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Genetic susceptibility to myocardial infarction and coronary artery disease.

Atherosclerotic involvement in the coronary arteries, which can result in heart attack and sudden death, is a common disease and prototypic of a complex human trait. To understand its genomic basis, eight linkage studies of sibling pairs have been performed. Although there was limited inter-study concordance of important loci, two gene variants in the leukotriene pathway (ALOX5AP and LTA4) have emerged as susceptibility factors for myocardial infarction (MI). Genome-wide association studies have also been undertaken, and the pro-inflammatory cytokine lymphotoxin-alpha (LTA), and its key ligand galectin-2 (LGALS2) have been identified as genes implicated in predisposition for heart attack. By cueing into the genomic basis for low serum LDL cholesterol levels, much work has been done to advance the importance of the serine protease PCSK9, which modulates LDL receptor function. Lifelong lowered LDL cholesterol associated with PCSK9 point mutations in 2-3% of individuals have been shown to provide marked protection from coronary artery disease (CAD). Most of the success in this field has been with the phenotype of MI, which is considerably more restrictive than CAD. Four principal and interdependent processes--lipoprotein handling, endothelial integrity, arterial inflammation, and thrombosis--have been supported as important via the clustering of genes, thus far implicated in CAD susceptibility. Of note, connecting genes in a single pathway (leukotriene), of a protein and its ligand (LTAalpha) or from one disease to another [age-related macular degeneration (AMD); complement factor H (CFH)], or even three disease characterized by inflammation (MHC2) have now been reported. Although the population attributable risk for any of the genes identified to date is limited, such discovery is likely to be accelerated in the future.

5-Lipoxygenase-Activating Proteins↗

Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. Molecular genetics of natural populations.

Significant progress in evolutionary genetics has been made by studying, on the one hand, patterns of DNA sequence polymorphism and, on the other, genetic architecture of complex adaptive traits. However, connections between nucleotide variants under selection and adaptively relevant phenotypes are missing. Such connections can be established using precise gene replacement. We review the recent successful introduction of this technique to the analysis of two evolutionarily interesting loci--Odysseus and desaturase2. Both genes have subtle phenotypes that nevertheless could be identified using gene replacement, demonstrating that effects of naturally occurring alleles can be measured in the laboratory. This is an important first step in connecting statistical signatures of selection with adaptation in nature. More candidate genes involved in adaptation, for example, through cloning of genes responsible for reproductive isolation, now need to be identified. Molecular genetic manipulation, DNA polymorphism analysis, and field studies then have to be integrated to provide fresh insights into the mechanisms of evolutionary change.

Alleles↗

Genetically engineered resistance to Fusarium head blight in wheat by expression of Arabidopsis NPR1.

Fusarium head blight (FHB) is a devastating disease of wheat and barley which causes extensive losses worldwide. Monogenic, gene-for-gene resistance to FHB has not been reported. The best source of resistance to FHB is a complex, quantitative trait derived from the wheat cv. Sumai 3. Here, we show that the Arabidopsis thaliana NPR1 gene (AtNPR1), which regulates the activation of systemic acquired resistance, when expressed in the FHB-susceptible wheat cv. Bobwhite, confers a heritable, type II resistance to FHB caused by Fusarium graminearum. The heightened FHB resistance in the transgenic AtNPRI -expressing wheat is associated with the faster activation of defense response when challenged by the fungus. PR1 expression is induced rapidly to a high level in the fungus-challenged spikes of the AtNPR1-expressing wheat. Furthermore, benzothiadiazole, a functional analog of salicylic acid, induced PR1 expression faster and to a higher level in the AtNPR1-expressing wheat than in the nontransgenic plants. We suggest that FHB resistance in the AtNPR1-expressing wheat is a result of these plants being more responsive to an endogenous activator of plant defense. Our results demonstrate that NPR1 is an effective candidate for controlling FHB.

Arabidopsis↗

New genetic concepts in hypertensive cardiovascular disease.

Hypertension is a complex quantitative trait under polygenic control. The identification of genes responsible for high blood pressure is of major importance, because it provides a mechanistic classification of the common phenotype and guide therapy tailored to the underlying primary abnormality. Experimental studies have identified several quantitative trait loci for blood pressure and other cardiovascular phenotypes. Further strategies that include congenic and subcongenic lines should ultimately lead to positional cloning of the causative genes, but this final step remains elusive at present. Human studies have focused on the rare Mendelian forms of human hypertension or candidate gene studies. Moreover, two recent examples show direct translation of a candidate gene and a quantitative trait locus from the experimental setting to human investigation. These strategies, together with new molecular genetic tools, will ultimately result in the identification of major genes contributing to human essential hypertension.

Animals↗

Pilot assessment of the subtelomeric regions of children with autism: detection of a 2q deletion.

PURPOSE: Autism is a chronic neurodevelopmental disorder characterized by deficits in reciprocal social interaction, language and communication, and by the presence of stereotypical behaviors. The disorder is a complex genetic trait with no known predisposing genes. We report the results of a pilot project to screen for aberrations in the gene-rich subtelomeric chromosomal regions of a cohort of children with autism. METHODS: For our pilot project, we used a multiprobe system that includes probes for the subtelomeric regions of all human chromosomes. We assessed the subtelomeric regions of chromosomes from 10 children with a diagnosis of autism. RESULTS: The screen identified one child with an apparent deletion of the subtelomeric region of chromosome 2q; nine children and pooled control samples yielded normal results. The deletion in our patient was confirmed with two other subtelomeric probes and a targeted cytogenetic study revealed a subtle difference in appearance for one chromosome 2 homologue. CONCLUSION: There have been several reports of children with dysmorphic features, autistic behaviors, and 2q deletions detectable with standard cytogenetic techniques. It may be that the distal region of chromosome 2q harbors a gene or genes that may predispose to autism.

Autistic Disorder↗

A comprehensive review of genetic association studies.

Most common diseases are complex genetic traits, with multiple genetic and environmental components contributing to susceptibility. It has been proposed that common genetic variants, including single nucleotide polymorphisms (SNPs), influence susceptibility to common disease. This proposal has begun to be tested in numerous studies of association between genetic variation at these common DNA polymorphisms and variation in disease susceptibility. We have performed an extensive review of such association studies. We find that over 600 positive associations between common gene variants and disease have been reported; these associations, if correct, would have tremendous importance for the prevention, prediction, and treatment of most common diseases. However, most reported associations are not robust: of the 166 putative associations which have been studied three or more times, only 6 have been consistently replicated. Interestingly, of the remaining 160 associations, well over half were observed again one or more times. We discuss the possible reasons for this irreproducibility and suggest guidelines for performing and interpreting genetic association studies. In particular, we emphasize the need for caution in drawing conclusions from a single report of an association between a genetic variant and disease susceptibility.

Alleles↗

Song and the song control pathway in the brain can develop independently of exposure to song in the sedge warbler.

Previous studies have shown that female sedge warblers choose to mate with males that have more complex songs, and sexual selection has driven the evolution of both song complexity and the size of the major song control area (HVc) in the brain. In songbirds, learning from conspecifics plays a major role in song development and this study investigates the effects of isolation and exposure to song on song structure and the underlying song control system. Sibling pairs of hand-reared nestling sedge warblers were reared to sexual maturity under two conditions. Siblings in one group were reared individually in acoustic isolation in separate soundproof chambers. In the other group, siblings were reared together in an aviary with playback of recorded songs. The following spring, analysis of songs revealed that siblings reared in acoustic isolation produced normal song structures, including larger syllable repertoires than those exposed to song. We found no significant differences in the volumes of HVc, nucleus robustus archistnatalis, the lateral portion of the magnocellular nucleus and the density of dendritic spines between the two groups. Males exceeded females in all these measures, and also had a larger telencephalon. Our experiments show that complex song, sexual dimorphism in brain structure, and the size of song nuclei can all develop independently of exposure to song. These findings have important implications for how sexual selection can operate upon a complex male trait such as song and how it may also shape the more general evolution of brain structure in songbirds.

Animals↗

Heterozygous carriers of Nijmegen Breakage Syndrome have a distinct gene expression phenotype.

Autosomal recessive diseases are those that require mutations in both alleles to exhibit the disorder. Although most recessive conditions are rare, heterozygous carriers of recessive mutations are quite common. In this study, we show that carriers of Nijmegen Breakage Syndrome (NBS) have a distinct gene expression phenotype that differs from that of noncarriers and also from that of carriers of a similar syndrome, Ataxia Telangiectasia (AT). We found 520 genes whose expression levels differ significantly (P < or = 0.001) between NBS carriers and controls. By linear discriminant analysis, we found a combination of 16 genes that allows 100% correct classification of individuals as either NBS carriers or noncarriers in a training set with 25 individuals, and in a test set with 52 individuals. When applied to AT carriers, the discriminant function misclassified only one out of 18 AT carriers as an NBS carrier. Our result shows that NBS carriers have a specific gene expression phenotype. It suggests that heterozygous mutations can contribute significantly to natural variation in gene expression. This has implications for the role that heterozygosity for recessive diseases plays in the overall genetic architecture of complex human traits and diseases.

Case-Control Studies↗

DNA analysis by fluorescence quenching detection.

The analysis of human genetic variations such as single nucleotide polymorphisms (SNPs) has great applications in genome-wide association studies of complex genetic traits. We have developed an SNP genotyping method based on the primer extension assay with fluorescence quenching as the detection. The template-directed dye-terminator incorporation with fluorescence quenching detection (FQ-TDI) assay is based on the observation that the intensity of fluorescent dye R110- and R6G-labeled acycloterminators is universally quenched once they are incorporated onto a DNA oligonucleotide primer. By comparing the rate of fluorescence quenching of the two allelic dyes in real time, we have extended this method for allele frequency estimation of SNPs in pooled DNA samples. The kinetic FQ-TDI assay is highly accurate and reproducible both in genotyping and in allele frequency estimation. Allele frequencies estimated by the kinetic FQ-TDI assay correlated well with known allele frequencies, with an r(2) value of 0.993. Applying this strategy to large-scale studies will greatly reduce the time and cost for genotyping hundreds and thousands of SNP markers between affected and control populations.

Alleles↗

Terminal investment induced by immune challenge and fitness traits associated with major histocompatibility complex in the house sparrow.

The terminal investment hypothesis predicts that individuals should invest more in their present reproduction if they are less likely to survive to future reproductive events. Infections, which reduce viability, may be used by individuals as a cue of a diminishing residual reproductive value and could therefore theoretically trigger an intensification of breeding effort. We tested this hypothesis in a natural population of house sparrows (Passer domesticus). We manipulated the immune system of breeding females by injecting them with a vaccine against the Paramyxo virus, the agent of Newcastle disease. Females were captured and treated immediately after completion of their first clutch either with the vaccine (NDV) or with phosphate buffered saline (PBS). The entire clutch was subsequently removed. We also screened Mhc class I genes of females to assess possible genotype-by-immune treatment interactions on reproductive investment. Our results indicate that vaccinated females were more likely to lay replacement clutches and that the difference in number of eggs between first and replacement clutches was greater for NDV females than for controls. In addition, chick size, both in terms of tarsus length and body mass, was affected by immune activation but in interaction with nestling age and female body mass, respectively. Mhc genotype-by-immune treatment interactions were never significant; however, allelic diversity was positively correlated with nestling survival. These results show that immune system activation is potentially used as a cue of reduced survival prospect and appears to induce a costly terminal investment behavior, and Mhc diversity might be under selection in a natural population of house sparrows.

Animals↗

Influence of major histocompatibility complex on reproduction and production traits in swine.

The effects of the swine lymphocyte antigen (SLA) system on different performance traits were investigated in Swiss pig breeds. Litter size and piglet weight at birth and at weaning were considered and in gilts the average daily weight gain, backfat and muscle thickness as well as percentage valuable cuts were measured. These data were analysed with least squares procedures. Although the effect of SLA on these traits was very small, a few haplotypes seemed to have some influence. Sows of the Large White breed carrying H12 had a significant smaller and those with H24 had a bigger litter size at weaning. Some mating studies were performed to investigate the effects of SLA homozygosity. The obtained results suggest that this has a negative effect on the litter size, especially when H19 in the Large White breed and H7 in Landrace are involved.

Analysis of Variance↗

A new endogenous retroviral sequence is expressed in skin of patients with psoriasis.

BACKGROUND: The origin of psoriasis, a chronic inflammatory skin disease involving keratinocyte proliferation, immune disturbances and complex inheritance, remains unknown. Human endogenous retroviruses (HERVs) are part of the normal human genome and their participation in the pathogenesis of various human diseases with complex genetic traits has been proposed. A possible role of HERVs in the induction of psoriasis was suggested many years ago. However, to date no study has searched for HERV expression in psoriasis. OBJECTIVES: To determine firstly, which HERV families are expressed in the psoriatic lesion and secondly, whether specific variants can be detected. METHODS: HERV expression was analysed at the mRNA level after degenerated reverse transcription-polymerase chain reaction (RT-PCR) of retroviral pol sequences followed by sequencing. Screening for a specific variant was performed by RT-PCR on lesional and nonlesional psoriatic skin and compared with normal and atopic dermatitis skin. RESULTS: We report the expression of three HERV families in psoriatic lesions, namely HERV-W, K and E. We then partially characterized a new endogenous retroviral variant, which was related to the ERV-9/HERV-W family. This sequence contains at least two open reading frames that could encode for a gag protein and a retroviral protease. The expression of this sequence was detected in 29 of 43 lesional psoriasis skin samples and rarely in normal (two of 21) or atopic dermatitis (three of 14) skin samples. CONCLUSIONS: In psoriatic lesions, HERV sequences of the W, K and E families are expressed and a new variant of the ERV-9/HERV-W family has been characterized. The possible role of HERV-related sequences in the pathogenesis of psoriasis is under investigation.

Amino Acid Sequence↗

Association of angiotensin II type 1 receptor gene polymorphism with essential hypertension.

The renin-angiotensin system is involved in control of blood pressure and salt and fluid homeostasis. Genes for components of this system have been of major focus in research on the causation of the common, complex, polygenic trait, essential hypertension (HT). Association of an A-->C variant at nucleotide 1166 of the angiotensin II type 1 receptor (AT1R) gene with HT, but an absence of linkage of this locus with this disease, has been reported recently. Since confirmation in a different setting is imperative, we performed a cross-sectional case-control study of the A1166C variant in a well-characterized group of 108 Caucasian HT subjects with a strong family history (two affected parents) and early onset disease. Genotyping was by mismatch polymerase chain reaction/BfrI restriction fragment length polymorphism analysis. Frequency of the C1166 allele was 0.40 in HTs and 0.29 in normotensives. The difference in genotype (chi 2 = 13, P = 0.0015) and allele (chi 2 = 5.3, P = 0.02) frequencies between the two groups was significant (odds ratio for CC vs AA + AC = 7.3 [95% CI, 1.9-31.9). The present results implicate the AT1R gene, or a locus in linkage disequilibrium with the variant tested, in the causation of essential HT.

Adult↗

Leaf hydraulic architecture correlates with regeneration irradiance in tropical rainforest trees.

The leaf hydraulic conductance (K(leaf)) is a major determinant of plant water transport capacity. Here, we measured K(leaf), and its basis in the resistances of leaf components, for fully illuminated leaves of five tree species that regenerate in deep shade, and five that regenerate in gaps or clearings, in Panamanian lowland tropical rainforest. We also determined coordination with stomatal characters and leaf mass per area. K(leaf) varied 10-fold across species, and was 3-fold higher in sun- than in shade-establishing species. On average, 12% of leaf hydraulic resistance (= 1/K(leaf)) was located in the petiole, 25% in the major veins, 25% in the minor veins, and 39% outside the xylem. Sun-establishing species had a higher proportion of leaf resistance in the xylem. Across species, component resistances correlated linearly with total leaf resistance. K(leaf) correlated tightly with indices of stomatal pore area, indicating a coordination of liquid- and vapor-phase conductances shifted relative to that of temperate woody species. Leaf hydraulic properties are integrally linked in the complex of traits that define differences in water use and carbon economy across habitats and vegetation zones.

Photobiology↗

Study of the PVRL1 gene in Italian nonsyndromic cleft lip patients with or without cleft palate.

Nonsyndromic cleft lip with or without cleft palate (CL/P) is a complex genetic trait and little is known about its aetiology. Recent investigations on rare clefting syndromes provided interesting clues about genes involved in face development. The PVRL1 gene encodes nectin1, a cell-to-cell adhesion molecule. Mutations in its sequence have been shown to cause the rare autosomal recessive syndrome CL/P-ectodermal dysplasia syndrome (CLPED1), while heterozygosity for the mutation W185X seemed to increase the risk of non syndromic CL/P in a population from northern Venezuela. In the present study, we screened 143 Italian CL/P patients for mutations in PVRL1. Three rare sequence variants in exon 3 that create amino-acid changes were detected in a total of 7 patients. Two of these mutations were not found in a panel of 292 unaffected controls, while the third was found in two controls. This study describes new mutations that may represent genetic risk factors for CL/P. Even though a study to look at the effects of the mutations on nectin1 function was not feasible, supporting evidence was reported, thus confirming the involvement of PVRL1 in the aetiology of non-syndromic CL/P malformation.

Cell Adhesion Molecules↗

Genetic linkage and association analysis in type 1 von Willebrand disease: results from the Canadian type 1 VWD study.

BACKGROUND: von Willebrand disease (VWD) is the most common bleeding disorder known in humans, with type 1 VWD representing the majority of cases. Unlike the other variant forms of VWD, type 1 disease represents a complex genetic trait, influenced by both genetic and environmental factors. AIM: To evaluate the contribution of the von Willebrand factor (VWF) and ABO blood group loci to the type 1 VWD phenotype, and to assess the potential for locus heterogeneity in this condition, we have performed genetic linkage and association studies on a large, unselected type 1 VWD population. METHOD: We initially collected samples from 194 Canadian type 1 VWD families for analysis. After the exclusion of families found to have either type 2 or type 3 VWD, and pedigrees with samples from single generations, linkage and association analysis was performed on 155 type 1 VWD families. RESULTS AND CONCLUSION: The linkage study has shown a low heterogeneity LOD score of 2.13 with the proportion of families linked to the VWF gene estimated to be 0.41. Linkage was not detected to the ABO locus in this type 1 VWD population. In the family-based association test, significant association was found between the type 1 VWD phenotype, the quantitative traits, VWF:Ag, VWF:RCo, and FVIII:C and the ABO 'O' and 'A' alleles and the VWF codon 1584 variant. There was also weak association with the -1185 promoter polymorphism and VWF:Ag, VWF:RCo, and FVIII:C plasma levels. These studies provide further evidence to support the role for genetic loci other than VWF and ABO in the pathogenesis of type 1 VWD.

ABO Blood-Group System↗

Heritability, correlations and in silico mapping of locomotor behavior and neurochemistry in inbred strains of mice.

The midbrain dopamine system mediates normal and pathologic behaviors related to motor activity, attention, motivation/reward and cognition. These are complex, quantitative traits whose variation among individuals is modulated by genetic, epigenetic and environmental factors. Conventional genetic methods have identified several genes important to this system, but the majority of factors contributing to the variation remain unknown. To understand these genetic and environmental factors, we initiated a study measuring 21 behavioral and neurochemical traits in 15 common inbred mouse strains. We report trait data, heritabilities and genetic and non-genetic correlations between pheno-types. In general, the behavioral traits were more heritable than neurochemical traits, and both genetic and non-genetic correlations within these trait sets were high. Surprisingly, there were few significant correlations between the behavioral and the individual neurochemical traits. However, striatal serotonin and one measure of dopamine turnover (DOPAC/DA) were highly correlated with most behavioral measures. The variable accounting for the most variation in behavior was mouse strain and not a specific neurochemical measure, suggesting that additional genetic factors remain to be determined to account for these behavioral differences. We also report the prospective use of the in silico method of quantitative trait loci (QTL) analysis and demonstrate difficulties in the use of this method, which failed to detect significant QTLs for the majority of these traits. These data serve as a framework for further studies of correlations between different midbrain dopamine traits and as a guide for experimental cross designs to identify QTLs and genes that contribute to these traits.

Animals↗

The effect of maternal responder status on the genetic control of the antibody response.

Various genetic models were examined with regard to the control of the antibody response in rats. Distributions of the response to poly(Glu52Lys33Tyr15) were determined in the inbred ACI (high responder) and F344 (low responder) strains and in the F1, F2 and backcross generations. Falconer's test for the effective number of genes showed that there was a larger number of genes involved if the maternal parent were the high responder strain. Studies in mating combinations involving high and moderate responders showed that the effective number of genes influencing the antibody response was much lower than in the mating between the high and low responders. Theoretical distributions of antibody response levels were generated using Monte Carlo techniques. The Kolmogorov-Smirnov goodness-of-fit test indicated that a three-gene model best fitted the matings involving the ACI female and that a two-gene model best fitted the matings involving the F344 female. These calculations indicate that the antibody response is a complex, multifactorial trait whose expression is significantly affected by the responder status of the maternal strain.

Animals↗