from the Framingham Heart Study using a new score statistic developed for the detection of potential pleiotropic, or cluster, genes. Univariate score statistics were also computed for each trait. At a significance level 0.001, linkage signals were found at markers GATA48B01 on chromosome 1, GATA21C12 on chromosome 8, and ATA55A11 on chromosome 16 using the bivariate analysis. At the same significance level, linkage signals were found at markers 036yb8 on chromosome 3 and GATA3F02 on chromosome 12 using the univariate analysis. A strong linkage signal was also found at marker GATA112F07 by both the bivariate analysis and the univariate analysis, a marker for which evidence for linkage had been reported previously in a related study.
Mapping complex traits using Random Forests
Authors: Bureau Alexandre , Dupuis Josée , Hayward Brooke , Falls Kathleen , Van Eerdewegh Paul
Published: December 2003

Random Forest is a prediction technique based on growing trees on bootstrap samples of data, in conjunction with a random selection of explanatory variables to define the best split at each node. In the case of a quantitative outcome, the tree predictor takes on a numerical value. We applied Random Forest to the first replicate of the Genetic Analysis Workshop 13 simulated data set, with the sibling pairs as our units of analysis and identity by descent (IBD) at selected loci as our explanatory variables. With the knowledge of the true model, we performed two sets of analyses on three phenotypes: HDL, triglycerides, and glucose. The goal was to approach the mapping of complex traits from a multivariate perspective. The first set of analyses mimics a candidate gene approach with a high proportion of true genes among the predictors while the second set represents a genome scan analysis using microsatellite markers. Random Forest was able to identify a few of the major genes influencing the phenotypes, such as baseline HDL and triglycerides, but failed to identify the major genes regulating baseline glucose levels.
Multivariate sib-pair linkage analysis of longitudinal phenotypes by three step-wise analysis approaches
Authors: Guo Zheng , Li Xia , Rao Shaoqi , Moser Kathy L , Zhang Tianwen , Gong Binsheng , Shen Gongqing , Li Lin , Cannata Ruth , Zirzow Erich , Topol Eric J , Wang Qing
Published: December 2003

Background

Current statistical methods for sib-pair linkage analysis of complex diseases include linear models, generalized linear models, and novel data mining techniques. The purpose of this study was to further investigate the utility and properties of a novel pattern recognition technique (step-wise discriminant analysis) using the chromosome 10 linkage data from the Framingham Heart Study and by comparing it with step-wise logistic regression and linear regression.

Results

The three step-wise approaches were compared in terms of statistical significance and gene localization. Step-wise discriminant linkage analysis approach performed best; next was step-wise logistic regression; and step-wise linear regression was the least efficient because it ignored the categorical nature of disease phenotypes. Nevertheless, all three methods successfully identified the previously reported chromosomal region linked to human hypertension, marker GATA64A09. We also explored the possibility of using the discriminant analysis to detect gene × gene and gene × environment interactions. There was evidence to suggest the existence of gene × environment interactions between markers GATA64A09 or GATA115E01 and hypertension treatment and gene × gene interactions between markers GATA64A09 and GATA115E01. Finally, we answered the theoretical question "Is a trichotomous phenotype more efficient than a binary?" Unlike logistic regression, discriminant sib-pair linkage analysis might have more power to detect linkage to a binary phenotype than a trichotomous one.

Conclusion

We confirmed our previous speculation that step-wise discriminant analysis is useful for genetic mapping of complex diseases. This analysis also supported the possibility of the pattern recognition technique for investigating gene × gene or gene × environment interactions.