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Genetic Loci (genetic + locus)
Kinds of Genetic Loci Selected AbstractsMultiple Genetic Loci From CAST/EiJ Chromosome 1 Affect vBMD Either Positively or Negatively in a C57BL/6J Background,JOURNAL OF BONE AND MINERAL RESEARCH, Issue 1 2006Bouchra Edderkaoui Abstract Skeletal phenotype analyses of 10 B6.CAST-1 congenic sublines of mice have revealed evidence for the presence of three closely linked QTLs in Chr 1 that influence femoral vBMD both positively and negatively. Introduction: BMD is an important component of bone strength and a recognized predictor of risk for osteoporotic fracture. Our goal in this study was to fine map the chromosomal location of volumetric BMD (vBMD) quantitative trait loci (QTLs) in mouse distal chromosome 1 (Chr 1). Materials and Methods: After several backcrosses of the B6.CAST-1T congenic strain, which carried the initial BMD QTL in Chr 1 with B6 mice, the N10F1 generation mice were intercrossed to obtain recombinations that yielded different regions of the QTL. Thirty-eight polymorphic markers were used to fine map the initial 1T QTL region (100-192 Mb). Different skeletal parameters were compared between the 10 sublines and B6 female mice at 16 weeks of age. A t -test was used to determine the significant difference between sublines and B6 control mice, whereas one-way ANOVA and posthoc (Newman-Keuls) tests were performed to compare the phenotype between the sublines. Results: Significantly higher femur vBMD was found in sublines that carried cast alleles from 100 to 169 and 172 to 185 Mb of the centromere compared with the B6 control mice (10-12%, p < 0.001). However, sublines that carried cast alleles from 185 to 192 Mb showed significantly lower femur vBMD compared with the control mice (,6%, p < 0.05). Furthermore, femur vBMD phenotype showed a negative correlation with endosteal circumference (r = ,0.8, p = 0.003), and a strong correlation with cortical thickness for combined data from the 10 sublines (r = 0.97, p < 0.001). Moreover, a high correlation was found between body weight and both periosteal and endosteal circumferences for sublines carrying cast alleles from 167 to 175, 168 to 185, and 169 to 185 Mb, whereas no significant correlation was found between these parameters for sublines carrying cast alleles from 172 to 185 Mb. Conclusions: Genetic analysis using congenic sublines revealed that the initial BMD QTL on Chr 1 is a complex site with multiple loci affecting bone phenotypes, showing the value of the congenic approach in clearly identifying loci that control specific traits. [source] Genetic loci influencing natural variations in femoral bone morphometry in mice,JOURNAL OF ORTHOPAEDIC RESEARCH, Issue 4 2001Thomas A. Drake This study identifies genetic loci affecting femoral bone length and width measures in mature mice. Sixteen month old female F2 progeny of a C57BL/6J and DBA/2J intercross were examined for femur length and width of the femoral head, intertrochanteric region and three locations of the diaphysis using digitized images of femur radiographs obtained in the anterior-posterior and lateral projections. A genome wide linkage map was constructed using microsatellite markers at an average density of 20 cM, and quantitative trait locus analysis used to identify regions of the genome showing linkage with the traits measured. Femur length showed significant linkage with loci on proximal chromosome 3 (lod 6.1), and suggestive linkage with a locus on chromosome 14. A major locus on mid-chromosome 7 controlled width of the diaphysis (lod 6.8). Other loci were identified on chromosomes 2 and 4. Width at the intertrochanteric region had suggestive linkage with loci on chromosomes 6 and 19. No loci were found with linkage for width of the femoral head. Candidate genes related to bone development or metabolism are present at most of these loci. These findings show that genetic regulation of femoral bone morphology is complex, and are consistent with the distinct biologic processes that control longitudinal and lateral growth of the femur. © 2001 Orthopaedic Research Society. Punlished by Elsevier Science Ltd. All rights reserved. [source] Frequent genetic recombination in natural populations of the marine cyanobacterium Microcoleus chthonoplastesENVIRONMENTAL MICROBIOLOGY, Issue 3 2005Nicole Lodders Summary A culture-independent method for multilocus sequence typing of Microcoleus chthonoplastes was developed based on mechanical separation of individual cyanobacterial filaments from natural microbial mat populations through micromanipulation, subsequent polymerase chain reaction (PCR) amplification and sequence analysis of three genetic loci (kaiC, petB/D, rDNA-ITS). Among 81 individuals sampled from intertidal sand flats of the North Sea and Baltic Sea, we found 8,14 different sequences (alleles) per genetic locus, resulting in 36 distinct genotypes with unique allele profiles. Non-congruent phylogenetic gene trees for the three loci analysed and split decomposition analysis indicated the occurrence of horizontal genetic exchange. The index of association determined for the entire population was 0.096, indicating that recombination occurs frequently enough to cause almost random association (linkage equilibrium) among alleles. Analysing individuals from three different locations in the North Sea and Baltic Sea, we did not find evidence for geographic subdivisions between populations. [source] Cadmium-regulated gene fusions in Pseudomonas fluorescensENVIRONMENTAL MICROBIOLOGY, Issue 4 2000Silvia Rossbach To study the mechanisms soil bacteria use to cope with elevated concentrations of heavy metals in the environment, a mutagenesis with the lacZ -based reporter gene transposon Tn5 -B20 was performed. Random gene fusions in the genome of the common soil bacterium Pseudomonas fluorescens strain ATCC 13525 were used to create a bank of 5000 P. fluorescens mutants. This mutant bank was screened for differential gene expression in the presence of the toxic metal cadmium. Fourteen mutants were identified that responded with increased or reduced gene expression to the presence of cadmium. The mutants were characterized with respect to their metal-dependent gene expression and their metal tolerance. Half the identified mutants reacted with differential gene expression specifically to the metal cadmium, whereas some of the other mutants also responded to elevated concentrations of copper and zinc ions. One of the mutants, strain C8, also showed increased gene expression in the presence of the solvent ethanol, but otherwise no overlap between cadmium-induced gene expression and general stress response was detected. Molecular analysis of the corresponding genetic loci was performed using arbitrary polymerase chain reaction (PCR), DNA sequencing and comparison of the deduced protein products with sequences deposited in genetic databases. Some of the genetic loci targeted by the transposon did not show any similarities to any known genes; thus, they may represent ,novel' loci. The hypothesis that genes that are differentially expressed in the presence of heavy metals play a role in metal tolerance was verified for one of the mutants. This mutant, strain C11, was hypersensitive to cadmium and zinc ions. In mutant C11, the transposon had inserted into a genetic region displaying similarity to genes encoding the sensor/regulator protein pairs of two-component systems that regulate gene expression in metal-resistant bacteria, including czcRS of Ralstonia eutropha, czrRS of Pseudomonas aeruginosa and copRS of Pseudomonas syringae. Although the P. fluorescens strain used in this study had not been isolated from a metal-rich environment, it nevertheless contained at least one genetic region enabling it to cope with elevated concentrations of heavy metals. [source] Genes involved in the determination of the rate of inversions at short inverted repeatsGENES TO CELLS, Issue 6 2000Malgorzata M. Slupska Background Not all of the enzymatic pathways involved in genetic rearrangements have been elucidated. While some rearrangements occur by recombination at areas of high homology, others are mediated by short, often interrupted homologies. We have previously constructed an Escherichia coli strain that allows us to examine inversions at microhomologies, and have shown that inversions can occur at short inverted repeats in a recB,C -dependent fashion. Results Here, we report on the use of this strain to define genetic loci involved in limiting rearrangements on an F, plasmid carrying the lac genes. Employing mini-Tn10 derivatives to generate insertions near or into genes of interest, we detected three loci (rmuA,B,C) that, when mutated, increase inversions. We have mapped, cloned and sequenced these mutator loci. In one case, inactivation of the sbcC gene leads to an increase in rearrangements, and in another, insertions near the recE gene lead to an even larger increase. The third gene involved in limiting inversions, rmuC, has been mapped at 86 min on the E. coli chromosome and encodes a protein of unknown function with a limited homology to myosins, and some of the SMC (structural maintenance of chromosomes) proteins. Conclusions This work presents the first example of an anti-mutator role of the sbcC,D genes, and defines a new gene (rmuC) involved in DNA recombination. [source] Gene position within chromosome territories correlates with their involvement in distinct rearrangement types in thyroid cancer cellsGENES, CHROMOSOMES AND CANCER, Issue 3 2009Manoj S. Gandhi Chromosomal rearrangements in human cancers are of two types, interchromosomal, which are rearrangements that involve exchange between loci located on different chromosomes, and intrachromosomal, which are rearrangements that involve loci located on the same chromosome. The type of rearrangement that typically activates a specific oncogene may be influenced by its nuclear location and that of its partner. In interphase nuclei, each chromosome occupies a distinct three-dimensional (3D) territory that tends to not overlap the territories of other chromosomes. It is also known that after double strand breaks in the genome, mobility of free DNA ends is limited. These considerations suggest that loci located deep within a chromosomal territory might not participate in interchromosomal rearrangements as readily as in intrachromosomal rearrangements. To test this hypothesis, we used fluorescence in situ hybridization with 3D high-resolution confocal microscopy to analyze the positions of six oncogenes known to be activated by recombination in human cancer cells. We found that loci involved in interchromosomal rearrangements were located closer to the periphery of chromosome territories as compared with the loci that were involved in intrachromosomal inversions. The results of this study provide evidence suggesting that nuclear architecture and location of specific genetic loci within chromosome territories may influence their participation in intrachromosomal or interchromosomal rearrangements in human thyroid cells. © 2008 Wiley-Liss, Inc. [source] Detecting interacting genetic loci with effects on quantitative traits where the nature and order of the interaction are unknownGENETIC EPIDEMIOLOGY, Issue 4 2010Joanna L. Davies Abstract Standard techniques for single marker quantitative trait mapping perform poorly in detecting complex interacting genetic influences. When a genetic marker interacts with other genetic markers and/or environmental factors to influence a quantitative trait, a sample of individuals will show different effects according to their exposure to other interacting factors. This paper presents a Bayesian mixture model, which effectively models heterogeneous genetic effects apparent at a single marker. We compute approximate Bayes factors which provide an efficient strategy for screening genetic markers (genome-wide) for evidence of a heterogeneous effect on a quantitative trait. We present a simulation study which demonstrates that the approximation is good and provide a real data example which identifies a population-specific genetic effect on gene expression in the HapMap CEU and YRI populations. We advocate the use of the model as a strategy for identifying candidate interacting markers without any knowledge of the nature or order of the interaction. The source of heterogeneity can be modeled as an extension. Genet. Epidemiol. 34: 299,308, 2010. © 2009 Wiley-Liss, Inc. [source] Power and robustness of linkage tests for quantitative traits in general pedigreesGENETIC EPIDEMIOLOGY, Issue 1 2005Wei-Min Chen Abstract There are numerous statistical methods for quantitative trait linkage analysis in human studies. An ideal such method would have high power to detect genetic loci contributing to the trait, would be robust to non-normality in the phenotype distribution, would be appropriate for general pedigrees, would allow the incorporation of environmental covariates, and would be appropriate in the presence of selective sampling. We recently described a general framework for quantitative trait linkage analysis, based on generalized estimating equations, for which many current methods are special cases. This procedure is appropriate for general pedigrees and easily accommodates environmental covariates. In this report, we use computer simulations to investigate the power and robustness of a variety of linkage test statistics built upon our general framework. We also propose two novel test statistics that take account of higher moments of the phenotype distribution, in order to accommodate non-normality. These new linkage tests are shown to have high power and to be robust to non-normality. While we have not yet examined the performance of our procedures in the context of selective sampling via computer simulations, the proposed tests satisfy all of the other qualities of an ideal quantitative trait linkage analysis method. Genet. Epidemiol. © 2004 Wiley-Liss, Inc. [source] G-substrate gene promoter SNP (,1323T>C) modifies plasma total cholesterol and triglyceride phenotype in familial hypercholesterolemia: Intra-familial association study in an eight-generation hyperlipidemic kindredGERIATRICS & GERONTOLOGY INTERNATIONAL, Issue 2 2004Yukiko Nobe Background: Plasma lipid and lipoprotein generally reflect the complex influences of multiple genetic loci, for instance, even familial hypercholesterolemia (FH), a representative example of monogenic hyperlipidemia, often presents with phenotypic heterogeneity. Methods: In the course of investigating familial coronary artery disease in Utah, we studied 160 members of an eight-generation extended family of FH, to examine possible genetic modification of lipoprotein phenotype by ,modifier locus'. G-substrate (GSBS) is an endogenous substrate for cGMP-dependent protein kinase. We carried out an intrafamilial correlation analysis of modifier effect of ,1323T>C substitution in the GSBS gene among 85 LDLR-mutation carriers and 75 non-carriers. Results: In the LDLR - mutation carriers, the plasma cholesterol levels were highest among ,1323C homozygotes (mean ± SD = 454 ± 101 mg/dL), lowest among ,1323T homozygotes (mean ± SD, 307 ± 72 mg/dL) and intermediate among ,1323T/C heterozygotes (mean ± SD, 314 ± 62 mg/dL; P = 0.015). Similarly, in the LDLR-mutation carriers, the plasma triglyceride levels were highest among ,1323C homozygotes (mean ± SD, 371 ± 381 mg/dL), lowest among ,323T homozygotes (mean ± SD, 171 ± 94 mg/dL), and intermediate among ,1323T/C heterozygotes (mean ± SD, 218 ± 130 mg/dL; P = 0.003). No such gene-interactive effect was observed among non-carriers of the LDLR-mutation. Conclusion: These results indicate a significant modification of the phenotype of FH with defective LDLR allele, by GSBS-1323C allele in the kindred studied. [source] Evidence for genetic heterogeneity in D -2-hydroxyglutaric aciduria,HUMAN MUTATION, Issue 3 2010Martijn Kranendijk Abstract We performed molecular, enzyme, and metabolic studies in 50 patients with D -2-hydroxyglutaric aciduria (D -2-HGA) who accumulated D -2-hydroxyglutarate (D -2-HG) in physiological fluids. Presumed pathogenic mutations were detected in 24 of 50 patients in the D -2-hydroxyglutarate dehydrogenase (D2HGDH) gene, which encodes D -2-hydroxyglutarate dehydrogenase (D -2-HGDH). Enzyme assay of D -2-HGDH confirmed that all patients with mutations had impaired enzyme activity, whereas patients with D -2-HGA whose enzyme activity was normal did not have mutations. Significantly lower D -2-HG concentrations in body fluids were observed in mutation-positive D -2-HGA patients than in mutation-negative patients. These results imply that multiple genetic loci may be associated with hyperexcretion of D -2-HG. Accordingly, we suggest a new classification: D -2-HGA Type I associates with D -2-HGDH deficiency, whereas idiopathic D -2-HGA manifests with normal D -2-HGDH activity and higher D -2-HG levels in body fluids compared with Type I patients. It remains possible that several classifications for idiopathic D -2-HGA patients with diverse genetic loci will be revealed in future studies. Hum Mutat 31:1,5, 2010. © 2009 Wiley-Liss, Inc. [source] A multicenter study on the prevalence and spectrum of mutations in the otoferlin gene (OTOF) in subjects with nonsyndromic hearing impairment and auditory neuropathy,HUMAN MUTATION, Issue 6 2008Montserrat Rodríguez-Ballesteros Abstract Autosomal recessive nonsyndromic hearing impairment (NSHI) is a heterogeneous condition, for which 53 genetic loci have been reported, and 29 genes have been identified to date. One of these, OTOF, encodes otoferlin, a membrane-anchored calcium-binding protein that plays a role in the exocytosis of synaptic vesicles at the auditory inner hair cell ribbon synapse. We have investigated the prevalence and spectrum of deafness-causing mutations in the OTOF gene. Cohorts of 708 Spanish, 83 Colombian, and 30 Argentinean unrelated subjects with autosomal recessive NSHI were screened for the common p.Gln829X mutation. In compound heterozygotes, the second mutant allele was identified by DNA sequencing. In total, 23 Spanish, two Colombian and two Argentinean subjects were shown to carry two mutant alleles of OTOF. Of these, one Colombian and 13 Spanish subjects presented with auditory neuropathy. In addition, a cohort of 20 unrelated subjects with a diagnosis of auditory neuropathy, from several countries, was screened for mutations in OTOF by DNA sequencing. A total of 11 of these subjects were shown to carry two mutant alleles of OTOF. In total, 18 pathogenic and four neutral novel alleles of the OTOF gene were identified. Haplotype analysis for markers close to OTOF suggests a common founder for the novel c.2905_2923delinsCTCCGAGCGCA mutation, frequently found in Argentina. Our results confirm that mutation of the OTOF gene correlates with a phenotype of prelingual, profound NSHI, and indicate that OTOF mutations are a major cause of inherited auditory neuropathy. Hum Mutat 29(6), 823,831, 2008. © 2008 Wiley-Liss, Inc. [source] Identification and characterization of multiple Spidroin 1 genes encoding major ampullate silk proteins in Nephila clavipesINSECT MOLECULAR BIOLOGY, Issue 5 2008W. A. Gaines IV Abstract Spider dragline silk is primarily composed of proteins called major ampullate spidroins (MaSps) that consist of a large repeat array flanked by nonrepetitive N- and C-terminal domains. Until recently, there has been little evidence for more than one gene encoding each of the two major spidroin silk proteins, MaSp1 and MaSp2. Here, we report the deduced N-terminal domain sequences for two distinct MaSp1 genes from Nephila clavipes (MaSp1A and MaSp1B) and for MaSp2. All three MaSp genes are co-expressed in the major ampullate gland. A search of the GenBank database also revealed two distinct MaSp1 C-terminal domain sequences. Sequencing confirmed that both MaSp1 genes are present in all seven Nephila clavipes spiders examined. The presence of nucleotide polymorphisms in these genes confirmed that MaSp1A and MaSp1B are distinct genetic loci and not merely alleles of the same gene. We experimentally determined the transcription start sites for all three MaSp genes and established preliminary pairing between the two MaSp1 N- and C-terminal domains. Phylogenetic analysis of these new sequences and other published MaSp N- and C-terminal domain sequences illustrated that duplications of MaSp genes may be widespread among spider species. [source] Prevalence and potential link between E. coli O157:H7 isolated from drinking water, meat and vegetables and stools of diarrhoeic confirmed and non-confirmed HIV/AIDS patients in the Amathole District , South AfricaJOURNAL OF APPLIED MICROBIOLOGY, Issue 2 2008B.O. Abong'o Abstract Aim:, The current study investigated the prevalence and molecular relatedness between Escherichia coli O157:H7 isolated from water, meat and meat products and vegetables and from stools of confirmed and non-confirmed Human Immune Virus/Acquired Immunodeficiency Syndrome (HIV/AIDS) patients with diarrhoea. Methods and Results:, Culture-based and polymerase chain reaction techniques were used to identify E. coli O157:H7. Thirty-five per cent of meat products, 25·5% of water, 21·7% of vegetables as well as 56·5% and 43·5% of stools of confirmed and non-confirmed HIV/AIDS patients, respectively, were presumptively positive with E. coli O157. Molecular results indicated that 10·3%, 8·6% and 7·8% of the vegetables, water and meat products examined carried E. coli O157:H7, which had homologous fliCH7, rfbEO157 and eaeA genetic loci to the genes of some E. coli O157:H7 isolated from 12·2% and 8·8% of the stools of confirmed and non-confirmed HIV/AIDS patients, respectively. Conclusions:, Water, meat and meat products and vegetables are potential sources of E. coli O157:H7 that are potentially capable of causing diarrhoea in humans especially HIV/AIDS patients. Significance and Impact of the Study:, Great care should be exercised to ensure that water and foods consumed by HIV/AIDS patients are safe, as contaminated water and foods can cause secondary infections in these patients. [source] Whole-Genome Scan for Linkage to Bone Strength and Structure in Inbred Fischer 344 and Lewis Rats,JOURNAL OF BONE AND MINERAL RESEARCH, Issue 9 2005Imranul Alam Abstract A genome-wide genetic linkage analysis identified several chromosomal regions influencing bone strength and structure in F2 progeny of Fischer 344 x Lewis inbred rats. Introduction: Inbred Fischer 344 (F344) and Lewis (LEW) rats are similar in body size, but the F344 rats have significantly lower BMD and biomechanical strength of the femur and spine compared with LEW rats. The goal of this study was to identify quantitative trait loci (QTL) linked to bone strength and structure in adult female F2 rats from F344 and LEW progenitors. Materials and Methods: The 595 F2 progeny from F344 x LEW rats were phenotyped for measures of bone strength (ultimate force {Fu}; energy to break {U}; stiffness {S}) of the femur and lumbar vertebra and structure (femur midshaft polar moment of inertia {Ip}; femur midshaft cortical area; vertebral area). A genome-wide scan was completed in the F2 rats using 118 microsatellite markers at an average interval of 20 cM. Multipoint quantitative linkage analysis was performed to identify chromosomal regions that harbor QTL for bone strength and structure phenotypes. Results: Evidence of linkage for femur and lumbar strength was observed on chromosomes (Chrs) 1, 2, 5, 10, and 19. Significant linkage for femoral structure was detected on Chrs 2, 4, 5, 7, and 15. QTLs affecting femoral strength on Chrs 2 and 5 were also found to influence femur structure. Unique QTLs on Chrs 1, 10, and 19 were found that contributed to variability in bone strength but had no significant effect on structure. Also, unique QTLs were observed on Chrs 4, 7, and 15 that affected only bone structure without any effect on biomechanics. Conclusion: We showed multiple genetic loci influencing bone strength and structure in F344 x LEW F2 rats. Some of these loci are homologous to mouse and human chromosomes previously linked to related bone phenotypes. [source] Congenic Strains of Mice for Verification and Genetic Decomposition of Quantitative Trait Loci for Femoral Bone Mineral Density,JOURNAL OF BONE AND MINERAL RESEARCH, Issue 2 2003Kathryn L Shultz Abstract Peak femoral volumetric bone mineral density (femoral bone mineral density) in C57BL/6J (B6) 4-month-old female mice is 50% lower than in C3H/HeJ (C3H) and 34% lower than in CAST/EiJ (CAST) females. Genome-wide analyses of (B6 × C3H)F2 and (B6 × CAST)F2 4-month-old female progeny demonstrated that peak femoral bone mineral density is a complex quantitative trait associated with genetic loci (QTL) on numerous chromosomes (Chrs) and with trait heritabilities of 83% (C3H) and 57% (CAST). To test the effect of each QTL on femoral bone mineral density, two sets of loci (six each from C3H and CAST) were selected to make congenic strains by repeated backcrossing of donor mice carrying a given QTL-containing chromosomal region to recipient mice of the B6 progenitor strain. At the N6F1 generation, each B6.C3H and B6.CAST congenic strain (statistically 98% B6-like in genomic composition) was intercrossed to obtain N6F2 progeny for testing the effect of each QTL on femoral bone mineral density. In addition, the femoral bone mineral density QTL region on Chr 1 of C3H was selected for congenic subline development to facilitate fine mapping of this strong femoral bone mineral density locus. In 11 of 12 congenic strains, 6 B6.C3H and 5 B6.CAST, femoral bone mineral density in mice carrying c3h or cast alleles in the QTL regions was significantly different from that of littermates carrying b6 alleles. Differences also were observed in body weight, femoral length, and mid-diaphyseal periosteal circumference among these 11 congenic strains when compared with control littermates; however, these latter three phenotypes were not consistently correlated with femoral bone mineral density. Analyses of eight sublines derived from the B6.C3H-1T congenic region revealed two QTLs: one located between 36.9 and 49.7 centiMorgans (cM) and the other located between 73.2 and 100.0 cM distal to the centromere. In conclusion, these congenic strains provide proof of principle that many QTLs identified in the F2 analyses for femoral bone mineral density exert independent effects when transferred and expressed in a common genetic background. Furthermore, significant differences in femoral bone mineral density among the congenic strains were not consistently accompanied by changes in body weight, femur length, or periosteal circumference. Finally, decomposition of QTL regions by congenic sublines can reveal additional loci for phenotypes assigned to a QTL region and can markedly refine genomic locations of quantitative trait loci, providing the opportunity for candidate gene testing. [source] Identification of genetic determinants of IGF-1 levels and longevity among mouse inbred strainsAGING CELL, Issue 5 2010Magalie S. Leduc Summary The IGF-1 signaling pathway plays an important role in regulating longevity. To identify the genetic loci and genes that regulate plasma IGF-1 levels, we intercrossed MRL/MpJ and SM/J, inbred mouse strains that differ in IGF-1 levels. Quantitative trait loci (QTL) analysis of IGF-1 levels of these F2 mice detected four QTL on chromosomes (Chrs) 9 (48 Mb), 10 (86 Mb), 15 (18 Mb), and 17 (85 Mb). Haplotype association mapping of IGF-1 levels in 28 domesticated inbred strains identified three suggestive loci in females on Chrs 2 (13 Mb), 10 (88 Mb), and 17 (28 Mb) and in four males on Chrs 1 (159 Mb), 3 (52 and 58 Mb), and 16 (74 Mb). Except for the QTL on Chr 9 and 16, all loci co-localized with IGF-1 QTL previously identified in other mouse crosses. The most significant locus was the QTL on Chr 10, which contains the Igf1 gene and which had a LOD score of 31.8. Haplotype analysis among 28 domesticated inbred strains revealed a major QTL on Chr 10 overlapping with the QTL identified in the F2 mice. This locus showed three major haplotypes; strains with haplotype 1 had significantly lower plasma IGF-1 and extended longevity (P < 0.05) than strains with haplotype 2 or 3. Bioinformatic analysis, combined with sequencing and expression studies, showed that Igf1 is the most likely QTL gene, but that other genes may also play a role in this strong QTL. [source] Association of candidate susceptible loci with chronic infection with hepatitis B virus in a Chinese populationJOURNAL OF MEDICAL VIROLOGY, Issue 3 2010Ding-Qiang Chen Abstract A number of genetic loci have been proposed to be associated with persistent hepatitis B virus (HBV) infection. This study aimed to evaluate the association and interaction of susceptible genes with HBV persistence in a Chinese population. A total of 17 polymorphisms in 9 candidate genes were studied in 361 Chinese chronic hepatitis B patients and 304 patients who recovered spontaneously. Distributions of susceptible polymorphisms were examined in healthy Chinese and Caucasian populations. Gene,gene interactions were tested by the multifactor dimensionality reduction (MDR) method. The TNF ,308 G/G genotype and G allele, IL-10RB codon 47 A allele, and MCP-1 ,2518 G/G genotype and G allele were more frequent in patients than controls (P,<,0.01, after multiple corrections Pc,<,0.05), while the frequencies of TNF ,308 A/G genotype and IL-10 ,592 A/A genotype were significantly higher in controls than in the patient group (Pc,<,0.05). The frequencies of the risk allele MCP-1 ,2518 G and CTLA4 6230 G were much higher in Chinese than in the Caucasian groups (P,<,0.001). An interaction between CCR5 ,2459, TNFA ,863, IL-10RB codon 47, and MCP-1 ,2518 was detected by MDR (P,=,0.001). The results indicate that genetic determinants may affect the outcome of HBV infection in both independent and synergic manners. J. Med. Virol. 82:371,378, 2010. © 2010 Wiley-Liss, Inc. [source] Genetic loci influencing natural variations in femoral bone morphometry in mice,JOURNAL OF ORTHOPAEDIC RESEARCH, Issue 4 2001Thomas A. Drake This study identifies genetic loci affecting femoral bone length and width measures in mature mice. Sixteen month old female F2 progeny of a C57BL/6J and DBA/2J intercross were examined for femur length and width of the femoral head, intertrochanteric region and three locations of the diaphysis using digitized images of femur radiographs obtained in the anterior-posterior and lateral projections. A genome wide linkage map was constructed using microsatellite markers at an average density of 20 cM, and quantitative trait locus analysis used to identify regions of the genome showing linkage with the traits measured. Femur length showed significant linkage with loci on proximal chromosome 3 (lod 6.1), and suggestive linkage with a locus on chromosome 14. A major locus on mid-chromosome 7 controlled width of the diaphysis (lod 6.8). Other loci were identified on chromosomes 2 and 4. Width at the intertrochanteric region had suggestive linkage with loci on chromosomes 6 and 19. No loci were found with linkage for width of the femoral head. Candidate genes related to bone development or metabolism are present at most of these loci. These findings show that genetic regulation of femoral bone morphology is complex, and are consistent with the distinct biologic processes that control longitudinal and lateral growth of the femur. © 2001 Orthopaedic Research Society. Punlished by Elsevier Science Ltd. All rights reserved. [source] The University of California, San Francisco Family Alcoholism Study.ALCOHOLISM, Issue 10 2004Background: The University of California, San Francisco (UCSF) Family Alcoholism Study is a project designed to identify genetic loci that influence susceptibility to alcohol dependence and related phenotypes. Evidence supports a substantial genetic contribution to alcoholism susceptibility. However, the genetic epidemiology of alcoholism is complex, and its clinical manifestation is heterogeneous, making phenotype definition and demonstration of linkage difficult. Despite these challenges, some progress has been made toward identifying genes. Methods: The UCSF Family Alcoholism Study used a small family design, focusing primarily on sibling pairs and parent-child trios for linkage and association studies. Alcoholism-related phenotypes were assessed through interview and self-report questionnaires, with a focus on unidimensional and subphenotypical traits. Data-driven approaches to determining the most promising phenotypes for genetic analysis are being used. Both genome-wide scan and candidate gene approaches were used. Results: The study enrolled 2154 individuals from 970 families from December 1995 through January 2003. Test-retest and interrater reliability for clinical data are very good, and power estimates suggest that this study will have adequate power by linkage analysis to detect loci with moderate effects. Design, methods, and sample demographics of the UCSF Family Study are presented, along with intrafamilial correlations for primary diagnostic phenotypes. Conclusions: Plans for genetic analysis, novel approaches to phenotype refinement, and the implications of ascertainment bias for heritability estimates are discussed. [source] Dopamine D2 Receptor Binding, Drd2 Expression and the Number of Dopamine Neurons in the BXD Recombinant Inbred Series: Genetic Relationships to Alcohol and Other Drug Associated PhenotypesALCOHOLISM, Issue 1 2003Robert Hitzemann Background: It has not been established to what extent the natural variation in dopamine systems contribute to the variation in ethanol response. The current study addresses this issue by measuring D2 dopamine (DA) receptor binding, the expression of Drd2, the number of midbrain DA neurons in the BXD recombinant inbred (RI) series and then compares these strain means with those previously reported for a variety of ethanol and other drug-related phenotypes. Methods: Data were collected for 21 to 23 of the BXD RI strains and the parental strains. D2 DA receptor autoradiography was performed using 125I-epidepride as the ligand [Kanes S, Dains K, Cipp L, Gatley J, Hitzemann B, Rasmussen E, Sanderson S, Silverman S, Hitzemann R (1996) Mapping the genes for haloperidol-induced catalepsy. J Pharmacol Exp Ther 277:1016,1025]. Drd2 expression was measured using the Affymetrix oligoarray system. Immunocytochemical techniques were used to determine the number of midbrain DA neurons [Hitzemann B, Dains K, Hitzemann R (1994) Further studies on the relationship between dopamine cell density and haloperidol response. J Pharmacol Exp Ther 271:969,976]. Results and Conclusions: The range of difference in receptor binding for the RI strains was approximately 2-fold in all regions examined, the core, the shell of the nucleus accumbens (NAc) and the dorsomedial caudate-putamen (CPu); heritability in all regions was moderate,(h 2,0.35). Drd2 expression in forebrain samples from the RI and parental strains ranged 1.5- to 2-fold and h2 was moderate,0.47. Variation in the number of tyrosine hydroxylase (TH) positive neurons was moderate, 41% and 26% and h2 was low,0.19 and 0.15 for the ventral tegmental area (VTA) and substantia nigra compacta (SNc), respectively. Significant correlations were found between D2 DA receptor binding and the low dose (1.33 g/kg) ethanol stimulant response. (p < 0.002) and between Drd2 expression and conditioned place preference (CPP) (p < 0.0005). No significant correlations were detected between ethanol preference and either receptor binding or Drd2 expression; however, a significant correlation was found between preference and Ncam expression. Ncam is approximately 0.2 Mb from Drd2. Overall, the data suggest ethanol preference and CPP are associated with the expression of Drd2 or closely linked genetic loci. [source] Genotype,phenotype correlation in some autosomal recessive hereditary spastic paraplegiasJOURNAL OF THE PERIPHERAL NERVOUS SYSTEM, Issue 2 2004F Manganelli Hereditary spastic paraplegias (HSPs) are a group of clinically and genetically inherited disorders. Spastic paraparesis (SP), the main clinical feature of all HSPs can occur in relative isolation in the "pure" form or in combination with other neurological deficits in "complicated" forms. Autosomal dominant, autosomal recessive (AR) and X-linked recessive inheritance pattern of HSPs have been reported. At present, among AR-HSPs, three genes, paraplegin (SPG7), spartin (SPG20 , Troyer syndrome) and maspardin (SPG21) have been identified and six genetic loci have been mapped (SPG5, SPG11, SPG14, SPG15, SPG24, SPG25). We have evaluated 11 patients belonging to six AR-HSP families genetically identified as SPG5, SPG7, SPG11 and SPG15. In all patients electromyography, nerve conduction velocity studies, visual (VEPs), somatosensory (SSEPs), brainstem auditory (BAEPs) and magnetic motor (MMEPs) evoked potentials were performed. All 4 SPG5 patients, affected by a pure form of SP, showed abnormalities of both MMEPs and SSEPs, and two of them also VEP alterations. In the two SPG7 patients with complicated SP, MMEP abnormalities only were discovered. Among the three SPG11 patients affected by SP, complicated by mental retardation and thin corpus callosum, electrophysiological studies revealed MMEP abnormalities and signs of motor neuropathy in one of them. Finally, in the SPG15 family, presenting with SP associated with mental retardation and neurosensorial deafness, MMEP and BAEP alterations were found. [source] A model selection approach for the identification of quantitative trait loci in experimental crossesJOURNAL OF THE ROYAL STATISTICAL SOCIETY: SERIES B (STATISTICAL METHODOLOGY), Issue 4 2002Karl W. Broman Summary. We consider the problem of identifying the genetic loci (called quantitative trait loci (QTLs)) contributing to variation in a quantitative trait, with data on an experimental cross. A large number of different statistical approaches to this problem have been described; most make use of multiple tests of hypotheses, and many consider models allowing only a single QTL. We feel that the problem is best viewed as one of model selection. We discuss the use of model selection ideas to identify QTLs in experimental crosses. We focus on a back-cross experiment, with strictly additive QTLs, and concentrate on identifying QTLs, considering the estimation of their effects and precise locations of secondary importance. We present the results of a simulation study to compare the performances of the more prominent methods. [source] Genome-wide association studies of cardiovascular risk factors: design, conduct and interpretationJOURNAL OF THROMBOSIS AND HAEMOSTASIS, Issue 2009J. C. BIS Summary., Relying on known biology, candidate-gene studies have been only modestly successful in identifying genetic variants associated with cardiovascular risk factors. Genome-wide association (GWA) studies, in contrast, allow broad scans across millions of loci in search of unsuspected genetic associations with phenotypes. The large numbers of statistical tests in GWA studies and the large sample sizes required to detect modest-sized associations have served as a powerful incentive for the development of large collaborative efforts such as the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium [1]. This article uses published data on three phenotypes, fibrinogen, uric acid, and electrocardiographic QT interval duration, from the CHARGE Consortium to describe several methodologic issues in the design, conduct, and interpretation of GWA studies, including the use of imputation and the need for additional genotyping. Even with large studies, novel genetic loci explain only a small proportion of the variance of cardiovascular phenotypes. [source] Analysis of mRNA in hemophilia A patients with undetectable mutations reveals normal splicing in the factor VIII geneJOURNAL OF THROMBOSIS AND HAEMOSTASIS, Issue 2 2005O. EL-MAARRI Summary.,Background: haemophilia A (HA) is characterized by partial or total deficiency of factor VIII (FVIII) protein activity. It is caused by a broad spectrum of mutations in the FVIII gene. Despite tremendous improvements in mutation screening methods, in about 2% of HA patients no DNA change could be found, even after sequencing the whole coding part of the FVIII gene including the flanking splice sites, as well as the promotor and the 3, UTR regions. Objectives, patients and methods: In the present study we performed a detailed RNA analysis of three groups of patients. The first included control patients with known splicing defects, the second included two patients with already identified nucleotide changes close to splicing sites, that could potentially alter the normal splicing process, and a third group of 11 unrelated patients whose genomic DNA have already been screened for mutations by DHPLC and direct sequencing with no mutation being identified. Results: Both candidate splice site mutations were shown to result in either skipping or alternative splicing of at least one exon, therefore these DNA changes must be considered as causal for the patients' HA phenotype. In contrast, no abnormalities on the RNA level were observed in any of 11 unrelated patients without mutations in the FVIII gene. Conclusions: These findings exclude mutations that could be located deep in the introns and affecting either normal splicing or lead to mechanisms causing some unknown rearrangements of the FVIII gene. In fact, our results point to the presence of still unknown factor(s) causing HA, which might be either allelic or in the close proximity of the FVIII gene or non-allelic associated with other genetic loci that are involved in the processing of the FVIII protein. [source] Characterization of RAT, an autolysis regulator in Staphylococcus aureusMOLECULAR MICROBIOLOGY, Issue 6 2003S. S. Ingavale Summary In trying to identify genetic loci involved in the regulation of cap5 genes in Staphylococcus aureus, we isolated a transposon mutant that exhibited a growth defect, enhanced autolysis and increased sensitivity to Triton X-100 and penicillin, attributable in part to increased murein hydrolase activity. Analysis of the chromosomal sequence flanking the transposon insertion site revealed that the gene disrupted in the mutant encodes an open reading frame of 147 amino acids. We named this gene rat, which stands for regulator of autolytic activity. Sequence analysis indicated that Rat is homologous to the MarR and, to a lesser extent, the SarA protein families. Mutations in rat resulted in decreased expression of known autolytic regulators lytSR, lrgAB and arlRS. Gel shift studies indicated that Rat binds to the lytRS and arlRS promoters, thus confirming Rat as a DNA-binding protein to these known repressors of autolytic activity. As anticipated, rat appears to be a negative regulator of autolysin genes including lytM and lytN. These data suggest that the rat gene product is an important regulator of autolytic activity in S. aureus. [source] Molecular diversity of the genetic loci responsible for lipopolysaccharide core oligosaccharide assembly within the genus SalmonellaMOLECULAR MICROBIOLOGY, Issue 5 2002Natalia A. Kaniuk Summary The waa locus on the chromosome of Salmonella enterica encodes enzymes involved in the assembly of the core oligosaccharide region of the lipopolysaccharide (LPS) molecule. To date, there are two known core structures in Salmonella, represented by serovars Typhimurium (subspecies I) and Arizonae (subspecies IIIA). The waa locus for serovar Typhimurium has been characterized. Here, the corresponding locus from serovar Arizonae is described, and the molecular basis for the distinctive structures is established. Eleven of the 13 open reading frames (ORFs) are shared by the two loci and encode conserved proteins of known function. Two polymorphic regions distinguish the waa loci. One involves the waaK gene, the product of which adds a terminal ,-1,2-linked N -acetylglucosamine residue that characterizes the serovar Typhimurium core oligosaccharide. There is an extensive internal deletion within waaK of serovar Arizonae. The serovar Arizonae locus contains a novel ORF (waaH) between the waaB and waaP genes. Structural analyses and in vitro glycosyltransferase assays identified WaaH as the UDP-glucose:(glucosyl) LPS ,-1,2-glucosyltransferase responsible for the addition of the characteristic terminal glucose residue found in serovar Arizonae. Isolates comprising the Salmonella Reference Collections, SARC (representing the eight subspecies of S. enterica) and SARB (representing subspecies I), were examined to assess the distribution of the waa locus polymorphic regions in natural populations. These comparative studies identified additional waa locus polymorphisms, shedding light on the genetic basis for diversity in the LPS core oligosaccharides of Salmonella isolates and identifying potential sources of further novel LPS structures. [source] Susceptibility genes in movement disordersMOVEMENT DISORDERS, Issue 7 2008Sonja Scholz MD Abstract During the last years, remarkable progress in our understanding of molecular genetic mechanisms underlying movement disorders has been achieved. The successes of linkage studies, followed by positional cloning, have dominated the last decade and several genes underlying monogenic disorders have been discovered. The pathobiological understanding garnered from these mutations has laid the foundation for much of the search for genetic loci that confer risk for, rather than cause, disease. With the introduction of whole genome association studies as a novel tool to investigate genetic variation underlying common, complex diseases, a new era in neurogenomics has just begun. As the field rapidly moves forward several new challenges and critical questions in clinical care have to be addressed. In this review, we summarize recent advances in the discovery of susceptibility loci underlying major movement disorders, explain the newest methodologies and tools employed for finding and characterizing genes and discuss how insights into the molecular genetic basis of neurological disorders will impact therapeutic concepts in patient care. © 2008 Movement Disorder Society [source] Familial essential tremor with apparent autosomal dominant inheritance: Should we also consider other inheritance modes?MOVEMENT DISORDERS, Issue 9 2006Shaochun Ma MD Abstract A positive family history is present in many patients with essential tremor (ET), but twin studies and segregation analysis have suggested that ET is not entirely a genetic disorder. Two genetic loci have been identified in autosomal dominant (AD) ET and polymorphisms in the DRD3 and HS1-BP3 genes have been proposed as the possible susceptibility factors for ET. There is also evidence for further genetic heterogeneity. We evaluated 4 unrelated large kindreds with ET with an apparent AD mode of transmission. Each kindred spanned at least 3 generations and contained at least 13 living affected subjects who met criteria for definitive ET. None of the pedigrees had evidence for inheritance of ET from both parents. Known genetic ET loci were excluded in these families. We detected a preferential transmission of ET in every kindred and the proportion of affected offspring varied from 75% to 90% (P < 0.05) in the generations with complete ascertainment. Our data indicate that non-Mendelian preferential transmission of an affected allele is a feature in many ET kindreds with multiple affected members and an apparent AD mode of inheritance. ET may have a complex etiology. Additional genetic models need to be considered, including an interaction of susceptibility genes and environmental risk factors. © 2006 Movement Disorder Society [source] Familial fibronectin glomerulopathy: analysis of chromosome 1q32 and uteroglobin gene loci in a large New Zealand familyNEPHROLOGY, Issue 5 2001Robert Walker SUMMARY: Recently, a newly recognized familial glomerulopathy with predominant fibronectin deposits has been reported. This is the first report of a family with this condition in Australasia and spans two generations over a 30-year period, with the histologically confirmed glomerulopathy present in the father and five out of eight siblings. The clinical presentations have ranged from asymptomatic proteinuria, pregnancy-associated proteinuria and the nephrotic syndrome to hypertension and proteinuria with progressive renal failure. The time-course from presentation to renal failure was over a 20 years. Histology demonstrated global and diffuse thickening of capillary loops, but no cellular proliferation. Immunofluorescence demonstrated granular positivity for IgM in the capillary loops only. Electron microscopy demonstrated massive electron-dense subendothelial granular deposits with occasional small fibrils and unremarkable epithelial cell foot processes. Immunohistochemical staining was strongly positive for fibronectin and negative for type I or type IV collagen and transforming growth factor , in all biopsies. Genetic studies of familial fibronectin glomerulopathy have recently highlighted two genetic loci. Firstly, a large five-generation pedigree has been described with linkage of fibronectin glomerulopathy to chromosome 1q32. Secondly, fibronectin glomerulopathy has been reported in uteroglobin gene knockout mice. In our studies, DNA sequence analysis of the uteroglobin gene showed that it was normal in all family members, and a DNA polymorphism in the uteroglobin gene did not co-segregate with the disease. In addition, DNA microsatellite markers at the 1q32 locus did not co-segregate with the disease in our family. We presume that the underlying abnormality involves as yet undefined glomerular extracellular matrix regulation and is inherited as an autosomal dominant condition. These data favour genetic heterogeneity for the aetiology of fibronectin glomerulopathy. [source] Enteric nervous system disorders: genetic and molecular insights for the neurogastroenterologistNEUROGASTROENTEROLOGY & MOTILITY, Issue 4 2001M. Camilleri The goals of this review are to summarize some of the novel observations on the genetic and molecular basis of enteric nervous system disorders, with particular emphasis on the relevance of these observations to the practicising neurogastroenterologist. In the last two decades, there has been a greater understanding of genetic loci involved in congenital forms of pseudo-obstruction and Hirschsprung's disease; and the contribution of endothelins and nuclear transcription factors to the development of the enteric nervous system. In addition, clarification of the molecules involved in the activation of the peristaltic reflex, the disorders of the interstitial cells of Cajal, the clinical manifestations of mitochondrial cytopathies affecting the gut, and the application of neurotrophic factors for disorders of colonic function have impacted on practical management of patients with gut dysmotility. [source] | ||||||||||||||||||||||||||||||||||