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Sample records for previous genetic analysis

  1. Case-control study for colorectal cancer genetic susceptibility in EPICOLON: previously identified variants and mucins

    International Nuclear Information System (INIS)

    Abulí, Anna; Morillas, Juan D; Rigau, Joaquim; Latorre, Mercedes; Fernández-Bañares, Fernando; Peña, Elena; Riestra, Sabino; Payá, Artemio; Jover, Rodrigo; Xicola, Rosa M; Llor, Xavier; Fernández-Rozadilla, Ceres; Carvajal-Carmona, Luis; Villanueva, Cristina M; Moreno, Victor; Piqué, Josep M; Carracedo, Angel; Castells, Antoni; Andreu, Montserrat; Ruiz-Ponte, Clara; Castellví-Bel, Sergi; Alonso-Espinaco, Virginia; Muñoz, Jenifer; Gonzalo, Victoria; Bessa, Xavier; González, Dolors; Clofent, Joan; Cubiella, Joaquin

    2011-01-01

    Colorectal cancer (CRC) is the second leading cause of cancer death in developed countries. Familial aggregation in CRC is also important outside syndromic forms and, in this case, a polygenic model with several common low-penetrance alleles contributing to CRC genetic predisposition could be hypothesized. Mucins and GALNTs (N-acetylgalactosaminyltransferase) are interesting candidates for CRC genetic susceptibility and have not been previously evaluated. We present results for ten genetic variants linked to CRC risk in previous studies (previously identified category) and 18 selected variants from the mucin gene family in a case-control association study from the Spanish EPICOLON consortium. CRC cases and matched controls were from EPICOLON, a prospective, multicenter, nationwide Spanish initiative, comprised of two independent stages. Stage 1 corresponded to 515 CRC cases and 515 controls, whereas stage 2 consisted of 901 CRC cases and 909 controls. Also, an independent cohort of 549 CRC cases and 599 controls outside EPICOLON was available for additional replication. Genotyping was performed for ten previously identified SNPs in ADH1C, APC, CCDN1, IL6, IL8, IRS1, MTHFR, PPARG, VDR and ARL11, and 18 selected variants in the mucin gene family. None of the 28 SNPs analyzed in our study was found to be associated with CRC risk. Although four SNPs were significant with a P-value < 0.05 in EPICOLON stage 1 [rs698 in ADH1C (OR = 1.63, 95% CI = 1.06-2.50, P-value = 0.02, recessive), rs1800795 in IL6 (OR = 1.62, 95% CI = 1.10-2.37, P-value = 0.01, recessive), rs3803185 in ARL11 (OR = 1.58, 95% CI = 1.17-2.15, P-value = 0.007, codominant), and rs2102302 in GALNTL2 (OR = 1.20, 95% CI = 1.00-1.44, P-value = 0.04, log-additive 0, 1, 2 alleles], only rs3803185 achieved statistical significance in EPICOLON stage 2 (OR = 1.34, 95% CI = 1.06-1.69, P-value = 0.01, recessive). In the joint analysis for both stages, results were only significant for rs3803185 (OR = 1.12, 95% CI = 1

  2. Case-control study for colorectal cancer genetic susceptibility in EPICOLON: previously identified variants and mucins

    Directory of Open Access Journals (Sweden)

    Moreno Victor

    2011-08-01

    Full Text Available Abstract Background Colorectal cancer (CRC is the second leading cause of cancer death in developed countries. Familial aggregation in CRC is also important outside syndromic forms and, in this case, a polygenic model with several common low-penetrance alleles contributing to CRC genetic predisposition could be hypothesized. Mucins and GALNTs (N-acetylgalactosaminyltransferase are interesting candidates for CRC genetic susceptibility and have not been previously evaluated. We present results for ten genetic variants linked to CRC risk in previous studies (previously identified category and 18 selected variants from the mucin gene family in a case-control association study from the Spanish EPICOLON consortium. Methods CRC cases and matched controls were from EPICOLON, a prospective, multicenter, nationwide Spanish initiative, comprised of two independent stages. Stage 1 corresponded to 515 CRC cases and 515 controls, whereas stage 2 consisted of 901 CRC cases and 909 controls. Also, an independent cohort of 549 CRC cases and 599 controls outside EPICOLON was available for additional replication. Genotyping was performed for ten previously identified SNPs in ADH1C, APC, CCDN1, IL6, IL8, IRS1, MTHFR, PPARG, VDR and ARL11, and 18 selected variants in the mucin gene family. Results None of the 28 SNPs analyzed in our study was found to be associated with CRC risk. Although four SNPs were significant with a P-value ADH1C (OR = 1.63, 95% CI = 1.06-2.50, P-value = 0.02, recessive, rs1800795 in IL6 (OR = 1.62, 95% CI = 1.10-2.37, P-value = 0.01, recessive, rs3803185 in ARL11 (OR = 1.58, 95% CI = 1.17-2.15, P-value = 0.007, codominant, and rs2102302 in GALNTL2 (OR = 1.20, 95% CI = 1.00-1.44, P-value = 0.04, log-additive 0, 1, 2 alleles], only rs3803185 achieved statistical significance in EPICOLON stage 2 (OR = 1.34, 95% CI = 1.06-1.69, P-value = 0.01, recessive. In the joint analysis for both stages, results were only significant for rs3803185 (OR = 1

  3. Proteomics Analysis Reveals Previously Uncharacterized Virulence Factors in Vibrio proteolyticus

    Directory of Open Access Journals (Sweden)

    Ann Ray

    2016-07-01

    Full Text Available Members of the genus Vibrio include many pathogens of humans and marine animals that share genetic information via horizontal gene transfer. Hence, the Vibrio pan-genome carries the potential to establish new pathogenic strains by sharing virulence determinants, many of which have yet to be characterized. Here, we investigated the virulence properties of Vibrio proteolyticus, a Gram-negative marine bacterium previously identified as part of the Vibrio consortium isolated from diseased corals. We found that V. proteolyticus causes actin cytoskeleton rearrangements followed by cell lysis in HeLa cells in a contact-independent manner. In search of the responsible virulence factor involved, we determined the V. proteolyticus secretome. This proteomics approach revealed various putative virulence factors, including active type VI secretion systems and effectors with virulence toxin domains; however, these type VI secretion systems were not responsible for the observed cytotoxic effects. Further examination of the V. proteolyticus secretome led us to hypothesize and subsequently demonstrate that a secreted hemolysin, belonging to a previously uncharacterized clan of the leukocidin superfamily, was the toxin responsible for the V. proteolyticus-mediated cytotoxicity in both HeLa cells and macrophages. Clearly, there remains an armory of yet-to-be-discovered virulence factors in the Vibrio pan-genome that will undoubtedly provide a wealth of knowledge on how a pathogen can manipulate host cells.

  4. Integrated genetic analysis microsystems

    International Nuclear Information System (INIS)

    Lagally, Eric T; Mathies, Richard A

    2004-01-01

    With the completion of the Human Genome Project and the ongoing DNA sequencing of the genomes of other animals, bacteria, plants and others, a wealth of new information about the genetic composition of organisms has become available. However, as the demand for sequence information grows, so does the workload required both to generate this sequence and to use it for targeted genetic analysis. Microfabricated genetic analysis systems are well poised to assist in the collection and use of these data through increased analysis speed, lower analysis cost and higher parallelism leading to increased assay throughput. In addition, such integrated microsystems may point the way to targeted genetic experiments on single cells and in other areas that are otherwise very difficult. Concomitant with these advantages, such systems, when fully integrated, should be capable of forming portable systems for high-speed in situ analyses, enabling a new standard in disciplines such as clinical chemistry, forensics, biowarfare detection and epidemiology. This review will discuss the various technologies available for genetic analysis on the microscale, and efforts to integrate them to form fully functional robust analysis devices. (topical review)

  5. Proteomics Analysis Reveals Previously Uncharacterized Virulence Factors in Vibrio proteolyticus.

    Science.gov (United States)

    Ray, Ann; Kinch, Lisa N; de Souza Santos, Marcela; Grishin, Nick V; Orth, Kim; Salomon, Dor

    2016-07-26

    Members of the genus Vibrio include many pathogens of humans and marine animals that share genetic information via horizontal gene transfer. Hence, the Vibrio pan-genome carries the potential to establish new pathogenic strains by sharing virulence determinants, many of which have yet to be characterized. Here, we investigated the virulence properties of Vibrio proteolyticus, a Gram-negative marine bacterium previously identified as part of the Vibrio consortium isolated from diseased corals. We found that V. proteolyticus causes actin cytoskeleton rearrangements followed by cell lysis in HeLa cells in a contact-independent manner. In search of the responsible virulence factor involved, we determined the V. proteolyticus secretome. This proteomics approach revealed various putative virulence factors, including active type VI secretion systems and effectors with virulence toxin domains; however, these type VI secretion systems were not responsible for the observed cytotoxic effects. Further examination of the V. proteolyticus secretome led us to hypothesize and subsequently demonstrate that a secreted hemolysin, belonging to a previously uncharacterized clan of the leukocidin superfamily, was the toxin responsible for the V. proteolyticus-mediated cytotoxicity in both HeLa cells and macrophages. Clearly, there remains an armory of yet-to-be-discovered virulence factors in the Vibrio pan-genome that will undoubtedly provide a wealth of knowledge on how a pathogen can manipulate host cells. The pan-genome of the genus Vibrio is a potential reservoir of unidentified toxins that can provide insight into how members of this genus have successfully risen as emerging pathogens worldwide. We focused on Vibrio proteolyticus, a marine bacterium that was previously implicated in virulence toward marine animals, and characterized its interaction with eukaryotic cells. We found that this bacterium causes actin cytoskeleton rearrangements and leads to cell death. Using a

  6. Genetics: modes of reproduction and genetic analysis.

    Science.gov (United States)

    Streit, Adrian

    2017-03-01

    Classical and reverse genetics remain invaluable tools for the scientific investigation of model organisms. Genetic analysis of endoparasites is generally difficult because the sexual adults required for crossing and other manipulations are usually hidden within their host. Strongyloides spp. and Parastrongyloides spp. are notable exceptions to this and their free-living adults offer unique opportunities to manipulate these parasites experimentally. Here I review the modes of inheritance in the two generations of Strongyloides/Parastrongyloides and I discuss the opportunities and the limitations of the currently available methodology for the genetic analysis of these two genera.

  7. Genetic structure of pike (Esox lucius) reveals a complex and previously unrecognized colonization history of Ireland.

    Science.gov (United States)

    Pedreschi, Debbi; Kelly-Quinn, Mary; Caffrey, Joe; O'Grady, Martin; Mariani, Stefano; Phillimore, Albert

    2014-03-01

    We investigated genetic variation of Irish pike populations and their relationship with European outgroups, in order to elucidate the origin of this species to the island, which is largely assumed to have occurred as a human-mediated introduction over the past few hundred years. We aimed thereby to provide new insights into population structure to improve fisheries and biodiversity management in Irish freshwaters. Ireland, Britain and continental Europe. A total of 752 pike ( Esox lucius ) were sampled from 15 locations around Ireland, and 9 continental European sites, and genotyped at six polymorphic microsatellite loci. Patterns and mechanisms of population genetic structure were assessed through a diverse array of methods, including Bayesian clustering, hierarchical analysis of molecular variance, and approximate Bayesian computation. Varying levels of genetic diversity and a high degree of population genetic differentiation were detected. Clear substructure within Ireland was identified, with two main groups being evident. One of the Irish populations showed high similarity with British populations. The other, more widespread, Irish strain did not group with any European population examined. Approximate Bayesian computation suggested that this widespread Irish strain is older, and may have colonized Ireland independently of humans. Population genetic substructure in Irish pike is high and comparable to the levels observed elsewhere in Europe. A comparison of evolutionary scenarios upholds the possibility that pike may have colonized Ireland in two 'waves', the first of which, being independent of human colonization, would represent the first evidence for natural colonization of a non-anadromous freshwater fish to the island of Ireland. Although further investigations using comprehensive genomic techniques will be necessary to confirm this, the present results warrant a reappraisal of current management strategies for this species.

  8. Genetic structure of pike (Esox lucius) reveals a complex and previously unrecognized colonization history of Ireland

    Science.gov (United States)

    Pedreschi, Debbi; Kelly-Quinn, Mary; Caffrey, Joe; O’Grady, Martin; Mariani, Stefano; Phillimore, Albert

    2014-01-01

    Aim We investigated genetic variation of Irish pike populations and their relationship with European outgroups, in order to elucidate the origin of this species to the island, which is largely assumed to have occurred as a human-mediated introduction over the past few hundred years. We aimed thereby to provide new insights into population structure to improve fisheries and biodiversity management in Irish freshwaters. Location Ireland, Britain and continental Europe. Methods A total of 752 pike (Esox lucius) were sampled from 15 locations around Ireland, and 9 continental European sites, and genotyped at six polymorphic microsatellite loci. Patterns and mechanisms of population genetic structure were assessed through a diverse array of methods, including Bayesian clustering, hierarchical analysis of molecular variance, and approximate Bayesian computation. Results Varying levels of genetic diversity and a high degree of population genetic differentiation were detected. Clear substructure within Ireland was identified, with two main groups being evident. One of the Irish populations showed high similarity with British populations. The other, more widespread, Irish strain did not group with any European population examined. Approximate Bayesian computation suggested that this widespread Irish strain is older, and may have colonized Ireland independently of humans. Main conclusions Population genetic substructure in Irish pike is high and comparable to the levels observed elsewhere in Europe. A comparison of evolutionary scenarios upholds the possibility that pike may have colonized Ireland in two ‘waves’, the first of which, being independent of human colonization, would represent the first evidence for natural colonization of a non-anadromous freshwater fish to the island of Ireland. Although further investigations using comprehensive genomic techniques will be necessary to confirm this, the present results warrant a reappraisal of current management strategies

  9. gap: Genetic Analysis Package

    Directory of Open Access Journals (Sweden)

    Jing Hua Zhao

    2007-06-01

    Full Text Available A preliminary attempt at collecting tools and utilities for genetic data as an R package called gap is described. Genomewide association is then described as a specific example, linking the work of Risch and Merikangas (1996, Long and Langley (1997 for family-based and population-based studies, and the counterpart for case-cohort design established by Cai and Zeng (2004. Analysis of staged design as outlined by Skol et al. (2006 and associate methods are discussed. The package is flexible, customizable, and should prove useful to researchers especially in its application to genomewide association studies.

  10. Further analysis of previously implicated linkage regions for Alzheimer's disease in affected relative pairs

    Directory of Open Access Journals (Sweden)

    Lannfelt Lars

    2009-12-01

    Full Text Available Abstract Background Genome-wide linkage studies for Alzheimer's disease have implicated several chromosomal regions as potential loci for susceptibility genes. Methods In the present study, we have combined a selection of affected relative pairs (ARPs from the UK and the USA included in a previous linkage study by Myers et al. (Am J Med Genet, 2002, with ARPs from Sweden and Washington University. In this total sample collection of 397 ARPs, we have analyzed linkage to chromosomes 1, 9, 10, 12, 19 and 21, implicated in the previous scan. Results The analysis revealed that linkage to chromosome 19q13 close to the APOE locus increased considerably as compared to the earlier scan. However, linkage to chromosome 10q21, which provided the strongest linkage in the previous scan could not be detected. Conclusion The present investigation provides yet further evidence that 19q13 is the only chromosomal region consistently linked to Alzheimer's disease.

  11. A Genetic Epidemiological Mega Analysis of Smoking Initiation in Adolescents

    NARCIS (Netherlands)

    Maes, Hermine H; Prom-Wormley, Elizabeth; Eaves, Lindon J; Rhee, Soo Hyun; Hewitt, John K; Young, Susan; Corley, Robin; McGue, Matt; Iacono, William G; Legrand, Lisa; Samek, Diana R; Murrelle, E Lenn; Silberg, Judy L; Miles, Donna R; Schieken, Richard M; Beunen, Gaston P; Thomis, Martine; Rose, Richard J.; Dick, Danielle M.; Boomsma, Dorret I; Bartels, Meike; Vink, Jacqueline M; Lichtenstein, Paul; White, Victoria; Kaprio, Jaakko; Neale, Michael C

    2017-01-01

    Introduction: Previous studies in adolescents were not adequately powered to accurately disentangle genetic and environmental influences on smoking initiation (SI) across adolescence. Methods: Mega-analysis of pooled genetically informative data on SI was performed, with structural equation

  12. COMPUTER METHODS OF GENETIC ANALYSIS.

    Directory of Open Access Journals (Sweden)

    A. L. Osipov

    2017-02-01

    Full Text Available The basic statistical methods used in conducting the genetic analysis of human traits. We studied by segregation analysis, linkage analysis and allelic associations. Developed software for the implementation of these methods support.

  13. Sacrococcygeal pilonidal disease: analysis of previously proposed risk factors

    Directory of Open Access Journals (Sweden)

    Ali Harlak

    2010-01-01

    Full Text Available PURPOSE: Sacrococcygeal pilonidal disease is a source of one of the most common surgical problems among young adults. While male gender, obesity, occupations requiring sitting, deep natal clefts, excessive body hair, poor body hygiene and excessive sweating are described as the main risk factors for this disease, most of these need to be verified with a clinical trial. The present study aimed to evaluate the value and effect of these factors on pilonidal disease. METHOD: Previously proposed main risk factors were evaluated in a prospective case control study that included 587 patients with pilonidal disease and 2,780 healthy control patients. RESULTS: Stiffness of body hair, number of baths and time spent seated per day were the three most predictive risk factors. Adjusted odds ratios were 9.23, 6.33 and 4.03, respectively (p<0.001. With an adjusted odds ratio of 1.3 (p<.001, body mass index was another risk factor. Family history was not statistically different between the groups and there was no specific occupation associated with the disease. CONCLUSIONS: Hairy people who sit down for more than six hours a day and those who take a bath two or less times per week are at a 219-fold increased risk for sacrococcygeal pilonidal disease than those without these risk factors. For people with a great deal of hair, there is a greater need for them to clean their intergluteal sulcus. People who engage in work that requires sitting in a seat for long periods of time should choose more comfortable seats and should also try to stand whenever possible.

  14. Radionuclides in Bayer process residues: previous analysis for radiological protection

    International Nuclear Information System (INIS)

    Cuccia, Valeria; Rocha, Zildete; Oliveira, Arno H. de

    2011-01-01

    Natural occurring radionuclides are present in many natural resources. Human activities may enhance concentrations of radionuclides and/or enhance potential of exposure to naturally occurring radioactive material (NORM). The industrial residues containing radionuclides have been receiving a considerable global attention, because of the large amounts of NORM containing wastes and the potential long term risks of long-lived radionuclides. Included in this global concern, this work focuses on the characterization of radioactivity in the main residues of Bayer process for alumina production: red mud and sand samples. Usually, the residues of Bayer process are named red mud, in their totality. However, in the industry where the samples were collected, there is an additional residues separation: sand and red mud. The analytical techniques used were gamma spectrometry (HPGe detector) and neutron activation analysis. The concentrations of radionuclides are higher in the red mud than in the sand. These solid residues present activities concentrations enhanced, when compared to bauxite. Further uses for the residues as building material must be more evaluated from the radiological point of view, due to its potential of radiological exposure enhancement, specially caused by radon emission. (author)

  15. Radionuclides in Bayer process residues: previous analysis for radiological protection

    Energy Technology Data Exchange (ETDEWEB)

    Cuccia, Valeria; Rocha, Zildete, E-mail: vc@cdtn.b, E-mail: rochaz@cdtn.b [Centro de Desenvolvimento da Tecnologia Nuclear (CDTN/CNEN-MG), Belo Horizonte, MG (Brazil); Oliveira, Arno H. de, E-mail: heeren@nuclear.ufmg.b [Universidade Federal de Minas Gerais (DEN/UFMG), Belo Horizonte, MG (Brazil). Dept. de Engenharia Nuclear

    2011-07-01

    Natural occurring radionuclides are present in many natural resources. Human activities may enhance concentrations of radionuclides and/or enhance potential of exposure to naturally occurring radioactive material (NORM). The industrial residues containing radionuclides have been receiving a considerable global attention, because of the large amounts of NORM containing wastes and the potential long term risks of long-lived radionuclides. Included in this global concern, this work focuses on the characterization of radioactivity in the main residues of Bayer process for alumina production: red mud and sand samples. Usually, the residues of Bayer process are named red mud, in their totality. However, in the industry where the samples were collected, there is an additional residues separation: sand and red mud. The analytical techniques used were gamma spectrometry (HPGe detector) and neutron activation analysis. The concentrations of radionuclides are higher in the red mud than in the sand. These solid residues present activities concentrations enhanced, when compared to bauxite. Further uses for the residues as building material must be more evaluated from the radiological point of view, due to its potential of radiological exposure enhancement, specially caused by radon emission. (author)

  16. High prevalence of genetic variants previously associated with LQT syndrome in new exome data

    DEFF Research Database (Denmark)

    Refsgaard, Lena; Holst, Anders G; Sadjadieh, Golnaz

    2012-01-01

    Exome Sequencing Project (ESP) has provided important knowledge on this topic. We aimed to investigate the prevalence of previously LQTS-associated variants in ESP (5400 individuals), in order to identify possible false-positive LQTS variants. With this aim, we performed a search for previously...... published LQTS-associated variants in ESP. In addition, a PolyPhen-2 prediction was conducted, and the four most prevalent LQTS-associated variants with significant functional effects present in ESP were genotyped in a second control population. We identified 33 missense variants previously associated...... with LQTS in ESP. These 33 variants affected 173 alleles and this corresponded to a LQTS prevalence of 1:31 in the ESP population. PolyPhen-2 predicted 30% of the 33 variants present in ESP to be benign compared with 13% among LQTS-associated variants not present in ESP (P=0.019). Genotyping of the four...

  17. The pathogenicity of genetic variants previously associated with left ventricular non-compaction

    DEFF Research Database (Denmark)

    Abbasi, Yeganeh; Jabbari, Javad; Jabbari, Reza

    2016-01-01

    an updated list of previously reported LVNC-associated variants with biologic description and investigate the prevalence of LVNC variants in healthy general population to find false-positive LVNC-associated variants. METHODS AND RESULTS: The Human Gene Mutation Database and PubMed were systematically...... searched to identify all previously reported LVNC-associated variants. Thereafter, the Exome Sequencing Project (ESP) and the Exome Aggregation Consortium (ExAC), that both represent the background population, was searched for all variants. Four in silico prediction tools were assessed to determine...

  18. High prevalence of genetic variants previously associated with Brugada syndrome in new exome data

    DEFF Research Database (Denmark)

    Risgaard, B; Jabbari, R; Refsgaard, L

    2013-01-01

    to a surprisingly high genotype prevalence of 1:23 (274:6258). Genotyping the four common ESP-derived variants CACNA2D1 S709N, SCN5A F2004L, CACNB2 S143F, and CACNB2 T450I in the Danish controls, we found a genotype prevalence comparable with that found in ESP. We suggest that exome data are used in research......More than 300 variants in 12 genes have been associated with Brugada syndrome (BrS) which has a prevalence ranging between 1:2000 and 1:100,000. Until recently, there has been little knowledge regarding the distribution of genetic variations in the general population. This problem was partly solved...

  19. Drug metabolism and genetic polymorphism in subjects with previous halothane hepatitis

    DEFF Research Database (Denmark)

    Ranek, L; Dalhoff, K; Poulsen, H E

    1993-01-01

    To test the hypothesis that halothane hepatitis is caused by a combination of altered drug metabolism and an immunoallergic disposition, the metabolism of antipyrine, metronidazole, sparteine, phenytoin, and racemic R- and S-mephenytoin was investigated in seven subjects with previous halothane h...... hepatitis do not appear to be different from controls with regard to drug metabolism and HLA tissue type. The possibility of a higher frequency of complement C3 phenotype F and FS needs further investigation....... hepatitis. The HLA tissue types and the complement C3 phenotypes were also determined. The metabolism of antipyrine and metronidazole was within normal range in all subjects, and they were all fast or extensive metabolizers of sparteine, mephenytoin, and phenytoin. HLA tissue types were unremarkable. Five...... of the seven subjects had complement C3 phenotypes F or FS. In the general population phenotype S is the most common, but the difference in complement C3 phenotypes is not statistically significant (p = 0.07). We conclude, although in a limited number of patients, that subjects with previous halothane...

  20. Arthritis Genetics Analysis Aids Drug Discovery

    Science.gov (United States)

    ... NIH Research Matters January 13, 2014 Arthritis Genetics Analysis Aids Drug Discovery An international research team identified 42 new ... Edition Distracted Driving Raises Crash Risk Arthritis Genetics Analysis Aids Drug Discovery Oxytocin Affects Facial Recognition Connect with Us ...

  1. Analysis Of Navy Hornet Squadron Mishap Costs With Regard To Previously Flown Flight Hours

    Science.gov (United States)

    2017-06-01

    HORNET SQUADRON MISHAP COSTS WITH REGARD TO PREVIOUSLY FLOWN FLIGHT HOURS by Jason R. Baumann June 2017 Thesis Advisor: Robert Eger Co...TYPE AND DATES COVERED Master’s thesis 4. TITLE AND SUBTITLE ANALYSIS OF NAVY HORNET SQUADRON MISHAP COSTS WITH REGARD TO PREVIOUSLY FLOWN...flown flight hours with mishap costs . It uses a macro level approach by evaluating how a squadron’s previously flown flight hours affect mishap cost and

  2. Biosystematic studies on Dactylis L. l. Review of the previous studies. 1.2. Cytology, genetics, experimental studies, and evolution

    Directory of Open Access Journals (Sweden)

    Marta Mizianty

    2014-01-01

    Full Text Available In this paper the author presents a review of the previous studies on Dactylis L., dealing with cytology,genetics, experimental studies and evolution. Following cytotypes of Dactylis are distributed mostly in Central Europe: 16 diploids, 7 tetraploids and also 2 hexaploids in North Africa. Some aneuploids and accessory chromosomes were also found in this genus. Data dealing with karyotypes of some taxa, and geographical distribution of cytotypes are also listed. Selected problems concerning crossing within diploids as well as tetraploids and also between diploids and teraploids were presented. Some opinions regarding the evolution in the genus Dactylis were also demonstrated. In all these hypotheses the following diploids are considered to be the oldest: D. smithii Link subsp. smithii, D. g. subsp. aschersoniana (Greabn. Thell. and D. g. subsp. himalayensis Dom.

  3. An analysis of the genetic diversity and genetic structure of ...

    African Journals Online (AJOL)

    Scientific approaches to conservation of threatened species depend on a good understanding of the genetic information of wild and artificial population. The genetic diversity and structure analysis of 10 Eucommia ulmoides population was analyzed using inter-simple sequence repeat (ISSR) markers in this paper.

  4. Intelligence, previous convictions and interrogative suggestibility: a path analysis of alleged false-confession cases.

    Science.gov (United States)

    Sharrock, R; Gudjonsson, G H

    1993-05-01

    The main purpose of this study was to investigate the relationship between interrogative suggestibility and previous convictions among 108 defendants in criminal trials, using a path analysis technique. It was hypothesized that previous convictions, which may provide defendants with interrogative experiences, would correlate negatively with 'shift' as measured by the Gudjonsson Suggestibility Scale (Gudjonsson, 1984a), after intelligence and memory had been controlled for. The hypothesis was partially confirmed and the theoretical and practical implications of the findings are discussed.

  5. Attitudes towards genetic testing: analysis of contradictions

    DEFF Research Database (Denmark)

    Jallinoja, P; Hakonen, A; Aro, A R

    1998-01-01

    and on the confidence in control of the process of genetic testing and its implications. Our analysis indicated that some of the respondents have contradictory attitudes towards genetic testing. It is proposed that contradictory attitudes towards genetic testing should be given greater significance both in scientific...

  6. Microsatellite data analysis for population genetics

    Science.gov (United States)

    Theories and analytical tools of population genetics have been widely applied for addressing various questions in the fields of ecological genetics, conservation biology, and any context where the role of dispersal or gene flow is important. Underlying much of population genetics is the analysis of ...

  7. Upon Further Review: V. An Examination of Previous Lightcurve Analysis from the Palmer Divide Observatory

    Science.gov (United States)

    Warner, Brian D.

    2011-01-01

    Updated results are given for nine asteroids previously reported from the Palmer Divide Observatory (PDO). The original images were re-measured to obtain new data sets using the latest version of MPO Canopus photometry software, analysis tools, and revised techniques for linking multiple observing runs covering several days to several weeks. Results that were previously not reported or were moderately different were found for 1659 Punkajarju, 1719 Jens, 1987 Kaplan, 2105 Gudy, 2961 Katsurahama, 3285 Ruth Wolfe, 3447 Burckhalter, 7816 Hanoi, and (34817) 2000 SE116. This is one in a series of papers that will examine results obtained during the initial years of the asteroid lightcurve program at PDO.

  8. Do emotional intelligence and previous caring experience influence student nurse performance? A comparative analysis.

    Science.gov (United States)

    Stenhouse, Rosie; Snowden, Austyn; Young, Jenny; Carver, Fiona; Carver, Hannah; Brown, Norrie

    2016-08-01

    Reports of poor nursing care have focused attention on values based selection of candidates onto nursing programmes. Values based selection lacks clarity and valid measures. Previous caring experience might lead to better care. Emotional intelligence (EI) might be associated with performance, is conceptualised and measurable. To examine the impact of 1) previous caring experience, 2) emotional intelligence 3) social connection scores on performance and retention in a cohort of first year nursing and midwifery students in Scotland. A longitudinal, quasi experimental design. Adult and mental health nursing, and midwifery programmes in a Scottish University. Adult, mental health and midwifery students (n=598) completed the Trait Emotional Intelligence Questionnaire-short form and Schutte's Emotional Intelligence Scale on entry to their programmes at a Scottish University, alongside demographic and previous caring experience data. Social connection was calculated from a subset of questions identified within the TEIQue-SF in a prior factor and Rasch analysis. Student performance was calculated as the mean mark across the year. Withdrawal data were gathered. 598 students completed baseline measures. 315 students declared previous caring experience, 277 not. An independent-samples t-test identified that those without previous caring experience scored higher on performance (57.33±11.38) than those with previous caring experience (54.87±11.19), a statistically significant difference of 2.47 (95% CI, 0.54 to 4.38), t(533)=2.52, p=.012. Emotional intelligence scores were not associated with performance. Social connection scores for those withdrawing (mean rank=249) and those remaining (mean rank=304.75) were statistically significantly different, U=15,300, z=-2.61, p$_amp_$lt;0.009. Previous caring experience led to worse performance in this cohort. Emotional intelligence was not a useful indicator of performance. Lower scores on the social connection factor were associated

  9. Analysis of Product Buying Decision on Lazada E-commerce based on Previous Buyers’ Comments

    OpenAIRE

    Neil Aldrin

    2017-01-01

    The aims of the present research are: 1) to know that product buying decision possibly occurs, 2) to know how product buying decision occurs on Lazada e-commerce’s customers, 3) how previous buyers’ comments can increase product buying decision on Lazada e-commerce. This research utilizes qualitative research method. Qualitative research is a research that investigates other researches and makes assumption or discussion result so that other analysis results can be made in order to widen idea ...

  10. Genetic analysis of Schizosaccharomyces pombe

    DEFF Research Database (Denmark)

    Ekwall, Karl; Thon, Genevieve

    2017-01-01

    In this introduction we discuss some basic genetic tools and techniques that are used with the fission yeast Schizosaccharomyces pombe. Genes commonly used for selection or as reporters are discussed, with an emphasis on genes that permit counterselection, intragenic complementation, or colony......-color assays. S. pombe is most stable as a haploid organism. We describe its mating-type system, how to perform genetic crosses and methods for selecting and propagating diploids. We discuss the relative merits of tetrad dissection and random spore preparation in strain construction and genetic analyses...

  11. Genetic analysis and location of a resistance gene to Puccinia ...

    Indian Academy of Sciences (India)

    Administrator

    Electrophoresis was carried out at 1400. V for 1.0 - 1.5 h. Gel staining and visualization was done as previously described (Chen et al. 1998). Polymorphic markers were used to genotype the F2 population. Genotype data were used to construct a genetic map and locate the resistance gene. Mapping and Data analysis.

  12. Gene set analysis for interpreting genetic studies

    DEFF Research Database (Denmark)

    Pers, Tune H

    2016-01-01

    Interpretation of genome-wide association study (GWAS) results is lacking behind the discovery of new genetic associations. Consequently, there is an urgent need for data-driven methods for interpreting genetic association studies. Gene set analysis (GSA) can identify aetiologic pathways...

  13. Genetic analysis of rare disorders

    DEFF Research Database (Denmark)

    van den Berg, Stéphanie M; von Bornemann Hjelmborg, Jacob

    2012-01-01

    Twin concordance rates provide insight into the possibility of a genetic background for a disease. These concordance rates are usually estimated within a frequentistic framework. Here we take a Bayesian approach. For rare diseases, estimation methods based on asymptotic theory cannot be applied due...

  14. Budget impact analysis of empagliflozin in T2D patients with a previous cardiovascular disease

    Directory of Open Access Journals (Sweden)

    Sergio Iannazzo

    2017-06-01

    Full Text Available Budget impact analysis of empagliflozin in T2D patients with a previous cardiovascular diseaseIntroductionThe EMPA-REG OUTCOME study demonstrated that empagliflozin is effective in reducing cardiovascular morbidity and mortality in T2D patients with high risk linked to a previous cardiovascular condition. The objective of this study is the budget impact analysis of the use of empagliflozin in this population in Italy.MethodsThe analysis was conducted from the cost perspective of the Italian NHS with a 3-year time horizon. The target population, defined as T2D patients with a known cardiovascular disease, was estimated based on epidemiologic and market data. An uptake of empagliflozin growing from 10% to 30% was considered to add up or substitute combinations of metformin, insulin, glitazones and DPP-4. The uptake of 80-100% was considered to substitute sulfonylureas and repaglinide. Costs, including drugs, glycaemia monitoring, management of severe hypoglycaemia events, and cardiovascular and renal events, were estimated based on published literature and current tariffs.ResultsThe target population was estimated in 243,693 in the first year. The incremental cost for drugs (17.6 million Euro is entirely offset by the savings in glycaemia monitoring (8.1 million Euro, cardiovascular and renal events (8.8 million Euro and severe hypoglycaemic events (3.1 million Euro, with a net saving of 2.3 million Euro, approximately corresponding to -0.7% of the total expenditure. The cumulative budget impact in the 3 years was 4.9 million Euro (-0.5%.ConclusionsThe progressive adoption of empagliflozin to treat T2D patients with known cardiovascular disease in Italy, would provide significant clinical benefit without entailing additional expense for the Italian NHS.

  15. The Analysis of Polyploid Genetic Data.

    Science.gov (United States)

    Meirmans, Patrick G; Liu, Shenglin; van Tienderen, Peter H

    2018-03-16

    Though polyploidy is an important aspect of the evolutionary genetics of both plants and animals, the development of population genetic theory of polyploids has seriously lagged behind that of diploids. This is unfortunate since the analysis of polyploid genetic data-and the interpretation of the results-requires even more scrutiny than with diploid data. This is because of several polyploidy-specific complications in segregation and genotyping such as tetrasomy, double reduction, and missing dosage information. Here, we review the theoretical and statistical aspects of the population genetics of polyploids. We discuss several widely used types of inferences, including genetic diversity, Hardy-Weinberg equilibrium, population differentiation, genetic distance, and detecting population structure. For each, we point out how the statistical approach, expected result, and interpretation differ between different ploidy levels. We also discuss for each type of inference what biases may arise from the polyploid-specific complications and how these biases can be overcome. From our overview, it is clear that the statistical toolbox that is available for the analysis of genetic data is flexible and still expanding. Modern sequencing techniques will soon be able to overcome some of the current limitations to the analysis of polyploid data, though the techniques are lagging behind those available for diploids. Furthermore, the availability of more data may aggravate the biases that can arise, and increase the risk of false inferences. Therefore, simulations such as we used throughout this review are an important tool to verify the results of analyses of polyploid genetic data.

  16. Rapid Genetic Analysis in Congenital Hyperinsulinism

    DEFF Research Database (Denmark)

    Christesen, Henrik Thybo; Brusgaard, Klaus; Alm, Jan

    2007-01-01

    BACKGROUND: In severe, medically unresponsive congenital hyperinsulinism (CHI), the histological differentiation of focal versus diffuse disease is vital, since the surgical management is completely different. Genetic analysis may help in the differential diagnosis, as focal CHI is associated...

  17. Analysis of Product Buying Decision on Lazada E-commerce based on Previous Buyers’ Comments

    Directory of Open Access Journals (Sweden)

    Neil Aldrin

    2017-06-01

    Full Text Available The aims of the present research are: 1 to know that product buying decision possibly occurs, 2 to know how product buying decision occurs on Lazada e-commerce’s customers, 3 how previous buyers’ comments can increase product buying decision on Lazada e-commerce. This research utilizes qualitative research method. Qualitative research is a research that investigates other researches and makes assumption or discussion result so that other analysis results can be made in order to widen idea and opinion. Research result shows that product which has many ratings and reviews will trigger other buyers to purchase or get that product. The conclusion is that product buying decision may occur because there are some processes before making decision which are: looking for recognition and searching for problems, knowing the needs, collecting information, evaluating alternative, evaluating after buying. In those stages, buying decision on Lazada e-commerce is supported by price, promotion, service, and brand.

  18. Service for victims of crime VDS info and victims’ support: Analysis of the previous work

    Directory of Open Access Journals (Sweden)

    Ćopić Sanja M.

    2004-01-01

    Full Text Available The first victim support service in our country VDS info and victims’ support started with its work in April 2003 within the Victimology Society of Serbia. This service is aimed at victims of crime (women and men, primarily at victims of violent crime, but also of some forms of property crime (such as burglary. The aim of the Service is to offer victims of crime information on their rights and the ways of how to realize them, emotional support, as well as to refer them to other institutions/organizations depending on the certain victim’s needs. Coordinators and volunteers, who passed the appropriate training, are responsible for that. Bearing that in mind, this paper will give the brief glens on the Service itself, its organization and the way of work, followed by the analysis of the results of previous work.

  19. New population-based exome data question the pathogenicity of some genetic variants previously associated with Marfan syndrome

    DEFF Research Database (Denmark)

    Yang, Ren-Qiang; Jabbari, Javad; Cheng, Xiao-Shu

    2014-01-01

    BACKGROUND: Marfan syndrome (MFS) is a rare autosomal dominantly inherited connective tissue disorder with an estimated prevalence of 1:5,000. More than 1000 variants have been previously reported to be associated with MFS. However, the disease-causing effect of these variants may be questionable...

  20. Integrated analysis of genetic data with R

    Directory of Open Access Journals (Sweden)

    Zhao Jing

    2006-01-01

    Full Text Available Abstract Genetic data are now widely available. There is, however, an apparent lack of concerted effort to produce software systems for statistical analysis of genetic data compared with other fields of statistics. It is often a tremendous task for end-users to tailor them for particular data, especially when genetic data are analysed in conjunction with a large number of covariates. Here, R http://www.r-project.org, a free, flexible and platform-independent environment for statistical modelling and graphics is explored as an integrated system for genetic data analysis. An overview of some packages currently available for analysis of genetic data is given. This is followed by examples of package development and practical applications. With clear advantages in data management, graphics, statistical analysis, programming, internet capability and use of available codes, it is a feasible, although challenging, task to develop it into an integrated platform for genetic analysis; this will require the joint efforts of many researchers.

  1. New population-based exome data are questioning the pathogenicity of previously cardiomyopathy-associated genetic variants

    DEFF Research Database (Denmark)

    Andreasen, Charlotte Hartig; Nielsen, Jonas B; Refsgaard, Lena

    2013-01-01

    variants in the NHLBI-Go Exome Sequencing Project (ESP) containing exome data from 6500 individuals. In ESP, we identified 94 variants out of 687 (14%) variants previously associated with HCM, 58 out of 337 (17%) variants associated with DCM, and 38 variants out of 209 (18%) associated with ARVC...... with these cardiomyopathies, but the disease-causing effect of reported variants is often dubious. In order to identify possible false-positive variants, we investigated the prevalence of previously reported cardiomyopathy-associated variants in recently published exome data. We searched for reported missense and nonsense...... times higher than expected from the phenotype prevalences in the general population (HCM 1:500, DCM 1:2500, and ARVC 1:5000) and our data suggest that a high number of these variants are not monogenic causes of cardiomyopathy....

  2. Event History Analysis in Quantitative Genetics

    DEFF Research Database (Denmark)

    Maia, Rafael Pimentel

    Event history analysis is a clas of statistical methods specially designed to analyze time-to-event characteristics, e.g. the time until death. The aim of the thesis was to present adequate multivariate versions of mixed survival models that properly represent the genetic aspects related to a given...... time-to-event characteristic of interest. Real genetic longevity studies based on female animals of different species (sows, dairy cows, and sheep) exemplifies the use of the methods. Moreover these studies allow to understand som genetic mechanisms related to the lenght of the productive life...

  3. Genetic divergence analysis in pumpkin

    International Nuclear Information System (INIS)

    Quamruzzaman, A.M.; Moniruzzaman, M.

    2013-01-01

    Genetic divergence among 18 punpkin genotypes was estimated using Mahalanohis's 1) statistic. Altogether lour clusters were formed where cluster I contained the highest number of genotypes (8) and cluster II contained the lowest (I). The highest intra-cluster distance was observed h.ir cluster I (0.83 I) and the lowest for clustcr IV (0.65 I). The highest inter-cluster distance was observed between cluster I and 11(24.346). Cluster II recorded the highest mean for fruit number/plant, TSS, fruit yield and niinitnuiii III cavity length and cavity diameter. Cluster III had the second highest mean for fruit diameter, fruit number/plant, individual unit weight, fruit yield and the fewest number of days to 1st Female flowering, earliness being a desirable trait. These crosses may produce new recombinants with desirable traits. (author)

  4. Genetic Analysis of Inherited Leukodystrophies

    Science.gov (United States)

    Bras, Jose; Rohrer, Jonathan D.; Taipa, Ricardo; Lashley, Tammaryn; Dupuits, Céline; Gurunlian, Nicole; Mochel, Fanny; Warren, Jason D.; Hannequin, Didier; Sedel, Frédéric; Depienne, Christel; Camuzat, Agnès; Golfier, Véronique; Du Boisguéheneuc, Foucaud; Schottlaender, Lucia; Fox, Nick C.; Beck, Jonathan; Mead, Simon; Rossor, Martin N.; Hardy, John; Revesz, Tamas; Brice, Alexis; Houlden, Henry

    2014-01-01

    Importance The leukodystrophies comprise a clinically and genetically heterogeneous group of progressive hereditary neurological disorders mainly affecting the myelin in the central nervous system. Their onset is variable from childhood to adulthood and presentation can be with a variety of clinical features that include mainly for adult-onset cases cognitive decline, seizures, parkinsonism, muscle weakness, neuropathy, spastic paraplegia, personality/behavioral problems, and dystonia. Recently, Rademakers and colleagues identified mutations in the CSF1R gene as the cause of hereditary diffuse leukoencephalopathy with spheroids (HDLS), offering the possibility for an in-life diagnosis. The detection of mutations in this gene in cases diagnosed with different clinical entities further demonstrated the difficulties in the clinical diagnosis of HDLS. Objective To better understand the genetic role of mutations in this gene, we sequenced a large cohort of adult-onset leukodystrophy cases. Design Whole-exome sequencing and follow up-screening by Sanger sequencing. Setting Collaborative study between the Institute of Neurology, University College London and the Inserm, Paris, France. Participants A total of 114 probands, mostly European patients, with a diagnosis of adult-onset leukodystrophy or atypical cases that could fit within a picture of leukodystrophy. These included 3 extended families within the spectrum of leukodystrophy phenotype. Interventions Whole-exome sequencing in a family and Sanger sequencing of CSF1R. Main Outcomes and Measures Mutations in CSF1R. Results We identified 12 probands with mutations in CSF1R. The clinical diagnoses given to these patients included dementia with spastic paraplegia, corticobasal degeneration syndrome, and stroke disorders. Our study shows that CSF1R mutations are responsible for a significant proportion of clinically and pathologically proven HDLS. Conclusions and Relevance These results give an indication of the frequency

  5. NMR-based phytochemical analysis of Vitis vinifera cv Falanghina leaves. Characterization of a previously undescribed biflavonoid with antiproliferative activity.

    Science.gov (United States)

    Tartaglione, Luciana; Gambuti, Angelita; De Cicco, Paola; Ercolano, Giuseppe; Ianaro, Angela; Taglialatela-Scafati, Orazio; Moio, Luigi; Forino, Martino

    2018-03-01

    Vitis vinifera cv Falanghina is an ancient grape variety of Southern Italy. A thorough phytochemical analysis of the Falanghina leaves was conducted to investigate its specialised metabolite content. Along with already known molecules, such as caftaric acid, quercetin-3-O-β-d-glucopyranoside, quercetin-3-O-β-d-glucuronide, kaempferol-3-O-β-d-glucopyranoside and kaempferol-3-O-β-d-glucuronide, a previously undescribed biflavonoid was identified. For this last compound, a moderate bioactivity against metastatic melanoma cells proliferation was discovered. This datum can be of some interest to researchers studying human melanoma. The high content in antioxidant glycosylated flavonoids supports the exploitation of grape vine leaves as an inexpensive source of natural products for the food industry and for both pharmaceutical and nutraceutical companies. Additionally, this study offers important insights into the plant physiology, thus prompting possible technological researches of genetic selection based on the vine adaptation to specific pedo-climatic environments. Copyright © 2017 Elsevier B.V. All rights reserved.

  6. Genetic analysis of dermatophilus spp. using multilocus enzyme electrophoresis.

    Science.gov (United States)

    Trott, D J; Masters, A M; Carson, J M; Ellis, T M; Hampson, D J

    1995-01-01

    Multilocus enzyme electrophoresis was used to examine a collection of 41 mainly Australian isolates of Dermatophilus congolensis that had been cultured from sheep, cattle, horses, a goat, a marsupial and Chelonids. Allelic variation was examined at 16 enzyme loci. The isolates were divided into eight distinct electrophoretic types (ETs) with a mean genetic diversity per locus of 0.41. The three isolates from Chelonids represented a distinct clone in ET 1 which was separated from the remaining cluster of isolates of D. congolensis by a genetic distance of 0.852. These findings supported a previous proposal that the isolates from Chelonids represent a new species of Dermatophilus. The other 38 D. congolensis isolates were separated into two divisions (I and II) by a genetic distance of 0.560. The divisions were both subdivided into groups that either only contained alpha-hemolytic or beta-hemolytic isolates, but all isolates in each ET had only one hemolytic pattern. Isolates originating from the same animal species, or from the same geographic location, were not all closely related genetically. The allocation of isolates into ETs correlated well with their distribution into DNA restriction endonuclease analysis patterns previously established for the collection. Although relatively few distinct strains of D. congolensis were identified amongst the collection, significant genetic diversity existed within this population.

  7. An integrated system for genetic analysis

    Directory of Open Access Journals (Sweden)

    Duan Xiao

    2006-04-01

    Full Text Available Abstract Background Large-scale genetic mapping projects require data management systems that can handle complex phenotypes and detect and correct high-throughput genotyping errors, yet are easy to use. Description We have developed an Integrated Genotyping System (IGS to meet this need. IGS securely stores, edits and analyses genotype and phenotype data. It stores information about DNA samples, plates, primers, markers and genotypes generated by a genotyping laboratory. Data are structured so that statistical genetic analysis of both case-control and pedigree data is straightforward. Conclusion IGS can model complex phenotypes and contain genotypes from whole genome association studies. The database makes it possible to integrate genetic analysis with data curation. The IGS web site http://bioinformatics.well.ox.ac.uk/project-igs.shtml contains further information.

  8. Optimization of genetic analysis for single cell

    Directory of Open Access Journals (Sweden)

    hussein mouawia

    2012-03-01

    Full Text Available The molecular genetic analysis of microdissected cells by laser, a method for selecting a starting material of pure DNA or RNA uncontaminated. Our study focuses on technical pre-PCR (polymerase chain reaction for the amplification of DNA from a single cell (leukocyte isolated from human blood after laser microdissection and aims to optimize the yield of DNA extracted of this cell to be amplified without errors and provide reliable genetic analyzes. This study has allowed us to reduce the duration of cell lysis in order to perform the step of expanding genomic PEP (primer extension preamplification directly after lysis the same day and the quality of genomic amplification and eliminate purification step of the product PEP, step with a risk of contamination and risk of loss of genetic material related to manipulation. This approach has shown that the combination of at least 3 STR (short tandem repeat markers for genetic analysis of single cell improves the efficiency and accuracy of PCR and minimizes the loss of allele (allele drop out; ADO. This protocol can be applied to large scale and an effective means suitable for genetic testing for molecular diagnostic from isolated single cell (cancerous - fetal.

  9. Genetic diversity analysis of Tinospora cordifolia germplasm ...

    Indian Academy of Sciences (India)

    2012-04-03

    Apr 3, 2012 ... c Indian Academy of Sciences. RESEARCH NOTE. Genetic diversity analysis of Tinospora cordifolia germplasm collected from northwestern Himalayan region of India. VIJAY RANA1, KALPANA THAKUR1, RITU SOOD1, VARUN SHARMA1 and T. R. SHARMA2∗. 1Rice and Wheat Research Centre, Malan ...

  10. Analysis of previous perceptual and motor experience in breaststroke kick learning

    Directory of Open Access Journals (Sweden)

    Ried Bettina

    2015-12-01

    Full Text Available One of the variables that influence motor learning is the learner’s previous experience, which may provide perceptual and motor elements to be transferred to a novel motor skill. For swimming skills, several motor experiences may prove effective. Purpose. The aim was to analyse the influence of previous experience in playing in water, swimming lessons, and music or dance lessons on learning the breaststroke kick. Methods. The study involved 39 Physical Education students possessing basic swimming skills, but not the breaststroke, who performed 400 acquisition trials followed by 50 retention and 50 transfer trials, during which stroke index as well as rhythmic and spatial configuration indices were mapped, and answered a yes/no questionnaire regarding previous experience. Data were analysed by ANOVA (p = 0.05 and the effect size (Cohen’s d ≥0.8 indicating large effect size. Results. The whole sample improved their stroke index and spatial configuration index, but not their rhythmic configuration index. Although differences between groups were not significant, two types of experience showed large practical effects on learning: childhood water playing experience only showed major practically relevant positive effects, and no experience in any of the three fields hampered the learning process. Conclusions. The results point towards diverse impact of previous experience regarding rhythmic activities, swimming lessons, and especially with playing in water during childhood, on learning the breaststroke kick.

  11. Retrospective analysis on malignant calcification previously misdiagnosed as benign on screening mammography

    Energy Technology Data Exchange (ETDEWEB)

    Ha, Su Min [Dept. of Radiology, Research Institute of Radiology, Chung Ang University Hospital, Seoul(Korea, Republic of); Cha, Joo Hee; Kim, Hak Hee; Shin, Hee Jung; Chae, Eun Young; Choi, Woo Jung [Dept. of Radiology, Research Institute of Radiology, Asan Medical Center, University of Ulsan College of Medicine, Seoul (Korea, Republic of)

    2017-04-15

    The purpose of our study was to investigate the morphology and distribution of calcifications initially interpreted as benign or probably benign, but proven to be malignant by subsequent stereotactic biopsy, and to identify the reason for misinterpretation or underestimation at the initial diagnosis. Out of 567 women who underwent stereotactic biopsy for calcifications at our hospital between January 2012 and December 2014, 167 women were diagnosed with malignancy. Forty-six of these 167 women had previous mammography assessed as benign or probably benign which was changed to suspicious malignancy on follow-up mammography. Of these 46 women, three women with biopsy-proven benign calcifications at the site of subsequent cancer were excluded, and 43 patients were finally included. The calcifications (morphology, distribution, extent, associated findings) in the previous and follow-up mammography examinations were analyzed according to the Breast Imaging Reporting and Data System (BI-RADS) lexicon and assessment category. We classified the patients into two groups: 1) group A patients who were still retrospectively re-categorized as less than or equal to BI-RADS 3 and 2) group B patients who were re-categorized as equal to or higher than BI-RADS 4a and whose results should have prompted previous diagnostic assessment. In the follow-up mammography examinations, change in calcification morphology (n = 27, 63%) was the most frequent cause of assessment change. The most frequent previous mammographic findings of malignant calcification were amorphous morphology (n = 26, 60%) and grouped distribution (n = 36, 84%). The most frequent calcification findings at reassessment were amorphous morphology (n = 4, 9%), fine pleomorphic calcification (n = 30, 70%), grouped distribution (n = 23, 53%), and segmental calcification (n = 12, 28%). There were 33 (77%) patients in group A, and 10 patients (23%) in group B. Amorphous morphology and grouped distribution were the most frequent

  12. Multilocus genetic analysis of brain images

    Directory of Open Access Journals (Sweden)

    Derrek Paul Hibar

    2011-10-01

    Full Text Available The quest to identify genes that influence disease is now being extended to find genes that affect biological markers of disease, or endophenotypes. Brain images, in particular, provide exquisitely detailed measures of anatomy, function, and connectivity in the living human brain, and have identified characteristic features of psychiatric and neurological disorders. The emerging field of imaging genomics is discovering important genetic variants associated with brain structure and function, which in turn influence disease risk and fundamental cognitive processes. Statistical approaches for testing genetic associations are not straightforward to apply to brain images because brain imaging phenotypes are generally high dimensional and spatially complex. Neuroimaging phenotypes comprise three dimensional maps across many points in the brain, fiber tracts, shape-based analysis, and connectivity matrices, or networks. These complex data types require new methods for data reduction and joint consideration of the image and the genome. Image-wide, genome-wide searches are now feasible, but they can be greatly empowered by sparse regression or hierarchical clustering methods that isolate promising features, boosting statistical power. Here we review the evolution of statistical approaches to assess genetic influences on the brain. We outline the current state of multivariate statistics in imaging genomics, and future directions, including meta-analysis. We emphasize the power of novel multivariate approaches to discover reliable genetic influences with small effect sizes.

  13. Kidney transplantation after previous liver transplantation: analysis of the organ procurement transplant network database.

    Science.gov (United States)

    Gonwa, Thomas A; McBride, Maureen A; Mai, Martin L; Wadei, Hani M

    2011-07-15

    Patients after liver transplant have a high incidence of chronic kidney disease and end-stage renal disease (ESRD). We investigated kidney transplantation after liver transplantation using the Organ Procurement Transplant Network database. The Organ Procurement Transplant Network database was queried for patients who received kidney transplantation after previous liver transplantation. These patients were compared with patients who received primary kidney transplantation alone during the same time period. Between 1997 and 2008, 157,086 primary kidney transplants were performed. Of these, 680 deceased donor kidney transplants and 410 living donor kidney transplants were performed in previous recipients of liver transplants. The number of kidney after liver transplants performed each year has increased from 37 per year to 124 per year in 2008. The time from liver transplant to kidney transplant increased from 8.2 to 9.0 years for living donor transplants and from 5.4 to 9.6 years for deceased donor. The 1, 3, and 5 year actuarial graft survival in both living donor kidney after liver transplant and deceased donor kidney after liver transplant are less than the kidney transplant alone patients. However, the death-censored graft survivals are equal. The patient survival is also less but is similar to what would be expected in liver transplant recipients who did not have ESRD. In 2008, kidney after liver transplantation represented 0.9% of the total kidney alone transplants performed in the United States. Kidney transplantation is an appropriate therapy for selected patients who develop ESRD after liver transplantation.

  14. Rhabdomyosarcoma Arising in a Previously Irradiated Field: An Analysis of 43 Patients

    Energy Technology Data Exchange (ETDEWEB)

    Dang, Nguyen D. [Department of Radiation Oncology, Baylor College of Medicine, Houston, Texas (United States); Teh, Bin S. [Department of Radiation Oncology, The Methodist Hospital and Methodist Hospital Research Institute, Houston, Texas (United States); Paulino, Arnold C., E-mail: apaulino@tmhs.org [Department of Radiation Oncology, The Methodist Hospital and Methodist Hospital Research Institute, Houston, Texas (United States)

    2013-03-01

    Patients with soft tissue sarcomas that arise from previously irradiated fields have traditionally been reported to have a poor prognosis. In this report, we examined the characteristics and outcomes of patients who developed a rhabdomyosarcoma in a previously irradiated field (RMS-RIF); we hypothesize that these patients should have a better outcome compared to other postradiation soft tissue sarcomas as these tumors are chemosensitive and radiosensitive. A PubMed search of the literature from 1961-2010 yielded 33 studies with data for patients with RMS-RIF. The study included 43 patients with a median age of 6.5 years at the time of radiation therapy (RT) for the initial tumor. The median RT dose was 48 Gy. The median latency period, the time from RT to development of RMS-RIF, was 8 years. The 3-year overall survival for RMS-RIF was 42%. The 3-year overall survival was 66% for patients receiving chemotherapy and local treatment (surgery and/or RT) compared to 29% for those who had systemic treatment only or local treatment only (P=.049). Other factors associated with increased 3-year overall survival included retinoblastoma initial diagnosis (P<.001), age ≤18 years at diagnosis of RMS-RIF (P=.003), favorable site (P=.008), and stage 1 disease (P=.002). Age at time of RMS-RIF, retinoblastoma initial tumor, favorable site, stage 1 disease, and use of both systemic and local treatment were found to be favorable prognostic factors for 3-year overall survival.

  15. Transcriptional profiling of human breast cancer cells cultured under microgravity conditions revealed the key role of genetic gravity sensors previously detected in Drosophila melanogaster

    Science.gov (United States)

    Valdivia-Silva, Julio E.; Lavan, David; Diego Orihuela-Tacuri, M.; Sanabria, Gabriela

    2016-07-01

    Currently, studies in Drosophila melanogaster has shown emerging evidence that microgravity stimuli can be detected at the genetic level. Analysis of the transcriptome in the pupal stage of the fruit flies under microgravity conditions versus ground controls has suggested the presence of a few candidate genes as "gravity sensors" which are experimentally validated. Additionally, several studies have shown that microgravity causes inhibitory effects in different types of cancer cells, although the genes involved and responsible for these effects are still unknown. Here, we demonstrate that the genes suggested as the sensors of gravitational waves in Drosophila melanogaster and their human counterpart (orthologous genes) are highly involved in carcinogenesis, proliferation, anti-apoptotic signals, invasiveness, and metastatic potential of breast cancer cell tumors. The transcriptome analyses suggested that the observed inhibitory effect in cancer cells could be due to changes in the genetic expression of these candidates. These results encourage the possibility of new therapeutic targets managed together and not in isolation.

  16. Analysis on Population Level Reveals Trappability of Wild Rodents Is Determined by Previous Trap Occupant.

    Directory of Open Access Journals (Sweden)

    Marc J Brouard

    Full Text Available Live trapping is central to the study of small mammals. Thus, any bias needs to be understood and accounted for in subsequent analyses to ensure accurate population estimates. One rarely considered bias is the behavioural response of individuals to the trap, in particular the olfactory cues left behind by previous occupants (PO. We used a data set of 8,115 trap nights spanning 17 separate trapping sessions between August 2002 and November 2013 in Wytham Woods, Oxfordshire, UK to examine if the decision to enter a trap was affected by the PO, if this was detectable in traditional Capture-Mark-Recapture trapping data (i.e., individuals not uniquely marked, and if it was possible for this effect to bias the population estimates obtained. Data were collected on Apodemus sylvaticus, Myodes glareolus, and Microtus agrestis. Three Generalised Linear Models revealed a significant tendency for the three species to enter traps with same-species PO. With, for example, A. sylvaticus 9.1 times more likely to enter a same species PO trap compared to one that contained a M. agrestis in the grassland during the nocturnal period. Simulation highlighted that, when all other factors are equal, the species with the highest PO effect will have the highest capture rate and therefore return more accurate population estimates. Despite the large dataset, certain species-, sex-, and/ or age-combinations were under-represented, and thus no effects of any additional individual-specific characteristics could be evaluated. Uniquely marking individuals would allow for the PO effect to be disentangled from other biases such as trap-shyness and spatial heterogeneity, but may not be possible in all cases and will depend on the aims of the study and the resources available.

  17. Association of single nucleotide polymorphisms in candidate genes previously related to genetic variation in fertility with phenotypic measurements of reproductive function in Holstein cows.

    Science.gov (United States)

    Ortega, M Sofia; Denicol, Anna C; Cole, John B; Null, Daniel J; Taylor, Jeremy F; Schnabel, Robert D; Hansen, Peter J

    2017-05-01

    Many genetic markers related to health or production traits are not evaluated in populations independent of the discovery population or related to phenotype. Here we evaluated 68 single nucleotide polymorphisms (SNP) in candidate genes previously associated with genetic merit for fertility and production traits for association with phenotypic measurements of fertility in a population of Holstein cows that was selected based on predicted transmitting ability (PTA) for daughter pregnancy rate (DPR; high, ≥1, n = 989; low, ≤ -1.0, n = 1,285). Cows with a high PTA for DPR had higher pregnancy rate at first service, fewer services per conception, and fewer days open than cows with a low PTA for DPR. Of the 68 SNP, 11 were associated with pregnancy rate at first service, 16 with services per conception, and 19 with days open. Single nucleotide polymorphisms in 12 genes (BDH2, BSP3, CAST, CD2, CD14, FUT1, FYB, GCNT3, HSD17B7, IBSP, OCLN, and PCCB) had significant associations with 2 fertility traits, and SNP in 4 genes (CSPP1, FCER1G, PMM2, and TBC1D24) had significant associations with each of the 3 traits. Results from this experiment were compared with results from 2 earlier studies in which the SNP were associated with genetic estimates of fertility. One study involved the same animals as used here, and the other study was of an independent population of bulls. A total of 13 SNP associated with 1 or more phenotypic estimates of fertility were directionally associated with genetic estimates of fertility in the same cow population. Moreover, 14 SNP associated with reproductive phenotype were directionally associated with genetic estimates of fertility in the bull population. Nine SNP (located in BCAS, BSP3, CAST, FUT1, HSD17B7, OCLN, PCCB, PMM2, and TBC1D24) had a directional association with fertility in all 3 studies. Examination of the function of the genes with SNP associated with reproduction in more than one study indicates the importance of steroid hormones

  18. Possible Detection of Perchlorates by the Sample Analysis at Mars (SAM) Instrument: Comparison with Previous Missions

    Science.gov (United States)

    Navarro-Gonzalex, Rafael; Sutter, Brad; Archer, Doug; Ming, Doug; Eigenbrode, Jennifer; Franz, Heather; Glavin, Daniel; McAdam, Amy; Stern, Jennifer; McKay, Christopher; hide

    2013-01-01

    The first chemical analysis of soluble salts in the soil was carried out by the Phoenix Lander in the Martian Arctic [1]. Surprisingly, chlorine was present as magnesium or calcium perchlorate at 0.4 to 0.6 percent. Additional support for the identification of perchlorate came from the evolved gas analysis which detected the release of molecular oxygen at 350-550C [1]. When Mars-like soils from the Atacama Desert were spiked with magnesium perchlorate (1 percent) and heated using the Viking GC-MS protocol, nearly all the organics were combusted but a small amount was chlorinated, forming chloromethane and dichloromethane [2]. These chlorohydrocarbons were detected by the Viking GC-MS experiments when the Martian soil was analyzed but they were considered to be terrestrial contaminants [3]. Reinterpretation of the Viking results suggests detected compounds (CH3Cl and CH2Cl2) were carried from Earth [4]. Recently the Sample Analysis at Mars (SAM) instrument on board the Mars Science Laboratory (MSL) ran four samples from an aeolian bedform named Rocknest. The samples analyzed were portioned from the fifth scoop at this location. The samples were heated to 835C at 35C/min with a He flow. The SAM QMS detected a major oxygen release (300-500C) [5], coupled with the release of chlorinated hydrocarbons (chloromethane, dichloromethane, trichloromethane, and chloromethylpropene) detected both by SAM QMS and GC-MS derived from known Earth organic contaminants in the instrument [6]. Calcium perchlorate appears to be the best candidate for evolved O2 in the Rocknest samples at this time but other Cl species (e.g., chlorates) are possible and must be evaluated. The potential detection of perchlorates in Rocknest material adds weight to the argument that both Viking Landers measured signatures of perchlorates. Even if the source of the organic carbon detected is still unknown, the chlorine source was likely Martian. Two mechanisms have been hypothesized for the formation of soil

  19. Analysis of genetic polymorphism and genetic distance among four ...

    African Journals Online (AJOL)

    use

    2011-11-21

    Nov 21, 2011 ... The genomes of 4 sheep populations {Yuanqu white Tan sheep (YWT), Baozhongchang white Tan sheep. (BWT), black Tan sheep (BT) and small-tailed Han sheep (Han)} were screened using 10 microsatellite. DNA markers to estimate the genetic diversities and genetic distances among these ...

  20. Hypothesis testing in genetic linkage analysis via Gibbs sampling ( )

    African Journals Online (AJOL)

    hope&shola

    2010-12-06

    Dec 6, 2010 ... Genetic linkage analysis involves estimating parameters in a genetic model in which a genetic trait is regressed on some factors such as ... Key words: Gibbs sampling, pedigree, linkage analysis, likelihood. INTRODUCTION ..... Pattern Analysis and Machine Intelligence, 6: 721-741. Guo SW, Thompson EA ...

  1. Segmental hair analysis after a single dose of zolpidem: comparison with a previous study.

    Science.gov (United States)

    Cui, Xiaopei; Xiang, Ping; Zhang, Jingshuo; Shi, Yan; Shen, Baohua; Shen, Min

    2013-01-01

    Hair is a useful aid and sometimes even the only matrix in the analytical strategy in drug-facilitated crime (DFC) investigations. In this novel study, segmental hair analysis was performed after a single 10 mg dose of zolpidem was given to 20 Chinese volunteers. Hair was collected 1 month after administration and was analyzed using ultra-high-pressure liquid chromatography/electrospray ionization tandem mass spectrometry. Zolpidem concentrations were found to be in the range of 135.0-554.6 pg/mg in the proximal 0-2 cm segments. These results were markedly different from those reported by Villain et al., who used volunteers administered equal doses of zolpidem. The analytical method used, as well as the volunteers' hair color, inter-individual variations such as metabolic capacity, hair growth rate, drug incorporation rates, physical state of the hair, age, gender, body weight, etc. and diffusion from sweat or other secretions are all factors that should be considered when interpreting the DFC results.

  2. Proteomics analysis in frozen horse mackerel previously high-pressure processed.

    Science.gov (United States)

    Pazos, Manuel; Méndez, Lucía; Vázquez, Manuel; Aubourg, Santiago P

    2015-10-15

    The effect of high-pressure processing (HPP) (150, 300 and 450 MPa for 0, 2.5 and 5 min) on total sodium dodecyl sulphate (SDS)-soluble and sarcoplasmic proteins in frozen (-10 °C for 3 months) horse mackerel (Trachurus trachurus) was evaluated. Proteomics tools based on image analysis of SDS-PAGE protein gels and protein identification by tandem mass spectrometry (MS/MS) were applied. Although total SDS-soluble fraction indicated no important changes induced by HPP, this processing modified the 1-D SDS-PAGE sarcoplasmic patterns in a direct-dependent manner and exerted a selective effect on particular proteins depending on processing conditions. Thus, application of the highest pressure (450 MPa) provoked a significant degradation of phosphoglycerate mutase 2, glycogen phosphorylase muscle form, pyruvate kinase muscle isozyme, beta-enolase and triosephosphate isomerase and phosphoglucomutase-1. Conversely, protein bands assigned to tropomyosin alpha-1 chain, fast myotomal muscle troponin T and parvalbumin beta 2 increased their intensity after applying a 450-MPa processing. Copyright © 2015 Elsevier Ltd. All rights reserved.

  3. Fate of manuscripts previously rejected by the American Journal of Neuroradiology: a follow-up analysis.

    Science.gov (United States)

    McDonald, R J; Cloft, H J; Kallmes, D F

    2009-02-01

    This is a follow-up article to "Fate of Submitted Manuscripts Rejected from the American Journal of Neuroradiology: Outcomes and Commentary." The purpose of this study was to quantify differences in citation frequency between manuscripts published in the American Journal of Neuroradiology (AJNR) and those published after AJNR rejection and to understand citation frequency differences among rejected manuscripts. In this study, a MEDLINE search identified all manuscripts published in AJNR in 2005 and those initially rejected by AJNR in 2004 but subsequently published elsewhere. Once identified, the citation frequencies of both groups were determined by using SCOPUS. Citation data were used in comparative studies between AJNR rejected and accepted articles and in studies comparing citation frequency differences among rejected manuscripts as a function of journal and/or publication classifications. Among 315 subsequently published rejections from AJNR in 2004, 696 citations accumulated between 2005 and 2007 (2.4 citations/journal year), whereas 441 AJNR articles published in 2005 accumulated 2490 citations between 2005 and 2007 (6.4 citations/journal year, P journals classified as either neuroradiology or general radiology had significantly higher citation frequencies than other submission types and journal classifications. Nonparametric analysis of citation frequency showed significant correlations with impact factors of respective publishing journals (rho = 0.444). Results from this study suggest that publications initially rejected from AJNR have a significantly lower citation frequency than those accepted by AJNR. Among rejected manuscripts, citations frequencies were highest in technical reports and among journals close to the neuroradiologic discipline.

  4. Convergence analysis of canonical genetic algorithms.

    Science.gov (United States)

    Rudolph, G

    1994-01-01

    This paper analyzes the convergence properties of the canonical genetic algorithm (CGA) with mutation, crossover and proportional reproduction applied to static optimization problems. It is proved by means of homogeneous finite Markov chain analysis that a CGA will never converge to the global optimum regardless of the initialization, crossover, operator and objective function. But variants of CGA's that always maintain the best solution in the population, either before or after selection, are shown to converge to the global optimum due to the irreducibility property of the underlying original nonconvergent CGA. These results are discussed with respect to the schema theorem.

  5. Genetic diversity analysis of the medicinal herb Plantago ovata ...

    African Journals Online (AJOL)

    Hierarchical cluster analysis using SPSS method showed genetic variation amongst genotypes dividing them into three major clusters comprising 10, seven and one genotypes, respectively. The result of present study indicates that RAPD analysis has determined the genetic relationships and estimated the genetic diversity ...

  6. Integrated genetic and epigenetic analysis of childhood acute lymphoblastic leukemia

    Science.gov (United States)

    Figueroa, Maria E.; Chen, Shann-Ching; Andersson, Anna K.; Phillips, Letha A.; Li, Yushan; Sotzen, Jason; Kundu, Mondira; Downing, James R.; Melnick, Ari; Mullighan, Charles G.

    2013-01-01

    Acute lymphoblastic leukemia (ALL) is the commonest childhood malignancy and is characterized by recurring structural genetic alterations. Previous studies of DNA methylation suggest epigenetic alterations may also be important, but an integrated genome-wide analysis of genetic and epigenetic alterations in ALL has not been performed. We analyzed 137 B-lineage and 30 T-lineage childhood ALL cases using microarray analysis of DNA copy number alterations and gene expression, and genome-wide cytosine methylation profiling using the HpaII tiny fragment enrichment by ligation-mediated PCR (HELP) assay. We found that the different genetic subtypes of ALL are characterized by distinct DNA methylation signatures that exhibit significant correlation with gene expression profiles. We also identified an epigenetic signature common to all cases, with correlation to gene expression in 65% of these genes, suggesting that a core set of epigenetically deregulated genes is central to the initiation or maintenance of lymphoid transformation. Finally, we identified aberrant methylation in multiple genes also targeted by recurring DNA copy number alterations in ALL, suggesting that these genes are inactivated far more frequently than suggested by structural genomic analyses alone. Together, these results demonstrate subtype- and disease-specific alterations in cytosine methylation in ALL that influence transcriptional activity, and are likely to exert a key role in leukemogenesis. PMID:23921123

  7. An analysis of the genetic diversity and genetic structure of ...

    African Journals Online (AJOL)

    ajl yemi

    2011-12-26

    Dec 26, 2011 ... levels of genetic diversity (Hamrick and Godt, 1996). In addition, E. ulmoides is distributed in a wide range of climatic and geographic conditions in China during the cultivation history of more than 2,000 years (Zhang,. 1992) and rich vitality and high adaptability accumulated through the long-term history.

  8. Analysis of Over 10,000 Cases Finds No Association between Previously-Reported Candidate Polymorphisms and Ovarian Cancer Outcome

    Science.gov (United States)

    White, Kristin L.; Vierkant, Robert A.; Fogarty, Zachary C.; Charbonneau, Bridget; Block, Matthew S.; Pharoah, Paul D.P.; Chenevix-Trench, Georgia; Rossing, Mary Anne; Cramer, Daniel W.; Pearce, C. Leigh; Schildkraut, Joellen M.; Menon, Usha; Kjaer, Susanne Kruger; Levine, Douglas A.; Gronwald, Jacek; Culver, Hoda Anton; Whittemore, Alice S.; Karlan, Beth Y.; Lambrechts, Diether; Wentzensen, Nicolas; Kupryjanczyk, Jolanta; Chang-Claude, Jenny; Bandera, Elisa V.; Hogdall, Estrid; Heitz, Florian; Kaye, Stanley B.; Fasching, Peter A.; Campbell, Ian; Goodman, Marc T.; Pejovic, Tanja; Bean, Yukie; Lurie, Galina; Eccles, Diana; Hein, Alexander; Beckmann, Matthias W.; Ekici, Arif B.; Paul, James; Brown, Robert; Flanagan, James; Harter, Philipp; du Bois, Andreas; Schwaab, Ira; Hogdall, Claus K.; Lundvall, Lene; Olson, Sara H.; Orlow, Irene; Paddock, Lisa E.; Rudolph, Anja; Eilber, Ursula; Dansonka-Mieszkowska, Agnieszka; Rzepecka, Iwona K.; Ziolkowska-Seta, Izabela; Brinton, Louise; Yang, Hannah; Garcia-Closas, Montserrat; Despierre, Evelyn; Lambrechts, Sandrina; Vergote, Ignace; Walsh, Christine; Lester, Jenny; Sieh, Weiva; McGuire, Valerie; Rothstein, Joseph H.; Ziogas, Argyrios; Lubiński, Jan; Cybulski, Cezary; Menkiszak, Janusz; Jensen, Allan; Gayther, Simon A.; Ramus, Susan J.; Gentry-Maharaj, Aleksandra; Berchuck, Andrew; Wu, Anna H.; Pike, Malcolm C.; Van Den Berg, David; Terry, Kathryn L.; Vitonis, Allison F.; Doherty, Jennifer A.; Johnatty, Sharon; deFazio, Anna; Song, Honglin; Tyrer, Jonathan; Sellers, Thomas A.; Phelan, Catherine M.; Kalli, Kimberly R.; Cunningham, Julie M.; Fridley, Brooke L.; Goode, Ellen L.

    2013-01-01

    Background Ovarian cancer is a leading cause of cancer-related death among women. In an effort to understand contributors to disease outcome, we evaluated single-nucleotide polymorphisms (SNPs) previously associated with ovarian cancer recurrence or survival, specifically in angiogenesis, inflammation, mitosis, and drug disposition genes. Methods Twenty-seven SNPs in VHL, HGF, IL18, PRKACB, ABCB1, CYP2C8, ERCC2, and ERCC1 previously associated with ovarian cancer outcome were genotyped in 10,084 invasive cases from 28 studies from the Ovarian Cancer Association Consortium with over 37,000 observed person-years and 4,478 deaths. Cox proportional hazards models were used to examine the association between candidate SNPs and ovarian cancer recurrence or survival with and without adjustment for key covariates. Results We observed no association between genotype and ovarian cancer recurrence or survival for any of the SNPs examined. Conclusions These results refute prior associations between these SNPs and ovarian cancer outcome and underscore the importance of maximally powered genetic association studies. Impact These variants should not be used in prognostic models. Alternate approaches to uncovering inherited prognostic factors, if they exist, are needed. PMID:23513043

  9. Analysis of over 10,000 Cases finds no association between previously reported candidate polymorphisms and ovarian cancer outcome.

    Science.gov (United States)

    White, Kristin L; Vierkant, Robert A; Fogarty, Zachary C; Charbonneau, Bridget; Block, Matthew S; Pharoah, Paul D P; Chenevix-Trench, Georgia; Rossing, Mary Anne; Cramer, Daniel W; Pearce, Celeste Leigh; Schildkraut, Joellen M; Menon, Usha; Kjaer, Susanne Kruger; Levine, Douglas A; Gronwald, Jacek; Culver, Hoda Anton; Whittemore, Alice S; Karlan, Beth Y; Lambrechts, Diether; Wentzensen, Nicolas; Kupryjanczyk, Jolanta; Chang-Claude, Jenny; Bandera, Elisa V; Hogdall, Estrid; Heitz, Florian; Kaye, Stanley B; Fasching, Peter A; Campbell, Ian; Goodman, Marc T; Pejovic, Tanja; Bean, Yukie; Lurie, Galina; Eccles, Diana; Hein, Alexander; Beckmann, Matthias W; Ekici, Arif B; Paul, James; Brown, Robert; Flanagan, James M; Harter, Philipp; du Bois, Andreas; Schwaab, Ira; Hogdall, Claus K; Lundvall, Lene; Olson, Sara H; Orlow, Irene; Paddock, Lisa E; Rudolph, Anja; Eilber, Ursula; Dansonka-Mieszkowska, Agnieszka; Rzepecka, Iwona K; Ziolkowska-Seta, Izabela; Brinton, Louise; Yang, Hannah; Garcia-Closas, Montserrat; Despierre, Evelyn; Lambrechts, Sandrina; Vergote, Ignace; Walsh, Christine; Lester, Jenny; Sieh, Weiva; McGuire, Valerie; Rothstein, Joseph H; Ziogas, Argyrios; Lubinski, Jan; Cybulski, Cezary; Menkiszak, Janusz; Jensen, Allan; Gayther, Simon A; Ramus, Susan J; Gentry-Maharaj, Aleksandra; Berchuck, Andrew; Wu, Anna H; Pike, Malcolm C; Van Denberg, David; Terry, Kathryn L; Vitonis, Allison F; Doherty, Jennifer A; Johnatty, Sharon E; Defazio, Anna; Song, Honglin; Tyrer, Jonathan; Sellers, Thomas A; Phelan, Catherine M; Kalli, Kimberly R; Cunningham, Julie M; Fridley, Brooke L; Goode, Ellen L

    2013-05-01

    Ovarian cancer is a leading cause of cancer-related death among women. In an effort to understand contributors to disease outcome, we evaluated single-nucleotide polymorphisms (SNP) previously associated with ovarian cancer recurrence or survival, specifically in angiogenesis, inflammation, mitosis, and drug disposition genes. Twenty-seven SNPs in VHL, HGF, IL18, PRKACB, ABCB1, CYP2C8, ERCC2, and ERCC1 previously associated with ovarian cancer outcome were genotyped in 10,084 invasive cases from 28 studies from the Ovarian Cancer Association Consortium with over 37,000-observed person-years and 4,478 deaths. Cox proportional hazards models were used to examine the association between candidate SNPs and ovarian cancer recurrence or survival with and without adjustment for key covariates. We observed no association between genotype and ovarian cancer recurrence or survival for any of the SNPs examined. These results refute prior associations between these SNPs and ovarian cancer outcome and underscore the importance of maximally powered genetic association studies. These variants should not be used in prognostic models. Alternate approaches to uncovering inherited prognostic factors, if they exist, are needed.

  10. Genetic diversity of Mycobacterium tuberculosis from Pará, Brazil, reveals a higher frequency of ancestral strains than previously reported in South America.

    Science.gov (United States)

    Conceição, Emilyn Costa; Rastogi, Nalin; Couvin, David; Lopes, Maria Luíza; Furlaneto, Ismari Perini; Gomes, Harrison Magdinier; Vasconcellos, Sidra Ezídio Gonçalves; Suffys, Philip Noel; Schneider, Maria Paula Cruz; de Sousa, Maísa Silva; Sola, Christophe; de Paula Souza E Guimarães, Ricardo José; Duarte, Rafael Silva; Batista Lima, Karla Valéria

    2017-12-01

    There is only scarce information available on genotypic diversity of the Mycobacterium tuberculosis complex (MTBC) clinical isolates circulating in the Northern part of Brazil, a relatively neglected region regarding research on tuberculosis. We therefore characterized 980 MTBC clinical isolates from the state of Pará, by spoligotyping and data was compared with patterns from around the world, besides analyzing drug susceptibility, and collecting sociodemographic data. We also performed 24 loci MIRU-VNTR typing to evaluate phylogenetic inferences among the East-African-Indian (EAI) lineage strains. The Geographic Information System analyses were performed to generate a descriptive visualization of MTBC strain distribution in the region. A total of 249 different spoligopatterns primarily belonging to evolutionary recent Euro-American lineages, as well as Central-Asian, Manu and ancestral EAI lineages, were identified, in addition to strains with reportedly unknown lineage signatures. The most frequent lineages were Latin American Mediterranean, T and Haarlem. Interestingly, EAI lineage strains were found in a significantly higher proportion in comparison with previous studies from South America. Regarding EAI lineage, the absence of spacers 4-9 and 23-24 co-related to 24 loci MIRU-VNTRs may suggest a close evolutionary relationship between such strains in Pará and those prevalent in Mozambique, which might have contributed to the genetic diversity of MTBC strains in this region. Copyright © 2017. Published by Elsevier B.V.

  11. Genetic analysis of haemophilia A in Bulgaria

    Directory of Open Access Journals (Sweden)

    Kremensky Ivo

    2004-03-01

    Full Text Available Abstract Background Haemophilias are the most common hereditary severe disorders of blood clotting. In families afflicted with heamophilia, genetic analysis provides opportunities to prevent recurrence of the disease. This study establishes a diagnostical strategy for carriership determination and prenatal diagnostics of haemophilia A in Bulgarian haemophilic population. Methods A diagnostical strategy consisting of screening for most common mutations in the factor VIII gene and analysis of a panel of eight linked to the factor VIII gene locus polymorphisms was established. Results Polymorphic analysis for carrier status determination of haemophilia A was successful in 30 families out of 32 (94%. Carrier status was determined in 25 of a total of 28 women at risk (89%. Fourteen prenatal diagnoses in women at high risk of having a haemophilia A – affected child were performed, resulting in 6 healthy boys and 5 girls. Conclusion The compound approach proves to be a highly informative and cost-effective strategy for prevention of recurrence of haemophilia A in Bulgaria. DNA analysis facilitates carriership determination and subsequent prenatal diagnosis in the majority of Bulgarian families affected by haemophilia A.

  12. Genetic diversity analysis of stress tolerant rice (Oryza sativa L.)

    African Journals Online (AJOL)

    MD.Farid Islam

    2012-10-23

    Oct 23, 2012 ... can be invaluable in crop breeding. Genetic diversity analysis is used for estimating and establishing of genetic relationship in germplasm collection, identifying diverse parental combinations to create segregating progenies with maximum genetic variability for further selection and introgressing desirable ...

  13. Genetic analysis of body weight of Takifugu rubripes at different ...

    African Journals Online (AJOL)

    To elucidate the genetic mechanism of growth trait in Takifugu rubripes during ontogeny, developmental genetic analysis of body weight was conducted by mixed genetic model with additive-dominance effects, using complete diallel cross with three different strains of T. rubripes from Laizhou Shandong, Tangshan Hebei ...

  14. Genetic analysis of the wild strawberry (Fragaria vesca) volatile composition.

    Science.gov (United States)

    Urrutia, María; Rambla, José L; Alexiou, Konstantinos G; Granell, Antonio; Monfort, Amparo

    2017-12-01

    The volatile composition of wild strawberry (Fragaria vesca) fruit differs from that of the cultivated strawberry, having more intense and fruity aromas. Over the last few years, the diploid F. vesca has been recognized as a model species for genetic studies of cultivated strawberry (F. x ananassa), and here a previously developed F. vesca/F. bucharica Near Isogenic Line collection (NIL) was used to explore genetic variability of fruit quality traits. Analysis of fruit volatiles by GC-MS in our NIL collection revealed a complex and highly variable profile. One hundred compounds were unequivocally identified, including esters, aldehydes, ketones, alcohols, terpenoids, furans and lactones. Those in a subset, named key volatile compounds (KVCs), are likely contributors to the special aroma/flavour of wild strawberry. Genetic analysis revealed 50 major quantitative trait loci (QTL) including 14 QTL for KVCs, and one segregating as a dominant monogenetic trait for nerolidol. The most determinant regions affecting QTLs for KVCs, were mapped on LG5 and LG7. New candidate genes for the volatile QTL are proposed, based on differences in gene expression between NILs containing specific fragments of F. bucharica and the F. vesca recurrent genome. A high percentage of these candidate genes/alleles were colocalized within the boundaries of introgressed regions that contain QTLs, appearing to affect volatile metabolite accumulation acting in cis. A NIL collection is a good tool for the genetic dissection of volatile accumulation in wild strawberry fruit and a source of information for genes and alleles which may enhance aroma in cultivated strawberry. Copyright © 2017 The Authors. Published by Elsevier Masson SAS.. All rights reserved.

  15. A Multivariate Genetic Analysis of Sensation Seeking

    NARCIS (Netherlands)

    Koopmans, J.R.; Boomsma, D.I.; Heath, A.C.; van Doornen, L.J.P.

    1995-01-01

    The genetic architecture of sensation seeking was analyzed in 1591 adolescent twin pairs. Individual differences in sensation seeking were best explained by a simple additive genetic model. Between 48 and 63% of the total variance in sensation seeking subscales was attributable to genetic factors.

  16. A new eigenfunction spatial analysis describing population genetic structure.

    Science.gov (United States)

    Diniz-Filho, José Alexandre Felizola; Diniz, João Vitor Barnez P L; Rangel, Thiago Fernando; Soares, Thannya Nascimento; Telles, Mariana Pires de Campos; Collevatti, Rosane Garcia; Bini, Luis Mauricio

    2013-12-01

    Several methods of spatial analyses have been proposed to infer the relative importance of evolutionary processes on genetic population structure. Here we show how a new eigenfunction spatial analysis can be used to model spatial patterns in genetic data. Considering a sample of n local populations, the method starts by modeling the response variable (allele frequencies or phenotypic variation) against the eigenvectors sequentially extracted from a geographic distance matrix (n × n). The relationship between the coefficient of determination (R(2)) of the models and the cumulative eigenvalues, which we named the spatial signal-representation (SSR) curve, can be more efficient than Moran's I correlograms in describing different patterns. The SSR curve was also applied to simulated data (under distinct scenarios of population differentiation) and to analyze spatial patterns in alleles from microsatellite data for 25 local populations of Dipteryx alata, a tree species endemic to the Brazilian Cerrado. The SSR curves are consistent with previous phylogeographical patterns of the species, revealing combined effects of isolation-by-distance and range expansion. Our analyses demonstrate that the SSR curve is a useful exploratory tool for describing spatial patterns of genetic variability and for selecting spatial eigenvectors for models aiming to explain spatial responses to environmental variables and landscape features.

  17. Quantitative genetic analysis of total glucosinolate, oil and protein ...

    African Journals Online (AJOL)

    Quantitative genetic analysis of total glucosinolate, oil and protein contents in Ethiopian mustard ( Brassica carinata A. Braun) ... Seeds were analyzed using HPLC (glucosinolates), NMR (oil) and NIRS (protein). Analyses of variance, Hayman's method of diallel analysis and a mixed linear model of genetic analysis were ...

  18. Improved Runtime Analysis of the Simple Genetic Algorithm

    DEFF Research Database (Denmark)

    Oliveto, Pietro S.; Witt, Carsten

    2013-01-01

    A runtime analysis of the Simple Genetic Algorithm (SGA) for the OneMax problem has recently been presented proving that the algorithm requires exponential time with overwhelming probability. This paper presents an improved analysis which overcomes some limitations of our previous one. Firstly......, the new result holds for population sizes up to mu = n1/4-epsilon which is an improvement up to a power of 2 larger. Secondly, we present a technique to bound the diversity of the population that does not require a bound on its bandwidth. Apart from allowing a stronger result, we believe this is a major...... improvement towards the reusability of the techniques in future systematic analyses of GAs. Finally, we consider the more natural SGA using selection with replacement rather than without replacement although the results hold for both algorithmic versions. Experiments are presented to explore the limits...

  19. The suitability of XRF analysis for compositional classification of archaeological ceramic fabric: A comparison with a previous NAA study

    Energy Technology Data Exchange (ETDEWEB)

    Padilla, R. [Centro de Aplicaciones Tecnologicas y Desarrollo Nuclear (CEADEN), Laboratorio de Analisis Quimico, Calle 30 no. 502, Playa, Ciudad Habana (Cuba)]. E-mail: roman.padilla@infomed.sld.cu; Espen, P. van [University of Antwerp (Belgium); Torres, P.P. Godo [Centro de Antropologia, Havana (Cuba)

    2006-02-03

    The main drawbacks of EDXRF techniques, restricting its more frequent use for the specific purpose of compositional analysis of archaeological ceramic fabric, have been the insufficient sensitivity to determine some important elements (like Cr, REE, among others), a somewhat worse precision and the inability to perform standard-less quantitative procedures in the absence of suitable certified reference materials (CRM) for ceramic fabric. This paper presents the advantages of combining two energy dispersive X-ray fluorescence methods for fast and non-destructive analysis of ceramic fabric with increased sensitivity. Selective polarized excitation using secondary targets (EDPXRF) and radioisotope excitation (R-XRF) using a {sup 241}Am source. The analytical performance of the methods was evaluated by analyzing several CRM of sediment type, and the fitness for the purpose of compositional classification was compared with that obtained by using Instrumental Neutron Activation Analysis in a previous study of Cuban aborigine pottery.

  20. GENETIC ANALYSIS OF ABSCISIC ACID BIOSYNTHESIS

    Energy Technology Data Exchange (ETDEWEB)

    MCCARTY D R

    2012-01-10

    The carotenoid cleavage dioxygenases (CCD) catalyze synthesis of a variety of apo-carotenoid secondary metabolites in plants, animals and bacteria. In plants, the reaction catalyzed by the 11, 12, 9-cis-epoxy carotenoid dioxygenase (NCED) is the first committed and key regulated step in synthesis of the plant hormone, abscisic acid (ABA). ABA is a key regulator of plant stress responses and has critical functions in normal root and seed development. The molecular mechanisms responsible for developmental control of ABA synthesis in plant tissues are poorly understood. Five of the nine CCD genes present in the Arabidopsis genome encode NCED's involved in control of ABA synthesis in the plant. This project is focused on functional analysis of these five AtNCED genes as a key to understanding developmental regulation of ABA synthesis and dissecting the role of ABA in plant development. For this purpose, the project developed a comprehensive set of gene knockouts in the AtNCED genes that facilitate genetic dissection of ABA synthesis. These mutants were used in combination with key molecular tools to address the following specific objectives: (1) the role of ABA synthesis in root development; (2) developmental control of ABA synthesis in seeds; (3) analysis of ATNCED over-expressers; (4) preliminary crystallography of the maize VP14 protein.

  1. Examining rare and low-frequency genetic variants previously associated with lone or familial forms of atrial fibrillation in an electronic medical record system

    DEFF Research Database (Denmark)

    Weeke, Peter; Denny, Joshua C; Basterache, Lisa

    2015-01-01

    of European or African ancestry with electronic medical records and exome chip data to compare the frequency of AF among carriers and noncarriers of these rare variants. METHODS AND RESULTS: The exome chip included 19 of 115 rare variants, in 9 genes, previously associated with lone or familial AF. Using......BACKGROUND: Studies in individuals or small kindreds have implicated rare variants in 25 different genes in lone and familial atrial fibrillation (AF) using linkage and segregation analysis, functional characterization, and rarity in public databases. Here, we used a cohort of 20 204 patients...... validated algorithms querying a combination of clinical notes, structured billing codes, ECG reports, and procedure codes, we identified 1056 AF cases (>18 years) and 19 148 non-AF controls (>50 years) with available genotype data on the Illumina HumanExome BeadChip v.1.0 in the Vanderbilt electronic...

  2. Molecular analysis of clinical isolates previously diagnosed as Mycobacterium intracellulare reveals incidental findings of "Mycobacterium indicus pranii" genotypes in human lung infection.

    Science.gov (United States)

    Kim, Su-Young; Park, Hye Yun; Jeong, Byeong-Ho; Jeon, Kyeongman; Huh, Hee Jae; Ki, Chang-Seok; Lee, Nam Yong; Han, Seung-Jung; Shin, Sung Jae; Koh, Won-Jung

    2015-09-30

    Mycobacterium intracellulare is a major cause of Mycobacterium avium complex lung disease in many countries. Molecular studies have revealed several new Mycobacteria species that are closely related to M. intracellulare. The aim of this study was to re-identify and characterize clinical isolates from patients previously diagnosed with M. intracellulare lung disease at the molecular level. Mycobacterial isolates from 77 patients, initially diagnosed with M. intracellulare lung disease were re-analyzed by multi-locus sequencing and pattern of insertion sequences. Among the 77 isolates, 74 (96 %) isolates were designated as M. intracellulare based on multigene sequence-based analysis. Interestingly, the three remaining strains (4 %) were re-identified as "Mycobacterium indicus pranii" according to distinct molecular phylogenetic positions in rpoB and hsp65 sequence-based typing. In hsp65 sequevar analysis, code 13 was found in the majority of cases and three unreported codes were identified. In 16S-23S rRNA internal transcribed spacer (ITS) sequevar analysis, all isolates of both species were classified within the Min-A ITS sequevar. Interestingly, four of the M. intracellulare isolates harbored IS1311, a M. avium-specific element. Two of three patients infected with "M. indicus pranii" had persistent positive sputum cultures after antibiotic therapy, indicating the clinical relevance of this study. This analysis highlights the importance of precise identification of clinical isolates genetically close to Mycobacterium species, and suggests that greater attention should be paid to nontuberculous mycobacteria lung disease caused by "M. indicus pranii".

  3. Longitudinal Genetic Analysis of Anxiety Sensitivity

    Science.gov (United States)

    Zavos, Helena M. S.; Gregory, Alice M.; Eley, Thalia C.

    2012-01-01

    Anxiety sensitivity is associated with both anxiety and depression and has been shown to be heritable. Little, however, is known about the role of genetic influence on continuity and change of symptoms over time. The authors' aim was to examine the stability of anxiety sensitivity during adolescence. By using a genetically sensitive design, the…

  4. Developments in statistical analysis in quantitative genetics

    DEFF Research Database (Denmark)

    Sorensen, Daniel

    2009-01-01

    A remarkable research impetus has taken place in statistical genetics since the last World Conference. This has been stimulated by breakthroughs in molecular genetics, automated data-recording devices and computer-intensive statistical methods. The latter were revolutionized by the bootstrap and ...

  5. Genetic Analysis of Termite Colonies in Wisconsin

    Science.gov (United States)

    R.A. Arango; D.A. Marschalek; F. Green III; K.F. Raffa; M.E. Berres

    2015-01-01

    The objective of this study was to document current areas of subterranean termite activity in Wisconsin and to evaluate genetic characteristics of these northern, peripheral colonies. Here, amplified fragment-length polymorphism was used to characterize levels of inbreeding, expected heterozygosity, and percent polymorphism within colonies as well as genetic structure...

  6. Genetic analysis of radiation-induced mouse thymic lymphomas

    International Nuclear Information System (INIS)

    Kominami, R.; Wakabayashi, Y.; Niwa, O.

    2003-01-01

    Mouse thymic lymphomas are one of the classic models of radiation-induced malignancies, and the model has been used for the study of genes involved in carcinogenesis. ras oncogenes are the first isolate which undergoes mutations in 10 to 30 % of lymphomas, and p16INK4a and p19ARF in the INK4a-ARF locus are also frequently inactivated. In our previous study, the inactivation of Ikaros, a key regurator of lymphoid system, was found in those lymphomas, and it was suggested that there are other responsible genes yet to be discovered. On the other hand, genetic predisposition to radiation-induced lymphoma often differs in different strains, and this reflects the presence of low penetrance genes that can modify the impact of a given mutation. Little study of such modifiers or susceptibility genes has been performed, either. Recent availability of databases on mouse genome information and the power of mouse genetic system underline usefulness of the lymphoma model in search for novel genes involved, which may provide clues to molecular mechanisms of development of the radiogenic lymphoma and also genes involved in human lymphomas and other malignancies. Accordingly, we have carried out positional cloning for the two different types of tumor-related genes. In this symposium, our current progress is presented that includes genetic mapping of susceptibility/ resistance loci on mouse chromosomes 4, 5 and 19, and also functional analysis of a novel tumor suppressor gene, Rit1/Bcl11b, that has been isolated from allelic loss (LOH) mapping and sequence analysis for γ -ray induced mouse thymic lymphomas

  7. At what price? A cost-effectiveness analysis comparing trial of labour after previous caesarean versus elective repeat caesarean delivery.

    Directory of Open Access Journals (Sweden)

    Christopher G Fawsitt

    Full Text Available BACKGROUND: Elective repeat caesarean delivery (ERCD rates have been increasing worldwide, thus prompting obstetric discourse on the risks and benefits for the mother and infant. Yet, these increasing rates also have major economic implications for the health care system. Given the dearth of information on the cost-effectiveness related to mode of delivery, the aim of this paper was to perform an economic evaluation on the costs and short-term maternal health consequences associated with a trial of labour after one previous caesarean delivery compared with ERCD for low risk women in Ireland. METHODS: Using a decision analytic model, a cost-effectiveness analysis (CEA was performed where the measure of health gain was quality-adjusted life years (QALYs over a six-week time horizon. A review of international literature was conducted to derive representative estimates of adverse maternal health outcomes following a trial of labour after caesarean (TOLAC and ERCD. Delivery/procedure costs derived from primary data collection and combined both "bottom-up" and "top-down" costing estimations. RESULTS: Maternal morbidities emerged in twice as many cases in the TOLAC group than the ERCD group. However, a TOLAC was found to be the most-effective method of delivery because it was substantially less expensive than ERCD (€ 1,835.06 versus € 4,039.87 per women, respectively, and QALYs were modestly higher (0.84 versus 0.70. Our findings were supported by probabilistic sensitivity analysis. CONCLUSIONS: Clinicians need to be well informed of the benefits and risks of TOLAC among low risk women. Ideally, clinician-patient discourse would address differences in length of hospital stay and postpartum recovery time. While it is premature advocate a policy of TOLAC across maternity units, the results of the study prompt further analysis and repeat iterations, encouraging future studies to synthesis previous research and new and relevant evidence under a single

  8. RESEARCH NOTE Molecular genetic analysis of consanguineous ...

    Indian Academy of Sciences (India)

    Navya

    Department of Biotechnology & Genetic Engineering, Kohat University of. Science & Technology, Kohat, Khyber Pakhtunkhwa, Pakistan. 7. Diagnostic Genomic Division, Department of Laboratory Medicine & Pathology,. Hamad Medical Corporation, Doha, 3050, Qatar. * These authors have equally contributed in this work.

  9. Genetic analysis of arsenic accumulation in maize using QTL mapping

    Science.gov (United States)

    Fu, Zhongjun; Li, Weihua; Xing, Xiaolong; Xu, Mengmeng; Liu, Xiaoyang; Li, Haochuan; Xue, Yadong; Liu, Zonghua; Tang, Jihua

    2016-02-01

    Arsenic (As) is a toxic heavy metal that can accumulate in crops and poses a threat to human health. The genetic mechanism of As accumulation is unclear. Herein, we used quantitative trait locus (QTL) mapping to unravel the genetic basis of As accumulation in a maize recombinant inbred line population derived from the Chinese crossbred variety Yuyu22. The kernels had the lowest As content among the different maize tissues, followed by the axes, stems, bracts and leaves. Fourteen QTLs were identified at each location. Some of these QTLs were identified in different environments and were also detected by joint analysis. Compared with the B73 RefGen v2 reference genome, the distributions and effects of some QTLs were closely linked to those of QTLs detected in a previous study; the QTLs were likely in strong linkage disequilibrium. Our findings could be used to help maintain maize production to satisfy the demand for edible corn and to decrease the As content in As-contaminated soil through the selection and breeding of As pollution-safe cultivars.

  10. Large-scale association analysis provides insights into the genetic architecture and pathophysiology of type 2 diabetes

    NARCIS (Netherlands)

    Morris, Andrew P.; Voight, Benjamin F.; Teslovich, Tanya M.; Ferreira, Teresa; Segrè, Ayellet V.; Steinthorsdottir, Valgerdur; Strawbridge, Rona J.; Khan, Hassan; Grallert, Harald; Mahajan, Anubha; Prokopenko, Inga; Kang, Hyun Min; Dina, Christian; Esko, Tonu; Fraser, Ross M.; Kanoni, Stavroula; Kumar, Ashish; Lagou, Vasiliki; Langenberg, Claudia; Luan, Jian'an; Lindgren, Cecilia M.; Müller-Nurasyid, Martina; Pechlivanis, Sonali; Rayner, N. William; Scott, Laura J.; Wiltshire, Steven; Yengo, Loic; Kinnunen, Leena; Rossin, Elizabeth J.; Raychaudhuri, Soumya; Johnson, Andrew D.; Dimas, Antigone S.; Loos, Ruth J. F.; Vedantam, Sailaja; Chen, Han; Florez, Jose C.; Fox, Caroline; Liu, Ching-Ti; Rybin, Denis; Couper, David J.; Kao, Wen Hong L.; Li, Man; Cornelis, Marilyn C.; Kraft, Peter; Sun, Qi; van Dam, Rob M.; Stringham, Heather M.; Chines, Peter S.; Fischer, Krista; Fontanillas, Pierre; Holmen, Oddgeir L.; Hunt, Sarah E.; Jackson, Anne U.; Kong, Augustine; Lawrence, Robert; Meyer, Julia; Perry, John R. B.; Platou, Carl G. P.; Potter, Simon; Rehnberg, Emil; Robertson, Neil; Sivapalaratnam, Suthesh; Stančáková, Alena; Stirrups, Kathleen; Thorleifsson, Gudmar; Tikkanen, Emmi; Wood, Andrew R.; Almgren, Peter; Atalay, Mustafa; Benediktsson, Rafn; Bonnycastle, Lori L.; Burtt, Noël; Carey, Jason; Charpentier, Guillaume; Crenshaw, Andrew T.; Doney, Alex S. F.; Dorkhan, Mozhgan; Edkins, Sarah; Emilsson, Valur; Eury, Elodie; Forsen, Tom; Gertow, Karl; Gigante, Bruna; Grant, George B.; Groves, Christopher J.; Guiducci, Candace; Herder, Christian; Hreidarsson, Astradur B.; Hui, Jennie; James, Alan; Jonsson, Anna; Rathmann, Wolfgang; Klopp, Norman; Kravic, Jasmina; Krjutškov, Kaarel; Langford, Cordelia; Leander, Karin; Lindholm, Eero; Lobbens, Stéphane; Männistö, Satu; Mirza, Ghazala; Mühleisen, Thomas W.; Musk, Bill; Parkin, Melissa; Rallidis, Loukianos; Saramies, Jouko; Sennblad, Bengt; Shah, Sonia; Sigurðsson, Gunnar; Silveira, Angela; Steinbach, Gerald; Thorand, Barbara; Trakalo, Joseph; Veglia, Fabrizio; Wennauer, Roman; Winckler, Wendy; Zabaneh, Delilah; Campbell, Harry; van Duijn, Cornelia; Uitterlinden, Andre G.; Hofman, Albert; Sijbrands, Eric; Abecasis, Goncalo R.; Owen, Katharine R.; Zeggini, Eleftheria; Trip, Mieke D.; Forouhi, Nita G.; Syvänen, Ann-Christine; Eriksson, Johan G.; Peltonen, Leena; Nöthen, Markus M.; Balkau, Beverley; Palmer, Colin N. A.; Lyssenko, Valeriya; Tuomi, Tiinamaija; Isomaa, Bo; Hunter, David J.; Qi, Lu; Shuldiner, Alan R.; Roden, Michael; Barroso, Ines; Wilsgaard, Tom; Beilby, John; Hovingh, Kees; Price, Jackie F.; Wilson, James F.; Rauramaa, Rainer; Lakka, Timo A.; Lind, Lars; Dedoussis, George; Njølstad, Inger; Pedersen, Nancy L.; Khaw, Kay-Tee; Wareham, Nicholas J.; Keinanen-Kiukaanniemi, Sirkka M.; Saaristo, Timo E.; Korpi-Hyövälti, Eeva; Saltevo, Juha; Laakso, Markku; Kuusisto, Johanna; Metspalu, Andres; Collins, Francis S.; Mohlke, Karen L.; Bergman, Richard N.; Tuomilehto, Jaakko; Boehm, Bernhard O.; Gieger, Christian; Hveem, Kristian; Cauchi, Stephane; Froguel, Philippe; Baldassarre, Damiano; Tremoli, Elena; Humphries, Steve E.; Saleheen, Danish; Danesh, John; Ingelsson, Erik; Ripatti, Samuli; Salomaa, Veikko; Erbel, Raimund; Jöckel, Karl-Heinz; Moebus, Susanne; Peters, Annette; Illig, Thomas; de Faire, Ulf; Hamsten, Anders; Morris, Andrew D.; Donnelly, Peter J.; Frayling, Timothy M.; Hattersley, Andrew T.; Boerwinkle, Eric; Melander, Olle; Kathiresan, Sekar; Nilsson, Peter M.; Deloukas, Panos; Thorsteinsdottir, Unnur; Groop, Leif C.; Stefansson, Kari; Hu, Frank; Pankow, James S.; Dupuis, Josée; Meigs, James B.; Altshuler, David; Boehnke, Michael; McCarthy, Mark I.

    2012-01-01

    To extend understanding of the genetic architecture and molecular basis of type 2 diabetes (T2D), we conducted a meta-analysis of genetic variants on the Metabochip, including 34,840 cases and 114,981 controls, overwhelmingly of European descent. We identified ten previously unreported T2D

  11. Molecular genetic analysis of Down syndrome.

    Science.gov (United States)

    Patterson, David

    2009-07-01

    Down syndrome (DS) is caused by trisomy of all or part of human chromosome 21 (HSA21) and is the most common genetic cause of significant intellectual disability. In addition to intellectual disability, many other health problems, such as congenital heart disease, Alzheimer's disease, leukemia, hypotonia, motor disorders, and various physical anomalies occur at an elevated frequency in people with DS. On the other hand, people with DS seem to be at a decreased risk of certain cancers and perhaps of atherosclerosis. There is wide variability in the phenotypes associated with DS. Although ultimately the phenotypes of DS must be due to trisomy of HSA21, the genetic mechanisms by which the phenotypes arise are not understood. The recent recognition that there are many genetically active elements that do not encode proteins makes the situation more complex. Additional complexity may exist due to possible epigenetic changes that may act differently in DS. Numerous mouse models with features reminiscent of those seen in individuals with DS have been produced and studied in some depth, and these have added considerable insight into possible genetic mechanisms behind some of the phenotypes. These mouse models allow experimental approaches, including attempts at therapy, that are not possible in humans. Progress in understanding the genetic mechanisms by which trisomy of HSA21 leads to DS is the subject of this review.

  12. Genetic analysis of amino acid content in wheat grain

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Genetics; Volume 93; Issue 2. Genetic analysis of amino acid content ... Shandong Agricultural University, No. 61 Daizong Road, Tai'an 271018, People's Republic of China; College of Food Science and Engineering, Shandong Agricultural University, Tai'an 271018, People's Republic of China ...

  13. Analysis of genetic diversity and estimation of inbreeding coefficient ...

    African Journals Online (AJOL)

    Analysis of genetic diversity and estimation of inbreeding coefficient within Caspian horse population using microsatellite markers. ... structure and to the assessment of genetic diversity that may be helpful to horse breeders in designing and managing breeding or conservation strategies for the Caspian horse breed.

  14. Analysis of genetic structure in Melia volkensii (Gurke.) populations ...

    African Journals Online (AJOL)

    Administrator

    2Farm Forestry Programme, Kenya Forestry Research Institute, P. O. Box 20412, Nairobi, Kenya. Accepted 5 ... were used to estimate genetic distances between populations and for construction of neighbour-joining phenograms. Analysis of Molecular Variance (AMOVA) indicated significant genetic differentiation between ...

  15. Molecular genetic analysis of grain protein content and flour ...

    Indian Academy of Sciences (India)

    is the most important trait for the nutritional value of grain and for the factors that influences the technological ... genotype–environment interaction. In a particular genetic background, quantitative trait locus ..... Triboï E. 2005 Genetic analysis of dry matter and nitrogen accu- mulation and protein composition in wheat kernels.

  16. Genetic analysis of 55 northern Vietnamese patients with Wilson ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Genetics; Volume 96; Issue 6. Genetic analysis of 55 northern Vietnamese patients with Wilson disease: seven novel mutations in ATP7B. LE ANH TUAN PHAM TRONG TUE NGUYEN HOANG BICH NGA LE DAT QUOC TRAN CAM TU HO THINH HUY TRAN VAN THANH TA THE HUNG BUI ...

  17. Molecular genetic analysis of grain protein content and flour ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Genetics; Volume 95; Issue 2. Molecular genetic analysis of grain protein content and flour whiteness degree using RILs in common wheat. XIANYIN SUN KE WU YAN ZHAO ZHAOGUO QIAN FANMEI KONG YING GUO YINGYING WANG SISHEN LI. RESEARCH ARTICLE Volume 95 Issue 2 ...

  18. Inter simple sequence repeat analysis of genetic diversity of five ...

    African Journals Online (AJOL)

    This paper studied the genetic diversity of five cultivated pepper species using inter simple sequence repeat (ISSR) analysis. The amplicons of 13 out of 15 designed primers were stable polymorphic and therefore were used as genetic biomarkers. 135 total clear bands were obtained, of which 102 were polymorphic bands ...

  19. VSX1 gene and keratoconus: genetic analysis in Korean patients.

    Science.gov (United States)

    Jeoung, Jin Wook; Kim, Mee Kum; Park, Sung Sup; Kim, Sung Yeun; Ko, Hyun Soo; Wee, Won Ryang; Lee, Jin Hak

    2012-07-01

    The visual system homeobox 1 (VSX1) gene variants have recently been shown to be associated with keratoconus. To replicate this finding, we performed a genetic analysis of the VSX1 gene in a Korean case-control sample. Patients with keratoconus and healthy control subjects were recruited from Seoul National University Hospital. A diagnosis of keratoconus was made based on clinical examinations and the presence of characteristic topographic features. For all patients and controls, the whole coding region and the exon-intron junctions of the VSX1 gene were analyzed by direct sequencing. Fifty-three patients with keratoconus and 100 healthy volunteers were included. We observed 2 novel missense substitutions (Leu17Val and Val199Leu) and 1 previously reported substitution (Gly160Val) in 6 of the 53 affected probands. Because these substitutions have been identified in unaffected individuals, they were not considered to be pathogenic. No intragenic polymorphism was associated with a significantly increased risk of keratoconus. We cannot confirm the previously reported association of the VSX1 gene variants with keratoconus. Our results suggest that the VSX1 gene and its mutations with amino acid changes do not play a major role in the pathogenesis of keratoconus.

  20. Genetic analysis of IgE expression

    Czech Academy of Sciences Publication Activity Database

    Kosařová, Marcela; Blažková, Hana; Havelková, Helena; Král, V.; Lipoldová, Marie

    Vol.57, Suppl.57 (2002), s. 140-140 ISSN 0108-1675. [The XXI Congress of the European Academy of Allergology and Clinical Immunology EAACI /2002./. 01.06.2002-05.06.2002, Itálie] R&D Projects: GA ČR GP310/02/P141 Keywords : IgE * Alergy * Genetipization Subject RIV: EB - Genetics ; Molecular Biology

  1. RESEARCH NOTE Molecular genetic analysis of consanguineous ...

    Indian Academy of Sciences (India)

    Navya

    proteins are involved in cell cycle and its regulation. Herein the present clinical genetic study, we present two consanguineous Pakistani families segregating primary microcephaly and intellectual disability. These families were ascertained from the Saraiki ethnic part of. Khyber-Pukhtunkhwa province in Pakistan.

  2. Analysis of genetic diversity inpigeonpeagermplasm using ...

    Indian Academy of Sciences (India)

    Navya

    2016-11-25

    Nov 25, 2016 ... techniques are useful and could be a better alternative to other marker techniques in analyzing the genetic diversity .... the SSR primer alone in REMAP reactions, in control experiments for REMAP, the retrotransposon ... Molecular marker technology has evolved into a very powerful tool in plant biology for.

  3. A markerless protocol for genetic analysis of Aggregatibacter actinomycetemcomitans

    Directory of Open Access Journals (Sweden)

    Ya-An Cheng

    2014-02-01

    Conclusion: The protocol described in this study is efficient and specific for genetic manipulation of A actinomycetemcomitans, and will be amenable for functional analysis of multiple genes in A actinomycetemcomitans.

  4. Phenotypic and molecular genetic analysis of Pyruvate Kinase ...

    African Journals Online (AJOL)

    Phenotypic and molecular genetic analysis of Pyruvate Kinase deficiency in a Tunisian family. Jaouani Mouna, Hamdi Nadia, Chaouch Leila, Kalai Miniar, Mellouli Fethi, Darragi Imen, Boudriga Imen, Chaouachi Dorra, Bejaoui Mohamed, Abbes Salem ...

  5. SNPs ANALYSIS AS A TOOL IN MOLECULAR GENETICS DIAGNOSTICS

    Directory of Open Access Journals (Sweden)

    Dewi Rusnita

    2015-05-01

    Full Text Available AbstrakSingle Nucleotide Polymorphism (SNP merupakan variasi genetik yang ditemukan pada lebih dari 1% populasi. Haplotipe, yang merupakan sekelompok SNP atau alel dalam satu kromosom, dapat di turunkan ke generasi selanjutnya dan dapat digunakan untuk menelusuri gen penyebab penyakit (marker genetik. Artikel ini bertujuan menjelaskan aplikasi analisis SNP dalam diagnosis beberapa sindrom yang disebabkan gangguan genetik. Berdasarkan laporan studi terdahulu, sindrom yang disebabkan oleh UPD (uniparental disomy maupun penyakit autosomal resesif yang muncul sebagai akibat perkawinan sedarah dapat dideteksi dengan SNP array melalui analisis block of homozygosity dalam kromosom. Kelebihan lain SNP array adalah kemampuannya dalam mendeteksi mosaicism level rendah yang tidak terdeteksi dengan pemeriksaan sitogenetik konvensional. Bahkan saat ini, SNP array sedang diujicobakan dalam IVF untuk mendapatkan bayi yang sehat. Hal ini dapat dilakukan dengan mendeteksi ada atau tidaknya gen tunggal penyebab penyakit pada embrio hasil bayi tabung sebelum embrio ditanamkan ke uterus. Analisis SNP dengan SNP array mempunyai banyak kelebihan dibanding metode pemeriksaan SNP lainnya dan diharapkan dapat digunakan secara luas dalam bidang diagnostik molekuler genetik di masa mendatang.AbstractSingle Nucleotide Polymorphism (SNP is a genetic variant with a frequency of >1% of a large population. Haplotypes, a combination of a set of SNPs/alleles that appear as “associated blocks” on one chromosome, tend to be inherited together to the next offspring and can be used as genetic markers to trace particular diseases. This article aimed at explaining of SNP analysis application in diagnosis of genetic-disorder related syndrome. Previous studies showed that syndromes caused by UPD or autosomal recessive disorder as a result of consanguineous marriage can be identified by SNP array through analysing block of homozygosity region in a chromosome. Another advantage of SNP

  6. Genetic analysis reveals diversity and genetic relationship among Trichoderma isolates from potting media, cultivated soil and uncultivated soil.

    Science.gov (United States)

    Al-Sadi, Abdullah M; Al-Oweisi, Fatma A; Edwards, Simon G; Al-Nadabi, Hamed; Al-Fahdi, Ahmed M

    2015-07-28

    Trichoderma is one of the most common fungi in soil. However, little information is available concerning the diversity of Trichoderma in soil with no previous history of cultivation. This study was conducted to investigate the most common species and the level of genetic relatedness of Trichoderma species from uncultivated soil in relation to cultivated soil and potting media. A total of 24, 15 and 13 Trichoderma isolates were recovered from 84 potting media samples, 45 cultivated soil samples and 65 uncultivated soil samples, respectively. Analysis based on the internal transcribed spacer region of the ribosomal RNA (rRNA) and the translation elongation factor gene (EF1) indicated the presence of 9 Trichoderma species: T. harzianum (16 isolates), T. asperellum (13), T. citrinoviride (9), T. orientalis (3), T. ghanense (3), T. hamatum (3), T. longibrachiatum (2), T. atroviride (2), and T. viride (1). All species were found to occur in potting media samples, while five Trichoderma species were recovered from the cultivated soils and four from the uncultivated soils. AFLP analysis of the 52 Trichoderma isolates produced 52 genotypes and 993 polymorphic loci. Low to moderate levels of genetic diversity were found within populations of Trichoderma species (H = 0.0780 to 0.2208). Analysis of Molecular Variance indicated the presence of very low levels of genetic differentiation (Fst = 0.0002 to 0.0139) among populations of the same Trichoderma species obtained from the potting media, cultivated soil and uncultivated soil. The study provides evidence for occurrence of Trichoderma isolates in soil with no previous history of cultivation. The lack of genetic differentiation among Trichoderma populations from potting media, cultivated soil and uncultivated soil suggests that some factors could have been responsible for moving Trichoderma propagules among the three substrates. The study reports for the first time the presence of 4 Trichoderma species in Oman: T

  7. Genetic analysis of sunflower chlorophyll mutants

    International Nuclear Information System (INIS)

    Mashkina, E.V.; Guskov, E.P.

    2001-01-01

    The method of getting the chlorophyll mutations in sunflower was developed by Y.D. Beletskii in 1969 with the use of N-nitroso-N-methylurea (NMH). Certain concentrations of NMH are known to induce plastid mutations in growing seeds, and their yield depends on the duration of the exposure. The given work presented studies on the influence of rifampicin (R) and 2,4-dinitrophenol (DNP) on the genetic activity NMH, as an inductor of plastid and nuclear mutations

  8. Population genetic analysis of cat populations from Mexico ...

    Indian Academy of Sciences (India)

    Unknown

    In this paper we identify new genetic profiles of eight Latin American cat populations. In addition, we combine data from the present study and previously published data on 70 other American and European populations to discuss (1) the points of introduction of mutant alleles for cat coat phenotypes from Europe into Latin ...

  9. The Genetic Analysis of an Acinetobacter johnsonii Clinical Strain Evidenced the Presence of Horizontal Genetic Transfer.

    Directory of Open Access Journals (Sweden)

    Sabrina Montaña

    Full Text Available Acinetobacter johnsonii rarely causes human infections. While most A. johnsonii isolates are susceptible to virtually all antibiotics, strains harboring a variety of β-lactamases have recently been described. An A. johnsonii Aj2199 clinical strain recovered from a hospital in Buenos Aires produces PER-2 and OXA-58. We decided to delve into its genome by obtaining the whole genome sequence of the Aj2199 strain. Genome comparison studies on Aj2199 revealed 240 unique genes and a close relation to strain WJ10621, isolated from the urine of a patient in China. Genomic analysis showed evidence of horizontal genetic transfer (HGT events. Forty-five insertion sequences and two intact prophages were found in addition to several resistance determinants such as blaPER-2, blaOXA-58, blaTEM-1, strA, strB, ereA, sul1, aacC2 and a new variant of blaOXA-211, called blaOXA-498. In particular, blaPER-2 and blaTEM-1 are present within the typical contexts previously described in the Enterobacteriaceae family. These results suggest that A. johnsonii actively acquires exogenous DNA from other bacterial species and concomitantly becomes a reservoir of resistance genes.

  10. Genetic analysis of abdominal aortic aneurysms (AAA)

    Energy Technology Data Exchange (ETDEWEB)

    St. Jean, P.L.; Hart, B.K.; Zhang, X.C. [Univ. of Pittsburgh, PA (United States)] [and others

    1994-09-01

    The association between AAA and gender, smoking (SM), hypertension (HTN) and inguinal herniation (IH) was examined in 141 AAA probands and 139 of their 1st degree relatives with aortic exam (36 affected, 103 unaffected). There was no significant difference between age at diagnosis of affecteds and age at exam of unaffecteds. Of 181 males, 142 had AAA; of 99 females, 35 had AAA. Using log-linear modeling AAA was significantly associated at the 5% level with gender, SM and HTN but not IH. The association of AAA with SM and HTN held when males and females were analyzed separately. HTN was -1.5 times more common in both affected males and females, while SM was 1.5 and 2 times more common in affected males and females, respectively. Tests of association and linkage analyses were performed with relevant candidate genes: 3 COL3A1 polymorphisms (C/T, ALA/THR, AvaII), 2 ELN polymorphisms (SER/GLY, (CA)n), FBN1(TAAA)n, 2 APOB polymorphisms (Xbal,Ins/Del), CLB4B (CA)n, PI and markers D1S243 (CA)n, HPR (CA)n and MFD23(CA)n. The loci were genotyped in > 100 AAA probands and > 95 normal controls. No statistically significant evidence of association at the 5% level was obtained for any of the loci using chi-square test of association. 28 families with 2 or more affecteds were analyzed using the affected pedigree member method (APM) and lod-score analyses. There was no evidence for linkage with any loci using APM. Lod-score analysis under an autosomal recessive model resulted in excluding linkage (lod score < -2) of all loci to AAA at {theta}=0.0. Under an autosomal dominant model, linkage was excluded at {theta}=0.0 to ELN, APOB, CLG4B, D1S243, HPR and MFD23. The various genes previously proposed in AAA pathogenesis are neither associated nor casually related in our study population.

  11. Bayesian population structure analysis reveals presence of phylogeographically specific sublineages within previously ill-defined T group of Mycobacterium tuberculosis

    Science.gov (United States)

    Reynaud, Yann; Zheng, Chao; Wu, Guihui; Sun, Qun; Rastogi, Nalin

    2017-01-01

    Mycobacterium tuberculosis genetic structure, and evolutionary history have been studied for years by several genotyping approaches, but delineation of a few sublineages remains controversial and needs better characterization. This is particularly the case of T group within lineage 4 (L4) which was first described using spoligotyping to pool together a number of strains with ill-defined signatures. Although T strains were not traditionally considered as a real phylogenetic group, they did contain a few phylogenetically meaningful sublineages as shown using SNPs. We therefore decided to investigate if this observation could be corroborated using other robust genetic markers. We consequently made a first assessment of genetic structure using 24-loci MIRU-VNTRs data extracted from the SITVIT2 database (n = 607 clinical isolates collected in Russia, Albania, Turkey, Iraq, Brazil and China). Combining Minimum Spanning Trees and Bayesian population structure analyses (using STRUCTURE and TESS softwares), we distinctly identified eight tentative phylogenetic groups (T1-T8) with a remarkable correlation with geographical origin. We further compared the present structure observed with other L4 sublineages (n = 416 clinical isolates belonging to LAM, Haarlem, X, S sublineages), and showed that 5 out of 8 T groups seemed phylogeographically well-defined as opposed to the remaining 3 groups that partially mixed with other L4 isolates. These results provide with novel evidence about phylogeographically specificity of a proportion of ill-defined T group of M. tuberculosis. The genetic structure observed will now be further validated on an enlarged worldwide dataset using Whole Genome Sequencing (WGS). PMID:28166309

  12. Bayesian population structure analysis reveals presence of phylogeographically specific sublineages within previously ill-defined T group of Mycobacterium tuberculosis.

    Directory of Open Access Journals (Sweden)

    Yann Reynaud

    Full Text Available Mycobacterium tuberculosis genetic structure, and evolutionary history have been studied for years by several genotyping approaches, but delineation of a few sublineages remains controversial and needs better characterization. This is particularly the case of T group within lineage 4 (L4 which was first described using spoligotyping to pool together a number of strains with ill-defined signatures. Although T strains were not traditionally considered as a real phylogenetic group, they did contain a few phylogenetically meaningful sublineages as shown using SNPs. We therefore decided to investigate if this observation could be corroborated using other robust genetic markers. We consequently made a first assessment of genetic structure using 24-loci MIRU-VNTRs data extracted from the SITVIT2 database (n = 607 clinical isolates collected in Russia, Albania, Turkey, Iraq, Brazil and China. Combining Minimum Spanning Trees and Bayesian population structure analyses (using STRUCTURE and TESS softwares, we distinctly identified eight tentative phylogenetic groups (T1-T8 with a remarkable correlation with geographical origin. We further compared the present structure observed with other L4 sublineages (n = 416 clinical isolates belonging to LAM, Haarlem, X, S sublineages, and showed that 5 out of 8 T groups seemed phylogeographically well-defined as opposed to the remaining 3 groups that partially mixed with other L4 isolates. These results provide with novel evidence about phylogeographically specificity of a proportion of ill-defined T group of M. tuberculosis. The genetic structure observed will now be further validated on an enlarged worldwide dataset using Whole Genome Sequencing (WGS.

  13. Genetic analysis in retinoblastoma and peripheral blood correlation.

    Science.gov (United States)

    Ruiz del Río, N; Abelairas Gómez, J M; Alonso García de la Rosa, F J; Peralta Calvo, J M; de las Heras Martín, A

    2015-12-01

    To determine the importance of intratumoral genetic analysis in the diagnosis of germ-line mutations in patients with retinoblastoma. To underline the importance of performing these genetic tests in every case of retinoblastoma. Intratumoral genetic analysis of RB1 mutation was performed on 17 enucleated eyes that were non-responsive to conservative treatment. Patients had no family history of retinoblastoma, and lesions were always single. The identified mutations were then also studied in peripheral blood analysis. There were 12 (70.6%) cases with positive results in intratumoral analysis. In 8 cases (47.1%) mutation of both RB1 alelli were detected, and in 4 (23.5%) cases only one allele was found mutated. In 5 patients (29.4%) no mutation was identified. In the first hit, mutations comprised 7 frameshift or nonsense and 2 splice, whereas in the second hit, one splice mutation, 2 nonsense and 8 loss of heterozygosity were identified. Among 6 patients where intratumoral analysis detected a single mutation associated with a loss of heterozygosity, the peripheral blood analysis was able to detect the same mutation in 3 cases (50%). Intratumoral genetic analysis of sporadic retinoblastoma can detect germ-line mutations. These patients are at higher risk of bilateralization and development of second tumors or trilateral retinoblastoma. Genetic screening is recommended in every patient diagnosed with retinoblastoma. Copyright © 2013 Sociedad Española de Oftalmología. Published by Elsevier España, S.L.U. All rights reserved.

  14. Population genetic analysis of Giardia duodenalis: genetic diversity and haplotype sharing between clinical and environmental sources.

    Science.gov (United States)

    Durigan, Mauricio; Ciampi-Guillardi, Maisa; Rodrigues, Ricardo C A; Greinert-Goulart, Juliane A; Siqueira-Castro, Isabel C V; Leal, Diego A G; Yamashiro, Sandra; Bonatti, Taís R; Zucchi, Maria I; Franco, Regina M B; de Souza, Anete P

    2017-04-01

    Giardia duodenalis is a flagellated intestinal protozoan responsible for infections in various hosts including humans and several wild and domestic animals. Few studies have correlated environmental contamination and clinical infections in the same region. The aim of this study was to compare groups of Giardia duodenalis from clinical and environmental sources through population genetic analyses to verify haplotype sharing and the degree of genetic similarity among populations from clinical and environmental sources in the metropolitan region of Campinas. The results showed high diversity of haplotypes and substantial genetic similarity between clinical and environmental groups of G. duodenalis. We demonstrated sharing of Giardia genotypes among the different populations studied. The comparison between veterinary and human sequences led us to identify new zoonotic genotypes, including human isolates from genetic assemblage C. The application of a population genetic analysis in epidemiological studies allows quantification of the degree of genetic similarity among populations of Giardia duodenalis from different sources of contamination. The genetic similarity of Giardia isolates among human, veterinary, and environmental groups reinforced the correlation between clinical and environmental isolates in this region, which is of great importance for public health. © 2017 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

  15. Evolutionary Analysis Predicts Sensitive Positions of MMP20 and Validates Newly- and Previously-Identified MMP20 Mutations Causing Amelogenesis Imperfecta

    Directory of Open Access Journals (Sweden)

    Barbara Gasse

    2017-06-01

    Full Text Available Amelogenesis imperfecta (AI designates a group of genetic diseases characterized by a large range of enamel disorders causing important social and health problems. These defects can result from mutations in enamel matrix proteins or protease encoding genes. A range of mutations in the enamel cleavage enzyme matrix metalloproteinase-20 gene (MMP20 produce enamel defects of varying severity. To address how various alterations produce a range of AI phenotypes, we performed a targeted analysis to find MMP20 mutations in French patients diagnosed with non-syndromic AI. Genomic DNA was isolated from saliva and MMP20 exons and exon-intron boundaries sequenced. We identified several homozygous or heterozygous mutations, putatively involved in the AI phenotypes. To validate missense mutations and predict sensitive positions in the MMP20 sequence, we evolutionarily compared 75 sequences extracted from the public databases using the Datamonkey webserver. These sequences were representative of mammalian lineages, covering more than 150 million years of evolution. This analysis allowed us to find 324 sensitive positions (out of the 483 MMP20 residues, pinpoint functionally important domains, and build an evolutionary chart of important conserved MMP20 regions. This is an efficient tool to identify new- and previously-identified mutations. We thus identified six functional MMP20 mutations in unrelated families, finding two novel mutated sites. The genotypes and phenotypes of these six mutations are described and compared. To date, 13 MMP20 mutations causing AI have been reported, making these genotypes and associated hypomature enamel phenotypes the most frequent in AI.

  16. Polyglot programming in applications used for genetic data analysis.

    Science.gov (United States)

    Nowak, Robert M

    2014-01-01

    Applications used for the analysis of genetic data process large volumes of data with complex algorithms. High performance, flexibility, and a user interface with a web browser are required by these solutions, which can be achieved by using multiple programming languages. In this study, I developed a freely available framework for building software to analyze genetic data, which uses C++, Python, JavaScript, and several libraries. This system was used to build a number of genetic data processing applications and it reduced the time and costs of development.

  17. On the runtime analysis of the Simple Genetic Algorithm

    DEFF Research Database (Denmark)

    Oliveto, Pietro S.; Witt, Carsten

    2014-01-01

    For many years it has been a challenge to analyze the time complexity of Genetic Algorithms (GAs) using stochastic selection together with crossover and mutation. This paper presents a rigorous runtime analysis of the well-known Simple Genetic Algorithm (SGA) for OneMax. It is proved that the SGA...... for a standard benchmark function. The presented techniques might serve as a first basis towards systematic runtime analyses of GAs....

  18. On the Analysis of the Simple Genetic Algorithm

    DEFF Research Database (Denmark)

    Oliveto, Pietro S.; Witt, Carsten

    2012-01-01

    For many years it has been a challenge to analyze the time complexity of Genetic Algorithms (GAs) using stochastic selection together with crossover and mutation. This paper presents a rigorous runtime analysis of the well-known Simple Genetic Algorithm (SGA) for OneMax. It is proved that the SGA...... benchmark function. The presented techniques might serve as a first basis towards systematic runtime analyses of GAs....

  19. Analysis of 60 706 Exomes Questions the Role of De Novo Variants Previously Implicated in Cardiac Disease

    DEFF Research Database (Denmark)

    Paludan-Müller, Christian; Ahlberg, Gustav; Ghouse, Jonas

    2017-01-01

    sought to evaluate the pathogenicity of de novo variants previously associated with cardiac disease based on a large population-representative exome database. METHODS AND RESULTS: We performed a literature search for previous publications on de novo variants associated with severe arrhythmias...... and structural heart diseases and investigated whether these variants were present in the Exome Aggregation Consortium (ExAC) database (n=60 706). We identified monogenic variants in single case reports and smaller studies (≤200 subjects) and variants considered to increase susceptibility of disease in 3 larger...

  20. Analysis of over 10,000 Cases finds no association between previously reported candidate polymorphisms and ovarian cancer outcome

    DEFF Research Database (Denmark)

    White, Kristin L; Vierkant, Robert A; Fogarty, Zachary C

    2013-01-01

    Ovarian cancer is a leading cause of cancer-related death among women. In an effort to understand contributors to disease outcome, we evaluated single-nucleotide polymorphisms (SNP) previously associated with ovarian cancer recurrence or survival, specifically in angiogenesis, inflammation, mitosis...

  1. The relationship between emotional intelligence, previous caring experience and mindfulness in student nurses and midwives: a cross sectional analysis.

    Science.gov (United States)

    Snowden, Austyn; Stenhouse, Rosie; Young, Jenny; Carver, Hannah; Carver, Fiona; Brown, Norrie

    2015-01-01

    Emotional Intelligence (EI), previous caring experience and mindfulness training may have a positive impact on nurse education. More evidence is needed to support the use of these variables in nurse recruitment and retention. To explore the relationship between EI, gender, age, programme of study, previous caring experience and mindfulness training. Cross sectional element of longitudinal study. 938year one nursing, midwifery and computing students at two Scottish Higher Education Institutes (HEIs) who entered their programme in September 2013. Participants completed a measure of 'trait' EI: Trait Emotional Intelligence Questionnaire Short Form (TEIQue-SF); and 'ability' EI: Schutte's et al. (1998) Emotional Intelligence Scale (SEIS). Demographics, previous caring experience and previous training in mindfulness were recorded. Relationships between variables were tested using non-parametric tests. Emotional intelligence increased with age on both measures of EI [TEIQ-SF H(5)=15.157 p=0.001; SEIS H(5)=11.388, p=0.044]. Females (n=786) scored higher than males (n=149) on both measures [TEIQ-SF, U=44,931, z=-4.509, pintelligence. Mindfulness training was associated with higher 'ability' emotional intelligence. Implications for recruitment, retention and further research are explored. Copyright © 2014. Published by Elsevier Ltd.

  2. Hierarchical Approaches to the Analysis of Genetic Diversity in ...

    African Journals Online (AJOL)

    Hierarchical Approaches to the Analysis of Genetic Diversity in Plants: A Systematic Overview. ME Osawaru, MC Ogwu, RO Aiwansoba. Abstract. Hierarchical analysis highlights the nature of relationship between and among type samples as outlined by standard descriptors. It produces an output called dendrogram, which ...

  3. GENETIC ANALYSIS OF YIELD AND YIELD COMPONENTS IN ...

    African Journals Online (AJOL)

    ACSS

    2017-11-16

    Nov 16, 2017 ... Sierra Leone Agricultural Research Institute, Rokupr Agricultural Research Centre, Sierra Leone .... The objectives of this study was to elucidate ... Data analysis. Generation mean analysis. (Equation 1) was used to estimates genetic control of the seven quantitative traits according to the methodology ...

  4. Genetic analysis of wild and cultivated germplasm of pigeonpea ...

    African Journals Online (AJOL)

    Ezedom Theresa

    RAPD profile obtained by primer OPA-10 is shown in. Figure 1. Out of a total of 22 loci (289-1511bp), all 22 were polymorphic (100%). In case of SSR analysis, CC based five microsatellite (SSR) primers out of total 40, were used to analyze the genetic diversity among 12 pigeon- pea germplasm (Table 3). The SSR analysis ...

  5. Improved time complexity analysis of the Simple Genetic Algorithm

    DEFF Research Database (Denmark)

    Oliveto, Pietro S.; Witt, Carsten

    2015-01-01

    A runtime analysis of the Simple Genetic Algorithm (SGA) for the OneMax problem has recently been presented proving that the algorithm with population size μ≤n1/8−ε requires exponential time with overwhelming probability. This paper presents an improved analysis which overcomes some limitations...

  6. Molecular genetic analysis of tumor suppressor genes in ovarian cancer

    International Nuclear Information System (INIS)

    Lee, Je Ho; Park, Sang Yun

    1992-04-01

    To examine the loci of putative tumor suppressor genes in ovarian cancers, we performed the molecular genetic analysis with fresh human ovarian cancers and observed the following data. Frequent allelic losses were observed on chromosomes 4p(42%), 6p(50%), 7p(43%), 8q(31%), 12p(38%), 12q(33%), 16p(33%), 16q(37%), and 19p(34%) in addition to the previously reported 6q, 11p, and 17p in ovarian caroinomas. we have used an additional probe, TCP10 to narrow down the deleted region on chromosome 6q. TCP10 was reported to be mapped to 6q 25-27. Allelic loss was found to be 40% in epithelial ovarian caroinomas. This finding suggests that chromosome 6q 24-27 is one of putative region haboring the tumor suppressor gene of epithelial ovarian cancer (particularly serous type). To examine the association between FAL(Fractional Allelic Loss) and histopathological features, the FAL value on each phenotypically different tumor was calculated as the ratio of the number of allelic losses versus the number of cases informative in each chromosomal arm. The average FALs for each phenotypically different tumor were: serous cystoadenocarcinomas. FAL=0.31 : mucinous 0.12 : and clear cell carcinoma. FAL=0.20. (Author)

  7. Genetic variability in the Iberian imperial eagle (Aquila adalberti) demonstrated by RAPD analysis.

    Science.gov (United States)

    Padilla, J A; Martínez-Trancón, M; Rabasco, A; Parejo, J C; Sansinforiano, M E; Guijo, M I

    2000-01-01

    RAPD analysis was used to estimate the genetic diversity in an Iberian imperial eagle (Aquila adalberti) population, one of the most threatened bird species in the world. Forty-five of 60 arbitrarily designed primers amplified 614 loci in 25 individual eagles, 59.7% of which were polymorphic. In contrast to the traditional allozyme analysis performed in a previous study, the RAPD method has revealed a high level of heterozygosity in this species (H = 0.267+/-0.008). The genetic distances estimated between 25 eagles can serve to establish more adequate mating in order to preserve genetic variability. Conservation efforts being carried out in Spain in this species might be successful based on the results obtained in the present work.

  8. Timing Analysis of Genetic Logic Circuits using D-VASim

    DEFF Research Database (Denmark)

    Baig, Hasan; Madsen, Jan

    and propagation delay analysis of single as well as cascaded geneticlogic circuits can be performed. D-VASim allows user to change the circuit parameters during runtime simulation to observe its effectson circuit’s timing behavior. The results obtained from D-VASim can be used not only to characterize the timing...... delay analysis may play a very significant role in the designing of genetic logic circuits. In thisdemonstration, we present the capability of D-VASim (Dynamic Virtual Analyzer and Simulator) to perform the timing and propagationdelay analysis of genetic logic circuits. Using D-VASim, the timing...... behavior of geneticlogic circuits but also to analyze the timing constraints of cascaded genetic logic circuits....

  9. Smoking and caffeine consumption: a genetic analysis of their association.

    Science.gov (United States)

    Treur, Jorien L; Taylor, Amy E; Ware, Jennifer J; Nivard, Michel G; Neale, Michael C; McMahon, George; Hottenga, Jouke-Jan; Baselmans, Bart M L; Boomsma, Dorret I; Munafò, Marcus R; Vink, Jacqueline M

    2017-07-01

    Smoking and caffeine consumption show a strong positive correlation, but the mechanism underlying this association is unclear. Explanations include shared genetic/environmental factors or causal effects. This study employed three methods to investigate the association between smoking and caffeine. First, bivariate genetic models were applied to data of 10 368 twins from the Netherlands Twin Register in order to estimate genetic and environmental correlations between smoking and caffeine use. Second, from the summary statistics of meta-analyses of genome-wide association studies on smoking and caffeine, the genetic correlation was calculated by LD-score regression. Third, causal effects were tested using Mendelian randomization analysis in 6605 Netherlands Twin Register participants and 5714 women from the Avon Longitudinal Study of Parents and Children. Through twin modelling, a genetic correlation of r0.47 and an environmental correlation of r0.30 were estimated between current smoking (yes/no) and coffee use (high/low). Between current smoking and total caffeine use, this was r0.44 and r0.00, respectively. LD-score regression also indicated sizeable genetic correlations between smoking and coffee use (r0.44 between smoking heaviness and cups of coffee per day, r0.28 between smoking initiation and coffee use and r0.25 between smoking persistence and coffee use). Consistent with the relatively high genetic correlations and lower environmental correlations, Mendelian randomization provided no evidence for causal effects of smoking on caffeine or vice versa. Genetic factors thus explain most of the association between smoking and caffeine consumption. These findings suggest that quitting smoking may be more difficult for heavy caffeine consumers, given their genetic susceptibility. © 2016 The Authors.Addiction Biology published by John Wiley & Sons Ltd on behalf of Society for the Study of Addiction.

  10. A roadmap for the genetic analysis of renal aging.

    Science.gov (United States)

    Noordmans, Gerda A; Hillebrands, Jan-Luuk; van Goor, Harry; Korstanje, Ron

    2015-10-01

    Several studies show evidence for the genetic basis of renal disease, which renders some individuals more prone than others to accelerated renal aging. Studying the genetics of renal aging can help us to identify genes involved in this process and to unravel the underlying pathways. First, this opinion article will give an overview of the phenotypes that can be observed in age-related kidney disease. Accurate phenotyping is essential in performing genetic analysis. For kidney aging, this could include both functional and structural changes. Subsequently, this article reviews the studies that report on candidate genes associated with renal aging in humans and mice. Several loci or candidate genes have been found associated with kidney disease, but identification of the specific genetic variants involved has proven to be difficult. CUBN, UMOD, and SHROOM3 were identified by human GWAS as being associated with albuminuria, kidney function, and chronic kidney disease (CKD). These are promising examples of genes that could be involved in renal aging, and were further mechanistically evaluated in animal models. Eventually, we will provide approaches for performing genetic analysis. We should leverage the power of mouse models, as testing in humans is limited. Mouse and other animal models can be used to explain the underlying biological mechanisms of genes and loci identified by human GWAS. Furthermore, mouse models can be used to identify genetic variants associated with age-associated histological changes, of which Far2, Wisp2, and Esrrg are examples. A new outbred mouse population with high genetic diversity will facilitate the identification of genes associated with renal aging by enabling high-resolution genetic mapping while also allowing the control of environmental factors, and by enabling access to renal tissues at specific time points for histology, proteomics, and gene expression. © 2015 The Authors. Aging Cell published by the Anatomical Society and John

  11. Genetic diversity analysis of common beans based on molecular markers

    Directory of Open Access Journals (Sweden)

    Homar R. Gill-Langarica

    2011-01-01

    Full Text Available A core collection of the common bean (Phaseolus vulgaris L., representing genetic diversity in the entire Mexican holding, is kept at the INIFAP (Instituto Nacional de Investigaciones Forestales, Agricolas y Pecuarias, Mexico Germplasm Bank. After evaluation, the genetic structure of this collection (200 accessions was compared with that of landraces from the states of Oaxaca, Chiapas and Veracruz (10 genotypes from each, as well as a further 10 cultivars, by means of four amplified fragment length polymorphisms (AFLP +3/+3 primer combinations and seven simple sequence repeats (SSR loci, in order to define genetic diversity, variability and mutual relationships. Data underwent cluster (UPGMA and molecular variance (AMOVA analyses. AFLP analysis produced 530 bands (88.5% polymorphic while SSR primers amplified 174 alleles, all polymorphic (8.2 alleles per locus. AFLP indicated that the highest genetic diversity was to be found in ten commercial-seed classes from two major groups of accessions from Central Mexico and Chiapas, which seems to be an important center of diversity in the south. A third group included genotypes from Nueva Granada, Mesoamerica, Jalisco and Durango races. Here, SSR analysis indicated a reduced number of shared haplotypes among accessions, whereas the highest genetic components of AMOVA variation were found within accessions. Genetic diversity observed in the common-bean core collection represents an important sample of the total Phaseolus genetic variability at the main Germplasm Bank of INIFAP. Molecular marker strategies could contribute to a better understanding of the genetic structure of the core collection as well as to its improvement and validation.

  12. Cellular and genetic analysis of mouse blastocyst development

    Energy Technology Data Exchange (ETDEWEB)

    Pedersen, R A; Spindle, A I

    1979-01-01

    The development of mouse embryos was studied by both cellular and genetic approaches. In the cellular analysis, determination of cell fate in blastocysts and in cell populations derived from them was studied in an attempt to estimate the time that these cells become committed to their fate. In the genetic analysis, existing mutations that are lethal to mouse embryos were used to discern essential features of early development. In this review, the timing of cell determination in the inner cell mass and the primary ectoderm, and the manifestation of defects in mouse embryos that are homozygous for the A/sup y/ allele of the agouti locus were considered.

  13. At what price? A cost-effectiveness analysis comparing trial of labour after previous Caesarean versus elective repeat Caesarean delivery.

    LENUS (Irish Health Repository)

    Fawsitt, Christopher G

    2013-01-01

    Elective repeat caesarean delivery (ERCD) rates have been increasing worldwide, thus prompting obstetric discourse on the risks and benefits for the mother and infant. Yet, these increasing rates also have major economic implications for the health care system. Given the dearth of information on the cost-effectiveness related to mode of delivery, the aim of this paper was to perform an economic evaluation on the costs and short-term maternal health consequences associated with a trial of labour after one previous caesarean delivery compared with ERCD for low risk women in Ireland.

  14. A genetic algorithm approach to routine gamma spectra analysis

    Energy Technology Data Exchange (ETDEWEB)

    Carlevaro, C M [Instituto de FIsica de LIquidos y Sistemas Biologicos, Calle 59 No 789, B1900BTE La Plata (Argentina); Wilkinson, M V [Autoridad Regulatoria Nuclear, Avda. del Libertador 8250, C1429BNP Buenos Aires (Argentina); Barrios, L A [Autoridad Regulatoria Nuclear, Avda. del Libertador 8250, C1429BNP Buenos Aires (Argentina)

    2008-01-15

    In this work we present an alternative method for performing routine gamma spectra analysis based on genetic algorithm techniques. The main idea is to search for patterns of single nuclide spectra obtained by simulation in a sample spectrum targeted for analysis. We show how this approach is applied to the analysis of simulated and real target spectra, and also to the study of interference resolution.

  15. A genetic analysis of Adh1 regulation

    Energy Technology Data Exchange (ETDEWEB)

    Freeling, M.

    1992-01-01

    The overall goal of our research proposal is to understand the meaning of the various cis-acting sites responsible for AdH1 expression in the entire maize plant. Progress is reported in the following areas: Studies on the TATA box and analysis of revertants of the Adh1-3F1124 allele; screening for more different mutants that affect Adh1 expression differentially; studies on cis-acting sequences required for root-specific Adh1 expression; refinement of the use of the particle gun; and functional analysis of a non- glycolytic anaerobic protein.

  16. Genetic diversity analysis of Tinospora cordifolia germplasm ...

    Indian Academy of Sciences (India)

    2012-04-03

    Apr 3, 2012 ... Wiley Eastern Limited, New Delhi, India. Shinde V. M. and Dhalwal K. 2010 DNA fingerprinting of. Tinospora cordifolia using RAPD analysis. J. Global Pharma. Tech. 2, 38–42. Singh S., Singh D. R., Faseela F., Kumar N., Damodaran V. and. Srivastava R. C. 2011. Diversity of 21 taro (Colocasia esculenta.

  17. A Genetic Analysis of Mortality in Pigs

    DEFF Research Database (Denmark)

    Varona, Luis; Sorensen, Daniel

    2010-01-01

    An analysis of mortality is undertaken in two breeds of pigs: Danish Landrace and Yorkshire. Zero-inflated and standard versions of hierarchical Poisson, binomial, and negative binomial Bayesian models were fitted using Markov chain Monte Carlo (MCMC). The objectives of the study were to investig...

  18. Genetic analysis of repeated, biparental, diploid, hydatidiform moles

    DEFF Research Database (Denmark)

    Sunde, L; Vejerslev, L O; Jensen, M P

    1993-01-01

    A woman presented with five consecutive pregnancies displaying molar morphology. In the fifth pregnancy, a non-malformed, liveborn infant was delivered. Genetic analyses (RFLP analysis, cytogenetics, flow cytometry) were performed in pregnancies II-V. It was demonstrated that these pregnancies...... originated in separate conceptions, all conceptuses were diploid, and all had maternally as well as paternally derived genetic markers. By cytogenetic analysis, aberrant heteromorphisms were noted; no other abnormalities were observed in chromosome structure or in DNA sequence. Many different causes...... for the abnormal development can be envisaged, environmental as well as genetic. To conform to current ideas of molar pathogenesis, it is suggested that the present conceptuses might have arisen from imbalances in imprinted genomic regions. This could be a consequence of uniparental disomy in critical regions...

  19. Genetic Characterization of a Novel HIV-1 Circulating Recombinant Form (CRF74_01B) Identified among Intravenous Drug Users in Malaysia: Recombination History and Phylogenetic Linkage with Previously Defined Recombinant Lineages.

    Science.gov (United States)

    Cheong, Hui Ting; Chow, Wei Zhen; Takebe, Yutaka; Chook, Jack Bee; Chan, Kok Gan; Al-Darraji, Haider Abdulrazzaq Abed; Koh, Clayton; Kamarulzaman, Adeeba; Tee, Kok Keng

    2015-01-01

    In many parts of Southeast Asia, the HIV-1 epidemic has been driven by the sharing of needles and equipment among intravenous drug users (IDUs). Over the last few decades, many studies have proven time and again that the diversity of HIV-1 epidemics can often be linked to the route of infection transmission. That said, the diversity and complexity of HIV-1 molecular epidemics in the region have been increasing at an alarming rate, due in part to the high tendency of the viral RNA to recombine. This scenario was exemplified by the discovery of numerous circulating recombinant forms (CRFs), especially in Thailand and Malaysia. In this study, we characterized a novel CRF designated CRF74_01B, which was identified in six epidemiologically unlinked IDUs in Kuala Lumpur, Malaysia. The near-full length genomes were composed of CRF01_AE and subtype B', with eight breakpoints dispersed in the gag-pol and nef regions. Remarkably, this CRF shared four and two recombination hotspots with the previously described CRF33_01B and the less prevalent CRF53_01B, respectively. Genealogy-based Bayesian phylogenetic analysis of CRF74_01B genomic regions showed that it is closely related to both CRF33_01B and CRF53_01B. This observation suggests that CRF74_01B was probably a direct descendent from specific lineages of CRF33_01B, CRF53_01B and subtype B' that could have emerged in the mid-1990s. Additionally, it illustrated the active recombination processes between prevalent HIV-1 subtypes and recombinants in Malaysia. In summary, we report a novel HIV-1 genotype designated CRF74_01B among IDUs in Kuala Lumpur, Malaysia. The characterization of the novel CRF74_01B is of considerable significance towards the understanding of the genetic diversity and population dynamics of HIV-1 circulating in the region.

  20. AFLP analysis of genetic variability in New Guinea impatiens.

    Science.gov (United States)

    Carr, Jason; Xu, Mingliang; Dudley, John W; Korban, Schuyler S

    2003-05-01

    New Guinea impatiens ( Impatiens hawkeri) is an economically important floral crop, however, little work has been conducted to further our understanding of the genetics of this crop. In this study, we used amplified fragment length polymorphism (AFLP) technology to investigate the level of polymorphism present among 41 commercial cultivars of New Guinea impatiens, study their genetic relatedness, and assess the genetic diversity in this material. An efficient DNA extraction protocol was developed, and a total of 48 EcoRI and MseI primer combinations were used for PCR amplification. Amplification products were then subjected to polyacrylamide gel electrophoresis. The AFLP analysis showed that all 41 cultivars generated between 73 and 130 scoreable polymorphic bands per primer combination. Gower's Genetic Dissimilarity estimates for the entire set of cultivars ranged between 0.940 and 0.488. A dendogram was generated from these dissimilarity data that revealed four groupings among these 41 cultivars. The implications of these results on genotypic variation, genetic relationships, and genetic diversity in New Guinea impatiens will be discussed.

  1. SSR Analysis of Genetic Diversity Among 192 Diploid Potato Cultivars

    Directory of Open Access Journals (Sweden)

    Xiaoyan Song

    2016-05-01

    Full Text Available In potato breeding, it is difficult to improve the traits of interest at the tetraploid level due to the tetrasomic inheritance. A promising alternative is diploid breeding. Thus it is necessary to assess the genetic diversity of diploid potato germplasm for efficient exploration and deployment of desirable traits. In this study, we used SSR markers to evaluate the genetic diversity of diploid potato cultivars. To screen polymorphic SSR markers, 55 pairs of SSR primers were employed to amplify 39 cultivars with relatively distant genetic relationships. Among them, 12 SSR markers with high polymorphism located at 12 chromosomes were chosen to evaluate the genetic diversity of 192 diploid potato cultivars. The primers produced 6 to 18 bands with an average of 8.2 bands per primer. In total, 98 bands were amplified from 192 cultivars, and 97 of them were polymorphic. Cluster analysis using UPGMA showed the genetic relationships of all accessions tested: 186 of the 192 accessions could be distinguished by only 12 pairs of SSR primers, and the 192 diploid cultivars were divided into 11 groups, and 83.3% constituted the first group. Clustering results showed relatively low genetic diversity among 192 diploid cultivars, with closer relationship at the molecular level. The results can provide molecular basis for diploid potato breeding.

  2. Meta-analysis of susceptibility of woody plants to loss of genetic diversity through habitat fragmentation.

    Science.gov (United States)

    Vranckx, Guy; Jacquemyn, Hans; Muys, Bart; Honnay, Olivier

    2012-04-01

    Shrubs and trees are assumed less likely to lose genetic variation in response to habitat fragmentation because they have certain life-history characteristics such as long lifespans and extensive pollen flow. To test this assumption, we conducted a meta-analysis with data on 97 woody plant species derived from 98 studies of habitat fragmentation. We measured the weighted response of four different measures of population-level genetic diversity to habitat fragmentation with Hedge's d and Spearman rank correlation. We tested whether the genetic response to habitat fragmentation was mediated by life-history traits (longevity, pollination mode, and seed dispersal vector) and study characteristics (genetic marker and plant material used). For both tests of effect size habitat fragmentation was associated with a substantial decrease in expected heterozygosity, number of alleles, and percentage of polymorphic loci, whereas the population inbreeding coefficient was not associated with these measures. The largest proportion of variation among effect sizes was explained by pollination mechanism and by the age of the tissue (progeny or adult) that was genotyped. Our primary finding was that wind-pollinated trees and shrubs appeared to be as likely to lose genetic variation as insect-pollinated species, indicating that severe habitat fragmentation may lead to pollen limitation and limited gene flow. In comparison with results of previous meta-analyses on mainly herbaceous species, we found trees and shrubs were as likely to have negative genetic responses to habitat fragmentation as herbaceous species. We also found that the genetic variation in offspring was generally less than that of adult trees, which is evidence of a genetic extinction debt and probably reflects the genetic diversity of the historical, less-fragmented landscape. ©2011 Society for Conservation Biology.

  3. A genetic analysis of Adhl regulation

    Energy Technology Data Exchange (ETDEWEB)

    Freeling, M.

    1992-01-01

    Several separate but related studies are reported on the mechanism of alcohol dehydrogenase (Adh-1) are reported. A study of a deletion mutation in the TATA box region which resulted in an increase from 6--60% of wildtype Adh-1 expression in the revertant has led to a focus on trans-acting protein factors that bind the TATA box. Analysis of another revertant has led to study of cis-acting sequences in Adh-1 expression. Screening efforts aimed at defining different mutants affecting Adh-1 expression are reported.

  4. A genetic analysis of segregation distortion revealed by molecular ...

    Indian Academy of Sciences (India)

    c Indian Academy of Sciences. RESEARCH NOTE. A genetic analysis of segregation ... 2College of Life Science, Northeast Forest University, Harbin 150040, People's Republic of China. [Cai J., Zhang X., Wang B., Yan M., Qi Y. and Kong L. ... elite agronomic traits (Zhang et al. 2011). However, there is still no report about ...

  5. Genetic analysis of japonica x indica recombinant inbred lines and ...

    African Journals Online (AJOL)

    Genetic analysis of japonica x indica recombinant inbred lines and characterization of major fragrance gene by microsatellite markers. ... At some SSR loci, new/recombinant alleles were observed, which indicate the active recombination between genomes of two rice varieties and can be used for linkage mapping once ...

  6. Analysis of genetic diversity of muga silkworm (Antheraea ...

    African Journals Online (AJOL)

    USER

    2010-03-22

    Mar 22, 2010 ... Eleven populations of muga silkworm, Antheraea assamensis Helfer, the golden silk yarn producer of northeast India, was subjected to RAPD marker analysis in order to assess its genetic diversity. The genomic DNA extracted from muga silkworms were analysed using 50 random primers among which 36.

  7. Analysis of genetic structure and relationship among nine ...

    Indian Academy of Sciences (India)

    The admixed individuals were distributed in all the nine chicken populations, while migrants were only distributed in TIB, XIA and LUY populations. These results indicated that the clustering analysis using the Structure program might provide an accurate representation of the genetic relationship among the breeds.

  8. Analysis of genetic diversity and construction of core collection of ...

    African Journals Online (AJOL)

    Analysis of genetic diversity and construction of core collection of local mulberry varieties from Shanxi Province based on ISSR marker. ... By using stepwise clustering and random methods and the modified heuristic algorithm, 21 core collections were constructed and the ratio of core collection was 28.77%. The result of ...

  9. Genetic diversity analysis in the Hypericum perforatum populations ...

    African Journals Online (AJOL)

    In conclusion, combined analysis of ISSR markers and hypericin content is an optimal approach for further progress and breeding programs. Keywords: Hypericum perforatum (St. John's Wort), inter-simple sequence repeats (ISSR) markers, unweighted pair-group method with arithmetic averages (UPGMA), Nei's genetic ...

  10. Analysis of three genetic polymorphisms in Malaysian essential ...

    African Journals Online (AJOL)

    Analysis of three genetic polymorphisms in Malaysian essential hypertensive and type 2 diabetic subjects. ... Genotyping of all the three polymorphisms was performed by PCR-RFLP method with the respective primers and restriction enzymes. The genotypic and allelic frequencies of the respective polymorphisms of the ...

  11. Genetic analysis of Myanmar Vigna species in responses to salt ...

    African Journals Online (AJOL)

    user

    2011-02-28

    Feb 28, 2011 ... Genetic parameters for STI values were estimated by using the following formulae (Singh and Chaudhary, 1977);. ;. SDS-PAGE analysis. Protein extraction was performed using upper young leaves from the treated plants. Protein electrophoresis and SDS polyacrylamide gel electrophoresis was performed ...

  12. Analysis of genetic diversity in mango ( Mangifera indica L.) using ...

    African Journals Online (AJOL)

    Glutamate oxaloacetate transaminase, malate dehydrogenase and peroxidase analysis possessed 8, 10 and 7 zymotypes, respectively, and genotypes were grouped into different electrophoretic zymotypes which indicated higher level of genetic diversity of mango. For glutamate oxaloacetate transminase, G6 was the most ...

  13. Genetic and phylogenetic analysis of ten Gobiidae species in China ...

    African Journals Online (AJOL)

    To study the genetic and phylogenetic relationship of gobioid fishes in China, the representatives of 10 gobioid fishes from 2 subfamilies in China were examined by amplified fragment length polymorphism (AFLP) analysis. We established 220 AFLP bands for 45 individuals from the 10 species, and the percentage of ...

  14. Molecular analysis of genetic diversity in elite II synthetic hexaploid ...

    African Journals Online (AJOL)

    The present study was conducted to assess the genetic diversity of Elite-II synthetic hexaploid (SH) wheat by genome DNA fingerprinting as revealed by random amplified polymorphic DNA (RAPD) analysis. Ten decamer RAPD primers (OPG-1, OPG-2, OPG-3, OPG-4, OPG-5, OPA-3, OPA-4, OPA-5, OPA-8, and OPA-15) ...

  15. Genetic analysis on the competitive ability of barley ( Hordeum ...

    African Journals Online (AJOL)

    Genetic analysis on the competitive ability of barley ( Hordeum vulgare L.) recombinant inbred lines intercropped with oat ( Avena sativa L.) weeds. ... Furthermore, the commonly used herbicide price is soaring from time to time and out of the reach of the poor farmers in the developing countries. Therefore, this method is an ...

  16. Genetic analysis of a consanguineous Pakistani family with Leber ...

    Indian Academy of Sciences (India)

    2014-08-01

    Aug 1, 2014 ... Genetic analysis of a consanguineous Pakistani family with Leber congenital amaurosis identifies a novel mutation in GUCY2D gene. MUZAMMIL AHMAD KHAN1, VERENA RUPP2, MUHAMMAD AYAZ KHAN1, MUHAMMAD PERVAIZ KHAN3,. MUHAMMAD ANSAR4 and CHRISTIAN WINDPASSINGER2 ...

  17. Genetic analysis of antibiotic production and other phenotypic traits ...

    African Journals Online (AJOL)

    So, the present study made an attempt to study the genetics of production of antibiotic and other phenotypic properties was demonstrated by plasmid DNA curing analysis. The DNA-intercalating agent ethidium bromide was used to eliminate plasmid DNA from streptomycetes and effects of curing agent (EB) on the antibiotic ...

  18. Genetic diversity analysis of stress tolerant rice ( Oryza sativa L ...

    African Journals Online (AJOL)

    Genetic diversity analysis of stress tolerant rice (Oryza sativa L.) A S M Faridul Islam, M Raihan Ali, Glenn B Gregorio, M Rafiqul Islam. Abstract. Fourteen rice genotypes, composed of six salt tolerant, three submergence tolerant, two drought tolerant genotypes along with three high yielding genotypes, released from ...

  19. Genetic diversity analysis of pearl millet ( Pennisetum glauccum [L ...

    African Journals Online (AJOL)

    between genotype PT 2835/1 and PT 5552 and lowest similarity index was observed between PT 5554 and PT 2835/1. Analysis of RAPD data appears to be helpful in determining the genetic relationship among 20 pearl millet genotypes. The associations among the 20 genotypes were also examined with Principle ...

  20. Genetic analysis of yield in peanut (Arachis hypogaea L.) using ...

    African Journals Online (AJOL)

    Jane

    2011-07-20

    Jul 20, 2011 ... only should the two major genes' effects be considered but also the polygene's effect should be considered in breeding to increase peanut yield. Key words: Peanut, yield, major gene plus polygene inheritance model, genetic analysis. INTRODUCTION. Peanut consists of diploid (2n = 2x = 20), tetraploid ...

  1. Genetic analysis of yield in peanut ( Arachis hypogaea L.) using ...

    African Journals Online (AJOL)

    The yield had significant major gene effect and the results implied that not only should the two major genes' effects be considered but also the polygene's effect should be considered in breeding to increase peanut yield. Key words: Peanut, yield, major gene plus polygene inheritance model, genetic analysis.

  2. RAPD analysis for genetic diversity of two populations of Mystus ...

    African Journals Online (AJOL)

    STORAGESEVER

    2009-09-01

    Sep 1, 2009 ... RAPD technique is the one of the most frequently used molecular methods for taxonomic and systematic analy- ... technique was applied to analyze the genetic relationship among Mystus vittatus populations. ..... (RAPD) Analysis of Atlantic coast Striped bass. Heredity, 78: 32-40. Brahmane MP, Das MK, ...

  3. Molecular analysis of genetic diversity in elite II synthetic hexaploid ...

    African Journals Online (AJOL)

    STORAGESEVER

    2009-07-20

    Jul 20, 2009 ... Full Length Research Paper. Molecular analysis of genetic diversity in elite II synthetic hexaploid wheat screened against Barley yellow dwarf virus. Huma Saffdar1 ... The history of cultiva- ted wheat and human .... and viewed under the UV light chamber using the computer pro- gram UVIPhotoMW.

  4. Genetic diversity analysis of Labeo gonius (Hamilton, 1822) in three ...

    African Journals Online (AJOL)

    a

    2013-05-08

    May 8, 2013 ... malic enzyme (ME), phosphoglucomutase (PGM), superoxide dismutase. (SOD) and xanthine dehydrogenase (XDH). These enzymes showed consistent phenotypic variations and were therefore useful for genetic analysis. They were coded by 19 putative loci (Table 2). LDH exhibited maximum number of.

  5. Comparative analysis of inter population genetic diversity in Puntius ...

    African Journals Online (AJOL)

    The genetic variation in different population of the freshwater cyprinid Puntius filamentosus was studied using restriction fragment length polymorphism (RFLP) analysis. Samples were collected from five different locations of southern Western Ghats, India. The morphometric characters of population from Alancholai showed ...

  6. [Use of coronary angioplasty in acute myocardial infarction without previous use of thrombolytic agents. Analysis of 201 patients].

    Science.gov (United States)

    Mattos, L A; Cano, M N; Maldonado, G; Feres, F; Pinto, I M; Tanajura, L F; Piegas, L S; Barbosa, M; Timerman, A; Paulista, P P

    1990-11-01

    To evaluate the experience with the use of primary PTCA in the set of acute myocardial infarction (AMI) without the previous administration of thrombolytic agents. Two hundred and one patients with AMI, aged 35 to 86 years (mean = 57.2). There were 83.5% men. Twenty patients were older than 70 years and 48.2% had an anterior AMI. PTCA was performed early in the AMI, with a delay no longer than 12 hours. In 95%, it was done solely to the infarct related artery. Seventy percent patients were in Killip class I, 21% in class II, and 8% in classes III and IV (more than 50% of this subset of patients were in cardiogenic shock). Primary success was achieved in 84.5%. In hospital mortality was 5.9%, and there were 7% reinfarctions. Among the 84 patients who underwent a late cinecoronariography study, there were 19% restenosis and 8.3% reocclusions. In the long term follow up 75% were asymptomatic. Repeat PTCA was required in 10.2% of the cases, late coronary surgery was performed on 10.8% of the patients, and post-hospital cardiac mortality was 8.8% during an average follow up of 28 months (range 2-72 months). Primary PTCA is a effective way of reperfusion in the AMI, with a high primary success, low complications rate and without any major contraindications.

  7. Borderline personality traits and adult attention-deficit hyperactivity disorder symptoms: a genetic analysis of comorbidity.

    Science.gov (United States)

    Distel, Marijn A; Carlier, Angela; Middeldorp, Christel M; Derom, Catherine A; Lubke, Gitta H; Boomsma, Dorret I

    2011-12-01

    Previous research has established the comorbidity of adult Attention-Deficit Hyperactivity Disorder (ADHD) with different personality disorders including Borderline Personality Disorder (BPD). The association between adult ADHD and BPD has primarily been investigated at the phenotypic level and not yet at the genetic level. The present study investigates the genetic and environmental contributions to the association between borderline personality traits (BPT) and ADHD symptoms in a sample of 7,233 twins and siblings (aged 18-90 years) registered with the Netherlands Twin Register and the East Flanders Prospective Twin Survey (EFPTS) . Participants completed the Conners' Adult ADHD Rating Scales (CAARS-S:SV) and the Personality Assessment Inventory-Borderline Features Scale (PAI-BOR). A bivariate genetic analysis was performed to determine the extent to which genetic and environmental factors influence variation in BPT and ADHD symptoms and the covariance between them. The heritability of BPT and ADHD symptoms was estimated at 45 and 36%, respectively. The remaining variance in BPT and ADHD symptoms was explained by unique environmental influences. The phenotypic correlation between BPT and ADHD symptoms was estimated at r = 0.59, and could be explained for 49% by genetic factors and 51% by environmental factors. The genetic and environmental correlations between BPT and ADHD symptoms were 0.72 and 0.51, respectively. The shared etiology between BPT and ADHD symptoms is thus a likely cause for the comorbidity of the two disorders. Copyright © 2011 Wiley-Liss, Inc.

  8. Genetic Architecture of Atherosclerosis in Mice: A Systems Genetics Analysis of Common Inbred Strains

    Science.gov (United States)

    Bennett, Brian J.; Davis, Richard C.; Civelek, Mete; Orozco, Luz; Wu, Judy; Qi, Hannah; Pan, Calvin; Packard, René R. Sevag; Eskin, Eleazar; Yan, Mujing; Kirchgessner, Todd; Wang, Zeneng; Li, Xinmin; Gregory, Jill C.; Hazen, Stanley L.; Gargalovic, Peter S.; Lusis, Aldons J.

    2015-01-01

    Common forms of atherosclerosis involve multiple genetic and environmental factors. While human genome-wide association studies have identified numerous loci contributing to coronary artery disease and its risk factors, these studies are unable to control environmental factors or examine detailed molecular traits in relevant tissues. We now report a study of natural variations contributing to atherosclerosis and related traits in over 100 inbred strains of mice from the Hybrid Mouse Diversity Panel (HMDP). The mice were made hyperlipidemic by transgenic expression of human apolipoprotein E-Leiden (APOE-Leiden) and human cholesteryl ester transfer protein (CETP). The mice were examined for lesion size and morphology as well as plasma lipid, insulin and glucose levels, and blood cell profiles. A subset of mice was studied for plasma levels of metabolites and cytokines. We also measured global transcript levels in aorta and liver. Finally, the uptake of acetylated LDL by macrophages from HMDP mice was quantitatively examined. Loci contributing to the traits were mapped using association analysis, and relationships among traits were examined using correlation and statistical modeling. A number of conclusions emerged. First, relationships among atherosclerosis and the risk factors in mice resemble those found in humans. Second, a number of trait-loci were identified, including some overlapping with previous human and mouse studies. Third, gene expression data enabled enrichment analysis of pathways contributing to atherosclerosis and prioritization of candidate genes at associated loci in both mice and humans. Fourth, the data provided a number of mechanistic inferences; for example, we detected no association between macrophage uptake of acetylated LDL and atherosclerosis. Fifth, broad sense heritability for atherosclerosis was much larger than narrow sense heritability, indicating an important role for gene-by-gene interactions. Sixth, stepwise linear regression

  9. Genetic Architecture of Atherosclerosis in Mice: A Systems Genetics Analysis of Common Inbred Strains.

    Directory of Open Access Journals (Sweden)

    Brian J Bennett

    2015-12-01

    Full Text Available Common forms of atherosclerosis involve multiple genetic and environmental factors. While human genome-wide association studies have identified numerous loci contributing to coronary artery disease and its risk factors, these studies are unable to control environmental factors or examine detailed molecular traits in relevant tissues. We now report a study of natural variations contributing to atherosclerosis and related traits in over 100 inbred strains of mice from the Hybrid Mouse Diversity Panel (HMDP. The mice were made hyperlipidemic by transgenic expression of human apolipoprotein E-Leiden (APOE-Leiden and human cholesteryl ester transfer protein (CETP. The mice were examined for lesion size and morphology as well as plasma lipid, insulin and glucose levels, and blood cell profiles. A subset of mice was studied for plasma levels of metabolites and cytokines. We also measured global transcript levels in aorta and liver. Finally, the uptake of acetylated LDL by macrophages from HMDP mice was quantitatively examined. Loci contributing to the traits were mapped using association analysis, and relationships among traits were examined using correlation and statistical modeling. A number of conclusions emerged. First, relationships among atherosclerosis and the risk factors in mice resemble those found in humans. Second, a number of trait-loci were identified, including some overlapping with previous human and mouse studies. Third, gene expression data enabled enrichment analysis of pathways contributing to atherosclerosis and prioritization of candidate genes at associated loci in both mice and humans. Fourth, the data provided a number of mechanistic inferences; for example, we detected no association between macrophage uptake of acetylated LDL and atherosclerosis. Fifth, broad sense heritability for atherosclerosis was much larger than narrow sense heritability, indicating an important role for gene-by-gene interactions. Sixth, stepwise linear

  10. Analysis of a genetically structured variance heterogeneity model using the Box-Cox transformation

    DEFF Research Database (Denmark)

    Yang, Ye; Christensen, Ole Fredslund; Sorensen, Daniel

    2011-01-01

    of the marginal distribution of the data. To investigate how the scale of measurement affects inferences, the genetically structured heterogeneous variance model is extended to accommodate the family of Box–Cox transformations. Litter size data in rabbits and pigs that had previously been analysed...... in the untransformed scale were reanalysed in a scale equal to the mode of the marginal posterior distribution of the Box–Cox parameter. In the rabbit data, the statistical evidence for a genetic component at the level of the environmental variance is considerably weaker than that resulting from an analysis...... in the original metric. In the pig data, the statistical evidence is stronger, but the coefficient of correlation between additive genetic effects affecting mean and variance changes sign, compared to the results in the untransformed scale. The study confirms that inferences on variances can be strongly affected...

  11. Transcriptomic analysis in a Drosophila model identifies previously implicated and novel pathways in the therapeutic mechanism in neuropsychiatric disorders

    Directory of Open Access Journals (Sweden)

    Priyanka eSingh

    2011-03-01

    Full Text Available We have taken advantage of a newly described Drosophila model to gain insights into the potential mechanism of antiepileptic drugs (AEDs, a group of drugs that are widely used in the treatment of several neurological and psychiatric conditions besides epilepsy. In the recently described Drosophila model that is inspired by pentylenetetrazole (PTZ induced kindling epileptogenesis in rodents, chronic PTZ treatment for seven days causes a decreased climbing speed and an altered CNS transcriptome, with the latter mimicking gene expression alterations reported in epileptogenesis. In the model, an increased climbing speed is further observed seven days after withdrawal from chronic PTZ. We used this post-PTZ withdrawal regime to identify potential AED mechanism. In this regime, treatment with each of the five AEDs tested, namely, ethosuximide (ETH, gabapentin (GBP, vigabatrin (VGB, sodium valproate (NaVP and levetiracetam (LEV, resulted in rescuing of the altered climbing behavior. The AEDs also normalized PTZ withdrawal induced transcriptomic perturbation in fly heads; whereas AED untreated flies showed a large number of up- and down-regulated genes which were enriched in several processes including gene expression and cell communication, the AED treated flies showed differential expression of only a small number of genes that did not enrich gene expression and cell communication processes. Gene expression and cell communication related upregulated genes in AED untreated flies overrepresented several pathways - spliceosome, RNA degradation, and ribosome in the former category, and inositol phosphate metabolism, phosphatidylinositol signaling, endocytosis and hedgehog signaling in the latter. Transcriptome remodeling effect of AEDs was overall confirmed by microarray clustering that clearly separated the profiles of AED treated and untreated flies. Besides being consistent with previously implicated pathways, our results provide evidence for a role of

  12. Genetic Investigation of Uterine Carcinosarcoma: Case Report and Cohort Analysis.

    Science.gov (United States)

    Hembree, Timothy N; Teer, Jamie K; Hakam, Ardeshir; Chiappori, Alberto A

    2016-01-01

    Uterine carcinosarcoma, a rare gynecological malignancy, often presents at the advanced stage with a poor prognosis because current therapies have not improved rates of survival. Genetic characterization of this tumor may lead to novel, specifically targeted drug targets to provide better treatment options for patients with this malignancy. We present a case of a woman aged 61 years with uterine carcinosarcoma and retrospectively analyzed 100 study patients with uterine carcinosarcoma. From this group, 9 study patients underwent targeted sequencing of 1,321 genes. All 9 study patients had at least 1 mutation in JAK2, KRAS, PIK3CA, CTNNB1, PTEN, FBXW7, TP53, and ERBB2; of these, TP53 was the most frequently mutated gene (6/9). In addition, ARID1A and KMT2C, which have been described and identified as part of a set of chromatin-remodeling genes, were also found in our analyses. From our 100-person cohort clinical analyses, study patients with stage 1 cancer had a median survival rate of 33 months (95% confidence interval, 19-109) compared with a median survival rate of 6 months (95% confidence interval, 3-12) in those with stage 4 disease. Disease stage alone predicted the rate of clinical survival. Up to 50% in the study group were identified at having early stage disease (stage 1/2), indicating improved rates of overall detection compared with previously reported data. Our mutational analysis findings add to the number of tumors in which these mutations have been found and suggest that chromatin-remodeling dysregulation may play a role in the tumorigenesis of carcinosarcoma.

  13. Analysis of guest binary mixtures by tert-butylcalix[6]arene using host memory of previously bound guests.

    Science.gov (United States)

    Safina, Goulnaz D; Ziganshin, Marat A; Gubaidullin, Aidar T; Gorbatchuk, Valery V

    2013-02-28

    A new principle of quantitative and qualitative analysis of binary organic mixtures is offered, which is based on an ability of calixarene receptor for specific polymorphic transitions related to the composition of the analyzed guest mixture. The ability of tert-butylcalix[6]arene to remember selectively some guests bound from headspace both of pure liquids and their binary mixtures is used. The image of guest mixture remains written in metastable polymorphs of host after partial or complete guest elimination from clathrates. The memory was read using differential scanning calorimetry as the enthalpy of exothermic polymorphic transition of host collapse. This enthalpy monotonously changes with the variation of guests' ratio in mixture, unlike the enthalpies of endothermic pseudopolymorphic transitions of guest release. So, the composition of volatile binary mixture can be estimated using only one receptor and only one its parameter even in absence of preferential binding from a binary mixture of guests. This is an example of a genuine molecular recognition.

  14. Accelerating epistasis analysis in human genetics with consumer graphics hardware

    Directory of Open Access Journals (Sweden)

    Cancare Fabio

    2009-07-01

    Full Text Available Abstract Background Human geneticists are now capable of measuring more than one million DNA sequence variations from across the human genome. The new challenge is to develop computationally feasible methods capable of analyzing these data for associations with common human disease, particularly in the context of epistasis. Epistasis describes the situation where multiple genes interact in a complex non-linear manner to determine an individual's disease risk and is thought to be ubiquitous for common diseases. Multifactor Dimensionality Reduction (MDR is an algorithm capable of detecting epistasis. An exhaustive analysis with MDR is often computationally expensive, particularly for high order interactions. This challenge has previously been met with parallel computation and expensive hardware. The option we examine here exploits commodity hardware designed for computer graphics. In modern computers Graphics Processing Units (GPUs have more memory bandwidth and computational capability than Central Processing Units (CPUs and are well suited to this problem. Advances in the video game industry have led to an economy of scale creating a situation where these powerful components are readily available at very low cost. Here we implement and evaluate the performance of the MDR algorithm on GPUs. Of primary interest are the time required for an epistasis analysis and the price to performance ratio of available solutions. Findings We found that using MDR on GPUs consistently increased performance per machine over both a feature rich Java software package and a C++ cluster implementation. The performance of a GPU workstation running a GPU implementation reduces computation time by a factor of 160 compared to an 8-core workstation running the Java implementation on CPUs. This GPU workstation performs similarly to 150 cores running an optimized C++ implementation on a Beowulf cluster. Furthermore this GPU system provides extremely cost effective

  15. Accelerating epistasis analysis in human genetics with consumer graphics hardware.

    Science.gov (United States)

    Sinnott-Armstrong, Nicholas A; Greene, Casey S; Cancare, Fabio; Moore, Jason H

    2009-07-24

    Human geneticists are now capable of measuring more than one million DNA sequence variations from across the human genome. The new challenge is to develop computationally feasible methods capable of analyzing these data for associations with common human disease, particularly in the context of epistasis. Epistasis describes the situation where multiple genes interact in a complex non-linear manner to determine an individual's disease risk and is thought to be ubiquitous for common diseases. Multifactor Dimensionality Reduction (MDR) is an algorithm capable of detecting epistasis. An exhaustive analysis with MDR is often computationally expensive, particularly for high order interactions. This challenge has previously been met with parallel computation and expensive hardware. The option we examine here exploits commodity hardware designed for computer graphics. In modern computers Graphics Processing Units (GPUs) have more memory bandwidth and computational capability than Central Processing Units (CPUs) and are well suited to this problem. Advances in the video game industry have led to an economy of scale creating a situation where these powerful components are readily available at very low cost. Here we implement and evaluate the performance of the MDR algorithm on GPUs. Of primary interest are the time required for an epistasis analysis and the price to performance ratio of available solutions. We found that using MDR on GPUs consistently increased performance per machine over both a feature rich Java software package and a C++ cluster implementation. The performance of a GPU workstation running a GPU implementation reduces computation time by a factor of 160 compared to an 8-core workstation running the Java implementation on CPUs. This GPU workstation performs similarly to 150 cores running an optimized C++ implementation on a Beowulf cluster. Furthermore this GPU system provides extremely cost effective performance while leaving the CPU available for other

  16. Random amplified polymorphic DNA analysis of genetically modified organisms.

    Science.gov (United States)

    Yoke-Kqueen, Cheah; Radu, Son

    2006-12-15

    Randomly amplified polymorphic DNA (RAPD) was used to analyzed 78 samples comprises of certified reference materials (soya and maize powder), raw seeds (soybean and maize), processed food and animal feed. Combination assay of two arbitrary primers in the RAPD analysis enable to distinguish genetically modified organism (GMO) reference materials from the samples tested. Dendrogram analysis revealed 13 clusters at 45% similarity from the RAPD. RAPD analysis showed that the maize and soybean samples were clustered differently besides the GMO and non-GMO products.

  17. Genetic analysis in the Collaborative Cross breeding population

    Energy Technology Data Exchange (ETDEWEB)

    Philip, Vivek [University of Tennessee, Knoxville (UTK); Sokoloff, Greta [ORNL; Ackert-Bicknell, Cheryl [Jackson Laboratory, The, Bar Harbor, ME; Striz, Martin [University of Kentucky, Lexington; Branstetter, Lisa R [ORNL; Beckmann, Melissa [ORNL; Spence, Jason S [ORNL; Jackson, Barbara L [ORNL; Galloway, Leslie D [ORNL; Barker, Gene [ORNL; Wymore, Ann M [Oak Ridge National Laboratory (ORNL); Hunsicker, Patricia R [ORNL; Durtschi, David W [University of Kentucky, Lexington; Shaw, Ginger S [University of Kentucky, Lexington; Shinpock, Sarah G [ORNL; Manly, Kenneth F [University of Kentucky, Lexington; Miller, Darla R [ORNL; Donahue, Kevin [University at Buffalo, NY; Culiat, Cymbeline T [ORNL; Churchill, Gary A [Jackson Laboratory, The, Bar Harbor, ME; Lariviere, William R [University of Pittsburgh; Palmer, Abraham [University of Chicago; O' Hara, Bruce [University of Kentucky; Voy, Brynn H [ORNL; Chesler, Elissa J [ORNL

    2011-01-01

    Genetic reference populations in model organisms are critical resources for systems genetic analysis of disease related phenotypes. The breeding history of these inbred panels may influence detectable allelic and phenotypic diversity. The existing panel of common inbred strains reflects historical selection biases, and existing recombinant inbred panels have low allelic diversity. All such populations may be subject to consequences of inbreeding depression. The Collaborative Cross (CC) is a mouse reference population with high allelic diversity that is being constructed using a randomized breeding design that systematically outcrosses eight founder strains, followed by inbreeding to obtain new recombinant inbred strains. Five of the eight founders are common laboratory strains, and three are wild-derived. Since its inception, the partially inbred CC has been characterized for physiological, morphological, and behavioral traits. The construction of this population provided a unique opportunity to observe phenotypic variation as new allelic combinations arose through intercrossing and inbreeding to create new stable genetic combinations. Processes including inbreeding depression and its impact on allelic and phenotypic diversity were assessed. Phenotypic variation in the CC breeding population exceeds that of existing mouse genetic reference populations due to both high founder genetic diversity and novel epistatic combinations. However, some focal evidence of allele purging was detected including a suggestive QTL for litter size in a location of changing allele frequency. Despite these inescapable pressures, high diversity and precision for genetic mapping remain. These results demonstrate the potential of the CC population once completed and highlight implications for development of related populations. Supplementary material consists of Supplementary Table 1 Phenotypic means, variances, ranges and heritabilities for all traits and generations, Supplementary Table

  18. Gene expression and genetic analysis during higher plants embryogenesis

    OpenAIRE

    Abid, Ghassen; Jaquemin, Jean-Marie; Sassi, Khaled; Muhovski, Yordan; Toussaint, André; Baudoin, Jean-Pierre

    2010-01-01

    This review describes and discusses recent attempts to analyze the embryogenesis process in higher plants, through combination of descriptive, experimental, and genetic approach. Analysis of gene expression profiles has permitted to build hypothesis concerning the induced mechanisms in early phases of embryogenesis in higher plants. Such mechanisms involve specific transcriptional and post-transcriptional regulatory pathways as well as diverse signal transduction processes at each stage of p...

  19. Genetic analysis of growth traits in Iranian Makuie sheep breed

    Directory of Open Access Journals (Sweden)

    Mohammad Farhadian

    2012-01-01

    Full Text Available The Makuie sheep is a fat-tailed sheep breed which can be found in the Azerbaijan province of Iran. In 1986, a Makuie sheep breeding station was established in the city of Maku in order to breed, protect and purify this breed. The genetic parameters for birth weight, weaning weight (3 months, 6-month, 9-month and yearling weight, and average daily gain from birth to weaning traits were estimated based on 25 years of data using DFREML software. Six different models were applied and a likelihood ratio test (LRT was used to select the appropriate model. Bivariate analysis was used to define the genetic correlation between studied traits. Based on the LRT, model II was selected as an appropriate model for all studied traits. Direct heritability estimates of birth, weaning, 6-month, 9-month and yearling weights and average daily gain from birth to weaning were 0.36, 0.41, 0.48, 0.42, 0.36 and 0.37, respectively. Estimates of direct genetic correlation between birth and weaning weights, birth and 6-month weights, birth and 9-month weights, as well as between birth and yearling weights were 0.57, 0.49, 0.46 and 0.32, respectively. The results suggest there is a substantial additive genetic variability for studied traits in the Makuie sheep breed population, and the direct additive effect and maternal permanent environment variance are the main source of phenotypic variance.

  20. Systematic documentation and analysis of human genetic variation using the microattribution approach

    Science.gov (United States)

    Giardine, Belinda; Borg, Joseph; Higgs, Douglas R.; Peterson, Kenneth R.; Maglott, Donna; Basak, A. Nazli; Clark, Barnaby; Faustino, Paula; Felice, Alex E.; Francina, Alain; Gallivan, Monica V. E.; Georgitsi, Marianthi; Gibbons, Richard J.; Giordano, Piero C.; Harteveld, Cornelis L.; Joly, Philippe; Kanavakis, Emmanuel; Kollia, Panagoula; Menzel, Stephan; Miller, Webb; Moradkhani, Kamran; Old, John; Papachatzopoulou, Adamantia; Papadakis, Manoussos N.; Papadopoulos, Petros; Pavlovic, Sonja; Philipsen, Sjaak; Radmilovic, Milena; Riemer, Cathy; Schrijver, Iris; Stojiljkovic, Maja; Thein, Swee Lay; Traeger-Synodinos, Jan; Tully, Ray; Wada, Takahito; Waye, John; Wiemann, Claudia; Zukic, Branka; Chui, David H. K.; Wajcman, Henri; Hardison, Ross C.; Patrinos, George P.

    2013-01-01

    We developed a series of interrelated locus-specific databases to store all published and unpublished genetic variation related to these disorders, and then implemented microattribution to encourage submission of unpublished observations of genetic variation to these public repositories 1. A total of 1,941 unique genetic variants in 37 genes, encoding globins (HBA2, HBA1, HBG2, HBG1, HBD, HBB) and other erythroid proteins (ALOX5AP, AQP9, ARG2, ASS1, ATRX, BCL11A, CNTNAP2, CSNK2A1, EPAS1, ERCC2, FLT1, GATA1, GPM6B, HAO2, HBS1L, KDR, KL, KLF1, MAP2K1, MAP3K5, MAP3K7, MYB, NOS1, NOS2, NOS3, NOX3, NUP133, PDE7B, SMAD3, SMAD6, and TOX) are currently documented in these databases with reciprocal attribution of microcitations to data contributors. Our project provides the first example of implementing microattribution to incentivise submission of all known genetic variation in a defined system. It has demonstrably increased the reporting of human variants and now provides a comprehensive online resource for systematically describing human genetic variation in the globin genes and other genes contributing to hemoglobinopathies and thalassemias. The large repository of previously reported data, together with more recent data, acquired by microattribution, demonstrates how the comprehensive documentation of human variation will provide key insights into normal biological processes and how these are perturbed in human genetic disease. Using the microattribution process set out here, datasets which took decades to accumulate for the globin genes could be assembled rapidly for other genes and disease systems. The principles established here for the globin gene system will serve as a model for other systems and the analysis of other common and/or complex human genetic diseases. PMID:21423179

  1. Genome-wide Comparative Analysis of Atopic Dermatitis and Psoriasis Gives Insight into Opposing Genetic Mechanisms

    Science.gov (United States)

    Baurecht, Hansjörg; Hotze, Melanie; Brand, Stephan; Büning, Carsten; Cormican, Paul; Corvin, Aiden; Ellinghaus, David; Ellinghaus, Eva; Esparza-Gordillo, Jorge; Fölster-Holst, Regina; Franke, Andre; Gieger, Christian; Hubner, Norbert; Illig, Thomas; Irvine, Alan D.; Kabesch, Michael; Lee, Young A.E.; Lieb, Wolfgang; Marenholz, Ingo; McLean, W.H. Irwin; Morris, Derek W.; Mrowietz, Ulrich; Nair, Rajan; Nöthen, Markus M.; Novak, Natalija; O’Regan, Grainne M.; Schreiber, Stefan; Smith, Catherine; Strauch, Konstantin; Stuart, Philip E.; Trembath, Richard; Tsoi, Lam C.; Weichenthal, Michael; Barker, Jonathan; Elder, James T.; Weidinger, Stephan; Cordell, Heather J.; Brown, Sara J.

    2015-01-01

    Atopic dermatitis and psoriasis are the two most common immune-mediated inflammatory disorders affecting the skin. Genome-wide studies demonstrate a high degree of genetic overlap, but these diseases have mutually exclusive clinical phenotypes and opposing immune mechanisms. Despite their prevalence, atopic dermatitis and psoriasis very rarely co-occur within one individual. By utilizing genome-wide association study and ImmunoChip data from >19,000 individuals and methodologies developed from meta-analysis, we have identified opposing risk alleles at shared loci as well as independent disease-specific loci within the epidermal differentiation complex (chromosome 1q21.3), the Th2 locus control region (chromosome 5q31.1), and the major histocompatibility complex (chromosome 6p21–22). We further identified previously unreported pleiotropic alleles with opposing effects on atopic dermatitis and psoriasis risk in PRKRA and ANXA6/TNIP1. In contrast, there was no evidence for shared loci with effects operating in the same direction on both diseases. Our results show that atopic dermatitis and psoriasis have distinct genetic mechanisms with opposing effects in shared pathways influencing epidermal differentiation and immune response. The statistical analysis methods developed in the conduct of this study have produced additional insight from previously published data sets. The approach is likely to be applicable to the investigation of the genetic basis of other complex traits with overlapping and distinct clinical features. PMID:25574825

  2. A strategy analysis for genetic association studies with known inbreeding

    Directory of Open Access Journals (Sweden)

    del Giacco Stefano

    2011-07-01

    Full Text Available Abstract Background Association studies consist in identifying the genetic variants which are related to a specific disease through the use of statistical multiple hypothesis testing or segregation analysis in pedigrees. This type of studies has been very successful in the case of Mendelian monogenic disorders while it has been less successful in identifying genetic variants related to complex diseases where the insurgence depends on the interactions between different genes and the environment. The current technology allows to genotype more than a million of markers and this number has been rapidly increasing in the last years with the imputation based on templates sets and whole genome sequencing. This type of data introduces a great amount of noise in the statistical analysis and usually requires a great number of samples. Current methods seldom take into account gene-gene and gene-environment interactions which are fundamental especially in complex diseases. In this paper we propose to use a non-parametric additive model to detect the genetic variants related to diseases which accounts for interactions of unknown order. Although this is not new to the current literature, we show that in an isolated population, where the most related subjects share also most of their genetic code, the use of additive models may be improved if the available genealogical tree is taken into account. Specifically, we form a sample of cases and controls with the highest inbreeding by means of the Hungarian method, and estimate the set of genes/environmental variables, associated with the disease, by means of Random Forest. Results We have evidence, from statistical theory, simulations and two applications, that we build a suitable procedure to eliminate stratification between cases and controls and that it also has enough precision in identifying genetic variants responsible for a disease. This procedure has been successfully used for the beta-thalassemia, which is

  3. DMPD: The Toll-like receptors: analysis by forward genetic methods. [Dynamic Macrophage Pathway CSML Database

    Lifescience Database Archive (English)

    Full Text Available 16001129 The Toll-like receptors: analysis by forward genetic methods. Beutler B. I...mmunogenetics. 2005 Jul;57(6):385-92. (.png) (.svg) (.html) (.csml) Show The Toll-like receptors: analysis by forwar...d genetic methods. PubmedID 16001129 Title The Toll-like receptors: analysis by forward genetic meth

  4. [Genetic analysis of family constellation for cochlear implant recipients].

    Science.gov (United States)

    Zhang, Chu-Qin; Chen, Bo-Bei; Huang, Jia-Yun; Sun, Dong-Mei; Chen, Ying-Ying; Xiang, Song-Jie; Guan, Min-Xin

    2008-11-01

    GJB2, SLC26A4 (PDS) and mitochondrial DNA (mtDNA) have been associated with sensorineural hearing loss. In the present study, the clinical, genetic and molecular analysis of 14 cochlear implant recipients and their parents was studied from April 2006 to September 2007. Of the 14 subjects, 35.7% had gene mutations; 28.6% had homozygous GJB2 235delC mutation, whose parents carried heterozygous GJB2 235delC mutation; and 7.1% had mtDNA A1555G mutation, whose mother carried mtDNA A1555G mutation too. There was no SLC26A4 (PDS) mutation. These results strongly suggested that the mutation in GJB2 gene was a major cause of deafness in cochlear implant recipients and the mutation of mtDNA A1555G was another important cause. Genetic test of hot-spots and analysis of family constellation can offer an accurate genetic counseling to deaf family and reduce the incidence of hearing loss.

  5. Analysis of genetic polymorphism of nine short tandem repeat loci in ...

    African Journals Online (AJOL)

    Yomi

    2012-03-15

    Mar 15, 2012 ... and they may be of great value in forensic science and human population genetics. Key words: short tandem repeat, repeat motif, genetic polymorphism, Han population, forensic genetics. INTRODUCTION. Short tandem repeat (STR) is widely used today for gene mapping, genetic linkage analysis, and ...

  6. Extended genetic analysis of Brazilian isolates of Bacillus cereus and Bacillus thuringiensis

    Directory of Open Access Journals (Sweden)

    Viviane Zahner

    2013-02-01

    Full Text Available Multiple locus sequence typing (MLST was undertaken to extend the genetic characterization of 29 isolates of Bacillus cereus and Bacillus thuringiensis previously characterized in terms of presence/absence of sequences encoding virulence factors and via variable number tandem repeat (VNTR. Additional analysis involved polymerase chain reaction for the presence of sequences (be, cytK, inA, pag, lef, cya and cap, encoding putative virulence factors, not investigated in the earlier study. MLST analysis ascribed novel and unique sequence types to each of the isolates. A phylogenetic tree was constructed from a single sequence of 2,838 bp of concatenated loci sequences. The strains were not monophyletic by analysis of any specific housekeeping gene or virulence characteristic. No clear association in relation to source of isolation or to genotypic profile based on the presence or absence of putative virulence genes could be identified. Comparison of VNTR profiling with MLST data suggested a correlation between these two methods of genetic analysis. In common with the majority of previous studies, MLST was unable to provide clarification of the basis for pathogenicity among members of the B. cereus complex. Nevertheless, our application of MLST served to reinforce the notion that B. cereus and B. thuringiensis should be considered as the same species.

  7. Standardization of RAPD assay for genetic analysis of olive

    African Journals Online (AJOL)

    PRECIOUS

    2009-12-15

    Dec 15, 2009 ... europaea L. Genetic variability and molecular cultivar identification. Genet. Res. Crop Evol. 54(1): 117-128. Mir Ali N, Nabulsi I (2003). Genetic diversity of almond (Prunus dulcis) using RAPD technique, Sci. Hort. 98: 461-471. Nei M (1972). Nei's Original Measures of Genetic Identity and Genetic. Distance.

  8. Genetic analysis of Aralia cordata thunb by RAPD | Qu | African ...

    African Journals Online (AJOL)

    The total genetic diversity (HT) of RAPD, intraspecific genetic diversity (HS) and genetic diversity (DST) of the various places was respectively 26.33%, 11.14%, and 49.36%. The differentiation among the species accounted for 98.76% of total genetic diversity (GST). Based on the cluster results of genetic distance, the 8 ...

  9. Pantoea ananatis Genetic Diversity Analysis Reveals Limited Genomic Diversity as Well as Accessory Genes Correlated with Onion Pathogenicity

    Science.gov (United States)

    Stice, Shaun P.; Stumpf, Spencer D.; Gitaitis, Ron D.; Kvitko, Brian H.; Dutta, Bhabesh

    2018-01-01

    Pantoea ananatis is a member of the family Enterobacteriaceae and an enigmatic plant pathogen with a broad host range. Although P. ananatis strains can be aggressive on onion causing foliar necrosis and onion center rot, previous genomic analysis has shown that P. ananatis lacks the primary virulence secretion systems associated with other plant pathogens. We assessed a collection of fifty P. ananatis strains collected from Georgia over three decades to determine genetic factors that correlated with onion pathogenic potential. Previous genetic analysis studies have compared strains isolated from different hosts with varying diseases potential and isolation sources. Strains varied greatly in their pathogenic potential and aggressiveness on different cultivated Allium species like onion, leek, shallot, and chive. Using multi-locus sequence analysis (MLSA) and repetitive extragenic palindrome repeat (rep)-PCR techniques, we did not observe any correlation between onion pathogenic potential and genetic diversity among strains. Whole genome sequencing and pan-genomic analysis of a sub-set of 10 strains aided in the identification of a novel series of genetic regions, likely plasmid borne, and correlating with onion pathogenicity observed on single contigs of the genetic assemblies. We named these loci Onion Virulence Regions (OVR) A-D. The OVR loci contain genes involved in redox regulation as well as pectate lyase and rhamnogalacturonase genes. Previous studies have not identified distinct genetic loci or plasmids correlating with onion foliar pathogenicity or pathogenicity on a single host pathosystem. The lack of focus on a single host system for this phytopathgenic disease necessitates the pan-genomic analysis performed in this study. PMID:29491851

  10. Systematic analysis, comparison, and integration of disease based human genetic association data and mouse genetic phenotypic information

    Directory of Open Access Journals (Sweden)

    Wang S Alex

    2010-01-01

    Full Text Available Abstract Background The genetic contributions to human common disorders and mouse genetic models of disease are complex and often overlapping. In common human diseases, unlike classical Mendelian disorders, genetic factors generally have small effect sizes, are multifactorial, and are highly pleiotropic. Likewise, mouse genetic models of disease often have pleiotropic and overlapping phenotypes. Moreover, phenotypic descriptions in the literature in both human and mouse are often poorly characterized and difficult to compare directly. Methods In this report, human genetic association results from the literature are summarized with regard to replication, disease phenotype, and gene specific results; and organized in the context of a systematic disease ontology. Similarly summarized mouse genetic disease models are organized within the Mammalian Phenotype ontology. Human and mouse disease and phenotype based gene sets are identified. These disease gene sets are then compared individually and in large groups through dendrogram analysis and hierarchical clustering analysis. Results Human disease and mouse phenotype gene sets are shown to group into disease and phenotypically relevant groups at both a coarse and fine level based on gene sharing. Conclusion This analysis provides a systematic and global perspective on the genetics of common human disease as compared to itself and in the context of mouse genetic models of disease.

  11. Genetic Analysis of Oncorhynchus Nerka : Life History and Genetic Analysis of Redfish Lake Oncorhynchus Nerka, 1993-1994 Completion Report.

    Energy Technology Data Exchange (ETDEWEB)

    Brannon, E.L.; Thorgaard, G.H.; Cummings, S.A.

    1994-10-01

    The study has shown through life history examination and DNA analysis that three forms of O. nerka are present in Redfish Lake. The three forms are closely related, but may be sufficiently different to be considered three separate stocks. Fishhook Creek kokanee are temporally isolated from the beach spawners, and may represent the gene pool most similar to the historic sockeye population that once spawned there. Fishhook Creek offers the best spawning area available in the lake system, and should be considered for use in reestablishing an anadromous Fishhook Creek sockeye swain. The resident beach spawning strain of O. nerka is likewise the most similar genetic form of the companion anadromous beach spawning O. nerka, and needs to be considered the most appropriate genetic source to help minimize reduced fitness of the sockeye from inbreeding.

  12. A meta-analysis of drug resistant tuberculosis in Sub-Saharan Africa: how strongly associated with previous treatment and HIV co-infection?

    Science.gov (United States)

    Berhan, Asres; Berhan, Yifru; Yizengaw, Desalegn

    2013-11-01

    In Sub-Saharan Africa, the fight against tuberculosis (TB) has encountered a great challenge because of the emergence of drug resistant TB strains and the high prevalence of HIV infection. The aim of this meta-analysis was to determine the association of drug-resistant TB with anti-TB drug treatment history and HIV co-infection. After electronic based literature search in the databases of Medline, HINARI, EMBASE and the Cochrane library, article selection and data extraction were carried out. HIV co-infection and previous history of TB treatment were used as predictors for the occurrence of any anti-TB drug resistant or multiple drug resistant TB (MDR-TB). The risk ratios for each included study and for the pooled sample were computed using the random-effects model. Heterogeneity test, sensitivity analyses and funnel plots were also done. The pooled analysis showed that the risk of developing drug-resistant TB to at least one anti-TB drug was about 3 times higher in individuals who had a previous history of anti-TB treatment than new TB cases. The risk of having MDR-TB in previously anti-TB treated TB cases was more than 5-fold higher than that of new TB cases. Resistance to Ethambutol and Rifampicin was more than fivefold higher among the previously treated with anti-TB drugs. However, HIV infection was not associated with drug-resistant TB. There was a strong association of previous anti-TB treatment with MDR-TB. Primary treatment warrants special emphasis, and screening for anti-TB drugs sensitivity has to be strengthened.

  13. PREVIOUS SECOND TRIMESTER ABORTION

    African Journals Online (AJOL)

    PNLC

    PREVIOUS SECOND TRIMESTER ABORTION: A risk factor for third trimester uterine rupture in three ... for accurate diagnosis of uterine rupture. KEY WORDS: Induced second trimester abortion - Previous uterine surgery - Uterine rupture. ..... scarred uterus during second trimester misoprostol- induced labour for a missed ...

  14. EMBO Course “Formal Analysis of Genetic Regulation”

    CERN Document Server

    1979-01-01

    The E M B 0 course on "Formal Analysis of Genetic Regulation" A course entitled "Formal analysis of Genetic Regulation" was held at the University of Brussels from 6 to 16 September 1977 under the auspices of EMBO (European Molecular Biology Organization). As indicated by the title of the book (but not explicitly enough by the title of the course), the main emphasis was put on a dynamic analysis of systems using logical methods, that is, methods in which functions and variables take only a limited number of values - typically two. In this respect, this course was complementary to an EMBO course using continuous methods which was held some months later in Israel by Prof. Segel. People from four very different laboratories took an active part in teaching our course in Brussels : Drs Anne LEUSSLER and Philippe VAN HAM, from the Laboratory of Prof. Jean FLORINE (Laboratoire des Systemes logiques et numeriques, Faculte des Sciences appliquees, Universite Libre de Bruxelles). Dr Stuart KAUFFMAN (Dept. of Biochemist...

  15. A cluster analysis on road traffic accidents using genetic algorithms

    Science.gov (United States)

    Saharan, Sabariah; Baragona, Roberto

    2017-04-01

    The analysis of traffic road accidents is increasingly important because of the accidents cost and public road safety. The availability or large data sets makes the study of factors that affect the frequency and severity accidents are viable. However, the data are often highly unbalanced and overlapped. We deal with the data set of the road traffic accidents recorded in Christchurch, New Zealand, from 2000-2009 with a total of 26440 accidents. The data is in a binary set and there are 50 factors road traffic accidents with four level of severity. We used genetic algorithm for the analysis because we are in the presence of a large unbalanced data set and standard clustering like k-means algorithm may not be suitable for the task. The genetic algorithm based on clustering for unknown K, (GCUK) has been used to identify the factors associated with accidents of different levels of severity. The results provided us with an interesting insight into the relationship between factors and accidents severity level and suggest that the two main factors that contributes to fatal accidents are "Speed greater than 60 km h" and "Did not see other people until it was too late". A comparison with the k-means algorithm and the independent component analysis is performed to validate the results.

  16. Genetic analysis of bulimia nervosa: methods and sample description.

    Science.gov (United States)

    Kaye, Walter H; Devlin, Bernie; Barbarich, Nicole; Bulik, Cynthia M; Thornton, Laura; Bacanu, Silviu-Alin; Fichter, Manfred M; Halmi, Katherine A; Kaplan, Allan S; Strober, Michael; Woodside, D Blake; Bergen, Andrew W; Crow, Scott; Mitchell, James; Rotondo, Alessandro; Mauri, Mauro; Cassano, Giovanni; Keel, Pamela; Plotnicov, Katherine; Pollice, Christine; Klump, Kelly L; Lilenfeld, Lisa R; Ganjei, J Kelly; Quadflieg, Norbert; Berrettini, Wade H

    2004-05-01

    Twin and family studies suggest that genetic variants contribute to the pathogenesis of bulimia nervosa (BN) and anorexia nervosa (AN). The Price Foundation has supported an international, multisite study of families with these disorders to identify these genetic variations. The current study presents the clinical characteristics of this sample as well as a description of the study methodology. All probands met modified criteria for BN or bulimia nervosa with a history of AN (BAN) as defined in the 4th ed. of the Diagnostic and Statistical Manual of Mental Disorders (DSM-IV; American Psychiatric Association, 1994). All affected relatives met DSM-IV criteria for BN, AN, BAN, or eating disorders not otherwise specified (EDNOS). Probands and affected relatives were assessed diagnostically using both trained-rater and self-report assessments. DNA samples were collected from probands, affected relatives, and available biologic parents. Assessments were obtained from 163 BN probands and 165 BAN probands. Overall, there were 365 relative pairs available for linkage analysis. Of the affected relatives of BN probands, 62 were diagnosed as BN (34.8%), 49 as BAN (27.5%), 35 as AN (19.7%), and 32 as EDNOS (18.0%). For the relatives of BAN probands, 42 were diagnosed as BN (22.5%), 67 as BAN (35.8%), 48 as AN (25.7%), and 30 as EDNOS (16.0%). This study represents the largest genetic study of eating disorders to date. Clinical data indicate that although there are a large number of individuals with BN disorders, a range of eating pathology is represented in the sample, allowing for the examination of several different phenotypes in molecular genetic analyses. Copyright 2004 by Wiley Periodicals, Inc. Int J Eat Disord 35: 556-570, 2004.

  17. [Wolfram syndrome: clinical and genetic analysis in two sisters].

    Science.gov (United States)

    Conart, J-B; Maalouf, T; Jonveaux, P; Guerci, B; Angioi, K

    2011-10-01

    Wolfram syndrome is a severe genetic disorder defined by the association of diabetes mellitus, optic atrophy, deafness, and diabetes insipidus. Two sisters complained of progressive visual loss. Fundus examination evidenced optic atrophy. Their past medical history revealed diabetes mellitus and deafness since childhood. The association of these symptoms made the diagnosis of Wolfram syndrome possible. It was confirmed by molecular analysis, which evidenced composite WFS1 heterozygous mutations inherited from both their mother and father. Ophthalmologists should be aware of the possibility of Wolfram syndrome when diagnosing optic atrophy in diabetic children. Copyright © 2011 Elsevier Masson SAS. All rights reserved.

  18. Population genetic structure of economically important Tortricidae (Lepidoptera) in South Africa: a comparative analysis.

    Science.gov (United States)

    Timm, A E; Geertsema, H; Warnich, L

    2010-08-01

    Comparative studies of the population genetic structures of agricultural pests can elucidate the factors by which their population levels are affected, which is useful for designing pest management programs. This approach was used to provide insight into the six Tortricidae of major economic importance in South Africa. The population genetic structure of the carnation worm E. acerbella and the false codling moth T. leucotreta, analyzed using amplified fragment length polymorphism (AFLP) analysis, is presented here for the first time. These results were compared with those obtained previously for the codling moth Cydia pomonella, the oriental fruit moth Grapholita molesta, the litchi moth Cryptophlebia peltastica and the macadamia nut borer T. batrachopa. Locally adapted populations were detected over local geographic areas for all species. No significant differences were found among population genetic structures as result of population history (whether native or introduced) although host range (whether oligophagous or polyphagous) had a small but significant effect. It is concluded that factors such as dispersal ability and agricultural practices have the most important effects on genetically structuring populations of the economically important Tortricidae in South Africa.

  19. Dielectrophoretic capture and genetic analysis of single neuroblastoma tumor cells

    Directory of Open Access Journals (Sweden)

    Erica L Carpenter

    2014-07-01

    Full Text Available Our understanding of the diversity of cells that escape the primary tumor and seed micrometastases remains rudimentary, and approaches for studying circulating and disseminated tumor cells have been limited by low throughput and sensitivity, reliance on single parameter sorting, and a focus on enumeration rather than phenotypic and genetic characterization. Here we utilize a highly sensitive microfluidic and dielectrophoretic approach for the isolation and genetic analysis of individual tumor cells. We employed fluorescence labeling to isolate 208 single cells from spiking experiments conducted with 11 cell lines, including 8 neuroblastoma cell lines, and achieved a capture sensitivity of 1 tumor cell per 106 white blood cells. Sample fixation or freezing had no detectable effect on cell capture. Point mutations were accurately detected in the whole genome amplification product of captured single tumor cells but not in negative control white blood cells. We applied this approach to capture 144 single tumor cells from 10 bone marrow samples from patients suffering from neuroblastoma. In this pediatric malignancy, high-risk patients often exhibit wide-spread hematogenous metastasis, but access to primary tumor can be difficult or impossible. Here we used flow-based sorting to pre-enrich samples with tumor involvement below 0.02%. For all patients for whom a mutation in the Anaplastic Lymphoma Kinase gene had already been detected in their primary tumor, the same mutation was detected in single cells from their marrow. These findings demonstrate a novel, non-invasive, and adaptable method for the capture and genetic analysis of single tumor cells from cancer patients.

  20. Analysis of current research addressing complementary use of life-cycle assessment and risk assessment for engineered nanomaterials: have lessons been learned from previous experience with chemicals?

    DEFF Research Database (Denmark)

    Grieger, Khara Deanne; Laurent, Alexis; Miseljic, Mirko

    2012-01-01

    While it is generally agreed that successful strategies to address the health and environmental impacts of engineered nanomaterials (NM) should consider the well-established frameworks for conducting life-cycle assessment (LCA) and risk assessment (RA), scientific research, and specific guidance...... on how to practically apply these methods are still very much under development. This paper evaluates how research efforts have applied LCA and RA together for NM, particularly reflecting on previous experiences with applying these methods to chemicals. Through a literature review and a separate analysis...... of research focused on applying LCA and RA together for NM, it appears that current research efforts have taken into account some key ‘‘lessons learned’’ from previous experience with chemicals while many key challenges remain for practically applying these methods to NM. We identified two main approaches...

  1. Genetic analysis of poliovirus strains isolated from sewage in Poland.

    Science.gov (United States)

    Kuryk, Ł; Wieczorek, M; Diedrich, S; Böttcher, S; Witek, A; Litwińska, B

    2014-07-01

    The study describes genetic characterization of poliovirus (PV) strains isolated from sewage samples in Poland. The analyses were performed for the detection of any putative polio revertants and recombinants in three genomic regions by sequencing analysis. Thirty-six strains were analyzed. The analyzed strains were identified by neutralization assay as 7 strains of serotype P1, 10 strains of serotype P2, and 19 strains of serotype P3. Sewage isolates were sequenced in 5'UTR, VP1, and 3D genomic regions. All detected PVs were classified as vaccine strains on the basis of VP1 sequence. Mutational differences in the VP1 sequences of isolated viruses ranged from 0.0% to 0.4%, indicating a limited replication period. The genetic analysis of the 3D region showed that some strains have recombinant genomes. Nine strains were found as dipartite recombinants (seven strains--S3/S2, one strain--S2/S1, one strain--S3/S1), while one strain was found as tripartite recombinant (S3/S2/S1). No recombinants with non-PV enteroviruses were identified. None of wild-type PVs or vaccine-derived polioviruses (VDPVs) were detected. This study showed the absence of wild or VDPV circulation in the country and demonstrated the usefulness of environmental surveillance in addition to acute flaccid paralysis (AFP) surveillance in support of polio eradication initiatives. © 2013 Wiley Periodicals, Inc.

  2. Genetic analysis of Apuleia leiocarpa as revealed by random amplified polymorphic DNA markers: prospects for population genetic studies.

    Science.gov (United States)

    Lencina, K H; Konzen, E R; Tsai, S M; Bisognin, D A

    2016-12-19

    Apuleia leiocarpa (Vogel) J.F. MacBride is a hardwood species native to South America, which is at serious risk of extinction. Therefore, it is of prime importance to examine the genetic diversity of this species, information required for developing conservation, sustainable management, and breeding strategies. Although scarcely used in recent years, random amplified polymorphic DNA markers are useful resources for the analysis of genetic diversity and structure of tree species. This study represents the first genetic analysis based on DNA markers in A. leiocarpa that aimed to investigate the levels of polymorphism and to select markers for the precise characterization of its genetic structure. We adapted the original DNA extraction protocol based on cetyltrimethyl ammonium bromide, and describe a simple procedure that can be used to obtain high-quality samples from leaf tissues of this tree. Eighteen primers were selected, revealing 92 bands, from which 75 were polymorphic and 61 were sufficient to represent the overall genetic structure of the population without compromising the precision of the analysis. Some fragments were conserved among individuals, which can be sequenced and used to analyze nucleotide diversity parameters through a wider set of A. leiocarpa individuals and populations. The individuals were separated into 11 distinct groups with variable levels of genetic diversity, which is important for selecting desirable genotypes and for the development of a conservation and sustainable management program. Our results are of prime importance for further investigations concerning the genetic characterization of this important, but vulnerable species.

  3. Analysis of Japanese newspaper articles on genetic modification

    Directory of Open Access Journals (Sweden)

    Ryuma Shineha

    2008-06-01

    Full Text Available The rapid spread of technologies involving the application of “Genetic Modification (GM” raised the need for science communication on this new technology in society. To consider the communication on GM in the society, an understanding of the current mass media is required. This paper shows the whole picture of newspaper discourses on GM in Japan. For the Japanese public, newspapers represent one of the major sources of information on GM. We subjected the two Japanese newspapers with the largest circulation, the Asahi Shimbun and Yomiuri Shimbun, to an analysis of the full text of approximately 4000 articles on GM published over the past to perform an assessment of the change of reportage on GM. As for the most important results, our analysis shows that there are two significant shifts with respect to the major topics addressed in articles on GM by Japanese newspapers.

  4. Genetics

    Science.gov (United States)

    ... Likelihood of getting certain diseases Mental abilities Natural talents An abnormal trait (anomaly) that is passed down ... one of them has a genetic disorder. Information Human beings have cells with 46 chromosomes . These consist ...

  5. Apixaban compared with warfarin in patients with atrial fibrillation and previous stroke or transient ischaemic attack: a subgroup analysis of the ARISTOTLE trial.

    Science.gov (United States)

    Easton, J Donald; Lopes, Renato D; Bahit, M Cecilia; Wojdyla, Daniel M; Granger, Christopher B; Wallentin, Lars; Alings, Marco; Goto, Shinya; Lewis, Basil S; Rosenqvist, Mårten; Hanna, Michael; Mohan, Puneet; Alexander, John H; Diener, Hans-Christoph

    2012-06-01

    In the ARISTOTLE trial, the rate of stroke or systemic embolism was reduced by apixaban compared with warfarin in patients with atrial fibrillation (AF). Patients with AF and previous stroke or transient ischaemic attack (TIA) have a high risk of stroke. We therefore aimed to assess the efficacy and safety of apixaban compared with warfarin in prespecified subgroups of patients with and without previous stroke or TIA. Between Dec 19, 2006, and April 2, 2010, patients were enrolled in the ARISTOTLE trial at 1034 clinical sites in 39 countries. 18,201 patients with AF or atrial flutter were randomly assigned to receive apixaban 5 mg twice daily or warfarin (target international normalised ratio 2·0-3·0). The median duration of follow-up was 1·8 years (IQR 1·4-2·3). The primary efficacy outcome was stroke or systemic embolism, analysed by intention to treat. The primary safety outcome was major bleeding in the on-treatment population. All participants, investigators, and sponsors were masked to treatment assignments. In this subgroup analysis, we estimated event rates and used Cox models to compare outcomes in patients with and without previous stroke or TIA. The ARISTOTLE trial is registered with ClinicalTrials.gov, number NTC00412984. Of the trial population, 3436 (19%) had a previous stroke or TIA. In the subgroup of patients with previous stroke or TIA, the rate of stroke or systemic embolism was 2·46 per 100 patient-years of follow-up in the apixaban group and 3·24 in the warfarin group (hazard ratio [HR] 0·76, 95% CI 0·56 to 1·03); in the subgroup of patients without previous stroke or TIA, the rate of stroke or systemic embolism was 1·01 per 100 patient-years of follow-up with apixaban and 1·23 with warfarin (HR 0·82, 95% CI 0·65 to 1·03; p for interaction=0·71). The absolute reduction in the rate of stroke and systemic embolism with apixaban versus warfarin was 0·77 per 100 patient-years of follow-up (95% CI -0·08 to 1·63) in patients with

  6. [Genetic constitution analysis of idiopathic sudden hearing loss].

    Science.gov (United States)

    Bora, Adem; Altuntaş, Emine Elif; Ozdemir, Oztürk; Uysal, Ismail Onder; Müderris, Suphi

    2010-01-01

    The purpose of this research is to understand the etiology of sudden hearing loss due to genetic factors in Turkish people. Determination of these genetic factors and better understanding of molecular pathogenesis may guide more realistic planning and treatment recommendations. Forty patients (Group 1; 19 males, 21 females; mean age 37.9+/-15.6 years; range 9 to 76 years) who presented with sudden hearing loss to the Ear, Nose and Throat Clinic of Medical Faculty Hospital of Cumhuriyet University between January 2008 and June 2009, and were diagnosed with sudden hearing loss through history, physical examination and review of audiometric findings, and 20 healthy volunteers (Group 2; 14 males, 6 females; mean age 31.7+/-4.4 years; range 24 to 43 years) for the control group were included in this study. All Patients were evaluated by the genetic clinic for the GJB2, GJB3, GJB6 and WFS1 gene using multiplex ligation-dependent probe amplification (MLPA) method mutation analysis. No difference was found in the peripheral blood sample analyses of the two groups at WFS1 exon 8 and connexin 26, 30 and 31 gene zones using the MLPA method with respect to heterozygous mutation (p=0.291, p>0.05). In four patients in group 1 heterozygous mutation was detected at the target gene zone. Heterozygous mutation was in the WFS1 exon 8 zone in two patients; and in the WFS1 exon 1 zone in other two patients. Sudden hearing loss studies in the future should include connexin 26, connexin 30 and other gene mutations that may affect the function of the gap-junction located in the region of the cochlea stria vascularis (stV), basal membrane (BM), spiral limbus (Li) and spiral ligament (SL). These studies should be performed on larger series, and should include family members of patients with sudden hearing loss.

  7. Genetic analysis of biosurfactant production in Ustilago maydis.

    Science.gov (United States)

    Hewald, Sandra; Josephs, Katharina; Bölker, Michael

    2005-06-01

    The dimorphic basidiomycete Ustilago maydis produces large amounts of surface-active compounds under conditions of nitrogen starvation. These biosurfactants consist of derivatives of two classes of amphipathic glycolipids. Ustilagic acids are cellobiose lipids in which the disaccharide is O-glycosidically linked to 15,16-dihydroxyhexadecanoic acid. Ustilipids are mannosylerythritol lipids derived from acylated beta-d-mannopyranosyl-d-erythritol. Whereas the chemical structure of these biosurfactants has been determined, the genetic basis for their biosynthesis and regulation is largely unknown. Here we report the first identification of two genes, emt1 and cyp1, that are essential for the production of fungal extracellular glycolipids. emt1 is required for mannosylerythritol lipid production and codes for a protein with similarity to prokaryotic glycosyltransferases involved in the biosynthesis of macrolide antibiotics. We suggest that Emt1 catalyzes the synthesis of mannosyl-d-erythritol by transfer of GDP-mannose. Deletion of the gene cyp1 resulted in complete loss of ustilagic acid production. Cyp1 encodes a cytochrome P450 monooxygenase which is highly related to a family of plant fatty acid hydroxylases. Therefore we assume that Cyp1 is directly involved in the biosynthesis of the unusual 15,16-dihydroxyhexadecanoic acid. We could show that mannosylerythritol lipid production is responsible for hemolytic activity on blood agar, whereas ustilagic acid secretion is required for long-range pheromone recognition. The mutants described here allow for the first time a genetic analysis of glycolipid production in fungi.

  8. Genetic Analysis of Southwestern Iranian Patients with Familial Mediterranean Fever

    Directory of Open Access Journals (Sweden)

    Mahmoud Haghighat

    2017-05-01

    Full Text Available Background: Familial Mediterranean fever (FMF is an autosomal recessive genetic disorder characterized by recurrent episodes of self-limited fever and serosal tissues inflammation. Methods: To evaluate clinical symptoms and common genetic mutations in southwestern Iranian patients with FMF, 20 unrelated patients were enrolled in this study based on clinical criteria. A panel of 12 common MEFV gene mutations was tested. Results: The most frequent clinical presentations of the patients were fever, colicky abdominal pain and arthritis. Eighteen patients responded completely to colchicine therapy. MEFV gene mutations were detected in only 40% of the patients. The most common mutation was E148Q, detected in five patients (25%. The V726A, M694V and P369S mutations were each observed in one patient. Conclusions: Although none of the 12 mutations we included in our test panel was detected in 60% of our patients, all of them had FMF symptoms and responded well to colchicine. MEFV full gene sequencing analysis in these patients may lead to finding new mutations in southwestern Iranian FMF patients which would be helpful in designing a local diagnostic kit.

  9. Genetically Modified Products in Lithuania: Situational Analysis and Consumers’ Attitudes

    OpenAIRE

    Dainora Grundey; Indre Rimkiene

    2012-01-01

    The paper analyses the genetically modified organism products (GMP) in relation to genetically modified organisms (GMO) from two perspectives: 1) from the theoretical standpoint, discussing the GMO and GMP trade conditions and 2) from the practical perspective, namely analysing the availability of GMP in the Lithuanian market. With the growing of genetically modified products (GMP) levels, it becomes important to examine the situation of genetically modified products. According to various stu...

  10. Genetic Analysis of Micro-environmental Plasticity in Drosophila melanogaster

    OpenAIRE

    Morgante, Fabio; Sorensen, Daniel A; Sørensen, Peter; Maltecca, Christian; Mackay, Trudy F C

    2014-01-01

    Quantitative genetic models recognize the potential for genotype by environment interaction, whereby different genotypes have different plastic responses to changes in macro-environmental conditions. Recently, it has been recognized that micro-environmental plasticity (‘residual’ variance) may also be genetically variable. This study utilized the Drosophila Genetic Reference Panel (DGRP) to accurately estimate the genetic variance of micro-environmental plasticity for chill coma recovery time...

  11. [Population genetic analysis of behaviour traits in Hovawart dogs].

    Science.gov (United States)

    Buse, Christina; Stock, Kathrin Friederike; Hamann, Henning; Distl, Ottmar

    2009-01-01

    The aim of this study was to determine genetic and environmental influences on behaviour traits in Hovawart dogs. Trait definition was based on a survey which was conducted by the breeding association for Hovawart dogs in Germany in 2002. Questionnaires of 601 dogs born between 1991 and 2001 were used for the analysis of 23 traits that were grouped to the following five trait complexes: behaviour towards strangers and kids, response to external influences, response to dominance gestures of the owner, response to other dogs, and behaviour towards other dogs. Analyses were performed using residual maximum likelihood in multivariate linear animal models. Heritability estimates ranged between h2 = 0.01 and h2 = 0.22 (standard error behaviour traits in the Hovawart dogs. Accordingly, traits like the response of the dog to unfamiliar situations (h2 = 0.20) and the behaviour towards strangers approaching the home property (h2 = 0.22) may be considered when selecting breeding animals.

  12. Risk of stillbirth, preterm delivery, and fetal growth restriction following exposure in a previous birth: systematic review and meta-analysis.

    Science.gov (United States)

    Malacova, E; Regan, A; Nassar, N; Raynes-Greenow, C; Leonard, H; Srinivasjois, R; W Shand, A; Lavin, T; Pereira, G

    2018-01-01

    Little is known about the risk of non-recurrent adverse birth outcomes. To evaluate the risk of stillbirth, preterm birth (PTB), and small for gestational age (SGA) as a proxy for fetal growth restriction (FGR) following exposure to one or more of these factors in a previous birth. We searched MEDLINE, EMBASE, Maternity and Infant Care, and Global Health from inception to 30 November 2016. Studies were included if they investigated the association between stillbirth, PTB, or SGA (as a proxy for FGR) in two subsequent births. Meta-analysis and pooled association presented as odds ratios (ORs) and adjusted odds ratios (aORs). Of the 3399 studies identified, 17 met the inclusion criteria. A PTB or SGA (as a proxy for FGR) infant increased the risk of subsequent stillbirth ((pooled OR 1.70; 95% confidence interval, 95% CI, 1.34-2.16) and (pooled OR 1.98; 95% CI 1.70-2.31), respectively). A combination of exposures, such as a preterm SGA (as a proxy for FGR) birth, doubled the risk of subsequent stillbirth (pooled OR 4.47; 95% CI 2.58-7.76). The risk of stillbirth also varied with prematurity, increasing three-fold following PTB preterm SGA (as a proxy for FGR) preterm (preterm or small for gestational age can increase the chance of long-term health problems. The effect of having a stillbirth, preterm birth, or small-for-gestational-age infant in a previous pregnancy on future pregnancy health has not been summarised. We identified 3399 studies of outcomes of previous pregnancies, and 17 were summarised by our study. What were the main findings? The outcome of the previous pregnancy influenced the risk of poor outcomes in the next pregnancy. Babies born to mothers who had a previous preterm birth or small-for-gestational-age birth were more likely to be stillborn. The smaller and the more preterm the previous baby, the higher the risk of stillbirth in the following pregnancy. The risk of stillbirth in the following pregnancy was doubled if the previous baby was born

  13. Laparoscopy After Previous Laparotomy

    Directory of Open Access Journals (Sweden)

    Zulfo Godinjak

    2006-11-01

    Full Text Available Following the abdominal surgery, extensive adhesions often occur and they can cause difficulties during laparoscopic operations. However, previous laparotomy is not considered to be a contraindication for laparoscopy. The aim of this study is to present that an insertion of Veres needle in the region of umbilicus is a safe method for creating a pneumoperitoneum for laparoscopic operations after previous laparotomy. In the last three years, we have performed 144 laparoscopic operations in patients that previously underwent one or two laparotomies. Pathology of digestive system, genital organs, Cesarean Section or abdominal war injuries were the most common causes of previouslaparotomy. During those operations or during entering into abdominal cavity we have not experienced any complications, while in 7 patients we performed conversion to laparotomy following the diagnostic laparoscopy. In all patients an insertion of Veres needle and trocar insertion in the umbilical region was performed, namely a technique of closed laparoscopy. Not even in one patient adhesions in the region of umbilicus were found, and no abdominal organs were injured.

  14. A cross-species genetic analysis identifies candidate genes for mouse anxiety and human bipolar disorder

    Directory of Open Access Journals (Sweden)

    David G Ashbrook

    2015-07-01

    Full Text Available Bipolar disorder (BD is a significant neuropsychiatric disorder with a lifetime prevalence of ~1%. To identify genetic variants underlying BD genome-wide association studies (GWAS have been carried out. While many variants of small effect associated with BD have been identified few have yet been confirmed, partly because of the low power of GWAS due to multiple comparisons being made. Complementary mapping studies using murine models have identified genetic variants for behavioral traits linked to BD, often with high power, but these identified regions often contain too many genes for clear identification of candidate genes. In the current study we have aligned human BD GWAS results and mouse linkage studies to help define and evaluate candidate genes linked to BD, seeking to use the power of the mouse mapping with the precision of GWAS. We use quantitative trait mapping for open field test and elevated zero maze data in the largest mammalian model system, the BXD recombinant inbred mouse population, to identify genomic regions associated with these BD-like phenotypes. We then investigate these regions in whole genome data from the Psychiatric Genomics Consortium’s bipolar disorder GWAS to identify candidate genes associated with BD. Finally we establish the biological relevance and pathways of these genes in a comprehensive systems genetics analysis.We identify four genes associated with both mouse anxiety and human BD. While TNR is a novel candidate for BD, we can confirm previously suggested associations with CMYA5, MCTP1 and RXRG. A cross-species, systems genetics analysis shows that MCTP1, RXRG and TNR coexpress with genes linked to psychiatric disorders and identify the striatum as a potential site of action. CMYA5, MCTP1, RXRG and TNR are associated with mouse anxiety and human BD. We hypothesize that MCTP1, RXRG and TNR influence intercellular signaling in the striatum.

  15. Population genetic analysis of cat populations from Mexico ...

    Indian Academy of Sciences (India)

    Unknown

    Bolivia, and the Dominican Republic: identification of different gene pools in Latin America. J. Genet. 84, 147–171]. Introduction. The genetic ... populations has led to the identification of genetic rela- tionships among populations and ...... Evolution 44, 689–697. Rao C. R. 1951. Advanced statistical methods in biometric re-.

  16. Genetic Analysis of Micro-environmental Plasticity in Drosophila melanogaster

    DEFF Research Database (Denmark)

    Morgante, Fabio; Sorensen, Daniel A; Sørensen, Peter

    be genetically variable. This study utilized the Drosophila Genetic Reference Panel (DGRP) to accurately estimate the genetic variance of micro-environmental plasticity for chill coma recovery time and startle response. Estimates of broad sense heritabilities for both traits are substantial (from 0.51 to 0...

  17. Genetic Analysis of Mice Skin Exposed by Hyper-Gravity

    Science.gov (United States)

    Takahashi, Rika; Terada, Masahiro; Seki, Masaya; Higashibata, Akira; Majima, Hideyuki J.; Ohira, Yoshinobu; Mukai, Chiaki; Ishioka, Noriaki

    2013-02-01

    In the space environment, physiological alterations, such as low bone density, muscle weakness and decreased immunity, are caused by microgravity and cosmic radiation. On the other hand, it is known that the leg muscles are hypertrophy by 2G-gravity. An understanding of the effects on human body from microgravity to hyper-gravity is very important. Recently, the Japan Aerospace Exploration Agency (JAXA) has started a project to detect the changes on gene expression and mineral metabolism caused by microgravity by analyzing the hair of astronauts who stay in the international Space Station (ISS) for a long time. From these results of human hair’s research, the genetic effects of human hair roots by microgravity will become clear. However, it is unclear how the gene expression of hair roots was effected by hypergravity. Therefore, in this experiment, we analyzed the effect on mice skin contained hair roots by comparing microgravity or hypergravity exposed mice. The purpose of this experiment is to evaluate the genetic effects on mice skin by microgravity or 2G-gravity. The samples were taken from mice exposed to space flight (FL) or hypergravity environment (2G) for 3-months, respectively. The extracted and amplified RNA from these mice skin was used to DNA microarray analysis. in this experiment, we analyzed the effect of gravity by using mice skin contained hair roots, which exposed space (FL) and hyper-gravity (2G) for 3 months and each control. By DNA microarray analysis, we found the common 98 genes changed in both FL and 2G. Among these 98 genes, the functions and pathways were identified by Gene Ontology (GO) analysis and Ingenuity Pathways Analysis (IPA) software. Next, we focused the one of the identified pathways and compared the effects on each molecules in this pathways by the different environments, such as FL and 2G. As the results, we could detect some interesting molecules, which might be depended on the gravity levels. In addition, to investigate

  18. Genetics

    International Nuclear Information System (INIS)

    Hubitschek, H.E.

    1975-01-01

    Progress is reported on the following research projects: genetic effects of high LET radiations; genetic regulation, alteration, and repair; chromosome replication and the division cycle of Escherichia coli; effects of radioisotope decay in the DNA of microorganisms; initiation and termination of DNA replication in Bacillus subtilis; mutagenesis in mouse myeloma cells; lethal and mutagenic effects of near-uv radiation; effect of 8-methoxypsoralen on photodynamic lethality and mutagenicity in Escherichia coli; DNA repair of the lethal effects of far-uv; and near uv irradiation of bacterial cells

  19. [Analysis of genetic diversity of Russian regional populations based on common STR markers used in DNA identification].

    Science.gov (United States)

    Pesik, V Yu; Fedunin, A A; Agdzhoyan, A T; Utevska, O M; Chukhraeva, M I; Evseeva, I V; Churnosov, M I; Lependina, I N; Bogunov, Yu V; Bogunova, A A; Ignashkin, M A; Yankovsky, N K; Balanovska, E V; Orekhov, V A; Balanovsky, O P

    2014-06-01

    We conducted the first genetic analysis of a wide a range of rural Russian populations in European Russia with a panel of common DNA markers commonly used in criminalistics genetic identification. We examined a total of 647 samples from indigenous ethnic Russian populations in Arkhangelsk, Belgorod, Voronezh, Kursk, Rostov, Ryazan, and Orel regions. We employed a multiplex genotyping kit, COrDIS Plus, to genotype Short Tandem Repeat (STR) loci, which included the genetic marker panel officially recommended for DNA identification in the Russian Federation, the United States, and the European Union. In the course of our study, we created a database of allelic frequencies, examined the distribution of alleles and genotypes in seven rural Russian populations, and defined the genetic relationships between these populations. We found that, although multidimensional analysis indicated a difference between the Northern gene pool and the rest of the Russian European populations, a pairwise comparison using 19 STR markers among all populations did not reveal significant differences. This is in concordance with previous studies, which examined up to 12 STR markers of urban Russian populations. Therefore, the database of allelic frequencies created in this study can be applied for forensic examinations and DNA identification among the ethnic Russian population over European Russia. We also noted a decrease in the levels of heterozygosity in the northern Russian population compared to ethnic populations in southern and central Russia, which is consistent with trends identified previously using classical gene markers and analysis of mitochondrial DNA.

  20. Genetic Analysis of Teosinte Alleles for Kernel Composition Traits in Maize

    Directory of Open Access Journals (Sweden)

    Avinash Karn

    2017-04-01

    Full Text Available Teosinte (Zea mays ssp. parviglumis is the wild ancestor of modern maize (Zea mays ssp. mays. Teosinte contains greater genetic diversity compared with maize inbreds and landraces, but its use is limited by insufficient genetic resources to evaluate its value. A population of teosinte near isogenic lines (NILs was previously developed to broaden the resources for genetic diversity of maize, and to discover novel alleles for agronomic and domestication traits. The 961 teosinte NILs were developed by backcrossing 10 geographically diverse parviglumis accessions into the B73 (reference genome inbred background. The NILs were grown in two replications in 2009 and 2010 in Columbia, MO and Aurora, NY, respectively, and near infrared reflectance spectroscopy and nuclear magnetic resonance calibrations were developed and used to rapidly predict total kernel starch, protein, and oil content on a dry matter basis in bulk whole grains of teosinte NILs. Our joint-linkage quantitative trait locus (QTL mapping analysis identified two starch, three protein, and six oil QTL, which collectively explained 18, 23, and 45% of the total variation, respectively. A range of strong additive allelic effects for kernel starch, protein, and oil content were identified relative to the B73 allele. Our results support our hypothesis that teosinte harbors stronger alleles for kernel composition traits than maize, and that teosinte can be exploited for the improvement of kernel composition traits in modern maize germplasm.

  1. Genetic Analysis of 'PAX6-Negative' Individuals with Aniridia or Gillespie Syndrome

    DEFF Research Database (Denmark)

    Ansari, Morad; Rainger, Jacqueline; Hanson, Isabel M

    2016-01-01

    We report molecular genetic analysis of 42 affected individuals referred with a diagnosis of aniridia who previously screened as negative for intragenic PAX6 mutations. Of these 42, the diagnoses were 31 individuals with aniridia and 11 individuals referred with a diagnosis of Gillespie syndrome......) to PAX6 and one within a gene desert 5' (telomeric) to PITX2. Sequence analysis of the FOXC1 and PITX2 coding regions identified two plausibly pathogenic de novo FOXC1 missense mutations (p.Pro79Thr and p.Leu101Pro). No intragenic mutations were detected in PITX2. FISH mapping in an individual...... with Gillespie-like syndrome with an apparently balanced X;11 reciprocal translocation revealed disruption of a gene at each breakpoint: ARHGAP6 on the X chromosome and PHF21A on chromosome 11. In the other individuals with Gillespie syndrome no mutations were identified in either of these genes, or in HCCS...

  2. Genetic analysis of the claret locus of Drosophila melanogaster

    International Nuclear Information System (INIS)

    Sequeira, W.; Nelson, C.R.; Szauter, P.

    1989-01-01

    The claret (ca) locus of Drosophila melanogaster comprises two separately mutable domains, one responsible for eye color and one responsible for proper disjunction of chromosomes in meiosis and early cleavage divisions. Previously isolated alleles are of three types: (1) alleles of the claret (ca) type that affect eye color only, (2) alleles of the claret-nondisjunctional (ca nd ) type that affect eye color and chromosome behavior, and (3) a meiotic mutation, non-claret disjunctional (ncd), that affects chromosome behavior only. In order to investigate the genetic structure of the claret locus, the authors have isolated 19 radiation-induced alleles of claret on the basis of the eye color phenotype. Two of these 19 new alleles are of the ca nd type, while 17 are of the ca type, demonstrating that the two domains do not often act as a single target for mutagenesis. This suggests that the two separately mutable functions are likely to be encoded by separate or overlapping genes rather than by a single gene. One of the new alleles of the ca nd type is a chromosome rearrangement with a breakpoint at the position of the claret locus. If this breakpoint is the cause of the mutant phenotype and there are no other mutations associated with the rearrangement, the two functions must be encoded by overlapping genes

  3. Analysis of current research addressing complementary use of life-cycle assessment and risk assessment for engineered nanomaterials: have lessons been learned from previous experience with chemicals?

    International Nuclear Information System (INIS)

    Grieger, Khara D.; Laurent, Alexis; Miseljic, Mirko; Christensen, Frans; Baun, Anders; Olsen, Stig I.

    2012-01-01

    While it is generally agreed that successful strategies to address the health and environmental impacts of engineered nanomaterials (NM) should consider the well-established frameworks for conducting life-cycle assessment (LCA) and risk assessment (RA), scientific research, and specific guidance on how to practically apply these methods are still very much under development. This paper evaluates how research efforts have applied LCA and RA together for NM, particularly reflecting on previous experiences with applying these methods to chemicals. Through a literature review and a separate analysis of research focused on applying LCA and RA together for NM, it appears that current research efforts have taken into account some key “lessons learned” from previous experience with chemicals while many key challenges remain for practically applying these methods to NM. We identified two main approaches for using these methods together for NM: “LC-based RA” (traditional RA applied in a life-cycle perspective) and “RA-complemented LCA” (conventional LCA supplemented by RA in specific life-cycle steps). Hence, the latter is the only identified approach which genuinely combines LC- and RA-based methods for NM-risk research efforts to date as the former is rather a continuation of normal RA according to standard assessment procedures (e.g., REACH). Both these approaches along with recommendations for using LCA and RA together for NM are similar to those made previously for chemicals, and thus, there does not appear to be much progress made specific for NM. We have identified one issue in particular that may be specific for NM when applying LCA and RA at this time: the need to establish proper dose metrics within both methods.

  4. Potential protective effect of lactation against incidence of type 2 diabetes mellitus in women with previous gestational diabetes mellitus: A systematic review and meta-analysis.

    Science.gov (United States)

    Tanase-Nakao, Kanako; Arata, Naoko; Kawasaki, Maki; Yasuhi, Ichiro; Sone, Hirohito; Mori, Rintaro; Ota, Erika

    2017-05-01

    Lactation may protect women with previous gestational diabetes mellitus (GDM) from developing type 2 diabetes mellitus, but the results of existing studies are inconsistent, ranging from null to beneficial. We aimed to conduct a systematic review to gather available evidence. Databases MEDLINE, CINAHL, PubMed, and EMBASE were searched on December 15, 2015, without restriction of language or publication year. A manual search was also conducted. We included observational studies (cross-sectional, case-control, and cohort study) with information on lactation and type 2 diabetes mellitus incidence among women with previous GDM. We excluded case studies without control data. Data synthesis was conducted by random-effect meta-analysis. Fourteen reports of 9 studies were included. Overall risk of bias using RoBANS ranged from low to unclear. Longer lactation for more than 4 to 12 weeks postpartum had risk reduction of type 2 diabetes mellitus compared with shorter lactation (OR 0.77, 95% CI 0.01-55.86; OR 0.56, 95% CI 0.35-0.89; OR 0.22, 95% CI 0.13-0.36; type 2 diabetes mellitus evaluation time 2 y, 2-5 y, and >5 y, respectively). Exclusive lactation for more than 6 to 9 weeks postpartum also had lower risk of type 2 diabetes mellitus compared with exclusive formula (OR 0.42, 95% CI 0.22-0.81). The findings support the evidence that longer and exclusive lactation may be beneficial for type 2 diabetes mellitus prevention in women with previous GDM. However, the evidence relies only on observational studies. Therefore, further studies are required to address the true causal effect. © 2017 The Authors. Diabetes/Metabolism Research and Reviews Published by John Wiley & Sons Ltd.

  5. Guidelines for complex genetic analysis of hereditary breast ovarian cancer syndrome in slovak population

    Directory of Open Access Journals (Sweden)

    Konecny M

    2015-12-01

    Full Text Available Genetic diagnostics of hereditary breast and ovarian cancer (HBOC has been performed in Slovakia in many different forms before the year 2000. Complex HBOC genetic analysis consists of many steps, including the initial genetic consultation, laboratory testing of genes associated with HBOC, interpretation and report of DNA analysis results, secondary explanatory genetic consultation and recommendation of clinical management for pathological mutation carriers. Many clinicians are participating on this workflow, such as clinical geneticists, laboratory diagnosticians as well as gynaecologists, oncologists or radio-diagnosticians. Currently, genetic testing is still technically and financially demanding and aimed only at selected families or patients who fulfil the defined clinical indication criteria.

  6. Genetic analysis of drug metabolizing phase-I enzymes CYP3A4 in ...

    Indian Academy of Sciences (India)

    The enzymatic activity of CYP3A4 results in broad interindividual variability in response to certain pharmacotherapies. The present study aimed to screen Tibetan volunteers for CYP3A4 genetic polymorphisms. Previous research has focussed on Han Chinese patients, while little is known about the genetic variation of ...

  7. Genetics

    DEFF Research Database (Denmark)

    Christensen, Kaare; McGue, Matt

    2016-01-01

    The sequenced genomes of individuals aged ≥80 years, who were highly educated, self-referred volunteers and with no self-reported chronic diseases were compared to young controls. In these data, healthy ageing is a distinct phenotype from exceptional longevity and genetic factors that protect...

  8. Genetic Code Analysis Toolkit: A novel tool to explore the coding properties of the genetic code and DNA sequences

    Science.gov (United States)

    Kraljić, K.; Strüngmann, L.; Fimmel, E.; Gumbel, M.

    2018-01-01

    The genetic code is degenerated and it is assumed that redundancy provides error detection and correction mechanisms in the translation process. However, the biological meaning of the code's structure is still under current research. This paper presents a Genetic Code Analysis Toolkit (GCAT) which provides workflows and algorithms for the analysis of the structure of nucleotide sequences. In particular, sets or sequences of codons can be transformed and tested for circularity, comma-freeness, dichotomic partitions and others. GCAT comes with a fertile editor custom-built to work with the genetic code and a batch mode for multi-sequence processing. With the ability to read FASTA files or load sequences from GenBank, the tool can be used for the mathematical and statistical analysis of existing sequence data. GCAT is Java-based and provides a plug-in concept for extensibility. Availability: Open source Homepage:http://www.gcat.bio/

  9. [Develop a statistics analysis software in population genetics using VBA language].

    Science.gov (United States)

    Cai, Ying; Zhou, Ni; Xu, Ye-li; Xiang, Da-peng; Su, Jiang-hui; Zhang, Lin-tian

    2006-12-01

    To develop a statistics analysis software that can be used in STR population genetics for the purpose of promoting and fastening the basic research of STR population genetics. Selecting the Microsoft VBA for Excel, which is simple and easy to use, as the program language and using its macro function to develop a statistics analysis software used in STR population genetics. The software "Easy STR Genetics" based on VBA language, by which the population genetic analysis of STR data can be made, were developed. The developed software "Easy STR Genetics" based on VBA language, can be spread in the domain of STR population genetics research domestically and internationally, due to its feature of full function, good compatibility for different formats of input data, distinct and easy to understand outputs for statistics and calculation results.

  10. Ameloblastic fibroma: a stage in the development of a hamartomatous odontoma or a true neoplasm? Critical analysis of 162 previously reported cases plus 10 new cases.

    Science.gov (United States)

    Buchner, Amos; Vered, Marilena

    2013-11-01

    To analyze neoplastic and hamartomatous variants of ameloblastic fibromas (AFs). Analysis of 172 cases (162 previously reported, 10 new). AF emerged as a lesion primarily of children and adolescents (mean age, 14.9 years), with about 80% diagnosed when odontogenesis is completed (age, 22 years are considered true neoplasms, while those in younger patients may be either true neoplasms or odontomas in early stages of development. Although the histopathology of hamartomatous and neoplastic variants of AF are indistinguishable, clinical and radiologic features can be of some help to distinguish between them. Asymptomatic small unilocular lesions with no or minimal bone expansion in young individuals are likely to be developing odontomas, and large, expansile lesions with extensive bone destruction are neoplasms. Copyright © 2013 Elsevier Inc. All rights reserved.

  11. Genetic and phylogenetic analysis of a novel parvovirus isolated from chickens in Guangxi, China.

    Science.gov (United States)

    Feng, Bin; Xie, Zhixun; Deng, Xianwen; Xie, Liji; Xie, Zhiqin; Huang, Li; Fan, Qin; Luo, Sisi; Huang, Jiaoling; Zhang, Yanfang; Zeng, Tingting; Wang, Sheng; Wang, Leyi

    2016-11-01

    A previously unidentified chicken parvovirus (ChPV) strain, associated with runting-stunting syndrome (RSS), is now endemic among chickens in China. To explore the genetic diversity of ChPV strains, we determined the first complete genome sequence of a novel ChPV isolate (GX-CH-PV-7) identified in chickens in Guang Xi, China, and showed moderate genome sequence similarity to reference strains. Analysis showed that the viral genome sequence is 86.4 %-93.9 % identical to those of other ChPVs. Genetic and phylogenetic analyses showed that this newly emergent GX-CH-PV-7 is closely related to Gallus gallus enteric parvovirus isolate ChPV 798 from the USA, indicating that they may share a common ancestor. The complete DNA sequence is 4612 bp long with an A+T content of 56.66 %. We determined the first complete genome sequence of a previously unidentified ChPV strain to elucidate its origin and evolutionary status.

  12. Genetic analysis of glucosinolate variability in broccoli florets using genome-anchored single nucleotide polymorphisms.

    Science.gov (United States)

    Brown, Allan F; Yousef, Gad G; Reid, Robert W; Chebrolu, Kranthi K; Thomas, Aswathy; Krueger, Christopher; Jeffery, Elizabeth; Jackson, Eric; Juvik, John A

    2015-07-01

    The identification of genetic factors influencing the accumulation of individual glucosinolates in broccoli florets provides novel insight into the regulation of glucosinolate levels in Brassica vegetables and will accelerate the development of vegetables with glucosinolate profiles tailored to promote human health. Quantitative trait loci analysis of glucosinolate (GSL) variability was conducted with a B. oleracea (broccoli) mapping population, saturated with single nucleotide polymorphism markers from a high-density array designed for rapeseed (Brassica napus). In 4 years of analysis, 14 QTLs were associated with the accumulation of aliphatic, indolic, or aromatic GSLs in floret tissue. The accumulation of 3-carbon aliphatic GSLs (2-propenyl and 3-methylsulfinylpropyl) was primarily associated with a single QTL on C05, but common regulation of 4-carbon aliphatic GSLs was not observed. A single locus on C09, associated with up to 40 % of the phenotypic variability of 2-hydroxy-3-butenyl GSL over multiple years, was not associated with the variability of precursor compounds. Similarly, QTLs on C02, C04, and C09 were associated with 4-methylsulfinylbutyl GSL concentration over multiple years but were not significantly associated with downstream compounds. Genome-specific SNP markers were used to identify candidate genes that co-localized to marker intervals and previously sequenced Brassica oleracea BAC clones containing known GSL genes (GSL-ALK, GSL-PRO, and GSL-ELONG) were aligned to the genomic sequence, providing support that at least three of our 14 QTLs likely correspond to previously identified GSL loci. The results demonstrate that previously identified loci do not fully explain GSL variation in broccoli. The identification of additional genetic factors influencing the accumulation of GSL in broccoli florets provides novel insight into the regulation of GSL levels in Brassicaceae and will accelerate development of vegetables with modified or enhanced GSL

  13. Mendelian randomization analysis with multiple genetic variants using summarized data.

    Science.gov (United States)

    Burgess, Stephen; Butterworth, Adam; Thompson, Simon G

    2013-11-01

    Genome-wide association studies, which typically report regression coefficients summarizing the associations of many genetic variants with various traits, are potentially a powerful source of data for Mendelian randomization investigations. We demonstrate how such coefficients from multiple variants can be combined in a Mendelian randomization analysis to estimate the causal effect of a risk factor on an outcome. The bias and efficiency of estimates based on summarized data are compared to those based on individual-level data in simulation studies. We investigate the impact of gene-gene interactions, linkage disequilibrium, and 'weak instruments' on these estimates. Both an inverse-variance weighted average of variant-specific associations and a likelihood-based approach for summarized data give similar estimates and precision to the two-stage least squares method for individual-level data, even when there are gene-gene interactions. However, these summarized data methods overstate precision when variants are in linkage disequilibrium. If the P-value in a linear regression of the risk factor for each variant is less than 1×10⁻⁵, then weak instrument bias will be small. We use these methods to estimate the causal association of low-density lipoprotein cholesterol (LDL-C) on coronary artery disease using published data on five genetic variants. A 30% reduction in LDL-C is estimated to reduce coronary artery disease risk by 67% (95% CI: 54% to 76%). We conclude that Mendelian randomization investigations using summarized data from uncorrelated variants are similarly efficient to those using individual-level data, although the necessary assumptions cannot be so fully assessed. © 2013 WILEY PERIODICALS, INC.

  14. Genetic Variation of Oriental Tobaccos Using Multivariate Analysis

    Directory of Open Access Journals (Sweden)

    H Hatami Maleki

    2012-07-01

    Full Text Available Tobacco (Nicotiana tabaccum is one of the valuable agricultural and industrial crops that there is little information about its variation. For studying genetic variation on the basis of morphological characteristics, a number of 100 exotic and endemic oriental tobacco genotypes were obtained from the germplasm collection of the Urmia Tobacco Research Center, Urmia, Iran, using simple lattice design with 2 replications. Eight traits include: stem height and diameter, leaf number per plot, leaf length and width, fresh and dry leaf weight and day to 50% flowering were examined. Principal component analysis could reduce the studied morphological traits to 5 components having 96% accumulative variance. In the first component, all traits (except stem height showed positive significant correlations with. Cluster analysis using UPGMA method distinguished genotypes in 4 different groups. Maximum distance was between groups 1 and 4. Mean comparison revealed that genotypes (Trimph and Ohdaruma belong to group 4 had the maximum value of most examined traits, therefore, they could be utilized as parents of crosses in breeding programs.

  15. Feature selection using genetic algorithms for fetal heart rate analysis

    International Nuclear Information System (INIS)

    Xu, Liang; Redman, Christopher W G; Georgieva, Antoniya; Payne, Stephen J

    2014-01-01

    The fetal heart rate (FHR) is monitored on a paper strip (cardiotocogram) during labour to assess fetal health. If necessary, clinicians can intervene and assist with a prompt delivery of the baby. Data-driven computerized FHR analysis could help clinicians in the decision-making process. However, selecting the best computerized FHR features that relate to labour outcome is a pressing research problem. The objective of this study is to apply genetic algorithms (GA) as a feature selection method to select the best feature subset from 64 FHR features and to integrate these best features to recognize unfavourable FHR patterns. The GA was trained on 404 cases and tested on 106 cases (both balanced datasets) using three classifiers, respectively. Regularization methods and backward selection were used to optimize the GA. Reasonable classification performance is shown on the testing set for the best feature subset (Cohen's kappa values of 0.45 to 0.49 using different classifiers). This is, to our knowledge, the first time that a feature selection method for FHR analysis has been developed on a database of this size. This study indicates that different FHR features, when integrated, can show good performance in predicting labour outcome. It also gives the importance of each feature, which will be a valuable reference point for further studies. (paper)

  16. Divulgative Discourse in Genetic Engineering. Pragmatic-Semantic Analysis

    Directory of Open Access Journals (Sweden)

    Alicia Pineda

    2010-08-01

    Full Text Available The objectives of this research are to identify, describe and explain the lexical, semantic and practical strategies and resources utilized in producing divulgative discourse related to genetic engineering. The applied methodology is qualitative and related to discourse analysis, which makes it possible, by using abduction, to reveal particularities of the message production process and its links with the intentionality of the emitter. The most important conclusions of the study reveal: 1 that the discourse analyzed as having a notable similarity to the specialized discourse of biology (traditional and molecular reiterates the presence of lexical, semantic and discursive strategies and resources connected with that discursive practice. 2 An adjustment exists between the use of these strategies and resources and the emitter’s intentionality: the objectives of informing, persuading and demonstrating configure an asymmetrical communicative relationship between the emitter and the receiver.  3 Methodologies provided by the pragmatic-semantic analysis that of constructing conceptual networks are appropriate for producing messages about science and technology with a low conceptual density, and therefore, with a greater possibility of being understood by the average mass receiver.

  17. An improved Agrobacterium-mediated transformation system for the functional genetic analysis of Penicillium marneffei.

    Science.gov (United States)

    Kummasook, Aksarakorn; Cooper, Chester R; Vanittanakom, Nongnuch

    2010-12-01

    We have developed an improved Agrobacterium-mediated transformation (AMT) system for the functional genetic analysis of Penicillium marneffei, a thermally dimorphic, human pathogenic fungus. Our AMT protocol included the use of conidia or pre-germinated conidia of P. marneffei as the host recipient for T-DNA from Agrobacterium tumefaciens and co-cultivation at 28°C for 36 hours. Bleomycin-resistant transformants were selected as yeast-like colonies following incubation at 37°C. The efficiency of transformation was approximately 123 ± 3.27 and 239 ± 13.12 transformants per plate when using 5 × 10(4) conidia and pre-germinated conidia as starting materials, respectively. Southern blot analysis demonstrated that 95% of transformants contained single copies of T-DNA. Inverse PCR was employed for identifying flanking sequences at the T-DNA insertion sites. Analysis of these sequences indicated that integration occurred as random recombination events. Among the mutants isolated were previously described stuA and gasC defective strains. These AMT-derived mutants possessed single T-DNA integrations within their particular coding sequences. In addition, other morphological and pigmentation mutants possessing a variety of gene-specific defects were isolated, including two mutants having T-DNA integrations within putative promoter regions. One of the latter integration events was accompanied by the deletion of the entire corresponding gene. Collectively, these results indicated that AMT could be used for large-scale, functional genetic analyses in P. marneffei. Such analyses can potentially facilitate the identification of those genetic elements related to morphogenesis, as well as pathogenesis in this medically important fungus.

  18. Artificial oocyte activation to improve reproductive outcomes in women with previous fertilization failure: a systematic review and meta-analysis of RCTs.

    Science.gov (United States)

    Sfontouris, Ioannis A; Nastri, Carolina O; Lima, Maria L S; Tahmasbpourmarzouni, Eisa; Raine-Fenning, Nick; Martins, Wellington P

    2015-08-01

    In couples with previous fertilization failure, are reproductive outcomes improved using ICSI followed by artificial oocyte activation (ICSI-AOA) compared with conventional ICSI? There is insufficient evidence available from RCTs to judge the efficacy and safety of ICSI-AOA for couples with previous fertilization failure. In cases with previous low fertilization rates or total fertilization failure using ICSI due to sperm-related, oocyte activation deficiency, several methods of AOA have been described, which employ mechanical, electrical or chemical stimuli. Reported fertilization and pregnancy rates appear to be improved after ICSI-AOA compared with conventional ICSI; however, the small studies performed to date make it difficult to assess the clinical efficacy or safety of AOA. The present systematic review and meta-analysis identified RCTs that compared ICSI-AOA and conventional ICSI. The last electronic search was conducted in August 2014 and there was no limitation regarding language, publication date, or publication status. We included studies that randomized either oocytes or women and included them in two different parts of this review: a women-based review and an oocyte-based review. For the women-based review, the primary outcome of effectiveness was live birth per randomized woman and the primary outcome for safety was congenital anomalies per clinical pregnancy. For the oocyte-based review, the primary outcome was embryo formation per oocyte randomized. Record screening and data extraction were performed independently by two authors and risk of bias was assessed by three authors. The effects of ICSI-AOA compared with conventional ICSI were summarized as risk ratio (RR) and the precision of the estimates was evaluated by the 95% confidence interval (CI). A total of 14 articles were assessed for eligibility and 9 included in the meta-analysis: 2 studies comprised the woman-based review (n = 168 women) and 7 studies the oocyte-based review (n = 4234

  19. No Genetic Influence for Childhood Behavior Problems From DNA Analysis

    OpenAIRE

    Trzaskowski, Maciej; Dale, Philip S.; Plomin, Robert

    2013-01-01

    Objective Twin studies of behavior problems in childhood point to substantial genetic influence. It is now possible to estimate genetic influence using DNA alone in samples of unrelated individuals, not relying on family-based designs such as twins. A linear mixed model, which incorporates DNA microarray data, has confirmed twin results by showing substantial genetic influence for diverse traits in adults. Here we present direct comparisons between twin and DNA heritability estimates for chil...

  20. Genetic analysis of candidate SNPs for metabolic syndrome in obstructive sleep apnea (OSA)

    Science.gov (United States)

    Grilo, Antonio; Ruiz-Granados, Elena S.; Moreno-Rey, Concha; Rivera, Jose M.; Ruiz, Agustin; Real, Luis M.; Sáez, Maria E.

    2014-01-01

    Obstructive sleep apnea (OSA) is a common disorder characterized by the reduction or complete cessation in airflow resulting from an obstruction of the upper airway. Several studies have observed an increased risk for cardiovascular morbidity and mortality among OSA patients. Metabolic syndrome (MetS), a cluster of cardiovascular risk factors characterized by the presence of insulin resistance, is often found in patients with OSA, but the complex interplay between these two syndromes is not well understood. In this study, we present the results of a genetic association analysis of 373 candidate SNPs for MetS selected in a previous genome wide association analysis (GWAS). The 384 selected SNPs were genotyped using the Illumina VeraCode Technology in 387 subjects retrospectively assessed at the Internal Medicine Unit of the “Virgen de Valme” University Hospital (Seville, Spain). In order to increase the power of this study and to validate our findings in an independent population, we used data from the Framingham Sleep study which comprises 368 individuals. Only the rs11211631 polymorphism was associated with OSA in both populations, with an estimated OR=0.57 (0.42-0.79) in the joint analysis (p=7.21 × 10-4). This SNP was selected in the previous GWAS for MetS components using a digenic approach, but was not significant in the monogenic study. We have also identified two SNPs (rs2687855 and rs4299396) with a protective effect from OSA only in the abdominal obese subpopulation. As a whole, our study does not support that OSA and MetS share major genetic determinants, although both syndromes share common epidemiological and clinical features. PMID:23524009

  1. Genetic diversity analysis of stress tolerant rice (Oryza sativa L.)

    African Journals Online (AJOL)

    MD.Farid Islam

    2012-10-23

    9208, Bangladesh. 2Plant Breeding Genetics and Biotechnology Division, International Rice Research Institute, Los Banos, Philippines. 3Plant Breeding Division, Bangladesh Rice Research Institute, Gazipur, Bangladesh.

  2. Genetic analysis of calf and heifer losses in Danish Holstein

    DEFF Research Database (Denmark)

    Fuerst-Walti, B; Sørensen, Morten Kargo

    2010-01-01

    of genetic parameters, linear and threshold sire models were applied. Effects accounted for were the random effects herd × year × season and sire as well as the fixed effects year × month, number of dam's parity (parities >5 were set to 5), calf size, and calving ease. In total, the pedigree consisted of 4...... calving was higher than the stillbirth rate. Genetic and phenotypic variation seemed to be sufficiently high to genetically improve the trait calf and heifer mortality. Hence, a routine genetic evaluation would be valuable for monitoring and for selecting fitter animals in the Danish Holstein cattle...

  3. Genetic analysis of three South African horse breeds

    Directory of Open Access Journals (Sweden)

    E.G. Cothran

    1998-07-01

    Full Text Available Genetic variability at 7 blood-group and 10 biochemical genetic loci was examined in 3 South African horse breeds, the Nooitgedacht, Boerperd and Basuto Pony. Observed heterozygosity for these breeds was intermediate for domestic horses, with the highest heterozygosity in the Boerperd and the lowest in the Basuto Pony. The 3 breeds show greater genetic similarity to each other than to other domestic horse breeds. Compared to other breeds, the South African breeds show greater genetic similarity to breeds such as the Thoroughbred, Holstein, Trakehner and Hanovarian and also to North American breeds such as the Saddlebred, Standardbred and Morgan Horse.

  4. Analysis of the genetic basis of disease in the context of worldwide human relationships and migration.

    Directory of Open Access Journals (Sweden)

    Erik Corona

    2013-05-01

    Full Text Available Genetic diversity across different human populations can enhance understanding of the genetic basis of disease. We calculated the genetic risk of 102 diseases in 1,043 unrelated individuals across 51 populations of the Human Genome Diversity Panel. We found that genetic risk for type 2 diabetes and pancreatic cancer decreased as humans migrated toward East Asia. In addition, biliary liver cirrhosis, alopecia areata, bladder cancer, inflammatory bowel disease, membranous nephropathy, systemic lupus erythematosus, systemic sclerosis, ulcerative colitis, and vitiligo have undergone genetic risk differentiation. This analysis represents a large-scale attempt to characterize genetic risk differentiation in the context of migration. We anticipate that our findings will enable detailed analysis pertaining to the driving forces behind genetic risk differentiation.

  5. Genetic analysis of Phytophthora infestans populations in the Nordic European countries reveals high genetic variability

    DEFF Research Database (Denmark)

    Brurberg, May Bente; Elameen, Abdelhameed; Le, Ving Hong

    2011-01-01

    Late blight, caused by the oomycete Phytophthora infestans, is the most important disease of potato (Solanum tuberosum). The pathogen is highly adaptable and to get an overview of the genetic variation in the Nordic countries, Denmark, Finland, Norway and Sweden we have analyzed 200 isolates from...... types (60 % A1) support the hypothesis that sexual reproduction is contributing notably to the genetic variation of P. infestans in the Nordic countries....

  6. Integrative genetic analysis suggests that skin color modifies the genetic architecture of melanoma.

    Science.gov (United States)

    Hulur, Imge; Skol, Andrew D; Gamazon, Eric R; Cox, Nancy J; Onel, Kenan

    2017-01-01

    Melanoma is the deadliest form of skin cancer and presents a significant health care burden in many countries. In addition to ultraviolet radiation in sunlight, the main causal factor for melanoma, genetic factors also play an important role in melanoma susceptibility. Although genome-wide association studies have identified many single nucleotide polymorphisms associated with melanoma, little is known about the proportion of disease risk attributable to these loci and their distribution throughout the genome. Here, we investigated the genetic architecture of melanoma in 1,888 cases and 990 controls of European non-Hispanic ancestry. We estimated the overall narrow-sense heritability of melanoma to be 0.18 (P < 0.03), indicating that genetics contributes significantly to the risk of sporadically-occurring melanoma. We then demonstrated that only a small proportion of this risk is attributable to known risk variants, suggesting that much remains unknown of the role of genetics in melanoma. To investigate further the genetic architecture of melanoma, we partitioned the heritability by chromosome, minor allele frequency, and functional annotations. We showed that common genetic variation contributes significantly to melanoma risk, with a risk model defined by a handful of genomic regions rather than many risk loci distributed throughout the genome. We also demonstrated that variants affecting gene expression in skin account for a significant proportion of the heritability, and are enriched among melanoma risk loci. Finally, by incorporating skin color into our analyses, we observed both a shift in significance for melanoma-associated loci and an enrichment of expression quantitative trait loci among melanoma susceptibility variants. These findings suggest that skin color may be an important modifier of melanoma risk. We speculate that incorporating skin color and other non-genetic factors into genetic studies may allow for an improved understanding of melanoma

  7. Genetic Analysis of Reduced γ-Tocopherol Content in Ethiopian Mustard Seeds.

    Science.gov (United States)

    García-Navarro, Elena; Fernández-Martínez, José M; Pérez-Vich, Begoña; Velasco, Leonardo

    2016-01-01

    Ethiopian mustard (Brassica carinata A. Braun) line BCT-6, with reduced γ-tocopherol content in the seeds, has been previously developed. The objective of this research was to conduct a genetic analysis of seed tocopherols in this line. BCT-6 was crossed with the conventional line C-101 and the F1, F2, and BC plant generations were analyzed. Generation mean analysis using individual scaling tests indicated that reduced γ-tocopherol content fitted an additive-dominant genetic model with predominance of additive effects and absence of epistatic interactions. This was confirmed through a joint scaling test and additional testing of the goodness of fit of the model. Conversely, epistatic interactions were identified for total tocopherol content. Estimation of the minimum number of genes suggested that both γ- and total tocopherol content may be controlled by two genes. A positive correlation between total tocopherol content and the proportion of γ-tocopherol was identified in the F2 generation. Additional research on the feasibility of developing germplasm with high tocopherol content and reduced concentration of γ-tocopherol is required.

  8. Spatio-temporal Genetic Structuring of Leishmania major in Tunisia by Microsatellite Analysis.

    Science.gov (United States)

    Harrabi, Myriam; Bettaieb, Jihène; Ghawar, Wissem; Toumi, Amine; Zaâtour, Amor; Yazidi, Rihab; Chaâbane, Sana; Chalghaf, Bilel; Hide, Mallorie; Bañuls, Anne-Laure; Ben Salah, Afif

    2015-01-01

    In Tunisia, cases of zoonotic cutaneous leishmaniasis caused by Leishmania major are increasing and spreading from the south-west to new areas in the center. To improve the current knowledge on L. major evolution and population dynamics, we performed multi-locus microsatellite typing of human isolates from Tunisian governorates where the disease is endemic (Gafsa, Kairouan and Sidi Bouzid governorates) and collected during two periods: 1991-1992 and 2008-2012. Analysis (F-statistics and Bayesian model-based approach) of the genotyping results of isolates collected in Sidi Bouzid in 1991-1992 and 2008-2012 shows that, over two decades, in the same area, Leishmania parasites evolved by generating genetically differentiated populations. The genetic patterns of 2008-2012 isolates from the three governorates indicate that L. major populations did not spread gradually from the south to the center of Tunisia, according to a geographical gradient, suggesting that human activities might be the source of the disease expansion. The genotype analysis also suggests previous (Bayesian model-based approach) and current (F-statistics) flows of genotypes between governorates and districts. Human activities as well as reservoir dynamics and the effects of environmental changes could explain how the disease progresses. This study provides new insights into the evolution and spread of L. major in Tunisia that might improve our understanding of the parasite flow between geographically and temporally distinct populations.

  9. Genetic Analysis of Reduced γ-Tocopherol Content in Ethiopian Mustard Seeds

    Directory of Open Access Journals (Sweden)

    Elena García-Navarro

    2016-01-01

    Full Text Available Ethiopian mustard (Brassica carinata A. Braun line BCT-6, with reduced γ-tocopherol content in the seeds, has been previously developed. The objective of this research was to conduct a genetic analysis of seed tocopherols in this line. BCT-6 was crossed with the conventional line C-101 and the F1, F2, and BC plant generations were analyzed. Generation mean analysis using individual scaling tests indicated that reduced γ-tocopherol content fitted an additive-dominant genetic model with predominance of additive effects and absence of epistatic interactions. This was confirmed through a joint scaling test and additional testing of the goodness of fit of the model. Conversely, epistatic interactions were identified for total tocopherol content. Estimation of the minimum number of genes suggested that both γ- and total tocopherol content may be controlled by two genes. A positive correlation between total tocopherol content and the proportion of γ-tocopherol was identified in the F2 generation. Additional research on the feasibility of developing germplasm with high tocopherol content and reduced concentration of γ-tocopherol is required.

  10. Genetic analysis of ewe stayability and its association with lamb growth and adult production.

    Science.gov (United States)

    Borg, R C; Notter, D R; Kott, R W

    2009-11-01

    Records from 2,525 adult Targhee ewes and 10,099 lambs were used to estimate genetic parameters in an animal model for ewe stayability (STAY), productive life (PL), adult BW (AW) and BCS, fleece characteristics, and number of lambs born (NLB) and for lamb BW at birth and approximately 45 d, 120 d (120W; weaning), 12 mo, and 18 mo of age. Stayabilities were analyzed as overall stayability (STAYn|2), which indicated presence or absence of a ewe at n yr of age, given that she was present at 2 yr of age, or marginal stayability (STAYn|n-1) recording the presence of a ewe at n yr of age, given that she was present in the previous year. Productive life was measured as the age of ewe in years at her last lambing. Lamb BW were corrected for age at weighing; BW taken at or before weaning were adjusted for effects of type of birth and rearing, age of dam, and sex using National Sheep Improvement Program methods. The NLB was likewise adjusted for effects of ewe age before analysis. Birth year was included as a fixed effect for all traits. Year of record and, for AW and CS, the number of lambs born or born and reared were also included in models for adult traits. Models for all traits included random additive genetic and residual effects. Random maternal genetic and dam permanent environmental effects were also included in the model for lamb (pre)weaning BW, and random permanent environmental effects of the ewe were included in models for adult traits. The heritability estimate for PL was 0.05 (P ewe fitness characteristics. Genetic correlations between STAY5|4 and 120W, AW, and NLB were not different from zero (0.06, 0.13, and -0.06, respectively; P > 0.10). However, genetic correlations between STAY6|2 and 120W, AW, and NLB were all negative, with values of -0.17, -0.32 (P < 0.05), and -0.03, respectively, indicating a possible small antagonism between STAY and genetic effects on body size.

  11. Delineation of genetic relatedness and population structure of oral and enteric Campylobacter concisus strains by analysis of housekeeping genes.

    Science.gov (United States)

    Mahendran, Vikneswari; Octavia, Sophie; Demirbas, Omer Faruk; Sabrina, Sheryl; Ma, Rena; Lan, Ruiting; Riordan, Stephen M; Grimm, Michael C; Zhang, Li

    2015-08-01

    Campylobacter concisus is an oral bacterium that has been shown to be associated with inflammatory bowel disease (IBD). In this study we examined clusters of oral C. concisus strains isolated from patients with IBD and healthy controls by analysing six housekeeping genes. In addition, we investigated the population structure of C. concisus strains. Whether oral and enteric strains form distinct clusters based on the sequences of these housekeeping genes was also investigated. The oral C. concisus strains were found to contain two genomospecies, which belong to the two genomospecies previously found in enteric C. concisus strains. C. concisus clusters formed based on the sequences of a single aspA gene were the same as that formed by using previously reported MLST schemes. The analysis of combined oral and enteric C. concisus strains found that enteric C. concisus strains did not form distinct clusters. Genetic structure analysis identified five subpopulations of C. concisus and showed that genetic recombination between C. concisus strains was common. However, genetic recombination was significantly less in oral strains isolated from patients with IBD than from healthy individuals. Previously reported oral and enteric intestinal epithelial invasive C. concisus strains were in cluster II and subpopulation III. Furthermore, this study shows that there are no distinct enteric C. concisus strain clusters or subpopulations.

  12. Genetic mapping and QTL analysis of agronomic traits in Indian ...

    Indian Academy of Sciences (India)

    Mucuna pruriens is a well-recognized agricultural and horticultural crop with important medicinal use. However, antinutritional factors in seed and adverse morphological characters have negatively affected its cultivation. To elucidate the genetic control of agronomic traits, an intraspecific genetic linkage map of Indian M.

  13. Analysis of genetic diversity in accessions of Irvingia gabonensis ...

    African Journals Online (AJOL)

    Amplified fragment length polymorphism (AFLP) was used to assess genetic diversity and relationships among 15 accessions of Irvingia gabonensis collected from Cameroun, Gabon, and Nigeria. Twelve AFLP+3 primers produced 384 polymorphic fragments. Average genetic distance (AGD) between the 15 accessions ...

  14. An existential analysis of genetic engineering and human rights ...

    African Journals Online (AJOL)

    Genetic engineering for purposes of human enhancement poses risks that justify regulation. However, this paper argues philosophically that it is inappropriate to use human rights treaties to prohibit germ-line genetic engineering whether therapeutic or for purposes of enhancement. When also looked at existentially, the ...

  15. Comparative analysis of genetic crossover operators in knapsack ...

    African Journals Online (AJOL)

    The Genetic Algorithm (GA) is an evolutionary algorithms and technique based on natural selections of individuals called chromosomes. In this paper, a method for solving Knapsack problem via GA (Genetic Algorithm) is presented. We compared six different crossovers: Crossover single point, Crossover Two point, ...

  16. Molecular genetic analysis of consanguineous families with primary ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Genetics; Volume 96; Issue 2 ... Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha 3050, Qatar; Gomal Centre of Biochemistry and Biotechnology,Gomal University Dera Ismail Khan, Khyber-Pakhtoonkhwa 29050, Pakistan; Institute of Human Genetics, ...

  17. Analysis of Genetic diversity and reltionships in local Tunisian barley ...

    African Journals Online (AJOL)

    Yomi

    Genetic diversity and environmental associations of wild barley, Hordeum spontaneum, in Turkey. Genetica, 68: 203-213. Nagaoka T, Ogihara Y (1997). Applicability of inter-simple sequence repeat polymorphism in wheat for use as DNA markers in comparison to RFLP and RAPD markers. Theor. Appl. Genet. 94: 597-602.

  18. An analysis of genetic architecture in populations of Ponderosa Pine

    Science.gov (United States)

    Yan B. Linhart; Jeffry B. Mitton; Kareen B. Sturgeon; Martha L. Davis

    1981-01-01

    Patterns of genetic variation were studied in three populations of ponderosa pine in Colorado by using electrophoretically variable protein loci. Significant genetic differences were found between separate clusters of trees and between age classes within populations. In addition, data indicate that differential cone production and differential animal damage have...

  19. A roadmap for the genetic analysis of renal aging

    NARCIS (Netherlands)

    Noordmans, Gerda A.; van Goor, Harry; Hillebrands, Jan-Luuk; Korstanje, Ron

    2015-01-01

    Several studies show evidence for the genetic basis of renal disease, which renders some individuals more prone than others to accelerated renal aging. Studying the genetics of renal aging can help us to identify genes involved in this process and to unravel the underlying pathways. First, this

  20. Multivariate Survival Mixed Models for Genetic Analysis of Longevity Traits

    DEFF Research Database (Denmark)

    Pimentel Maia, Rafael; Madsen, Per; Labouriau, Rodrigo

    2014-01-01

    A class of multivariate mixed survival models for continuous and discrete time with a complex covariance structure is introduced in a context of quantitative genetic applications. The methods introduced can be used in many applications in quantitative genetics although the discussion presented co...

  1. Genetic diversity analysis of pearl millet (Pennisetum glauccum [L ...

    African Journals Online (AJOL)

    PRECIOUS

    2009-11-16

    Nov 16, 2009 ... assess the degree of polymorphisms within and among genotypes and to investigate if this approach was suitable for genetic studies of pearl ... markers for the assessment of genetic diversity and choosing parents for developing ..... RAPD mapping in a doubled haploid population of rice (Oryza sativa L.).

  2. Comparative Analysis of Genetic Crossover Operators in Knapsack ...

    African Journals Online (AJOL)

    ADOWIE PERE

    ABSTRACT: The Genetic Algorithm (GA) is an evolutionary algorithms and technique based on natural selections of individuals called chromosomes. In this paper, a method for solving. Knapsack problem via GA (Genetic Algorithm) is presented. We compared six different crossovers: Crossover single point, Crossover Two ...

  3. Genetic diversity of Ardi goat based on microsatellite analysis ...

    African Journals Online (AJOL)

    The aim of this study was to analyze the genetic variability of Ardi goats found in the central regions of the kingdom of Saudi Arabia using 14 microsatellite markers. Allelic richness was considerably high in this population indicating high genetic polymorphism as expected heterozygozity was 0.675. Furthermore, the ...

  4. Genetic diversity of Najdi sheep based on microsatellite analysis

    African Journals Online (AJOL)

    MUNEEB

    2012-10-16

    Oct 16, 2012 ... Handley LJL, Byrne K, Santucci F, Townsend S, Taylor M, Bruford MW,. Hewitt GM (2007). Genetic structure of European sheep breeds. Heredity 99:620-631. Hoda A, Dobi P, Hyka G (2009). Genetic diversity and distances of. Albanian local sheep breeds using microsatellite markers. Livest. res. rural Dev.

  5. Molecular genetic analysis of consanguineous families with primary ...

    Indian Academy of Sciences (India)

    Abstract. Autosomal recessive primary microcephaly is a rare genetic disorder that is characterized by reduced head circumference and a varying degree of intellectual disability. Genetic studies on consanguineous families with primary microcephaly have identified 15 (MCPH) causative genes that include MCPH1, WDR62, ...

  6. Molecular-genetic analysis of two cases with retinoblastoma ...

    Indian Academy of Sciences (India)

    Unknown

    Effective counselling and management of retinoblastoma families using genetic information is presently practised in many parts of the world. We studied histopathological, chromosomal and molecular-genetic data of two retinoblastoma pa- tients from India. The two patients, one with bilateral and the other with unilateral ...

  7. Genetic diversity analysis and conservation of the Chinese herb ...

    African Journals Online (AJOL)

    Salvia miltiorrhiza is an economically important floral herb. However, little work has been conducted to further our understanding of the genetics of this herb. In this study, a representative set of germplasm of. S. miltiorrhiza populations was used to analyze genetic diversity using amplified fragment length polymorphism ...

  8. Analysis of embryo, cytoplasmic and maternal genetic correlations ...

    Indian Academy of Sciences (India)

    Genetic correlations of nutrient quality traits including lysine, methionine, leucine, isoleucine, phenylalanine, valine and threonine contents in rapeseed meal were analysed by the genetic model for quantitative traits of diploid plants using a diallel design with nine parents of Brassica napus L. These results indicated that the ...

  9. Genetic analysis of some Egyptian rice genotypes using RAPD, SSR ...

    African Journals Online (AJOL)

    nformation of genetic similarities and diversity among superior Egyptian rice genotypes is necessary for future rice breeding programs and derivation of plant lines. Genetic variability and relationships among seven Egyptian rice genotypes namely Giza 178, Giza177, Giza 175, Giza171 Giza 172, Sakha 102, and Sakha 101 ...

  10. Molecular-genetic analysis of two cases with retinoblastoma ...

    Indian Academy of Sciences (India)

    Effective counselling and management of retinoblastoma families using genetic information is presently practised in many parts of the world. We studied histopathological, chromosomal and molecular-genetic data of two retinoblastoma patients from India. The two patients, one with bilateral and the other with unilateral ...

  11. Analysis of genetic diversity in pigeon pea germplasm using ...

    Indian Academy of Sciences (India)

    Pigeon pea (Cajanus cajan), an important legume crop is predominantly cultivated in tropical and subtropical regions of Asia and Africa. It is normally considered to have a low degree of genetic diversity, an impediment in undertaking crop improvement programmes.We have analysed genetic polymorphism of domesticated ...

  12. Genetic diversity of Najdi sheep based on microsatellite analysis ...

    African Journals Online (AJOL)

    The prime objective of this research was to measure the genetic polymorphism of main sheep breed of Saudi Arabia, Najdi. Randomly selected 49 blood samples were used to extract the DNA followed by polymerase chain reaction (PCR), using 19 microsatellite markers, which were used to investigate the genetic ...

  13. Genetic diversity analysis of rice cultivars from various origins using ...

    African Journals Online (AJOL)

    Genetic diversity is of paramount importance for the success of any plant breeding program. An experiment was conducted to assess the extent of genetic diversity and similarity of 24 rice cultivars from various origins using 29 simple sequence repeat (SSR) markers. A total of 144 alleles were detected at the 29 SSR primer ...

  14. Genetic analysis of seed proteins contents in cowpea ( Vigna ...

    African Journals Online (AJOL)

    In order to select cowpea genotypes with high food value, 10 varieties were genetically screened in Ngaoundéré (Cameroon) for seed crude protein and its soluble fractions contents. Five divergent lines were studied through a 5 x 5 half diallel cross mating. The genotypes presented a significant genetic variability for these ...

  15. Microsatellite and mitochondrial DNA analysis of the genetic ...

    African Journals Online (AJOL)

    Chinese horseshoe crab (Tachypleus tridentatus) is a Xiphosura animal of significant commercial importance and in danger of extinction in China. To better estimate how genetic structure can be used to obtain a conservation perspective of the species, genetic variation was examined in nine locations covering its ...

  16. Analysis of the genetic diversity of four rabbit genotypes using ...

    African Journals Online (AJOL)

    Dr.Ola

    2013-05-15

    May 15, 2013 ... Genetic variations were detected in four different rabbit genotypes; Animal Production Research. Institute (APRI) line, New-Zealand White (NZW), ... (RAPD) is a technology of molecular genetics marker. As the technology is simple, quick, ..... head bacteriophage T4. Nature 227:680-685. Liping Y, Yusheng ...

  17. Strategic analysis in evolutionary genetics and the theory of games

    Indian Academy of Sciences (India)

    Unknown

    the theory of games. PETER HAMMERSTEIN*. Institute for Theoretical Biology, Humboldt University Berlin,. Invalidenstrasse 43, D-10115 Berlin, Germany ... John Maynard Smith; game theory; evolutionarily stable strategy; population genetics; genetic constraint; phenotypic ..... redundant activation signalling paths. If one of ...

  18. Mouse-based genetic modeling and analysis of Down syndrome

    Science.gov (United States)

    Xing, Zhuo; Li, Yichen; Pao, Annie; Bennett, Abigail S.; Tycko, Benjamin; Mobley, William C.; Yu, Y. Eugene

    2016-01-01

    Introduction Down syndrome (DS), caused by human trisomy 21 (Ts21), can be considered as a prototypical model for understanding the effects of chromosomal aneuploidies in other diseases. Human chromosome 21 (Hsa21) is syntenically conserved with three regions in the mouse genome. Sources of data A review of recent advances in genetic modeling and analysis of DS. Using Cre/loxP-mediated chromosome engineering, a substantial number of new mouse models of DS have recently been generated, which facilitates better understanding of disease mechanisms in DS. Areas of agreement Based on evolutionary conservation, Ts21 can be modeled by engineered triplication of Hsa21 syntenic regions in mice. The validity of the models is supported by the exhibition of DS-related phenotypes. Areas of controversy Although substantial progress has been made, it remains a challenge to unravel the relative importance of specific candidate genes and molecular mechanisms underlying the various clinical phenotypes. Growing points Further understanding of mechanisms based on data from mouse models, in parallel with human studies, may lead to novel therapies for clinical manifestations of Ts21 and insights to the roles of aneuploidies in other developmental disorders and cancers. PMID:27789459

  19. Genetic variation analysis of the Bali street dog using microsatellites

    Directory of Open Access Journals (Sweden)

    Wilton Alan N

    2005-02-01

    Full Text Available Abstract Background Approximately 800,000 primarily feral dogs live on the small island of Bali. To analyze the genetic diversity in this population, forty samples were collected at random from dogs in the Denpasar, Bali region and tested using 31 polymorphic microsatellites. Australian dingoes and 28 American Kennel Club breeds were compared to the Bali Street Dog (BSD for allelic diversity, heterozygosities, F-statistics, GST estimates, Nei's DA distance and phylogenetic relationships. Results The BSD proved to be the most heterogeneous, exhibiting 239 of the 366 total alleles observed across all groups and breeds and had an observed heterozygosity of 0.692. Thirteen private alleles were observed in the BSD with an additional three alleles observed only in the BSD and the Australian dingo. The BSD was related most closely to the Chow Chow with a FST of 0.088 and also with high bootstrap support to the Australian dingo and Akita in the phylogenetic analysis. Conclusions This preliminary study into the diversity and relationship of the BSD to other domestic and feral dog populations shows the BSD to be highly heterogeneous and related to populations of East Asian origin. These results indicate that a viable and diverse population of dogs existed on the island of Bali prior to its geographic isolation approximately 12,000 years ago and has been little influenced by domesticated European dogs since that time.

  20. Genetic analysis of processed in-line mastitis indicator data

    DEFF Research Database (Denmark)

    Sørensen, Lars Peter; Løvendahl, Peter

    2013-01-01

    The aim of this study was to estimate heritability of elevated mastitis risk (EMR), a trait derived from in-line measurements of cell counts expressing risk of mastitis on a continuous scale, and its genetic correlation with in-line somatic cell counts. Log-transformed somatic cell counts (SCC; n...... on exponential smoothing of the SCC values followed by factor analysis for estimation of the latent variable EMR was used. Finally, EMR was expressed as a continuum on the interval [0;1] using sigmoid transformation. Thus, an EMR value close to zero indicates low risk of mastitis and a value close to one...... indicates high risk of mastitis. The EMR values were summarized for each cow using the log-transformed median EMR. A second trait was defined as the median of the log-transformed SCC values from 5 to 305 d in milk. A bivariate animal model was used for estimation of co-variance components for the 2 traits...

  1. A quantitative genetic analysis of intermediate asthma phenotypes

    DEFF Research Database (Denmark)

    Thomsen, S.F.; Ferreira, M.A.R.; Kyvik, K.O.

    2009-01-01

    AIM: To study the relative contribution of genetic and environmental factors to the correlation between exhaled nitric oxide (FeNO), airway responsiveness, airway obstruction, and serum total immunoglobulin E (IgE). METHODS: Within a sampling frame of 21,162 twin subjects, 20-49 years of age, from...... to the observed data using maximum likelihood methods. RESULTS: Additive genetic factors explained 67% of the variation in FeNO, 43% in airway responsiveness, 22% in airway obstruction, and 81% in serum total IgE. In general, traits had genetically and environmentally distinct variance structures. The most...... substantial genetic similarity was observed between FeNO and serum total IgE, genetic correlation (rhoA) = 0.37, whereas the strongest environmental resemblance was observed between airway responsiveness and airway obstruction, specific environmental correlation (rhoE) = -0.46, and between FeNO and airway...

  2. Genetic analysis of male reproductive success in relation to density in the zebrafish, Danio rerio

    Directory of Open Access Journals (Sweden)

    Jordan William C

    2006-04-01

    Full Text Available Abstract Background We used behavioural and genetic data to investigate the effects of density on male reproductive success in the zebrafish, Danio rerio. Based on previous measurements of aggression and courtship behaviour by territorial males, we predicted that they would sire more offspring than non-territorial males. Results Microsatellite analysis of paternity showed that at low densities territorial males had higher reproductive success than non-territorial males. However, at high density territorial males were no more successful than non-territorials and the sex difference in the opportunity for sexual selection, based on the parameter Imates, was low. Conclusion Male zebrafish exhibit two distinct mating tactics; territoriality and active pursuit of females. Male reproductive success is density dependent and the opportunity for sexual selection appears to be weak in this species.

  3. Synchronous Onset of Breast and Pancreatic Cancers: Results of Germline and Somatic Genetic Analysis

    Directory of Open Access Journals (Sweden)

    Michael Castro

    2016-07-01

    Full Text Available Background: Synchronous cancers have occasionally been detected at initial diagnosis among patients with breast and ovarian cancer. However, simultaneous coexistence and diagnosis of breast and pancreas cancer has not previously been reported. Case Report: Paternal transmission of a germline BRCA2 mutation to a patient who was diagnosed at age 40 with locally advanced breast and pancreas cancer is presented. Somatic genomic analysis of both cancers with next-generation DNA sequencing confirmed the germline result and reported a variety of variants of unknown significance alterations, of which two were present in both the breast and pancreas cancers. Discussion: The possibility that genomic alterations could have been responsible for modulating the phenotypic or clinical expression of this rare presentation is considered. The authors call attention to the practice of privatizing the clinicogenetic information gained from genetic testing and call for health policy that will facilitate sharing in order to advance the outcomes of patients diagnosed with hereditary cancers.

  4. Genetic analysis of a type IV pili-like locus in the archaeon Methanococcus maripaludis.

    Science.gov (United States)

    Nair, Divya B; Uchida, Kaoru; Aizawa, Shin-Ichi; Jarrell, Ken F

    2014-03-01

    Methanococcus maripaludis is a stringently anaerobic archaeon with two studied surface structures, archaella and type IV pili. Previously, it was shown that three pilin genes (mmp0233 [epdA], mmp0236 [epdB] and mmp0237 [epdC]) located within an 11 gene cluster in the genome were necessary for normal piliation. This study focused on analysis of the remaining genes to determine their potential involvement in piliation. Reverse transcriptase PCR experiments demonstrated the 11 genes formed a single transcriptional unit. Deletions were made in all the non-pilin genes except mmp0231. Electron microscopy revealed that all the genes in the locus except mmp0235 and mmp0238 were essential for piliation. Complementation with a plasmid-borne wild-type copy of the deleted gene restored at least some piliation. We identified genes for an assembly ATPase and two versions of the conserved pilin platform forming protein necessary for pili assembly at a separate genetic locus.

  5. Analysis of Plasminogen Genetic Variants in Multiple Sclerosis Patients

    Science.gov (United States)

    Sadovnick, A. Dessa; Traboulsee, Anthony L.; Bernales, Cecily Q.; Ross, Jay P.; Forwell, Amanda L.; Yee, Irene M.; Guillot-Noel, Lena; Fontaine, Bertrand; Cournu-Rebeix, Isabelle; Alcina, Antonio; Fedetz, Maria; Izquierdo, Guillermo; Matesanz, Fuencisla; Hilven, Kelly; Dubois, Bénédicte; Goris, An; Astobiza, Ianire; Alloza, Iraide; Antigüedad, Alfredo; Vandenbroeck, Koen; Akkad, Denis A.; Aktas, Orhan; Blaschke, Paul; Buttmann, Mathias; Chan, Andrew; Epplen, Joerg T.; Gerdes, Lisa-Ann; Kroner, Antje; Kubisch, Christian; Kümpfel, Tania; Lohse, Peter; Rieckmann, Peter; Zettl, Uwe K.; Zipp, Frauke; Bertram, Lars; Lill, Christina M; Fernandez, Oscar; Urbaneja, Patricia; Leyva, Laura; Alvarez-Cermeño, Jose Carlos; Arroyo, Rafael; Garagorri, Aroa M.; García-Martínez, Angel; Villar, Luisa M.; Urcelay, Elena; Malhotra, Sunny; Montalban, Xavier; Comabella, Manuel; Berger, Thomas; Fazekas, Franz; Reindl, Markus; Schmied, Mascha C.; Zimprich, Alexander; Vilariño-Güell, Carles

    2016-01-01

    Multiple sclerosis (MS) is a prevalent neurological disease of complex etiology. Here, we describe the characterization of a multi-incident MS family that nominated a rare missense variant (p.G420D) in plasminogen (PLG) as a putative genetic risk factor for MS. Genotyping of PLG p.G420D (rs139071351) in 2160 MS patients, and 886 controls from Canada, identified 10 additional probands, two sporadic patients and one control with the variant. Segregation in families harboring the rs139071351 variant, identified p.G420D in 26 out of 30 family members diagnosed with MS, 14 unaffected parents, and 12 out of 30 family members not diagnosed with disease. Despite considerably reduced penetrance, linkage analysis supports cosegregation of PLG p.G420D and disease. Genotyping of PLG p.G420D in 14446 patients, and 8797 controls from Canada, France, Spain, Germany, Belgium, and Austria failed to identify significant association with disease (P = 0.117), despite an overall higher prevalence in patients (OR = 1.32; 95% CI = 0.93–1.87). To assess whether additional rare variants have an effect on MS risk, we sequenced PLG in 293 probands, and genotyped all rare variants in cases and controls. This analysis identified nine rare missense variants, and although three of them were exclusively observed in MS patients, segregation does not support pathogenicity. PLG is a plausible biological candidate for MS owing to its involvement in immune system response, blood-brain barrier permeability, and myelin degradation. Moreover, components of its activation cascade have been shown to present increased activity or expression in MS patients compared to controls; further studies are needed to clarify whether PLG is involved in MS susceptibility. PMID:27194806

  6. Genetic and evolutionary analysis of the Drosophila larval neuromuscular junction

    Science.gov (United States)

    Campbell, Megan

    Although evolution of brains and behaviors is of fundamental biological importance, we lack comprehensive understanding of the general principles governing these processes or the specific mechanisms and molecules through which the evolutionary changes are effected. Because synapses are the basic structural and functional units of nervous systems, one way to address these problems is to dissect the genetic and molecular pathways responsible for morphological evolution of a defined synapse. I have undertaken such an analysis by examining morphology of the larval neuromuscular junction (NMJ) in wild caught D. melanogaster as well as in over 20 other species of Drosophila. Whereas variation in NMJ morphology within a species is limited, I discovered a surprisingly extensive variation among different species. Compared with evolution of other morphological traits, NMJ morphology appears to be evolving very rapidly. Moreover, my data indicate that natural selection rather than genetic drift is primarily responsible for evolution of NMJ morphology. To dissect underlying molecular mechanisms that may govern NMJ growth and evolutionary divergence, I focused on a naturally occurring variant in D. melanogaster that causes NMJ overgrowth. I discovered that the variant mapped to Mob2, a gene encoding a kinase adapter protein originally described in yeast as a member of the Mitotic Exit Network (MEN). I have subsequently examined mutations in the Drosophila orthologs of all the core components of the yeast MEN and found that all of them function as part of a common pathway that acts presynaptically to negatively regulate NMJ growth. As in the regulation of yeast cytokinesis, these components of the MEN appear to act ultimately by regulating actin dynamics during the process of bouton growth and division. These studies have thus led to the discovery of an entirely new role for the MEN---regulation of synaptic growth---that is separate from its function in cell division. This work

  7. Genetic analysis and clinical phenotype of two Indian families with X-linked choroideremia

    Directory of Open Access Journals (Sweden)

    Rajani Battu

    2016-01-01

    Full Text Available Purpose: This study aims to describe the phenotype and genotype of two Indian families affected with X-linked choroideremia (CHM. Materials and Methods: In these two families, the affected individuals and unaffected family members underwent a comprehensive ophthalmic examination including an optical coherence tomography (OCT and electroretinogram. Blood samples were collected from the families for genetic analysis. Next generation sequencing (NGS was done using a panel of 184 genes, which covered previously associated genes with retinal dystrophies. Sequencing data were analyzed for the CHM, RPGR, and RP2 genes that have been implicated in CHM and X-linked retinitis pigmentosa (XLRP, respectively. The identified variants were confirmed by Sanger sequencing in available individuals and unrelated controls. Results: In two unrelated male patients, NGS analysis revealed a previously reported 3'-splice site change c.820-1G>C in the CHM gene in the first family and hemizygous mutation c.653G>C (p.Ser218X in the second family. The asymptomatic family members were carriers for these mutations. Spectral domain-OCT showed loss of outer retina, preservation of the inner retina, and choroidal thinning in the affected males and retinal pigment epithelial changes in the asymptomatic carriers. The identified mutations were not present in 100 controls of Indian origin. There were no potential mutations found in XLRP-associated (RPGR and RP2 genes. Conclusion: This report describes the genotype and phenotype findings in patients with CHM from India. The identified genetic mutation leads to lack of Rab escort protein-1 (REP-1 or affects the production of a REP-1 protein that is likely to cause retinal abnormalities in patients.

  8. Diagnostic and therapeutic implications of genetic heterogeneity in myeloid neoplasms uncovered by comprehensive mutational analysis

    Directory of Open Access Journals (Sweden)

    Sarah M. Choi

    2017-01-01

    Full Text Available While growing use of comprehensive mutational analysis has led to the discovery of innumerable genetic alterations associated with various myeloid neoplasms, the under-recognized phenomenon of genetic heterogeneity within such neoplasms creates a potential for diagnostic confusion. Here, we describe two cases where expanded mutational testing led to amendment of an initial diagnosis of chronic myelogenous leukemia with subsequent altered treatment of each patient. We demonstrate the power of comprehensive testing in ensuring appropriate classification of genetically heterogeneous neoplasms, and emphasize thoughtful analysis of molecular and genetic data as an essential component of diagnosis and management.

  9. Simulation Approach for Timing Analysis of Genetic Logic Circuits

    DEFF Research Database (Denmark)

    Baig, Hasan; Madsen, Jan

    2017-01-01

    in a manner similar to electronic logic circuits, but they are much more stochastic and hence much harder to characterize. In this article, we introduce an approach to analyze the threshold value and timing of genetic logic circuits. We show how this approach can be used to analyze the timing behavior...... of single and cascaded genetic logic circuits. We further analyze the timing sensitivity of circuits by varying the degradation rates and concentrations. Our approach can be used not only to characterize the timing behavior but also to analyze the timing constraints of cascaded genetic logic circuits...

  10. Gregor Mendel's Genetic Experiments: A Statistical Analysis after 150 Years

    Czech Academy of Sciences Publication Activity Database

    Kalina, Jan

    2016-01-01

    Roč. 12, č. 2 (2016), s. 20-26 ISSN 1801-5603 Institutional support: RVO:67985807 Keywords : genetics * history of science * biostatistics * design of experiments Subject RIV: BB - Applied Statistics, Operational Research

  11. Systems genetics analysis of pharmacogenomics variation during antidepressant treatment

    DEFF Research Database (Denmark)

    Madsen, M. B.; Kogelman, L. J. A.; Kadarmideen, H. N.

    2018-01-01

    Selective serotonin reuptake inhibitors (SSRIs) are the most widely used antidepressants, but the efficacy of the treatment varies significantly among individuals. It is believed that complex genetic mechanisms play a part in this variation. We have used a network based approach to unravel...... the involved genetic components. Moreover, we investigated the potential difference in the genetic interaction networks underlying SSRI treatment response over time. We found four hub genes (ASCC3, PPARGC1B, SCHIP1 and TMTC2) with different connectivity in the initial SSRI treatment period (baseline to week 4......) compared with the subsequent period (4-8 weeks after initiation), suggesting that different genetic networks are important at different times during SSRI treatment. The strongest interactions in the initial SSRI treatment period involved genes encoding transcriptional factors, and in the subsequent period...

  12. Genetic Analysis of Micro-environmental Plasticity in Drosophila melanogaster

    DEFF Research Database (Denmark)

    Morgante, Fabio; Sorensen, Daniel A; Sørensen, Peter

    Quantitative genetic models recognize the potential for genotype by environment interaction, whereby different genotypes have different plastic responses to changes in macro-environmental conditions. Recently, it has been recognized that micro-environmental plasticity (‘residual’ variance) may also...... be genetically variable. This study utilized the Drosophila Genetic Reference Panel (DGRP) to accurately estimate the genetic variance of micro-environmental plasticity for chill coma recovery time and startle response. Estimates of broad sense heritabilities for both traits are substantial (from 0.51 to 0.......77), of the same order as the heritability at the level of the trait mean for startle response and even larger for chill coma recovery. Genome wide association analyses identified molecular variants (from 15 to 31 depending on the sex and the trait) associated with micro-environmental plasticity. These findings...

  13. Smoking and caffeine consumption: a genetic analysis of their association

    NARCIS (Netherlands)

    Treur, J.L.; Taylor, A.E.; Ware, J.J.; Nivard, M.G.; Neale, M.C.; McMahon, G.; Hottenga, J.J.; Baselmans, B.M.L.; Boomsma, D.I.; Munafò, M.; Vink, J.M.

    2017-01-01

    Smoking and caffeine consumption show a strong positive correlation, but the mechanism underlying this association is unclear. Explanations include shared genetic/environmental factors or causal effects. This study employed three methods to investigate the association between smoking and caffeine.

  14. Genetic diversity analysis of various red spider mite- resistant ...

    African Journals Online (AJOL)

    User

    2011-05-02

    resistant cotton (Gossypium hirsutum) cultivars that are applied in cultivar identification and breeder's right protection of cottons. The genomic DNA was used as template and random primers were used to analyze the genetic diversity.

  15. Genetic diversity analysis of various red spider miteresistant upland ...

    African Journals Online (AJOL)

    resistant cotton (Gossypium hirsutum) cultivars that are applied in cultivar identification and breeder's right protection of cottons. The genomic DNA was used as template and random primers were used to analyze the genetic diversity of 21 accessions ...

  16. Killer Whale Genetic Data - Southern resident killer whale pedigree analysis

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — In this project, we are using genetic variation to infer mating patterns in the southern killer whale community. In Canada, this population was listed as threatened...

  17. (AFLP) analysis of genetic diversity and relationship of Chinese ...

    African Journals Online (AJOL)

    Administrator

    2011-05-30

    May 30, 2011 ... and 25 cultivars that originated from China with fluorescent amplified fragment length polymorphism molecular markers were ... Key words: Rosa rugosa, genetic diversity and relationship, amplified fragment length polymorphism. INTRODUCTION ... northern Japan (Ohwi, 1965), the Korean Peninsula.

  18. Safety and tolerability of frovatriptan in the acute treatment of migraine and prevention of menstrual migraine: Results of a new analysis of data from five previously published studies.

    Science.gov (United States)

    MacGregor, E Anne; Pawsey, Stephen P; Campbell, John C; Hu, Xiaojun

    2010-04-01

    Triptans are a recommended first-line treatment for moderate to severe migraine. Using clinical trial data, we evaluated the safety and tolerability of frovatriptan as acute treatment (AT) and as short-term preventive (STP) therapy for menstrual migraine (MM). Data from 2 Phase III AT trials (AT1: randomized, placebo controlled, 1 attack; AT2: 12-months, noncomparative, open label) and 3 Phase IIIb STP trials in MM (MMP1 and MMP2: randomized, placebo controlled, double blind, 3 perimenstrual periods; MMP3: open label, noncomparative, 12 perimenstrual periods) were analyzed. In AT1, patients treated each attack with frovatriptan 2.5 mg, sumatriptan 100 mg, or placebo. In AT2, they used frovatriptan 2.5 mg. In MMP1 and MMP2, women administered frovatriptan 2.5 mg for 6 days during the perimenstrual period, taking a loading dose of 2 or 4 tablets on day 1, followed by once-daily or BID frovatriptan 2.5 mg, respectively; in MMP3, they used BID frovatriptan 2.5 mg. In AT1, which was previously published in part, group differences in adverse events (AEs) were analyzed using the Fisher exact test, and response rates were compared using logistic regression. Post hoc analyses of sustained pain-free status with no AEs (SNAE) and sustained pain response with no AEs (SPRNAE) were performed using a 2-sample test for equality of proportions without continuity correction. For AT2 and the STP studies, data were summarized using descriptive statistics. Results of individual safety analyses for the STP studies were previously reported; the present report includes new results from a pooled analysis of MMP1 and MMP2 and a new analysis of MMP3 in which AEs were coded using Medical Dictionary for Regulatory Activities version 8.0. AT1 included 1206 patients in the safety group; AT2 included 496. In the STP studies, safety data were collected for 1487 women. In AT1 and AT2, 85.6% and 88.3%, respectively, of enrolled patients were women. Overall, AEs were generally mild to moderate (AT

  19. Common standards in facial esthetics: craniofacial analysis of most attractive black and white subjects according to People magazine during previous 10 years.

    Science.gov (United States)

    Iglesias-Linares, Alejandro; Yáñez-Vico, Rosa-María; Moreno-Manteca, Blanca; Moreno-Fernández, Ana María; Mendoza-Mendoza, Asunción; Solano-Reina, Enrique

    2011-06-01

    The aim of the present case-control study was to determine--using the 10 most recent annual listings of the most beautiful black and white people--whether any common, measurable esthetic parameter could be extracted from both groups. A total of 80 women (40 white and 40 black), who had been included in the list of People magazine's 100 most beautiful people during the previous 10 years, were selected. Lateral photographs of all 80 subjects were obtained from Internet databases, oriented, and sized. A modified photogrammetric analysis was performed on the lateral view of each subject to obtain the angle and proportion measurements. Differences between the 2 groups were compared with 95% significance using the Student t test for independent samples. Facial similarities in the 2 ethnic groups were observed for the angle of the inferior facial third, labiomental angle, angle of facial convexity, and cervicomental angle. These results point to a similar conformation of the lower part of the face in relation to the neck that was shared by both groups of beautiful women. Additionally, both groups showed similar results for the lower lip projection. Likewise, similar proportional measurements were found for the upper lip proportion, notwithstanding differences in protrusion. Modern society is changing the classic concept of facial beauty because of globalization and the prevalence of multiethnic communities in the developed world. Independently of ethnic origin, beautiful women tend to have similar facial features that are a mixture of both black and white features. Copyright © 2011 American Association of Oral and Maxillofacial Surgeons. Published by Elsevier Inc. All rights reserved.

  20. Systems genetic analysis of brown adipose tissue function

    Czech Academy of Sciences Publication Activity Database

    Pravenec, Michal; Saba, L. M.; Zídek, Václav; Landa, Vladimír; Mlejnek, Petr; Šilhavý, Jan; Šimáková, Miroslava; Strnad, Hynek; Trnovská, J.; Škop, V.; Hüttl, M.; Marková, I.; Oliyarnyk, O.; Malínská, H.; Kazdová, L.; Smith, H.; Tabakoff, B.

    2018-01-01

    Roč. 50, č. 1 (2018), s. 52-66 ISSN 1094-8341 R&D Projects: GA ČR(CZ) GA13-04420S Institutional support: RVO:67985823 Keywords : brown adipose tissue * coexpression modules * quantitative trait locus * recombinant inbred strains * spontaneously hypertensive rat Subject RIV: EB - Genetics ; Molecular Biology OBOR OECD: Human genetics Impact factor: 3.044, year: 2016

  1. Systematic Complex Haploinsufficiency-Based Genetic Analysis of Candida albicans Transcription Factors: Tools and Applications to Virulence-Associated Phenotypes.

    Science.gov (United States)

    Glazier, Virginia E; Murante, Thomas; Koselny, Kristy; Murante, Daniel; Esqueda, Marisol; Wall, Gina A; Wellington, Melanie; Hung, Chiung-Yu; Kumar, Anuj; Krysan, Damian J

    2018-03-28

    Genetic interaction analysis is a powerful approach to the study of complex biological processes that are dependent on multiple genes. Because of the largely diploid nature of the human fungal pathogen Candida albicans , genetic interaction analysis has been limited to a small number of large-scale screens and a handful for gene-by-gene studies. Complex haploinsufficiency, which occurs when a strain containing two heterozygous mutations at distinct loci shows a phenotype that is distinct from either of the corresponding single heterozygous mutants, is an expedient approach to genetic interactions analysis in diploid organisms. Here, we describe the construction of a barcoded-library of 133 heterozygous TF deletion mutants and deletion cassettes for designed to facilitate complex haploinsufficiency-based genetic interaction studies of the TF networks in C. albicans We have characterized the phenotypes of these heterozygous mutants under a broad range of in vitro conditions using both agar-plate and pooled signature tag-based assays. Consistent with previous studies, haploinsufficiency is relative uncommon. In contrast, a set of 12 TFs enriched in mutants with a role in adhesion were found to have altered competitive fitness at early time points in a murine model of disseminated candidiasis. Finally, we characterized the genetic interactions of a set of biofilm related TFs in the first two steps of biofilm formation, adherence and filamentation of adherent cells. The genetic interaction networks at each stage of biofilm formation are significantly different indicating that the network is not static but dynamic. Copyright © 2018 Glazier et al.

  2. Multivariate analysis in a genetic divergence study of Psidium guajava.

    Science.gov (United States)

    Nogueira, A M; Ferreira, M F S; Guilhen, J H S; Ferreira, A

    2014-12-18

    The family Myrtaceae is widespread in the Atlantic Forest and is well-represented in the Espírito Santo State in Brazil. In the genus Psidium of this family, guava (Psidium guajava L.) is the most economically important species. Guava is widely cultivated in tropical and subtropical countries; however, the widespread cultivation of only a small number of guava tree cultivars may cause the genetic vulnerability of this crop, making the search for promising genotypes in natural populations important for breeding programs and conservation. In this study, the genetic diversity of 66 guava trees sampled in the southern region of Espírito Santo and in Caparaó, MG, Brazil were evaluated. A total of 28 morphological descriptors (11 quantitative and 17 multicategorical) and 18 microsatellite markers were used. Principal component, discriminant and cluster analyses, descriptive analyses, and genetic diversity analyses using simple sequence repeats were performed. Discrimination of accessions using molecular markers resulted in clustering of genotypes of the same origin, which was not observed using morphological data. Genetic diversity was detected between and within the localities evaluated, regardless of the methodology used. Genetic differentiation among the populations using morphological and molecular data indicated the importance of the study area for species conservation, genetic erosion estimation, and exploitation in breeding programs.

  3. Early Onset Diabetes - Genetic And Hormonal Analysis In Pakistani Population.

    Science.gov (United States)

    Wahid, Maryam; Kamran, Mohammad

    2016-01-01

    Mitochondrial DNA mutation and hormonal imbalance is involved in the pathogenesis of early onset diabetes but data is lacking in Pakistani population. The study was planned to delineate the clinical presentation of early onset diabetes with possible hormonal and genetic etiological factors and aascertain the possible etiological role of insulin and glucagon in these patients either on oral hypoglycaemic or subcutaneous insulin therapy. Retrospective, analytical case control study with conventional sampling technique carried at Centre for Research in Experimental and Applied Medicine (CREAM) affiliated with the department of Biochemistry and Molecular Biology, Army Medical College Rawalpindi from Dec 2006 to July 2011. Study included the patients (20-35 years of age) with early onset diabetes on oral hypoglycemic (n=240), insulin therapy (n=280), and compared with non-diabetic healthy controls (n=150). A fragment surrounding tRNALeu (UUR) gene was amplified by AmpliTaq from mtDNA which was extracted from peripheral blood leucocytes. Then it was subjected to restriction endonucleases, ApaI for A3242G mutation and HaeIII for G3316A mutation detection. Plasma glucose, glycosylated Hb, osmolality, insulin and glucagon levels along with ABGs analysis was also done. Non diabetic controls comprised of 51% males and 49% females, diabetics on oral hypoglycemic 60% males and 40 % females and on insulin therapy 54% males and 46% females. Insulin dependent diabetics had statistically significant hyperglucagonemia, acidemia and bicarbonate deficit. MtDNA A3242G and G3316A mutations were not detected. relative hyperglucagonemia and acidemia in Insulin dependent diabetics was a potent threat leading to DKA. The absence of two mtDNA mutations in ND1 gene rules out the possibility of involvement of these mutations in early onset diabetes in Pakistani population.

  4. Genetic and genomic analysis of RNases in model cyanobacteria.

    Science.gov (United States)

    Cameron, Jeffrey C; Gordon, Gina C; Pfleger, Brian F

    2015-10-01

    Cyanobacteria are diverse photosynthetic microbes with the ability to convert CO2 into useful products. However, metabolic engineering of cyanobacteria remains challenging because of the limited resources for modifying the expression of endogenous and exogenous biochemical pathways. Fine-tuned control of protein production will be critical to optimize the biological conversion of CO2 into desirable molecules. Messenger RNAs (mRNAs) are labile intermediates that play critical roles in determining the translation rate and steady-state protein concentrations in the cell. The majority of studies on mRNA turnover have focused on the model heterotrophic bacteria Escherichia coli and Bacillus subtilis. These studies have elucidated many RNA modifying and processing enzymes and have highlighted the differences between these Gram-negative and Gram-positive bacteria, respectively. In contrast, much less is known about mRNA turnover in cyanobacteria. We generated a compendium of the major ribonucleases (RNases) and provide an in-depth analysis of RNase III-like enzymes in commonly studied and diverse cyanobacteria. Furthermore, using targeted gene deletion, we genetically dissected the RNases in Synechococcus sp. PCC 7002, one of the fastest growing and industrially attractive cyanobacterial strains. We found that all three cyanobacterial homologs of RNase III and a member of the RNase II/R family are not essential under standard laboratory conditions, while homologs of RNase E/G, RNase J1/J2, PNPase, and a different member of the RNase II/R family appear to be essential for growth. This work will enhance our understanding of native control of gene expression and will facilitate the development of an RNA-based toolkit for metabolic engineering in cyanobacteria.

  5. Mitochondrial DNA analysis of eneolithic trypillians from Ukraine reveals neolithic farming genetic roots.

    Directory of Open Access Journals (Sweden)

    Alexey G Nikitin

    Full Text Available The agricultural revolution in Eastern Europe began in the Eneolithic with the Cucuteni-Trypillia culture complex. In Ukraine, the Trypillian culture (TC existed for over two millennia (ca. 5,400-2,700 BCE and left a wealth of artifacts. Yet, their burial rituals remain a mystery and to date almost nothing is known about the genetic composition of the TC population. One of the very few TC sites where human remains can be found is a cave called Verteba in western Ukraine. This report presents four partial and four complete mitochondrial genomes from nine TC individuals uncovered in the cave. The results of this analysis, combined with the data from previous reports, indicate that the Trypillian population at Verteba carried, for the most part, a typical Neolithic farmer package of mitochondrial DNA (mtDNA lineages traced to Anatolian farmers and Neolithic farming groups of central Europe. At the same time, the find of two specimens belonging to haplogroup U8b1 at Verteba can be viewed as a connection of TC with the Upper Paleolithic European populations. At the level of mtDNA haplogroup frequencies, the TC population from Verteba demonstrates a close genetic relationship with population groups of the Funnel Beaker/ Trichterbecker cultural complex from central and northern Europe (ca. 3,950-2,500 BCE.

  6. Population genetics analysis of Phlebotomus papatasi sand flies from Egypt and Jordan based on mitochondrial cytochrome b haplotypes.

    Science.gov (United States)

    Flanley, Catherine M; Ramalho-Ortigao, Marcelo; Coutinho-Abreu, Iliano V; Mukbel, Rami; Hanafi, Hanafi A; El-Hossary, Shabaan S; Fawaz, Emad El-Din Y; Hoel, David F; Bray, Alexander W; Stayback, Gwen; Shoue, Douglas A; Kamhawi, Shaden; Karakuş, Mehmet; Jaouadi, Kaouther; Yaghoobie-Ershadi, Mohammad Reza; Krüger, Andreas; Amro, Ahmad; Kenawy, Mohamed Amin; Dokhan, Mostafa Ramadhan; Warburg, Alon; Hamarsheh, Omar; McDowell, Mary Ann

    2018-03-27

    Phlebotomus papatasi sand flies are major vectors of Leishmania major and phlebovirus infection in North Africa and across the Middle East to the Indian subcontinent. Population genetics is a valuable tool in understanding the level of genetic variability present in vector populations, vector competence, and the development of novel control strategies. This study investigated the genetic differentiation between P. papatasi populations in Egypt and Jordan that inhabit distinct ecotopes and compared this structure to P. papatasi populations from a broader geographical range. A 461 base pair (bp) fragment from the mtDNA cytochrome b (cyt b) gene was PCR amplified and sequenced from 116 individual female sand flies from Aswan and North Sinai, Egypt, as well as Swaimeh and Malka, Jordan. Haplotypes were identified and used to generate a median-joining network, F ST values and isolation-by-distance were also evaluated. Additional sand fly individuals from Afghanistan, Iran, Israel, Jordan, Libya, Tunisia and Turkey were included as well as previously published haplotypes to provide a geographically broad genetic variation analysis. Thirteen haplotypes displaying nine variant sites were identified from P. papatasi collected in Egypt and Jordan. No private haplotypes were identified from samples in North Sinai, Egypt, two were observed in Aswan, Egypt, four from Swaimeh, Jordan and two in Malka, Jordan. The Jordan populations clustered separately from the Egypt populations and produced more private haplotypes than those from Egypt. Pairwise F ST values fall in the range 0.024-0.648. The clustering patterns and pairwise F ST values indicate a strong differentiation between Egyptian and Jordanian populations, although this population structure is not due to isolation-by-distance. Other factors, such as environmental influences and the genetic variability in the circulating Le. major parasites, could possibly contribute to this heterogeneity. The present study aligns with

  7. Quantitative Genetic Analysis Reveals Potential to Genetically Improve Fruit Yield and Drought Resistance Simultaneously in Coriander.

    Science.gov (United States)

    Khodadadi, Mostafa; Dehghani, Hamid; Jalali Javaran, Mokhtar

    2017-01-01

    Enhancing water use efficiency of coriander ( Coriandrum sativum L.) is a major focus for coriander breeding to cope with drought stress. The purpose of this study was; (a) to identify the predominant mechanism(s) of drought resistance in coriander and (b) to evaluate the genetic control mechanism(s) of traits associated with drought resistance and higher fruit yield. To reach this purpose, 15 half-diallel hybrids of coriander and their six parents were evaluated under well-watered and water deficit stressed (WDS) in both glasshouse lysimetric and field conditions. The parents were selected for their different response to water deficit stress following preliminary experiments. Results revealed that the genetic control mechanism of fruit yield is complex, variable and highly affected by environment. The mode of inheritance and nature of gene action for percent assimilate partitioned to fruits were similar to those for flowering time in both well-watered and WDS conditions. A significant negative genetic linkage was found between fruit yield and percent assimilate partitioned to root, percent assimilate partitioned to shoot, root number, root diameter, root dry mass, root volume, and early flowering. Thus, to improve fruit yield under water deficit stress, selection of low values of these traits could be used. In contrast, a significant positive genetic linkage between fruit yield and percent assimilate partitioned to fruits, leaf relative water content and chlorophyll content indicate selection for high values of these traits. These secondary or surrogate traits could be selected during early segregating generations. The early ripening parent (P 1 ; TN-59-230) contained effective genes involved in preferred percent assimilate partitioning to fruit and drought stress resistance. In conclusion, genetic improvement of fruit yield and drought resistance could be simultaneously gained in coriander when breeding for drought resistance.

  8. Genetic diversity analysis of tropical sugar beet (Beta vulgaris L.) varieties in Bangladesh using RAPD markers

    OpenAIRE

    Saclain Saidin; Latif Abdul; Bala Babul; Mallik Mithun; Islam Shahidul

    2016-01-01

    Knowledge on intra-specific genetic variation of an organism is important for its genetic improvement and conservation. In order to estimate genetic variation and relatedness in eleven tropical Sugar beet varieties we used randomly amplified polymorphic DNA (RAPD) markers. The RAPD analysis was performed using six decamer random primers, which amplified a total of 63 DNA fragments of which 43 (68.25%) were found polymorphic. The average polymorphic bands pe...

  9. Identification of Genetic Susceptibility to Childhood Cancer through Analysis of Genes in Parallel

    Science.gov (United States)

    Plon, Sharon E.; Wheeler, David A.; Strong, Louise C.; Tomlinson, Gail E.; Pirics, Michael; Meng, Qingchang; Cheung, Hannah C.; Begin, Phyllis R.; Muzny, Donna M.; Lewis, Lora; Biegel, Jaclyn A.; Gibbs, Richard A.

    2011-01-01

    Clinical cancer genetic susceptibility analysis typically proceeds sequentially beginning with the most likely causative gene. The process is time consuming and the yield is low particularly for families with unusual patterns of cancer. We determined the results of in parallel mutation analysis of a large cancer-associated gene panel. We performed deletion analysis and sequenced the coding regions of 45 genes (8 oncogenes and 37 tumor suppressor or DNA repair genes) in 48 childhood cancer patients who also (1) were diagnosed with a second malignancy under age 30, (2) have a sibling diagnosed with cancer under age 30 and/or (3) have a major congenital anomaly or developmental delay. Deleterious mutations were identified in 6 of 48 (13%) families, 4 of which met the sibling criteria. Mutations were identified in genes previously implicated in both dominant and recessive childhood syndromes including SMARCB1, PMS2, and TP53. No pathogenic deletions were identified. This approach has provided efficient identification of childhood cancer susceptibility mutations and will have greater utility as additional cancer susceptibility genes are identified. Integrating parallel analysis of large gene panels into clinical testing will speed results and increase diagnostic yield. The failure to detect mutations in 87% of families highlights that a number of childhood cancer susceptibility genes remain to be discovered. PMID:21356188

  10. Quantitative genetic analysis indicates natural selection on leaf phenotypes across wild tomato species (Solanum sect. Lycopersicon; Solanaceae).

    Science.gov (United States)

    Muir, Christopher D; Pease, James B; Moyle, Leonie C

    2014-12-01

    Adaptive evolution requires both raw genetic material and an accessible path of high fitness from one fitness peak to another. In this study, we used an introgression line (IL) population to map quantitative trait loci (QTL) for leaf traits thought to be associated with adaptation to precipitation in wild tomatoes (Solanum sect. Lycopersicon; Solanaceae). A QTL sign test showed that several traits likely evolved under directional natural selection. Leaf traits correlated across species do not share a common genetic basis, consistent with a scenario in which selection maintains trait covariation unconstrained by pleiotropy or linkage disequilibrium. Two large effect QTL for stomatal distribution colocalized with key genes in the stomatal development pathway, suggesting promising candidates for the molecular bases of adaptation in these species. Furthermore, macroevolutionary transitions between vastly different stomatal distributions may not be constrained when such large-effect mutations are available. Finally, genetic correlations between stomatal traits measured in this study and data on carbon isotope discrimination from the same ILs support a functional hypothesis that the distribution of stomata affects the resistance to CO2 diffusion inside the leaf, a trait implicated in climatic adaptation in wild tomatoes. Along with evidence from previous comparative and experimental studies, this analysis indicates that leaf traits are an important component of climatic niche adaptation in wild tomatoes and demonstrates that some trait transitions between species could have involved few, large-effect genetic changes, allowing rapid responses to new environmental conditions. Copyright © 2014 by the Genetics Society of America.

  11. Mapping Genetic Diversity of Cherimoya (Annona cherimola Mill.): Application of Spatial Analysis for Conservation and Use of Plant Genetic Resources

    Science.gov (United States)

    van Zonneveld, Maarten; Scheldeman, Xavier; Escribano, Pilar; Viruel, María A.; Van Damme, Patrick; Garcia, Willman; Tapia, César; Romero, José; Sigueñas, Manuel; Hormaza, José I.

    2012-01-01

    There is a growing call for inventories that evaluate geographic patterns in diversity of plant genetic resources maintained on farm and in species' natural populations in order to enhance their use and conservation. Such evaluations are relevant for useful tropical and subtropical tree species, as many of these species are still undomesticated, or in incipient stages of domestication and local populations can offer yet-unknown traits of high value to further domestication. For many outcrossing species, such as most trees, inbreeding depression can be an issue, and genetic diversity is important to sustain local production. Diversity is also crucial for species to adapt to environmental changes. This paper explores the possibilities of incorporating molecular marker data into Geographic Information Systems (GIS) to allow visualization and better understanding of spatial patterns of genetic diversity as a key input to optimize conservation and use of plant genetic resources, based on a case study of cherimoya (Annona cherimola Mill.), a Neotropical fruit tree species. We present spatial analyses to (1) improve the understanding of spatial distribution of genetic diversity of cherimoya natural stands and cultivated trees in Ecuador, Bolivia and Peru based on microsatellite molecular markers (SSRs); and (2) formulate optimal conservation strategies by revealing priority areas for in situ conservation, and identifying existing diversity gaps in ex situ collections. We found high levels of allelic richness, locally common alleles and expected heterozygosity in cherimoya's putative centre of origin, southern Ecuador and northern Peru, whereas levels of diversity in southern Peru and especially in Bolivia were significantly lower. The application of GIS on a large microsatellite dataset allows a more detailed prioritization of areas for in situ conservation and targeted collection across the Andean distribution range of cherimoya than previous studies could do, i.e. at

  12. Mapping genetic diversity of cherimoya (Annona cherimola Mill.): application of spatial analysis for conservation and use of plant genetic resources.

    Science.gov (United States)

    Zonneveld, Maarten van; Scheldeman, Xavier; Escribano, Pilar; Viruel, María A; Van Damme, Patrick; Garcia, Willman; Tapia, César; Romero, José; Sigueñas, Manuel; Hormaza, José I

    2012-01-01

    There is a growing call for inventories that evaluate geographic patterns in diversity of plant genetic resources maintained on farm and in species' natural populations in order to enhance their use and conservation. Such evaluations are relevant for useful tropical and subtropical tree species, as many of these species are still undomesticated, or in incipient stages of domestication and local populations can offer yet-unknown traits of high value to further domestication. For many outcrossing species, such as most trees, inbreeding depression can be an issue, and genetic diversity is important to sustain local production. Diversity is also crucial for species to adapt to environmental changes. This paper explores the possibilities of incorporating molecular marker data into Geographic Information Systems (GIS) to allow visualization and better understanding of spatial patterns of genetic diversity as a key input to optimize conservation and use of plant genetic resources, based on a case study of cherimoya (Annona cherimola Mill.), a Neotropical fruit tree species. We present spatial analyses to (1) improve the understanding of spatial distribution of genetic diversity of cherimoya natural stands and cultivated trees in Ecuador, Bolivia and Peru based on microsatellite molecular markers (SSRs); and (2) formulate optimal conservation strategies by revealing priority areas for in situ conservation, and identifying existing diversity gaps in ex situ collections. We found high levels of allelic richness, locally common alleles and expected heterozygosity in cherimoya's putative centre of origin, southern Ecuador and northern Peru, whereas levels of diversity in southern Peru and especially in Bolivia were significantly lower. The application of GIS on a large microsatellite dataset allows a more detailed prioritization of areas for in situ conservation and targeted collection across the Andean distribution range of cherimoya than previous studies could do, i.e. at

  13. Mapping genetic diversity of cherimoya (Annona cherimola Mill.: application of spatial analysis for conservation and use of plant genetic resources.

    Directory of Open Access Journals (Sweden)

    Maarten van Zonneveld

    Full Text Available There is a growing call for inventories that evaluate geographic patterns in diversity of plant genetic resources maintained on farm and in species' natural populations in order to enhance their use and conservation. Such evaluations are relevant for useful tropical and subtropical tree species, as many of these species are still undomesticated, or in incipient stages of domestication and local populations can offer yet-unknown traits of high value to further domestication. For many outcrossing species, such as most trees, inbreeding depression can be an issue, and genetic diversity is important to sustain local production. Diversity is also crucial for species to adapt to environmental changes. This paper explores the possibilities of incorporating molecular marker data into Geographic Information Systems (GIS to allow visualization and better understanding of spatial patterns of genetic diversity as a key input to optimize conservation and use of plant genetic resources, based on a case study of cherimoya (Annona cherimola Mill., a Neotropical fruit tree species. We present spatial analyses to (1 improve the understanding of spatial distribution of genetic diversity of cherimoya natural stands and cultivated trees in Ecuador, Bolivia and Peru based on microsatellite molecular markers (SSRs; and (2 formulate optimal conservation strategies by revealing priority areas for in situ conservation, and identifying existing diversity gaps in ex situ collections. We found high levels of allelic richness, locally common alleles and expected heterozygosity in cherimoya's putative centre of origin, southern Ecuador and northern Peru, whereas levels of diversity in southern Peru and especially in Bolivia were significantly lower. The application of GIS on a large microsatellite dataset allows a more detailed prioritization of areas for in situ conservation and targeted collection across the Andean distribution range of cherimoya than previous studies could

  14. Genome-wide association study and meta-analysis in multiple populations identifies new loci for peanut allergy and establishes C11orf30/EMSY as a genetic risk factor for food allergy

    NARCIS (Netherlands)

    Asai, Yuka; Eslami, Aida; van Ginkel, C Dorien; Akhabir, Loubna; Wan, Ming; Ben-Shoshan, Moshe; Martino, David; Ferreira, Manuel A; Allen, Katrina; Mazer, Bruce; de Jong, Nicolette W; Gerth van Wijk, Roy N; Dubois, Anthony E J; Chin, Rick; Cheuk, Steven; Hoffman, Joshua; Jorgensen, Eric; Witte, John S; Melles, Ronald B; Hong, Xiumei; Wang, Xiaobin; Hui, Jennie; Musk, Arthur W Bill; Hunter, Michael; James, Alan L; Koppelman, Gerard H; Sandford, Andrew J; Clarke, Ann E; Daley, Denise

    BACKGROUND: Peanut allergy (PA) is a complex disease with both environmental and genetic risk factors. Previously PA loci were identified in FLG and HLA in candidate gene studies, and loci in HLA in a genome-wide association study and meta-analysis. OBJECTIVE: To investigate genetic susceptibility

  15. VNTR analysis reveals unexpected genetic diversity within Mycoplasma agalactiae, the main causative agent of contagious agalactia

    Directory of Open Access Journals (Sweden)

    Ayling Roger D

    2008-11-01

    Full Text Available Abstract Background Mycoplasma agalactiae is the main cause of contagious agalactia, a serious disease of sheep and goats, which has major clinical and economic impacts. Previous studies of M. agalactiae have shown it to be unusually homogeneous and there are currently no available epidemiological techniques which enable a high degree of strain differentiation. Results We have developed variable number tandem repeat (VNTR analysis using the sequenced genome of the M. agalactiae type strain PG2. The PG2 genome was found to be replete with tandem repeat sequences and 4 were chosen for further analysis. VNTR 5 was located within the hypothetical protein MAG6170 a predicted lipoprotein. VNTR 14 was intergenic between the hypothetical protein MAG3350 and the hypothetical protein MAG3340. VNTR 17 was intergenic between the hypothetical protein MAG4060 and the hypothetical protein MAG4070 and VNTR 19 spanned the 5' end of the pseudogene for a lipoprotein MAG4310 and the 3' end of the hypothetical lipoprotein MAG4320. We have investigated the genetic diversity of 88 M. agalactiae isolates of wide geographic origin using VNTR analysis and compared it with pulsed field gel electrophoresis (PFGE and random amplified polymorphic DNA (RAPD analysis. Simpson's index of diversity was calculated to be 0.324 for PFGE and 0.574 for VNTR analysis. VNTR analysis revealed unexpected diversity within M. agalactiae with 9 different VNTR types discovered. Some correlation was found between geographical origin and the VNTR type of the isolates. Conclusion VNTR analysis represents a useful, rapid first-line test for use in molecular epidemiological analysis of M. agalactiae for outbreak tracing and control.

  16. Genetic and immunohistochemical analysis of HSPA5 in mouse and human retinas

    OpenAIRE

    Chintalapudi, Sumana R.; Wang, XiaoFei; Li, Huiling; Lau, Yin H. Chan; Williams, Robert W.; Jablonski, Monica M.

    2016-01-01

    Purpose Photoreceptor degenerative diseases?are among the leading causes of vision loss. Although the causative genetic mutations are often known, mechanisms leading to photoreceptor degeneration remain poorly defined. We have previously demonstrated that the photoreceptor membrane-associated protein XAP-1 antigen is a product of the HSPA5 gene. In this study, we used systems genetic methods, statistical modeling, and immunostaining to identify and analyze candidate genes that modulate Hspa5 ...

  17. Previous Adverse Infant Outcomes as Predictors of Preconception Care Use: An Analysis of the 2010 and 2012 Los Angeles Mommy and Baby (LAMB) Surveys.

    Science.gov (United States)

    Batra, Priya; Higgins, Chandra; Chao, Shin M

    2016-06-01

    Objectives This study aimed to understand the impact of a previous adverse infant outcome (AIO) on use of preconception care prior to a subsequent pregnancy. Methods Responses from the 2010 and 2012 Los Angeles Mommy and Baby Surveys were analyzed. Weighted multivariate logistic regression was employed to identify significant associations between having had a previous AIO (preterm delivery, low birth weight infant, stillbirth, or major birth defect) and receipt of preconception care prior to the most recent pregnancy. Select patient-level covariates were included: chronic disease, age, education level, race/ethnicity, country of birth, insurance status prior to pregnancy and pregnancy intent. Adjustment for missing responses was performed using multiple chained imputation. Results After controlling for covariates, having had a previous AIO was associated with an increased odds of having utilized preconception care in the most recent pregnancy (OR 1.237, p = 0.040). Per the final regression model, a woman reporting a previous AIO and an intended subsequent pregnancy had a 42.4 % likelihood of having used preconception care. Of these women, only 28.8 % reported doing so because of concern regarding a previous birth complication. Discussion Women reporting a previous AIO were more likely to have used preconception care in a subsequent pregnancy. The prevalence of preconception care utilization remained low overall. Pregnancy intent emerged as a strong secondary predictor; any concerted strategy to improve access to preconception care must include initiatives to help ensure that pregnancies are planned.

  18. Meningococcal genetic variation mechanisms viewed through comparative analysis of serogroup C strain FAM18.

    Directory of Open Access Journals (Sweden)

    Stephen D Bentley

    2007-02-01

    Full Text Available The bacterium Neisseria meningitidis is commonly found harmlessly colonising the mucosal surfaces of the human nasopharynx. Occasionally strains can invade host tissues causing septicaemia and meningitis, making the bacterium a major cause of morbidity and mortality in both the developed and developing world. The species is known to be diverse in many ways, as a product of its natural transformability and of a range of recombination and mutation-based systems. Previous work on pathogenic Neisseria has identified several mechanisms for the generation of diversity of surface structures, including phase variation based on slippage-like mechanisms and sequence conversion of expressed genes using information from silent loci. Comparison of the genome sequences of two N. meningitidis strains, serogroup B MC58 and serogroup A Z2491, suggested further mechanisms of variation, including C-terminal exchange in specific genes and enhanced localised recombination and variation related to repeat arrays. We have sequenced the genome of N. meningitidis strain FAM18, a representative of the ST-11/ET-37 complex, providing the first genome sequence for the disease-causing serogroup C meningococci; it has 1,976 predicted genes, of which 60 do not have orthologues in the previously sequenced serogroup A or B strains. Through genome comparison with Z2491 and MC58 we have further characterised specific mechanisms of genetic variation in N. meningitidis, describing specialised loci for generation of cell surface protein variants and measuring the association between noncoding repeat arrays and sequence variation in flanking genes. Here we provide a detailed view of novel genetic diversification mechanisms in N. meningitidis. Our analysis provides evidence for the hypothesis that the noncoding repeat arrays in neisserial genomes (neisserial intergenic mosaic elements provide a crucial mechanism for the generation of surface antigen variants. Such variation will have an

  19. Clinical evaluation of recombinant factor VIII preparation (Kogenate) in previously treated patients with hemophilia A: descriptive meta-analysis of post-marketing study data.

    Science.gov (United States)

    Yoshioka, A; Fukutake, K; Takamatsu, J; Shirahata, A

    2006-08-01

    The safety and efficacy of Kogenate, a recombinant factor VIII (rFVIII) preparation for the treatment of bleeding episodes, were studied in a 123-patient meta-analysis population of previously treated patients (PTPs), including 15 enrolled in the registration Phase III trial (PTP-I group), 93 from the post-marketing special investigation (PTP-II group), and 15 from short-term special investigations in surgery or tooth extraction (SI group). These patients (82 severe, 31 moderate, 9 mild, and 1 unknown), aged 11 months to 72 years, were enrolled in 28 centers in Japan. Blood samples taken at the baseline and at 3, 6, 9, 12, 18, and 24 months after the introduction of Kogenate were evaluated for FVIII inhibitor antibodies, antibodies formed against trace proteins derived from the rFVIII production process, and for general changes in laboratory test results. Mean exposure to Kogenate was 1103 days in PTP-I, 86 days in PTP-II, 27 days in patients in surgery, and 2 days in patients with tooth extraction. Assessment of FVIII inhibitor activity was conducted in 115 of the 123 patients by means of the Bethesda assay. Twelve patients were found to have a low titer of FVIII inhibitor (0.5-3.0 BU/mL) prior to any administration of Kogenate, and 103 were inhibitor-negative at the baseline. Among this latter group, 3 patients (2.9%) tested inhibitor-positive, with titers ranging from 1.2 to 2.1 BU/mL, with 4 patients below 1.0 BU/mL. One patient in the 11 PTPs investigated (PTP-I) developed antibodies against baby hamster kidney protein and mouse immunoglobulin G, but these findings were transient and asymptomatic. Hemostasis was achieved (markedly effective or effective) in 3666 of the 3855 bleeding episodes (95.1%) observed in 108 patients. Only 1 infusion was necessary in 3790 (98.3%) of these episodes. These data indicate that Kogenate is safe and very effective for the treatment of bleeding in PTPs with hemophilia A.

  20. Mosaic trisomy 17 at amniocentesis: Prenatal diagnosis, molecular genetic analysis, and literature review

    Directory of Open Access Journals (Sweden)

    Chih-Ping Chen

    2016-10-01

    Conclusion: Low-level mosaicism for trisomy 17 detected by amniocentesis without ultrasound abnormality can be associated with a favorable outcome. Molecular genetic analysis of uncultured amniocytes at repeat amniocentesis is useful for genetic counseling. A review of the literature shows a correlation between an adverse fetal outcome and a higher trisomy 17 mosaicism level at amniocentesis associated with ultrasound abnormality.

  1. Analysis of genetic diversity of Piper spp. in Hainan Island (China ...

    African Journals Online (AJOL)

    use

    2011-10-26

    Oct 26, 2011 ... Inter-simple sequence repeat (ISSR) analysis was used to evaluate the genetic variation of Piper spp. from Hainan, China. 247 polymorphic bands out of a total of 248 (99.60%) were generated from 74 individual plants of Piper spp. The overall level of genetic diversity among Piper spp. in Hainan was.

  2. Analysis of genetic diversity of Piper spp. in Hainan Island (China ...

    African Journals Online (AJOL)

    Inter-simple sequence repeat (ISSR) analysis was used to evaluate the genetic variation of Piper spp. from Hainan, China. 247 polymorphic bands out of a total of 248 (99.60%) were generated from 74 individual plants of Piper spp. The overall level of genetic diversity among Piper spp. in Hainan was high, with the mean ...

  3. Combined sequence-based and genetic mapping analysis of complex traits in outbred rats

    NARCIS (Netherlands)

    Baud, Amelie; Hermsen, Roel; Guryev, Victor; Stridh, Pernilla; Graham, Delyth; McBride, Martin W.; Foroud, Tatiana; Calderari, Sophie; Diez, Margarita; Ockinger, Johan; Beyeen, Amennai D.; Gillett, Alan; Abdelmagid, Nada; Guerreiro-Cacais, Andre Ortlieb; Jagodic, Maja; Tuncel, Jonatan; Norin, Ulrika; Beattie, Elisabeth; Huynh, Ngan; Miller, William H.; Koller, Daniel L.; Alam, Imranul; Falak, Samreen; Osborne-Pellegrin, Mary; Martinez-Membrives, Esther; Canete, Toni; Blazquez, Gloria; Vicens-Costa, Elia; Mont-Cardona, Carme; Diaz-Moran, Sira; Tobena, Adolf; Hummel, Oliver; Zelenika, Diana; Saar, Kathrin; Patone, Giannino; Bauerfeind, Anja; Bihoreau, Marie-Therese; Heinig, Matthias; Lee, Young-Ae; Rintisch, Carola; Schulz, Herbert; Wheeler, David A.; Worley, Kim C.; Muzny, Donna M.; Gibbs, Richard A.; Lathrop, Mark; Lansu, Nico; Toonen, Pim; Ruzius, Frans Paul; de Bruijn, Ewart; Hauser, Heidi; Adams, David J.; Keane, Thomas; Atanur, Santosh S.; Aitman, Tim J.; Flicek, Paul; Malinauskas, Tomas; Jones, E. Yvonne; Ekman, Diana; Lopez-Aumatell, Regina; Dominiczak, Anna F.; Johannesson, Martina; Holmdahl, Rikard; Olsson, Tomas; Gauguier, Dominique; Hubner, Norbert; Fernandez-Teruel, Alberto; Cuppen, Edwin; Mott, Richard; Flint, Jonathan

    Genetic mapping on fully sequenced individuals is transforming understanding of the relationship between molecular variation and variation in complex traits. Here we report a combined sequence and genetic mapping analysis in outbred rats that maps 355 quantitative trait loci for 122 phenotypes. We

  4. Multicolor Super-Resolution DNA Imaging for Genetic Analysis

    Science.gov (United States)

    Baday, Murat; Cravens, Aaron; Hastie, Alex; Kim, HyeongJun; Kudeki, Deren E.; Kwok, Pui-Yan; Xiao, Ming; Selvin, Paul R.

    2013-01-01

    Many types of cancer and neurodegenerative diseases are caused by abnormalities and variations in the genome. We have designed a high-resolution imaging technique with high throughput and low cost for determining structural variations of genes related to genetic diseases. We initially mapped all seven nicking sites of Nb.BbvCI endonuclease enzyme on lambda DNA. Then we resolved densely labeled patterns of 107 nicking sites on human BAC DNA that is digested by Nb.BsmI and Nb.BbvCI endonuclease enzymes. This high density resulted in several dyes being closer together than the diffraction limit. Overall, detailed DNA nicking sites mapping with 100bp resolution was achieved, which has the potential to reveal information about genetic variance and to facilitate medical diagnosis of several genetic diseases. PMID:22698062

  5. GPFrontend and GPGraphics: graphical analysis tools for genetic association studies.

    Science.gov (United States)

    Uebe, Steffen; Pasutto, Francesca; Krumbiegel, Mandy; Schanze, Denny; Ekici, Arif B; Reis, André

    2010-09-21

    Most software packages for whole genome association studies are non-graphical, purely text based programs originally designed to run with UNIX-like operating systems. Graphical output is often not intended or supposed to be performed with other command line tools, e.g. gnuplot. Using the Microsoft .NET 2.0 platform and Visual Studio 2005, we have created a graphical software package to analyze data from microarray whole genome association studies, both for a DNA-pooling based approach as well as regular single sample data. Part of this package was made to integrate with GenePool 0.8.2, a previously existing software suite for GNU/Linux systems, which we have modified to run in a Microsoft Windows environment. Further modifications cause it to generate some additional data. This enables GenePool to interact with the .NET parts created by us. The programs we developed are GPFrontend, a graphical user interface and frontend to use GenePool and create metadata files for it, and GPGraphics, a program to further analyze and graphically evaluate output of different WGA analysis programs, among them also GenePool. Our programs enable regular MS Windows users without much experience in bioinformatics to easily visualize whole genome data from a variety of sources.

  6. GPFrontend and GPGraphics: graphical analysis tools for genetic association studies

    Directory of Open Access Journals (Sweden)

    Schanze Denny

    2010-09-01

    Full Text Available Abstract Background Most software packages for whole genome association studies are non-graphical, purely text based programs originally designed to run with UNIX-like operating systems. Graphical output is often not intended or supposed to be performed with other command line tools, e.g. gnuplot. Results Using the Microsoft .NET 2.0 platform and Visual Studio 2005, we have created a graphical software package to analyze data from microarray whole genome association studies, both for a DNA-pooling based approach as well as regular single sample data. Part of this package was made to integrate with GenePool 0.8.2, a previously existing software suite for GNU/Linux systems, which we have modified to run in a Microsoft Windows environment. Further modifications cause it to generate some additional data. This enables GenePool to interact with the .NET parts created by us. The programs we developed are GPFrontend, a graphical user interface and frontend to use GenePool and create metadata files for it, and GPGraphics, a program to further analyze and graphically evaluate output of different WGA analysis programs, among them also GenePool. Conclusions Our programs enable regular MS Windows users without much experience in bioinformatics to easily visualize whole genome data from a variety of sources.

  7. Genetic Analysis of 'PAX6-Negative' Individuals with Aniridia or Gillespie Syndrome.

    Directory of Open Access Journals (Sweden)

    Morad Ansari

    Full Text Available We report molecular genetic analysis of 42 affected individuals referred with a diagnosis of aniridia who previously screened as negative for intragenic PAX6 mutations. Of these 42, the diagnoses were 31 individuals with aniridia and 11 individuals referred with a diagnosis of Gillespie syndrome (iris hypoplasia, ataxia and mild to moderate developmental delay. Array-based comparative genomic hybridization identified six whole gene deletions: four encompassing PAX6 and two encompassing FOXC1. Six deletions with plausible cis-regulatory effects were identified: five that were 3' (telomeric to PAX6 and one within a gene desert 5' (telomeric to PITX2. Sequence analysis of the FOXC1 and PITX2 coding regions identified two plausibly pathogenic de novo FOXC1 missense mutations (p.Pro79Thr and p.Leu101Pro. No intragenic mutations were detected in PITX2. FISH mapping in an individual with Gillespie-like syndrome with an apparently balanced X;11 reciprocal translocation revealed disruption of a gene at each breakpoint: ARHGAP6 on the X chromosome and PHF21A on chromosome 11. In the other individuals with Gillespie syndrome no mutations were identified in either of these genes, or in HCCS which lies close to the Xp breakpoint. Disruption of PHF21A has previously been implicated in the causation of intellectual disability (but not aniridia. Plausibly causative mutations were identified in 15 out of 42 individuals (12/32 aniridia; 3/11 Gillespie syndrome. Fourteen of these mutations presented in the known aniridia genes; PAX6, FOXC1 and PITX2. The large number of individuals in the cohort with no mutation identified suggests greater locus heterogeneity may exist in both isolated and syndromic aniridia than was previously appreciated.

  8. Genetic and systems level analysis of Drosophila sticky/citron kinase and dFmr1 mutants reveals common regulation of genetic networks

    Directory of Open Access Journals (Sweden)

    Zarnescu Daniela C

    2008-11-01

    Full Text Available Abstract Background In Drosophila, the genes sticky and dFmr1 have both been shown to regulate cytoskeletal dynamics and chromatin structure. These genes also genetically interact with Argonaute family microRNA regulators. Furthermore, in mammalian systems, both genes have been implicated in neuronal development. Given these genetic and functional similarities, we tested Drosophila sticky and dFmr1 for a genetic interaction and measured whole genome expression in both mutants to assess similarities in gene regulation. Results We found that sticky mutations can dominantly suppress a dFmr1 gain-of-function phenotype in the developing eye, while phenotypes produced by RNAi knock-down of sticky were enhanced by dFmr1 RNAi and a dFmr1 loss-of-function mutation. We also identified a large number of transcripts that were misexpressed in both mutants suggesting that sticky and dFmr1 gene products similarly regulate gene expression. By integrating gene expression data with a protein-protein interaction network, we found that mutations in sticky and dFmr1 resulted in misexpression of common gene networks, and consequently predicted additional specific phenotypes previously not known to be associated with either gene. Further phenotypic analyses validated these predictions. Conclusion These findings establish a functional link between two previously unrelated genes. Microarray analysis indicates that sticky and dFmr1 are both required for regulation of many developmental genes in a variety of cell types. The diversity of transcripts regulated by these two genes suggests a clear cause of the pleiotropy that sticky and dFmr1 mutants display and provides many novel, testable hypotheses about the functions of these genes. As both of these genes are implicated in the development and function of the mammalian brain, these results have relevance to human health as well as to understanding more general biological processes.

  9. Logic analysis and verification of n-input genetic logic circuits

    DEFF Research Database (Denmark)

    Baig, Hasan; Madsen, Jan

    2017-01-01

    accordingly. As compared to electronic circuits, genetic circuits exhibit stochastic behavior and do not always behave as intended. Therefore, there is a growing interest in being able to analyze and verify the logical behavior of a genetic circuit model, prior to its physical implementation in a laboratory....... In this paper, we present an approach to analyze and verify the Boolean logic of a genetic circuit from the data obtained through stochastic analog circuit simulations. The usefulness of this analysis is demonstrated through different case studies illustrating how our approach can be used to verify the expected...... behavior of an n-input genetic logic circuit....

  10. Multivariate Survival Mixed Models for Genetic Analysis of Longevity Traits

    DEFF Research Database (Denmark)

    Pimentel Maia, Rafael; Madsen, Per; Labouriau, Rodrigo

    2013-01-01

    A class of multivariate mixed survival models for continuous and discrete time with a complex covariance structure is introduced in a context of quantitative genetic applications. The methods introduced can be used in many applications in quantitative genetics although the discussion presented....... The discrete time models used are multivariate variants of the discrete relative risk models. These models allow for regular parametric likelihood-based inference by exploring a coincidence of their likelihood functions and the likelihood functions of suitably defined multivariate generalized linear mixed...

  11. Genetic analysis of intracapillary glomerular lipoprotein deposits in aging mice.

    Directory of Open Access Journals (Sweden)

    Gerda A Noordmans

    Full Text Available Renal aging is characterized by functional and structural changes like decreased glomerular filtration rate, and glomerular, tubular and interstitial damage. To gain insight in pathways involved in renal aging, we studied aged mouse strains and used genetic analysis to identify genes associated with aging phenotypes.Upon morphological screening in kidneys from 20-month-old mice from 26 inbred strains we noted intracapillary PAS-positive deposits. The severity of these deposits was quantified by scoring of a total of 50 glomeruli per section (grade 0-4. Electron microscopy and immunohistochemical staining for apoE, apoB, apoA-IV and perilipin-2 was performed to further characterize the lesions. To identify loci associated with these PAS-positive intracapillary glomerular deposits, we performed haplotype association mapping.Six out of 26 mouse strains showed glomerular PAS-positive deposits. The severity of these deposits varied: NOD(0.97, NZW(0.41, NON(0.30, B10(0.21, C3 H(0.9 and C57BR(0.7. The intracapillary deposits were strongly positive for apoE and weakly positive for apoB and apoA-IV. Haplotype association mapping showed a strong association with a 30-Kb haplotype block on Chr 1 within the Esrrg gene. We investigated 1 Mb on each site of this region, which includes the genes Spata17, Gpatch2, Esrrg, Ush2a and Kctd3.By analyzing 26 aged mouse strains we found that some strains developed an intracapillary PAS and apoE-positive lesion and identified a small haplotype block on Chr 1 within the Esrrg gene to be associated with these lipoprotein deposits. The region spanning this haplotype block contains the genes Spata17, Gpatch2, Esrrg, Ush2a and Kctd3, which are all highly expressed in the kidney. Esrrg might be involved in the evolvement of these glomerular deposits by influencing lipid metabolism and possibly immune reponses.

  12. Genetic Analysis of Pinus sylvestris L. and Pinus sylvestris forma turfosa L. Using RAPD Markers

    Directory of Open Access Journals (Sweden)

    Beáta ÁBRAHÁM

    2010-03-01

    Full Text Available The purpose of the present study was to determine the level of genetic diversity within and among Ciuc basin, Romania (populations from Mohos and Luci raised bogs in Harghita Mountain and Sumuleu in Ciuc Mountain Pinus sylvestris populations using molecular markers. Two of populations (Mohos and Luci seems to be the descendants that survived the continental glaciation. Genetic diversity was analyzed by RAPD (Random Amplified Polymorphic DNA. Nine primers were selected for analysis, which generated reproducible bands. On base of presence or absence of homologues bands Nei’s gene diversity, the percentage of polymorphic loci and Nei’s unbiased genetic distance were calculated. The level of genetic variation among populations was found to be low. For both populations the variation values among populations were higher than within populations. The fossil records and geological historical data explain the extremely low genetic diversity of this species. Pinus sylvestris experienced strong bottlenecks during its evolutionary history, which caused the loss of genetic variation. Genetic drift and breeding in post-bottlenecked small populations may be the major forces that contribute to low genetic diversity and genetic differentiation of populations. Human activities may have accelerated the loss of genetic diversity in Pinus sylvestris.

  13. Bayesian analysis of genetic association across tree-structured routine healthcare data in the UK Biobank.

    Science.gov (United States)

    Cortes, Adrian; Dendrou, Calliope A; Motyer, Allan; Jostins, Luke; Vukcevic, Damjan; Dilthey, Alexander; Donnelly, Peter; Leslie, Stephen; Fugger, Lars; McVean, Gil

    2017-09-01

    Genetic discovery from the multitude of phenotypes extractable from routine healthcare data can transform understanding of the human phenome and accelerate progress toward precision medicine. However, a critical question when analyzing high-dimensional and heterogeneous data is how best to interrogate increasingly specific subphenotypes while retaining statistical power to detect genetic associations. Here we develop and employ a new Bayesian analysis framework that exploits the hierarchical structure of diagnosis classifications to analyze genetic variants against UK Biobank disease phenotypes derived from self-reporting and hospital episode statistics. Our method displays a more than 20% increase in power to detect genetic effects over other approaches and identifies new associations between classical human leukocyte antigen (HLA) alleles and common immune-mediated diseases (IMDs). By applying the approach to genetic risk scores (GRSs), we show the extent of genetic sharing among IMDs and expose differences in disease perception or diagnosis with potential clinical implications.

  14. Genetic polymorphisms of Bcl-2 promoter in cancer susceptibility and prognosis: a meta-analysis.

    Science.gov (United States)

    Yao, Zhongqiang; Yang, Binhui; Liu, Zhongqiu; Li, Wei; He, Qihua; Peng, Xingchun

    2017-04-11

    Bcl-2 is critical for tumorigenesis. However, previous studies on the association of Bcl-2 promoter polymorphisms with predisposition to different cancer types are somewhat contradictory. Therefore, we performed this meta-analysis regarding the relationship between Bcl-2 promoter single nucleotide polymorphisms (SNPs) and cancer susceptibility and prognosis. Up to August 2016, 32 original publications were identified covering two Bcl-2 promoter SNPs (rs2279115 and rs1801018). Our results showed statistically significant association between rs2279115 and cancer susceptibility and prognosis in all four genetic models but not in rs1801018. Subgroups analysis indicated that rs2279115 was associated with a significantly higher risk of cancer susceptibility in Asia but not in Caucasian. Furthermore, rs2279115 was associated with a significantly higher risk in digestive system cancer and endocrine system cancer but not in breast cancer, respiratory cancer and hematopoietic cancer. Simultaneously, rs2279115 was correlated with a significantly higher risk of cancer prognosis in Asia but not in Caucasian. Considering these promising results, rs2279115 may be a tumor marker for cancertherapy in Asia. Sensitivity analysis show four gene model were stable, and no publication bias was observed in all four gene model. Large sample size, different ethnic population and different cancer type are warranted to validate this association.

  15. An analysis of 97 previously diagnosed de novo adult acute erythroid leukemia patients following the 2016 revision to World Health Organization classification.

    Science.gov (United States)

    Qiu, Shaowei; Jiang, Erlie; Wei, Hui; Lin, Dong; Zhang, Guangji; Wei, Shuning; Zhou, Chunlin; Liu, Kaiqi; Wang, Ying; Liu, Bingcheng; Liu, Yuntao; Gong, Benfa; Gong, Xiaoyuan; Feng, Sizhou; Mi, Yingchang; Han, Mingzhe; Wang, Jianxiang

    2017-08-09

    The incidence of acute erythroid leukemia subtype (AEL) is rare, accounting for 5% of cases of acute myeloid leukemia (AML), and the outcome is dismal. However, in 2016 revision to the WHO classification, the subcategory of AEL has been removed. Myeloblasts are redefined as the percentage of total marrow cells, not non-erythroid cells. Therefore, the previously diagnosed AEL cases are currently diagnosed as AML or myelodyspalstic syndrome (MDS) according to new criteria. We respectively reviewed cases of 97 de novo previously diagnosed AEL and all the patients were diagnosed as AML or MDS according to the new classification scheme, and then the clinical characteristics of these two subtypes were compared. Statistical analyses were performed by SPSS software version 18.0. The median age was 37 years-old, the two-thirds of previous AEL cases were diagnosed as MDS, and there was no obvious difference between two subtypes except for male/female ratio and age. Cytogenetic, rather than MDS/AML subtypes, can better represent the prognostic factor of previously diagnosed AEL patients. When the cytogenetic risk of patients belonged to MRC intermediate category and age were below 40 years-old in previous AEL cases, the patients who received induction chemotherapy without transplantation had a similar survival compared with the patients who underwent transplantation (3-year OS: 67.2% vs 68.5%). Cytogenetic, rather than MDS/AML subtypes, can better represent the prognostic factor of previously diagnosed AEL patients. Transplantation was a better choice for those whose cytogenetic category was unfavorable.

  16. Genetic origin and dispersal of the invasive soybean aphid inferred from population genetic analysis and approximate Bayesian computation.

    Science.gov (United States)

    Fang, Fang; Chen, Jing; Jiang, Li-Yun; Qu, Yan-Hua; Qiao, Ge-Xia

    2018-01-09

    Biological invasion is considered one of the most important global environmental problems. Knowledge of the source and dispersal routes of invasion could facilitate the eradication and control of invasive species. Soybean aphid, Aphis glycines Matsumura, is one of the most destructive soybean pests. For effective management of this pest, we conducted genetic analyses and approximate Bayesian computation (ABC) analysis to determine the origins and dispersal of the aphid species, as well as the source of its invasion in the USA, using eight microsatellite loci and the mitochondrial cytochrome c oxidase subunit I (COI) gene. We were able to identify a significant isolation by distance (IBD) pattern and three genetic lineages in the microsatellite data but not in the mtDNA dataset. The genetic structure showed that the USA population has the closest relationship with those from Korea and Japan, indicating that the two latter populations might be the sources of the invasion to the USA. Both population genetic analyses and ABC showed that the northeastern populations in China were the possible sources of the further spread of A. glycines to Indonesia. The dispersal history of this aphid can provide useful information for pest management strategies and can further help predict areas at risk of invasion. This article is protected by copyright. All rights reserved.

  17. Genetic diversity and relationship analysis among accessions of ...

    African Journals Online (AJOL)

    Amplified fragment length polymorphism (AFLP) DNA markers were used to assess the genetic diversity and relationships between 55 accessions of genus Aegilops, including the species Aegilops triuncialis L. (UUCC), Aegilops geniculata Roth (MMUU), Aegilops cylindrica Host (CCDD) and Aegilops umbellulata Zhuk ...

  18. RAPD analysis for genetic diversity of two populations of Mystus ...

    African Journals Online (AJOL)

    ) was applied to analyze the genetic variation of the 2 populations of Mystus vittatus (Bloch) of Madhya Pradesh, India. 10 random 10-mer primers were primarily scored in 3 individuals from each of the 2 locations. Five primers, which gave ...

  19. Historical analysis of Newfoundland dog fur colour genetics ...

    African Journals Online (AJOL)

    This article makes use of digitized historic newspapers to analyze Newfoundland dog fur colour genetics, and fur colour variations over time. The results indicate that contrary to the accepted view, the 'Solid' gene was introduced into the British population of Newfoundland dogs in the 1840s. Prior to that time, the dogs were ...

  20. Genetic Analysis of Meiotic Recombination in Schizosaccharomyces pombe

    OpenAIRE

    Smith, Gerald R.

    2009-01-01

    The fission yeast Schizosaccharomyces pombe is well-suited for studying meiotic recombination. Methods are described here for culturing S. pombe and for genetic assays of intragenic recombination (gene conversion), intergenic recombination (crossing-over), and spore viability. Both random spore and tetrad analyses are described.

  1. Genetic and phylogenetic analysis of ten Gobiidae species in China ...

    African Journals Online (AJOL)

    Administrator

    2011-09-07

    Sep 7, 2011 ... The results agreed with the traditional taxonomy of the morphological characters. AFLP fingerprints were ... It allows fast and efficient generation of a large amount of genetic data. Until now, AFLP ..... Hamamatsu C, Sugiyama K, Ikeda Y, Sakamoto K, Fumihito A, Ohno. Han et al. 10535. S, Gojobori T (2000).

  2. Genetic diversity analysis and conservation of the Chinese herb ...

    African Journals Online (AJOL)

    STORAGESEVER

    2009-10-05

    Oct 5, 2009 ... Production of rosmarinic acid and lithospermic acid B in Ti transformed Salvia miltiorrhiza cell suspension cultures. Process Biochem. 34: 777-784. Clarke GM, Dwyer CO (2000). Genetic variability and population structure of the endangered golden sun moth, Synemon plana. Biol. Conserv. 92: 371- 381.

  3. AFLP analysis of genetic diversity in main cultivated strains of ...

    African Journals Online (AJOL)

    Ganoderma mushroom is one of the most prescribed traditional medicines, which has been used for medicinal purposes for centuries particularly in China, Japan, Korea and other Asian countries. In this article, the different strains of Ganoderma spp. used in production and their genetic relations of the closely related strains ...

  4. Genetic analysis of amino acid content in wheat grain

    Indian Academy of Sciences (India)

    2014-08-22

    Aug 22, 2014 ... Therefore, it is important to enhance the level of nutrition in food by increasing the protein content of wheat, especially improving the amino acid composition of protein. Contents of wheat grain amino acids are quantitative traits, controlled by many genes, and their genetic basis was. ∗For correspondence.

  5. Genetic analysis of fertility restoration under CGMS system in rice ...

    Indian Academy of Sciences (India)

    Cytoplasmic genetic male sterility (CGMS) resulting from nuclear-cytoplasmic interaction has been commercially exploited for the production of F1 hybrid seed in rice. The. CGMS system involves three lines, namely a cytoplasmic male sterile (CMS) line, a maintainer line and a restorer line where restorer line (R line) ...

  6. Analysis of genetic divergence in Durum wheat (Triticum Durum Desf.)

    African Journals Online (AJOL)

    A field experiment was conducted at Geregera and Kone testing sites of Sirinka Agricultural Research Center, northeastern Ethiopia. The objective of the experiment was to estimate the genetic divergence among durum wheat germplasm of diverse origin and clustering them into homogenous groups for further hybridization ...

  7. Induction, characterization and genetic analysis of Aspergillus flavus ...

    African Journals Online (AJOL)

    The Aspergillus flavus infection of peanut (Arachis hypogaea) results in the accumulation of aflatoxins in seeds, which are very harmful to humans and animals. Mutation breeding programs are an effective way of inducing resistant mutants. In this study, we induced a genetic variation by using ethyl methanesulfonate (EMS) ...

  8. Analysis of genetic diversity and population structure among exotic ...

    African Journals Online (AJOL)

    The present study was performed to study genetic relationships and population differentiation of 90 introduced sugarcane accessions in Ethiopia by means of 22 SSR molecular markers. The 22 SSR markers amplified a total of 260 alleles, of which 230 were polymorphic with a mean of 10.45 alleles per SSR locus.

  9. Assessment of genetic diversity analysis in contrasting sugarcane ...

    African Journals Online (AJOL)

    Sugarcane is an important crop in the country economically, politically and sociologically. It is the second largest agro-industry next to textiles. The selection and combination of parents for crossing rely on an understanding of their genetic structures and molecular diversity. In the present study, 28 sugarcane genotypes were ...

  10. Analysis of genetic variation among accessions of critically ...

    African Journals Online (AJOL)

    STORAGESEVER

    2009-05-18

    May 18, 2009 ... Differentiation between ecological groups was higher than that revealed within groups. Conservation programs should take into account the level of genetic diversity within population revealed by these markers according to soil types. Key words: Rhaponticoides iconiensis, endangered, SDS-PAGE, RAPD.

  11. Pushing the envelope in genetic analysis of species invasion

    Science.gov (United States)

    Samuel A. Cushman

    2015-01-01

    How a species spreads once introduced into a new environment is a major question in landscape genetics. When the species in question is a potential disease vector, the findings are important not only for fundamental science, but can impact applied science and public health as well. In this issue of Molecular Ecology Medley et al. (2014) study, the invasion...

  12. Analysis of genetic diversity within and among four rabbit genotypes ...

    African Journals Online (AJOL)

    The results show a variation in biochemical activity levels since, esterase profiles showed higher percentage of polymorphism (67.21%) than peroxidase (34.78%) and SDS-protein profiles (39.11 %). Moreover, the mean of the genetic similarity within the genotypes based on overall biochemical markers were 0.81 (APRI), ...

  13. Standardization of RAPD assay for genetic analysis of olive | Sesli ...

    African Journals Online (AJOL)

    ... also PCR cycles I and II; however, favorable results were attained by PCR Mix III and. PCR cycle III. Evaluable bands were obtained for defining the olive samples by using primers from OP-I. Thus, it was concluded that RAPD profiles are effective in the study of genetic similarities and distances of wild and cultivated olives ...

  14. Genetic diversity and bottleneck analysis of Yunnan mithun ( Bos ...

    African Journals Online (AJOL)

    Despite the smaller population size, the normal L-shaped distribution of allelic frequencies without any mode-shift indicate the absence of genetic bottleneck in Yunnan mithun population, suggesting that Yunnan mithun population might moderately have underwent gene introgression from zebu and yellow cattle.

  15. Genetic algorithms in supply chain management: A critical analysis ...

    Indian Academy of Sciences (India)

    Genetic algorithms (GAs) are perhaps the oldest and most frequently used search techniques for dealing with complex and intricate real-life problems that are otherwise difficult to solve by the traditional methods. The present article provides an extensive literature review of the application of GA on supply chain management ...

  16. Analysis of the genetic diversity of four rabbit genotypes using ...

    African Journals Online (AJOL)

    Dr.Ola

    2013-05-15

    May 15, 2013 ... diseases or market conditions. A considerable number of genetic diversity studies for several livestock species have been carried out during recent years by research. *Corresponding author. E-mail: ola.galal@agr.kfs.edu.eg or olagalal2002@yahoo.com , Tel/Fax: +2-0479102930. Abbreviations: APRI ...

  17. Genetic analysis of maternal and paternal lineages in Kabardian ...

    African Journals Online (AJOL)

    The high mitochondrial and also remarkable paternal diversity of the Kabardian horse is caused by its long history with a widely spread maternal origin and the introduction of Arabian as well as Thoroughbred influenced stallions for improvement. This high genetic diversity provides a good situation for the ongoing breed ...

  18. Fusion genetic analysis of jasmonate-signalling mutants in Arabidopsis

    DEFF Research Database (Denmark)

    Jensen, Anders Bøgh; Raventos, D.; Mundy, John Williams

    2002-01-01

    Jasmonates induce plant-defence responses and act to regulate defence-related genes including positive feedback of the lipoxygenase 2 (LOX2) gene involved in jasmonate synthesis. To identify jasmonate-signalling mutants, we used a fusion genetic strategy in which the firefly luciferase (FLUC) and...

  19. Microsatellite analysis of the genetic relationships between wild

    Indian Academy of Sciences (India)

    In the present study, we isolated 11 microsatellite DNA markers, and analysed the genetic diversity and differentiation between cultured stocks and wild populations of the giant grouper originating from the South China Sea. A total of 390 alleles at 11 microsatellite loci were detected in 130 individuals from five different ...

  20. 1 Hierarchical Approaches to the Analysis of Genetic Diversity in ...

    African Journals Online (AJOL)

    2015-04-14

    Apr 14, 2015 ... of calculating them easily which include Ms-Excel, SPSS, PAST e.t.c.. Multivariate Methods: With increases in the sample size of germplasm accession used in crop improvement programs, classification and to create order in genetic variability assuming considerable significance. The use of established ...

  1. Genetic analysis of wild apple resources in Shandong province ...

    African Journals Online (AJOL)

    Apple (malus domestica Borkh.), which is a widely cultivated, important and economic fruit crop with nutritive and medicinal importance, has emerged as a model horticultural crop in this post-genomic era. Wild apple resources are important and they develop gradually in apple industry and genetic diversity. In this study, two ...

  2. Genetic analysis of fertility restoration under CGMS system in rice ...

    Indian Academy of Sciences (India)

    Abstract. We studied the genetics of fertility restoration by producing three-way test cross (TWTC) hybrids involved different combi- nations of restorers, maintainers and partial restorers of rice. Pollen and spikelet fertility of 16 TWTC hybrids were studied. Six TWTC involving restorer/restorer combinations as male parents ...

  3. Analysis of embryo, cytoplasmic and maternal genetic correlations ...

    Indian Academy of Sciences (India)

    maintenance, reproduction and immunity in farm animals. (Wu 2009). An accurate ... Keywords. genetic main correlations; genotype × environment interaction correlations; rapeseed meal; amino acids contents; nutrient quality. Journal of ... cytoplasmic effects, maternal additive and dominance effects for individual amino ...

  4. Strategic analysis in evolutionary genetics and the theory of games

    Indian Academy of Sciences (India)

    Unknown

    This paper is written in memory of John Maynard Smith. In a brief survey it discusses essential aspects of how game theory in biology relates to its counterpart in eco- nomics, the major transition in game theory initiated by. Maynard Smith, the discrepancies between genetic and phenotypic models in evolutionary biology, ...

  5. A quantitative genetic analysis of intermediate asthma phenotypes

    DEFF Research Database (Denmark)

    Thomsen, S F; Ferreira, M A R; Kyvik, K O

    2009-01-01

    Aim: To study the relative contribution of genetic and environmental factors to the correlation between exhaled nitric oxide (FeNO), airway responsiveness, airway obstruction, and serum total immunoglobulin E (IgE). Methods: Within a sampling frame of 21 162 twin subjects, 20-49 years of age, fro...

  6. Genetic analysis of 55 northern Vietnamese patients with Wilson ...

    Indian Academy of Sciences (India)

    Le Anh Tuan Pham

    2017-12-19

    Yoo 2002; Liu et al. 2004;. Wan et al. 2006; Li et al. 2013; Diao et al. 2014; Wei et al. 2014). Identification of mutation hot spots may significantly reduce the time of genetic test processing. However, in Vietnam, no such study was ...

  7. Genetic diversity analysis of mustard (Brassica spp.) germplasm ...

    African Journals Online (AJOL)

    sunny t

    successfully cultivated between Aman and Boro rice rotation without affecting this popular cropping pattern. So, it is urgent to analyze the genetic diversity and its response for the selection of short duration mustard genotypes for increasing our cropping intensity. Diversity at marker loci is currently the most feasible strategy ...

  8. Molecular genetic analysis of consanguineous families with primary ...

    Indian Academy of Sciences (India)

    MUZAMMIL AHMAD KHAN

    Physiologically, most of these MCPH proteins are involved in cell cycle and its regulation. ... in ASPM presumably truncates the protein synthesis that results in loss of armadillo-type fold domain. [Khan M. A., Windpassinger C., Ali M. Z., ..... 2014 A Drosophila genetic resource of mutats to study mechanism underlying human ...

  9. Comparative and genetic analysis of the porcine glucocerebrosidase (GBA) gene

    Czech Academy of Sciences Publication Activity Database

    Stratil, Antonín; Wagenknecht, Daniel; Van Poucke, M.; Kubíčková, S.; Bartenschlager, H.; Musilová, P.; Rubeš, J.; Geldermann, H.; Peelman, L. J.

    2004-01-01

    Roč. 138, - (2004), s. 377-383 ISSN 1096-4959 R&D Projects: GA ČR GA523/00/0669 Institutional research plan: CEZ:AV0Z5045916 Keywords : acid beta-glucosidase * gene mapping * fluorescence in situ hybridization Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 1.393, year: 2004

  10. Genetic variation and DNA markers in forensic analysis | Hameed ...

    African Journals Online (AJOL)

    The light has been focused and directed in this study to establish the basic forensic genetic information, knowledge, data and statistics which might be so ultimately helpful practically in forensic science and criminology and to let evaluate and present the DNA weight evidences in medico-legal institute and courts of law.

  11. Genetic analysis of silver-fir populations in the Beskids

    Directory of Open Access Journals (Sweden)

    Leon Mejnartowicz

    2011-01-01

    Full Text Available Twenty-eight isozymic loci were studied in the Beskid Mts., in four populations of common silver-fir (Abies alba: one in Beskid Makowski (BM and three populations in Beskid Sądecki (BS. Their genetic variation and diversity were analyzed, and Nei's genetic distances between the populations were calculated. The results show that the geographical distance between the BM population and the three BS populations is reflected in genetic distances. The BM population is clearly distinct from the others. It has the lowest genetic diversity (I = 0.42, percentage of polymorphic loci (%PoL = 64.29 and number of rare alleles (NoRa = 5. Besides, the BM population has the highest observed heterozygosity (Ho = 0.291, which exceeds the expected heterozygosity (He = 0.254, estimated on the basis of the Hardy-Weinberg Principle. On the contrary, BS populations are in the state of equilibrium, which is manifested, in similar values of He = 0.262 and Ho = 0.264.

  12. Analysis of genetic variation in different banana ( Musa species ...

    African Journals Online (AJOL)

    The banana (Musa acuminata Colla) is considered as an important crop plant due to its high economic value as good dietary source. Here, we analyze the genetic relationship of four different banana varieties that are cultivated in south India. Random amplified polymorphic DNAs (RAPDs) fingerprinting of these banana ...

  13. Genetic analysis of body weight of Takifugu rubripes at different ...

    African Journals Online (AJOL)

    Tuoyo Aghomotsegin

    2016-11-09

    Nov 9, 2016 ... 3Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, China .... During the larval-culture period, water ... The measured values at time t were conditioned on measured values at time t – 1. Thus, the conditional genetic model can be written as follows (Zhu, 1995; Atchley ...

  14. Development of mapping populations for genetic analysis in yams ...

    African Journals Online (AJOL)

    Progress is being made at the International Institute of Tropical Agriculture (IITA, Ibadan, Nigeria) to develop molecular tools for marker-assisted selection that would complement and expedite conventional breeding approaches for genetic improvement of yams (Dioscorea spp.). F1 full-sib mapping populations were ...

  15. Genetic diversity and relationship analysis of the Brassica napus ...

    African Journals Online (AJOL)

    Oilseed rape (Brassica napus L.) is an important oilseed crop worldwide. The objective of this research was to study the genetic diversity and relationships of B. napus accessions using simple sequence repeat (SSR). A set of 217 genotypes was characterized using 37 SSR markers of mapping on the B. napus genome.

  16. Genetic analysis of baculovirus resistance in lepidopteran model ...

    African Journals Online (AJOL)

    In order to clarify the resistant mechanism of BmNPV in silkworm, and from negative to prove agricultural pest inheritance of virus resistance, in this study, we used the highly resistant strain NB and susceptible strain 306 as the material through the method of classical genetics experiment, and proved that the baculovirus ...

  17. Analysis of genetic structure of white croaker using amplified ...

    African Journals Online (AJOL)

    STORAGESEVER

    2009-09-15

    Sep 15, 2009 ... continental margins (Grant and Bowen, 1998; Hewitt,. 2000). White croaker with long planktonic larval stage might confirm to this pattern. Preliminary allozyme analy- sis of white croaker in the same area showed a similar trend with weak genetic differentiation (Pairwise FST values between populations ...

  18. Potato leafroll virus : molecular analysis and genetically engineered resistance

    NARCIS (Netherlands)

    Wilk, van der F.

    1995-01-01

    The nucleotide sequence of the genomic RNA of potato leafroll virus (PLRV) was elucidated and its genetic organization deduced (Chapter 2). Six open reading frames (ORFs) were shown to be present on the genome. Both the PLRV coat protein gene and the RNA- dependent RNA polymerase gene were

  19. Analysis of embryo, cytoplasmic and maternal genetic correlations ...

    Indian Academy of Sciences (India)

    2School of Agriculture and Food Science, Zhejiang A & F University, Linan, 311300, People's Republic of China. Abstract. Genetic correlations of nutrient quality traits including lysine, ...... spectroscopy (NIRS) enables the fast and accurate prediction of essential amino acid contents. 2. Results for wheat, barley, corn, triticale ...

  20. Preliminary molecular analysis of the genetic diversity of some ...

    African Journals Online (AJOL)

    In the arid and semi arid areas, salt bush (Atriplex) represents an important forage resource. The characterization of the genetic diversity of these species is useful for their classification, their conservation and their improvement. In this context, we used the random amplified polymorphic DNA-polymerase chain reaction ...

  1. Evaluation of schistosome promoter expression for transgenesis and genetic analysis.

    Directory of Open Access Journals (Sweden)

    Shuang Liang

    Full Text Available Schistosome worms of the genus Schistosoma are the causative agents of schistosomiasis, a devastating parasitic disease affecting more than 240 million people worldwide. Schistosomes have complex life cycles, and have been challenging to manipulate genetically due to the dearth of molecular tools. Although the use of gene overexpression, gene knockouts or knockdowns are straight-forward genetic tools applied in many model systems, gene misexpression and genetic manipulation of schistosome genes in vivo has been exceptionally challenging, and plasmid based transfection inducing gene expression is limited. We recently reported the use of polyethyleneimine (PEI as a simple and effective method for schistosome transfection and gene expression. Here, we use PEI-mediated schistosome plasmid transgenesis to define and compare gene expression profiles from endogenous and nonendogenous promoters in the schistosomula stage of schistosomes that are potentially useful to misexpress (underexpress or overexpress gene product levels. In addition, we overexpress schistosome genes in vivo using a strong promoter and show plasmid-based misregulation of genes in schistosomes, producing a clear and distinct phenotype--death. These data focus on the schistosomula stage, but they foreshadow strong potential for genetic characterization of schistosome molecular pathways, and potential for use in overexpression screens and drug resistance studies in schistosomes using plasmid-based gene expression.

  2. Analysis of genetic variability among plantain cultivars (Musa ...

    African Journals Online (AJOL)

    SERVER

    2008-04-17

    Apr 17, 2008 ... In Nigeria the genetic similarities of the plantains among each other were greater than that of Jamaica. There was a 75% similarity between the 'Horn' plantains. Also, there was a 50% similarity between the 'French' plantain and the 'Horn' plantain (dwarf mutant) and. 66.7% similarity between the 'French' ...

  3. Genetic analysis of wild and cultivated germplasm of pigeonpea ...

    African Journals Online (AJOL)

    To compare the efficiency of the use of single versus multiple markers, the genetic diversity was quantified among 12 diverse pigeonpea germplasm comprised of eight wild and four cultivated using both random amplified polymorphic DNA (RAPD) and simple sequence repeat (SSR) markers, and how well these two types ...

  4. Microsatellite analysis of the genetic relationships between wild and ...

    Indian Academy of Sciences (India)

    In the present study, we isolated 11 microsatellite DNA markers, and analysed the genetic diversity and differentiation between cultured stocks and wild populations of the giant grouper originating from the South China Sea. A total of 390 alleles at 11 microsatellite loci were detected in 130 individuals from five different ...

  5. Genetic analysis of resistance to soybean rust disease | Kiryowa ...

    African Journals Online (AJOL)

    Soybean rust (Phakopsora pachyrhizi Sydow.) causes the most damage of all the pathogens known to attack soybean (Glycine max. Merril). A study was conducted in Uganda to estimate the magnitude of genetic parameters controlling soybean rust resistance and to estimate narrow sense heritability of the resistance.

  6. Analysis of genetic diversity in bambara groundnut [ Vigna ...

    African Journals Online (AJOL)

    Amplified fragment length polymorphism (AFLP) was used to assess genetic diversity among 100 selected bambara groundnut [Vigna subterranea (L.) Verdc] landraces from a diverse geographic area of Tanzania. Eleven informative AFLP primer combinations generated a total of 49 scorable polymorphic amplification ...

  7. Genetic Diversity of Rose germplasm based on RAPD analysis

    African Journals Online (AJOL)

    AHSAN IQBAL

    2012-06-12

    Jun 12, 2012 ... Random amplified polymorphic DNA (RAPD) markers have been found to be very useful in studying the genetic variability of ... produced by primer GLD-20, while GLC-02 produced the minimum number of bands (2). Maximum polymorphism in ..... ability and occurrence of pseudo bands. However, it can.

  8. Analysis of genetic variation of inducible nitric oxide synthase and ...

    African Journals Online (AJOL)

    The genetic diversity of 100 Malaysian native chickens was investigated using polymerase chain reaction-restriction fragment polymorphism (PCR-RFLP) for two candidate genes: inducible nitric oxide synthase (INOS) and natural resistance-associated macrophage protein 1 (NRAMP1). The two genes were selected ...

  9. Analysis of genetic diversity and construction of core collection of ...

    African Journals Online (AJOL)

    Jane

    2011-06-03

    Jun 3, 2011 ... Genetic diversity of 73 local mulberry varieties from Shanxi Province were screened using ISSR markers, with l5 primers combinations selected for their reproducibility and polymorphism. 129 bands were amplified, of which 115 bands showed polymorphism and the ratio of polymorphism bands was.

  10. Molecular genetic analysis of the Chinese Erhualian pig breed | Yue ...

    African Journals Online (AJOL)

    The Chinese Erhualian is one of the most prolific pig breeds in the world, but it is in danger of being replaced by other exotic pig breeds because of its slow growth rate and high fat content in the body. To obtain some genetic information for conservation, we analysed the Erhualian pigs by using a PCR-RFLP for the ...

  11. Analysis of genetic diversity in pigeon pea germplasm using ...

    Indian Academy of Sciences (India)

    MANEESHA

    2017-08-16

    Aug 16, 2017 ... Asia and Africa. It is normally considered to have a low degree of genetic diversity, an impediment in undertaking crop improvement programmes. ... of environmental conditions. ..... Th, Thailand; It, Italy; B, Barbados; Ta, Taiwan; J, Jamaica; V, Venezuela; UK, United Kingdom; My, Myanmar; U, Uganda; G,.

  12. DNA methylation and genetic diversity analysis of genus Cycas in ...

    African Journals Online (AJOL)

    mallory

    2012-01-12

    Jan 12, 2012 ... Key words: Cycas, DNA methylation, genetic diversity, methylation sensitive amplification polymorphism .... Cliffs and steep slopes on Khao Chamao mountain (eastern. Thailand). C. clivicola subsp. clivicola (Cli). 7-9, 10-12. M, F. Limestone cliffs, sea shore, evergreen forest, dry ... cytosine at both strands.

  13. Microsatellite analysis of the genetic relationships between wild and ...

    Indian Academy of Sciences (India)

    Abstract. The giant grouper (Epinephelus lanceolatus) is a coral fish with high commercial value in Southeast Asia. In the present study, we isolated 11 microsatellite DNA markers, and analysed the genetic diversity and differentiation between cultured stocks and wild populations of the giant grouper originating from the ...

  14. Genetic diversity analysis and subspecies classification of Thailand ...

    African Journals Online (AJOL)

    Genetic diversity among 126 rice accessions, including 110 Thai landraces and 16 varieties used as subspecies reference, were evaluated by three types of DNA markers, InDel (Insertion/Deletion), inter-simple sequence repeat (ISSR) and simple sequence repeat (SSR) markers. Twelve InDel primer pairs, based on DNA ...

  15. Genetic analysis of wild apple resources in Shandong province ...

    African Journals Online (AJOL)

    Jane

    2011-08-22

    Aug 22, 2011 ... Apple (malus domestica Borkh.), which is a widely cultivated, important and economic fruit crop with nutritive and medicinal importance, has emerged as a model horticultural crop in this post-genomic era. Wild apple resources are important and they develop gradually in apple industry and genetic diversity.

  16. Isolation, characterization and genetic analysis of canine GATA4 ...

    Indian Academy of Sciences (India)

    Biol. 13, 2235–2246. Basson C. T., Bachinsky D. R., Lin R. C., Bachinsky D. R., Wer- emowicz S., Vaglio A. et al. 1997 Mutations in human cause limb and cardiac malformation in Holt-Oram syndrome. Nature. Genet. 15, 30–35. Brickner M. E., Hillis D. and Lange R. A. 2000 Congenital heart disease in adult I. Medicine 342, ...

  17. Sonographic Measurement of Lower Uterine Segment Thickness to Predict Uterine Rupture During a Trial of Labor in Women With Previous Cesarean Section: A Meta-analysis

    NARCIS (Netherlands)

    Kok, N.; Wiersma, I. C.; Opmeer, B. C.; de Graaf, I. M.; Mol, B. W.; Pajkrt, E.

    2014-01-01

    Along with the increasing rate of cesarean section (CS) births has been a concomitant decrease in the rate of vaginal birth after cesarean (VBAC), mostly due to concerns about uterine rupture during a trial of labor (TOL). The risk of uterine rupture in laboring women with a previous CS must be

  18. Bayesian methods for meta-analysis of causal relationships estimated using genetic instrumental variables

    DEFF Research Database (Denmark)

    Burgess, Stephen; Thompson, Simon G; Thompson, Grahame

    2010-01-01

    Genetic markers can be used as instrumental variables, in an analogous way to randomization in a clinical trial, to estimate the causal relationship between a phenotype and an outcome variable. Our purpose is to extend the existing methods for such Mendelian randomization studies to the context...... of multiple genetic markers measured in multiple studies, based on the analysis of individual participant data. First, for a single genetic marker in one study, we show that the usual ratio of coefficients approach can be reformulated as a regression with heterogeneous error in the explanatory variable....... This can be implemented using a Bayesian approach, which is next extended to include multiple genetic markers. We then propose a hierarchical model for undertaking a meta-analysis of multiple studies, in which it is not necessary that the same genetic markers are measured in each study. This provides...

  19. Metal loading in Soda Butte Creek upstream of Yellowstone National Park, Montana and Wyoming; a retrospective analysis of previous research; and quantification of metal loading, August 1999

    Science.gov (United States)

    Boughton, G.K.

    2001-01-01

    Acid drainage from historic mining activities has affected the water quality and aquatic biota of Soda Butte Creek upstream of Yellowstone National Park. Numerous investigations focusing on metals contamination have been conducted in the Soda Butte Creek basin, but interpretations of how metals contamination is currently impacting Soda Butte Creek differ greatly. A retrospective analysis of previous research on metal loading in Soda Butte Creek was completed to provide summaries of studies pertinent to metal loading in Soda Butte Creek and to identify data gaps warranting further investigation. Identification and quantification of the sources of metal loading to Soda Butte Creek was recognized as a significant data gap. The McLaren Mine tailings impoundment and mill site has long been identified as a source of metals but its contribution relative to the total metal load entering Yellowstone National Park was unknown. A tracer-injection and synoptic-sampling study was designed to determine metal loads upstream of Yellowstone National Park.A tracer-injection and synoptic-sampling study was conducted on an 8,511-meter reach of Soda Butte Creek from upstream of the McLaren Mine tailings impoundment and mill site downstream to the Yellowstone National Park boundary in August 1999. Synoptic-sampling sites were selected to divide the creek into discrete segments. A lithium bromide tracer was injected continuously into Soda Butte Creek for 24.5 hours. Downstream dilution of the tracer and current-meter measurements were used to calculate the stream discharge. Stream discharge values, combined with constituent concentrations obtained by synoptic sampling, were used to quantify constituent loading in each segment of Soda Butte Creek.Loads were calculated for dissolved calcium, silica, and sulfate, as well as for dissolved and total-recoverable iron, aluminum, and manganese. Loads were not calculated for cadmium, copper, lead, and zinc because these elements were infrequently

  20. Ellis-van Creveld syndrome: prenatal diagnosis, molecular analysis and genetic counseling.

    Science.gov (United States)

    Chen, Chih-Ping; Su, Yi-Ning; Hsu, Chin-Yuan; Chern, Schu-Rern; Tsai, Fuu-Jen; Wu, Pei-Chen; Chen, Po-Tsang; Wang, Wayseen

    2010-12-01

    To present the perinatal findings and molecular genetic analysis of two siblings with Ellis-van Creveld (EvC) syndrome. A 33-year-old woman, gravida 3, para 1, was referred for genetic counseling at 18 gestational weeks because of recurrent fetal skeletal dysplasia. Two years previously, she had delivered a 1,316-g dead male baby at 28 gestational weeks with a karyotype of 46,XY, postaxial polydactyly of the hands, thoracic narrowness, endocardial cushion defects, transposition of the great arteries, shortening of the long bones, malposition of the toes, and hypoplastic nails. During this pregnancy, prenatal ultrasound at 18 gestational weeks revealed shortening of the long bones (equivalent to 15 weeks), postaxial polydactyly of both hands, thoracic narrowness, and endocardial cushion defects. The pregnancy was subsequently terminated, and a 236-g female fetus was delivered with a karyotype of 46,XX, postaxial polydactyly of the hands, thoracic dysplasia, endocardial cushion defects, shortening of the long bones, and malposition of the toes and hypoplastic nails. The phenotype of each of the two siblings was consistent with EVC syndrome. Molecular analysis of the EVC and EVC2 genes revealed heterozygous mutations in the EVC2 gene. A heterozygous deletion mutation of a 26-bp deletion of c.871-2_894del26 encompassing the junction between intron 7 and exon 8 of the EVC2 gene was found in the mother and two siblings, and a heterozygous nonsense mutation of c.1195C >T, p.R399X in exon 10 of the EVC2 gene was found in the father and two siblings. Prenatal sonographic identification of endocardial cushion defects in association with shortening of the long bones should alert clinicians to the possibility of EvC syndrome and prompt a careful search of hexadactyly of the hands. Molecular analysis of the EVC and EVC2 genes is helpful in genetic counseling in cases with prenatally detected postaxial polydactyly, thoracic narrowness, short limbs and endocardial cushion defects

  1. Genome-wide Analysis of Genetic Loci Associated with Alzheimer’s Disease

    Science.gov (United States)

    Seshadri, Sudha; Fitzpatrick, Annette L.; Arfan Ikram, M; DeStefano, Anita L.; Gudnason, Vilmundur; Boada, Merce; Bis, Joshua C.; Smith, Albert V.; Carassquillo, Minerva M.; Charles Lambert, Jean; Harold, Denise; Schrijvers, Elisabeth M. C.; Ramirez-Lorca, Reposo; Debette, Stephanie; Longstreth, W.T.; Janssens, A. Cecile J.W.; Shane Pankratz, V.; Dartigues, Jean François; Hollingworth, Paul; Aspelund, Thor; Hernandez, Isabel; Beiser, Alexa; Kuller, Lewis H.; Koudstaal, Peter J.; Dickson, Dennis W.; Tzourio, Christophe; Abraham, Richard; Antunez, Carmen; Du, Yangchun; Rotter, Jerome I.; Aulchenko, Yurii S.; Harris, Tamara B.; Petersen, Ronald C.; Berr, Claudine; Owen, Michael J.; Lopez-Arrieta, Jesus; Varadarajan, Badri N.; Becker, James T.; Rivadeneira, Fernando; Nalls, Michael A.; Graff-Radford, Neill R.; Campion, Dominique; Auerbach, Sanford; Rice, Kenneth; Hofman, Albert; Jonsson, Palmi V.; Schmidt, Helena; Lathrop, Mark; Mosley, Thomas H.; Au, Rhoda; Psaty, Bruce M.; Uitterlinden, Andre G.; Farrer, Lindsay A.; Lumley, Thomas; Ruiz, Agustin; Williams, Julie; Amouyel, Philippe; Younkin, Steve G.; Wolf, Philip A.; Launer, Lenore J.; Lopez, Oscar L.; van Duijn, Cornelia M.; Breteler, Monique M. B.

    2010-01-01

    Context Genome wide association studies (GWAS) have recently identified CLU, PICALM and CR1 as novel genes for late-onset Alzheimer’s disease (AD). Objective In a three-stage analysis of new and previously published GWAS on over 35000 persons (8371 AD cases), we sought to identify and strengthen additional loci associated with AD and confirm these in an independent sample. We also examined the contribution of recently identified genes to AD risk prediction. Design, Setting, and Participants We identified strong genetic associations (p<10−3) in a Stage 1 sample of 3006 AD cases and 14642 controls by combining new data from the population-based Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) consortium (1367 AD cases (973 incident)) with previously reported results from the Translational Genomics Research Institute (TGEN) and Mayo AD GWAS. We identified 2708 single nucleotide polymorphisms (SNPs) with p-values<10−3, and in Stage 2 pooled results for these SNPs with the European AD Initiative (2032 cases, 5328 controls) to identify ten loci with p-values<10−5. In Stage 3, we combined data for these ten loci with data from the Genetic and Environmental Risk in AD consortium (3333 cases, 6995 controls) to identify four SNPs with a p-value<1.7×10−8. These four SNPs were replicated in an independent Spanish sample (1140 AD cases and 1209 controls). Main outcome measure Alzheimer’s Disease. Results We showed genome-wide significance for two new loci: rs744373 near BIN1 (OR:1.13; 95%CI:1.06–1.21 per copy of the minor allele; p=1.6×10−11) and rs597668 near EXOC3L2/BLOC1S3/MARK4 (OR:1.18; 95%CI1.07–1.29; p=6.5×10−9). Associations of CLU, PICALM, BIN1 and EXOC3L2 with AD were confirmed in the Spanish sample (p<0.05). However, CLU and PICALM did not improve incident AD prediction beyond age, sex, and APOE (improvement in area under receiver-operating-characteristic curve <0.003). Conclusions Two novel genetic loci for AD are reported

  2. Methods of Sports Genetics: dermatoglyphic analysis of human fingerprints (information 1

    Directory of Open Access Journals (Sweden)

    Serhiyenko L.P.

    2010-02-01

    Full Text Available The article provides data on the dermatoglyphic analysis of human fingerprints. The most informative dermatoglyphic traits of fingerprints are defined. They can be used as genetic markers to prognosticate sports endowments. The recommendations to use the technology of dermatoglyphic analysis of human fingerprints in sports genetics are given. There are certain national and racial differences in phenotypical expressed of dermatoglyphics of digit patterns.

  3. Study on characteristic points of boiling curve by using wavelet analysis and genetic algorithm

    International Nuclear Information System (INIS)

    Wei Huiming; Su Guanghui; Qiu Suizheng; Yang Xingbo

    2009-01-01

    Based on the wavelet analysis theory of signal singularity detection,the critical heat flux (CHF) and minimum film boiling starting point (q min ) of boiling curves can be detected and analyzed by using the wavelet multi-resolution analysis. To predict the CHF in engineering, empirical relations were obtained based on genetic algorithm. The results of wavelet detection and genetic algorithm prediction are consistent with experimental data very well. (authors)

  4. A novel genetic tool for clonal analysis of fourth chromosome mutations

    OpenAIRE

    Sousa-Neves, Rui; Schinaman, Joseph M.

    2012-01-01

    The fourth chromosome of Drosophila remains one of the most intractable regions of the fly genome to genetic analysis. The main difficulty posed to the genetic analyses of mutations on this chromosome arises from the fact that it does not undergo meiotic recombination, which makes recombination mapping impossible, and also prevents clonal analysis of mutations, a technique which relies on recombination to introduce the prerequisite recessive markers and FLP-recombinase recognition targets (FR...

  5. A new statistical framework for genetic pleiotropic analysis of high dimensional phenotype data.

    Science.gov (United States)

    Wang, Panpan; Rahman, Mohammad; Jin, Li; Xiong, Momiao

    2016-11-07

    The widely used genetic pleiotropic analyses of multiple phenotypes are often designed for examining the relationship between common variants and a few phenotypes. They are not suited for both high dimensional phenotypes and high dimensional genotype (next-generation sequencing) data. To overcome limitations of the traditional genetic pleiotropic analysis of multiple phenotypes, we develop sparse structural equation models (SEMs) as a general framework for a new paradigm of genetic analysis of multiple phenotypes. To incorporate both common and rare variants into the analysis, we extend the traditional multivariate SEMs to sparse functional SEMs. To deal with high dimensional phenotype and genotype data, we employ functional data analysis and the alternative direction methods of multiplier (ADMM) techniques to reduce data dimension and improve computational efficiency. Using large scale simulations we showed that the proposed methods have higher power to detect true causal genetic pleiotropic structure than other existing methods. Simulations also demonstrate that the gene-based pleiotropic analysis has higher power than the single variant-based pleiotropic analysis. The proposed method is applied to exome sequence data from the NHLBI's Exome Sequencing Project (ESP) with 11 phenotypes, which identifies a network with 137 genes connected to 11 phenotypes and 341 edges. Among them, 114 genes showed pleiotropic genetic effects and 45 genes were reported to be associated with phenotypes in the analysis or other cardiovascular disease (CVD) related phenotypes in the literature. Our proposed sparse functional SEMs can incorporate both common and rare variants into the analysis and the ADMM algorithm can efficiently solve the penalized SEMs. Using this model we can jointly infer genetic architecture and casual phenotype network structure, and decompose the genetic effect into direct, indirect and total effect. Using large scale simulations we showed that the proposed

  6. Systems Genetics Analysis to Identify the Genetic Modulation of a Glaucoma-Associated Gene.

    Science.gov (United States)

    Chintalapudi, Sumana R; Jablonski, Monica M

    2017-01-01

    Loss of retinal ganglion cells (RGCs) is one of the hallmarks of retinal neurodegenerative diseases, glaucoma being one of the most common. Recently, γ-synuclein (SNCG) was shown to be highly expressed in the somas and axons of RGCs. In various mouse models of glaucoma, downregulation of Sncg gene expression correlates with RGC loss. To investigate the regulation of Sncg in RGCs, we used a systems genetics approach to identify a gene that modulates the expression of Sncg, followed by confirmatory studies in both healthy and diseased retinas. We found that chromosome 1 harbors an eQTL that modulates the expression of Sncg in the mouse retina and identified Pfdn2 as the candidate upstream modulator of Sncg expression. Downregulation of Pfdn2 in enriched RGCs causes a concomitant reduction in Sncg. In this chapter, we describe our strategy and methods for identifying and confirming a genetic modulation of a glaucoma-associated gene. A similar method can be applied to other genes expressed in other tissues.

  7. Rivaroxaban compared with warfarin in patients with atrial fibrillation and previous stroke or transient ischaemic attack: a subgroup analysis of ROCKET AF.

    Science.gov (United States)

    Hankey, Graeme J; Patel, Manesh R; Stevens, Susanna R; Becker, Richard C; Breithardt, Günter; Carolei, Antonio; Diener, Hans-Christoph; Donnan, Geoffrey A; Halperin, Jonathan L; Mahaffey, Kenneth W; Mas, Jean-Louis; Massaro, Ayrton; Norrving, Bo; Nessel, Christopher C; Paolini, John F; Roine, Risto O; Singer, Daniel E; Wong, Lawrence; Califf, Robert M; Fox, Keith A A; Hacke, Werner

    2012-04-01

    In ROCKET AF, rivaroxaban was non-inferior to adjusted-dose warfarin in preventing stroke or systemic embolism among patients with atrial fibrillation (AF). We aimed to investigate whether the efficacy and safety of rivaroxaban compared with warfarin is consistent among the subgroups of patients with and without previous stroke or transient ischaemic attack (TIA). In ROCKET AF, patients with AF who were at increased risk of stroke were randomly assigned (1:1) in a double-blind manner to rivaroxaban 20 mg daily or adjusted dose warfarin (international normalised ratio 2·0-3·0). Patients and investigators were masked to treatment allocation. Between Dec 18, 2006, and June 17, 2009, 14 264 patients from 1178 centres in 45 countries were randomly assigned. The primary endpoint was the composite of stroke or non-CNS systemic embolism. In this substudy we assessed the interaction of the treatment effects of rivaroxaban and warfarin among patients with and without previous stroke or TIA. Efficacy analyses were by intention to treat and safety analyses were done in the on-treatment population. ROCKET AF is registered with ClinicalTrials.gov, number NCT00403767. 7468 (52%) patients had a previous stroke (n=4907) or TIA (n=2561) and 6796 (48%) had no previous stroke or TIA. The number of events per 100 person-years for the primary endpoint in patients treated with rivaroxaban compared with warfarin was consistent among patients with previous stroke or TIA (2·79% rivaroxaban vs 2·96% warfarin; hazard ratio [HR] 0·94, 95% CI 0·77-1·16) and those without (1·44%vs 1·88%; 0·77, 0·58-1·01; interaction p=0·23). The number of major and non-major clinically relevant bleeding events per 100 person-years in patients treated with rivaroxaban compared with warfarin was consistent among patients with previous stroke or TIA (13·31% rivaroxaban vs 13·87% warfarin; HR 0·96, 95% CI 0·87-1·07) and those without (16·69%vs 15·19%; 1·10, 0·99-1·21; interaction p=0·08

  8. Large-scale association analysis provides insights into the genetic architecture and pathophysiology of type 2 diabetes

    Science.gov (United States)

    Morris, Andrew P; Voight, Benjamin F; Teslovich, Tanya M; Ferreira, Teresa; Segrè, Ayellet V; Steinthorsdottir, Valgerdur; Strawbridge, Rona J; Khan, Hassan; Grallert, Harald; Mahajan, Anubha; Prokopenko, Inga; Kang, Hyun Min; Dina, Christian; Esko, Tonu; Fraser, Ross M; Kanoni, Stavroula; Kumar, Ashish; Lagou, Vasiliki; Langenberg, Claudia; Luan, Jian'an; Lindgren, Cecilia M; Müller-Nurasyid, Martina; Pechlivanis, Sonali; Rayner, N William; Scott, Laura J; Wiltshire, Steven; Yengo, Loic; Kinnunen, Leena; Rossin, Elizabeth J; Raychaudhuri, Soumya; Johnson, Andrew D; Dimas, Antigone S; Loos, Ruth J F; Vedantam, Sailaja; Chen, Han; Florez, Jose C; Fox, Caroline; Liu, Ching-Ti; Rybin, Denis; Couper, David J; Kao, Wen Hong L; Li, Man; Cornelis, Marilyn C; Kraft, Peter; Sun, Qi; van Dam, Rob M; Stringham, Heather M; Chines, Peter S; Fischer, Krista; Fontanillas, Pierre; Holmen, Oddgeir L; Hunt, Sarah E; Jackson, Anne U; Kong, Augustine; Lawrence, Robert; Meyer, Julia; Perry, John RB; Platou, Carl GP; Potter, Simon; Rehnberg, Emil; Robertson, Neil; Sivapalaratnam, Suthesh; Stančáková, Alena; Stirrups, Kathleen; Thorleifsson, Gudmar; Tikkanen, Emmi; Wood, Andrew R; Almgren, Peter; Atalay, Mustafa; Benediktsson, Rafn; Bonnycastle, Lori L; Burtt, Noël; Carey, Jason; Charpentier, Guillaume; Crenshaw, Andrew T; Doney, Alex S F; Dorkhan, Mozhgan; Edkins, Sarah; Emilsson, Valur; Eury, Elodie; Forsen, Tom; Gertow, Karl; Gigante, Bruna; Grant, George B; Groves, Christopher J; Guiducci, Candace; Herder, Christian; Hreidarsson, Astradur B; Hui, Jennie; James, Alan; Jonsson, Anna; Rathmann, Wolfgang; Klopp, Norman; Kravic, Jasmina; Krjutškov, Kaarel; Langford, Cordelia; Leander, Karin; Lindholm, Eero; Lobbens, Stéphane; Männistö, Satu; Mirza, Ghazala; Mühleisen, Thomas W; Musk, Bill; Parkin, Melissa; Rallidis, Loukianos; Saramies, Jouko; Sennblad, Bengt; Shah, Sonia; Sigurðsson, Gunnar; Silveira, Angela; Steinbach, Gerald; Thorand, Barbara; Trakalo, Joseph; Veglia, Fabrizio; Wennauer, Roman; Winckler, Wendy; Zabaneh, Delilah; Campbell, Harry; van Duijn, Cornelia; Uitterlinden89-, Andre G; Hofman, Albert; Sijbrands, Eric; Abecasis, Goncalo R; Owen, Katharine R; Zeggini, Eleftheria; Trip, Mieke D; Forouhi, Nita G; Syvänen, Ann-Christine; Eriksson, Johan G; Peltonen, Leena; Nöthen, Markus M; Balkau, Beverley; Palmer, Colin N A; Lyssenko, Valeriya; Tuomi, Tiinamaija; Isomaa, Bo; Hunter, David J; Qi, Lu; Shuldiner, Alan R; Roden, Michael; Barroso, Ines; Wilsgaard, Tom; Beilby, John; Hovingh, Kees; Price, Jackie F; Wilson, James F; Rauramaa, Rainer; Lakka, Timo A; Lind, Lars; Dedoussis, George; Njølstad, Inger; Pedersen, Nancy L; Khaw, Kay-Tee; Wareham, Nicholas J; Keinanen-Kiukaanniemi, Sirkka M; Saaristo, Timo E; Korpi-Hyövälti, Eeva; Saltevo, Juha; Laakso, Markku; Kuusisto, Johanna; Metspalu, Andres; Collins, Francis S; Mohlke, Karen L; Bergman, Richard N; Tuomilehto, Jaakko; Boehm, Bernhard O; Gieger, Christian; Hveem, Kristian; Cauchi, Stephane; Froguel, Philippe; Baldassarre, Damiano; Tremoli, Elena; Humphries, Steve E; Saleheen, Danish; Danesh, John; Ingelsson, Erik; Ripatti, Samuli; Salomaa, Veikko; Erbel, Raimund; Jöckel, Karl-Heinz; Moebus, Susanne; Peters, Annette; Illig, Thomas; de Faire, Ulf; Hamsten, Anders; Morris, Andrew D; Donnelly, Peter J; Frayling, Timothy M; Hattersley, Andrew T; Boerwinkle, Eric; Melander, Olle; Kathiresan, Sekar; Nilsson, Peter M; Deloukas, Panos; Thorsteinsdottir, Unnur; Groop, Leif C; Stefansson, Kari; Hu, Frank; Pankow, James S; Dupuis, Josée; Meigs, James B; Altshuler, David; Boehnke, Michael; McCarthy, Mark I

    2012-01-01

    To extend understanding of the genetic architecture and molecular basis of type 2 diabetes (T2D), we conducted a meta-analysis of genetic variants on the Metabochip involving 34,840 cases and 114,981 controls, overwhelmingly of European descent. We identified ten previously unreported T2D susceptibility loci, including two demonstrating sex-differentiated association. Genome-wide analyses of these data are consistent with a long tail of further common variant loci explaining much of the variation in susceptibility to T2D. Exploration of the enlarged set of susceptibility loci implicates several processes, including CREBBP-related transcription, adipocytokine signalling and cell cycle regulation, in diabetes pathogenesis. PMID:22885922

  9. Genetic Analysis of Histamine Signaling in Larval Zebrafish Sleep

    Science.gov (United States)

    Oikonomou, Grigorios

    2017-01-01

    Abstract Pharmacological studies in mammals and zebrafish suggest that histamine plays an important role in promoting arousal. However, genetic studies using rodents with disrupted histamine synthesis or signaling have revealed only subtle or no sleep/wake phenotypes. Studies of histamine function in mammalian arousal are complicated by its production in cells of the immune system and its roles in humoral and cellular immunity, which can have profound effects on sleep/wake states. To avoid this potential confound, we used genetics to explore the role of histamine in regulating sleep in zebrafish, a diurnal vertebrate in which histamine production is restricted to neurons in the brain. Similar to rodent genetic studies, we found that zebrafish that lack histamine due to mutation of histidine decarboxylase (hdc) exhibit largely normal sleep/wake behaviors. Zebrafish containing predicted null mutations in several histamine receptors also lack robust sleep/wake phenotypes, although we are unable to verify that these mutants are completely nonfunctional. Consistent with some rodent studies, we found that arousal induced by overexpression of the neuropeptide hypocretin (Hcrt) or by stimulation of hcrt-expressing neurons is not blocked in hdc or hrh1 mutants. We also found that the number of hcrt-expressing or histaminergic neurons is unaffected in animals that lack histamine or Hcrt signaling, respectively. Thus, while acute pharmacological manipulation of histamine signaling has been shown to have profound effects on zebrafish and mammalian sleep, our results suggest that chronic loss of histamine signaling due to genetic mutations has only subtle effects on sleep in zebrafish, similar to rodents. PMID:28275716

  10. Genetic Analysis of Histamine Signaling in Larval Zebrafish Sleep.

    Science.gov (United States)

    Chen, Audrey; Singh, Chanpreet; Oikonomou, Grigorios; Prober, David A

    2017-01-01

    Pharmacological studies in mammals and zebrafish suggest that histamine plays an important role in promoting arousal. However, genetic studies using rodents with disrupted histamine synthesis or signaling have revealed only subtle or no sleep/wake phenotypes. Studies of histamine function in mammalian arousal are complicated by its production in cells of the immune system and its roles in humoral and cellular immunity, which can have profound effects on sleep/wake states. To avoid this potential confound, we used genetics to explore the role of histamine in regulating sleep in zebrafish, a diurnal vertebrate in which histamine production is restricted to neurons in the brain. Similar to rodent genetic studies, we found that zebrafish that lack histamine due to mutation of histidine decarboxylase ( hdc ) exhibit largely normal sleep/wake behaviors. Zebrafish containing predicted null mutations in several histamine receptors also lack robust sleep/wake phenotypes, although we are unable to verify that these mutants are completely nonfunctional. Consistent with some rodent studies, we found that arousal induced by overexpression of the neuropeptide hypocretin (Hcrt) or by stimulation of hcrt -expressing neurons is not blocked in hdc or hrh1 mutants. We also found that the number of hcrt -expressing or histaminergic neurons is unaffected in animals that lack histamine or Hcrt signaling, respectively. Thus, while acute pharmacological manipulation of histamine signaling has been shown to have profound effects on zebrafish and mammalian sleep, our results suggest that chronic loss of histamine signaling due to genetic mutations has only subtle effects on sleep in zebrafish, similar to rodents.

  11. The genetics and functional analysis of primary osteoarthritis susceptibility

    OpenAIRE

    Reynard, Louise N.; Loughlin, John

    2013-01-01

    Recent genome-wide association scans (GWASs) along with several adequately powered candidate gene studies have yielded a number of risk alleles for osteoarthritis (OA). This number is now sufficiently large to allow conclusions to be drawn regarding the nature of genetic susceptibility, including the fact that the risk alleles have variable effects depending on sex, ethnicity and on the skeletal site of the disease. Several of the alleles that have emerged from the GWASs are within or close t...

  12. Quantitative genetic analysis of anxiety trait in bipolar disorder.

    Science.gov (United States)

    Contreras, J; Hare, E; Chavarría, G; Raventós, H

    2018-01-01

    Bipolar disorder type I (BPI) affects approximately 1% of the world population. Although genetic influences on bipolar disorder are well established, identification of genes that predispose to the illness has been difficult. Most genetic studies are based on categorical diagnosis. One strategy to overcome this obstacle is the use of quantitative endophenotypes, as has been done for other medical disorders. We studied 619 individuals, 568 participants from 61 extended families and 51 unrelated healthy controls. The sample was 55% female and had a mean age of 43.25 (SD 13.90; range 18-78). Heritability and genetic correlation of the trait scale from the Anxiety State and Trait Inventory (STAI) was computed by using the general linear model (SOLAR package software). we observed that anxiety trait meets the following criteria for an endophenotype of bipolar disorder type I (BPI): 1) association with BPI (individuals with BPI showed the highest trait score (F = 15.20 [5,24], p = 0.009), 2) state-independence confirmed after conducting a test-retest in 321 subjects, 3) co-segregation within families 4) heritability of 0.70 (SE: 0.060), p = 2.33 × 10 -14 and 5) genetic correlation with BPI was 0.20, (SE = 0.17, p = 3.12 × 10 -5 ). Confounding factors such as comorbid disorders and pharmacological treatment could affect the clinical relationship between BPI and anxiety trait. Further research is needed to evaluate if anxiety traits are specially related to BPI in comparison with other traits such as anger, attention or response inhibition deficit, pathological impulsivity or low self-directedness. Anxiety trait is a heritable phenotype that follows a normal distribution when measured not only in subjects with BPI but also in unrelated healthy controls. It could be used as an endophenotype in BPI for the identification of genomic regions with susceptibility genes for this disorder. Published by Elsevier B.V.

  13. RESEARCH ARTICLE Genetic analysis of drug-metabolizing phase ...

    Indian Academy of Sciences (India)

    Navya

    Uighur, Hui and Mongolian populations were 0.8162, 0.8598, 0.8079, 0.7975, respectively. (ZUO et al. 2012). The differences .... Lee JS., Cheong HS., Kim LH., Kim JO., Seo DW., Kim YH et al. 2013 Screening of genetic ... enzymes CYP3A4, CYP2C9, CYP2C19 and CYP2D6 in Han, Uighur, Hui and. Mongolian Chinese ...

  14. (SSR) markers for analysis of genetic diversity in African rice ...

    African Journals Online (AJOL)

    Bonny Oloka

    2015-05-06

    May 6, 2015 ... 161/161. 194/196. 32 WAC 116. AfricaRice. 116/122. 121/121. 182/182. 146/146. 217/217. 210/210. 157/189. 231/257. 157/157. 174/177. 33 AER-75 ..... Life Technologies Inc., USA. Table 3. Estimated genetic diversity parameters obtained at each locus across 99 genotypes. Marker. No. of Alleles. He. Ho.

  15. A landscape genetic analysis of important agricultural pest species in Tunisia: The whitefly Bemisia tabaci.

    Science.gov (United States)

    Ben Abdelkrim, Ahmed; Hattab, Tarek; Fakhfakh, Hatem; Belkadhi, Mohamed Sadok; Gorsane, Faten

    2017-01-01

    Combining landscape ecology and genetics provides an excellent framework to appreciate pest population dynamics and dispersal. The genetic architectures of many species are always shaped by environmental constraints. Because little is known about the ecological and genetic traits of Tunisian whitefly populations, the main objective of this work is to highlight patterns of biodiversity, genetic structure and migration routes of this pest. We used nuclear microsatellite loci to analyze B. tabaci populations collected from various agricultural areas across the country and we determine their biotype status. Molecular data were subsequently interpreted in an ecological context supplied from a species distribution model to infer habitat suitability and hereafter the potential connection paths between sampling localities. An analysis of landscape resistance to B. tabaci genetic flow was thus applied to take into account habitat suitability, genetic relatedness and functional connectivity of habitats within a varied landscape matrix. We shed light on the occurrence of three geographically delineated genetic groups with high levels of genetic differentiation within each of them. Potential migration corridors of this pest were then established providing significant advances toward the understanding of genetic features and the dynamic dispersal of this pest. This study supports the hypothesis of a long-distance dispersal of B. tabaci followed by infrequent long-term isolations. The Inference of population sources and colonization routes is critical for the design and implementation of accurate management strategies against this pest.

  16. A landscape genetic analysis of important agricultural pest species in Tunisia: The whitefly Bemisia tabaci.

    Directory of Open Access Journals (Sweden)

    Ahmed Ben Abdelkrim

    Full Text Available Combining landscape ecology and genetics provides an excellent framework to appreciate pest population dynamics and dispersal. The genetic architectures of many species are always shaped by environmental constraints. Because little is known about the ecological and genetic traits of Tunisian whitefly populations, the main objective of this work is to highlight patterns of biodiversity, genetic structure and migration routes of this pest. We used nuclear microsatellite loci to analyze B. tabaci populations collected from various agricultural areas across the country and we determine their biotype status. Molecular data were subsequently interpreted in an ecological context supplied from a species distribution model to infer habitat suitability and hereafter the potential connection paths between sampling localities. An analysis of landscape resistance to B. tabaci genetic flow was thus applied to take into account habitat suitability, genetic relatedness and functional connectivity of habitats within a varied landscape matrix. We shed light on the occurrence of three geographically delineated genetic groups with high levels of genetic differentiation within each of them. Potential migration corridors of this pest were then established providing significant advances toward the understanding of genetic features and the dynamic dispersal of this pest. This study supports the hypothesis of a long-distance dispersal of B. tabaci followed by infrequent long-term isolations. The Inference of population sources and colonization routes is critical for the design and implementation of accurate management strategies against this pest.

  17. Longitudinal Analysis of Genetic Susceptibility and BMI Throughout Adult Life.

    Science.gov (United States)

    Song, Mingyang; Zheng, Yan; Qi, Lu; Hu, Frank B; Chan, Andrew T; Giovannucci, Edward L

    2018-02-01

    Little is known about the genetic influence on BMI trajectory throughout adulthood. We created a genetic risk score (GRS) comprising 97 adult BMI-associated variants among 9,971 women and 6,405 men of European ancestry. Serial measures of BMI were assessed from 18 (women) or 21 (men) years to 85 years of age. We also examined BMI change in early (from 18 or 21 to 45 years of age), middle (from 45 to 65 years of age), and late adulthood (from 65 to 80 years of age). GRS was positively associated with BMI across all ages, with stronger associations in women than in men. The associations increased from early to middle adulthood, peaked at 45 years of age in men and at 60 years of age in women (0.91 and 1.35 kg/m 2 per 10-allele increment, respectively) and subsequently declined in late adulthood. For women, each 10-allele increment in the GRS was associated with an average BMI gain of 0.54 kg/m 2 in early adulthood, whereas no statistically significant association was found for BMI change in middle or late adulthood or for BMI change in any life period in men. Our findings indicate that genetic predisposition exerts a persistent effect on adiposity throughout adult life and increases early adulthood weight gain in women. © 2017 by the American Diabetes Association.

  18. Genetic Analysis of the Henry Mountains Bison Herd.

    Directory of Open Access Journals (Sweden)

    Dustin H Ranglack

    Full Text Available Wild American plains bison (Bison bison populations virtually disappeared in the late 1800s, with some remnant animals retained in what would become Yellowstone National Park and on private ranches. Some of these private bison were intentionally crossbred with cattle for commercial purposes. This forced hybridization resulted in both mitochondrial and nuclear introgression of cattle genes into some of the extant bison genome. As the private populations grew, excess animals, along with their history of cattle genetics, provided founders for newly established public bison populations. Of the US public bison herds, only those in Yellowstone and Wind Cave National Parks (YNP and WCNP appear to be free of detectable levels of cattle introgression. However, a small free-ranging population (~350 animals exists on public land, along with domestic cattle, in the Henry Mountains (HM of southern Utah. This isolated bison herd originated from a founder group translocated from YNP in the 1940s. Using genetic samples from 129 individuals, we examined the genetic status of the HM population and found no evidence of mitochondrial or nuclear introgression of cattle genes. This new information confirms it is highly unlikely for free-living bison to crossbreed with cattle, and this disease-free HM bison herd is valuable for the long-term conservation of the species. This bison herd is a subpopulation of the YNP/WCNP/HM metapopulation, within which it can contribute significantly to national efforts to restore the American plains bison to more of its native range.

  19. Methods of Sports Genetics: toe and plantar dermatoglyphic analysis (information 3)

    OpenAIRE

    Serhiyenko L.P.; Lyshevskaya V.H.

    2010-01-01

    The article summarized the data and dermatoglyphic analysis of human toe and plantar prints. It is defined that toe and plantar triradii, papillary ridge patterns, the main plantar lines, the types of dermatoglyphic patterns can be the objects of the dermatoglyphic analysis. The recommendations to use the technology of dermatoglyphic analysis of human toe and plantar prints in sport genetics are given.

  20. A set of autosomal multiple InDel markers for forensic application and population genetic analysis in the Chinese Xinjiang Hui group.

    Science.gov (United States)

    Xie, Tong; Guo, Yuxin; Chen, Ling; Fang, Yating; Tai, Yunchun; Zhou, Yongsong; Qiu, Pingming; Zhu, Bofeng

    2018-03-13

    In recent years, insertion/deletion (InDel) markers have become a promising and useful supporting tool in forensic identification cases and biogeographic research field. In this study, 30 InDel loci were explored to reveal the genetic diversities and genetic relationships between Chinese Xinjiang Hui group and the 25 previously reported populations using various biostatistics methods such as forensic statistical parameter analysis, phylogenetic reconstruction, multi-dimensional scaling, principal component analysis, and STRUCTURE analysis. No deviations from Hardy-Weinberg equilibrium tests were found at all 30 loci in the Chinese Xinjiang Hui group. The observed heterozygosity and expected heterozygosity ranged from 0.1971 (HLD118) to 0.5092 (HLD92), 0.2222 (HLD118) to 0.5000 (HLD6), respectively. The cumulative probability of exclusion and combined power of discrimination were 0.988849 and 0.99999999999378, respectively, which indicated that these 30 loci could be qualified for personal identification and used as complementary genetic markers for paternity tests in forensic cases. The results of present research based on the different methods of population genetic analysis revealed that the Chinese Xinjiang Hui group had close relationships with most Chinese groups, especially Han populations. In spite of this, for a better understanding of genetic background of the Chinese Xinjiang Hui group, more molecular genetic markers such as ancestry informative markers, single nucleotide polymorphisms (SNPs), and copy number variations will be conducted in future studies. Copyright © 2018 Elsevier B.V. All rights reserved.

  1. Multi-locus analysis of human infective Cryptosporidium species and subtypes using ten novel genetic loci

    Directory of Open Access Journals (Sweden)

    Bouzid Maha

    2010-08-01

    Full Text Available Abstract Background Cryptosporidium is a protozoan parasite that causes diarrheal illness in a wide range of hosts including humans. Two species, C. parvum and C. hominis are of primary public health relevance. Genome sequences of these two species are available and show only 3-5% sequence divergence. We investigated this sequence variability, which could correspond either to sequence gaps in the published genome sequences or to the presence of species-specific genes. Comparative genomic tools were used to identify putative species-specific genes and a subset of these genes was tested by PCR in a collection of Cryptosporidium clinical isolates and reference strains. Results The majority of the putative species-specific genes examined were in fact common to C. parvum and C. hominis. PCR product sequence analysis revealed interesting SNPs, the majority of which were species-specific. These genetic loci allowed us to construct a robust and multi-locus analysis. The Neighbour-Joining phylogenetic tree constructed clearly discriminated the previously described lineages of Cryptosporidium species and subtypes. Conclusions Most of the genes identified as being species specific during bioinformatics in Cryptosporidium sp. are in fact present in multiple species and only appear species specific because of gaps in published genome sequences. Nevertheless SNPs may offer a promising approach to studying the taxonomy of closely related species of Cryptosporidia.

  2. A systematic analysis of genetic dilated cardiomyopathy reveals numerous ubiquitously expressed and muscle-specific genes

    NARCIS (Netherlands)

    Harakalova, Magdalena; Kummeling, Gijs; Sammani, Arjan; Linschoten, Marijke; Baas, Annette F.; van der Smagt, Jasper; Doevendans, Pieter A.; van Tintelen, J. Peter; Dooijes, Dennis; Mokry, Michal; Asselbergs, Folkert W.

    2015-01-01

    Despite considerable progress being made in genetic diagnostics for dilated cardiomyopathy (DCM) using panels of the most prevalent genes, the cause remains unsolved in a substantial percentage of patients. We hypothesize that several previously described DCM genes with low or unknown prevalence

  3. Genetic Analysis of the Pathogenic Molecular Sub-phenotype Interferon Alpha Identifies Multiple Novel Loci Involved in Systemic Lupus Erythematosus

    Science.gov (United States)

    Kariuki, Silvia N.; Ghodke-Puranik, Yogita; Dorschner, Jessica M.; Chrabot, Beverly S.; Kelly, Jennifer A.; Tsao, Betty P.; Kimberly, Robert P.; Alarcón-Riquelme, Marta E.; Jacob, Chaim O.; Criswell, Lindsey A.; Sivils, Kathy L.; Langefeld, Carl D.; Harley, John B.; Skol, Andrew D.; Niewold, Timothy B.

    2014-01-01

    Systemic Lupus Erythematosus (SLE) is a chronic autoimmune disorder characterized by inflammation of multiple organ systems and dysregulated interferon responses. SLE is both genetically and phenotypically heterogeneous, greatly reducing the power of case-control studies in SLE. Elevated circulating interferon alpha (IFN-α) is a stable, heritable trait in SLE, which has been implicated in primary disease pathogenesis. 40–50% of patients have high IFN-α, and high levels correspond with clinical differences. To study genetic heterogeneity in SLE, we performed a case-case study comparing patients with high vs. low IFN-α in over 1550 SLE cases, including GWAS and replication cohorts. In meta-analysis, the top associations in European ancestry were PRKG1 rs7897633 (PMeta=2.75 × 10−8) and PNP rs1049564 (PMeta=1.24 × 10−7). We also found evidence for cross-ancestral background associations with the ANKRD44 and PLEKHF2 loci. These loci have not been previously identified in case-control SLE genetic studies. Bioinformatic analyses implicated these loci functionally in dendritic cells and natural killer cells, both of which are involved in IFN-α production in SLE. As case-control studies of heterogeneous diseases reach a limit of feasibility with respect to subject number and detectable effect size, the study of informative pathogenic subphenotypes becomes an attractive strategy for genetic discovery in complex disease. PMID:25338677

  4. Genetic and immunohistochemical analysis of HSPA5 in mouse and human retinas.

    Science.gov (United States)

    Chintalapudi, Sumana R; Wang, XiaoFei; Li, Huiling; Lau, Yin H Chan; Williams, Robert W; Jablonski, Monica M

    2016-01-01

    Photoreceptor degenerative diseases are among the leading causes of vision loss. Although the causative genetic mutations are often known, mechanisms leading to photoreceptor degeneration remain poorly defined. We have previously demonstrated that the photoreceptor membrane-associated protein XAP-1 antigen is a product of the HSPA5 gene. In this study, we used systems genetic methods, statistical modeling, and immunostaining to identify and analyze candidate genes that modulate Hspa5 expression in the retina. Quantitative trait locus (QTL) mapping was used to map the genomic region that regulates Hspa5 in the cross between C57BL/6J X DBA/2J mice (BXD) genetic reference panel. The stepwise refinement of candidate genes was based on expression QTL mapping, gene expression correlation analyses (direct and partial), and analysis of regional sequence variants. The subcellular localization of candidate proteins and HSPA5 in mouse and human retinas was evaluated by immunohistochemistry. Differences in the localization of extracellular HSPA5 were assessed between healthy human donor and atrophic age-related macular degeneration (AMD) donor eyes. In the eyes of healthy mice, extracellular HSPA5 was confined to the area around the cone photoreceptor outer segments. Mapping variation in Hspa5 mRNA expression levels in the retina revealed a statistically significant trans -acting expression QTL (eQTL) on Chromosome 2 (Chr 2) and a suggestive locus on Chr 15. Sulf2 on Chr 2 was the strongest candidate gene based on partial correlation analysis, Pearson correlation with Hspa5 , expression levels in the retina, a missense variant in exon 14, and its reported function in the extracellular matrix and interphotoreceptor matrix. SULF2 is localized to the rod and cone photoreceptors in both human and mouse retinas. In human retinas with no pathology, extracellular HSPA5 was localized around many cones within the macular area. In contrast, fewer HSPA5-immunopositive cones were

  5. Genetic and immunohistochemical analysis of HSPA5 in mouse and human retinas

    Science.gov (United States)

    Chintalapudi, Sumana R.; Wang, XiaoFei; Li, Huiling; Lau, Yin H. Chan; Williams, Robert W.; Jablonski, Monica M.

    2016-01-01

    Purpose Photoreceptor degenerative diseases are among the leading causes of vision loss. Although the causative genetic mutations are often known, mechanisms leading to photoreceptor degeneration remain poorly defined. We have previously demonstrated that the photoreceptor membrane-associated protein XAP-1 antigen is a product of the HSPA5 gene. In this study, we used systems genetic methods, statistical modeling, and immunostaining to identify and analyze candidate genes that modulate Hspa5 expression in the retina. Methods Quantitative trait locus (QTL) mapping was used to map the genomic region that regulates Hspa5 in the cross between C57BL/6J X DBA/2J mice (BXD) genetic reference panel. The stepwise refinement of candidate genes was based on expression QTL mapping, gene expression correlation analyses (direct and partial), and analysis of regional sequence variants. The subcellular localization of candidate proteins and HSPA5 in mouse and human retinas was evaluated by immunohistochemistry. Differences in the localization of extracellular HSPA5 were assessed between healthy human donor and atrophic age-related macular degeneration (AMD) donor eyes. Results In the eyes of healthy mice, extracellular HSPA5 was confined to the area around the cone photoreceptor outer segments. Mapping variation in Hspa5 mRNA expression levels in the retina revealed a statistically significant trans-acting expression QTL (eQTL) on Chromosome 2 (Chr 2) and a suggestive locus on Chr 15. Sulf2 on Chr 2 was the strongest candidate gene based on partial correlation analysis, Pearson correlation with Hspa5, expression levels in the retina, a missense variant in exon 14, and its reported function in the extracellular matrix and interphotoreceptor matrix. SULF2 is localized to the rod and cone photoreceptors in both human and mouse retinas. In human retinas with no pathology, extracellular HSPA5 was localized around many cones within the macular area. In contrast, fewer HSPA5

  6. Clinical genetic testing using a custom-designed steroid-resistant nephrotic syndrome gene panel: analysis and recommendations.

    Science.gov (United States)

    Sen, Ethan S; Dean, Philip; Yarram-Smith, Laura; Bierzynska, Agnieszka; Woodward, Geoff; Buxton, Chris; Dennis, Gemma; Welsh, Gavin I; Williams, Maggie; Saleem, Moin A

    2017-12-01

    There are many single-gene causes of steroid-resistant nephrotic syndrome (SRNS) and the list continues to grow rapidly. Prompt comprehensive diagnostic testing is key to realising the clinical benefits of a genetic diagnosis. This report describes a bespoke-designed, targeted next-generation sequencing (NGS) diagnostic gene panel assay to detect variants in 37 genes including the ability to identify copy number variants (CNVs). This study reports results of 302 patients referred for SRNS diagnostic gene panel analysis. Phenotype and clinical impact data were collected using a standard proforma. Candidate variants detected by NGS were confirmed by Sanger sequencing/Multiplex Ligation-dependent Probe Amplification with subsequent family segregation analysis where possible. Clinical presentation was nephrotic syndrome in 267 patients and suspected Alport syndrome (AS) in 35. NGS panel testing determined a likely genetic cause of disease in 44/220 (20.0%) paediatric and 10/47 (21.3%) adult nephrotic cases, and 17/35 (48.6%) of haematuria/AS patients. Of 71 patients with genetic disease, 32 had novel pathogenic variants without a previous disease association including two with deletions of one or more exons of NPHS1 or NPHS2 . Gene panel testing provides a genetic diagnosis in a significant number of patients presenting with SRNS or suspected AS. It should be undertaken at an early stage of the care pathway and include the ability to detect CNVs as an emerging mechanism for genes associated with this condition. Use of clinical genetic testing after diagnosis of SRNS has the potential to stratify patients and assist decision-making regarding management. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

  7. Identification of a previously undetected metabolic defect in the Complex II Caenorhabditis elegans mev-1 mutant strain using respiratory control analysis.

    Science.gov (United States)

    Fong, Sheng; Ng, Li Fang; Ng, Li Theng; Moore, Philip K; Halliwell, Barry; Gruber, Jan

    2017-04-01

    Hypometabolism may play an important role in the pathogenesis of ageing and ageing-related diseases. The nematode Caenorhabditis elegans offers the opportunity to study "living mitochondria" in a small (~1 mm) animal replete with a highly stereotypical, yet complex, anatomy and physiology. Basal oxygen consumption rate is often employed as a proxy for energy metabolism in this context. This parameter is traditionally measured using single-chamber Clark electrodes without the addition of metabolic modulators. Recently, multi-well oxygen electrodes, facilitating addition of metabolic modulators and hence study of respiratory control during different mitochondrial respiration states, have been developed. However, only limited official protocols exist for C. elegans, and key limitations of these techniques are therefore unclear. Following modification and testing of some of the existing protocols, we used these methods to explore mitochondrial bioenergetics in live nematodes of an electron transfer chain Complex II mutant strain, mev-1, and identified a previously undetected metabolic defect. We find that mev-1 mutants cannot respond adequately to increased energy demands, suggesting that oxidative phosphorylation is more severely impaired in these animals than has previously been appreciated.

  8. Two-level mixed modeling of longitudinal pedigree data for genetic association analysis

    DEFF Research Database (Denmark)

    Tan, Q.

    2013-01-01

    Genetic association analysis on complex phenotypes under a longitudinal design involving pedigrees encounters the problem of correlation within pedigrees which could affect statistical assessment of the genetic effects on both the mean level of the phenotype and its rate of change over the time...... of follow-up. Approaches have been proposed to integrate kinship correlation into the mixed effect models to explicitly model the genetic relationship which have been proven as an efficient way for dealing with sample clustering in pedigree data. Although useful for adjusting relatedness in the mixed...... assess the genetic associations with the mean level and the rate of change in a phenotype both with kinship correlation integrated in the mixed effect models. We apply our method to longitudinal pedigree data to estimate the genetic effects on systolic blood pressure measured over time in large pedigrees...

  9. [Determining mitochondrial molecular markers suitable for genetic diversity analysis of Cordyceps militaris].

    Science.gov (United States)

    Zhang, Yongjie; Guo, Lihong; Zhang, Shu; Liu, Xingzhong

    2015-07-04

    To screen efficient molecular markers suitable for genetic diversity analysis of Cordyceps militaris from mitochondrial DNA. We amplified 12 mitochondrial DNA fragments and 3 nuclear DNA fragments from each of 20 C. militaris isolates and analyzed nucleotide variations on these DNA fragments. We revealed a greatly higher genetic variation in mitochondrial DNA fragments than in nuclear DNA fragments. Specifically, C. militaris isolates exhibited intron presence/absence diversity in some mitochondrial fragments, and more variable sites were found in mitochondrial fragments than in nuclear fragments. The extent of nucleotide variations also varied by mitochondrial fragment, and intronic proteins seemed to be more vulnerable to amino acid changes than exonic proteins. Genetic diversity increased with the number of molecular markers used. We recommended using (in order) nad3-cox2. cox2-nad5, cox2, cox3, cob, and cox1 for future genetic diversity and population genetic studies of C. militaris.

  10. Forward genetic analysis of visual behavior in zebrafish.

    Directory of Open Access Journals (Sweden)

    Akira Muto

    2005-11-01

    Full Text Available The visual system converts the distribution and wavelengths of photons entering the eye into patterns of neuronal activity, which then drive motor and endocrine behavioral responses. The gene products important for visual processing by a living and behaving vertebrate animal have not been identified in an unbiased fashion. Likewise, the genes that affect development of the nervous system to shape visual function later in life are largely unknown. Here we have set out to close this gap in our understanding by using a forward genetic approach in zebrafish. Moving stimuli evoke two innate reflexes in zebrafish larvae, the optomotor and the optokinetic response, providing two rapid and quantitative tests to assess visual function in wild-type (WT and mutant animals. These behavioral assays were used in a high-throughput screen, encompassing over half a million fish. In almost 2,000 F2 families mutagenized with ethylnitrosourea, we discovered 53 recessive mutations in 41 genes. These new mutations have generated a broad spectrum of phenotypes, which vary in specificity and severity, but can be placed into only a handful of classes. Developmental phenotypes include complete absence or abnormal morphogenesis of photoreceptors, and deficits in ganglion cell differentiation or axon targeting. Other mutations evidently leave neuronal circuits intact, but disrupt phototransduction, light adaptation, or behavior-specific responses. Almost all of the mutants are morphologically indistinguishable from WT, and many survive to adulthood. Genetic linkage mapping and initial molecular analyses show that our approach was effective in identifying genes with functions specific to the visual system. This collection of zebrafish behavioral mutants provides a novel resource for the study of normal vision and its genetic disorders.

  11. Forward Genetic Analysis of Visual Behavior in Zebrafish.

    Directory of Open Access Journals (Sweden)

    2005-11-01

    Full Text Available The visual system converts the distribution and wavelengths of photons entering the eye into patterns of neuronal activity, which then drive motor and endocrine behavioral responses. The gene products important for visual processing by a living and behaving vertebrate animal have not been identified in an unbiased fashion. Likewise, the genes that affect development of the nervous system to shape visual function later in life are largely unknown. Here we have set out to close this gap in our understanding by using a forward genetic approach in zebrafish. Moving stimuli evoke two innate reflexes in zebrafish larvae, the optomotor and the optokinetic response, providing two rapid and quantitative tests to assess visual function in wild-type (WT and mutant animals. These behavioral assays were used in a high-throughput screen, encompassing over half a million fish. In almost 2,000 F2 families mutagenized with ethylnitrosourea, we discovered 53 recessive mutations in 41 genes. These new mutations have generated a broad spectrum of phenotypes, which vary in specificity and severity, but can be placed into only a handful of classes. Developmental phenotypes include complete absence or abnormal morphogenesis of photoreceptors, and deficits in ganglion cell differentiation or axon targeting. Other mutations evidently leave neuronal circuits intact, but disrupt phototransduction, light adaptation, or behavior-specific responses. Almost all of the mutants are morphologically indistinguishable from WT, and many survive to adulthood. Genetic linkage mapping and initial molecular analyses show that our approach was effective in identifying genes with functions specific to the visual system. This collection of zebrafish behavioral mutants provides a novel resource for the study of normal vision and its genetic disorders.

  12. The multi-niche crowding genetic algorithm: Analysis and applications

    Energy Technology Data Exchange (ETDEWEB)

    Cedeno, Walter [Univ. of California, Davis, CA (United States)

    1995-09-01

    The ability of organisms to evolve and adapt to the environment has provided mother nature with a rich and diverse set of species. Only organisms well adapted to their environment can survive from one generation to the next, transferring on the traits, that made them successful, to their offspring. Competition for resources and the ever changing environment drives some species to extinction and at the same time others evolve to maintain the delicate balance in nature. In this disertation we present the multi-niche crowding genetic algorithm, a computational metaphor to the survival of species in ecological niches in the face of competition. The multi-niche crowding genetic algorithm maintains stable subpopulations of solutions in multiple niches in multimodal landscapes. The algorithm introduces the concept of crowding selection to promote mating among members with qirnilar traits while allowing many members of the population to participate in mating. The algorithm uses worst among most similar replacement policy to promote competition among members with similar traits while allowing competition among members of different niches as well. We present empirical and theoretical results for the success of the multiniche crowding genetic algorithm for multimodal function optimization. The properties of the algorithm using different parameters are examined. We test the performance of the algorithm on problems of DNA Mapping, Aquifer Management, and the File Design Problem. Applications that combine the use of heuristics and special operators to solve problems in the areas of combinatorial optimization, grouping, and multi-objective optimization. We conclude by presenting the advantages and disadvantages of the algorithm and describing avenues for future investigation to answer other questions raised by this study.

  13. Genetic analysis of metabolic defects in the spontaneously hypertensive rat

    Czech Academy of Sciences Publication Activity Database

    Pravenec, Michal; Zídek, Václav; Musilová, Alena; Šimáková, Miroslava; Kostka, Vlastimil; Mlejnek, Petr; Křen, Vladimír; Křenová, D.; Bílá, V.; Míková, B.; Jáchymová, M.; Horký, K.; Kazdová, L.; St.Lezin, E.; Kurtz, W. T.

    2002-01-01

    Roč. 13, č. 5 (2002), s. 253-258 ISSN 0938-8990 R&D Projects: GA MŠk LN00A079; GA ČR GV204/98/K015; GA ČR GA305/00/1646; GA MŠk NB5299 Grant - others:NIH(US) RO1 HL56028; NIH(US) PO1 HL35018; HHMI(US) 55000331 Institutional research plan: CEZ:AV0Z5011922 Keywords : metabolic defects * spontaneously hypertensive rat Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.233, year: 2002

  14. Analysis of Genetic and Non-Genetic Factors Influencing Timing and Time Perception.

    Science.gov (United States)

    Bartholomew, Alex J; Meck, Warren H; Cirulli, Elizabeth T

    2015-01-01

    Performance on different psychophysical tasks measuring the sense of time indicates a large amount of individual variation in the accuracy and precision of timing in the hundredths of milliseconds-to-minutes range. Quantifying factors with an influence on timing is essential to isolating a biological (genetic) contribution to the perception and estimation of time. In the largest timing study to date, 647 participants completed a duration-discrimination task in the sub-second range and a time-production task in the supra-second range. We confirm the stability of a participant's time sense across multiple sessions and substantiate a modest sex difference on time production. Moreover, we demonstrate a strong correlation between performance on a standardized cognitive battery and performance in both duration-discrimination and time-production tasks; we further show that performance is uncorrelated with age after controlling for general intelligence. Additionally, we find an effect of ethnicity on time sense, with African Americans and possibly Hispanics in our cohort differing in accuracy and precision from other ethnic groups. Finally, a preliminary genome-wide association and exome chip study was performed on 148 of the participants, ruling out the possibility for a single common variant or groups of low-frequency coding variants within a single gene to explain more than ~18% of the variation in the sense of time.

  15. Analysis of the genetic diversity of Candida isolates obtained from diabetic patients and kidney transplant recipients

    Directory of Open Access Journals (Sweden)

    Volmir Pitt Benedetti

    2016-01-01

    Full Text Available Yeasts of the genus Candida have high genetic variability and are the most common opportunistic pathogenic fungi in humans. In this study, we evaluated the genetic diversity among 120 isolates of Candida spp. obtained from diabetic patients, kidney transplant recipients and patients without any immune deficiencies from Paraná state, Brazil. The analysis was performed using the ITS1-5.8S-ITS2 region and a partial sequence of 28S rDNA. In the phylogenetic analysis, we observed a consistent separation of the species C. albicans, C. dubliniensis, C. glabrata, C. tropicalis, C. parapsilosis, C. metapsilosis and C. orthopsilosis, however with low intraspecific variability. In the analysis of the C. albicans species, two clades were formed. Clade A included the largest number of isolates (91.2% and the majority of isolates from GenBank (71.4%. The phylogenetic analysis showed low intraspecific genetic diversity, and the genetic polymorphisms between C. albicans isolates were similar to genetic divergence found in other studies performed with isolates from Brazil. This low genetic diversity of isolates can be explained by the geographic proximity of the patients evaluated. It was observed that yeast colonisation was highest in renal transplant recipients and diabetic patients and that C. albicans was the species most frequently isolated.

  16. Population genetic analysis and trichothecene profiling of Fusarium graminearum from wheat in Uruguay.

    Science.gov (United States)

    Pan, D; Mionetto, A; Calero, N; Reynoso, M M; Torres, A; Bettucci, L

    2016-03-11

    Fusarium graminearum sensu stricto (F. graminearum s.s.) is the major causal agent of Fusarium head blight of wheat worldwide, and contaminates grains with trichothecene mycotoxins that cause serious threats to food safety and animal health. An important aspect of managing this pathogen and reducing mycotoxin contamination of wheat is knowledge regarding its population genetics. Therefore, isolates of F. graminearum s.s. from the major wheat-growing region of Uruguay were analyzed by amplified fragment length polymorphism assays, PCR genotyping, and chemical analysis of trichothecene production. Of the 102 isolates identified as having the 15-ADON genotype via PCR genotyping, all were DON producers, but only 41 strains were also 15-ADON producers, as determined by chemical analysis. The populations were genotypically diverse but genetically similar, with significant genetic exchange occurring between them. Analysis of molecular variance indicated that most of the genetic variability resulted from differences between isolates within populations. Multilocus linkage disequilibrium analysis suggested that the isolates had a panmictic population genetic structure and that there is significant recombination occurs in F. graminearum s.s. In conclusion, tour findings provide the first detailed description of the genetic structure and trichothecene production of populations of F. graminearum s.s. from Uruguay, and expands our understanding of the agroecology of F. graminearum and of the correlation between genotypes and trichothecene chemotypes.

  17. Thalidomide for previously untreated elderly patients with multiple myeloma: meta-analysis of 1685 individual patient data from 6 randomized clinical trials

    DEFF Research Database (Denmark)

    Fayers, Peter M; Palumbo, Antonio; Hulin, Cyrille

    2011-01-01

    The role of thalidomide for previously untreated elderly patients with multiple myeloma remains unclear. Six randomized controlled trials, launched in or after 2000, compared melphalan and prednisone alone (MP) and with thalidomide (MPT). The effect on overall survival (OS) varied across trials. We...... interval 0.73-0.94, P = .004), representing increased median OS time of 6.6 months, from 32.7 months (MP) to 39.3 months (MPT). The thalidomide regimen was also associated with superior PFS (hazard ratio = 0.68, 95% confidence interval 0.61-0.76, P ... or better was 59% on MPT and 37% on MP). Although the trials differed in terms of patient baseline characteristics and thalidomide regimens, there was no evidence that treatment affected OS differently according to levels of the prognostic factors. We conclude that thalidomide added to MP improves OS...

  18. Thalidomide for previously untreated elderly patients with multiple myeloma: meta-analysis of 1685 individual patient data from 6 randomized clinical trials

    DEFF Research Database (Denmark)

    Fayers, Peter M; Palumbo, Antonio; Hulin, Cyrille

    2011-01-01

    carried out a meta-analysis of the 1685 individual patients in these trials. The primary endpoint was OS, and progression-free survival (PFS) and 1-year response rates were secondary endpoints. There was a highly significant benefit to OS from adding thalidomide to MP (hazard ratio = 0.83; 95% confidence...

  19. Genetic diversity, population structure and association analysis in cut chrysanthemum (Chrysanthemum morifolium Ramat.).

    Science.gov (United States)

    Li, Pirui; Zhang, Fei; Chen, Sumei; Jiang, Jiafu; Wang, Haibin; Su, Jiangshuo; Fang, Weimin; Guan, Zhiyong; Chen, Fadi

    2016-06-01

    Characterizing the genetic diversity present in a working set of plant germplasm can contribute to its effective management and genetic improvement. The cut flower chrysanthemum (Chrysanthemum morifolium Ramat.) is an economically important ornamental species. With the repeated germplasm exchange and intensive breeding activities, it remains a major task in genetic research. The purpose of the present study was to characterize the genetic diversity and the population structure of a worldwide collection of 159 varieties, and to apply an association mapping approach to identify DNA-based markers linked to five plant architecture traits and six inflorescence traits. The genotyping demonstrated that there was no lack of genetic diversity in the collection and that pair-wise kinship values were relatively low. The clustering based on a Bayesian model of population structure did not reflect known variation in either provenance or inflorescence type. A principal coordinate analysis was, however, able to discriminate most of the varieties according to both of these criteria. About 1 in 100 marker pairs exhibited a degree of linkage disequilibrium. The association analysis identified a number of markers putatively linked to one or more of the traits. Some of these associations were robust over two seasons. The findings provide an in-depth understanding of genetic diversity and population structure present in cut flower chrysanthemum varieties, and an insight into the genetic control of plant architecture and inflorescence-related traits.

  20. Genetic variability and population structure of Disanthus cercidifolius subsp. longipes (Hamamelidaceae based on AFLP analysis.

    Directory of Open Access Journals (Sweden)

    Yi Yu

    Full Text Available Disanthus cercidifolius subsp. longipes is an endangered species in China. Genetic diversity and structure analysis of this species was investigated using amplified fragments length polymorphism (AFLP fingerprinting. Nei's gene diversity ranged from 0.1290 to 0.1394. The AMOVA indicated that 75.06% of variation was distributed within populations, while the between-group component 5.04% was smaller than the between populations-within-group component 19.90%. Significant genetic differentiation was detected between populations. Genetic and geographical distances were not correlated. PCA and genetic structure analysis showed that populations from East China were together with those of the Nanling Range. These patterns of genetic diversity and levels of genetic variation may be the result of D. c. subsp. longipes restricted to several isolated habitats and "excess flowers production, but little fruit set". It is necessary to protect all existing populations of D. c. subsp. longipes in order to preserve as much genetic variation as possible.

  1. Genetic diversity and structure analysis based on hordein protein polymorphism in barley landrace populations from jordan

    International Nuclear Information System (INIS)

    Baloch, A.W.; Ali, M.; Baloch, A.M.; Mangan, B.U.N.; Song, W

    2014-01-01

    Jordan is unanimously considered to be one of the centers of genetic diversity for barley, where wild and landraces of barley has been grown under different climatic conditions. The genetic diversity and genetic structure based on hordein polymorphism was assessed in 90 different accessions collected from four different sites of Jordan. A-PAGE was used to reveal hordein polymorphism among the genotypes. A total of 29 distinct bands were identified, out of them 9 bands were distinguished for D, 11 for C, and 9 for the B hordein regions. The observed genetic similarity was an exceptionally high between the populations than expected, which is probably due to high gene flow estimated between them. The genetic diversity parameters were not differ largely among the populations, indicating that local selection of a particular site did not play a key role in shaping genetic diversity. Analysis of molecular variance (AMOVA) revealed significant population structure when accessions were structured according to population site. There was 94% of hordein variation resided within the populations and only 8% present among the populations. Both Bayesian and Principale Coordinate Analysis (PCoA) concordantly demonstrated admixture genotypes of the landraces barley populations. Consequently, none of the population found to be clustered separately according to its population site. It is concluded that this approach can be useful to explore the germplasm for genetic diversity but perhaps is not suitable for determining phylogenic relations in barley. (author)

  2. Genetic structure of pig breeds from Korea and China using microsatellite loci analysis.

    Science.gov (United States)

    Kim, T H; Kim, K S; Choi, B H; Yoon, D H; Jang, G W; Lee, K T; Chung, H Y; Lee, H Y; Park, H S; Lee, J W

    2005-10-01

    To understand molecular genetic characteristics of Korean pigs, the genetic relationships of nine pig breeds including two Korean pigs (Korean native pig and Korean wild pig), three Chinese pigs (Min pig, Xiang pig, and Wuzhishan pig), and four European breeds (Berkshire, Duroc, Landrace, and Yorkshire) were characterized from a 16-microsatellite loci analysis. The mean heterozygosity within breeds ranged from 0.494 to 0.703. Across multiple loci, significant deviation from Hardy-Weinberg equilibrium was observed in most pig breeds, except for two Chinese pigs (Min pig and Wuzhishan pig). This deviation was in the direction of heterozygote deficit. Across population loci, 36 of 144 significantly deviated (P Relationship trees based on the Nei's DA genetic distance and scatter diagram from principal component analysis consistently displayed pronounced genetic differentiation among the Korean wild pig, Xiang pig, and Wuzhishan pig. Individual assignment test using a Bayesian method showed 100% success in assigning Korean and Chinese individual pigs into their correct breeds of origin and 100% exclusion success from all alternative reference populations at P China pig breed with a black coat color. Considering the close genetic relationship of Korean pigs to the Western breeds such as Berkshire and Landrace, our findings can be used as valuable genetic information for the preservation and further genetic improvement of the Korean native pig.

  3. Genetic Analysis for Two Italian Siblings with Usher Syndrome and Schizophrenia

    Directory of Open Access Journals (Sweden)

    Daniela Domanico

    2012-01-01

    Full Text Available Usher syndrome is a group of autosomal recessive genetic disorders characterized by deafness, retinitis pigmentosa, and sometimes vestibular areflexia. The relationship between Usher syndrome and mental disorders, most commonly a “schizophrenia-like” psychosis, is sometimes described in the literature. The etiology of psychiatric expression of Usher syndrome is still unclear. We reported a case of two natural siblings with congenital hypoacusis, retinitis pigmentosa, and psychiatric symptoms. Clinical features and genetic analysis were also reported. We analyzed possible causes to explain the high prevalence of psychiatric manifestations in Usher syndrome: genetic factors, brain damage, and “stress-related” hypothesis.

  4. [Analysis of genetic control of maize response in anther culture within a diallelic set].

    Science.gov (United States)

    Satarova, T N

    2002-01-01

    The androgenic ability in anther culture in vitro was examined within a diallel set of five maize lines. The complex analysis of genetic variation components, Hayman's diagram, and genetic parameters showed that the anther response is under the control of an additive-dominant genetic system. The examined lines possessed the different correlation of dominant and recessive alleles controlling androgenesis. And 44 was the line with the biggest number of recessive genes, which determined the increase in the trait. The level of dominance varied in different loci, though in the whole the degree of dominance approached to the complete one.

  5. Population genetic analysis and bioclimatic modeling in Agave striata in the Chihuahuan Desert indicate higher genetic variation and lower differentiation in drier and more variable environments.

    Science.gov (United States)

    Trejo, Laura; Alvarado-Cárdenas, Leonardo O; Scheinvar, Enrique; Eguiarte, Luis E

    2016-06-01

    Is there an association between bioclimatic variables and genetic variation within species? This question can be approached by a detailed analysis of population genetics parameters along environmental gradients in recently originated species (so genetic drift does not further obscure the patterns). The genus Agave, with more than 200 recent species encompassing a diversity of morphologies and distributional patterns, is an adequate system for such analyses. We studied Agave striata, a widely distributed species from the Chihuahuan Desert, with a distinctive iteroparous reproductive ecology and two recognized subspecies with clear morphological differences. We used population genetic analyses along with bioclimatic studies to understand the effect of environment on the genetic variation and differentiation of this species. We analyzed six populations of the subspecies A. striata subsp. striata, with a southern distribution, and six populations of A. striata subsp. falcata, with a northern distribution, using 48 ISSR loci and a total of 541 individuals (averaging 45 individuals per population). We assessed correlations between population genetics parameters (the levels of genetic variation and differentiation) and the bioclimatic variables of each population. We modeled each subspecies distribution and used linear correlations and multifactorial analysis of variance. Genetic variation (measured as expected heterozygosity) increased at higher latitudes. Higher levels of genetic variation in populations were associated with a higher variation in environmental temperature and lower precipitation. Stronger population differentiation was associated with wetter and more variable precipitation in the southern distribution of the species. The two subspecies have genetic differences, which coincide with their climatic differences and potential distributions. Differences in genetic variation among populations and the genetic differentiation between A. striata subsp. striata

  6. Genetic analysis of X-linked hybrid sterility in the house mouse

    Czech Academy of Sciences Publication Activity Database

    Storchová, Radka; Gregorová, Soňa; Buckiová, Daniela; Kyselová, Vendula; Divina, Petr; Forejt, Jiří

    2004-01-01

    Roč. 15, - (2004), s. 515-524 ISSN 0938-8990 R&D Projects: GA MŠk LN00A079; GA ČR GA204/02/1373 Grant - others:EU(XE) QLRI-2000-00233; HHMI(US) 555000306 Institutional research plan: CEZ:AV0Z5052915 Keywords : X-linked hybrid sterility * genetic analysis Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.658, year: 2004

  7. Detecting the genetic link between Alzheimer's disease and obesity using bioinformatics analysis of GWAS data

    OpenAIRE

    Zhuang, Qi-Shuai; Zheng, Hao; Gu, Xiao-Dan; Shen, Liang; Ji, Hong-Fang

    2017-01-01

    Alzheimer's disease (AD) represents the major form of dementia in the elderly. In recent years, accumulating evidence indicate that obesity may act as a risk factor for AD, while the genetic link between the two conditions remains unclear. This bioinformatics analysis aimed to detect the genetic link between AD and obesity on single nucleotide polymorphisms (SNPs), gene, and pathway levels based on genome-wide association studies data. A total of 31 SNPs were found to be shared by AD and obes...

  8. Emerging Global Initiatives in Neurogenetics: The Enhancing Neuroimaging Genetics through Meta-analysis (ENIGMA) Consortium.

    Science.gov (United States)

    Bearden, Carrie E; Thompson, Paul M

    2017-04-19

    The Enhancing Neuroimaging Genetics through Meta-analysis (ENIGMA) Consortium is a global team science effort, now including over 800 scientists spread across 340 institutions in 35 countries, with the shared goal of understanding disease and genetic influences on the brain. This "crowdsourcing" approach to team neuroscience has unprecedented power for advancing our understanding of both typical and atypical human brain development. Copyright © 2017 Elsevier Inc. All rights reserved.

  9. Phenopolis: an open platform for harmonization and analysis of genetic and phenotypic data

    OpenAIRE

    Pontikos, N.; Yu, J.; Moghul, I.; Withington, L.; Blanco-Kelly, F.; Vulliamy, T.; Wong, T. L.; Murphy, C.; Cipriani, V.; Fiorentino, A.; Arno, G.; Greene, D.; Jacobsen, J. O.; Clark, T.; Gregory, D. S.

    2017-01-01

    SUMMARY: Phenopolis is an open-source web server providing an intuitive interface to genetic and phenotypic databases. It integrates analysis tools such as variant filtering and gene prioritization based on phenotype. The Phenopolis platform will accelerate clinical diagnosis, gene discovery and encourage wider adoption of the Human Phenotype Ontology in the study of rare genetic diseases. AVAILABILITY AND IMPLEMENTATION: A demo of the website is available at https://phenopolis.github.io. ...

  10. Prevalence of high-risk human papillomavirus and cervical intraepithelial neoplasias in a previously unscreened population--a pooled analysis from three studies.

    Science.gov (United States)

    Basu, Partha; Mittal, Srabani; Bhaumik, Suchismita; Mandal, Shyam Sunder; Samaddar, Anusree; Ray, Chinmayi; Siddiqi, Maqsood; Biswas, Jaydip; Sankaranarayanan, Rengaswamy

    2013-04-01

    Population prevalence of human papillomavirus (HPV) and cervical intraepithelial neoplasias (CIN) is an important indicator to judge the disease burden in the community, to monitor the performance of cervical cancer screening program and to assess the impact of HPV vaccination program. India being a country without any cervical cancer screening program has no published data on the population prevalence of CIN and only a few large community-based studies to report the high-risk HPV prevalence. The objective of our study was to study HPV and CIN prevalence in a previously unscreened population. We pooled together the results of three research studies originally designed to assess the performance of visual inspection after acetic acid application and Hybrid Capture 2 (HC 2). Nearly 60% of the screened women had colposcopy irrespective of their screening test results. The diagnosis and grading of cervical neoplasias were based on histology. The age standardized prevalence of HPV by HC 2 test was 6.0%. Age-adjusted prevalence of CIN1 and CIN2 was 2.3% and 0.5%, respectively. The age-adjusted prevalence of CIN3 was 0.4% and that of invasive cancer was 0.2%. The prevalence of high-risk HPV was relatively low in the population we studied, which is reflected in the low prevalence of high-grade CIN. The prevalence of CIN3 remained constant across age groups due to absence of screening. Copyright © 2012 UICC.

  11. GENETIC STABILITY ANALYSIS OF RB GENE IN GENETICALLY MODIFIED POTATO LINES TOLERANT TO Phytophthora infestans

    Directory of Open Access Journals (Sweden)

    Edy Listanto

    2016-02-01

    Full Text Available Development of potato cultivars with high levels of broad spectrum resistance is a key long-term management strategy against late blight disease caused by Phytophthora infestans. Six progeny lines of hybridization between transgenic potato Katahdin SP951 with non-transgenic Granola and Atlantic were selected based on agronomical characteristics and resistance to late blight disease. The study aimed to analyze the number of insertions and stability of inserted RB gene in the transgenic potato lines. The research was carried out through plant DNA extraction, southern blot analysis and polymerase chain reaction (PCR. Southern blot analysis was used to detect the number of inserts integrated into potato genome, while PCR analysis was used to detect stability of RB gene from generation to generation. The results showed that the progenies obtained from hybridization between Atlantic and transgenic Katahdin SP951 (lines No. 20 and 27 and between Granola and transgenic Katahdin SP951 (line No. 69 contained one copy number of RB gene, according to the probing of nptII. The result is similar to that of inserted RB gene found in the parental transgenic Katahdin SP951. The presence of RB gene in four different generations (G0, G1, G2 and G3 showed stable integration of the gene into the plant genome. The single copy number of RB gene will repress the occurrence of silencing gene expression. The stability analysis of RB gene can determine that the gene is still present in plant genome after several generations.

  12. Analysis of Shrinkage on Thick Plate Part using Genetic Algorithm

    Directory of Open Access Journals (Sweden)

    Najihah S.N.

    2016-01-01

    Full Text Available Injection moulding is the most widely used processes in manufacturing plastic products. Since the quality of injection improves plastic parts are mostly influenced by process conditions, the method to determine the optimum process conditions becomes the key to improving the part quality. This paper presents a systematic methodology to analyse the shrinkage of the thick plate part during the injection moulding process. Genetic Algorithm (GA method was proposed to optimise the process parameters that would result in optimal solutions of optimisation goals. Using the GA, the shrinkage of the thick plate part was improved by 39.1% in parallel direction and 17.21% in the normal direction of melt flow.

  13. Metabolic Engineering: Techniques for analysis of targets for genetic manipulations

    DEFF Research Database (Denmark)

    Nielsen, Jens Bredal

    1998-01-01

    enzymes. Despite the prospect of obtaining major improvement through metabolic engineering, this approach is, however, not expected to completely replace the classical approach to strain improvement-random mutagenesis followed by screening. Identification of the optimal genetic changes for improvement......Metabolic engineering has been defined as the purposeful modification of intermediary metabolism using recombinant DNA techniques. With this definition metabolic engineering includes: (1) inserting new pathways in microorganisms with the aim of producing novel metabolites, e.g., production...... of polyketides by Streptomyces; (2) production of heterologous peptides, e.g., production of human insulin, erythropoitin, and tPA; and (3) improvement of both new and existing processes, e.g., production of antibiotics and industrial enzymes. Metabolic engineering is a multidisciplinary approach, which involves...

  14. Genetic analysis of anther culture response in maize.

    Science.gov (United States)

    Petolino, J F; Thompson, S A

    1987-06-01

    Response frequencies in maize (Zea mays L.) anthers cultured in vitro were examined in a diallel set of crosses among four commercial inbred lines. Significant differences among the genotypes were observed, with the crosses H99xFR16 and Pa91xFR16 displaying the highest responses. General (GCA) and specific (SCA) combining ability mean squares were calculated and determined to be highly significant. GCA effects among the parental lines were highest for FR16 and lowest for LH38. Nongenotypic, plant-toplant differences were also found to make a significant contribution to the overall variation observed. The results from this study indicate that parents which give rise to highly responsive hybrids can be identified and that genetic improvement is possible through selection.

  15. Sucrose accumulation in watermelon fruits: genetic variation and biochemical analysis.

    Science.gov (United States)

    Yativ, Merav; Harary, Idan; Wolf, Shmuel

    2010-05-15

    Sugar accumulation, the key process determining fruit quality, is controlled by both the translocation of sugars and their metabolism in developing fruits. Sugar composition in watermelon, as in all cucurbit fruits, includes sucrose, fructose and glucose. The proportions of these three sugars are determined primarily by three enzyme families: invertases, sucrose synthases (SuSys) and sucrose phosphate synthases (SPSs). The goal of the present research was to explore the process of sugar metabolism in watermelon fruits. Crosses between the domestic watermelon (Citrullus lanatus) and three wild species provided a wide germplasm to explore genetic variability in sugar composition and metabolism. This survey demonstrated great genetic variability in sugar content and in the proportions of sucrose, glucose and fructose in mature fruits. Genotypes accumulating high and low percentage of sucrose provided an experimental system to study sugar metabolism in developing fruits. Insoluble invertase activity was high and constant throughout fruit development in control lines and in genotypes accumulating low levels of sucrose, while in genotypes accumulating high levels of sucrose, activity declined sharply 4 weeks after pollination. Soluble acid invertase activity was significantly lower in genotypes accumulating high levels of sucrose than in low-sucrose-accumulating genotypes. Conversely, activities of SuSy and SPS were higher in the high-sucrose-accumulating genotypes. The present results establish that, within the genus Citrullus, there are genotypes that accumulate a high percentage of sucrose in the fruit, while others accumulate high percentages of glucose and fructose. The significant negative correlation between insoluble invertase activity and fruit sucrose level suggests that sucrose accumulation is affected by both phloem unloading and sugar metabolism. (c) 2009 Elsevier GmbH. All rights reserved.

  16. Wolf population genetics in Europe: a systematic review, meta-analysis and suggestions for conservation and management.

    Science.gov (United States)

    Hindrikson, Maris; Remm, Jaanus; Pilot, Malgorzata; Godinho, Raquel; Stronen, Astrid Vik; Baltrūnaité, Laima; Czarnomska, Sylwia D; Leonard, Jennifer A; Randi, Ettore; Nowak, Carsten; Åkesson, Mikael; López-Bao, José Vicente; Álvares, Francisco; Llaneza, Luis; Echegaray, Jorge; Vilà, Carles; Ozolins, Janis; Rungis, Dainis; Aspi, Jouni; Paule, Ladislav; Skrbinšek, Tomaž; Saarma, Urmas

    2017-08-01

    The grey wolf (Canis lupus) is an iconic large carnivore that has increasingly been recognized as an apex predator with intrinsic value and a keystone species. However, wolves have also long represented a primary source of human-carnivore conflict, which has led to long-term persecution of wolves, resulting in a significant decrease in their numbers, genetic diversity and gene flow between populations. For more effective protection and management of wolf populations in Europe, robust scientific evidence is crucial. This review serves as an analytical summary of the main findings from wolf population genetic studies in Europe, covering major studies from the 'pre-genomic era' and the first insights of the 'genomics era'. We analyse, summarize and discuss findings derived from analyses of three compartments of the mammalian genome with different inheritance modes: maternal (mitochondrial DNA), paternal (Y chromosome) and biparental [autosomal microsatellites and single nucleotide polymorphisms (SNPs)]. To describe large-scale trends and patterns of genetic variation in European wolf populations, we conducted a meta-analysis based on the results of previous microsatellite studies and also included new data, covering all 19 European countries for which wolf genetic information is available: Norway, Sweden, Finland, Estonia, Latvia, Lithuania, Poland, Czech Republic, Slovakia, Germany, Belarus, Russia, Italy, Croatia, Bulgaria, Bosnia and Herzegovina, Greece, Spain and Portugal. We compared different indices of genetic diversity in wolf populations and found a significant spatial trend in heterozygosity across Europe from south-west (lowest genetic diversity) to north-east (highest). The range of spatial autocorrelation calculated on the basis of three characteristics of genetic diversity was 650-850 km, suggesting that the genetic diversity of a given wolf population can be influenced by populations up to 850 km away. As an important outcome of this synthesis, we

  17. Genetic stability evaluation of quercus suber l. somatic embryogenesis by rapd analysis

    International Nuclear Information System (INIS)

    Fernandes, P.; Costa, A.; Rocha, A.C.C.; Santos, C.

    2011-01-01

    A reliable protocol for adult Quercus suber L. somatic embryogenesis (SE) was developed recently. To evaluate the potential use of this protocol in cork oak forest breeding programs, it is essential to guarantee somatic embryos/emblings genetic stability. Random Amplification of Polymorphic DNA (RAPD) is currently used to assess somaclonal variation providing information on genetic variability of the micropropagation process. In this work, SE was induced from adult trees by growing leaf explants on MS medium supplemented with 2,4-D and zeatin. Embling conversion took place on MS medium without growth regulators. DNA from donor tree, somatic embryos and emblings was used to assess genetic variability by RAPD fingerprinting. Fourteen primers produced 165 genetic loci with high quality and reproducibility. Despite somatic embryos originated some poor quality PCR-profiles, replicable and excellent fingerprints were obtained for both donor plant and embling. Results presented no differences among regenerated emblings and donor plant. Hence, the SE protocol used did not induce, up to moment, any genetic variability, confirming data previously obtained with other molecular/genetic techniques, supporting that this protocol may be used to provide true-to-type plants from important forestry species. (author)

  18. Genetic diversity analysis of five cattle breeds native to China using ...

    Indian Academy of Sciences (India)

    Unknown

    Animal Diversity Information System (http://www.fao.org/ dad-is). Microsatellite analysis. Ten microsatellite markers for the genetic diversity study in cattle were used for the analysis of five native Chinese cattle breeds. The polymerase chain reaction (PCR) was accomplished in a total volume of 25 µl containing 50 ng.

  19. Genetic analysis and location of gene for resistance to stripe rust in ...

    Indian Academy of Sciences (India)

    Bulked segregant analysis (BSA) and F2 segregation analysis were used for detecting polymorphic primers to locate the gene. The resistance of the NIL Taichung 29*6/Strubes Dickkopf to CYR26 was controlled by a single dominant gene, named YrSD. The primer pair Xbarc59 on 5B was linked to YrSD and the genetic ...

  20. Analysis of the genetic diversity of selected East African sweet potato

    African Journals Online (AJOL)

    Aghomotsegin

    Key words: Sweet potato, cluster analysis, genetic diversity, principal component analysis, Simple Sequence ... Author(s) agree that this article remains permanently open access under the terms of the Creative Commons Attribution License 4.0 ..... Karuri HW, Ateka EM, Amata R, Nyende AB, Muigai AWT, Mwasame E,.

  1. Genetic programming system for building block analysis to enhance data analysis and data mining techniques

    Science.gov (United States)

    Eick, Christoph F.; Sanz, Walter D.; Zhang, Ruijian

    1999-02-01

    Recently, many computerized data mining tools and environments have been proposed for finding interesting patterns in large data collections. These tools employ techniques that originate from research in various areas, such as machine learning, statistical data analysis, and visualization. Each of these techniques makes assumptions concerning the composition of the data collection to be analyzed. If the particular data collection does not meet these assumptions well, the technique usually performs poorly. For example, decision tree tools, such as C4.5, rely on rectangular approximations, which do not perform well if the boundaries between different classes have other shapes, such as a 45 degree line or elliptical shapes. However, if we could find a transformation f that transforms the original attribute space, in which class boundaries are more, better rectangular approximations could be obtained. In this paper, we address the problem of finding such transformations f. We describe the features of the tool, WOLS, whose goal is the discovery of ingredients for such transformation functions f, which we call building blocks. The tool employs genetic programming and symbolic regression for this purpose. We also present and discuss the results of case studies, using the building block analysis tool, in the areas of decision tree learning and regression analysis.

  2. Radiological and genetic analysis of a Late Iron Age mummy from the Tuli Block, Botswana

    Directory of Open Access Journals (Sweden)

    Frank J. Rühli

    2016-02-01

    Full Text Available Mummified human remains are valuable sources of information on past populations. Here we report on the radiological and molecular findings of a partially mummified individual found in northern Botswana. This desiccated mummy from the Tuli region is the first to have been reported from this region. The remains were those of an older male adult of African origin. He was interred in a tightly flexed position and wrapped in an animal skin. Computerised tomography (CT scanning revealed that none of the internal organs was preserved. Multiple post-mortem alterations are seen, but apart from some degenerative changes of the lower vertebral column, the axial skeleton has remained intact. The advanced osteophytosis suggests an older age than what was previously estimated. The aDNA analysis confirms Sotho-Tswana and possibly Khoesan genetic relatedness, as could be expected from individuals from that region. These results represent one of the first CT scans of a mummified individual from southern Africa, and also the first successful aDNA extraction from such remains.

  3. Genetic analysis of seedling resistance to crown rust in five diploid oat (Avena strigosa) accessions.

    Science.gov (United States)

    Cabral, A L; Park, R F

    2016-02-01

    Crown rust, caused by Puccinia coronata Corda f. sp. avenae Eriks., is a serious menace in oats, for which resistance is an effective means of control. Wild diploid oat accessions are a source of novel resistances that first need to be characterised prior to introgression into locally adapted oat cultivars. A genetic analysis of resistance to crown rust was carried out in three diverse diploid oat accessions (CIav6956, CIav9020, PI292226) and two cultivars (Saia and Glabrota) of A. strigosa. A single major gene conditioning resistance to Australian crown rust pathotype (Pt) 0000-2 was identified in each of the three accessions. Allelism tests suggested that these genes are either the same, allelic, or tightly linked with less than 1 % recombination. Similarly, a single gene was identified in Glabrota, and possibly two genes in Saia; both cultivars previously reported to carry two and three crown rust resistance genes, respectively. The identified seedling resistance genes could be deployed in combination with other resistance gene(s) to enhance durability of resistance to crown rust in hexaploid oat. Current diploid and hexaploid linkage maps and molecular anchor markers (simple sequence repeat [SSR] and diversity array technology [DArT] markers) should facilitate their mapping and introgression into hexaploid oat.

  4. Genetic analysis of the CHD7 gene in Korean patients with CHARGE syndrome.

    Science.gov (United States)

    Cho, Hyun-Ju; Song, Mee Hyun; Choi, Soo-Young; Kim, Jeongho; Lee, Jinwook; Kim, Un-Kyung; Bok, Jinwoong; Choi, Jae Young

    2013-04-01

    CHARGE syndrome is an autosomal dominant congenital disorder known to be caused by the haploinsufficiency of the CHD7 gene. Heterozygous mutations in the CHD7 gene have been identified in approximately 60-70% of patients clinically diagnosed with CHARGE syndrome. Although there have been many reports on the mutational spectrum of the CHD7 gene in patients with CHARGE syndrome worldwide, little is known about this syndrome in the Korean population. In this study, three Korean patients with CHARGE syndrome including one patient with Patau syndrome were evaluated for genetic analysis of the CHD7 gene using direct sequencing of all 38 exons and the flanking intronic regions. One nonsense and two novel missense mutations were identified in the CHD7 gene. Clinical symptoms caused by the missense mutations were much milder compared to the nonsense mutation, confirming the previously determined genotype-phenotype correlation in CHARGE syndrome. Our study demonstrates the importance of mutational screening of CHD7 in patients who have been diagnosed with other syndromes but display clinical features of CHARGE syndrome. Copyright © 2013 Elsevier B.V. All rights reserved.

  5. Structural analysis of eight novel and 112 previously reported missense mutations in the interactive FXI mutation database reveals new insight on FXI deficiency.

    Science.gov (United States)

    Saunders, Rebecca E; Shiltagh, Nuha; Gomez, Keith; Mellars, Gillian; Cooper, Carolyn; Perry, David J; Tuddenham, Edward G; Perkins, Stephen J

    2009-08-01

    Factor XI (FXI) functions in blood coagulation. FXI is composed of four apple (Ap) domains and a serine protease (SP) domain. Deficiency of FXI leads to an injury-related bleeding disorder, which is remarkable for the lack of correlation between bleeding symptoms and FXI coagulant activity (FXI:C). The number of mutations previously reported in our interactive web database (http://www.FactorXI.org) is now significantly increased to 183 through our new patient studies and from literature surveys. Eight novel missense mutations give a total of 120 throughout the FXI gene (F11). The most abundant defects in FXI are revealed to be those from low-protein plasma levels (Type I: CRM-) that originate from protein misfolding, rather than from functional defects (Type II: CRM+). A total of 70 Ap missense mutations were analysed using a consensus Ap domain structure generated from the FXI dimer crystal structure. This showed that all parts of the Ap domain were affected. The 47 SP missense mutations were also distributed throughout the SP domain structure. The periphery of the Ap beta-sheet structure is sensitive to structural perturbation caused by residue changes throughout the Ap domain, yet this beta-sheet is crucial for FXI dimer formation. Residues located at the Ap4:Ap4 interface in the dimer are much less directly involved. We conclude that the abundance of Type I defects in FXI results from the sensitivity of the Ap domain folding to residue changes within this, and discuss how structural knowledge of the mutations improves our understanding of FXI deficiencies.

  6. An analysis of discrepancies between United Kingdom cancer research funding and societal burden and a comparison to previous and United States values.

    Science.gov (United States)

    Carter, Ashley J R; Delarosa, Beverly; Hur, Hannah

    2015-11-02

    Ideally, the allocation of research funding for each specific type of cancer should be proportional to its societal burden. This burden can be estimated with the metric 'years of life lost' (YLL), which combines overall mortality and age at death. Using United Kingdom data from 2010, we compared research funding from the National Cancer Research Institute to this YLL burden metric for 26 types of cancers in order to identify the discrepancies between cancer research funding allocation and societal burden. We also compared these values to United States data from 2010 and United Kingdom data published in 2005. Our study revealed a number of discrepancies between cancer research funding and burden. Some cancers are funded at levels far higher than their relative burden suggests (testicular, leukaemia, Hodgkin's lymphoma, breast, cervical, ovarian, prostate) while other cancers appear under-funded (gallbladder, lung, nasopharyngeal, intestine, stomach, pancreatic, thyroid, oesophageal, liver, kidney, bladder, and brain/central nervous system). United Kingdom funding patterns over the past decade have generally moved to increase funding to previously under-funded cancers with one notable exception showing a converse trend (breast cancer). The broad relationship between United Kingdom and United States funding patterns is similar with a few exceptions (e.g. leukaemia, Hodgkin's lymphoma, prostate, testicular cancer). There are discrepancies between cancer research funding allocation and societal burden in the United Kingdom. These discrepancies are broadly similar in both the United Kingdom and the United States and, while they appear to be improving, this is not consistent across all types of cancer.

  7. Cross-Disorder Genetic Analysis of Tic Disorders, Obsessive-Compulsive, and Hoarding Symptoms.

    Science.gov (United States)

    Zilhão, Nuno R; Smit, Dirk J; Boomsma, Dorret I; Cath, Danielle C

    2016-01-01

    Hoarding, obsessive-compulsive disorder (OCD), and Tourette's disorder (TD) are psychiatric disorders that share symptom overlap, which might partly be the result of shared genetic variation. Population-based twin studies have found significant genetic correlations between hoarding and OCD symptoms, with genetic correlations varying between 0.1 and 0.45. For tic disorders, studies examining these correlations are lacking. Other lines of research, including clinical samples and GWAS or CNV data to explore genetic relationships between tic disorders and OCD, have only found very modest if any shared genetic variation. Our aim was to extend current knowledge on the genetic structure underlying hoarding, OC symptoms (OCS), and lifetime tic symptoms and, in a trivariate analysis, assess the degree of common and unique genetic factors contributing to the etiology of these disorders. Data have been gathered from participants in the Netherlands Twin Register comprising a total of 5293 individuals from a sample of adult monozygotic (n = 2460) and dizygotic (n = 2833) twin pairs (mean age 33.61 years). The data on Hoarding, OCS, and tic symptoms were simultaneously analyzed in Mplus. A liability threshold model was fitted to the twin data, analyzing heritability of phenotypes and of their comorbidity. Following the criteria for a probable clinical diagnosis in all phenotypes, 6.8% of participants had a diagnosis of probable hoarding disorder (HD), 6.3% of OCS, and 12.8% of any probable lifetime tic disorder. Genetic factors explained 50.4, 70.1, and 61.1% of the phenotypic covariance between hoarding-OCS, hoarding-tics, and OCS-tics, respectively. Substantial genetic correlations were observed between hoarding and OCS (0.41), hoarding and tics (0.35), and between OCS and tics (0.37). These results support the contribution of genetic factors in the development of these disorders and their comorbidity. Furthermore, tics were mostly influenced by specific

  8. Clinical features and genetic analysis of 7 patients with late-onset glycogen storage disease typeⅡ

    Directory of Open Access Journals (Sweden)

    Juan YANG

    2014-05-01

    Full Text Available Objective In order to make a well understanding on glycogen storage disease typeⅡ (GSDⅡ, this paper explored clinical features and genetic analysis of 7 patients with late-onset glycogen storage disease typeⅡ.  Methods Clinical data of 7 patients with late-onset glycogen storage disease type Ⅱ were collected and acid α-glucosidase (GAA gene sequencing was performed.  Results Seven patients who belong to 4 families were at the age of 13-31 years old. The first symptom occurred at 6-17 years old, and the age at first and definitive diagnosis was 12-29 and 12-30 years old, respectively. The initial symptoms were mostly related to limb girdle muscular atrophy and weakness. The GAA activity ranged from 0 to 5.27 nmol/(mg·h. Sequencing analysis revealed 14 sequence variants, including 2 novel mutations (Q81X and c.1355_1356delC, 2 pseudodeficiency alleles (G576S and E689K, 8 polymorphic loci, and 2 sequence variants previously related with glycogen storage disease type Ⅱ pathogenesis (W746C and D645E.  Conclusions Due to the apparently diagnostic delay, prognosis of patients with glycogen storage disease type Ⅱ could be improved by increasing the clinician's awareness of the disease. It is essential to combine clinical history with GAA activity and GAA gene analysis when we make a definitive diagnosis of glycogen storage disease type Ⅱ. Though siblings share the same set of GAA mutations, the phenotype regarding the course and severity of disease could vary substantially. doi: 10.3969/j.issn.1672-6731.2014.05.008

  9. Shortest-path network analysis is a useful approach toward identifying genetic determinants of longevity.

    Directory of Open Access Journals (Sweden)

    J R Managbanag

    Full Text Available BACKGROUND: Identification of genes that modulate longevity is a major focus of aging-related research and an area of intense public interest. In addition to facilitating an improved understanding of the basic mechanisms of aging, such genes represent potential targets for therapeutic intervention in multiple age-associated diseases, including cancer, heart disease, diabetes, and neurodegenerative disorders. To date, however, targeted efforts at identifying longevity-associated genes have been limited by a lack of predictive power, and useful algorithms for candidate gene-identification have also been lacking. METHODOLOGY/PRINCIPAL FINDINGS: We have utilized a shortest-path network analysis to identify novel genes that modulate longevity in Saccharomyces cerevisiae. Based on a set of previously reported genes associated with increased life span, we applied a shortest-path network algorithm to a pre-existing protein-protein interaction dataset in order to construct a shortest-path longevity network. To validate this network, the replicative aging potential of 88 single-gene deletion strains corresponding to predicted components of the shortest-path longevity network was determined. Here we report that the single-gene deletion strains identified by our shortest-path longevity analysis are significantly enriched for mutations conferring either increased or decreased replicative life span, relative to a randomly selected set of 564 single-gene deletion strains or to the current data set available for the entire haploid deletion collection. Further, we report the identification of previously unknown longevity genes, several of which function in a conserved longevity pathway believed to mediate life span extension in response to dietary restriction. CONCLUSIONS/SIGNIFICANCE: This work demonstrates that shortest-path network analysis is a useful approach toward identifying genetic determinants of longevity and represents the first application of

  10. Genetic analysis shows that morphology alone cannot distinguish asian carp eggs from those of other cyprinid species

    Science.gov (United States)

    Larson, James H.; McCalla, Sunnie; Chapman, Duane C.; Rees, Christopher B.; Knights, Brent C.; Vallazza, Jon; George, Amy E.; Richardson, William B.; Amberg, Jon

    2016-01-01

    Fish eggs and embryos (hereafter collectively referred to as “eggs”) were collected in the upper Mississippi River main stem (~300 km upstream of previously reported spawning by invasive Asian carp) during summer 2013. Based on previously published morphological characteristics, the eggs were identified as belonging to Asian carp. A subsample of the eggs was subsequently analyzed by using molecular methods to determine species identity. Genetic identification using the cytochrome-c oxidase 1 gene was attempted for a total of 41 eggs. Due to the preservation technique used (formalin) and the resulting DNA degradation, sequences were recovered from only 17 individual eggs. In all 17 cases, cyprinids other than Asian carp (usually Notropis sp.) were identified as the most likely species. In previously published reports, a key characteristic that distinguished Asian carp eggs from those of other cyprinids was size: Asian carp eggs exhibited diameters ranging from 4.0 to 6.0 mm and were thought to be much larger than the otherwise similar eggs of native species. Eggs from endemic cyprinids were believed to rarely reach 3.0 mm and had not been observed to exceed 3.3 mm. However, many of the eggs that were genetically identified as originating from native cyprinids were as large as 4.0 mm in diameter (at early developmental stages) and were therefore large enough to over- lap with the lower end of the size range observed for Asian carp eggs. Researchers studying the egg stages of Asian carp and other cyprinids should plan on preserving subsets of eggs for genetic analysis to confirm morphological identifications.

  11. [Lower uterine segment thickness measurement in pregnant women with previous caesarean section: intra- and interobserver reliability analysis using bi- and tridimensional ultrasonography].

    Science.gov (United States)

    Barra, Daniela de Abreu; Martins, Wellington de Paula; Gallarretta, Francisco Maximilliano; Nastri, Carolina Oliveira; Nicolau, Luis Guilherme; Mauad Filho, Francisco

    2008-03-01

    to compare the intra and interobserver reproducibility of the total thickness measurement of the inferior uterine segment (IUS), through the abdominal route, and of the muscle layer measurement, through the vaginal route, using bi and tridimensional ultrasonography. the IUS thickness measurement of 30 women, between the 36th and 39th weeks of gestation with previous caesarean section, done by two observers, was studied. Abdominal ultrasonography with the patient in both supine and lithotomy position was performed. In the sagittal section, the IUS was identified and four bidimensional images and two tridimensional blocks of the total thickness were collected through the abdominal route, and the same for the muscle layer, through the vaginal route. Tridimensional acquisitions were manipulated in the multiplanar mode. The time was measured with a chronometer. Reproducibility was evaluated by the computation of the absolute difference between measurements, the ratio of differences smaller than 1 mm, the intraclass coefficient (ICC), and the Bland and Altman's concordance limits. the average bidimensional measurement of IUS thickness was 7.4 mm through the abdominal and 2.7 mm through the vaginal route, and the tridimensional measurement was 6.9 mm through the abdominal and 5.1 mm through the vaginal route. Intra- and interobserver reproducibility of vaginal versus abdominal route: smaller absolute difference (0.2-0.4 mm versus 0.8-1.5 mm), greater ratio of differences (85.8-97.8% versus 48.7-72,8%), with p0.05[A1] and similar lower concordance limits (-38 to 3.4 versus -3.6 to 4 mm) for tridimensional ultrasonography and ICC (0.6-0.9 versus 0.7-0.9). from the above, we came to the conclusion that the measurement of the IUS muscle layer, through the vaginal route using tridimensional ultrasonography is more reproducible. Nevertheless, our results do not indicate that this measurement shows any clinical evidence to predict uterine tear, as that was not the aim of this

  12. Analysis of genetic diversity of southern Spain fig tree (Ficus carica L.) and reference materials as a tool for breeding and conservation.

    Science.gov (United States)

    Perez-Jiménez, M; López, B; Dorado, G; Pujadas-Salvá, A; Guzmán, G; Hernandez, P

    2012-06-01

    The common fig tree (Ficus carica L.) is a Mediterranean crop with problematic cultivar identification. The recovery and conservation of possible local varieties for ecological production requires the previous genetic characterization of the available germplasm. In this context, 42 lines corresponding to 12 local varieties and two caprifigs, in addition to 15 reference samples have been fingerprinted using 21 SSR markers. A total of 77 alleles were revealed, detecting a useful level of genetic variability within the local germplasm pools. UPGMA clustering analysis has revealed the genetic structure and relationships among the local and reference germplasm. Eleven of the local varieties could be identified and defined as obtained clusters, showing that SSR analysis is an efficient method to evaluate the Andalusian fig tree diversity for on-farm conservation. © 2012 The Authors.

  13. [Genetic variation and clustal analysis of Trichomonas vaginalis cysteine proteases].

    Science.gov (United States)

    Jia, Wan-Zhong; Li, Zhi; Zhao, Liang; Lun, Zhao-Rong

    2008-06-30

    To clone the genes coding for cysteine proteases (CPs, TvCPs) from Trichomonas vaginalis and to analyze their genetic variations with the related sequences from NCBI database (GenBank) and T. vaginalis Genome Project database from The Institute for Genomic Research (TIGR). TvCP genes were amplified using PCR, and inserted into vector pET28b or pBS-T. The recombinant plasmids were then transformed to Escherichia coli BL21 or Topl0 strain. The recombinant plasmids were used for sequencing. Homologous TvCP genes were blasted based on NCBI GenBank and TIGR T. vaginalis Genome Project database. The sequences of cloned TvCP genes were aligned and clustered by Clustal X (1.83 version) with retrieved sequences. Comparisons of amino acids among cathepsin L-like TvCPs, human L-like cathepsins and papaya papain were performed using DNAstar software, and their phylogenic tree was constructed based on neighbor-joining method using Clustal X. Two TvCP3 clones and one TvCP2 had a high identity of more than 99% with their responding TvCPs. Three clones of TvCP4 genes, GZ-CP4-clone 1-3, belonged to two members of a family showing a high percentage identity of more than 97.5% with the sequences of TvCP4 genes from databases (GenBank and TIGR) both at amino acid and nucleotide levels. Nine homologous TvCP4 pro-enzymes with 304 amino acids and other two members with deletions of N-terminal sequence existed in T. vaginalis sharing a similarity of 62.3-96.7% amino acids, which may evolve by means of gene replication and deletion. TvCP1-4, TvCP12, TvCP25 and CP65 had an identity of 61-88.2% at amino acid levels. So far, all reported sequences of C1 family from T. vaginalis belonged to capanthesin L-like subfamily with the same enzymatic active sites, conserved cysteine residues and similar structural features such as ERFNIN-like motif in pro-enzyme region, suggesting that they might result from gene duplication and mutations. TvCPs belong to cathepsin L-like family with genetic diversity

  14. Analysis of genetic diversity and differentiation of seven stocks of Litopenaeus vannamei using microsatellite markers

    Science.gov (United States)

    Zhang, Kai; Wang, Weiji; Li, Weiya; Zhang, Quanqi; Kong, Jie

    2014-08-01

    Seven microsatellite markers were used to evaluate the genetic diversity and differentiation of seven stocks of Litopenaeus vannamei, which were introduced from Central and South America to China. All seven microsatellite loci were polymorphic, with polymorphism information content ( PIC) values ranging from 0.593 to 0.952. Totally 92 alleles were identified, and the number of alleles ( Na) and effective alleles ( Ne) varied between 4 and 21 and 2.7 and 14.6, respectively. Observed heterozygosity ( H o) values were lower than the expected heterozygosity ( H e) values (0.526-0.754), which indicated that the seven stocks possessed a rich genetic diversity. Thirty-seven tests were detected for reasonable significant deviation from Hardy-Weinberg equilibrium. F is values were positive at five loci, suggesting that there was a relatively high degree of inbreeding within stocks. Pairwise F st values ranged from 0.0225 to 0.151, and most of the stock pairs were moderately differentiated. Genetic distance and cluster analysis using UPGMA revealed a close genetic relationship of L. vannamei between Pop2 and Pop3. AMOVA indicated that the genetic variation among stocks (11.3%) was much lower than that within stocks (88.7%). Although the seven stocks had a certain degree of genetic differentiation and a rich genetic diversity, there is an increasing risk of decreased performance due to inbreeding in subsequent generations.

  15. Genetic diversity in cultivated carioca common beans based on molecular marker analysis

    Directory of Open Access Journals (Sweden)

    Juliana Morini Küpper Cardoso Perseguini

    2011-01-01

    Full Text Available A wide array of molecular markers has been used to investigate the genetic diversity among common bean species. However, the best combination of markers for studying such diversity among common bean cultivars has yet to be determined. Few reports have examined the genetic diversity of the carioca bean, commercially one of the most important common beans in Brazil. In this study, we examined the usefulness of two molecular marker systems (simple sequence repeats - SSRs and amplified fragment length polymorphisms - AFLPs for assessing the genetic diversity of carioca beans. The amount of information provided by Roger's modified genetic distance was used to analyze SSR data and Jaccards similarity coefficient was used for AFLP data. Seventy SSRs were polymorphic and 20 AFLP primer combinations produced 635 polymorphic bands. Molecular analysis showed that carioca genotypes were quite diverse. AFLPs revealed greater genetic differentiation and variation within the carioca genotypes (Gst = 98% and Fst = 0.83, respectively than SSRs and provided better resolution for clustering the carioca genotypes. SSRs and AFLPs were both suitable for assessing the genetic diversity of Brazilian carioca genotypes since the number of markers used in each system provided a low coefficient of variation. However, fingerprint profiles were generated faster with AFLPs, making them a better choice for assessing genetic diversity in the carioca germplasm.

  16. Relationship of genetic diversity and niche centrality: a survey and analysis.

    Science.gov (United States)

    Lira-Noriega, Andrés; Manthey, Joseph D

    2014-04-01

    The distribution of genetic diversity within and among populations in relation to species' geographic ranges is important to understanding processes of evolution, speciation, and biogeography. One hypothesis predicts that natural populations at geographic range margins will have lower genetic diversity relative to those located centrally in species' distributions owing to a link between geographic and environmental marginality; alternatively, genetic variation may be unrelated with geographic marginality via decoupling of geographic and environmental marginality. We investigate the predictivity of geographic patterns of genetic variation based on geographic and environmental marginality using published genetic diversity data for 40 species (insects, plants, birds, mammals, worms). Only about half of species showed positive relationships between geographic and environmental marginality. Three analyses (sign test, multiple linear regression, and meta-analysis of correlation effect sizes) showed a negative relationship between genetic diversity and distance to environmental niche centroid, but no consistent relationship of genetic diversity with distance to geographic range center. © 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.

  17. The genetic diversity of the mangrove kandelia obovata in China revealed by ISSR analysis

    International Nuclear Information System (INIS)

    Chen, Shao-Bo; Ding, When-Young; Qiu, Jia-Biao; Wang, Guang-Yin; Zhou, Zhi-Min; Chen- Jiao-Fei; Ai, Wewi-ming; Wang, Cheng-Yi; Xie, Qi-Lang

    2010-01-01

    The genetic diversity of 7 populations of Kandelia obovata in China was characterized using inter simple sequence repeats (ISSR) technique. A total of 50 primers were screened, of which 9 polymorphic and informative patterns were selected to determine genetic relationships. ISSR amplification was conducted on 140 individuals from 7 populations, and 88 polymorphic loci were detected from 106 total loci. The total percentage of polymorphic loci (PPL) was 83.02%. The percentage of PPL at the population level ranged from 32.08% to 47.17%, with an average of 39.89%. Nei's gene diversity (H) and Shannon's information index (I) of K. obovata at the species level were 0.3631 and 0.5203, respectively. The genetic differentiation coefficient (Gst) among populations was 0.5548. Among populations component accounted for 55.48% of the total variation, whereas the within populations component accounted for 44.52%, suggesting that genetic differentiation among K. obovata populations was relatively high. The gene flow among populations was 0.4012, indicating that gene flow was low among geographically diverse populations of K. obovata. The results of the genetic diversity and cluster analysis suggest that geographical isolation of K. obovata populations mainly results in low gene flow and random genetic drift, leading to genetic differentiation. (author)

  18. A theoretical analysis of population genetics of plants on restored habitats

    Energy Technology Data Exchange (ETDEWEB)

    Bogoliubov, A.G. [Botanical Institute, Russian Academy of Science, St. Petersburg (Russian Federation); Loehle, C. [Argonne National Lab., IL (United States)

    1995-02-01

    Seed and propagules used for habitat restoration are not likely to be closely adapted to local site conditions. Rapid changes of genotypes frequencies on local microsites and/or microevolution would allow plants to become better adapted to a site. These same factors would help to maintain genetic diversity and ensure the survival of small endangered populations. We used population genetics models to examine the selection of genotypes during establishment on restored sites. Vegetative spread was shown to affect selection and significantly reduce genetic diversity. To study general microevolution, we linked a model of resource usage with a genetics model and analyzed competition between genotypes. A complex suite of feasible ecogenetic states was shown to result. The state actually resulting would depend strongly on initial conditions. This analysis indicated that genetic structure can vary locally and can produce overall genetic variability that is not simply the result of microsite adaptations. For restoration activities, the implication is that small differences in seed source could lead to large differences in local genetic structure after selection.

  19. A theoretical analysis of population genetics of plants on restored habitats

    Energy Technology Data Exchange (ETDEWEB)

    Bogoliubov, A.G. [Russian Academy of Science, St. Petersburg (Russian Federation). Botanical Inst.; Loehle, C. [Argonne National Lab., IL (United States). Environmental Research Div.

    1997-07-01

    Seed and propagules used for habitat restoration are not likely to be closely adapted to local site conditions. Rapid changes of genotypes frequencies on local microsites and/or microevolution would allow plants to become better adapted to a site. These same factors would help to maintain genetic diversity and ensure the survival of small endangered populations. The authors used population genetics models to examine the selection of genotypes during establishment on restored sites. Vegetative spread was shown to affect selection and significantly reduce genetic diversity. To study general microevolution, the authors linked a model of resource usage with a genetics model and analyzed competition between genotypes. A complex suite of feasible ecogenetic states was shown to result. The state actually resulting would depend strongly on initial conditions. This analysis indicated that genetic structure can vary locally and can produce overall genetic variability that is not simply the result of microsite adaptations. For restoration activities, the implication is that small differences in seed source could lead to large differences in local genetic structure after selection.

  20. Genetic analysis of albuminuria in collaborative cross and multiple mouse intercross populations

    Science.gov (United States)

    Thaisz, Jill; Tsaih, Shirng-Wern; Feng, Minjie; Philip, Vivek M.; Zhang, Yunyu; Yanas, Liane; Sheehan, Susan; Xu, Lingfei; Miller, Darla R.; Paigen, Beverly; Chesler, Elissa J.; Churchill, Gary A.

    2012-01-01

    Albuminuria is an important marker of nephropathy that increases the risk of progressive renal and chronic cardiovascular diseases. The genetic basis of kidney disease is well-established in humans and rodent models, but the causal genes remain to be identified. We applied several genetic strategies to map and refine genetic loci affecting albuminuria in mice and translated the findings to human kidney disease. First, we measured albuminuria in mice from 33 inbred strains, used the data for haplotype association mapping (HAM), and detected 10 genomic regions associated with albuminuria. Second, we performed eight F2 intercrosses between genetically diverse strains to identify six loci underlying albuminuria, each of which was concordant to kidney disease loci in humans. Third, we used the Oak Ridge National Laboratory incipient Collaborative Cross subpopulation to detect an additional novel quantitative trait loci (QTL) underlying albuminuria. We also performed a ninth intercross, between genetically similar strains, that substantially narrowed an albuminuria QTL on Chromosome 17 to a region containing four known genes. Finally, we measured renal gene expression in inbred mice to detect pathways highly correlated with albuminuria. Expression analysis also identified Glcci1, a gene known to affect podocyte structure and function in zebrafish, as a strong candidate gene for the albuminuria QTL on Chromosome 6. Overall, these findings greatly enhance our understanding of the genetic basis of albuminuria in mice and may guide future studies into the genetic basis of kidney disease in humans. PMID:22859403

  1. Genetic diversity of Centella asiatica in China analyzed by inter-simple sequence repeat (ISSR) markers: combination analysis with chemical diversity.

    Science.gov (United States)

    Zhang, Xiao-Gang; Han, Ting; He, Zhi-Gao; Zhang, Qiao-Yan; Zhang, Lei; Rahman, Khalid; Qin, Lu-Ping

    2012-01-01

    Centella asiatica is an important plant species used in traditional Chinese medicine. To help the efficient use and conservation of this species, the genetic diversity of C. asiatica populations in China was investigated using inter-simple sequence repeat (ISSR) markers. Fourteen natural populations comprising 162 individuals were included to estimate genetic diversity. At the species level, genetic diversity was relatively high (P = 66.33%, H = 0.2183, I = 0.3305). At the population level, the genetic diversity of JH (Jinhua, Zhejiang Province, China) and JJ (Jiujiang, Jiangxi Province, China) populations was relatively high (P = 43.88%, 38.78%, H = 0.1610, 0.1301, I = 0.2376, 0.1957, respectively), whereas the genetic diversity of GA (Guang'an, Sichuan Province, China) and EM (E'mei, Sichuan Province, China) was relatively low (P = 10.2%, 5.1%, H = 0.0383, 0.0211, I = 0.0570, 0.0309, respectively). On the basis of Nei's G(st) value, more genetic differentiation among populations was determined (G(st) = 0.6573). In addition, the 14 populations were clustered into four groups in view of abundant ISSR data, which further defined the genetic relationship among populations. Interestingly, the genetic clustering result was similar to previous chemical clustering results based on high-performance liquid chromatography (HPLC) data, which would also classify the 14 populations into four groups. Thus, we combined the clustering results and compared their difference. The combined analysis and genetic diversity data provide a scientific basis for conserving populations of relatively high genetic diversity such as JH and JJ populations and establishing good agricultural practices (GAP) for C. asiatica.

  2. [Spinal muscular atrophy mimicking myotonic dystrophy: a case report and clinical, pathological and genetic analysis].

    Science.gov (United States)

    Luo, Li-xia; Pan, Qian; Xia, Kun; Tang, Bei-sha; Jiang, Hong

    2012-08-01

    To investigate a patient featuring a complex neuromuscular disease phenotype. A comprehensive analysis integrating clinical investigation, electrophysiological testing, pathological analysis and mutation screening was carried out. The patient has presented clinical and pathological manifestations mimicking Duchenne muscular dystrophy. However, genetic analysis has identified no deletion in 21 exons of Dystrophin gene, no pathologic expansion of CTG repeats in DMPK gene or CCTG repeats in ZFN9 gene. Instead, a homozygous deletion of exons 7 and 8 in SMN gene was discovered. A rare case of spinal muscular atrophy (SMA) was verified by genetic diagnosis. SMA is a group of neuromuscular disorders with great phenotypic heterogeneity and sometimes cannot be diagnosed by clinical manifestations, electrophysiological and pathological changes alone. Genetic diagnosis has become indispensable for accurate diagnosis for patients suspected to have the disease.

  3. Molecular genetic analysis of activation-tagged transcription factors thought to be involved in photomorphogenesis

    Energy Technology Data Exchange (ETDEWEB)

    Neff, Michael M.

    2011-06-23

    This is a final report for Department of Energy Grant No. DE-FG02-08ER15927 entitled “Molecular Genetic Analysis of Activation-Tagged Transcription Factors Thought to be Involved in Photomorphogenesis”. Based on our preliminary photobiological and genetic analysis of the sob1-D mutant, we hypothesized that OBP3 is a transcription factor involved in both phytochrome and cryptochrome-mediated signal transduction. In addition, we hypothesized that OBP3 is involved in auxin signaling and root development. Based on our preliminary photobiological and genetic analysis of the sob2-D mutant, we also hypothesized that a related gene, LEP, is involved in hormone signaling and seedling development.

  4. [Genetic monitoring of populations of Matthiola fragrans (Bunge) using RAPD and AFLP analysis].

    Science.gov (United States)

    Khadeeva, N V; Goriunova, S V; Kochumova, A A; Iakovleva, E Iu; Mel'nikova, N V; Zholobova, O O; Korotkov, O I; Kudriavtsev, A M

    2011-01-01

    The possibility of using RAPD and AFLP methods for genetic monitoring of populations of Matthiola fragrans (Bunge), a species included in the Red Book of the USSR, was shown for the first time. An analysis of inter- and intrapopulation and interspecies genome polymorphism was performed. Differences in the genetic structure of Matthiola populations from various geographical collection points were revealed. A simple method of performing RAPD analysis and the great number of unique markers found in each population compared with the AFLP analysis, as well as the good division of populations under statistical treatment, allow us to draw the conclusion that using the RAPD method in genetic monitoring of rare and insufficiently studied species is well founded.

  5. Viral Genetic Linkage Analysis in the Presence of Missing Data.

    Directory of Open Access Journals (Sweden)

    Shelley H Liu

    Full Text Available Analyses of viral genetic linkage can provide insight into HIV transmission dynamics and the impact of prevention interventions. For example, such analyses have the potential to determine whether recently-infected individuals have acquired viruses circulating within or outside a given community. In addition, they have the potential to identify characteristics of chronically infected individuals that make their viruses likely to cluster with others circulating within a community. Such clustering can be related to the potential of such individuals to contribute to the spread of the virus, either directly through transmission to their partners or indirectly through further spread of HIV from those partners. Assessment of the extent to which individual (incident or prevalent viruses are clustered within a community will be biased if only a subset of subjects are observed, especially if that subset is not representative of the entire HIV infected population. To address this concern, we develop a multiple imputation framework in which missing sequences are imputed based on a model for the diversification of viral genomes. The imputation method decreases the bias in clustering that arises from informative missingness. Data from a household survey conducted in a village in Botswana are used to illustrate these methods. We demonstrate that the multiple imputation approach reduces bias in the overall proportion of clustering due to the presence of missing observations.

  6. Functional analysis of the Gonococcal Genetic Island of Neisseria gonorrhoeae.

    Directory of Open Access Journals (Sweden)

    Emilia Pachulec

    Full Text Available Neisseria gonorrhoeae is an obligate human pathogen that is responsible for the sexually-transmitted disease gonorrhea. N. gonorrhoeae encodes a T4SS within the Gonococcal Genetic Island (GGI, which secretes ssDNA directly into the external milieu. Type IV secretion systems (T4SSs play a role in horizontal gene transfer and delivery of effector molecules into target cells. We demonstrate that GGI-like T4SSs are present in other β-proteobacteria, as well as in α- and γ-proteobacteria. Sequence comparison of GGI-like T4SSs reveals that the GGI-like T4SSs form a highly conserved unit that can be found located both on chromosomes and on plasmids. To better understand the mechanism of DNA secretion by N. gonorrhoeae, we performed mutagenesis of all genes encoded within the GGI, and studied the effects of these mutations on DNA secretion. We show that genes required for DNA secretion are encoded within the yaa-atlA and parA-parB regions, while genes encoded in the yfeB-exp1 region could be deleted without any effect on DNA secretion. Genes essential for DNA secretion are encoded within at least four different operons.

  7. Genetic analysis of water-deficit response traits in maize.

    Science.gov (United States)

    Ahmad, M; Saleem, M; Ahsan, M; Ahmad, A

    2016-03-28

    A set of sixty inbred lines of maize (Zea mays L.) were screened in the greenhouse at the seedling stage under both normal and water-deficit conditions. Six water deficit-tolerant inbred lines were selected based on root to shoot ratios. These selected lines were crossed in a diallel pattern. The parental, F1, and reciprocal cross plants were planted in a field under both normal and water-deficit conditions. Normal irrigation was applied to the control set, while the water-deficit set received 50% of normal irrigation levels. Analyses of variance of various morpho-physiological parameters identified significant differences among the selected lines under both conditions, indicating the presence of significant genetic variability. Variance components for general combining ability (GCA), specific combining ability (SCA), and reciprocal effects for all the parameters were estimated to determine the relative importance of additive and non-additive or dominance type of gene action. Variance components for GCA were larger than for SCA indicating the preponderance of additive types of gene action for all the traits under study. Hybrids developed from inbred lines W-10 and W-64SP proved to have the best grain yield under normal and water-deficit conditions. Under water-deficit conditions, the best performing cross was B-34 x W-10. Hence, these inbred lines and the hybrids might be of value in future breeding programs.

  8. Genetic analysis of CHARGE syndrome identifies overlapping molecular biology.

    Science.gov (United States)

    Moccia, Amanda; Srivastava, Anshika; Skidmore, Jennifer M; Bernat, John A; Wheeler, Marsha; Chong, Jessica X; Nickerson, Deborah; Bamshad, Michael; Hefner, Margaret A; Martin, Donna M; Bielas, Stephanie L

    2018-01-04

    PurposeCHARGE syndrome is an autosomal-dominant, multiple congenital anomaly condition characterized by vision and hearing loss, congenital heart disease, and malformations of craniofacial and other structures. Pathogenic variants in CHD7, encoding adenosine triphosphate-dependent chromodomain helicase DNA binding protein 7, are present in the majority of affected individuals. However, no causal variant can be found in 5-30% (depending on the cohort) of individuals with a clinical diagnosis of CHARGE syndrome.MethodsWe performed whole-exome sequencing (WES) on 28 families from which at least one individual presented with features highly suggestive of CHARGE syndrome.ResultsPathogenic variants in CHD7 were present in 15 of 28 individuals (53.6%), whereas 4 (14.3%) individuals had pathogenic variants in other genes (RERE, KMT2D, EP300, or PUF60). A variant of uncertain clinical significance in KDM6A was identified in one (3.5%) individual. The remaining eight (28.6%) individuals were not found to have pathogenic variants by WES.ConclusionThese results demonstrate that the phenotypic features of CHARGE syndrome overlap with multiple other rare single-gene syndromes. Additionally, they implicate a shared molecular pathology that disrupts epigenetic regulation of multiple-organ development.GENETICS in MEDICINE advance online publication, 4 January 2018; doi:10.1038/gim.2017.233.

  9. Differential Analysis of Genetic, Epigenetic, and Cytogenetic Abnormalities in AML

    Directory of Open Access Journals (Sweden)

    Mirazul Islam

    2017-01-01

    Full Text Available Acute myeloid leukemia (AML is a haematological malignancy characterized by the excessive proliferation of immature myeloid cells coupled with impaired differentiation. Many AML cases have been reported without any known cytogenetic abnormalities and carry no mutation in known AML-associated driver genes. In this study, 200 AML cases were selected from a publicly available cohort and differentially analyzed for genetic, epigenetic, and cytogenetic abnormalities. Three genes (FLT3, DNMT3A, and NPMc are found to be predominantly mutated. We identified several aberrations to be associated with genome-wide methylation changes. These include Del (5q, T (15; 17, and NPMc mutations. Four aberrations—Del (5q, T (15; 17, T (9; 22, and T (9; 11—are significantly associated with patient survival. Del (5q-positive patients have an average survival of less than 1 year, whereas T (15; 17-positive patients have a significantly better prognosis. Combining the methylation and mutation data reveals three distinct patient groups and four clusters of genes. We speculate that combined signatures have the better potential to be used for subclassification of AML, complementing cytogenetic signatures. A larger sample cohort and further investigation of the effects observed in this study are required to enable the clinical application of our patient classification aided by DNA methylation.

  10. [Molecular, genetic and physiological analysis of photoinhibition and photosynthetic

    Energy Technology Data Exchange (ETDEWEB)

    1992-01-01

    A major goal of this project is to use a combined molecular genetic, biochemical and physiological approach to understand the relationship between photosynthetic performance and the structure of the multifunctional D1 reaction center protein of Photosystem II encoded by the chloroplast psbA gene. Relative to other chloroplast proteins, turover of D1 is rapid and highly light dependent and de novo synthesis of D1 is required for a plant's recovery from short term exposure to irradiances which induce photoinhibitory damage. These observations have led to models for a damage/repair cycle of PSII involving the targeted degradation and replacement of photodamaged D1. To investigate the effects of perturbing the D1 cycle on photosynthesis and autotrophic growth under high and low irradiance, we have examined the consequences of site-specific mutations of the psbA and 16S rRNA genes affecting synthesis, maturation and function/stability of the D1 protein introduced into the chloroplast genome of wildtype strain of the green alga Chlamydomonas reinhardtii using biolistic transformation.

  11. Genetic analysis of a morphologically heterogeneous ovarian endometrioid carcinoma.

    Science.gov (United States)

    Geyer, Felipe C; Pareja, Fresia; Burke, Kathleen A; Schultheis, Anne M; Hussein, Yaser R; Ye, Jiqing; De Filippo, Maria R; Marchio, Caterina; Macedo, Gabriel S; Piscuoglio, Salvatore; Lim, Raymond S; Toy, Eugene; Murali, Rajmohan; Jungbluth, Achim A; Reis-Filho, Jorge S; Soslow, Robert A; Weigelt, Britta

    2017-09-01

    Low-grade ovarian endometrioid carcinomas may be associated with high-grade components. Whether the latter are clonally related to and originate from the low-grade endometrioid carcinoma remains unclear. The aim of this study was to use massively parallel sequencing to characterize the genomic landscape and clonal relatedness of an ovarian endometrioid carcinoma containing low-grade and high-grade components. DNA samples extracted from each tumour component (low-grade endometrioid, high-grade anaplastic and high-grade squamous) and matched normal tissue were subjected to targeted massively parallel sequencing with the 410-gene Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT) sequencing assay. Somatic single nucleotide variants, small insertions and deletions, and copy number alterations were detected with state-of-the-art bioinformatics algorithms, and validated with orthogonal methods. The endometrioid carcinoma and the associated high-grade components shared copy number alterations and four clonal mutations, including SMARCA4 mutations, which resulted in loss of BRG1 protein expression. Subclonal mutations and mutations restricted to single components were also identified, such as distinct TP53 mutations restricted to each histological component. Histologically distinct components of ovarian endometrioid carcinomas may show intratumour genetic heterogeneity but be clonally related, harbouring a complex clonal composition. In the present case, SMARCA4 mutations were probably early events, whereas TP53 somatic mutations were acquired later in evolution. © 2017 John Wiley & Sons Ltd.

  12. Genetic analysis of presbycusis by arrayed primer extension.

    Science.gov (United States)

    Rodriguez-Paris, Juan; Ballay, Charles; Inserra, Michelle; Stidham, Katrina; Colen, Tahl; Roberson, Joseph; Gardner, Phyllis; Schrijver, Iris

    2008-01-01

    Using the Hereditary Hearing Loss arrayed primer extension (APEX) array, which contains 198 mutations across 8 hearing loss-associated genes (GJB2, GJB6, GJB3, GJA1, SLC26A4, SLC26A5, 12S-rRNA, and tRNA Ser), we compared the frequency of sequence variants in 94 individuals with early presbycusis to 50 unaffected controls and aimed to identify possible genetic contributors. This cross-sectional study was performed at Stanford University with presbycusis samples from the California Ear Institute. The patients were between ages 20 and 65 yr, with adult-onset sensorineural hearing loss of unknown etiology, and carried a clinical diagnosis of early presbycusis. Exclusion criteria comprised known causes of hearing loss such as significant noise exposure, trauma, ototoxic medication, neoplasm, and congenital infection or syndrome, as well as congenital or pediatric onset. Sequence changes were identified in 11.7% and 10% of presbycusis and control alleles, respectively. Among the presbycusis group, these solely occurred within the GJB2 and SLC26A4 genes. Homozygous and compound heterozygous pathogenic mutations were exclusively seen in affected individuals. We were unable to detect a statistically significant difference between our control and affected populations regarding the frequency of sequence variants detected with the APEX array. Individuals who carry two mild mutations in the GJB2 gene possibly have an increased risk of developing early presbycusis.

  13. Genetic and phylogenetic analysis of ten Gobiidae species in China ...

    African Journals Online (AJOL)

    Administrator

    2011-09-07

    In Chinese). Xu F, Sun M (2001). Comparative analysis of phylogenetic relationships of grain amaranths and their wild relatives (Amaranthus;. Amaranthaceae) using internal transcribed spacer, amplified fragment length ...

  14. Genetic diversity and population structure analysis to construct a core collection from a large Capsicum germplasm.

    Science.gov (United States)

    Lee, Hea-Young; Ro, Na-Young; Jeong, Hee-Jin; Kwon, Jin-Kyung; Jo, Jinkwan; Ha, Yeaseong; Jung, Ayoung; Han, Ji-Woong; Venkatesh, Jelli; Kang, Byoung-Cheorl

    2016-11-14

    Conservation of genetic diversity is an essential prerequisite for developing new cultivars with desirable agronomic traits. Although a large number of germplasm collections have been established worldwide, many of them face major difficulties due to large size and a lack of adequate information about population structure and genetic diversity. Core collection with a minimum number of accessions and maximum genetic diversity of pepper species and its wild relatives will facilitate easy access to genetic material as well as the use of hidden genetic diversity in Capsicum. To explore genetic diversity and population structure, we investigated patterns of molecular diversity using a transcriptome-based 48 single nucleotide polymorphisms (SNPs) in a large germplasm collection comprising 3,821 accessions. Among the 11 species examined, Capsicum annuum showed the highest genetic diversity (H E  = 0.44, I = 0.69), whereas the wild species C. galapagoense showed the lowest genetic diversity (H E  = 0.06, I = 0.07). The Capsicum germplasm collection was divided into 10 clusters (cluster 1 to 10) based on population structure analysis, and five groups (group A to E) based on phylogenetic analysis. Capsicum accessions from the five distinct groups in an unrooted phylogenetic tree showed taxonomic distinctness and reflected their geographic origins. Most of the accessions from European countries are distributed in the A and B groups, whereas the accessions from Asian countries are mainly distributed in C and D groups. Five different sampling strategies with diverse genetic clustering methods were used to select the optimal method for constructing the core collection. Using a number of allelic variations based on 48 SNP markers and 32 different phenotypic/morphological traits, a core collection 'CC240' with a total of 240 accessions (5.2 %) was selected from within the entire Capsicum germplasm. Compared to the other core collections, CC240 displayed higher

  15. Trans-ethnic Meta-analysis and Functional Annotation Illuminates the Genetic Architecture of Fasting Glucose and Insulin.

    Science.gov (United States)

    Liu, Ching-Ti; Raghavan, Sridharan; Maruthur, Nisa; Kabagambe, Edmond Kato; Hong, Jaeyoung; Ng, Maggie C Y; Hivert, Marie-France; Lu, Yingchang; An, Ping; Bentley, Amy R; Drolet, Anne M; Gaulton, Kyle J; Guo, Xiuqing; Armstrong, Loren L; Irvin, Marguerite R; Li, Man; Lipovich, Leonard; Rybin, Denis V; Taylor, Kent D; Agyemang, Charles; Palmer, Nicholette D; Cade, Brian E; Chen, Wei-Min; Dauriz, Marco; Delaney, Joseph A C; Edwards, Todd L; Evans, Daniel S; Evans, Michele K; Lange, Leslie A; Leong, Aaron; Liu, Jingmin; Liu, Yongmei; Nayak, Uma; Patel, Sanjay R; Porneala, Bianca C; Rasmussen-Torvik, Laura J; Snijder, Marieke B; Stallings, Sarah C; Tanaka, Toshiko; Yanek, Lisa R; Zhao, Wei; Becker, Diane M; Bielak, Lawrence F; Biggs, Mary L; Bottinger, Erwin P; Bowden, Donald W; Chen, Guanjie; Correa, Adolfo; Couper, David J; Crawford, Dana C; Cushman, Mary; Eicher, John D; Fornage, Myriam; Franceschini, Nora; Fu, Yi-Ping; Goodarzi, Mark O; Gottesman, Omri; Hara, Kazuo; Harris, Tamara B; Jensen, Richard A; Johnson, Andrew D; Jhun, Min A; Karter, Andrew J; Keller, Margaux F; Kho, Abel N; Kizer, Jorge R; Krauss, Ronald M; Langefeld, Carl D; Li, Xiaohui; Liang, Jingling; Liu, Simin; Lowe, William L; Mosley, Thomas H; North, Kari E; Pacheco, Jennifer A; Peyser, Patricia A; Patrick, Alan L; Rice, Kenneth M; Selvin, Elizabeth; Sims, Mario; Smith, Jennifer A; Tajuddin, Salman M; Vaidya, Dhananjay; Wren, Mary P; Yao, Jie; Zhu, Xiaofeng; Ziegler, Julie T; Zmuda, Joseph M; Zonderman, Alan B; Zwinderman, Aeilko H; Adeyemo, Adebowale; Boerwinkle, Eric; Ferrucci, Luigi; Hayes, M Geoffrey; Kardia, Sharon L R; Miljkovic, Iva; Pankow, James S; Rotimi, Charles N; Sale, Michele M; Wagenknecht, Lynne E; Arnett, Donna K; Chen, Yii-Der Ida; Nalls, Michael A; Province, Michael A; Kao, W H Linda; Siscovick, David S; Psaty, Bruce M; Wilson, James G; Loos, Ruth J F; Dupuis, Josée; Rich, Stephen S; Florez, Jose C; Rotter, Jerome I; Morris, Andrew P; Meigs, James B

    2016-07-07

    Knowledge of the genetic basis of the type 2 diabetes (T2D)-related quantitative traits fasting glucose (FG) and insulin (FI) in African ancestry (AA) individuals has been limited. In non-diabetic subjects of AA (n = 20,209) and European ancestry (EA; n = 57,292), we performed trans-ethnic (AA+EA) fine-mapping of 54 established EA FG or FI loci with detailed functional annotation, assessed their relevance in AA individuals, and sought previously undescribed loci through trans-ethnic (AA+EA) meta-analysis. We narrowed credible sets of variants driving association signals for 22/54 EA-associated loci; 18/22 credible sets overlapped with active islet-specific enhancers or transcription factor (TF) binding sites, and 21/22 contained at least one TF motif. Of the 54 EA-associated loci, 23 were shared between EA and AA. Replication with an additional 10,096 AA individuals identified two previously undescribed FI loci, chrX FAM133A (rs213676) and chr5 PELO (rs6450057). Trans-ethnic analyses with regulatory annotation illuminate the genetic architecture of glycemic traits and suggest gene regulation as a target to advance precision medicine for T2D. Our approach to utilize state-of-the-art functional annotation and implement trans-ethnic association analysis for discovery and fine-mapping offers a framework for further follow-up and characterization of GWAS signals of complex trait loci. Copyright © 2016 American Society of Human Genetics. All rights reserved.

  16. Genetic Analysis of Oculocutaneous Albinism Type1A (OCA1A) in an Iranian Family

    Science.gov (United States)

    Pour-Jafari, H; Zamanian, A; Pour-Jafari, B

    2010-01-01

    Background: Oculocutaneous albinism type1 (OCA1) is characterized by the absence of melanin pigmentation. The mutation on TYR gene makes OCA1 as an autosomal recessive genetic disorder. In this study, we delineated the genetic analysis of an Iranian family with four members affected with OCA1. Methods: Clinical exams and paraclinical test were performed for all patients of the case family, also proband, her husband, and her parents. Pedigree chart was drawn too. We extracted the genomic DNA from the leukocytes of seven members of the family. Haplotype analysis at the TYR locus was done and informative microsatellite markers were employed. In order to amplify the entire coding region of the TYR gene, for bidirectional direct sequencing mutation analysis, eight sets of primers were used. Results: Our patients were diagnosed as affected with Oculocutaneous albinism type1a. Analysis of pedigree pattern showed an autosomal recessive inheritance. Analysis with different markers in chromosomes 5, 6, 9, 11 and 15 showed that cause of albinism in our case family was on chromosome 11 (D11S1887 marker was informative). Conclusions: The results offered a more developed method of diagnosis for OCA1 carrier identification and genetic counseling for OCA1 affected families as well; also submit a sample of mutation involved with oculocutaneous albinism in Iran. Genetic analysis is necessary for determining the type of albinism in an individual patient. PMID:23112997

  17. The complex genetics of gait speed: genome-wide meta-analysis approach.

    Science.gov (United States)

    Ben-Avraham, Dan; Karasik, David; Verghese, Joe; Lunetta, Kathryn L; Smith, Jennifer A; Eicher, John D; Vered, Rotem; Deelen, Joris; Arnold, Alice M; Buchman, Aron S; Tanaka, Toshiko; Faul, Jessica D; Nethander, Maria; Fornage, Myriam; Adams, Hieab H; Matteini, Amy M; Callisaya, Michele L; Smith, Albert V; Yu, Lei; De Jager, Philip L; Evans, Denis A; Gudnason, Vilmundur; Hofman, Albert; Pattie, Alison; Corley, Janie; Launer, Lenore J; Knopman, Davis S; Parimi, Neeta; Turner, Stephen T; Bandinelli, Stefania; Beekman, Marian; Gutman, Danielle; Sharvit, Lital; Mooijaart, Simon P; Liewald, David C; Houwing-Duistermaat, Jeanine J; Ohlsson, Claes; Moed, Matthijs; Verlinden, Vincent J; Mellström, Dan; van der Geest, Jos N; Karlsson, Magnus; Hernandez, Dena; McWhirter, Rebekah; Liu, Yongmei; Thomson, Russell; Tranah, Gregory J; Uitterlinden, Andre G; Weir, David R; Zhao, Wei; Starr, John M; Johnson, Andrew D; Ikram, M Arfan; Bennett, David A; Cummings, Steven R; Deary, Ian J; Harris, Tamara B; Kardia, Sharon L R; Mosley, Thomas H; Srikanth, Velandai K; Windham, Beverly G; Newman, Ann B; Walston, Jeremy D; Davies, Gail; Evans, Daniel S; Slagboom, Eline P; Ferrucci, Luigi; Kiel, Douglas P; Murabito, Joanne M; Atzmon, Gil

    2017-01-10

    Emerging evidence suggests that the basis for variation in late-life mobility is attributable, in part, to genetic factors, which may become increasingly important with age. Our objective was to systematically assess the contribution of genetic variation to gait speed in older individuals. We conducted a meta-analysis of gait speed GWASs in 31,478 older adults from 17 cohorts of the CHARGE consortium, and validated our results in 2,588 older adults from 4 independent studies. We followed our initial discoveries with network and eQTL analysis of candidate signals in tissues. The meta-analysis resulted in a list of 536 suggestive genome wide significant SNPs in or near 69 genes. Further interrogation with Pathway Analysis placed gait speed as a polygenic complex trait in five major networks. Subsequent eQTL analysis revealed several SNPs significantly associated with the expression of PRSS16, WDSUB1 and PTPRT, which in addition to the meta-analysis and pathway suggested that genetic effects on gait speed may occur through synaptic function and neuronal development pathways. No genome-wide significant signals for gait speed were identified from this moderately large sample of older adults, suggesting that more refined physical function phenotypes will be needed to identify the genetic basis of gait speed in aging.

  18. Methods of sports genetics: dermatoglyphic analysis of human palmarprints (information 2

    Directory of Open Access Journals (Sweden)

    Serhiyenko L.P.

    2010-01-01

    Full Text Available Information is generalized about the dermatoglyphic analysis of hands of hands of man. The quantitative dermatoglyphic indexes of hands of hands are presented for youths and girls of the Podol region of Ukraine. The quantitative indexes of palm's dermatoglyphics are rotined for youths and girls of Ukrainian and Russian nationality in Kharkov. The most informing dermatoglyphic indexes of hands of hands which it is possible to use in sporting genetics are certain. Formed recommendation on technology of dermatoglyphic analysis of hands of hands of man in sporting genetics.

  19. Genetic and biochemical analysis of peptide transport in Escherichia coli

    International Nuclear Information System (INIS)

    Andrews, J.C.

    1986-01-01

    E. coli peptide transport mutants have been isolated based on their resistance to toxic tripeptides. These genetic defects were found to map in two distinct chromosomal locations. The transport systems which require expression of the trp-linked opp genes and the oppE gene(s) for activity were shown to have different substrate preferences. Growth of E. coli in medium containing leucine results in increased entry of exogenously supplied tripeptides into the bacterial cell. This leucine-mediated elevation of peptide transport required expression of the trp-linked opp operon and was accompanied by increased sensitivity to toxic tripeptides, by an enhanced capacity to utilize nutritional peptides, and by an increase in both the velocity and apparent steady-state level of L-(U- 14 C)alanyl-L-alanyl-L-alanine accumulation for E. coli grown in leucine-containing medium relative to these parameters of peptide transport measured with bacteria grown in media lacking leucine. Direct measurement of opp operon expression by pulse-labeling experiments demonstrated that growth of E. coli in the presence of leucine resulted in increased synthesis of the oppA-encoded periplasmic binding protein. The transcriptional regulation of the trp-linked opp operon of E. coli was investigated using λ placMu51-generated lac operon fusions. Synthesis of β-galactosidase by strains harboring oppA-lac, oppB-lac, and oppD-lac fusions occurred at a basal level when the fusion-containing strains were grown in minimal medium

  20. Methods of Sports Genetics: toe and plantar dermatoglyphic analysis (information 3

    Directory of Open Access Journals (Sweden)

    Serhiyenko L.P.

    2010-03-01

    Full Text Available The article summarized the data and dermatoglyphic analysis of human toe and plantar prints. It is defined that toe and plantar triradii, papillary ridge patterns, the main plantar lines, the types of dermatoglyphic patterns can be the objects of the dermatoglyphic analysis. The recommendations to use the technology of dermatoglyphic analysis of human toe and plantar prints in sport genetics are given.