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Genomic Regions (genomic + regions)
Selected AbstractsA common cortactin gene variation confers differential susceptibility to severe asthmaGENETIC EPIDEMIOLOGY, Issue 8 2008Shwu-Fan Ma Abstract Genomic regions with replicated linkage to asthma-related phenotypes likely harbor multiple susceptibility loci with relatively minor effects on disease susceptibility. The 11q13 chromosomal region has repeatedly been linked to asthma with five genes residing in this region with reported replicated associations. Cortactin, an actin-binding protein encoded by the CTTN gene in 11q13, constitutes a key regulator of cytoskeletal dynamics and contractile cell machinery, events facilitated by interaction with myosin light chain kinase; encoded by MYLK, a gene we recently reported as associated with severe asthma in African Americans. To evaluate potential association of CTTN gene variation with asthma susceptibility, CTTN exons and flanking regions were re-sequenced in 48 non-asthmatic multiethnic samples, leading to selection of nine tagging polymorphisms for case-control association studies in individuals of European and African descent. After ancestry adjustments, an intronic variant (rs3802780) was significantly associated with severe asthma (odds ratio [OR]: 1.71; 95% confidence interval [CI]: 1.20,2.43; p=0.003) in a joint analysis. Further analyses evidenced independent and additive effects of CTTN and MYLK risk variants for severe asthma susceptibility in African Americans (accumulated OR: 2.93, 95% CI: 1.40,6.13, p=0.004). These data suggest that CTTN gene variation may contribute to severe asthma and that the combined effects of CTTN and MYLK risk polymorphisms may further increase susceptibility to severe asthma in African Americans harboring both genetic variants. Genet. Epidemiol. 2008. © 2008 Wiley-Liss, Inc. [source] Design and testing of ,genome-proxy' microarrays to profile marine microbial communitiesENVIRONMENTAL MICROBIOLOGY, Issue 2 2008Virginia I. Rich Summary Microarrays are useful tools for detecting and quantifying specific functional and phylogenetic genes in natural microbial communities. In order to track uncultivated microbial genotypes and their close relatives in an environmental context, we designed and implemented a ,genome-proxy' microarray that targets microbial genome fragments recovered directly from the environment. Fragments consisted of sequenced clones from large-insert genomic libraries from microbial communities in Monterey Bay, the Hawaii Ocean Time-series station ALOHA, and Antarctic coastal waters. In a prototype array, we designed probe sets to 13 of the sequenced genome fragments and to genomic regions of the cultivated cyanobacterium Prochlorococcus MED4. Each probe set consisted of multiple 70-mers, each targeting an individual open reading frame, and distributed along each ,40,160 kbp contiguous genomic region. The targeted organisms or clones, and close relatives, were hybridized to the array both as pure DNA mixtures and as additions of cells to a background of coastal seawater. This prototype array correctly identified the presence or absence of the target organisms and their relatives in laboratory mixes, with negligible cross-hybridization to organisms having , ,75% genomic identity. In addition, the array correctly identified target cells added to a background of environmental DNA, with a limit of detection of ,0.1% of the community, corresponding to ,103 cells ml,1 in these samples. Signal correlated to cell concentration with an R2 of 1.0 across six orders of magnitude. In addition, the array could track a related strain (at 86% genomic identity to that targeted) with a linearity of R2 = 0.9999 and a limit of detection of ,1% of the community. Closely related genotypes were distinguishable by differing hybridization patterns across each probe set. This array's multiple-probe, ,genome-proxy' approach and consequent ability to track both target genotypes and their close relatives is important for the array's environmental application given the recent discoveries of considerable intrapopulation diversity within marine microbial communities. [source] DIFFERENTIAL PATTERNS OF INTROGRESSION ACROSS THE X CHROMOSOME IN A HYBRID ZONE BETWEEN TWO SPECIES OF HOUSE MICEEVOLUTION, Issue 9 2004Bret A. Payseur Abstract A complete understanding of the speciation process requires the identification of genomic regions and genes that confer reproductive barriers between species. Empirical and theoretical research has revealed two important patterns in the evolution of reproductive isolation in animals: isolation typically arises as a result of disrupted epistatic interactions between multiple loci and these disruptions map disproportionately to the X chromosome. These patterns suggest that a targeted examination of natural gene flow between closely related species at X-linked markers with known positions would provide insight into the genetic basis of speciation. We take advantage of the existence of genomic data and a well-documented European zone of hybridization between two species of house mice, Mus domesticus and M. musculus, to conduct such a survey. We evaluate patterns of introgression across the hybrid zone for 13 diagnostic X-linked loci with known chromosomal positions using a maximum likelihood model. Interlocus comparisons clearly identify one locus with reduced introgression across the center of the hybrid zone, pinpointing a candidate region for reproductive isolation. Results also reveal one locus with high frequencies of M. domesticus alleles in populations on the M. musculus side of the zone, suggesting the possibility that positive selection may act to drive the spread of alleles from one species on to the genomic background of the other species. Finally, cline width and cline center are strongly positively correlated across the X chromosome, indicating that gene flow of the X chromosome may be asymmetrical. This study highlights the utility of natural populations of hybrids for mapping speciation genes and suggests that the middle of the X chromosome may be important for reproductive isolation between species of house mice. [source] Variation in fiber number of a male-specific muscle between Drosophila species: a genetic and developmental analysisEVOLUTION AND DEVELOPMENT, Issue 4 2007Virginie Orgogozo SUMMARY We characterize a newly discovered morphological difference between species of the Drosophila melanogaster subgroup. The muscle of Lawrence (MOL) contains about four to five fibers in D. melanogaster and Drosophila simulans and six to seven fibers in Drosophila mauritiana and Drosophila sechellia. The same number of nuclei per fiber is present in these species but their total number of MOL nuclei differs. This suggests that the number of muscle precursor cells has changed during evolution. Our comparison of MOL development indicates that the species difference appears during metamorphosis. We mapped the quantitative trait loci responsible for the change in muscle fiber number between D. sechellia and D. simulans to two genomic regions on chromosome 2. Our data eliminate the possibility of evolving mutations in the fruitless gene and suggest that a change in the twist might be partly responsible for this evolutionary change. [source] DNA methylation of Sleeping Beauty with transposition into the mouse genomeGENES TO CELLS, Issue 8 2005Chang Won Park The Sleeping Beauty transposon is a recently developed non-viral vector that can mediate insertion of transgenes into the mammalian genome. Foreign DNA elements that are introduced tend to invoke a host-defense mechanism resulting in epigenetic changes, such as DNA methylation, which may induce transcriptional inactivation of mammalian genes. To assess potential epigenetic modifications associated with Sleeping Beauty transposition, we investigated the DNA methylation pattern of transgenes inserted into the mouse genome as well as genomic regions flanking the insertion sites with bisulfite-mediated genomic sequencing. Transgenic mouse lines were created with two different Sleeping Beauty transposons carrying either the Agouti or eGFP transgene. Our results showed that DNA methylation in the keratin-14 promoter and Agouti transgene were negligible. In addition, two different genomic loci flanking the Agouti insertion site exhibited patterns of DNA methylation similar to wild-type mice. In contrast, high levels of DNA methylation were observed in the eGFP transgene and its ROSA26 promoter. These results indicate that transposition via Sleeping Beauty into the mouse genome may result in a significant level of de novo DNA methylation. This may depend on a number of different factors including the cargo DNA sequence, chromosomal context of the insertion site, and/or host genetic background. [source] Molecular characterization of the spectrum of genomic deletions in the mismatch repair genes MSH2, MLH1, MSH6, and PMS2 responsible for hereditary nonpolyposis colorectal cancer (HNPCC)GENES, CHROMOSOMES AND CANCER, Issue 2 2005Heleen van der Klift A systematic search by Southern blot analysis in a cohort of 439 hereditary nonpolyposis colorectal cancer (HNPCC) families for genomic rearrangements in the main mismatch repair (MMR) genes, namely, MSH2, MLH1, MSH6, and PMS2, identified 48 genomic rearrangements causative of this inherited predisposition to colorectal cancer in 68 unrelated kindreds. Twenty-nine of the 48 rearrangements were found in MSH2, 13 in MLH1, 2 in MSH6, and 4 in PMS2. The vast majority were deletions, although one previously described large inversion, an intronic insertion, and a more complex rearrangement also were found. Twenty-four deletion breakpoints have been identified and sequenced in order to determine the underlying recombination mechanisms. Most fall within repetitive sequences, mainly Alu repeats, in agreement with the differential distribution of deletions between the MSH2 and MLH1 genes: the higher number and density of Alu repeats in MSH2 corresponded with a higher incidence of genomic rearrangement at this disease locus when compared with other MMR genes. Long interspersed nuclear element (LINE) repeats, relatively abundant in, for example, MLH1, did not seem to contribute to the genesis of the deletions, presumably because of their older evolutionary age and divergence among individual repeat units when compared with short interspersed nuclear element (SINE) repeats, including Alu repeats. Moreover, Southern blot analysis of the introns and the genomic regions flanking the MMR genes allowed us to detect 6 novel genomic rearrangements that left the coding region of the disease-causing gene intact. These rearrangements comprised 4 deletions upstream of the coding region of MSH2 (3 cases) and MSH6 (1 case), a 2-kb insertion in intron 7 of PMS2, and a small (459-bp) deletion in intron 13 of MLH1. The characterization of these genomic rearrangements underlines the importance of genomic deletions in the etiology of HNPCC and will facilitate the development of PCR-based tests for their detection in diagnostic laboratories. © 2005 Wiley-Liss, Inc. [source] Genomic imbalances in CML blast crisis: 8q24.12,q24.13 Segment identified as a common region of over-representationGENES, CHROMOSOMES AND CANCER, Issue 4 2003Susan M. Gribble The acute phase of chronic myeloid leukemia (CML) is accompanied by secondary chromosomal changes. The additional changes have a non-random pattern; however, highly abnormal (marker) chromosomes are reported in some 20% of abnormal karyotypes. These marker chromosomes have proved to be beyond the resolution of conventional G-banding analysis. We used molecular cytogenetic techniques to determine the structure of complex chromosome markers in 10 CML-derived cell lines after our investigations of CML patients in blast crisis. Multicolor fluorescence in situ hybridization identified a multitude of structural chromosome aberrations. In addition, genomic gains identified by comparative genomic hybridization (CGH) were mapped to highly complex marker chromosomes in more than one cell line. The most common genomic loss detected by CGH affected chromosome 9, whereas the most common genomic gains affected, in order of frequency, the sequences of 8q, 6, and 13q. The smallest discrete amplification on 8q was identified in cell line MEG-01. This amplicon contains sequences represented by the marker D8S263/RMC08P029 but did not contain the proximal MYC gene or a more distal marker, D8S256/RMC08P025. We determined the size of the amplicon to be less than the chromosome segment 8q24.12,q24.13. The use of region- and locus-specific probes to analyze the organization of highly complex marker structures aided the identification of preferentially amplified genomic regions. The resultant amplifications could harbor gene(s) driving disease progression. © 2003 Wiley-Liss, Inc. [source] Comprehensive linkage and linkage heterogeneity analysis of 4344 sibling pairs affected with hypertension from the Family Blood Pressure ProgramGENETIC EPIDEMIOLOGY, Issue 3 2007Tiffany A. Greenwood Abstract Linkage analyses of complex, multifactorial traits and diseases, such as essential hypertension, have been difficult to interpret and reconcile. Many published studies provide evidence suggesting that different genes and genomic regions influence hypertension, but knowing which of these studies reflect true positive results is challenging. The reasons for this include the diversity of analytical methods used across these studies, the different samples and sample sizes in each study, and the complicated biological underpinnings of hypertension. We have undertaken a comprehensive linkage analysis of 371 autosomal microsatellite markers genotyped on 4,334 sibling pairs affected with hypertension from five ethnic groups sampled from 13 different field centers associated with the Family Blood Pressure Program (FBPP). We used a single analytical technique known to be robust to interpretive problems associated with a lack of completely informative markers to assess evidence for linkage to hypertension both within and across the ethnic groups and field centers. We find evidence for linkage to a number of genomic regions, with the most compelling evidence from analyses that combine data across field center and ethnic groups (e.g., chromosomes 2 and 9). We also pursued linkage analyses that accommodate locus heterogeneity, which is known to plague the identification of disease susceptibility loci in linkage studies of complex diseases. We find evidence for linkage heterogeneity on chromosomes 2 and 17. Ultimately our results suggest that evidence for linkage heterogeneity can only be detected with large sample sizes, such as the FBPP, which is consistent with theoretical sample size calculations. Genet. Epidemiol. 2007. © 2007 Wiley-Liss, Inc. [source] Haplotype interaction analysis of unlinked regionsGENETIC EPIDEMIOLOGY, Issue 4 2005Tim Becker Abstract Genetically complex diseases are caused by interacting environmental factors and genes. As a consequence, statistical methods that consider multiple unlinked genomic regions simultaneously are desirable. Such consideration, however, may lead to a vast number of different high-dimensional tests whose appropriate analysis pose a problem. Here, we present a method to analyze case-control studies with multiple SNP data without phase information that considers gene-gene interaction effects while correcting appropriately for multiple testing. In particular, we allow for interactions of haplotypes that belong to different unlinked regions, as haplotype analysis often proves to be more powerful than single marker analysis. In addition, we consider different marker combinations at each unlinked region. The multiple testing issue is settled via the minP approach; the P value of the "best" marker/region configuration is corrected via Monte-Carlo simulations. Thus, we do not explicitly test for a specific pre-defined interaction model, but test for the global hypothesis that none of the considered haplotype interactions shows association with the disease. We carry out a simulation study for case-control data that confirms the validity of our approach. When simulating two-locus disease models, our test proves to be more powerful than association methods that analyze each linked region separately. In addition, when one of the tested regions is not involved in the etiology of the disease, only a small amount of power is lost with interaction analysis as compared to analysis without interaction. We successfully applied our method to a real case-control data set with markers from two genes controlling a common pathway. While classical analysis failed to reach significance, we obtained a significant result even after correction for multiple testing with our proposed haplotype interaction analysis. The method described here has been implemented in FAMHAP. Genet. Epidemiol. 2005. © 2005 Wiley-Liss, Inc. [source] Gene conversion causing human inherited disease: Evidence for involvement of non-B-DNA-forming sequences and recombination-promoting motifs in DNA breakage and repair,HUMAN MUTATION, Issue 8 2009Nadia Chuzhanova Abstract A variety of DNA sequence motifs including inverted repeats, minisatellites, and the , recombination hotspot, have been reported in association with gene conversion in human genes causing inherited disease. However, no methodical statistically based analysis has been performed to formalize these observations. We have performed an in silico analysis of the DNA sequence tracts involved in 27 nonoverlapping gene conversion events in 19 different genes reported in the context of inherited disease. We found that gene conversion events tend to occur within (C+G)- and CpG-rich regions and that sequences with the potential to form non-B-DNA structures, and which may be involved in the generation of double-strand breaks that could, in turn, serve to promote gene conversion, occur disproportionately within maximal converted tracts and/or short flanking regions. Maximal converted tracts were also found to be enriched (P<0.01) in a truncated version of the ,-element (a TGGTGG motif), immunoglobulin heavy chain class switch repeats, translin target sites and several novel motifs including (or overlapping) the classical meiotic recombination hotspot, CCTCCCCT. Finally, gene conversions tend to occur in genomic regions that have the potential to fold into stable hairpin conformations. These findings support the concept that recombination-inducing motifs, in association with alternative DNA conformations, can promote recombination in the human genome. Hum Mutat 30:1,10, 2009. © 2009 Wiley-Liss, Inc. [source] Annotated chromosome maps for renal disease,HUMAN MUTATION, Issue 3 2009Amy Jayne McKnight Abstract A combination of linkage analyses and association studies are currently employed to promote the identification of genetic factors contributing to inherited renal disease. We have standardized and merged complex genetic data from disparate sources, creating unique chromosomal maps to enhance genetic epidemiological investigations. This database and novel renal maps effectively summarize genomic regions of suggested linkage, association, or chromosomal abnormalities implicated in renal disease. Chromosomal regions associated with potential intermediate clinical phenotypes have been integrated, adding support for particular genomic intervals. More than 500 reports from medical databases, published scientific literature, and the World Wide Web were interrogated for relevant renal-related information. Chromosomal regions highlighted for prioritized investigation of renal complications include 3q13,26, 6q22,27, 10p11,15, 16p11,13, and 18q22. Combined genetic and physical maps are effective tools to organize genetic data for complex diseases. These renal chromosome maps provide insights into renal phenotype-genotype relationships and act as a template for future genetic investigations into complex renal diseases. New data from individual researchers and/or future publications can be readily incorporated to this resource via a user-friendly web-form accessed from the website: www.qub.ac.uk/neph-res/CORGI/index.php. Hum Mutat 0, 1,8, 2008. © 2008 Wiley-Liss, Inc. [source] GENOMIZER: an integrated analysis system for genome-wide association data,HUMAN MUTATION, Issue 6 2006Andre Franke Abstract Genome-wide association analysis appears to be a promising way to identify heritable susceptibility factors for complex human disorders. However, the feasibility of large-scale genotyping experiments is currently limited by an incomplete marker coverage of the genome, a restricted understanding of the functional role of given genomic regions, and the small sample sizes used. Thus, genome-wide association analysis will be a screening tool to facilitate subsequent gene discovery rather than a means to completely resolve individual genetic risk profiles. The validation of association findings will continue to rely upon the replication of "leads" in independent samples from either the same or different populations. Even under such pragmatic conditions, the timely analysis of the large data sets in question poses serious technical challenges. We have therefore developed public-domain software, GENOMIZER, that implements the workflow of an association experiment, including data management, single-point and haplotype analysis, "lead" definition, and data visualization. GENOMIZER (www.ikmb.uni-kiel.de/genomizer) comes with a complete user manual, and is open-source software licensed under the GNU Lesser General Public License. We suggest that the use of this software will facilitate the handling and interpretation of the currently emerging genome-wide association data. Hum Mutat 27(6), 583,588, 2006. © 2006 Wiley-Liss, Inc. [source] A Bivariate Whole Genome Linkage Study Identified Genomic Regions Influencing Both BMD and Bone Structure,JOURNAL OF BONE AND MINERAL RESEARCH, Issue 11 2008Xiao-Gang Liu Abstract Areal BMD (aBMD) and areal bone size (ABS) are biologically correlated traits and are each important determinants of bone strength and risk of fractures. Studies showed that aBMD and ABS are genetically correlated, indicating that they may share some common genetic factors, which, however, are largely unknown. To study the genetic factors influencing both aBMD and ABS, bivariate whole genome linkage analyses were conducted for aBMD-ABS at the femoral neck (FN), lumbar spine (LS), and ultradistal (UD)-forearm in a large sample of 451 white pedigrees made up of 4498 individuals. We detected significant linkage on chromosome Xq27 (LOD = 4.89) for LS aBMD-ABS. In addition, we detected suggestive linkages at 20q11 (LOD = 3.65) and Xp11 (LOD = 2.96) for FN aBMD-ABS; at 12p11 (LOD = 3.39) and 17q21 (LOD = 2.94) for LS aBMD-ABS; and at 5q23 (LOD = 3.54), 7p15 (LOD = 3.45), Xq27 (LOD = 2.93), and 12p11 (LOD = 2.92) for UD-forearm aBMD-ABS. Subsequent discrimination analyses indicated that quantitative trait loci (QTLs) at 12p11 and 17q21 may have pleiotropic effects on aBMD and ABS. This study identified several genomic regions that may contain QTLs important for both aBMD and ABS. Further endeavors are necessary to follow these regions to eventually pinpoint the genetic variants affecting bone strength and risk of fractures. [source] X-linked mental retardation and epigeneticsJOURNAL OF CELLULAR AND MOLECULAR MEDICINE, Issue 4 2006Guy Froyen Abstract The search for the genetic defects in constitutional diseases has so far been restricted to direct methods for the identification of genetic mutations in the patients' genome. Traditional methods such as karyotyping, FISH, mutation screening, positional cloning and CGH, have been complemented with newer methods including array-CGH and PCR-based approaches (MLPA, qPCR). These methods have revealed a high number of genetic or genomic aberrations that result in an altered expression or reduced functional activity of key proteins. For a significant percentage of patients with congenital disease however, the underlying cause has not been resolved strongly suggesting that yet other mechanisms could play important roles in their etiology. Alterations of the ,native' epigenetic imprint might constitute such a novel mechanism. Epigenetics, heritable changes that do not rely on the nucleotide sequence, has already been shown to play a determining role in embryonic development, X-inactivation, and cell differentiation in mammals. Recent progress in the development of techniques to study these processes on full genome scale has stimulated researchers to investigate the role of epigenetic modifications in cancer as well as in constitutional diseases. We will focus on mental impairment because of the growing evidence for the contribution of epigenetics in memory formation and cognition. Disturbance of the epigenetic profile due to direct alterations at genomic regions, or failure of the epigenetic machinery due to genetic mutations in one of its components, has been demonstrated in cognitive derangements in a number of neurological disorders now. It is therefore tempting to speculate that the cognitive deficit in a significant percentage of patients with unexplained mental retardation results from epigenetic modifications. [source] Effects of interferon alpha therapy on the catalytic domains of the polymerase gene and basal core promoter, precore and core regions of hepatitis B virusJOURNAL OF GASTROENTEROLOGY AND HEPATOLOGY, Issue 6 2003ROBERT YUNG MING CHEN Aims: The aim of the present study was to examine the catalytic domains of the polymerase gene, the basal core promoter and the precore and core regions of the hepatitis B virus (HBV) genome for specific mutations. These may account for the response to interferon alpha (IFN-,) treatment, which may have prognostic value. Methods: Multiple serum samples were collected prospectively from 30 patients with chronic active hepatitis B who were treated with IFN-,. Patients were assigned to one of three groups: group A (n = 11) and group B (n = 10) individuals were hepatitis B e antigen (HBeAg)-positive prior to treatment. Group A patients underwent HBeAg seroconversion after treatment while group B patients did not. Group C (n = 9) patients were HBeAg-negative prior to treatment. The HBV DNA was extracted from the sera collected before, during and after treatment and the various genomic regions were amplified, sequenced and examined for mutations. Results: During IFN-, therapy, multiple changes were found in the catalytic domains of the HBV polymerase gene in all groups. The frequency of mutations and associated amino acid changes were highest in virus from group C patients and lowest in group A patients. The interdomain regions of the viral polymerase were the most affected. Multiple mutations were also found in the precore, core and core promoter regions. However, no specific mutations were associated with clinical response or outcome. Conclusions: During IFN-, treatment, multiple mutations occurred in the HBV genome, including the catalytic domains of the polymerase gene. Changes that did occur could not be correlated to the clinical response or treatment outcome. However, no mutations were found that have been linked to lamivudine escape, indicating that lamivudine therapy would be effective in IFN-, non-responder patients. [source] Molecular epidemiology of hepatitis A in St. Petersburg, Russia, 1997,2003JOURNAL OF MEDICAL VIROLOGY, Issue 6 2007Irja Davidkin Abstract The molecular epidemiology of hepatitis A virus (HAV) strains circulating in the St. Petersburg and Karelia regions was studied during 1997,2003. Hepatitis A virus RNA was isolated from both clinical samples (stools or sera) and environmental samples (sewage water). RT-PCR was carried out using different primer pairs from the VP1/2A and VP1 genomic regions, the variable parts of the HAV genome. PCR products were sequenced and 306 nucleotides from the VP1/2A and 332 nucleotides from the VP1 region were used for phylogenetic analysis. The results show that the IA subtype was the most common during the follow-up period: >90% of the isolated HAV strains belonged to that subtype. The HAV strains found in intravenous drug users belonged to subtypes IA and IIIA. Only one out of a total of 88 sequenced strains was of the IB subtype. The subtypes IB and IIIA were found only in 2001,2003, which suggests that new strains were introduced into the endemic situation. The results indicate the usefulness of molecular epidemiological methods in studying changes in the circulating HAV strains and in tracing transmission routes. J. Med. Virol. 79: 657,662, 2007. © 2007 Wiley-Liss, Inc. [source] Cerebellar Gene Expression Profiling and eQTL Analysis in Inbred Mouse Strains Selected for Ethanol SensitivityALCOHOLISM, Issue 9 2005Erik J. MacLaren Background: Inbred Long-Sleep (ILS) and Inbred Short-Sleep (ISS) mice exhibit striking differences in a number of alcohol and drug related behaviors. This study examined the expression levels of more than 39,000 transcripts in these strains in the cerebellum, a major target of ethanol's actions in the CNS, to find differentially expressed (DE) candidate genes for these phenotypes. Methods: Genes that were differentially expressed between the strains were identified using oligonucleotide arrays as well as complimentary DNA arrays. Sequence alignment was used to locate DE genes in the mouse genome assembly. In silico expression QTL (eQTL) mapping was used to identify chromosomal regions likely to control the transcription level of DE genes, and the EASE program identified overrepresented functional themes. The genomic region immediately upstream of the cyclase associated protein homolog 1 (Cap1) gene was directly sequenced from PCR products. Results: Nearly 300 genes were identified as differentially expressed between the cerebella of ILS and ISS. These genes and their corresponding eQTLs map to genomic regions linked to several phenotypes that differ between the ILS and ISS strains, including ethanol preference and cocaine-induced locomotor activation on Chromosomes 4 and 7 respectively. Eight genes were cross-platform validated, four of which are more highly expressed in ILS cerebellum. Three SNPs, one of which disrupts a predicted Sp1 binding site, were found in the upstream region of Cap1, a strong candidate for influencing ethanol phenotypes. Conclusions: Many of these DE genes are candidates to influence ethanol and drug regulated phenotypes because they either map to ethanol related QTLs in the genome or are linked to them through eQTL mapping. Genes involved in calcium ion binding and transcriptional regulation are overrepresented and therefore these gene classes may influence ethanol behaviors in mice and humans. [source] Prospects for using marker-assisted breeding to improve maize production in AfricaJOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE, Issue 5 2008Robyn Stevens Abstract Maize (Zea mays L.) production in sub-Saharan Africa has historically been constrained by a number of biotic and abiotic factors, including drought, insects, disease, and weeds. New agricultural research involving genomics and molecular markers may assist plant breeders in developing new varieties that will benefit producers and consumers in this region. Over the past few decades, plant breeders have used molecular markers to identify numerous genomic regions affecting maize production and nutritional value. Marker-assisted selection (MAS) presents the potential to improve the efficiency of plant breeding by allowing for the transfer of these specific genomic regions of interest and accelerating the recovery of the elite parent background. However, to this point, few examples of successful MAS in breeding programs, particularly those with benefits in Africa, have been noted. This review discusses the use of molecular markers in the identification of quantitative trait loci (QTL) affecting the production and nutritional quality of maize, as well as the potential to use the results from the vast number of QTL studies that have been performed in MAS breeding programs. Copyright © 2008 Society of Chemical Industry [source] Genome scan in the mosquito Aedes rusticus: population structure and detection of positive selection after insecticide treatmentMOLECULAR ECOLOGY, Issue 2 2010MARGOT PARIS Abstract Identification of genes involved in local adaptation is particularly challenging for species functioning as a network of interconnected populations undergoing frequent extinctions,recolonizations, because populations are submitted to contrasted evolutionary pressures. Using amplified fragment length polymorphism markers, population genetic structure of the mosquito Aedes rusticus was analysed in five geographical areas of the French Rhône-Alpes region. We included a number of sites that were treated with the bio-insecticide Bacillus thuringiensis israelensis (Bti) for more than 15 years. Analysis of molecular variance revealed that most of the genetic variability was found within populations (96%), with no significant variation among geographical areas, although variation among populations within areas (4%) was significant. The global genetic differentiation index FST was low (0.0366 ± 0.167). However, pairwise FST values were significant and no isolation-by-distance at the regional level was observed, suggesting a metapopulation structure in this species. Bti -treatment had no effect on genetic structure and on within-population genetic diversity. Potential signatures of positive selection associated with Bti -treatment were detected for five loci, even though toxicological bioassays performed on field-collected larvae showed no significant difference in mortality between Bti -treated and nontreated sites. The difficulty of detecting moderate resistance in field-collected larvae together with possible differential persistence of toxins in the environment may explain our inability to detect a toxicological response to Bti in treated sites. The evidence for positive selection occurring at several genomic regions suggests a first step towards Bti resistance in natural mosquito populations treated with this bio-insecticide. Furthermore, this signal was detectable using genomic tools before any toxicological evidence for resistance could be identified. [source] A population genomic approach to map recent positive selection in model speciesMOLECULAR ECOLOGY, Issue 16 2008P. PAVLIDIS Abstract Based on nearly complete genome sequences from a variety of organisms data on naturally occurring genetic variation on the scale of hundreds of loci to entire genomes have been collected in recent years. In parallel, new statistical tests have been developed to infer evidence of recent positive selection from these data and to localize the target regions of selection in the genome. These methods have now been successfully applied to Drosophila melanogaster, humans, mice and a few plant species. In genomic regions of normal recombination rates, the targets of positive selection have been mapped down to the level of individual genes. [source] Variation of haplotype distributions of two genomic regions of Citrus tristeza virus populations from eastern SpainMOLECULAR ECOLOGY, Issue 2 2003F. D'Urso Abstract Genetic variation in natural populations of Citrus tristeza virus (CTV) was studied using haplotypes detected by single-strand conformation polymorphism (SSCP) analysis of two genomic regions (p20 gene and segment A, located in ORF1a). Analysis of 254 samples from 125 trees, collected at 12 different sites, yielded 8 different haplotypes for p20 and 5 for segment A. The most frequent haplotype of p20 was predominant at all sites, but several sites differed in the predominance of segment A haplotypes. At most sites, the homozygosity observed for the p20 gene tended to be higher than expected in a neutral evolution, whereas the opposite was true for segment A. Comparison of the populations at different sites showed that 44 of the 66 possible population pairs were genetically distinct for segment A, but only six pairs differed for the p20 gene. Analysis of molecular variance grouping trees by site, scion variety, rootstock or age, showed that variation in segment A was significantly affected by site, tree age and rootstock, and that variation between trees in each group and within trees was even more important. In contrast, variation in p20 was affected only by site and rootstock, each factor contributing to < 2% of the variation. The data suggest that sequence variations in segment A must be functionally less important and that it has less evolutionary constraints than p20. Detection of different haplotypes in neighbour trees or in samples from the same tree may help explain part of the variability observed in CTV symptom expression. [source] Identifying genetic components controlling fertility in the outcrossing grass species perennial ryegrass (Lolium perenne) by quantitative trait loci analysis and comparative geneticsNEW PHYTOLOGIST, Issue 3 2008I. P. Armstead Summary ,,Mutational load and resource allocation factors and their effects on limiting seed set were investigated in ryegrass by comparative mapping genomics and quantitative trait loci (QTL) analysis in two perennial ryegrass (Lolium perenne) mapping families sharing common genetic markers. ,,Quantitative trait loci for seed-set were identified on chromosome (LG) 7 in both families and on LG4 of the F2/WSC family. On LG7, seed-set and heading date QTLs colocalized in both families and cannot be unequivocally resolved. Comparative genomics suggests that the LG7 region is syntenous to a region of rice LG6 which contains both fertility (S5n) and heading date (Hd1, Hd3a) candidate genes. The LG4 region is syntenous to a region of rice LG3 which contains a fertility (S33) candidate gene. QTL maxima for seed-set and heading date on LG4 in the F2/WSC family are separated by c. 8 cm, indicating distinct genetic control. ,,Low seed set is under the control of recessive genes at both LG4 and LG7 locations. ,,The identification of QTLs associated with seed set, a major component of seed yield in perennial ryegrass, indicates that mutational load associated with these genomic regions can be mitigated through marker-assisted selection. [source] Genetic control over silica deposition in wheat awnsPHYSIOLOGIA PLANTARUM, Issue 1 2010Zvi Peleg Awns are long, stiff filamentous extensions of glumes in many grasses. In wheat, awns contribute up to 40% of the grain's photosynthetic assimilates, and assist in seed dispersal. Awns accumulate silica in epidermal hairs and papillae, and silica has been positively associated with yield and environmental stress tolerance. Here, the awns of a set of domesticated wheat genotypes and their direct progenitor, Triticum turgidum ssp. dicoccoides were characterized. In addition, the silica concentration in awns was genetically dissected in a tetraploid wheat population of recombinant inbred lines (RILs) derived from a cross between durum wheat (cv. Langdon) and wild emmer (accession G18-16). Scanning electron micrographs revealed a continuous silica layer under the cuticle. Extended silicification was identified in the epidermis cell wall and in sclerenchyma cells near the vascular bundles, but not in the stomata, suggesting that an active process directs the soluble silica away from the water evaporation stream. The number of silicified cells was linearly correlated to silica concentration in dry weight (DW), suggesting cellular control over silicification. Domesticated wheat awns contained up to 19% silica per DW, as compared with 7% in the wild accessions, suggesting selection pressure associated with the domestication process. Six quantitative trait loci (QTLs) for silica were identified in the awns, with a LOD score of 3.7,6.3, three of which overlapped genomic regions that contribute to high grain protein. Localization of silica in the awns and identification of QTLs help illuminate mechanisms associated with silica metabolism in wheat. [source] Informatic and genomic analysis of melanocyte cDNA libraries as a resource for the study of melanocyte development and functionPIGMENT CELL & MELANOMA RESEARCH, Issue 3 2007Laura L. Baxter Summary As part of the RIKEN mouse encyclopedia project, two cDNA libraries were prepared from melanocyte-derived cell lines, using techniques of full-length clone selection and subtraction/normalization to enrich for rare transcripts. End sequencing showed that these libraries display over 83% complete coding sequence at the 5, end and 96,97% complete coding sequence at the 3, end. Evaluation of the libraries, derived from B16F10Y tumor cells and melan-c cells, revealed that they contain clones for a majority of the genes previously demonstrated to function in melanocyte biology. Analysis of genomic locations for transcripts revealed that the distribution of melanocyte genes is non-random throughout the genome. Three genomic regions identified that showed significant clustering of melanocyte-expressed genes contain one or more genes previously shown to regulate melanocyte development or function. A catalog of genes expressed in these libraries is presented, providing a valuable resource of cDNA clones and sequence information that can be used for identification of new genes important for melanocyte development, function, and disease. [source] Detection of loci controlling seed glucosinolate content and their association with Sclerotinia resistance in Brassica napusPLANT BREEDING, Issue 1 2003J. Zhao Abstract A genetic linkage map of Brassica napus constructed from a cross between a low glucosinolate cultivar ,H5200' and a high glucosinolate line ,NingRS-1' was used to identify loci associated with seed glucosinolate content and to understand the association between specific glucosinolate components and Sclerotinia resistance. Seed glucosinolate content was assessed by standard High pressure Liquid Chromatogram (HPLC) protocol. Seven components of seed glucosinolate, including four types of aliphatic glucosinolate, two types of indolyl glucosinolates and one aromatic glucosinolate were detected in the seeds. Three quantitative trait loci (QTLs) were identified for seed total glucosinolate content. From three to 15 loci were found to be responsible for different types of glucosinolates, and by comparing the overlapped intervals, eight genomic regions were defined. One of the nine loci associated with aliphatic glucosinolate content was found to be associated with Sclerotinia resistance on the leaf at the seedling stage, and one locus, responsible for 3-indolyl-methyl glucosinolate content, was probably linked with Sclerotinia resistance on the stem of the maturing plant. The association between seed glucosinolate content and Sclerotinia resistance is discussed. [source] Genetic dissection of cotton physiological responses to arid conditions and their inter-relationships with productivityPLANT CELL & ENVIRONMENT, Issue 3 2004Y. SARANGA ABSTRACT Testing of the extent to which different complex traits share common genetic control provides a means to distinguish associations that are truly diagnostic of genetic potential for improved adaptation to abiotic stress, from incidental phenotypic correlations. In two generations of progeny from a cross between Gossypium hirsutum and Gossypium barbadense, quantitative trait loci (QTL) mapping was used to evaluate correspondence in genetic control of selected physiological measures and productivity under water-limited and well-watered environments, respectively. A total of 33 QTLs were detected for five physiological variables [osmotic potential (OP), carbon isotope ratio (,13C; indicator of water use efficiency), canopy temperature, chlorophyll a and b], and 46 QTLs for five measures of crop productivity [dry matter, seed cotton yield (SC), harvest index, boll weight, and boll number]. QTL likelihood intervals for high SC and low OP corresponded in three genomic regions, two of which mapped to homoeologous locations on the two subgenomes of tetraploid cotton. QTLs for ,13C showed only incidental association with productivity, indicating that high water use efficiency can be associated with either high or low productivity. Different cotton species have evolved different alleles related to physiological responses and productivity under water deficit, which may permit the development of genotypes that are better-adapted to arid conditions. [source] Genome-wide analysis of DNA copy number alterations and gene expression in gastric cancer,THE JOURNAL OF PATHOLOGY, Issue 4 2008Y Tsukamoto Abstract Genomic copy number aberrations (CNAs) are believed to play a major role in the development and progression of human cancers. Although many CNAs have been reported in gastric cancer, their genome-wide transcriptional consequences are poorly understood. In this study, to reveal the impact of CNAs on genome-wide expression in gastric cancer, we analysed 30 cases of gastric cancers for their CNAs by array comparative genomic hybridization (array CGH) and 24 of these 30 cases for their expression profiles by oligonucleotide-expression microarray. We found that with the application of laser microdissection, most CNAs were detected at higher frequency than in previous studies. Notably, gain at 20q13 was detected in almost all cases (97%), suggesting that this may play an important role in the pathogenesis of gastric cancer. By comparing the array CGH data with expression profiles of the same samples, we showed that both genomic amplification and deletion strongly influence the expression of genes in altered genomic regions. Furthermore, we identified 125 candidate genes, consisting of 114 up-regulated genes located in recurrent regions (>10%) of amplification and 11 down-regulated genes located in recurrent regions of deletion. Up-regulation of several candidate genes, such as CDC6, SEC61G, ANP32E, BYSL and FDFT1, was confirmed by immunohistochemistry. Interestingly, some candidate genes were localized at genomic loci adjacent to well-known genes such as EGFR, ERBB2 and SMAD4, and concordantly deregulated by genomic alterations. Based on these results, we propose that our list of candidate genes may contain novel genes involved in the pathogenesis of advanced gastric cancer. Copyright © 2008 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd. [source] Arabidopsis proteins important for modulating defense responses to Pseudomonas syringae that secrete HopW1-1THE PLANT JOURNAL, Issue 3 2008Min Woo Lee Summary Plant infection responses result from the interaction of pathogen-derived molecules with host components. For the bacterial pathogen Pseudomonas syringae, these molecules are often effector proteins (Hops) that are injected into plant cells. P. syringae carrying hopW1-1 have restricted host range on some Arabidopsis thaliana accessions. At least two Arabidopsis genomic regions are important for the natural variation that conditions resistance to P. syringae/hopW1-1. HopW1-1 elicits a resistance response, and consequently the accumulation of the signal molecule salicylic acid (SA) and transcripts of HWI1 (HopW1-1-Induced Gene1). This work identified three HopW1-1-interacting (WIN) plant proteins: a putative acetylornithine transaminase (WIN1), a protein phosphatase (WIN2) and a firefly luciferase superfamily protein (WIN3). Importantly, WIN2 and WIN3 are partially required for HopW1-1-induced disease resistance, SA production and HWI1 expression. The requirement for WIN2 is specific for HopW1-1-induced resistance, whereas WIN3 is important for responses to several effectors. Overexpression of WIN2 or WIN3 confers resistance to virulent P. syringae, which is consistent with these proteins being defense components. Several known genes important for SA production or signaling are also partially (EDS1, NIM1/NPR1, ACD6 and ALD1) or strongly (PAD4) required for the robust resistance induced by HopW1-1, suggesting a key role for SA in the HopW1-1-induced resistance response. Finally, WIN1 is an essential protein, the overexpression of which over-rides the resistance response to HopW1-1 (and several other defense-inducing effectors), and delays SA and HWI1 induction. Thus, the WIN proteins have different roles in modulating plant defense. [source] The maize (Zea mays L.) RTCS gene encodes a LOB domain protein that is a key regulator of embryonic seminal and post-embryonic shoot-borne root initiationTHE PLANT JOURNAL, Issue 4 2007Graziana Taramino Summary Maize has a complex root system composed of different root types formed during different stages of development. The rtcs (rootless concerning crown and seminal roots) mutant is impaired in the initiation of the embryonic seminal roots and the post-embryonic shoot-borne root system. The primary root of the mutant shows a reduced gravitropic response, while its elongation, lateral root density and reaction to exogenously applied auxin is not affected. We report here the map-based cloning of the RTCS gene which encodes a 25.5 kDa LOB domain protein located on chromosome 1S. The RTCS gene has been duplicated during evolution. The RTCS-LIKE (RTCL) gene displays 72% sequence identity on the protein level. Both genes are preferentially expressed in roots. Expression of RTCS in coleoptilar nodes is confined to emerging shoot-borne root primordia. Sequence analyses of the RTCS and RTCL upstream genomic regions identified auxin response elements. Reverse transcriptase-PCR revealed that both genes are auxin induced. Microsynteny analyses between maize and rice genomes revealed co-linearity of 14 genes in the RTCS region. We conclude from our data that RTCS and RTCL are auxin-responsive genes involved in the early events that lead to the initiation and maintenance of seminal and shoot-borne root primordia formation. [source] DNA copy number alterations in prostate cancers: A combined analysis of published CGH studiesTHE PROSTATE, Issue 7 2007Jishan Sun Abstract BACKGROUND Identifying genomic regions that are commonly deleted or gained in neoplastic cells is an important approach to identify tumor suppressor genes and oncogenes. Studies in the last two decades have identified a number of common DNA copy number alterations in prostate cancer. However, because of various sample sizes, diverse tumor types and sources, as well as a variety of detection methods with various sensitivities and resolutions, it is difficult to summarize and fully interpret the overall results. METHODS We performed a combined analysis of all published comparative genomic hybridization (CGH) studies of prostate cancer and estimated the frequency of alterations across the genome for all tumors, as well as in advanced and localized tumors separately. A total of 41 studies examining 872 cancers were included in this study. RESULTS The frequency of deletions and gains were estimated in all tumors, as well as in advanced and localized tumors. Eight deleted and five gained regions were found in more than 10% of the prostate tumors. An additional six regions were commonly deleted and seven were commonly gained in advanced tumors. While 8p was the most common location of deletion, occurring in about a third of all tumors and about half of advanced tumors, 8q was the most commonly gained region, affecting about a quarter of all tumors and about half of all advanced tumors. CONCLUSIONS The large number of tumors examined in this combined analysis provides better estimates of the frequency of specific alterations in the prostate cancer cell genome, and offers important clues for prioritizing efforts to identify tumor suppressor genes and oncogenes in these altered regions. Prostate 67: 692,700, 2007. © 2007 Wiley-Liss, Inc. [source] | |||||||||||||||||||||||||||||||