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Sample records for lesions genetic analyses

  1. Graphical models for genetic analyses

    DEFF Research Database (Denmark)

    Lauritzen, Steffen Lilholt; Sheehan, Nuala A.

    2003-01-01

    This paper introduces graphical models as a natural environment in which to formulate and solve problems in genetics and related areas. Particular emphasis is given to the relationships among various local computation algorithms which have been developed within the hitherto mostly separate areas...... of graphical models and genetics. The potential of graphical models is explored and illustrated through a number of example applications where the genetic element is substantial or dominating....

  2. Genetic Heterogeneity of Benign Thyroid Lesions

    Directory of Open Access Journals (Sweden)

    O. Ferrer-Roca

    1998-01-01

    Full Text Available The present series includes 75 thyroid lesions (38 goiters, 30 adenomas, 3 follicullo‐papillary encapsulated carcinomas and 4 normal thyroid that were studied by static and flow cytometry. Four cases were also analyzed by in situ hybridization (centromeric probes for chromosomes 1 and 17 and 10 cases by G‐banding cytogenetics. Results demonstrate a polymorphysm and genetic instability in the thyroid tissue that may be related to the spontaneous polyploidization of their cells. The most consistent finding in cytometry was the presence of two clones associated with clinical or histological hyperactivity (46% versus 23% in non‐functioning cases; X2 distribution with a p < 0.05.

  3. Genetic analyses for deciphering the status and role of ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Genetics; Volume 96; Issue 1. Genetic analyses for deciphering the status and role of photoperiodic and maturity genes in major Indian soybean cultivars. SANJAY GUPTA VIRENDER SINGH BHATIA GIRIRAJ KUMAWAT DEVSHREE THAKUR GOURAV SINGH RACHANA TRIPATHI GYANESH ...

  4. Spontaneous chromosome aberrations in cancer cells. Evidence of existence of hidden genetic lesions in genetic structures

    International Nuclear Information System (INIS)

    Poryadkova-Luchnik, N.A.; Kuz'mina, E.G.

    1996-01-01

    Chromosome aberrations spontaneously observed in cancer cells were quantitively studied under the effect of non-mutagenic (suboptimal temperature, low content of propilgallate and caffeine) and mutagenic (ionizing radiation) factors. Human larynx cancer cells during several years or gamma-irradiation were used to carry out experiments. The experiments linked with cloning of the initial population and investigation into chromosome aberrations in 22 clones demonstrated persuasively the occurrence of latent genetic lesions in cancer cells

  5. A review of multivariate analyses in imaging genetics

    Directory of Open Access Journals (Sweden)

    Jingyu eLiu

    2014-03-01

    Full Text Available Recent advances in neuroimaging technology and molecular genetics provide the unique opportunity to investigate genetic influence on the variation of brain attributes. Since the year 2000, when the initial publication on brain imaging and genetics was released, imaging genetics has been a rapidly growing research approach with increasing publications every year. Several reviews have been offered to the research community focusing on various study designs. In addition to study design, analytic tools and their proper implementation are also critical to the success of a study. In this review, we survey recent publications using data from neuroimaging and genetics, focusing on methods capturing multivariate effects accommodating the large number of variables from both imaging data and genetic data. We group the analyses of genetic or genomic data into either a prior driven or data driven approach, including gene-set enrichment analysis, multifactor dimensionality reduction, principal component analysis, independent component analysis (ICA, and clustering. For the analyses of imaging data, ICA and extensions of ICA are the most widely used multivariate methods. Given detailed reviews of multivariate analyses of imaging data available elsewhere, we provide a brief summary here that includes a recently proposed method known as independent vector analysis. Finally, we review methods focused on bridging the imaging and genetic data by establishing multivariate and multiple genotype-phenotype associations, including sparse partial least squares, sparse canonical correlation analysis, sparse reduced rank regression and parallel ICA. These methods are designed to extract latent variables from both genetic and imaging data, which become new genotypes and phenotypes, and the links between the new genotype-phenotype pairs are maximized using different cost functions. The relationship between these methods along with their assumptions, advantages, and

  6. How distributed processing produces false negatives in voxel-based lesion-deficit analyses.

    Science.gov (United States)

    Gajardo-Vidal, Andrea; Lorca-Puls, Diego L; Crinion, Jennifer T; White, Jitrachote; Seghier, Mohamed L; Leff, Alex P; Hope, Thomas M H; Ludersdorfer, Philipp; Green, David W; Bowman, Howard; Price, Cathy J

    2018-07-01

    In this study, we hypothesized that if the same deficit can be caused by damage to one or another part of a distributed neural system, then voxel-based analyses might miss critical lesion sites because preservation of each site will not be consistently associated with preserved function. The first part of our investigation used voxel-based multiple regression analyses of data from 359 right-handed stroke survivors to identify brain regions where lesion load is associated with picture naming abilities after factoring out variance related to object recognition, semantics and speech articulation so as to focus on deficits arising at the word retrieval level. A highly significant lesion-deficit relationship was identified in left temporal and frontal/premotor regions. Post-hoc analyses showed that damage to either of these sites caused the deficit of interest in less than half the affected patients (76/162 = 47%). After excluding all patients with damage to one or both of the identified regions, our second analysis revealed a new region, in the anterior part of the left putamen, which had not been previously detected because many patients had the deficit of interest after temporal or frontal damage that preserved the left putamen. The results illustrate how (i) false negative results arise when the same deficit can be caused by different lesion sites; (ii) some of the missed effects can be unveiled by adopting an iterative approach that systematically excludes patients with lesions to the areas identified in previous analyses, (iii) statistically significant voxel-based lesion-deficit mappings can be driven by a subset of patients; (iv) focal lesions to the identified regions are needed to determine whether the deficit of interest is the consequence of focal damage or much more extensive damage that includes the identified region; and, finally, (v) univariate voxel-based lesion-deficit mappings cannot, in isolation, be used to predict outcome in other patients

  7. A weighted U statistic for association analyses considering genetic heterogeneity.

    Science.gov (United States)

    Wei, Changshuai; Elston, Robert C; Lu, Qing

    2016-07-20

    Converging evidence suggests that common complex diseases with the same or similar clinical manifestations could have different underlying genetic etiologies. While current research interests have shifted toward uncovering rare variants and structural variations predisposing to human diseases, the impact of heterogeneity in genetic studies of complex diseases has been largely overlooked. Most of the existing statistical methods assume the disease under investigation has a homogeneous genetic effect and could, therefore, have low power if the disease undergoes heterogeneous pathophysiological and etiological processes. In this paper, we propose a heterogeneity-weighted U (HWU) method for association analyses considering genetic heterogeneity. HWU can be applied to various types of phenotypes (e.g., binary and continuous) and is computationally efficient for high-dimensional genetic data. Through simulations, we showed the advantage of HWU when the underlying genetic etiology of a disease was heterogeneous, as well as the robustness of HWU against different model assumptions (e.g., phenotype distributions). Using HWU, we conducted a genome-wide analysis of nicotine dependence from the Study of Addiction: Genetics and Environments dataset. The genome-wide analysis of nearly one million genetic markers took 7h, identifying heterogeneous effects of two new genes (i.e., CYP3A5 and IKBKB) on nicotine dependence. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

  8. Genetic analyses of bolting in bulb onion (Allium cepa L.).

    Science.gov (United States)

    Baldwin, Samantha; Revanna, Roopashree; Pither-Joyce, Meeghan; Shaw, Martin; Wright, Kathryn; Thomson, Susan; Moya, Leire; Lee, Robyn; Macknight, Richard; McCallum, John

    2014-03-01

    We present the first evidence for a QTL conditioning an adaptive trait in bulb onion, and the first linkage and population genetics analyses of candidate genes involved in photoperiod and vernalization physiology. Economic production of bulb onion (Allium cepa L.) requires adaptation to photoperiod and temperature such that a bulb is formed in the first year and a flowering umbel in the second. 'Bolting', or premature flowering before bulb maturation, is an undesirable trait strongly selected against by breeders during adaptation of germplasm. To identify genome regions associated with adaptive traits we conducted linkage mapping and population genetic analyses of candidate genes, and QTL analysis of bolting using a low-density linkage map. We performed tagged amplicon sequencing of ten candidate genes, including the FT-like gene family, in eight diverse populations to identify polymorphisms and seek evidence of differentiation. Low nucleotide diversity and negative estimates of Tajima's D were observed for most genes, consistent with purifying selection. Significant population differentiation was observed only in AcFT2 and AcSOC1. Selective genotyping in a large 'Nasik Red × CUDH2150' F2 family revealed genome regions on chromosomes 1, 3 and 6 associated (LOD > 3) with bolting. Validation genotyping of two F2 families grown in two environments confirmed that a QTL on chromosome 1, which we designate AcBlt1, consistently conditions bolting susceptibility in this cross. The chromosome 3 region, which coincides with a functionally characterised acid invertase, was not associated with bolting in other environments, but showed significant association with bulb sucrose content in this and other mapping pedigrees. These putative QTL and candidate genes were placed on the onion map, enabling future comparative studies of adaptive traits.

  9. White Matter Lesion Progression: Genome-Wide Search for Genetic Influences

    NARCIS (Netherlands)

    E. Hofer (Edith); M. Cavalieri (Margherita); J.C. Bis (Joshua); C. DeCarli (Charles); M. Fornage (Myriam); S. Sigurdsson (Sigurdur); V. Srikanth (Velandai); S. Trompet (Stella); B.F.J. Verhaaren (Benjamin); C. Wolf (Christiane); Q. Yang (Qiong Fang); H.H.H. Adams (Hieab); P. Amouyel (Philippe); A. Beiser (Alexa); B.M. Buckley (Brendan M.); M. Callisaya (Michele); G. Chauhan (Ganesh); A.J.M. De Craen (Anton J. M.); C. Dufouil (Carole); C.M. van Duijn (Cornelia); I. Ford; P. Freudenberger (Paul); R.F. Gottesman (Rebecca); V. Gudnason (Vilmundur); G. Heiss (Gerardo); A. Hofman (Albert); T. Lumley (Thomas); O. Martinez (Oliver); B. Mazoyer (Bernard); C. Moran (Chris); W.J. Niessen (Wiro); T.G. Phan (Thanh); B.M. Psaty (Bruce); C.L. Satizabal (Claudia L.); N. Sattar (Naveed); S. Schilling (Sabrina); D.K. Shibata (Dean); P.E. Slagboom (Eline); G.D. Smith; D.J. Stott (David. J.); K.D. Taylor (Kent); R. Thomson (Russell); A.M. Töglhofer (Anna Maria); C. Tzourio (Christophe); M.A. van Buchem (Mark); J. Wang (Jing); R.G.J. Westendorp (Rudi); B. Gwen Windham; M.W. Vernooij (Meike); A.P. Zijdenbos; R.J. Beare (Richard); S. Debette (Stéphanie); M.A. Ikram (Arfan); J.W. Jukema (Jan Wouter); L.J. Launer (Lenore); W.T. Longstreth Jr; T.H. Mosley (Thomas H.); S. Seshadri (Sudha); R. Schmidt (Reinhold); R. Schmidt (Reinhold)

    2015-01-01

    textabstractBackground and Purpose-White matter lesion (WML) progression on magnetic resonance imaging is related to cognitive decline and stroke, but its determinants besides baseline WML burden are largely unknown. Here, we estimated heritability of WML progression, and sought common genetic

  10. Genetic analyses for conformation traits in South African Jersey and ...

    African Journals Online (AJOL)

    JACO

    Genetic trends for conformation traits of the South African Holstein show that ... conformation traits can be used to improve stayability, fertility and disease resistance (Rogers et al., 1999; .... Genetic correlations among protein yield, productive.

  11. Litter size, fur quality and genetic analyses of American mink

    DEFF Research Database (Denmark)

    Thirstrup, Janne Pia

    of the skin, have been analyzed. Both fur quality traits and litter size are complex traits underlying quantitative genetic variation. Methods for estimating genetic variance, spanning from pedigree information to the use of different genetic markers, have been utilized in order to gain knowledge about...

  12. Characteristics and genetic mapping of a lesion mimic mutant pl(t) in japonica rice variety zhejing 22

    International Nuclear Information System (INIS)

    Chen Pingping; Zhang Xiaoming; Ye Shenghai; Zhao Ningchun; Lu Yanting; Liu Heqin; Jin Qingsheng; Yang Ling

    2010-01-01

    A lesion mimic mutant,obtained by radiation mutagenesis on the seeds of a japonica rice variety Zhejing 22, exhibited a lesion mimic phenotype during the whole growth stage under different environments. Genetic analysis indicated that the mutant trait was controlled by a single recessive gene named spl (t). Relying on simple sequence repeat (SSR) and recessive class analysis method to map the spl (t) gene with a F 2 population was constructed by crossing the mutant spl (t) with Zhenshan 97B.spl (t) was mapped in the interval of 0.8cM between RM7195 and RM27929 near centromere region on the short arm of chromosome 12.Blue trypan dye analyses indicated that the lesion mimic trait of the mutant was caused by the programmer cell death. Further study showed that the programmer cell death was caused by H 2 O 2 oxidative burst. By inoculation of bacterial leaf blight and blast strains, the resistances of the mutant were similar to the wild variety Zhejing 22. (authors)

  13. Genetic, molecular and functional analyses of complement factor I deficiency

    DEFF Research Database (Denmark)

    Nilsson, S.C.; Trouw, L.A.; Renault, N.

    2009-01-01

    Complete deficiency of complement inhibitor factor I (FI) results in secondary complement deficiency due to uncontrolled spontaneous alternative pathway activation leading to susceptibility to infections. Current genetic examination of two patients with near complete FI deficiency and three patie...

  14. Genetic analyses of agronomic and seed quality traits of synthetic ...

    Indian Academy of Sciences (India)

    As for protein content, similar results were found in the F2 plants and their maternal parents. ... doubled haploid; genetic analysis; gene interaction; agronomic traits; seed ..... Han J. Q. and Liu H. L. 1993 Principal component analysis for main.

  15. Meta-analyses: does long-term PPI use increase the risk of gastric premalignant lesions?

    Science.gov (United States)

    Eslami, Layli; Nasseri-Moghaddam, Siavosh

    2013-08-01

    Proton pump inhibitors (PPIs) are the most effective agents available for reducing acid secretion. They are used for medical treatment of various acid-related disorders. PPIs are used extensively and for extended periods of time in gastroesophageal reflux disease (GERD). A troublesome issue regarding maintenance therapy has been the propensity of PPI-treated patients to develop chronic atrophic gastritis while on therapy that could theoretically lead to an increased incidence of gastric cancer. In addition, animal studies have raised concern for development of enterochromaffin-like cell hyperplasia and carcinoid tumors in the stomachs of mice receiving high dose PPIs. Current literature does not provide a clear-cut conclusion on the subject and the reports are sometimes contradictory. Therefore, this study is a systematic review of the available literature to address the safety of long-term PPI use and its relation to the development of malignant/premalignant gastric lesions. A literature search of biomedical databases was performed. The reference lists of retrieved articles were reviewed to further identify relevant trials. We hand-searched the abstracts of the American Digestive Disease Week (DDW) and the United European Gastroenterology Week (UEGW) from 1995 to 2013. Only randomized clinical trials (RCTs) that used PPIs as the primary treatment for at least six month versus no treatment, placebo, antacid or anti-reflux surgery (ARS) were included. Two reviewers independently extracted the data. Discrepancies in the interpretation were resolved by consensus. All analyses of outcomes were based on the intention-to-treat principle. We performed statistical analysis using Review Manager software. The effect measure of choice was relative risk (RR) for dichotomous data. Six RCTs with a total of 785 patients met the inclusion criteria. Two multicenter RCTs compared Esomeprazole with placebo. One RCT compared omeprazole with ARS. Two RCTs compared omeprazole with

  16. A supervised framework for lesion segmentation and automated VLSM analyses in left hemispheric stroke

    Directory of Open Access Journals (Sweden)

    Dorian Pustina

    2015-05-01

    Full Text Available INTRODUCTION: Voxel-based lesion-symptom mapping (VLSM is conventionally performed using skill and knowledge of experts to manually delineate brain lesions. This process requires time, and is likely to have substantial inter-rater variability. Here, we propose a supervised machine learning framework for lesion segmentation capable of learning from a single modality and existing manual segmentations in order to delineate lesions in new patients. METHODS: Data from 60 patients with chronic stroke aphasia were utilized in the study (age: 59.7±11.5yrs, post-stroke interval: 5±2.9yrs, male/female ratio: 34/26. Using a single T1 image of each subject, additional features were created that provided complementary information, such as, difference from template, tissue segmentation, brain asymmetries, gradient magnitude, and deviances of these images from 80 age and gender matched controls. These features were fed into MRV-NRF (multi-resolution voxel-wise neighborhood random forest; Tustison et al., 2014 prediction algorithm implemented in ANTsR (Avants, 2015. The algorithm incorporates information from each voxel and its surrounding neighbors from all above features, in a hierarchy of random forest predictions from low to high resolution. The validity of the framework was tested with a 6-fold cross validation (i.e., train from 50 subjects, predict 10. The process was repeated ten times, producing ten segmentations for each subject, from which the average solution was binarized. Predicted lesions were compared to manually defined lesions, and VLSM models were built on 4 language measures: repetition and comprehension subscores from the WAB (Kertesz, 1982, WAB-AQ, and PNT naming accuracy (Roach, Schwartz, Martin, Grewal, & Brecher, 1996. RESULTS: Manual and predicted lesion size showed high correlation (r=0.96. Compared to manual lesions, the predicted lesions had a dice overlap of 0.72 (±0.14 STD, a case-wise maximum distance (Hausdorff of 21mm (±16

  17. Diagnostic accuracy of pit pattern and vascular pattern analyses in colorectal lesions.

    Science.gov (United States)

    Wada, Yoshiki; Kashida, Hiroshi; Kudo, Shin-ei; Misawa, Masashi; Ikehara, Nobunao; Hamatani, Shigeharu

    2010-07-01

    The aim of this prospective study is to compare the usefulness of magnifying narrow band imaging (NBI) and magnifying chromoendoscopy in the diagnosis of colorectal lesions. The subjects were 1185 patients who underwent a complete colonoscopic examination and endoscopic or surgical treatment, from January 2006 to February 2008. A total of 1473 lesions were evaluated (53 hyperplastic polyps, 1317 adenomas, 103 submucosally invasive cancers). The digital images with NBI or chromoendoscopy were recorded and diagnosed independently from each other by two endoscopists who were blinded to the final pathological diagnosis. We could differentiate between neoplastic and non-neoplastic lesions with sensitivity of 88.9%, specificity of 98.5% and accuracy of 98.2% according to the vascular pattern. By recognizing an irregular or sparse pattern with NBI, massively invasive submucosal cancer could be diagnosed with the sensitivity and specificity of 94.9% and 76.0%. Using chromoendoscopy, we could differentiate between neoplastic and non-neoplastic lesions with sensitivity of 86.8% and specificity of 99.2%. We were able to differentiate between massively invasive cancers and slightly invasive cancers using the pit patterns with sensitivity of 89.7% and specificity of 88.0%. The specificity was superior to that of NBI colonoscopy. Both NBI and chromoendoscopy can be useful for distinguishing between neoplastic and non-neoplastic lesions. In the diagnosis of submucosal cancer, pit pattern diagnosis was slightly superior to vascular pattern diagnosis. It is desirable to perform chromoendoscopy in addition to NBI for distinguishing between slightly and massively invasive submucosal cancer lesions and determining the treatment.

  18. gPGA: GPU Accelerated Population Genetics Analyses.

    Directory of Open Access Journals (Sweden)

    Chunbao Zhou

    Full Text Available The isolation with migration (IM model is important for studies in population genetics and phylogeography. IM program applies the IM model to genetic data drawn from a pair of closely related populations or species based on Markov chain Monte Carlo (MCMC simulations of gene genealogies. But computational burden of IM program has placed limits on its application.With strong computational power, Graphics Processing Unit (GPU has been widely used in many fields. In this article, we present an effective implementation of IM program on one GPU based on Compute Unified Device Architecture (CUDA, which we call gPGA.Compared with IM program, gPGA can achieve up to 52.30X speedup on one GPU. The evaluation results demonstrate that it allows datasets to be analyzed effectively and rapidly for research on divergence population genetics. The software is freely available with source code at https://github.com/chunbaozhou/gPGA.

  19. Genetic recombinational and physical linkage analyses on slash pine

    Science.gov (United States)

    Rob Doudrick

    1996-01-01

    Slash pine is native to the southeastern USA, but is commercially valuable world-wide as a timber-,fiber- and resin-producing species. Breeding objectives emphasize selection for fusiform rust disease resistance. Identification of markers linked to genetic factors conditioning specificity should expand our knowledge of disease development. Towards this end, random...

  20. Biodiversity analyses for risk assessment of genetically modified potato

    NARCIS (Netherlands)

    Lazebnik, Jenny; Dicke, Marcel; Braak, ter Cajo J.F.; Loon, van Joop J.A.

    2017-01-01

    An environmental risk assessment for the introduction of genetically modified crops includes assessing the consequences for biodiversity. In this study arthropod biodiversity was measured using pitfall traps in potato agro-ecosystems in Ireland and The Netherlands over two years. We tested the

  1. RESEARCH NOTE Genetic Analyses for Deciphering the Status and ...

    Indian Academy of Sciences (India)

    Precision breeding for developing varieties for a specific area would involve ... Presently India is the fifth largest soybean producing country after US, Brazil, ... Genetic analysis at E3 and E4 loci and assessment of effect of photoperiodic ... outsourced (Scigenom, Banglore) for Sanger sequencing of coding region of E1.

  2. Dermatitis Herpetiformis: From the Genetics to the Development of Skin Lesions

    Directory of Open Access Journals (Sweden)

    Diletta Bonciani

    2012-01-01

    Full Text Available Dermatitis herpetiformis (DH is a rare autoimmune disease linked to gluten sensitivity with a chronic-relapsing course. It is currently considered to be the specific cutaneous manifestation of celiac disease (CD. Both conditions are mediated by the IgA class of autoantibodies, and the diagnosis of DH is dependent on the detection of granular deposits of IgA in the skin. There is an underlying genetic predisposition to the development of DH, but environmental factors are also important. This paper describes these different factors and discusses the known mechanism that lead to the development of skin lesions.

  3. Skin barrier and contact allergy: Genetic risk factor analyses

    DEFF Research Database (Denmark)

    Ross-Hansen, Katrine

    2013-01-01

    allergy. Objectives To evaluate the effect of specific gene polymorphisms on the risk of developing contact allergy by a candidate gene approach. These included polymorphisms in the glutathione S-transferase genes (GSTM1, -T1 and -P1 variants), the claudin-1 gene (CLDN1), and the filaggrin gene (FLG......) in particular. Methods Epidemiological genetic association studies were performed on a general Danish population. Participants were patch tested, answered a questionnaire on general health and were genotyped for GST, CLDN1 and FLG polymorphisms. Filaggrin’s nickel binding potential was evaluated biochemically...

  4. Ascorbic acid deficiency aggravates stress-induced gastric mucosal lesions in genetically scorbutic ODS rats.

    Science.gov (United States)

    Ohta, Y; Chiba, S; Imai, Y; Kamiya, Y; Arisawa, T; Kitagawa, A

    2006-12-01

    We examined whether ascorbic acid (AA) deficiency aggravates water immersion restraint stress (WIRS)-induced gastric mucosal lesions in genetically scorbutic ODS rats. ODS rats received scorbutic diet with either distilled water containing AA (1 g/l) or distilled water for 2 weeks. AA-deficient rats had 12% of gastric mucosal AA content in AA-sufficient rats. AA-deficient rats showed more severe gastric mucosal lesions than AA-sufficient rats at 1, 3 or 6 h after the onset of WIRS, although AA-deficient rats had a slight decrease in gastric mucosal AA content, while AA-sufficient rats had a large decrease in that content. AA-deficient rats had more decreased gastric mucosal nonprotein SH and vitamin E contents and increased gastric mucosal lipid peroxide content than AA-sufficient rats at 1, 3 or 6 h of WIRS. These results indicate that AA deficiency aggravates WIRS-induced gastric mucosal lesions in ODS rats by enhancing oxidative damage in the gastric mucosa.

  5. Genetic ablation of soluble TNF does not affect lesion size and functional recovery after moderate spinal cord injury in mice

    DEFF Research Database (Denmark)

    Ellman, Ditte Gry; Degn, Matilda; Lund, Minna Christiansen

    2016-01-01

    Traumatic spinal cord injury (SCI) is followed by an instant increase in expression of the microglial-derived proinflammatory cytokine tumor necrosis factor (TNF) within the lesioned cord. TNF exists both as membrane-anchored TNF (mTNF) and as cleaved soluble TNF (solTNF). We previously demonstra......, and MHCII), lesion size, and functional outcome after moderate SCI were comparable between genotypes. Collectively, our data demonstrate that genetic ablation of solTNF does not significantly modulate postlesion outcome after SCI....

  6. Histologic and molecular-genetic characteristics of precancerous lesions in chronic gastritis

    Directory of Open Access Journals (Sweden)

    Nina Zidar

    2014-03-01

    Full Text Available Chronic gastritis is an inflammatory condition of the gastric mucosa, which may include glandular alterations. It is most frequently caused by infection with Helicobacter pylori, a smaller proportion is related to chemical agents and autoimmune mechanisms. Chronic gastritis may lead to the development of gastric adenocarcinoma, depending on environmental factors, bacterial strain and host immune response. The vast majority of gastric adenocarcinomas are the final step in a complex cascade process of cancerogenesis involving sequential steps of precancerous lesions – atrophy, intestinal metaplasia and dysplasia.The process of cancerogenesis is associated with progressive genetic and epigenetic alterations, these being more frequent in dysplasia than in atrophic gastritis and intestinal metaplasia. Despite extensive research of gastric cancerogenesis, there are no molecular markers to be used for detecting patients at risk for cancer development.Biopsy remains among the most reliable ways of detecting gastric precancerous lesions. Apart from the correct histologic diagnosis, the assessment of topography is important. Biopsies must be taken according to the updated Sydney protocol. For further classifying patients at risk for gastric cancer, two systems have been developed: OLGA (Operative Link for Gastritis Assessment and OLGIM (Operative Link for Gastric Intestinal Metaplasia Assessment.Slovenian Society for Gastroenterology and Hepatology, and Slovenian Society for Pathology and Forensic Medicine have accepted guidelines for endoscopic and histologic management of patients with gastric precancerosis. The aim of these recommendations is to diagnose gastric cancer at an early stage and to improve survival of patients with gastric cancer in Slovenia.

  7. The preponderance and dye-tissue receptive variability analyses of malignant and benign lesions of the female genitalia

    Directory of Open Access Journals (Sweden)

    F.M. Onyije

    2017-04-01

    Conclusion: Our study reported the preponderance of benign lesions than malignant lesions in the sample population. Comparatively, MT exhibited the best dye-tissue receptivity in both benign and malignant lesions than the baseline dye (H&E and remains a valuable tool for the diagnosis of gynecological lesions.

  8. Children with severe early childhood caries: streptococci genetic strains within carious and white spot lesions.

    Science.gov (United States)

    Gilbert, Kenneth; Joseph, Raphael; Vo, Alex; Patel, Trusha; Chaudhry, Samiya; Nguyen, Uyen; Trevor, Amy; Robinson, Erica; Campbell, Margaret; McLennan, John; Houran, Farielle; Wong, Tristan; Flann, Kendra; Wages, Melissa; Palmer, Elizabeth A; Peterson, John; Engle, John; Maier, Tom; Machida, Curtis A

    2014-01-01

    Mutans streptococci (MS) are one of the major microbiological determinants of dental caries. The objectives of this study are to identify distinct MS and non-MS streptococci strains that are located at carious sites and non-carious enamel surfaces in children with severe early childhood caries (S-ECC), and assess if cariogenic MS and non-cariogenic streptococci might independently exist as primary bacterial strains on distinct sites within the dentition of individual children. Dental plaque from children (N=20; aged 3-6) with S-ECC was collected from carious lesions (CLs), white spot lesions (WSLs) and non-carious enamel surfaces. Streptococcal isolates (N=10-20) from each site were subjected to polymerase chain reaction (PCR) to identify MS, and arbitrarily primed-PCR for assignment of genetic strains. Primary strains were identified as ≥50% of the total isolates surveyed at any site. In several cases, strains were characterized for acidurity using ATP-driven bioluminescence and subjected to PCR-determination of potential MS virulence products. Identification of non-MS was determined by 16S rRNA gene sequencing. Sixty-four independent MS or non-MS streptococcal strains were identified. All children contained 1-6 strains. In many patients (N=11), single primary MS strains were identified throughout the dentition. In other patients (N=4), primary MS strains were identified within CLs that were distinct from primary strains found on enamel. Streptococcus gordonii strains were identified as primary strains on enamel or WSLs in four children, and in general were less aciduric than MS strains. Many children with S-ECC contained only a single primary MS strain that was present in both carious and non-carious sites. In some cases, MS and non-cariogenic S. gordonii strains were found to independently exist as dominant strains at different locations within the dentition of individual children, and the aciduric potential of these strains may influence susceptibility in the

  9. Children with severe early childhood caries: streptococci genetic strains within carious and white spot lesions

    Directory of Open Access Journals (Sweden)

    Kenneth Gilbert

    2014-10-01

    Full Text Available Background and objectives: Mutans streptococci (MS are one of the major microbiological determinants of dental caries. The objectives of this study are to identify distinct MS and non-MS streptococci strains that are located at carious sites and non-carious enamel surfaces in children with severe early childhood caries (S-ECC, and assess if cariogenic MS and non-cariogenic streptococci might independently exist as primary bacterial strains on distinct sites within the dentition of individual children. Design: Dental plaque from children (N=20; aged 3–6 with S-ECC was collected from carious lesions (CLs, white spot lesions (WSLs and non-carious enamel surfaces. Streptococcal isolates (N=10–20 from each site were subjected to polymerase chain reaction (PCR to identify MS, and arbitrarily primed-PCR for assignment of genetic strains. Primary strains were identified as ≥50% of the total isolates surveyed at any site. In several cases, strains were characterized for acidurity using ATP-driven bioluminescence and subjected to PCR-determination of potential MS virulence products. Identification of non-MS was determined by 16S rRNA gene sequencing. Results: Sixty-four independent MS or non-MS streptococcal strains were identified. All children contained 1–6 strains. In many patients (N=11, single primary MS strains were identified throughout the dentition. In other patients (N=4, primary MS strains were identified within CLs that were distinct from primary strains found on enamel. Streptococcus gordonii strains were identified as primary strains on enamel or WSLs in four children, and in general were less aciduric than MS strains. Conclusions: Many children with S-ECC contained only a single primary MS strain that was present in both carious and non-carious sites. In some cases, MS and non-cariogenic S. gordonii strains were found to independently exist as dominant strains at different locations within the dentition of individual children, and

  10. Phylogeographic analyses and genetic structure illustrate the complex evolutionary history of Phragmites australis in Mexico.

    Science.gov (United States)

    Colin, Ricardo; Eguiarte, Luis E

    2016-05-01

    Genetic data suggest that three lineages of Phragmites australis are found in North America: the Native North American lineage, the Gulf Coast lineage, and the Invasive lineage. In Mexico, P. australis is a common species, but nothing is known about the distribution or ecology of these lineages. We examined the phylogeography of P. australis to analyze the current geographic distribution of genetic variation, demographic history, and dispersal patterns to better understand its evolutionary history in Mexico. We sampled 427 individuals from 28 populations. We used two noncoding regions of chloroplast DNA to estimate the levels of genetic variation and identified the genetic groups across the species' geographical range in Mexico. We compared the genealogical relationships among haplotypes with those previously reported. A hypothesis of demographic expansion was also tested for the Mexican P. australis lineages. We found 13 new haplotypes native to Mexico that might be undergoing an active process of expansion and diversification. Genealogical analyses provided evidence that two independent lineages of P. australis are present in Mexico. The invasive lineage was not detected with our sampling. Our estimates of population expansions in Mexico ranged from 0.202 to 0.726 mya. Phragmites australis is a native species that has been in Mexico for thousands of years. Genetic data suggest that climatic changes during the Pleistocene played an important role in the demographic expansion of the populations that constitute the different genetic groups of P. australis in Mexico. © 2016 Botanical Society of America.

  11. Multicollinearity in spatial genetics: separating the wheat from the chaff using commonality analyses.

    Science.gov (United States)

    Prunier, J G; Colyn, M; Legendre, X; Nimon, K F; Flamand, M C

    2015-01-01

    Direct gradient analyses in spatial genetics provide unique opportunities to describe the inherent complexity of genetic variation in wildlife species and are the object of many methodological developments. However, multicollinearity among explanatory variables is a systemic issue in multivariate regression analyses and is likely to cause serious difficulties in properly interpreting results of direct gradient analyses, with the risk of erroneous conclusions, misdirected research and inefficient or counterproductive conservation measures. Using simulated data sets along with linear and logistic regressions on distance matrices, we illustrate how commonality analysis (CA), a detailed variance-partitioning procedure that was recently introduced in the field of ecology, can be used to deal with nonindependence among spatial predictors. By decomposing model fit indices into unique and common (or shared) variance components, CA allows identifying the location and magnitude of multicollinearity, revealing spurious correlations and thus thoroughly improving the interpretation of multivariate regressions. Despite a few inherent limitations, especially in the case of resistance model optimization, this review highlights the great potential of CA to account for complex multicollinearity patterns in spatial genetics and identifies future applications and lines of research. We strongly urge spatial geneticists to systematically investigate commonalities when performing direct gradient analyses. © 2014 John Wiley & Sons Ltd.

  12. Thirty years of Alzheimer's disease genetics: the implications of systematic meta-analyses.

    Science.gov (United States)

    Bertram, Lars; Tanzi, Rudolph E

    2008-10-01

    The genetic underpinnings of Alzheimer's disease (AD) remain largely elusive despite early successes in identifying three genes that cause early-onset familial AD (those that encode amyloid precursor protein (APP) and the presenilins (PSEN1 and PSEN2)), and one genetic risk factor for late-onset AD (the gene that encodes apolipoprotein E (APOE)). A large number of studies that aimed to help uncover the remaining disease-related loci have been published in recent decades, collectively proposing or refuting the involvement of over 500 different gene candidates. Systematic meta-analyses of these studies currently highlight more than 20 loci that have modest but significant effects on AD risk. This Review discusses the putative pathogenetic roles and common biochemical pathways of some of the most genetically and biologically compelling of these potential AD risk factors.

  13. Clinical Perspectives of Genetic Analyses on Dyslipidemia and Coronary Artery Disease

    Science.gov (United States)

    Kawashiri, Masa-aki; Yamagishi, Masakazu

    2017-01-01

    We have learned that low-density lipoprotein (LDL) cholesterol is the cause of atherosclerosis from various aspects, including a single case with familial hypercholesterolemia, other cases with different types of Mendelian dyslipidemias, large-scale randomized controlled trials using LDL cholesterol lowering therapies, and Mendelian randomization studies using common as well as rare variants associated with LDL cholesterol levels. There is no doubt that determinations of genotypes in lipid-associated genes have contributed not only to the genetic diagnosis for Mendelian dyslipidemias but also to the discoveries of novel therapeutic targets. Furthermore, recent studies have shown that such genetic information could provide useful clues for the risk prediction as well as risk stratification in general and in particular population. We provide the current understanding of genetic analyses relating to plasma lipids and coronary artery disease. PMID:28250266

  14. Whole exome sequencing in 342 congenital cardiac left sided lesion cases reveals extensive genetic heterogeneity and complex inheritance patterns

    Directory of Open Access Journals (Sweden)

    Alexander H. Li

    2017-10-01

    Full Text Available Abstract Background Left-sided lesions (LSLs account for an important fraction of severe congenital cardiovascular malformations (CVMs. The genetic contributions to LSLs are complex, and the mutations that cause these malformations span several diverse biological signaling pathways: TGFB, NOTCH, SHH, and more. Here, we use whole exome sequence data generated in 342 LSL cases to identify likely damaging variants in putative candidate CVM genes. Methods Using a series of bioinformatics filters, we focused on genes harboring population-rare, putative loss-of-function (LOF, and predicted damaging variants in 1760 CVM candidate genes constructed a priori from the literature and model organism databases. Gene variants that were not observed in a comparably sequenced control dataset of 5492 samples without severe CVM were then subjected to targeted validation in cases and parents. Whole exome sequencing data from 4593 individuals referred for clinical sequencing were used to bolster evidence for the role of candidate genes in CVMs and LSLs. Results Our analyses revealed 28 candidate variants in 27 genes, including 17 genes not previously associated with a human CVM disorder, and revealed diverse patterns of inheritance among LOF carriers, including 9 confirmed de novo variants in both novel and newly described human CVM candidate genes (ACVR1, JARID2, NR2F2, PLRG1, SMURF1 as well as established syndromic CVM genes (KMT2D, NF1, TBX20, ZEB2. We also identified two genes (DNAH5, OFD1 with evidence of recessive and hemizygous inheritance patterns, respectively. Within our clinical cohort, we also observed heterozygous LOF variants in JARID2 and SMAD1 in individuals with cardiac phenotypes, and collectively, carriers of LOF variants in our candidate genes had a four times higher odds of having CVM (odds ratio = 4.0, 95% confidence interval 2.5–6.5. Conclusions Our analytical strategy highlights the utility of bioinformatic resources, including human

  15. The Autism Simplex Collection : an international, expertly phenotyped autism sample for genetic and phenotypic analyses

    OpenAIRE

    Buxbaum, Joseph D.; Bolshakova, Nadia; Brownfeld, Jessica M.; Anney, Richard J. L.; Bender, Patrick; Bernier, Raphael; Cook, Edwin H.; Coon, Hilary; Cuccaro, Michael L.; Freitag, Christine M.; Hallmayer, Joachim; Geschwind, Daniel H.; Klauck, Sabine M.; Nurnberger, John I.; Oliveira, Guiomar

    2014-01-01

    Background: There is an urgent need for expanding and enhancing autism spectrum disorder (ASD) samples, in order to better understand causes of ASD. Methods: In a unique public-private partnership, 13 sites with extensive experience in both the assessment and diagnosis of ASD embarked on an ambitious, 2-year program to collect samples for genetic and phenotypic research and begin analyses on these samples. The program was called The Autism Simplex Collection (TASC). TASC sample collection ...

  16. [Noonan syndrome can be diagnosed clinically and through molecular genetic analyses].

    Science.gov (United States)

    Henningsen, Marie Krab; Jelsig, Anne Marie; Andersen, Helle; Brusgaard, Klaus; Ousager, Lilian Bomme; Hertz, Jens Michael

    2015-08-03

    Noonan syndrome is part of the group of RASopathies caused by germ line mutations in genes involved in the RAS/MAPK pathway. There is substantial phenotypic overlap among the RASopathies. Diagnosis of Noonan syndrome is often based on clinical features including dysmorphic facial features, short stature and congenital heart disease. Rapid advances in sequencing technology have made molecular genetic analyses a helpful tool in diagnosing and distinguishing Noonan syndrome from other RASopathies.

  17. Molecular - and genetic aspects of the repair of the lesions induced by the furocoumarin photoaddition in Sacharomyces cerevisiae : role of the PSO genes

    International Nuclear Information System (INIS)

    Henriques, J.A.P.

    1982-01-01

    Experiences with strains of Sacharomyces cerevisiae with the aim to obtain informations about molecular steps and genetic control of the DNA photo-induced lesion repair by furocoumarins are described. (M.A.) [pt

  18. Analysing the Progression Rates of Macular Lesions with Autofluorescence Imaging Modes in Dry Age-Related Macular Degeneration

    Directory of Open Access Journals (Sweden)

    Kenan Olcay

    2015-12-01

    Full Text Available Objectives: In this study we aimed to compare the sensitivity of blue-light fundus autofluorescence (FAF and near-infrared autofluorescence (NI-AF imaging for determining the progression rates of macular lesions in dry age-related macular degeneration (AMD. Materials and Methods: The study was designed retrospectively and included patients diagnosed with intermediate and advanced stage dry AMD. Best corrected visual acuities and FAF and NI-AF images were recorded in 46 eyes of 33 patients. Lesion borders were drawn manually on the images using Heidelberg Eye Explorer software and lesion areas were calculated by using Microsoft Excel software. BCVA and lesion areas were compared with each other. Results: Patients’ mean follow-up time was 30.98±13.30 months. The lesion area progression rates were 0.85±0.93 mm2/y in FAF and 0.93±1.01 mm2/y in NI-AF, showing statistically significant correlation with each other (r=0.883; p<0.01. Both imaging methods are moderately correlated with visual acuity impairment (r=0.362; p<0.05 and r=0.311; p<0.05, respectively. In addition, larger lesions showed higher progression rates than smaller ones in both imaging methods. Conclusion: NI-AF imaging is as important and effective as FAF imaging for follow-up of dry AMD patients.

  19. Molecular responses of genetically modified maize to abiotic stresses as determined through proteomic and metabolomic analyses.

    Directory of Open Access Journals (Sweden)

    Rafael Fonseca Benevenuto

    Full Text Available Some genetically modified (GM plants have transgenes that confer tolerance to abiotic stressors. Meanwhile, other transgenes may interact with abiotic stressors, causing pleiotropic effects that will affect the plant physiology. Thus, physiological alteration might have an impact on the product safety. However, routine risk assessment (RA analyses do not evaluate the response of GM plants exposed to different environmental conditions. Therefore, we here present a proteome profile of herbicide-tolerant maize, including the levels of phytohormones and related compounds, compared to its near-isogenic non-GM variety under drought and herbicide stresses. Twenty differentially abundant proteins were detected between GM and non-GM hybrids under different water deficiency conditions and herbicide sprays. Pathway enrichment analysis showed that most of these proteins are assigned to energetic/carbohydrate metabolic processes. Among phytohormones and related compounds, different levels of ABA, CA, JA, MeJA and SA were detected in the maize varieties and stress conditions analysed. In pathway and proteome analyses, environment was found to be the major source of variation followed by the genetic transformation factor. Nonetheless, differences were detected in the levels of JA, MeJA and CA and in the abundance of 11 proteins when comparing the GM plant and its non-GM near-isogenic variety under the same environmental conditions. Thus, these findings do support molecular studies in GM plants Risk Assessment analyses.

  20. Mobile Genome Express (MGE: A comprehensive automatic genetic analyses pipeline with a mobile device.

    Directory of Open Access Journals (Sweden)

    Jun-Hee Yoon

    Full Text Available The development of next-generation sequencing (NGS technology allows to sequence whole exomes or genome. However, data analysis is still the biggest bottleneck for its wide implementation. Most laboratories still depend on manual procedures for data handling and analyses, which translates into a delay and decreased efficiency in the delivery of NGS results to doctors and patients. Thus, there is high demand for developing an automatic and an easy-to-use NGS data analyses system. We developed comprehensive, automatic genetic analyses controller named Mobile Genome Express (MGE that works in smartphones or other mobile devices. MGE can handle all the steps for genetic analyses, such as: sample information submission, sequencing run quality check from the sequencer, secured data transfer and results review. We sequenced an Actrometrix control DNA containing multiple proven human mutations using a targeted sequencing panel, and the whole analysis was managed by MGE, and its data reviewing program called ELECTRO. All steps were processed automatically except for the final sequencing review procedure with ELECTRO to confirm mutations. The data analysis process was completed within several hours. We confirmed the mutations that we have identified were consistent with our previous results obtained by using multi-step, manual pipelines.

  1. Mobile Genome Express (MGE): A comprehensive automatic genetic analyses pipeline with a mobile device.

    Science.gov (United States)

    Yoon, Jun-Hee; Kim, Thomas W; Mendez, Pedro; Jablons, David M; Kim, Il-Jin

    2017-01-01

    The development of next-generation sequencing (NGS) technology allows to sequence whole exomes or genome. However, data analysis is still the biggest bottleneck for its wide implementation. Most laboratories still depend on manual procedures for data handling and analyses, which translates into a delay and decreased efficiency in the delivery of NGS results to doctors and patients. Thus, there is high demand for developing an automatic and an easy-to-use NGS data analyses system. We developed comprehensive, automatic genetic analyses controller named Mobile Genome Express (MGE) that works in smartphones or other mobile devices. MGE can handle all the steps for genetic analyses, such as: sample information submission, sequencing run quality check from the sequencer, secured data transfer and results review. We sequenced an Actrometrix control DNA containing multiple proven human mutations using a targeted sequencing panel, and the whole analysis was managed by MGE, and its data reviewing program called ELECTRO. All steps were processed automatically except for the final sequencing review procedure with ELECTRO to confirm mutations. The data analysis process was completed within several hours. We confirmed the mutations that we have identified were consistent with our previous results obtained by using multi-step, manual pipelines.

  2. Variability of Cutaneous Leishmaniasis Lesions Is Not Associated with Genetic Diversity of Leishmania tropica in Khyber Pakhtunkhwa Province of Pakistan.

    Science.gov (United States)

    Khan, Nazma Habib; Llewellyn, Martin S; Schönian, Gabriele; Sutherland, Colin J

    2017-11-01

    Leishmania tropica is the causative agent of cutaneous leishmaniasis in Pakistan. Here, intraspecific diversity of L. tropica from northern Pakistan was investigated using multilocus microsatellite typing. Fourteen polymorphic microsatellite markers were typed in 34 recently collected L. tropica isolates from Pakistan along with 158 archival strains of diverse Afro-Eurasian origins. Previously published profiles for 145 strains of L. tropica originating from different regions of Africa, Central Asia, Iran, and Middle East were included for comparison. Six consistently well-supported genetic groups were resolved: 1) Asia, 2) Morroco A, 3) Namibia and Kenya A, 4) Kenya B/Tunisia and Galilee, 5) Morocco B, and 6) Middle East. Strains from northern Pakistan were assigned to Asian cluster except for three that were placed in a geographically distant genetic group; Morocco A. Lesion variability among these Pakistani strains was not associated with specific L. tropica genetic profile. Pakistani strains showed little genetic differentiation from strains of Iraq, Afghanistan, and Syria (F ST = 0.00-0.06); displayed evidence of modest genetic flow with India (F ST = 0.14). Furthermore, genetic structuring within these isolates was not geographically defined. Pak-Afghan cluster was in significant linkage disequilibrium (I A = 1.43), had low genetic diversity, and displayed comparatively higher heterozygosity (F IS = -0.62). Patterns of genetic diversity observed suggest dominance of a minimally diverse clonal lineage within northern Pakistan. This is surprising as a wide clinical spectrum was observed in patients, suggesting the importance of host and other factors. Further genotyping studies of L. tropica isolates displaying different clinical phenotypes are required to validate this potentially important observation.

  3. Genetic Ablation of Soluble TNF Does Not Affect Lesion Size and Functional Recovery after Moderate Spinal Cord Injury in Mice

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    Ditte Gry Ellman

    2016-01-01

    Full Text Available Traumatic spinal cord injury (SCI is followed by an instant increase in expression of the microglial-derived proinflammatory cytokine tumor necrosis factor (TNF within the lesioned cord. TNF exists both as membrane-anchored TNF (mTNF and as cleaved soluble TNF (solTNF. We previously demonstrated that epidural administration of a dominant-negative inhibitor of solTNF, XPro1595, to the contused spinal cord resulted in changes in Iba1 protein expression in microglia/macrophages, decreased lesion volume, and improved locomotor function. Here, we extend our studies using mice expressing mTNF, but no solTNF (mTNFΔ/Δ, to study the effect of genetic ablation of solTNF on SCI. We demonstrate that TNF levels were significantly decreased within the lesioned spinal cord 3 days after SCI in mTNFΔ/Δ mice compared to littermates. This decrease did, however, not translate into significant changes in other pro- and anti-inflammatory cytokines (IL-10, IL-1β, IL-6, IL-5, IL-2, CXCL1, CCL2, or CCL5, despite a tendency towards increased IL-10 and decreased IL-1β, TNFR1, and TNFR2 levels in mTNFΔ/Δ mice. In addition, microglial and leukocyte infiltration, activation state (Iba1, CD11b, CD11c, CD45, and MHCII, lesion size, and functional outcome after moderate SCI were comparable between genotypes. Collectively, our data demonstrate that genetic ablation of solTNF does not significantly modulate postlesion outcome after SCI.

  4. Mitochondrial DNA analyses reveal low genetic diversity in Culex quinquefasciatus from residential areas in Malaysia.

    Science.gov (United States)

    Low, V L; Lim, P E; Chen, C D; Lim, Y A L; Tan, T K; Norma-Rashid, Y; Lee, H L; Sofian-Azirun, M

    2014-06-01

    The present study explored the intraspecific genetic diversity, dispersal patterns and phylogeographic relationships of Culex quinquefasciatus Say (Diptera: Culicidae) in Malaysia using reference data available in GenBank in order to reveal this species' phylogenetic relationships. A statistical parsimony network of 70 taxa aligned as 624 characters of the cytochrome c oxidase subunit I (COI) gene and 685 characters of the cytochrome c oxidase subunit II (COII) gene revealed three haplotypes (A1-A3) and four haplotypes (B1-B4), respectively. The concatenated sequences of both COI and COII genes with a total of 1309 characters revealed seven haplotypes (AB1-AB7). Analysis using tcs indicated that haplotype AB1 was the common ancestor and the most widespread haplotype in Malaysia. The genetic distance based on concatenated sequences of both COI and COII genes ranged from 0.00076 to 0.00229. Sequence alignment of Cx. quinquefasciatus from Malaysia and other countries revealed four haplotypes (AA1-AA4) by the COI gene and nine haplotypes (BB1-BB9) by the COII gene. Phylogenetic analyses demonstrated that Malaysian Cx. quinquefasciatus share the same genetic lineage as East African and Asian Cx. quinquefasciatus. This study has inferred the genetic lineages, dispersal patterns and hypothetical ancestral genotypes of Cx. quinquefasciatus. © 2013 The Royal Entomological Society.

  5. Detection of Genetic Relationship in the Tree of Life of Some Quail Through Molecular Markers Analyses

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    Lamiaa Elsayed Mokhtar Deef

    2017-08-01

    Full Text Available ABSTRACT Quail is an important and interesting group of galliform birds. The Common quail (Coturnix coturnix; the Japanese quail (Coturnix japonica; the Panda quail (Coturnix japonica; the Dotted white quail (Coturnix japonica and the Bobwhite quail (Colinus virginianus were used in this study. PCR-RFLP and SDS-proteins were performed to reveal the genetic characterization and genetic relationship of the studied quails. Analysis of fragments generated by digestion of PCR product with restriction enzyme NlaIII recorded highly polymorphic restriction profiles. There is a wide intraspecific COI, SEMA3E and TLX genes variability among the studied quails. Protein bands varied from10 to 18 between quails with minimum number of bands were in the Dotted white quail (10 bands and the maximum were in the Japanese quail (18 bands as measured by SDS-polyacrylamide gel electrophoresis. The Dotted white quail revealed the lowest similarity to the Bobwhite with a coefficient of 0.18 while The similarity coefficients between the Common quail and each one of the other quails were 0.67, 0.62, 0.45 and 0.42 for the Japanese, Panda, Dotted white and the Bobwhite quails, respectively. The results indicate that, PCR-RFLP and protein analyses are good techniques to evaluate genetic characterization and genetic relationship of these quails.

  6. Chemometrical characterization of four italian rice varieties based on genetic and chemical analyses.

    Science.gov (United States)

    Brandolini, Vincenzo; Coïsson, Jean Daniel; Tedeschi, Paola; Barile, Daniela; Cereti, Elisabetta; Maietti, Annalisa; Vecchiati, Giorgio; Martelli, Aldo; Arlorio, Marco

    2006-12-27

    This paper describes a method for achieving qualitative identification of four rice varieties from two different Italian regions. To estimate the presence of genetic diversity among the four rice varieties, we used polymerase chain reaction-randomly amplified polymorphic DNA (PCR-RAPD) markers, and to elucidate whether a relationship exists between the ground and the specific characteristics of the product, we studied proximate composition, fatty acid composition, mineral content, and total antioxidant capacity. Using principal component analysis on genomic and compositional data, we were able to classify rice samples according to their variety and their district of production. This work also examined the discrimination ability of different parameters. It was found that genomic data give the best discrimination based on varieties, indicating that RAPD assays could be useful in discriminating among closely related species, while compositional analyses do not depend on the genetic characters only but are related to the production area.

  7. Complete genome of a European hepatitis C virus subtype 1g isolate: phylogenetic and genetic analyses.

    Science.gov (United States)

    Bracho, Maria A; Saludes, Verónica; Martró, Elisa; Bargalló, Ana; González-Candelas, Fernando; Ausina, Vicent

    2008-06-05

    Hepatitis C virus isolates have been classified into six main genotypes and a variable number of subtypes within each genotype, mainly based on phylogenetic analysis. Analyses of the genetic relationship among genotypes and subtypes are more reliable when complete genome sequences (or at least the full coding region) are used; however, so far 31 of 80 confirmed or proposed subtypes have at least one complete genome available. Of these, 20 correspond to confirmed subtypes of epidemic interest. We present and analyse the first complete genome sequence of a HCV subtype 1g isolate. Phylogenetic and genetic distance analyses reveal that HCV-1g is the most divergent subtype among the HCV-1 confirmed subtypes. Potential genomic recombination events between genotypes or subtype 1 genomes were ruled out. We demonstrate phylogenetic congruence of previously deposited partial sequences of HCV-1g with respect to our sequence. In light of this, we propose changing the current status of its subtype-specific designation from provisional to confirmed.

  8. Complete genome of a European hepatitis C virus subtype 1g isolate: phylogenetic and genetic analyses

    Directory of Open Access Journals (Sweden)

    Bargalló Ana

    2008-06-01

    Full Text Available Abstract Background Hepatitis C virus isolates have been classified into six main genotypes and a variable number of subtypes within each genotype, mainly based on phylogenetic analysis. Analyses of the genetic relationship among genotypes and subtypes are more reliable when complete genome sequences (or at least the full coding region are used; however, so far 31 of 80 confirmed or proposed subtypes have at least one complete genome available. Of these, 20 correspond to confirmed subtypes of epidemic interest. Results We present and analyse the first complete genome sequence of a HCV subtype 1g isolate. Phylogenetic and genetic distance analyses reveal that HCV-1g is the most divergent subtype among the HCV-1 confirmed subtypes. Potential genomic recombination events between genotypes or subtype 1 genomes were ruled out. We demonstrate phylogenetic congruence of previously deposited partial sequences of HCV-1g with respect to our sequence. Conclusion In light of this, we propose changing the current status of its subtype-specific designation from provisional to confirmed.

  9. Electron Microscopic, Genetic and Protein Expression Analyses of Helicobacter acinonychis Strains from a Bengal Tiger

    Science.gov (United States)

    Tegtmeyer, Nicole; Rivas Traverso, Francisco; Rohde, Manfred; Oyarzabal, Omar A.; Lehn, Norbert; Schneider-Brachert, Wulf; Ferrero, Richard L.; Fox, James G.; Berg, Douglas E.; Backert, Steffen

    2013-01-01

    Colonization by Helicobacter species is commonly noted in many mammals. These infections often remain unrecognized, but can cause severe health complications or more subtle host immune perturbations. The aim of this study was to isolate and characterize putative novel Helicobacter spp. from Bengal tigers in Thailand. Morphological investigation (Gram-staining and electron microscopy) and genetic studies (16SrRNA, 23SrRNA, flagellin, urease and prophage gene analyses, RAPD DNA fingerprinting and restriction fragment polymorphisms) as well as Western blotting were used to characterize the isolated Helicobacters. Electron microscopy revealed spiral-shaped bacteria, which varied in length (2.5–6 µm) and contained up to four monopolar sheathed flagella. The 16SrRNA, 23SrRNA, sequencing and protein expression analyses identified novel H. acinonychis isolates closely related to H. pylori. These Asian isolates are genetically very similar to H. acinonychis strains of other big cats (cheetahs, lions, lion-tiger hybrid and other tigers) from North America and Europe, which is remarkable in the context of the great genetic diversity among worldwide H. pylori strains. We also found by immunoblotting that the Bengal tiger isolates express UreaseA/B, flagellin, BabA adhesin, neutrophil-activating protein NapA, HtrA protease, γ-glutamyl-transpeptidase GGT, Slt lytic transglycosylase and two DNA transfer relaxase orthologs that were known from H. pylori, but not the cag pathogenicity island, nor CagA, VacA, SabA, DupA or OipA proteins. These results give fresh insights into H. acinonychis genetics and the expression of potential pathogenicity-associated factors and their possible pathophysiological relevance in related gastric infections. PMID:23940723

  10. Electron microscopic, genetic and protein expression analyses of Helicobacter acinonychis strains from a Bengal tiger.

    Directory of Open Access Journals (Sweden)

    Nicole Tegtmeyer

    Full Text Available Colonization by Helicobacter species is commonly noted in many mammals. These infections often remain unrecognized, but can cause severe health complications or more subtle host immune perturbations. The aim of this study was to isolate and characterize putative novel Helicobacter spp. from Bengal tigers in Thailand. Morphological investigation (Gram-staining and electron microscopy and genetic studies (16SrRNA, 23SrRNA, flagellin, urease and prophage gene analyses, RAPD DNA fingerprinting and restriction fragment polymorphisms as well as Western blotting were used to characterize the isolated Helicobacters. Electron microscopy revealed spiral-shaped bacteria, which varied in length (2.5-6 µm and contained up to four monopolar sheathed flagella. The 16SrRNA, 23SrRNA, sequencing and protein expression analyses identified novel H. acinonychis isolates closely related to H. pylori. These Asian isolates are genetically very similar to H. acinonychis strains of other big cats (cheetahs, lions, lion-tiger hybrid and other tigers from North America and Europe, which is remarkable in the context of the great genetic diversity among worldwide H. pylori strains. We also found by immunoblotting that the Bengal tiger isolates express UreaseA/B, flagellin, BabA adhesin, neutrophil-activating protein NapA, HtrA protease, γ-glutamyl-transpeptidase GGT, Slt lytic transglycosylase and two DNA transfer relaxase orthologs that were known from H. pylori, but not the cag pathogenicity island, nor CagA, VacA, SabA, DupA or OipA proteins. These results give fresh insights into H. acinonychis genetics and the expression of potential pathogenicity-associated factors and their possible pathophysiological relevance in related gastric infections.

  11. Electron microscopic, genetic and protein expression analyses of Helicobacter acinonychis strains from a Bengal tiger.

    Science.gov (United States)

    Tegtmeyer, Nicole; Rivas Traverso, Francisco; Rohde, Manfred; Oyarzabal, Omar A; Lehn, Norbert; Schneider-Brachert, Wulf; Ferrero, Richard L; Fox, James G; Berg, Douglas E; Backert, Steffen

    2013-01-01

    Colonization by Helicobacter species is commonly noted in many mammals. These infections often remain unrecognized, but can cause severe health complications or more subtle host immune perturbations. The aim of this study was to isolate and characterize putative novel Helicobacter spp. from Bengal tigers in Thailand. Morphological investigation (Gram-staining and electron microscopy) and genetic studies (16SrRNA, 23SrRNA, flagellin, urease and prophage gene analyses, RAPD DNA fingerprinting and restriction fragment polymorphisms) as well as Western blotting were used to characterize the isolated Helicobacters. Electron microscopy revealed spiral-shaped bacteria, which varied in length (2.5-6 µm) and contained up to four monopolar sheathed flagella. The 16SrRNA, 23SrRNA, sequencing and protein expression analyses identified novel H. acinonychis isolates closely related to H. pylori. These Asian isolates are genetically very similar to H. acinonychis strains of other big cats (cheetahs, lions, lion-tiger hybrid and other tigers) from North America and Europe, which is remarkable in the context of the great genetic diversity among worldwide H. pylori strains. We also found by immunoblotting that the Bengal tiger isolates express UreaseA/B, flagellin, BabA adhesin, neutrophil-activating protein NapA, HtrA protease, γ-glutamyl-transpeptidase GGT, Slt lytic transglycosylase and two DNA transfer relaxase orthologs that were known from H. pylori, but not the cag pathogenicity island, nor CagA, VacA, SabA, DupA or OipA proteins. These results give fresh insights into H. acinonychis genetics and the expression of potential pathogenicity-associated factors and their possible pathophysiological relevance in related gastric infections.

  12. Genetic analyses of partial egg production in Japanese quail using multi-trait random regression models.

    Science.gov (United States)

    Karami, K; Zerehdaran, S; Barzanooni, B; Lotfi, E

    2017-12-01

    1. The aim of the present study was to estimate genetic parameters for average egg weight (EW) and egg number (EN) at different ages in Japanese quail using multi-trait random regression (MTRR) models. 2. A total of 8534 records from 900 quail, hatched between 2014 and 2015, were used in the study. Average weekly egg weights and egg numbers were measured from second until sixth week of egg production. 3. Nine random regression models were compared to identify the best order of the Legendre polynomials (LP). The most optimal model was identified by the Bayesian Information Criterion. A model with second order of LP for fixed effects, second order of LP for additive genetic effects and third order of LP for permanent environmental effects (MTRR23) was found to be the best. 4. According to the MTRR23 model, direct heritability for EW increased from 0.26 in the second week to 0.53 in the sixth week of egg production, whereas the ratio of permanent environment to phenotypic variance decreased from 0.48 to 0.1. Direct heritability for EN was low, whereas the ratio of permanent environment to phenotypic variance decreased from 0.57 to 0.15 during the production period. 5. For each trait, estimated genetic correlations among weeks of egg production were high (from 0.85 to 0.98). Genetic correlations between EW and EN were low and negative for the first two weeks, but they were low and positive for the rest of the egg production period. 6. In conclusion, random regression models can be used effectively for analysing egg production traits in Japanese quail. Response to selection for increased egg weight would be higher at older ages because of its higher heritability and such a breeding program would have no negative genetic impact on egg production.

  13. Genome sequencing elucidates Sardinian genetic architecture and augments association analyses for lipid and blood inflammatory markers

    Science.gov (United States)

    Zoledziewska, Magdalena; Mulas, Antonella; Pistis, Giorgio; Steri, Maristella; Danjou, Fabrice; Kwong, Alan; Ortega del Vecchyo, Vicente Diego; Chiang, Charleston W. K.; Bragg-Gresham, Jennifer; Pitzalis, Maristella; Nagaraja, Ramaiah; Tarrier, Brendan; Brennan, Christine; Uzzau, Sergio; Fuchsberger, Christian; Atzeni, Rossano; Reinier, Frederic; Berutti, Riccardo; Huang, Jie; Timpson, Nicholas J; Toniolo, Daniela; Gasparini, Paolo; Malerba, Giovanni; Dedoussis, George; Zeggini, Eleftheria; Soranzo, Nicole; Jones, Chris; Lyons, Robert; Angius, Andrea; Kang, Hyun M.; Novembre, John; Sanna, Serena; Schlessinger, David; Cucca, Francesco; Abecasis, Gonçalo R

    2015-01-01

    We report ~17.6M genetic variants from whole-genome sequencing of 2,120 Sardinians; 22% are absent from prior sequencing-based compilations and enriched for predicted functional consequence. Furthermore, ~76K variants common in our sample (frequency >5%) are rare elsewhere (Genomes Project). We assessed the impact of these variants on circulating lipid levels and five inflammatory biomarkers. Fourteen signals, including two major new loci, were observed for lipid levels, and 19, including two novel loci, for inflammatory markers. New associations would be missed in analyses based on 1000 Genomes data, underlining the advantages of large-scale sequencing in this founder population. PMID:26366554

  14. Genetic analyses of linear profiling data on 3-year-old Swedish Warmblood horses.

    Science.gov (United States)

    Viklund, Å; Eriksson, S

    2018-02-01

    A linear profiling protocol was introduced in 2013 at tests for 3-year-old Swedish Warmblood horses. In this protocol, traits are subjectively described on a nine-point linear scale from one biological extreme to the other. This complements the traditional scoring where horses are evaluated in relation to the breeding objective. This study aimed to investigate the suitability of the linear information for genetic evaluation. Data on 22 conformation traits, 17 movement traits, 14 jumping traits and one temperament trait from 3,410 horses tested between 2013 and 2016 were analysed using an animal model. For conformation traits, the heritabilities ranged from 0.10 for description of hock joint from behind to 0.52 for shape of the neck. For movement traits, the highest heritability (0.54) was estimated for elasticity in trot and the lowest (0.08) for energy in walk. The heritabilities for jumping traits ranged from 0.05 for the ability to focus on the assignment to 0.57 for scope. Genetic correlations between linear traits and corresponding traditionally scored traits were strong (-0.37 to in many cases <-0.9). The results show that the linear information is suitable for genetic evaluation and can be a useful tool for breeders. © 2018 Blackwell Verlag GmbH.

  15. Mitochondrial DNA analyses revealed low genetic diversity in the endangered Indian wild ass Equus hemionus khur.

    Science.gov (United States)

    Khaire, Devendra; Atkulwar, Ashwin; Farah, Sameera; Baig, Mumtaz

    2017-09-01

    The Indian wild ass Equus hemionus khur, belonging to ass-like equid branch, inhabits the dry and arid desert of the Little Rann of Kutch, Gujarat. The E. h. khur is the sole survivor of Asiatic wild ass species/subspecies in South Asia. To provide first ever insights into the genetic diversity, phylogeny, and demography of the endangered Indian wild ass, we sampled 52 free-ranging individuals from the Little Rann of Kutch by using a non-invasive methodology. The sequencing of 230 bp in cytochrome b (Cyt b) and displacement loop (D-loop) region revealed that current ∼4000 extant population of Indian wild ass harbours low genetic diversity. Phylogenetic analyses confirmed that E. h. khur, E. h. onager, and E. h. kulan belong to a single strict monophyletic clade. Therefore, we suggest the delimitation of the five E. hemionus subspecies in vogue to a single species E. hemionus. The application of molecular clock confirmed that the Asiatic wild ass had undergone diversification 0.65 Million years ago. Demographic measurements assessed using a Bayesian skyline plot demonstrated decline in the maternal effective population size of the Indian wild ass during different periods; these periods coincided with the origin and rise of the Indus civilization in the northwest of the Indian subcontinent during the Neolithic. In conclusion, maintaining high genetic diversity in the existing isolated population of 4000 Indian wild asses inhabiting the wild ass sanctuary is important compared with subspecies preservation alone.

  16. Will an "island" population of voles be recolonized if eradicated? Insights from molecular genetic analyses

    Science.gov (United States)

    Miller, Mark P.; Haig, Susan M.; Ledig, David B.; Vander Heyden, Madeleine F.; Bennett, Gregory

    2011-01-01

    We performed genetic analyses of Microtus longicaudus populations within the Crook Point Unit of the Oregon Islands National Wildlife Refuge. A M. longicaudus population at Saddle Rock (located approx. 65 m off-shore from the Crook Point mainland) is suspected to be partially responsible for declines of a Leach's storm-petrel colony at this important nesting site. Using Amplified Fragment Length Polymorphism markers and mitochondrial DNA, we illustrate that Saddle Rock and Crook Point function as separate island and mainland populations despite their close proximity. In addition to genetic structure, we also observed reduced genetic diversity at Saddle Rock, suggesting that little individual movement occurs between populations. If local resource managers decide to perform an eradication at Saddle Rock, we conclude that immediate recolonization of the island by M. longicaudus would be unlikely. Because M. longicaudus is native to Oregon, we also consider the degree with which the differentiation of Saddle Rock signifies the presence of a unique entity that warrants conservation rather than eradication. ?? The Wildlife Society, 2011.

  17. Comprehensive research synopsis and systematic meta-analyses in Parkinson's disease genetics: The PDGene database.

    Directory of Open Access Journals (Sweden)

    Christina M Lill

    Full Text Available More than 800 published genetic association studies have implicated dozens of potential risk loci in Parkinson's disease (PD. To facilitate the interpretation of these findings, we have created a dedicated online resource, PDGene, that comprehensively collects and meta-analyzes all published studies in the field. A systematic literature screen of -27,000 articles yielded 828 eligible articles from which relevant data were extracted. In addition, individual-level data from three publicly available genome-wide association studies (GWAS were obtained and subjected to genotype imputation and analysis. Overall, we performed meta-analyses on more than seven million polymorphisms originating either from GWAS datasets and/or from smaller scale PD association studies. Meta-analyses on 147 SNPs were supplemented by unpublished GWAS data from up to 16,452 PD cases and 48,810 controls. Eleven loci showed genome-wide significant (P < 5 × 10(-8 association with disease risk: BST1, CCDC62/HIP1R, DGKQ/GAK, GBA, LRRK2, MAPT, MCCC1/LAMP3, PARK16, SNCA, STK39, and SYT11/RAB25. In addition, we identified novel evidence for genome-wide significant association with a polymorphism in ITGA8 (rs7077361, OR 0.88, P  =  1.3 × 10(-8. All meta-analysis results are freely available on a dedicated online database (www.pdgene.org, which is cross-linked with a customized track on the UCSC Genome Browser. Our study provides an exhaustive and up-to-date summary of the status of PD genetics research that can be readily scaled to include the results of future large-scale genetics projects, including next-generation sequencing studies.

  18. Testing Genetic Pleiotropy with GWAS Summary Statistics for Marginal and Conditional Analyses.

    Science.gov (United States)

    Deng, Yangqing; Pan, Wei

    2017-12-01

    working independence model for robust inference. We provide numerical examples based on both simulated and real data, including two large lipid GWAS summary association datasets based on ∼100,000 and ∼189,000 samples, respectively, to demonstrate the difference between marginal and conditional analyses, as well as the effectiveness of our new approach. Copyright © 2017 by the Genetics Society of America.

  19. Intra-specific genetic relationship analyses of Elaeagnus angustifolia based on RP-HPLC biochemical markers

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    Elaeagnus angustifolia Linn. has various ecological, medicinal and economical uses. An approach was established using RP-HPLC (reversed-phase high-performance liquid chromatography) to classify and analyse the intra-specific genetic relationships of seventeen populations of E. angustifolia, collected from the Xinjiang areas of China. Chromatograms of alcohol-soluble proteins produced by seventeen populations ofE. angustifolia, were compared. Each chromatogram of alcohol-soluble proteins came from a single seed of one wild plant only. The results showed that when using a Waters Delta Pak. C18, 5 μm particle size reversed phase column (150 mm×3.9 mm), a linear gradient of 25%~60% solvent B with flow rate of 1 ml/min and run time of 67 min, the chromatography yielded optimum separation ofE. angustifolia alcohol-soluble proteins. Representative peaks in each population were chosen according to peak area and occurrence in every seed. The converted data on the elution peaks of each population were different and could be used to represent those populations. GSC (genetic similarity coefficients) of 41% to 62% showed a medium degree of genetic diversity among the populations in these eco-areas. Cluster analysis showed that the seventeen populations ofE. angustifolia could be divided into six clusters at the GSC=0.535 level and indicated the general and unique biochemical markers of these clusters. We suggest that E. angustifolia distribution in these eco-areas could be classified into six variable species. RP-HPLC was shown to be a rapid, repeatable and reliable method for E. angustifolia classification and identification and for analysis of genetic diversity.

  20. Rationale, Design, and Methodological Aspects of the BUDAPEST-GLOBAL Study (Burden of Atherosclerotic Plaques Study in Twins-Genetic Loci and the Burden of Atherosclerotic Lesions).

    Science.gov (United States)

    Maurovich-Horvat, Pál; Tárnoki, Dávid L; Tárnoki, Ádám D; Horváth, Tamás; Jermendy, Ádám L; Kolossváry, Márton; Szilveszter, Bálint; Voros, Viktor; Kovács, Attila; Molnár, Andrea Á; Littvay, Levente; Lamb, Hildo J; Voros, Szilard; Jermendy, György; Merkely, Béla

    2015-12-01

    The heritability of coronary atherosclerotic plaque burden, coronary geometry, and phenotypes associated with increased cardiometabolic risk are largely unknown. The primary aim of the Burden of Atherosclerotic Plaques Study in Twins-Genetic Loci and the Burden of Atherosclerotic Lesions (BUDAPEST-GLOBAL) study is to evaluate the influence of genetic and environmental factors on the burden of coronary artery disease. By design this is a prospective, single-center, classical twin study. In total, 202 twins (61 monozygotic pairs, 40 dizygotic same-sex pairs) were enrolled from the Hungarian Twin Registry database. All twins underwent non-contrast-enhanced computed tomography (CT) for the detection and quantification of coronary artery calcium and for the measurement of epicardial fat volumes. In addition, a single non-contrast-enhanced image slice was acquired at the level of L3-L4 to assess abdominal fat distribution. Coronary CT angiography was used for the detection and quantification of plaque, stenosis, and overall coronary artery disease burden. For the primary analysis, we will assess the presence and volume of atherosclerotic plaques. Furthermore, the 3-dimensional coronary geometry will be assessed based on the coronary CT angiography datasets. Additional phenotypic analyses will include per-patient epicardial and abdominal fat quantity measurements. Measurements obtained from monozygotic and dizygotic twin pairs will be compared to evaluate the genetic or environmental effects of the given phenotype. The BUDAPEST-GLOBAL study provides a unique framework to shed some light on the genetic and environmental influences of cardiometabolic disorders. © 2015 Wiley Periodicals, Inc.

  1. Correlation and regression analyses of genetic effects for different types of cells in mammals under radiation and chemical treatment

    International Nuclear Information System (INIS)

    Slutskaya, N.G.; Mosseh, I.B.

    2006-01-01

    Data about genetic mutations under radiation and chemical treatment for different types of cells have been analyzed with correlation and regression analyses. Linear correlation between different genetic effects in sex cells and somatic cells have found. The results may be extrapolated on sex cells of human and mammals. (authors)

  2. Molecular markers for analyses of intraspecific genetic diversity in the Asian Tiger mosquito, Aedes albopictus.

    Science.gov (United States)

    Manni, Mosè; Gomulski, Ludvik M; Aketarawong, Nidchaya; Tait, Gabriella; Scolari, Francesca; Somboon, Pradya; Guglielmino, Carmela R; Malacrida, Anna R; Gasperi, Giuliano

    2015-03-28

    The dramatic worldwide expansion of Aedes albopictus (the Asian tiger mosquito) and its vector competence for numerous arboviruses represent a growing threat to public health security. Molecular markers are crucially needed for tracking the rapid spread of this mosquito and to obtain a deeper knowledge of population structure. This is a fundamental requirement for the development of strict monitoring protocols and for the improvement of sustainable control measures. Wild population samples from putative source areas and from newly colonised regions were analysed for variability at the ribosomal DNA internal transcribed spacer 2 (ITS2). Moreover, a new set of 23 microsatellite markers (SSR) was developed. Sixteen of these SSRs were tested in an ancestral (Thailand) and two adventive Italian populations. Seventy-six ITS2 sequences representing 52 unique haplotypes were identified, and AMOVA indicated that most of their variation occurred within individuals (74.36%), while only about 8% was detected among populations. Spatial analyses of molecular variance revealed that haplotype genetic similarity was not related to the geographic proximity of populations and the haplotype phylogeny clearly indicated that highly related sequences were distributed across populations from different geographical regions. The SSR markers displayed a high level of polymorphism both in the ancestral and in adventive populations, and F ST estimates suggested the absence of great differentiation. The ancestral nature of the Thai population was corroborated by its higher level of variability. The two types of genetic markers here implemented revealed the distribution of genetic diversity within and between populations and provide clues on the dispersion dynamics of this species. It appears that the diffusion of this mosquito does not conform to a progressive expansion from the native Asian source area, but to a relatively recent and chaotic propagule distribution mediated by human activities

  3. Bayesian analyses of genetic parameters for growth traits in Nellore cattle raised on pasture.

    Science.gov (United States)

    Lopes, F B; Ferreira, J L; Lobo, R B; Rosa, G J M

    2017-07-06

    This study was carried out to investigate (co)variance components and genetic parameters for growth traits in beef cattle using a multi-trait model by Bayesian methods. Genetic and residual (co)variances and parameters were estimated for weights at standard ages of 120 (W120), 210 (W210), 365 (W365), and 450 days (W450), and for pre- and post-weaning daily weight gain (preWWG and postWWG) in Nellore cattle. Data were collected over 16 years (1993-2009), and all animals were raised on pasture in eight farms in the North of Brazil that participate in the National Association of Breeders and Researchers. Analyses were run by the Bayesian approach using Gibbs sampler. Additive direct heritabilities for W120, W210, W365, and W450 and for preWWG and postWWG were 0.28 ± 0.013, 0.32 ± 0.002, 0.31 ± 0.002, 0.50 ± 0.026, 0.61 ± 0.047, and 0.79 ± 0.055, respectively. The estimates of maternal heritability were 0.32 ± 0.012, 0.29 ± 0.004, 0.30 ± 0.005, 0.25 ± 0.015, 0.23 ± 0.017, and 0.22 ± 0.016, respectively, for W120, W210, W365, and W450 and for preWWG and postWWG. The estimates of genetic direct additive correlation among all traits were positive and ranged from 0.25 ± 0.03 (preWWG and postWWG) to 0.99 ± 0.00 (W210 and preWWG). The moderate to high estimates of heritability and genetic correlation for weights and daily weight gains at different ages is suggestive of genetic improvement in these traits by selection at an appropriate age. Maternal genetic effects seemed to be significant across the traits. When the focus is on direct and maternal effects, W210 seems to be a good criterium for the selection of Nellore cattle considering the importance of this breed as a major breed of beef cattle not only in Northern Brazil but all regions covered by tropical pastures. As in this study the genetic correlations among all traits were high, the selection based on weaning weight might be a good choice because at this age there are two important effects (maternal

  4. Genetic Markers Analyses and Bioinformatic Approaches to Distinguish Between Olive Tree (Olea europaea L.) Cultivars.

    Science.gov (United States)

    Ben Ayed, Rayda; Ben Hassen, Hanen; Ennouri, Karim; Rebai, Ahmed

    2016-12-01

    The genetic diversity of 22 olive tree cultivars (Olea europaea L.) sampled from different Mediterranean countries was assessed using 5 SNP markers (FAD2.1; FAD2.3; CALC; SOD and ANTHO3) located in four different genes. The genotyping analysis of the 22 cultivars with 5 SNP loci revealed 11 alleles (average 2.2 per allele). The dendrogram based on cultivar genotypes revealed three clusters consistent with the cultivars classification. Besides, the results obtained with the five SNPs were compared to those obtained with the SSR markers using bioinformatic analyses and by computing a cophenetic correlation coefficient, indicating the usefulness of the UPGMA method for clustering plant genotypes. Based on principal coordinate analysis using a similarity matrix, the first two coordinates, revealed 54.94 % of the total variance. This work provides a more comprehensive explanation of the diversity available in Tunisia olive cultivars, and an important contribution for olive breeding and olive oil authenticity.

  5. Phylogeographic and population genetic analyses reveal multiple species of Boa and independent origins of insular dwarfism.

    Science.gov (United States)

    Card, Daren C; Schield, Drew R; Adams, Richard H; Corbin, Andrew B; Perry, Blair W; Andrew, Audra L; Pasquesi, Giulia I M; Smith, Eric N; Jezkova, Tereza; Boback, Scott M; Booth, Warren; Castoe, Todd A

    2016-09-01

    Boa is a Neotropical genus of snakes historically recognized as monotypic despite its expansive distribution. The distinct morphological traits and color patterns exhibited by these snakes, together with the wide diversity of ecosystems they inhabit, collectively suggest that the genus may represent multiple species. Morphological variation within Boa also includes instances of dwarfism observed in multiple offshore island populations. Despite this substantial diversity, the systematics of the genus Boa has received little attention until very recently. In this study we examined the genetic structure and phylogenetic relationships of Boa populations using mitochondrial sequences and genome-wide SNP data obtained from RADseq. We analyzed these data at multiple geographic scales using a combination of phylogenetic inference (including coalescent-based species delimitation) and population genetic analyses. We identified extensive population structure across the range of the genus Boa and multiple lines of evidence for three widely-distributed clades roughly corresponding with the three primary land masses of the Western Hemisphere. We also find both mitochondrial and nuclear support for independent origins and parallel evolution of dwarfism on offshore island clusters in Belize and Cayos Cochinos Menor, Honduras. Copyright © 2016 Elsevier Inc. All rights reserved.

  6. A weighted U-statistic for genetic association analyses of sequencing data.

    Science.gov (United States)

    Wei, Changshuai; Li, Ming; He, Zihuai; Vsevolozhskaya, Olga; Schaid, Daniel J; Lu, Qing

    2014-12-01

    With advancements in next-generation sequencing technology, a massive amount of sequencing data is generated, which offers a great opportunity to comprehensively investigate the role of rare variants in the genetic etiology of complex diseases. Nevertheless, the high-dimensional sequencing data poses a great challenge for statistical analysis. The association analyses based on traditional statistical methods suffer substantial power loss because of the low frequency of genetic variants and the extremely high dimensionality of the data. We developed a Weighted U Sequencing test, referred to as WU-SEQ, for the high-dimensional association analysis of sequencing data. Based on a nonparametric U-statistic, WU-SEQ makes no assumption of the underlying disease model and phenotype distribution, and can be applied to a variety of phenotypes. Through simulation studies and an empirical study, we showed that WU-SEQ outperformed a commonly used sequence kernel association test (SKAT) method when the underlying assumptions were violated (e.g., the phenotype followed a heavy-tailed distribution). Even when the assumptions were satisfied, WU-SEQ still attained comparable performance to SKAT. Finally, we applied WU-SEQ to sequencing data from the Dallas Heart Study (DHS), and detected an association between ANGPTL 4 and very low density lipoprotein cholesterol. © 2014 WILEY PERIODICALS, INC.

  7. Genetic analyses of herding traits in the Border Collie using sheepdog trial data.

    Science.gov (United States)

    Storteig Horn, S; Steinheim, G; Fjerdingby Olsen, H; Gjerjordet, H F; Klemetsdal, G

    2017-04-01

    The aim of this study was to evaluate the quality of the data provided from sheepdog trials in Norway, estimate heritabilities, repeatabilities and genetic correlations for the traits included in the trial and make recommendations on how sheepdog trials best can be utilized in the breeding of Border Collies in Norway. The analyses were based on test results from sheepdog trials carried out in Norway from 1993 to 2012. A total of 45 732 records from 3841 Border Collies were available, but after quality assurance only a third was left. The results demonstrated little information in the data. Heritabilities varied between 0.010 and 0.056 with standard errors ranging from 0.010 to 0.023, while repeatabilities ranged from 0.041 to 0.286. There is a need to assure the quality of data to improve the information in the test results. We recommend adding new traits based on the Herding Trait Characterization scheme evaluated in Sweden, and on traits from the predatory motor pattern, regarded as common for all dogs. These new traits may be scored across the elements that make up the current trial system, which should be kept in place to stimulate participation in the genetic evaluation scheme. © 2016 Blackwell Verlag GmbH.

  8. Correlation of Klebsiella pneumoniae comparative genetic analyses with virulence profiles in a murine respiratory disease model.

    Directory of Open Access Journals (Sweden)

    Ramy A Fodah

    Full Text Available Klebsiella pneumoniae is a bacterial pathogen of worldwide importance and a significant contributor to multiple disease presentations associated with both nosocomial and community acquired disease. ATCC 43816 is a well-studied K. pneumoniae strain which is capable of causing an acute respiratory disease in surrogate animal models. In this study, we performed sequencing of the ATCC 43816 genome to support future efforts characterizing genetic elements required for disease. Furthermore, we performed comparative genetic analyses to the previously sequenced genomes from NTUH-K2044 and MGH 78578 to gain an understanding of the conservation of known virulence determinants amongst the three strains. We found that ATCC 43816 and NTUH-K2044 both possess the known virulence determinant for yersiniabactin, as well as a Type 4 secretion system (T4SS, CRISPR system, and an acetonin catabolism locus, all absent from MGH 78578. While both NTUH-K2044 and MGH 78578 are clinical isolates, little is known about the disease potential of these strains in cell culture and animal models. Thus, we also performed functional analyses in the murine macrophage cell lines RAW264.7 and J774A.1 and found that MGH 78578 (K52 serotype was internalized at higher levels than ATCC 43816 (K2 and NTUH-K2044 (K1, consistent with previous characterization of the antiphagocytic properties of K1 and K2 serotype capsules. We also examined the three K. pneumoniae strains in a novel BALB/c respiratory disease model and found that ATCC 43816 and NTUH-K2044 are highly virulent (LD50<100 CFU while MGH 78578 is relatively avirulent.

  9. Molecular genetic analyses of 300-year old skeletons from Auersperg tomb

    Directory of Open Access Journals (Sweden)

    Irena Zupanič Pajnič

    2014-01-01

    Full Text Available Background: In 2009 the archaeologists excavated five skeletons from a 17th-century archaeological site in Ljubljana. They were found in the side chapel of the church in the Franciscans monastery, which was the Auerspergs’ tomb. Beside the skeletons, the finds revealed a bronze bowl with the heart , and the name of Ferdinand II and the years of birth and death (1655–1706 engraved. In 2011, we were asked to identify those five skeletons. The skeletons were poorly preserved and bones degraded to small pieces. Fragments of femurs and teeth were preserved only in two skeletons, therefore for the remaining three the fragments of cranium were used for molecular genetic analyses.Methods: We cleaned the bones and teeth, removed surface contamination, and ground them into powder. Prior to DNA isolation, bone or tooth powder was decalcified. DNA was purified in the Biorobot EZ1 device (Qiagen. Nuclear DNA of the samples was quantified using real-time polymerase chain reaction (PCR. Short tandem repeat (STR typing of autosomal DNA was performed using Investigator ESSplex Kit (Qiagen, the NGM Kit (Applied Biosystems and the MiniFiler Kit (Applied Biosystems. Typing of the Y-STRs was performed using the YFiler Kit (Applied Biosystems. The two hypervariable regions HVI and HVII of the mtDNA were sequenced.Results: We were able to extract up to 10.7 ng DNA/g of tooth powder from Auersperg chapel archaeological site skeletal remains. We managed to obtain nuclear DNA for successful STR typing from skeletal remains that were over 300 years old. From one skeleton we obtained a complete male genetic profile of autosomal DNA, almost complete Y-STR haplotype, which enabled us to track the paternal line and mtDNA haplotype for HVI and HVII regions, which enabled us to track the maternal line. After comparing the profiles with elimination database, no match was found, and thus the authenticity of genetic profiles was confirmed.Conclusions: Now we are waiting for

  10. Genetic analysis of Enterobius vermicularis isolated from a chimpanzee with lethal hemorrhagic colitis and pathology of the associated lesions.

    Science.gov (United States)

    Yaguchi, Yuji; Okabayashi, Sachi; Abe, Niichiro; Masatou, Haruhisa; Iida, Shinya; Teramoto, Isao; Matsubayashi, Makoto; Shibahara, Tomoyuki

    2014-11-01

    Human pinworms, Enterobius vermicularis, are normally recognized as minor pathogens. However, a fatal case of human pinworm infection has been reported in a nonhuman primate, a zoo reared chimpanzee. Here, we histopathologically examined the lesions in tissues from the deceased chimpanzee and genetically characterized the isolated worms to investigate the pathogenicity and determine the phylogeny. We identified ulcers deep in the submucosa where many parasites were found to have invaded the lamina propria mucosa or submucous tissue. An inflammatory reaction consisting mainly of neutrophils and lymphocytes but not eosinophils was observed around the parasites, and intense hemorrhage in the lamina propria was confirmed. The parasites were morphologically similar to E. vermicularis based on the shape of the copulatory spicules. Mitochondrial cytochrome c oxidase subunit 1 gene products were amplified from worm DNA by PCR and were genetically identified as E. vermicularis based on >98.7% similarity of partial sequences. Phylogenetic analysis revealed that the sequences clustered together with other chimpanzee E. vermicularis isolates in a group which has been referred to as type C and which differs from human isolates (type A). The samples were negative for bacterial pathogens and Entamoeba histolytica indicating that E. vermicularis could be pathogenic in chimpanzees. Phylogenetic clustering of the isolates indicated that the parasite may be host specific.

  11. Genetic Analyses of a Three Generation Family Segregating Hirschsprung Disease and Iris Heterochromia.

    Directory of Open Access Journals (Sweden)

    Long Cui

    Full Text Available We present the genetic analyses conducted on a three-generation family (14 individuals with three members affected with isolated-Hirschsprung disease (HSCR and one with HSCR and heterochromia iridum (syndromic-HSCR, a phenotype reminiscent of Waardenburg-Shah syndrome (WS4. WS4 is characterized by pigmentary abnormalities of the skin, eyes and/or hair, sensorineural deafness and HSCR. None of the members had sensorineural deafness. The family was screened for copy number variations (CNVs using Illumina-HumanOmni2.5-Beadchip and for coding sequence mutations in WS4 genes (EDN3, EDNRB, or SOX10 and in the main HSCR gene (RET. Confocal microscopy and immunoblotting were used to assess the functional impact of the mutations. A heterozygous A/G transition in EDNRB was identified in 4 affected and 3 unaffected individuals. While in EDNRB isoforms 1 and 2 (cellular receptor the transition results in the abolishment of translation initiation (M1V, in isoform 3 (only in the cytosol the replacement occurs at Met91 (M91V and is predicted benign. Another heterozygous transition (c.-248G/A; -predicted to affect translation efficiency- in the 5'-untranslated region of EDN3 (EDNRB ligand was detected in all affected individuals but not in healthy carriers of the EDNRB mutation. Also, a de novo CNVs encompassing DACH1 was identified in the patient with heterochromia iridum and HSCR Since the EDNRB and EDN3 variants only coexist in affected individuals, HSCR could be due to the joint effect of mutations in genes of the same pathway. Iris heterochromia could be due to an independent genetic event and would account for the additional phenotype within the family.

  12. Comprehensive analyses of imprinted differentially methylated regions reveal epigenetic and genetic characteristics in hepatoblastoma

    International Nuclear Information System (INIS)

    Rumbajan, Janette Mareska; Aoki, Shigehisa; Kohashi, Kenichi; Oda, Yoshinao; Hata, Kenichiro; Saji, Tsutomu; Taguchi, Tomoaki; Tajiri, Tatsuro; Soejima, Hidenobu; Joh, Keiichiro; Maeda, Toshiyuki; Souzaki, Ryota; Mitsui, Kazumasa; Higashimoto, Ken; Nakabayashi, Kazuhiko; Yatsuki, Hitomi; Nishioka, Kenichi; Harada, Ryoko

    2013-01-01

    Aberrant methylation at imprinted differentially methylated regions (DMRs) in human 11p15.5 has been reported in many tumors including hepatoblastoma. However, the methylation status of imprinted DMRs in imprinted loci scattered through the human genome has not been analyzed yet in any tumors. The methylation statuses of 33 imprinted DMRs were analyzed in 12 hepatoblastomas and adjacent normal liver tissue by MALDI-TOF MS and pyrosequencing. Uniparental disomy (UPD) and copy number abnormalities were investigated with DNA polymorphisms. Among 33 DMRs analyzed, 18 showed aberrant methylation in at least 1 tumor. There was large deviation in the incidence of aberrant methylation among the DMRs. KvDMR1 and IGF2-DMR0 were the most frequently hypomethylated DMRs. INPP5Fv2-DMR and RB1-DMR were hypermethylated with high frequencies. Hypomethylation was observed at certain DMRs not only in tumors but also in a small number of adjacent histologically normal liver tissue, whereas hypermethylation was observed only in tumor samples. The methylation levels of long interspersed nuclear element-1 (LINE-1) did not show large differences between tumor tissue and normal liver controls. Chromosomal abnormalities were also found in some tumors. 11p15.5 and 20q13.3 loci showed the frequent occurrence of both genetic and epigenetic alterations. Our analyses revealed tumor-specific aberrant hypermethylation at some imprinted DMRs in 12 hepatoblastomas with additional suggestion for the possibility of hypomethylation prior to tumor development. Some loci showed both genetic and epigenetic alterations with high frequencies. These findings will aid in understanding the development of hepatoblastoma

  13. Diallel analyses and estimation of genetic parameters of hot pepper (Capsicum chinense Jacq.

    Directory of Open Access Journals (Sweden)

    Sousa João Alencar de

    2003-01-01

    Full Text Available The degree of heterosis in the genus Capsicum spp. is considered high; however, most of the studies refer to the species Capsicum annuum L. In spite of the potential use of F1 hybrids in pungent peppers of the species Capsicum chinense, few studies are available which assess the magnitude of heterosis in this species . This study was carried out to assess heterosis and its components in F1 hybrids from a diallel cross between hot pepper lines (Capsicum chinense and to obtain data on the allelic interaction between the parents involved in the crosses. Trials were made in Rio Branco-Acre, Brazil, from March through October 1997. A randomized complete block design with fifteen treatments and three replications was used. The treatments were five C. chinense accessions (from the Vegetable Germplasm Bank of the Universidade Federal de Viçosa - BGH/UFV and 10 F1 hybrids derived from single crosses between them (reciprocals excluded. Diallel analyses were performed for total yield, fruit length/diameter ratio, fruit dry matter per plant, Xanthomonas campestris pv. vesicatoria incidence, capsaicin yield per plant and number of seeds per fruit. Non-additive genetic effects were larger than additive effects for all the traits assessed. Epistasis was detected for fruit dry matter per plant, capsaicin yield per plant and number of seeds per fruit. In these cases, epistasis seemed to be largely responsible for heterosis expression. Dominant gene action, ranging from incomplete dominance to probable overdominance, was responsible for heterosis in those traits where no epistatic genetic action was detected.

  14. Human papillomavirus virus (HPV) genotype- and age-specific analyses of external genital lesions among men in the HPV Infection in Men (HIM) Study.

    Science.gov (United States)

    Ingles, Donna J; Pierce Campbell, Christine M; Messina, Jane A; Stoler, Mark H; Lin, Hui-Yi; Fulp, William J; Abrahamsen, Martha; Sirak, Bradley A; O'Keefe, Michael T; Papenfuss, Mary; Gage, Christine; Carvalho da Silva, Roberto; Gonzalez Sosa, Rossana; Rojas Juarez, Oscar; Villa, Luisa L; Lazcano Ponce, Eduardo; Giuliano, Anna R

    2015-04-01

    Human papillomavirus (HPV) causes external genital lesions (EGLs) in men, including condyloma and penile intraepithelial neoplasia (PeIN). We sought to determine the incidence of pathologically confirmed EGLs, by lesion type, among men in different age groups and to evaluate the HPV types that were associated with EGL development. HPV Infection in Men (HIM) study participants who contributed ≥2 visits from 2009-2013 were included in the biopsy cohort. Genotyping by an HPV line-probe assay was performed on all pathologically confirmed EGLs. Age-specific analyses were conducted for incident EGLs, with Kaplan-Meier estimation of cumulative incidence. This biopsy cohort included 2754 men (median follow-up duration, 12.4 months [interquartile range, 6.9-19.2 months]). EGLs (n = 377) were pathologically confirmed in 228 men, 198 of whom had incident EGLs. The cumulative incidence of any EGL was highest among men <45 years old and, for condyloma, decreased significantly over time with age. The genotype-specific incidence of EGL varied by pathological diagnoses, with high- and low-risk genotypes found in 15.6% and 73.2% of EGLs, respectively. Condyloma primarily contained HPV 6 or 11. While PeIN lesions primarily contained HPV 16, 1 PeIN III lesion was positive for HPV 6 only. Low- and high-risk HPV genotypes contribute to the EGL burden. Men remain susceptible to HPV-related EGLs throughout the life span, making it necessary to ensure the longevity of immune protection against the most common causative HPV genotypes. © The Author 2014. Published by Oxford University Press on behalf of the Infectious Diseases Society of America. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  15. Integrating genetic data and population viability analyses for the identification of harbour seal (Phoca vitulina) populations and management units

    DEFF Research Database (Denmark)

    Olsen, Morten Tange; Andersen, Liselotte Wesley; Dietz, Rune

    2014-01-01

    present a novel approach, integrating genetic, life-history and demographic data to identify populations and management units in southern Scandinavian harbour seals. First, 15 microsatellite markers and model- and distance-based genetic clustering methods were used to determine the population genetic...... structure in harbour seals. Second, we used harbour seal demographic and life-history data to conduct population viability analyses (PVAs) in the VORTEX simulation model in order to determine whether the inferred genetic units could be classified as management units according to Lowe and Allendorf's (2010......, and that the combined use of genetic data and PVAs constitute a promising approach for delineating populations and management units. This article is protected by copyright. All rights reserved....

  16. Systems genetics of obesity in an F2 pig model by genome-wide association, genetic network and pathway analyses

    DEFF Research Database (Denmark)

    Kogelman, Lisette; Pant, Sameer Dinkar; Fredholm, Merete

    2014-01-01

    .g. metabolic processes. WISH networks based on genotypic correlations allowed further identification of various gene ontology terms and pathways related to obesity and related traits, which were not identified by the GWA study. In conclusion, this is the first study to develop a (genetic) obesity index...... investigations focusing on single genetic variants have achieved limited success, and the importance of including genetic interactions is becoming evident. Here, the aim was to perform an integrative genomic analysis in an F2 pig resource population that was constructed with an aim to maximize genetic variation...... of obesity-related phenotypes and genotyped using the 60K SNP chip. Firstly, Genome Wide Association (GWA) analysis was performed on the Obesity Index to locate candidate genomic regions that were further validated using combined Linkage Disequilibrium Linkage Analysis and investigated by evaluation...

  17. TAXONOMY AND GENETIC RELATIONSHIPS OF PANGASIIDAE, ASIAN CATFISHES, BASED ON MORPHOLOGICAL AND MOLECULAR ANALYSES

    Directory of Open Access Journals (Sweden)

    Rudhy Gustiano

    2007-12-01

    Full Text Available Pangasiids are economically important riverine catfishes generally residing in freshwater from the Indian subcontinent to the Indonesian Archipelago. The systematics of this family are still poorly known. Consequently, lack of such basic information impedes the understanding of the biology of the Pangasiids and the study of their aquaculture potential as well as improvement of seed production and growth performance. The objectives of the present study are to clarify phylogeny of this family based on a biometric analysis and molecular evidence using 12S ribosomal mtDNA on the total of 1070 specimens. The study revealed that 28 species are recognised as valid in Pangasiidae. Four genera are also recognized as Helicophagus Bleeker 1858, Pangasianodon Chevey 1930, Pteropangasius Fowler 1937, and Pangasius Valenciennes 1840 instead of two as reported by previous workers. The phylogenetic analysis demonstrated the recognised genera, and genetic relationships among taxa. Overall, trees from the different analyses show similar topologies and confirm the hypothesis derived from geological history, palaeontology, and similar models in other taxa of fishes from the same area. The oldest genus may already have existed when the Asian mainland was still connected to the islands in the southern part about 20 million years ago.

  18. From sexless to sexy: Why it is time for human genetics to consider and report analyses of sex.

    Science.gov (United States)

    Powers, Matthew S; Smith, Phillip H; McKee, Sherry A; Ehringer, Marissa A

    2017-01-01

    Science has come a long way with regard to the consideration of sex differences in clinical and preclinical research, but one field remains behind the curve: human statistical genetics. The goal of this commentary is to raise awareness and discussion about how to best consider and evaluate possible sex effects in the context of large-scale human genetic studies. Over the course of this commentary, we reinforce the importance of interpreting genetic results in the context of biological sex, establish evidence that sex differences are not being considered in human statistical genetics, and discuss how best to conduct and report such analyses. Our recommendation is to run stratified analyses by sex no matter the sample size or the result and report the findings. Summary statistics from stratified analyses are helpful for meta-analyses, and patterns of sex-dependent associations may be hidden in a combined dataset. In the age of declining sequencing costs, large consortia efforts, and a number of useful control samples, it is now time for the field of human genetics to appropriately include sex in the design, analysis, and reporting of results.

  19. Morphological and Genetic Analyses of the Invasive Forest Pathogen Phytophthora austrocedri Reveal that Two Clonal Lineages Colonized Britain and Argentina from a Common Ancestral Population.

    Science.gov (United States)

    Henricot, Béatrice; Pérez-Sierra, Ana; Armstrong, April C; Sharp, Paul M; Green, Sarah

    2017-12-01

    Phytophthora austrocedri is causing widespread mortality of Austrocedrus chilensis in Argentina and Juniperus communis in Britain. The pathogen has also been isolated from J. horizontalis in Germany. Isolates from Britain, Argentina, and Germany are homothallic, with no clear differences in the dimensions of sporangia, oogonia, or oospores. Argentinian and German isolates grew faster than British isolates across a range of media and had a higher temperature tolerance, although most isolates, regardless of origin, grew best at 15°C and all isolates were killed at 25°C. Argentinian and British isolates caused lesions when inoculated onto both A. chilensis and J. communis; however, the Argentinian isolate caused longer lesions on A. chilensis than on J. communis and vice versa for the British isolate. Genetic analyses of nuclear and mitochondrial loci showed that all British isolates are identical. Argentinian isolates and the German isolate are also identical but differ from the British isolates. Single-nucleotide polymorphisms are shared between the British and Argentinian isolates. We concluded that British isolates and Argentinian isolates conform to two distinct clonal lineages of P. austrocedri founded from the same as-yet-unidentified source population. These lineages should be recognized and treated as separate risks by international plant health legislation.

  20. Mutational analyses of molecularly cloned satellite tobacco mosaic virus during serial passage in plants: Evidence for hotspots of genetic change

    Science.gov (United States)

    Kurath, G.; Dodds, J.A.

    1995-01-01

    The high level of genetic diversity and rapid evolution of viral RNA genomes are well documented, but few studies have characterized the rate and nature of ongoing genetic change over time under controlled experimental conditions, especially in plant hosts. The RNA genome of satellite tobacco mosaic virus (STMV) was used as an effective model for such studies because of advantageous features of its genome structure and because the extant genetic heterogeneity of STMV has been characterized previously. In the present study, the process of genetic change over time was studied by monitoring multiple serial passage lines of STMV populations for changes in their consensus sequences. A total of 42 passage lines were initiated by inoculation of tobacco plants with a helper tobamovirus and one of four STMV RNA inocula that were transcribed from full-length infectious STMV clones or extracted from purified STMV type strain virions. Ten serial passages were carried out for each line and the consensus genotypes of progeny STMV populations were assessed for genetic change by RNase protection analyses of the entire 1,059-nt STMV genome. Three different types of genetic change were observed, including the fixation of novel mutations in 9 of 42 lines, mutation at the major heterogeneity site near nt 751 in 5 of the 19 lines inoculated with a single genotype, and selection of a single major genotype in 6 of the 23 lines inoculated with mixed genotypes. Sequence analyses showed that the majority of mutations were single base substitutions. The distribution of mutation sites included three clusters in which mutations occurred at or very near the same site, suggesting hot spots of genetic change in the STMV genome. The diversity of genetic changes in sibling lines is clear evidence for the important role of chance and random sampling events in the process of genetic diversification of STMV virus populations.

  1. A new automated assign and analysing method for high-resolution rotationally resolved spectra using genetic algorithms

    NARCIS (Netherlands)

    Meerts, W.L.; Schmitt, M.

    2006-01-01

    This paper describes a numerical technique that has recently been developed to automatically assign and fit high-resolution spectra. The method makes use of genetic algorithms (GA). The current algorithm is compared with previously used analysing methods. The general features of the GA and its

  2. The role of host genetic factors in respiratory tract infectious diseases: systematic review, meta-analyses and field synopsis

    NARCIS (Netherlands)

    Patarčić, Inga; Gelemanović, Andrea; Kirin, Mirna; Kolčić, Ivana; Theodoratou, Evropi; Baillie, Kenneth J.; de Jong, Menno D.; Rudan, Igor; Campbell, Harry; Polašek, Ozren

    2015-01-01

    Host genetic factors have frequently been implicated in respiratory infectious diseases, often with inconsistent results in replication studies. We identified 386 studies from the total of 24,823 studies identified in a systematic search of four bibliographic databases. We performed meta-analyses of

  3. Genetic Diversity among Rhizobium leguminosarum bv. Trifolii Strains Revealed by Allozyme and Restriction Fragment Length Polymorphism Analyses

    Science.gov (United States)

    Demezas, David H.; Reardon, Terry B.; Watson, John M.; Gibson, Alan H.

    1991-01-01

    Allozyme electrophoresis and restriction fragment length polymorphism (RFLP) analyses were used to examine the genetic diversity of a collection of 18 Rhizobium leguminosarum bv. trifolii, 1 R. leguminosarum bv. viciae, and 2 R. meliloti strains. Allozyme analysis at 28 loci revealed 16 electrophoretic types. The mean genetic distance between electrophoretic types of R. leguminosarum and R. meliloti was 0.83. Within R. leguminosarum, the single strain of bv. viciae differed at an average of 0.65 from strains of bv. trifolii, while electrophoretic types of bv. trifolii differed at a range of 0.23 to 0.62. Analysis of RFLPs around two chromosomal DNA probes also delineated 16 unique RFLP patterns and yielded genetic diversity similar to that revealed by the allozyme data. Analysis of RFLPs around three Sym (symbiotic) plasmid-derived probes demonstrated that the Sym plasmids reflect genetic divergence similar to that of their bacterial hosts. The large genetic distances between many strains precluded reliable estimates of their genetic relationships. PMID:16348600

  4. Genetic analyses of the NF1 gene in Turkish neurofibromatosis type I patients and definition of three novel variants

    Directory of Open Access Journals (Sweden)

    Ulusal SD

    2017-06-01

    Full Text Available Neurofibromatosis Type I (NF1 is a multi systemic autosomal dominant neurocutaneous disorder predisposing patients to have benign and/or malignant lesions predominantly of the skin, nervous system and bone. Loss of function mutations or deletions of the NF1 gene is responsible for NF1 disease. Involvement of various pathogenic variants, the size of the gene and presence of pseudogenes makes it difficult to analyze. We aimed to report the results of 2 years of multiplex ligation-dependent probe amplification (MLPA and next generation sequencing (NGS for genetic diagnosis of NF1 applied at our genetic diagnosis center. The MLPA, semiconductor sequencing and Sanger sequencing were performed in genomic DNA samples from 24 unrelated patients and their affected family members referred to our center suspected of having NF1. In total, three novel and 12 known pathogenic variants and a whole gene deletion were determined. We suggest that next generation sequencing is a practical tool for genetic analysis of NF1. Deletion/duplication analysis with MLPA may also be helpful for patients clinically diagnosed to carry NF1 but do not have a detectable mutation in NGS.

  5. Simulation, prediction, and genetic analyses of daily methane emissions in dairy cattle.

    Science.gov (United States)

    Yin, T; Pinent, T; Brügemann, K; Simianer, H; König, S

    2015-08-01

    This study presents an approach combining phenotypes from novel traits, deterministic equations from cattle nutrition, and stochastic simulation techniques from animal breeding to generate test-day methane emissions (MEm) of dairy cows. Data included test-day production traits (milk yield, fat percentage, protein percentage, milk urea nitrogen), conformation traits (wither height, hip width, body condition score), female fertility traits (days open, calving interval, stillbirth), and health traits (clinical mastitis) from 961 first lactation Brown Swiss cows kept on 41 low-input farms in Switzerland. Test-day MEm were predicted based on the traits from the current data set and 2 deterministic prediction equations, resulting in the traits labeled MEm1 and MEm2. Stochastic simulations were used to assign individual concentrate intake in dependency of farm-type specifications (requirement when calculating MEm2). Genetic parameters for MEm1 and MEm2 were estimated using random regression models. Predicted MEm had moderate heritabilities over lactation and ranged from 0.15 to 0.37, with highest heritabilities around DIM 100. Genetic correlations between MEm1 and MEm2 ranged between 0.91 and 0.94. Antagonistic genetic correlations in the range from 0.70 to 0.92 were found for the associations between MEm2 and milk yield. Genetic correlations between MEm with days open and with calving interval increased from 0.10 at the beginning to 0.90 at the end of lactation. Genetic relationships between MEm2 and stillbirth were negative (0 to -0.24) from the beginning to the peak phase of lactation. Positive genetic relationships in the range from 0.02 to 0.49 were found between MEm2 with clinical mastitis. Interpretation of genetic (co)variance components should also consider the limitations when using data generated by prediction equations. Prediction functions only describe that part of MEm which is dependent on the factors and effects included in the function. With high

  6. Genetic and QTL analyses of yield and a set of physiological traits in pepper

    NARCIS (Netherlands)

    Alimi, N.A.; Bink, M.C.A.M.; Dieleman, J.A.; Nicolaï, M.; Wubs, M.; Heuvelink, E.; Magan, J.; Voorrips, R.E.; Jansen, J.; Rodrigues, P.C.; Heijden, van der G.W.A.M.; Vercauteren, A.; Vuylsteke, M.; Song, Y.; Glasbey, C.; Barocsi, A.; Lefebvre, V.; Palloix, A.; Eeuwijk, van F.A.

    2013-01-01

    An interesting strategy for improvement of a complex trait dissects the complex trait in a number of physiological component traits, with the latter having hopefully a simple genetic basis. The complex trait is then improved via improvement of its component traits. As first part of such a strategy

  7. The ENIGMA Consortium : large-scale collaborative analyses of neuroimaging and genetic data

    NARCIS (Netherlands)

    Thompson, Paul M.; Stein, Jason L.; Medland, Sarah E.; Hibar, Derrek P.; Vasquez, Alejandro Arias; Renteria, Miguel E.; Toro, Roberto; Jahanshad, Neda; Schumann, Gunter; Franke, Barbara; Wright, Margaret J.; Martin, Nicholas G.; Agartz, Ingrid; Alda, Martin; Alhusaini, Saud; Almasy, Laura; Almeida, Jorge; Alpert, Kathryn; Andreasen, Nancy C.; Andreassen, Ole A.; Apostolova, Liana G.; Appel, Katja; Armstrong, Nicola J.; Aribisala, Benjamin; Bastin, Mark E.; Bauer, Michael; Bearden, Carrie E.; Bergmann, Orjan; Binder, Elisabeth B.; Blangero, John; Bockholt, Henry J.; Boen, Erlend; Bois, Catherine; Boomsma, Dorret I.; Booth, Tom; Bowman, Ian J.; Bralten, Janita; Brouwer, Rachel M.; Brunner, Han G.; Brohawn, David G.; Buckner, Randy L.; Buitelaar, Jan; Bulayeva, Kazima; Bustillo, Juan R.; Calhoun, Vince D.; Hartman, Catharina A.; Hoekstra, Pieter J.; Penninx, Brenda W.; Schmaal, Lianne; van Tol, Marie-Jose

    The Enhancing NeuroImaging Genetics through Meta-Analysis (ENIGMA) Consortium is a collaborative network of researchers working together on a range of large-scale studies that integrate data from 70 institutions worldwide. Organized into Working Groups that tackle questions in neuroscience,

  8. The ENIGMA Consortium: large-scale collaborative analyses of neuroimaging and genetic data

    NARCIS (Netherlands)

    Thompson, Paul M.; Stein, Jason L.; Medland, Sarah E.; Hibar, Derrek P.; Vasquez, Alejandro Arias; Renteria, Miguel E.; Toro, Roberto; Jahanshad, Neda; Schumann, Gunter; Franke, Barbara; Wright, Margaret J.; Martin, Nicholas G.; Agartz, Ingrid; Alda, Martin; Alhusaini, Saud; Almasy, Laura; Almeida, Jorge; Alpert, Kathryn; Andreasen, Nancy C.; Andreassen, Ole A.; Apostolova, Liana G.; Appel, Katja; Armstrong, Nicola J.; Aribisala, Benjamin; Bastin, Mark E.; Bauer, Michael; Bearden, Carrie E.; Bergmann, Orjan; Binder, Elisabeth B.; Blangero, John; Bockholt, Henry J.; Bøen, Erlend; Bois, Catherine; Boomsma, Dorret I.; Booth, Tom; Bowman, Ian J.; Bralten, Janita; Brouwer, Rachel M.; Brunner, Han G.; Brohawn, David G.; Buckner, Randy L.; Buitelaar, Jan; Bulayeva, Kazima; Bustillo, Juan R.; Calhoun, Vince D.; Cannon, Dara M.; Cantor, Rita M.; Carless, Melanie A.; Caseras, Xavier; Cavalleri, Gianpiero L.; Chakravarty, M. Mallar; Chang, Kiki D.; Ching, Christopher R. K.; Christoforou, Andrea; Cichon, Sven; Clark, Vincent P.; Conrod, Patricia; Coppola, Giovanni; Crespo-Facorro, Benedicto; Curran, Joanne E.; Czisch, Michael; Deary, Ian J.; de Geus, Eco J. C.; den Braber, Anouk; Delvecchio, Giuseppe; Depondt, Chantal; de Haan, Lieuwe; de Zubicaray, Greig I.; Dima, Danai; Dimitrova, Rali; Djurovic, Srdjan; Dong, Hongwei; Donohoe, Gary; Duggirala, Ravindranath; Dyer, Thomas D.; Ehrlich, Stefan; Ekman, Carl Johan; Elvsåshagen, Torbjørn; Emsell, Louise; Erk, Susanne; Espeseth, Thomas; Fagerness, Jesen; Fears, Scott; Fedko, Iryna; Fernández, Guillén; Fisher, Simon E.; Foroud, Tatiana; Fox, Peter T.; Francks, Clyde; Frangou, Sophia; Frey, Eva Maria; Frodl, Thomas; Frouin, Vincent; Garavan, Hugh; Giddaluru, Sudheer; Glahn, David C.; Godlewska, Beata; Goldstein, Rita Z.; Gollub, Randy L.; Grabe, Hans J.; Grimm, Oliver; Gruber, Oliver; Guadalupe, Tulio; Gur, Raquel E.; Gur, Ruben C.; Göring, Harald H. H.; Hagenaars, Saskia; Hajek, Tomas; Hall, Geoffrey B.; Hall, Jeremy; Hardy, John; Hartman, Catharina A.; Hass, Johanna; Hatton, Sean N.; Haukvik, Unn K.; Hegenscheid, Katrin; Heinz, Andreas; Hickie, Ian B.; Ho, Beng-Choon; Hoehn, David; Hoekstra, Pieter J.; Hollinshead, Marisa; Holmes, Avram J.; Homuth, Georg; Hoogman, Martine; Hong, L. Elliot; Hosten, Norbert; Hottenga, Jouke-Jan; Hulshoff Pol, Hilleke E.; Hwang, Kristy S.; Jack, Clifford R.; Jenkinson, Mark; Johnston, Caroline; Jönsson, Erik G.; Kahn, René S.; Kasperaviciute, Dalia; Kelly, Sinead; Kim, Sungeun; Kochunov, Peter; Koenders, Laura; Krämer, Bernd; Kwok, John B. J.; Lagopoulos, Jim; Laje, Gonzalo; Landen, Mikael; Landman, Bennett A.; Lauriello, John; Lawrie, Stephen M.; Lee, Phil H.; Le Hellard, Stephanie; Lemaître, Herve; Leonardo, Cassandra D.; Li, Chiang-Shan; Liberg, Benny; Liewald, David C.; Liu, Xinmin; Lopez, Lorna M.; Loth, Eva; Lourdusamy, Anbarasu; Luciano, Michelle; Macciardi, Fabio; Machielsen, Marise W. J.; Macqueen, Glenda M.; Malt, Ulrik F.; Mandl, René; Manoach, Dara S.; Martinot, Jean-Luc; Matarin, Mar; Mather, Karen A.; Mattheisen, Manuel; Mattingsdal, Morten; Meyer-Lindenberg, Andreas; McDonald, Colm; McIntosh, Andrew M.; McMahon, Francis J.; McMahon, Katie L.; Meisenzahl, Eva; Melle, Ingrid; Milaneschi, Yuri; Mohnke, Sebastian; Montgomery, Grant W.; Morris, Derek W.; Moses, Eric K.; Mueller, Bryon A.; Muñoz Maniega, Susana; Mühleisen, Thomas W.; Müller-Myhsok, Bertram; Mwangi, Benson; Nauck, Matthias; Nho, Kwangsik; Nichols, Thomas E.; Nilsson, Lars-Göran; Nugent, Allison C.; Nyberg, Lars; Olvera, Rene L.; Oosterlaan, Jaap; Ophoff, Roel A.; Pandolfo, Massimo; Papalampropoulou-Tsiridou, Melina; Papmeyer, Martina; Paus, Tomas; Pausova, Zdenka; Pearlson, Godfrey D.; Penninx, Brenda W.; Peterson, Charles P.; Pfennig, Andrea; Phillips, Mary; Pike, G. Bruce; Poline, Jean-Baptiste; Potkin, Steven G.; Pütz, Benno; Ramasamy, Adaikalavan; Rasmussen, Jerod; Rietschel, Marcella; Rijpkema, Mark; Risacher, Shannon L.; Roffman, Joshua L.; Roiz-Santiañez, Roberto; Romanczuk-Seiferth, Nina; Rose, Emma J.; Royle, Natalie A.; Rujescu, Dan; Ryten, Mina; Sachdev, Perminder S.; Salami, Alireza; Satterthwaite, Theodore D.; Savitz, Jonathan; Saykin, Andrew J.; Scanlon, Cathy; Schmaal, Lianne; Schnack, Hugo G.; Schork, Andrew J.; Schulz, S. Charles; Schür, Remmelt; Seidman, Larry; Shen, Li; Shoemaker, Jody M.; Simmons, Andrew; Sisodiya, Sanjay M.; Smith, Colin; Smoller, Jordan W.; Soares, Jair C.; Sponheim, Scott R.; Sprooten, Emma; Starr, John M.; Steen, Vidar M.; Strakowski, Stephen; Strike, Lachlan; Sussmann, Jessika; Sämann, Philipp G.; Teumer, Alexander; Toga, Arthur W.; Tordesillas-Gutierrez, Diana; Trabzuni, Daniah; Trost, Sarah; Turner, Jessica; van den Heuvel, Martijn; van der Wee, Nic J.; van Eijk, Kristel; van Erp, Theo G. M.; van Haren, Neeltje E. M.; van 't Ent, Dennis; van Tol, Marie-Jose; Valdés Hernández, Maria C.; Veltman, Dick J.; Versace, Amelia; Völzke, Henry; Walker, Robert; Walter, Henrik; Wang, Lei; Wardlaw, Joanna M.; Weale, Michael E.; Weiner, Michael W.; Wen, Wei; Westlye, Lars T.; Whalley, Heather C.; Whelan, Christopher D.; White, Tonya; Winkler, Anderson M.; Wittfeld, Katharina; Woldehawariat, Girma; Wolf, Christiane; Zilles, David; Zwiers, Marcel P.; Thalamuthu, Anbupalam; Schofield, Peter R.; Freimer, Nelson B.; Lawrence, Natalia S.; Drevets, Wayne

    2014-01-01

    The Enhancing NeuroImaging Genetics through Meta-Analysis (ENIGMA) Consortium is a collaborative network of researchers working together on a range of large-scale studies that integrate data from 70 institutions worldwide. Organized into Working Groups that tackle questions in neuroscience,

  9. The ENIGMA Consortium: Large-scale collaborative analyses of neuroimaging and genetic data

    NARCIS (Netherlands)

    P.M. Thompson (Paul); J.L. Stein; S.E. Medland (Sarah Elizabeth); D.P. Hibar (Derrek); A.A. Vásquez (Arias); M.E. Rentería (Miguel); R. Toro (Roberto); N. Jahanshad (Neda); G. Schumann (Gunter); B. Franke (Barbara); M.J. Wright (Margaret); N.G. Martin (Nicholas); I. Agartz (Ingrid); M. Alda (Martin); S. Alhusaini (Saud); L. Almasy (Laura); K. Alpert (Kathryn); N.C. Andreasen; O.A. Andreassen (Ole); L.G. Apostolova (Liana); K. Appel (Katja); N.J. Armstrong (Nicola); B. Aribisala (Benjamin); M.E. Bastin (Mark); M. Bauer (Michael); C.E. Bearden (Carrie); Ø. Bergmann (Ørjan); E.B. Binder (Elisabeth); J. Blangero (John); H.J. Bockholt; E. Bøen (Erlend); M. Bois (Monique); D.I. Boomsma (Dorret); T. Booth (Tom); I.J. Bowman (Ian); L.B.C. Bralten (Linda); R.M. Brouwer (Rachel); H.G. Brunner; D.G. Brohawn (David); M. Buckner; J.K. Buitelaar (Jan); K. Bulayeva (Kazima); J. Bustillo; V.D. Calhoun (Vince); D.M. Cannon (Dara); R.M. Cantor; M.A. Carless (Melanie); X. Caseras (Xavier); G. Cavalleri (Gianpiero); M.M. Chakravarty (M. Mallar); K.D. Chang (Kiki); C.R.K. Ching (Christopher); A. Christoforou (Andrea); S. Cichon (Sven); V.P. Clark; P. Conrod (Patricia); D. Coppola (Domenico); B. Crespo-Facorro (Benedicto); J.E. Curran (Joanne); M. Czisch (Michael); I.J. Deary (Ian); E.J.C. de Geus (Eco); A. den Braber (Anouk); G. Delvecchio (Giuseppe); C. Depondt (Chantal); L. de Haan (Lieuwe); G.I. de Zubicaray (Greig); D. Dima (Danai); R. Dimitrova (Rali); S. Djurovic (Srdjan); H. Dong (Hongwei); D.J. Donohoe (Dennis); A. Duggirala (Aparna); M.D. Dyer (Matthew); S.M. Ehrlich (Stefan); C.J. Ekman (Carl Johan); T. Elvsåshagen (Torbjørn); L. Emsell (Louise); S. Erk; T. Espeseth (Thomas); J. Fagerness (Jesen); S. Fears (Scott); I. Fedko (Iryna); G. Fernandez (Guillén); S.E. Fisher (Simon); T. Foroud (Tatiana); P.T. Fox (Peter); C. Francks (Clyde); S. Frangou (Sophia); E.M. Frey (Eva Maria); T. Frodl (Thomas); V. Frouin (Vincent); H. Garavan (Hugh); S. Giddaluru (Sudheer); D.C. Glahn (David); B. Godlewska (Beata); R.Z. Goldstein (Rita); R.L. Gollub (Randy); H.J. Grabe (Hans Jörgen); O. Grimm (Oliver); O. Gruber (Oliver); T. Guadalupe (Tulio); R.E. Gur (Raquel); R.C. Gur (Ruben); H.H.H. Göring (Harald); S. Hagenaars (Saskia); T. Hajek (Tomas); G.B. Hall (Garry); J. Hall (Jeremy); J. Hardy (John); C.A. Hartman (Catharina); J. Hass (Johanna); W. Hatton; U.K. Haukvik (Unn); K. Hegenscheid (Katrin); J. Heinz (Judith); I.B. Hickie (Ian); B.C. Ho (Beng ); D. Hoehn (David); P.J. Hoekstra (Pieter); M. Hollinshead (Marisa); A.J. Holmes (Avram); G. Homuth (Georg); M. Hoogman (Martine); L.E. Hong (L.Elliot); N. Hosten (Norbert); J.J. Hottenga (Jouke Jan); H.E. Hulshoff Pol (Hilleke); K.S. Hwang (Kristy); C.R. Jack Jr. (Clifford); S. Jenkinson (Sarah); C. Johnston; E.G. Jönsson (Erik); R.S. Kahn (René); D. Kasperaviciute (Dalia); S. Kelly (Steve); S. Kim (Shinseog); P. Kochunov (Peter); L. Koenders (Laura); B. Krämer (Bernd); J.B.J. Kwok (John); J. Lagopoulos (Jim); G. Laje (Gonzalo); M. Landén (Mikael); B.A. Landman (Bennett); J. Lauriello; S. Lawrie (Stephen); P.H. Lee (Phil); S. Le Hellard (Stephanie); H. Lemaître (Herve); C.D. Leonardo (Cassandra); C.-S. Li (Chiang-shan); B. Liberg (Benny); D.C. Liewald (David C.); X. Liu (Xinmin); L.M. Lopez (Lorna); E. Loth (Eva); A. Lourdusamy (Anbarasu); M. Luciano (Michelle); F. MacCiardi (Fabio); M.W.J. Machielsen (Marise); G.M. MacQueen (Glenda); U.F. Malt (Ulrik); R. Mandl (René); D.S. Manoach (Dara); J.-L. Martinot (Jean-Luc); M. Matarin (Mar); R. Mather; M. Mattheisen (Manuel); M. Mattingsdal (Morten); A. Meyer-Lindenberg; C. McDonald (Colm); A.M. McIntosh (Andrew); F.J. Mcmahon (Francis J); K.L. Mcmahon (Katie); E. Meisenzahl (Eva); I. Melle (Ingrid); Y. Milaneschi (Yuri); S. Mohnke (Sebastian); G.W. Montgomery (Grant); D.W. Morris (Derek W); E.K. Moses (Eric); B.A. Mueller (Bryon ); S. Muñoz Maniega (Susana); T.W. Mühleisen (Thomas); B. Müller-Myhsok (Bertram); B. Mwangi (Benson); M. Nauck (Matthias); K. Nho (Kwangsik); T.E. Nichols (Thomas); L.G. Nilsson; A.C. Nugent (Allison); L. Nyberg (Lisa); R.L. Olvera (Rene); J. Oosterlaan (Jaap); R.A. Ophoff (Roel); M. Pandolfo (Massimo); M. Papalampropoulou-Tsiridou (Melina); M. Papmeyer (Martina); T. Paus (Tomas); Z. Pausova (Zdenka); G. Pearlson (Godfrey); B.W.J.H. Penninx (Brenda); C.P. Peterson (Charles); A. Pfennig (Andrea); M. Phillips (Mary); G.B. Pike (G Bruce); J.B. Poline (Jean Baptiste); S.G. Potkin (Steven); B. Pütz (Benno); A. Ramasamy (Adaikalavan); J. Rasmussen (Jerod); M. Rietschel (Marcella); M. Rijpkema (Mark); S.L. Risacher (Shannon); J.L. Roffman (Joshua); R. Roiz-Santiañez (Roberto); N. Romanczuk-Seiferth (Nina); E.J. Rose (Emma); N.A. Royle (Natalie); D. Rujescu (Dan); M. Ryten (Mina); P.S. Sachdev (Perminder); A. Salami (Alireza); T.D. Satterthwaite (Theodore); J. Savitz (Jonathan); A.J. Saykin (Andrew); C. Scanlon (Cathy); L. Schmaal (Lianne); H. Schnack (Hugo); N.J. Schork (Nicholas); S.C. Schulz (S.Charles); R. Schür (Remmelt); L.J. Seidman (Larry); L. Shen (Li); L. Shoemaker (Lawrence); A. Simmons (Andrew); S.M. Sisodiya (Sanjay); C. Smith (Colin); J.W. Smoller; J.C. Soares (Jair); S.R. Sponheim (Scott); R. Sprooten (Roy); J.M. Starr (John); V.M. Steen (Vidar); S. Strakowski (Stephen); L.T. Strike (Lachlan); J. Sussmann (Jessika); P.G. Sämann (Philipp); A. Teumer (Alexander); A.W. Toga (Arthur); D. Tordesillas-Gutierrez (Diana); D. Trabzuni (Danyah); S. Trost (Sarah); J. Turner (Jessica); M. van den Heuvel (Martijn); N.J. van der Wee (Nic); K.R. van Eijk (Kristel); T.G.M. van Erp (Theo G.); N.E.M. van Haren (Neeltje E.); D. van 't Ent (Dennis); M.J.D. van Tol (Marie-José); M.C. Valdés Hernández (Maria); D.J. Veltman (Dick); A. Versace (Amelia); H. Völzke (Henry); R. Walker (Robert); H.J. Walter (Henrik); L. Wang (Lei); J.M. Wardlaw (J.); M.E. Weale (Michael); M.W. Weiner (Michael); W. Wen (Wei); L.T. Westlye (Lars); H.C. Whalley (Heather); C.D. Whelan (Christopher); T.J.H. White (Tonya); A.M. Winkler (Anderson); K. Wittfeld (Katharina); G. Woldehawariat (Girma); A. Björnsson (Asgeir); D. Zilles (David); M.P. Zwiers (Marcel); A. Thalamuthu (Anbupalam); J.R. Almeida (Jorge); C.J. Schofield (Christopher); N.B. Freimer (Nelson); N.S. Lawrence (Natalia); D.A. Drevets (Douglas)

    2014-01-01

    textabstractThe Enhancing NeuroImaging Genetics through Meta-Analysis (ENIGMA) Consortium is a collaborative network of researchers working together on a range of large-scale studies that integrate data from 70 institutions worldwide. Organized into Working Groups that tackle questions in

  10. Assessment of RAPD Markers to Analyse the Genetic Diversity among Sunflower (Helianthus annuus L. Genotypes

    Directory of Open Access Journals (Sweden)

    Ali Raza

    2018-02-01

    Full Text Available Genetic diversity estimation among different species is an important tool for genetic improvement to maximize the yield, desirable quality, wider adaptation, pest and insect resistance that ultimately boosting traditional plant breeding methods. The most efficient way of diversity estimation is application of molecular markers. In this study, twenty random amplified polymorphic DNA (RAPD primers were utilized to estimate the genetic diversity between ten sunflower genotypes. Overall 227 bands were amplified by 20 primers with an average of 11.35 bands per primer. RAPD data showed 86.34% polymorophic bands and 13.65% of monomorophic bands. Genetic similarity was ranged from 50.22% to 87.22%. The lowest similarity (50.22% was observed between FH-352 and FH-359 and the maximum similarity 87.22% was observed between A-23 and G-46. Polymorphic information content (PIC values were varying from 0.05 to 0.12 with a mean of 0.09. Cluster analysis based on RAPD results displayed two major distinct groups 1 and 2. Group-2 contains FH-352 which was the most diverse genotype, while group-1 consists of few sub groups with all other genotypes. Ample diversity was found in all the genotypes. Present study reveals novel information about sunflower genome which can be used in future studies for sunflower improvement.

  11. Genetic analysis of seed development in Arabidopsis thaliana = [Genetische analyse van de zaadontwikkeling in Arabidopsis thaliana

    NARCIS (Netherlands)

    Leon - Kloosterziel, K.

    1997-01-01


    This thesis deals with the genetic aspects of seed development in Arabidopsisthaliana. Mutants affected in several aspects of seed development and, more specifically, in seed maturation have been isolated by various selection

  12. Integrating genetic, transcriptional, and functional analyses to identify 5 novel genes for atrial fibrillation

    DEFF Research Database (Denmark)

    Sinner, Moritz F; Tucker, Nathan R; Lunetta, Kathryn L

    2014-01-01

    BACKGROUND: Atrial fibrillation (AF) affects >30 million individuals worldwide and is associated with an increased risk of stroke, heart failure, and death. AF is highly heritable, yet the genetic basis for the arrhythmia remains incompletely understood. METHODS AND RESULTS: To identify new AF-re...

  13. Marshes as "Mountain Tops": Genetic Analyses of the Critically Endangered São Paulo Marsh Antwren (Aves: Thamnophilidae).

    Science.gov (United States)

    de Camargo, Crisley; Gibbs, H Lisle; Costa, Mariellen C; Del-Rio, Glaucia; Silveira, Luís F; Wasko, Adriane P; Francisco, Mercival R

    2015-01-01

    Small populations of endangered species can be impacted by genetic processes such as drift and inbreeding that reduce population viability. As such, conservation genetic analyses that assess population levels of genetic variation and levels of gene flow can provide important information for managing threatened species. The São Paulo Marsh Antwren (Formicivora paludicola) is a recently-described and critically endangered bird from São Paulo State (Brazil) whose total estimated population is around 250-300 individuals, distributed in only 15 isolated marshes around São Paulo metropolitan region. We used microsatellite DNA markers to estimate the population genetic characteristics of the three largest remaining populations of this species all within 60 km of each other. We detected a high and significant genetic structure between all populations (overall FST = 0.103) which is comparable to the highest levels of differentiation ever documented for birds, (e.g., endangered birds found in isolated populations on the tops of African mountains), but also evidence for first-generation immigrants, likely from small local unsampled populations. Effective population sizes were small (between 28.8-99.9 individuals) yet there are high levels of genetic variability within populations and no evidence for inbreeding. Conservation implications of this work are that the high levels of genetic structure suggests that translocations between populations need to be carefully considered in light of possible local adaptation and that remaining populations of these birds should be managed as conservation units that contain both main populations studied here but also small outlying populations which may be a source of immigrants.

  14. A Report on Molecular Diagnostic Testing for Inherited Retinal Dystrophies by Targeted Genetic Analyses.

    Science.gov (United States)

    Ramkumar, Hema L; Gudiseva, Harini V; Kishaba, Kameron T; Suk, John J; Verma, Rohan; Tadimeti, Keerti; Thorson, John A; Ayyagari, Radha

    2017-02-01

    To test the utility of targeted sequencing as a method of clinical molecular testing in patients diagnosed with inherited retinal degeneration (IRD). After genetic counseling, peripheral blood was drawn from 188 probands and 36 carriers of IRD. Single gene testing was performed on each patient in a Clinical Laboratory Improvement Amendment (CLIA) certified laboratory. DNA was isolated, and all exons in the gene of interest were analyzed along with 20 base pairs of flanking intronic sequence. Genetic testing was most often performed on ABCA4, CTRP5, ELOV4, BEST1, CRB1, and PRPH2. Pathogenicity of novel sequence changes was predicted by PolyPhen2 and sorting intolerant from tolerant (SIFT). Of the 225 genetic tests performed, 150 were for recessive IRD, and 75 were for dominant IRD. A positive molecular diagnosis was made in 70 (59%) of probands with recessive IRD and 19 (26%) probands with dominant IRD. Analysis confirmed 12 (34%) of individuals as carriers of familial mutations associated with IRD. Thirty-two novel variants were identified; among these, 17 sequence changes in four genes were predicted to be possibly or probably damaging including: ABCA4 (14), BEST1 (2), PRPH2 (1), and TIMP3 (1). Targeted analysis of clinically suspected genes in 225 subjects resulted in a positive molecular diagnosis in 26% of patients with dominant IRD and 59% of patients with recessive IRD. Novel damaging mutations were identified in four genes. Single gene screening is not an ideal method for diagnostic testing given the phenotypic and genetic heterogeneity among IRD cases. High-throughput sequencing of all genes associated with retinal degeneration may be more efficient for molecular diagnosis.

  15. Comparative Genetic Analyses of Human Rhinovirus C (HRV-C) Complete Genome from Malaysia

    Science.gov (United States)

    Khaw, Yam Sim; Chan, Yoke Fun; Jafar, Faizatul Lela; Othman, Norlijah; Chee, Hui Yee

    2016-01-01

    Human rhinovirus-C (HRV-C) has been implicated in more severe illnesses than HRV-A and HRV-B, however, the limited number of HRV-C complete genomes (complete 5′ and 3′ non-coding region and open reading frame sequences) has hindered the in-depth genetic study of this virus. This study aimed to sequence seven complete HRV-C genomes from Malaysia and compare their genetic characteristics with the 18 published HRV-Cs. Seven Malaysian HRV-C complete genomes were obtained with newly redesigned primers. The seven genomes were classified as HRV-C6, C12, C22, C23, C26, C42, and pat16 based on the VP4/VP2 and VP1 pairwise distance threshold classification. Five of the seven Malaysian isolates, namely, 3430-MY-10/C22, 8713-MY-10/C23, 8097-MY-11/C26, 1570-MY-10/C42, and 7383-MY-10/pat16 are the first newly sequenced complete HRV-C genomes. All seven Malaysian isolates genomes displayed nucleotide similarity of 63–81% among themselves and 63–96% with other HRV-Cs. Malaysian HRV-Cs had similar putative immunogenic sites, putative receptor utilization and potential antiviral sites as other HRV-Cs. The genomic features of Malaysian isolates were similar to those of other HRV-Cs. Negative selections were frequently detected in HRV-Cs complete coding sequences indicating that these sequences were under functional constraint. The present study showed that HRV-Cs from Malaysia have diverse genetic sequences but share conserved genomic features with other HRV-Cs. This genetic information could provide further aid in the understanding of HRV-C infection. PMID:27199901

  16. Genetic analyses of nonfluorescent root mutants induced by mutagenesis in soybean

    International Nuclear Information System (INIS)

    Sawada, S.; Palmer, R.G.

    1987-01-01

    Nonfluorescent root mutants in soybean [Glycine max (L.) Merr.] are useful as markers in genetic studies and in tissue culture research. Our objective was to obtain mutagen-induced nonfluorescent root mutants and to conduct genetic studies with them. Thirteen nonfluorescent mutants were detected among 154016 seedlings derived from soybean lines treated with six mutagens. One of these mutants, derived from Williams treated with 20 kR gamma rays, did not correspond to any of the known (standard) nonfluorescent spontaneous mutants. This is the first mutagen-induced nonfluorescent root mutant in soybean. It was assigned Genetic Type Collection no. T285 and the gene symbol fr5 fr5. The fr5 allele was not located on trisomics A, B, or C and was not linked to five chlorophyll-deficient mutants (y9, y11, y12, y13, and y20-k2) or flower color mutant w1. The remaining nonfluorescent root mutants were at the same loci as known spontaneous mutants; i.e., four had the fr1 allele, five had the fr2 allele, and three had the fr4 allele

  17. The ENIGMA Consortium: large-scale collaborative analyses of neuroimaging and genetic data.

    Science.gov (United States)

    Thompson, Paul M; Stein, Jason L; Medland, Sarah E; Hibar, Derrek P; Vasquez, Alejandro Arias; Renteria, Miguel E; Toro, Roberto; Jahanshad, Neda; Schumann, Gunter; Franke, Barbara; Wright, Margaret J; Martin, Nicholas G; Agartz, Ingrid; Alda, Martin; Alhusaini, Saud; Almasy, Laura; Almeida, Jorge; Alpert, Kathryn; Andreasen, Nancy C; Andreassen, Ole A; Apostolova, Liana G; Appel, Katja; Armstrong, Nicola J; Aribisala, Benjamin; Bastin, Mark E; Bauer, Michael; Bearden, Carrie E; Bergmann, Orjan; Binder, Elisabeth B; Blangero, John; Bockholt, Henry J; Bøen, Erlend; Bois, Catherine; Boomsma, Dorret I; Booth, Tom; Bowman, Ian J; Bralten, Janita; Brouwer, Rachel M; Brunner, Han G; Brohawn, David G; Buckner, Randy L; Buitelaar, Jan; Bulayeva, Kazima; Bustillo, Juan R; Calhoun, Vince D; Cannon, Dara M; Cantor, Rita M; Carless, Melanie A; Caseras, Xavier; Cavalleri, Gianpiero L; Chakravarty, M Mallar; Chang, Kiki D; Ching, Christopher R K; Christoforou, Andrea; Cichon, Sven; Clark, Vincent P; Conrod, Patricia; Coppola, Giovanni; Crespo-Facorro, Benedicto; Curran, Joanne E; Czisch, Michael; Deary, Ian J; de Geus, Eco J C; den Braber, Anouk; Delvecchio, Giuseppe; Depondt, Chantal; de Haan, Lieuwe; de Zubicaray, Greig I; Dima, Danai; Dimitrova, Rali; Djurovic, Srdjan; Dong, Hongwei; Donohoe, Gary; Duggirala, Ravindranath; Dyer, Thomas D; Ehrlich, Stefan; Ekman, Carl Johan; Elvsåshagen, Torbjørn; Emsell, Louise; Erk, Susanne; Espeseth, Thomas; Fagerness, Jesen; Fears, Scott; Fedko, Iryna; Fernández, Guillén; Fisher, Simon E; Foroud, Tatiana; Fox, Peter T; Francks, Clyde; Frangou, Sophia; Frey, Eva Maria; Frodl, Thomas; Frouin, Vincent; Garavan, Hugh; Giddaluru, Sudheer; Glahn, David C; Godlewska, Beata; Goldstein, Rita Z; Gollub, Randy L; Grabe, Hans J; Grimm, Oliver; Gruber, Oliver; Guadalupe, Tulio; Gur, Raquel E; Gur, Ruben C; Göring, Harald H H; Hagenaars, Saskia; Hajek, Tomas; Hall, Geoffrey B; Hall, Jeremy; Hardy, John; Hartman, Catharina A; Hass, Johanna; Hatton, Sean N; Haukvik, Unn K; Hegenscheid, Katrin; Heinz, Andreas; Hickie, Ian B; Ho, Beng-Choon; Hoehn, David; Hoekstra, Pieter J; Hollinshead, Marisa; Holmes, Avram J; Homuth, Georg; Hoogman, Martine; Hong, L Elliot; Hosten, Norbert; Hottenga, Jouke-Jan; Hulshoff Pol, Hilleke E; Hwang, Kristy S; Jack, Clifford R; Jenkinson, Mark; Johnston, Caroline; Jönsson, Erik G; Kahn, René S; Kasperaviciute, Dalia; Kelly, Sinead; Kim, Sungeun; Kochunov, Peter; Koenders, Laura; Krämer, Bernd; Kwok, John B J; Lagopoulos, Jim; Laje, Gonzalo; Landen, Mikael; Landman, Bennett A; Lauriello, John; Lawrie, Stephen M; Lee, Phil H; Le Hellard, Stephanie; Lemaître, Herve; Leonardo, Cassandra D; Li, Chiang-Shan; Liberg, Benny; Liewald, David C; Liu, Xinmin; Lopez, Lorna M; Loth, Eva; Lourdusamy, Anbarasu; Luciano, Michelle; Macciardi, Fabio; Machielsen, Marise W J; Macqueen, Glenda M; Malt, Ulrik F; Mandl, René; Manoach, Dara S; Martinot, Jean-Luc; Matarin, Mar; Mather, Karen A; Mattheisen, Manuel; Mattingsdal, Morten; Meyer-Lindenberg, Andreas; McDonald, Colm; McIntosh, Andrew M; McMahon, Francis J; McMahon, Katie L; Meisenzahl, Eva; Melle, Ingrid; Milaneschi, Yuri; Mohnke, Sebastian; Montgomery, Grant W; Morris, Derek W; Moses, Eric K; Mueller, Bryon A; Muñoz Maniega, Susana; Mühleisen, Thomas W; Müller-Myhsok, Bertram; Mwangi, Benson; Nauck, Matthias; Nho, Kwangsik; Nichols, Thomas E; Nilsson, Lars-Göran; Nugent, Allison C; Nyberg, Lars; Olvera, Rene L; Oosterlaan, Jaap; Ophoff, Roel A; Pandolfo, Massimo; Papalampropoulou-Tsiridou, Melina; Papmeyer, Martina; Paus, Tomas; Pausova, Zdenka; Pearlson, Godfrey D; Penninx, Brenda W; Peterson, Charles P; Pfennig, Andrea; Phillips, Mary; Pike, G Bruce; Poline, Jean-Baptiste; Potkin, Steven G; Pütz, Benno; Ramasamy, Adaikalavan; Rasmussen, Jerod; Rietschel, Marcella; Rijpkema, Mark; Risacher, Shannon L; Roffman, Joshua L; Roiz-Santiañez, Roberto; Romanczuk-Seiferth, Nina; Rose, Emma J; Royle, Natalie A; Rujescu, Dan; Ryten, Mina; Sachdev, Perminder S; Salami, Alireza; Satterthwaite, Theodore D; Savitz, Jonathan; Saykin, Andrew J; Scanlon, Cathy; Schmaal, Lianne; Schnack, Hugo G; Schork, Andrew J; Schulz, S Charles; Schür, Remmelt; Seidman, Larry; Shen, Li; Shoemaker, Jody M; Simmons, Andrew; Sisodiya, Sanjay M; Smith, Colin; Smoller, Jordan W; Soares, Jair C; Sponheim, Scott R; Sprooten, Emma; Starr, John M; Steen, Vidar M; Strakowski, Stephen; Strike, Lachlan; Sussmann, Jessika; Sämann, Philipp G; Teumer, Alexander; Toga, Arthur W; Tordesillas-Gutierrez, Diana; Trabzuni, Daniah; Trost, Sarah; Turner, Jessica; Van den Heuvel, Martijn; van der Wee, Nic J; van Eijk, Kristel; van Erp, Theo G M; van Haren, Neeltje E M; van 't Ent, Dennis; van Tol, Marie-Jose; Valdés Hernández, Maria C; Veltman, Dick J; Versace, Amelia; Völzke, Henry; Walker, Robert; Walter, Henrik; Wang, Lei; Wardlaw, Joanna M; Weale, Michael E; Weiner, Michael W; Wen, Wei; Westlye, Lars T; Whalley, Heather C; Whelan, Christopher D; White, Tonya; Winkler, Anderson M; Wittfeld, Katharina; Woldehawariat, Girma; Wolf, Christiane; Zilles, David; Zwiers, Marcel P; Thalamuthu, Anbupalam; Schofield, Peter R; Freimer, Nelson B; Lawrence, Natalia S; Drevets, Wayne

    2014-06-01

    The Enhancing NeuroImaging Genetics through Meta-Analysis (ENIGMA) Consortium is a collaborative network of researchers working together on a range of large-scale studies that integrate data from 70 institutions worldwide. Organized into Working Groups that tackle questions in neuroscience, genetics, and medicine, ENIGMA studies have analyzed neuroimaging data from over 12,826 subjects. In addition, data from 12,171 individuals were provided by the CHARGE consortium for replication of findings, in a total of 24,997 subjects. By meta-analyzing results from many sites, ENIGMA has detected factors that affect the brain that no individual site could detect on its own, and that require larger numbers of subjects than any individual neuroimaging study has currently collected. ENIGMA's first project was a genome-wide association study identifying common variants in the genome associated with hippocampal volume or intracranial volume. Continuing work is exploring genetic associations with subcortical volumes (ENIGMA2) and white matter microstructure (ENIGMA-DTI). Working groups also focus on understanding how schizophrenia, bipolar illness, major depression and attention deficit/hyperactivity disorder (ADHD) affect the brain. We review the current progress of the ENIGMA Consortium, along with challenges and unexpected discoveries made on the way.

  18. Analyses of fixed effects for genetic evaluation of dairy cattle using test day records in Indonesia

    Directory of Open Access Journals (Sweden)

    Asep Anang

    2010-06-01

    Full Text Available Season, rainfall, day of rain, temperature, humidity, year and farm are fixed effects, which have been reported to influence milk yield. Those factors are often linked together to contribute to the variation of milk production. This research is addressed to study the fixed effect factors, including lactation curve, which should be considered for genetic evaluation of milk yield based on test day records of dairy cattle. The data were taken from four different farms, which were PT. Taurus Dairy Farm, BPPT Cikole, Bandang Dairy Farm, and BBPTU Baturraden. In total of 16806 test day records were evaluated, consisting of 9,302 at first and 7,504 at second lactation, respectively. The results indicated that fixed effects were very specific and the influences had different patterns for each farm. Consequently, in a genetic evaluation, these factors such as lactation, temperature, year, day of rain, and humidity need to be evaluated first. Ali-Schaeffer curve represented the most appropriate curve to use in the genetic evaluation of dairy cattle in Indonesia.

  19. Genetic architecture and bottleneck analyses of Salem Black goat breed based on microsatellite markers

    Directory of Open Access Journals (Sweden)

    A. K. Thiruvenkadan

    2014-09-01

    Full Text Available Aim: The present study was undertaken in Salem Black goat population for genetic analysis at molecular level to exploit the breed for planning sustainable improvement, conservation and utilization, which subsequently can improve the livelihood of its stakeholders. Materials and Methods: Genomic DNA was isolated from blood samples of 50 unrelated Salem Black goats with typical phenotypic features in several villages in the breeding tract and the genetic characterization and bottleneck analysis in Salem Black goat was done using 25 microsatellite markers as recommended by the Food and Agricultural Organization, Rome, Italy. The basic measures of genetic variation were computed using bioinformatic software. To evaluate the Salem Black goats for mutation drift equilibrium, three tests were performed under three different mutation models, viz., infinite allele model (IAM, stepwise mutation model (SMM and two-phase model (TPM and the observed gene diversity (He and expected equilibrium gene diversity (Heq were estimated under different models of microsatellite evolution. Results: The study revealed that the observed number of alleles ranged from 4 (ETH10, ILSTS008 to 17 (BM64444 with a total of 213 alleles and mean of 10.14±0.83 alleles across loci. The overall observed heterozygosity, expected heterozygosity, inbreeding estimate and polymorphism information content values were 0.631±0.041, 0.820±0.024, 0.233±0.044 and 0.786±0.023 respectively indicating high genetic diversity. The average observed gene diversities (He pooled over different markers was 0.829±0.024 and the average expected gene diversities under IAM, TPM and SMM models were 0.769±0.026, 0.808±0.024 and 0.837±0.020 respectively. The number of loci found to exhibit gene diversity excess under IAM, TPM and SMM models were 18, 17 and 12 respectively. Conclusion: All the three statistical tests, viz., sign test, standardized differences test and Wilcoxon sign rank test, revealed

  20. Population Genetic Analyses of the Fungal Pathogen Colletotrichum fructicola on Tea-Oil Trees in China.

    Directory of Open Access Journals (Sweden)

    He Li

    Full Text Available The filamentous fungus Colletotrichum fructicola is found in all five continents and is capable of causing severe diseases in a number of economically important plants such as avocado, fig, cocoa, pear, and tea-oil trees. However, almost nothing is known about its patterns of genetic variation and epidemiology on any of its host plant species. Here we analyzed 167 isolates of C. fructicola obtained from the leaves of tea-oil tree Camellia oleifera at 15 plantations in seven Chinese provinces. Multilocus sequence typing was conducted for all isolates based on DNA sequences at fragments of four genes: the internal transcribed spacers of the nuclear ribosomal RNA gene cluster (539 bp, calmodulin (633 bp, glutamine synthetase (711 bp, and glyceraldehyde-3-phosphate dehydrogenase (190 bp, yielding 3.52%, 0.63%, 8.44%, and 7.89% of single nucleotide polymorphic sites and resulting in 15, 5, 12 and 11 alleles respectively at the four gene fragments in the total sample. The combined allelic information from all four loci identified 53 multilocus genotypes with the most frequent represented by 21 isolates distributed in eight tea-oil plantations in three provinces, consistent with long-distance clonal dispersal. However, despite evidence for clonal dispersal, statistically significant genetic differentiation among geographic populations was detected. In addition, while no evidence of recombination was found within any of the four gene fragments, signatures of recombination were found among the four gene fragments in most geographic populations, consistent with sexual mating of this species in nature. Our study provides the first insights into the population genetics and epidemiology of the important plant fungal pathogen C. fructicola.

  1. GSEVM v.2: MCMC software to analyse genetically structured environmental variance models

    DEFF Research Database (Denmark)

    Ibáñez-Escriche, N; Garcia, M; Sorensen, D

    2010-01-01

    This note provides a description of software that allows to fit Bayesian genetically structured variance models using Markov chain Monte Carlo (MCMC). The gsevm v.2 program was written in Fortran 90. The DOS and Unix executable programs, the user's guide, and some example files are freely available...... for research purposes at http://www.bdporc.irta.es/estudis.jsp. The main feature of the program is to compute Monte Carlo estimates of marginal posterior distributions of parameters of interest. The program is quite flexible, allowing the user to fit a variety of linear models at the level of the mean...

  2. Genetic analyses, phenotypic adaptability and stability in sugarcane genotypes for commercial cultivation in Pernambuco.

    Science.gov (United States)

    Dutra Filho, J A; Junior, T C; Simões Neto, D E

    2015-10-05

    In the present study, we assessed the agro-industrial performance of 22 sugarcane genotypes adaptable to edaphoclimatic conditions in production microregions in the State of Pernambuco, Brazil, and we recommended the commercial cultivation of select genotypes. The variables analyzed were as follows: sucrose percentage in cane juice, tonnage of saccharose per hectare (TPH), sugarcane tonnage per hectare (TCH), fiber, solid soluble contents, total recoverable sugar tonnage (ATR), and total recoverable sugar tonnage per hectare (ATR t/ha). A randomized block design with 4 repeats was used. Combined variance of the experiments, genetic parameter estimates, and environment stratification were analyzed. Phenotypic adaptability and stability were analyzed using the Annicchiarico and Wricke methods and analysis of variance. Genetic gain was estimated using the classic index and sum of ranks. Genotype selection was efficient for TPH, TCH, and ATR t/ha. Genotypes presented a great potential for improvement and a similar response pattern in Litoral Norte and Mata Sul microregions for TPH and TCH and Litoral Norte and Litoral Sul microregions for ATR t/ha. Genotypes SP78-4764, RB813804, and SP79-101 showed better productivity and phenotypic adaptability and stability, according to the Wricke and Annicchiarico methods. These genotypes can be recommended for cultivation in the sugarcane belt in the State of Pernambuco.

  3. Evaluation of Kalman filters and genetic algorithms for delayed-neutron nondestructive assay data analyses

    International Nuclear Information System (INIS)

    Aumeier, S.E.; Forsmann, J.H.

    1998-01-01

    The ability to nondestructively determine the presence and quantity of fissile/fertile nuclei in various matrices is important in several areas of nuclear applications, including international and domestic safeguards, radioactive waste characterization, and nuclear facility operations. An analysis was performed to determine the feasibility of identifying the masses of individual fissionable isotopes from a cumulative delayed-neutron signal resulting form the neutron irradiation of several uranium and plutonium isotopes. The feasibility of two separate data-processing techniques was studied: Kalman filtering and genetic algorithms. The basis of each technique is reviewed, and the structure of the algorithms as applied to the delayed-neutron analysis problem is presented. The results of parametric studies performed using several variants of the algorithms are presented. The effect of including additional constraining information such as additional measurements and known relative isotopic concentration is discussed. The parametric studies were conducted using simulated delayed-neutron data representative of the cumulative delayed-neutron response following irradiation of a sample containing 238 U, 235 U, 239 Pu, and 240 Pu. The results show that by processing delayed-neutron data representative of two significantly different fissile/fertile fission ratios, both Kalman filters and genetic algorithms are capable of yielding reasonably accurate estimates of the mass of individual isotopes contained in a given assay sample

  4. What Risk Assessments of Genetically Modified Organisms Can Learn from Institutional Analyses of Public Health Risks

    Directory of Open Access Journals (Sweden)

    S. Ravi Rajan

    2012-01-01

    Full Text Available The risks of genetically modified organisms (GMOs are evaluated traditionally by combining hazard identification and exposure estimates to provide decision support for regulatory agencies. We question the utility of the classical risk paradigm and discuss its evolution in GMO risk assessment. First, we consider the problem of uncertainty, by comparing risk assessment for environmental toxins in the public health domain with genetically modified organisms in the environment; we use the specific comparison of an insecticide to a transgenic, insecticidal food crop. Next, we examine normal accident theory (NAT as a heuristic to consider runaway effects of GMOs, such as negative community level consequences of gene flow from transgenic, insecticidal crops. These examples illustrate how risk assessments are made more complex and contentious by both their inherent uncertainty and the inevitability of failure beyond expectation in complex systems. We emphasize the value of conducting decision-support research, embracing uncertainty, increasing transparency, and building interdisciplinary institutions that can address the complex interactions between ecosystems and society. In particular, we argue against black boxing risk analysis, and for a program to educate policy makers about uncertainty and complexity, so that eventually, decision making is not the burden that falls upon scientists but is assumed by the public at large.

  5. What risk assessments of genetically modified organisms can learn from institutional analyses of public health risks.

    Science.gov (United States)

    Rajan, S Ravi; Letourneau, Deborah K

    2012-01-01

    The risks of genetically modified organisms (GMOs) are evaluated traditionally by combining hazard identification and exposure estimates to provide decision support for regulatory agencies. We question the utility of the classical risk paradigm and discuss its evolution in GMO risk assessment. First, we consider the problem of uncertainty, by comparing risk assessment for environmental toxins in the public health domain with genetically modified organisms in the environment; we use the specific comparison of an insecticide to a transgenic, insecticidal food crop. Next, we examine normal accident theory (NAT) as a heuristic to consider runaway effects of GMOs, such as negative community level consequences of gene flow from transgenic, insecticidal crops. These examples illustrate how risk assessments are made more complex and contentious by both their inherent uncertainty and the inevitability of failure beyond expectation in complex systems. We emphasize the value of conducting decision-support research, embracing uncertainty, increasing transparency, and building interdisciplinary institutions that can address the complex interactions between ecosystems and society. In particular, we argue against black boxing risk analysis, and for a program to educate policy makers about uncertainty and complexity, so that eventually, decision making is not the burden that falls upon scientists but is assumed by the public at large.

  6. Longitudinal changes in telomere length and associated genetic parameters in dairy cattle analysed using random regression models.

    Directory of Open Access Journals (Sweden)

    Luise A Seeker

    Full Text Available Telomeres cap the ends of linear chromosomes and shorten with age in many organisms. In humans short telomeres have been linked to morbidity and mortality. With the accumulation of longitudinal datasets the focus shifts from investigating telomere length (TL to exploring TL change within individuals over time. Some studies indicate that the speed of telomere attrition is predictive of future disease. The objectives of the present study were to 1 characterize the change in bovine relative leukocyte TL (RLTL across the lifetime in Holstein Friesian dairy cattle, 2 estimate genetic parameters of RLTL over time and 3 investigate the association of differences in individual RLTL profiles with productive lifespan. RLTL measurements were analysed using Legendre polynomials in a random regression model to describe TL profiles and genetic variance over age. The analyses were based on 1,328 repeated RLTL measurements of 308 female Holstein Friesian dairy cattle. A quadratic Legendre polynomial was fitted to the fixed effect of age in months and to the random effect of the animal identity. Changes in RLTL, heritability and within-trait genetic correlation along the age trajectory were calculated and illustrated. At a population level, the relationship between RLTL and age was described by a positive quadratic function. Individuals varied significantly regarding the direction and amount of RLTL change over life. The heritability of RLTL ranged from 0.36 to 0.47 (SE = 0.05-0.08 and remained statistically unchanged over time. The genetic correlation of RLTL at birth with measurements later in life decreased with the time interval between samplings from near unity to 0.69, indicating that TL later in life might be regulated by different genes than TL early in life. Even though animals differed in their RLTL profiles significantly, those differences were not correlated with productive lifespan (p = 0.954.

  7. Genetic analyses of the human eye colours using a novel objective method for eye colour classification

    DEFF Research Database (Denmark)

    Andersen, Jeppe D.; Johansen, Peter; Harder, Stine

    2013-01-01

    In this study, we present a new objective method for measuring the eye colour on a continuous scale that allows researchers to associate genetic markers with different shades of eye colour. With the use of the custom designed software Digital Iris Analysis Tool (DIAT), the iris was automatically...... and TYR rs1393350) on the eye colour. We evaluated the two published prediction models for eye colour (IrisPlex [1] and Snipper[2]) and compared the predictions with the PIE-scores. We found good concordance with the prediction from individuals typed as HERC2 rs12913832 G. However, both methods had......-score ranged from −1 to 1 (brown to blue). The software eliminated the need for user based interpretation and qualitative eye colour categories. In 94% (570) of 605 analyzed eye images, the iris region was successfully extracted and a PIE-score was calculated. A very high correlation between the PIE...

  8. Subtypes of familial hemophagocytic lymphohistiocytosis in Japan based on genetic and functional analyses of cytotoxic T lymphocytes.

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    Kozo Nagai

    Full Text Available BACKGROUND: Familial hemophagocytic lymphohistiocytosis (FHL is a rare disease of infancy or early childhood. To clarify the incidence and subtypes of FHL in Japan, we performed genetic and functional analyses of cytotoxic T lymphocytes (CTLs in Japanese patients with FHL. DESIGN AND METHODS: Among the Japanese children with hemophagocytic lymphohistiocytosis (HLH registered at our laboratory, those with more than one of the following findings were eligible for study entry under a diagnosis of FHL: positive for known genetic mutations, a family history of HLH, and impaired CTL-mediated cytotoxicity. Mutations of the newly identified causative gene for FHL5, STXBP2, and the cytotoxicity and degranulation activity of CTLs in FHL patients, were analyzed. RESULTS: Among 31 FHL patients who satisfied the above criteria, PRF1 mutation was detected in 17 (FHL2 and UNC13D mutation was in 10 (FHL3. In 2 other patients, 3 novel mutations of STXBP2 gene were confirmed (FHL5. Finally, the remaining 2 were classified as having FHL with unknown genetic mutations. In all FHL patients, CTL-mediated cytotoxicity was low or deficient, and degranulation activity was also low or absent except FHL2 patients. In 2 patients with unknown genetic mutations, the cytotoxicity and degranulation activity of CTLs appeared to be deficient in one patient and moderately impaired in the other. CONCLUSIONS: FHL can be diagnosed and classified on the basis of CTL-mediated cytotoxicity, degranulation activity, and genetic analysis. Based on the data obtained from functional analysis of CTLs, other unknown gene(s responsible for FHL remain to be identified.

  9. Landscape genetic analyses reveal fine-scale effects of forest fragmentation in an insular tropical bird.

    Science.gov (United States)

    Khimoun, Aurélie; Peterman, William; Eraud, Cyril; Faivre, Bruno; Navarro, Nicolas; Garnier, Stéphane

    2017-10-01

    Within the framework of landscape genetics, resistance surface modelling is particularly relevant to explicitly test competing hypotheses about landscape effects on gene flow. To investigate how fragmentation of tropical forest affects population connectivity in a forest specialist bird species, we optimized resistance surfaces without a priori specification, using least-cost (LCP) or resistance (IBR) distances. We implemented a two-step procedure in order (i) to objectively define the landscape thematic resolution (level of detail in classification scheme to describe landscape variables) and spatial extent (area within the landscape boundaries) and then (ii) to test the relative role of several landscape features (elevation, roads, land cover) in genetic differentiation in the Plumbeous Warbler (Setophaga plumbea). We detected a small-scale reduction of gene flow mainly driven by land cover, with a negative impact of the nonforest matrix on landscape functional connectivity. However, matrix components did not equally constrain gene flow, as their conductivity increased with increasing structural similarity with forest habitat: urban areas and meadows had the highest resistance values whereas agricultural areas had intermediate resistance values. Our results revealed a higher performance of IBR compared to LCP in explaining gene flow, reflecting suboptimal movements across this human-modified landscape, challenging the common use of LCP to design habitat corridors and advocating for a broader use of circuit theory modelling. Finally, our results emphasize the need for an objective definition of landscape scales (landscape extent and thematic resolution) and highlight potential pitfalls associated with parameterization of resistance surfaces. © 2017 John Wiley & Sons Ltd.

  10. Direct radiocarbon dating and genetic analyses on the purported Neanderthal mandible from the Monti Lessini (Italy).

    Science.gov (United States)

    Talamo, Sahra; Hajdinjak, Mateja; Mannino, Marcello A; Fasani, Leone; Welker, Frido; Martini, Fabio; Romagnoli, Francesca; Zorzin, Roberto; Meyer, Matthias; Hublin, Jean-Jacques

    2016-07-08

    Anatomically modern humans replaced Neanderthals in Europe around 40,000 years ago. The demise of the Neanderthals and the nature of the possible relationship with anatomically modern humans has captured our imagination and stimulated research for more than a century now. Recent chronological studies suggest a possible overlap between Neanderthals and anatomically modern humans of more than 5,000 years. Analyses of ancient genome sequences from both groups have shown that they interbred multiple times, including in Europe. A potential place of interbreeding is the notable Palaeolithic site of Riparo Mezzena in Northern Italy. In order to improve our understanding of prehistoric occupation at Mezzena, we analysed the human mandible and several cranial fragments from the site using radiocarbon dating, ancient DNA, ZooMS and isotope analyses. We also performed a more detailed investigation of the lithic assemblage of layer I. Surprisingly we found that the Riparo Mezzena mandible is not from a Neanderthal but belonged to an anatomically modern human. Furthermore, we found no evidence for the presence of Neanderthal remains among 11 of the 13 cranial and post-cranial fragments re-investigated in this study.

  11. University Students' Knowledge Structures and Informal Reasoning on the Use of Genetically Modified Foods: Multidimensional Analyses

    Science.gov (United States)

    Wu, Ying-Tien

    2013-10-01

    This study aims to provide insights into the role of learners' knowledge structures about a socio-scientific issue (SSI) in their informal reasoning on the issue. A total of 42 non-science major university students' knowledge structures and informal reasoning were assessed with multidimensional analyses. With both qualitative and quantitative analyses, this study revealed that those students with more extended and better-organized knowledge structures, as well as those who more frequently used higher-order information processing modes, were more oriented towards achieving a higher-level informal reasoning quality. The regression analyses further showed that the "richness" of the students' knowledge structures explained 25 % of the variation in their rebuttal construction, an important indicator of reasoning quality, indicating the significance of the role of students' sophisticated knowledge structure in SSI reasoning. Besides, this study also provides some initial evidence for the significant role of the "core" concept within one's knowledge structure in one's SSI reasoning. The findings in this study suggest that, in SSI-based instruction, science instructors should try to identify students' core concepts within their prior knowledge regarding the SSI, and then they should try to guide students to construct and structure relevant concepts or ideas regarding the SSI based on their core concepts. Thus, students could obtain extended and well-organized knowledge structures, which would then help them achieve better learning transfer in dealing with SSIs.

  12. Genetic and functional analyses demonstrate a role for abnormal glycinergic signaling in autism.

    Science.gov (United States)

    Pilorge, M; Fassier, C; Le Corronc, H; Potey, A; Bai, J; De Gois, S; Delaby, E; Assouline, B; Guinchat, V; Devillard, F; Delorme, R; Nygren, G; Råstam, M; Meier, J C; Otani, S; Cheval, H; James, V M; Topf, M; Dear, T N; Gillberg, C; Leboyer, M; Giros, B; Gautron, S; Hazan, J; Harvey, R J; Legendre, P; Betancur, C

    2016-07-01

    Autism spectrum disorder (ASD) is a common neurodevelopmental condition characterized by marked genetic heterogeneity. Recent studies of rare structural and sequence variants have identified hundreds of loci involved in ASD, but our knowledge of the overall genetic architecture and the underlying pathophysiological mechanisms remains incomplete. Glycine receptors (GlyRs) are ligand-gated chloride channels that mediate inhibitory neurotransmission in the adult nervous system but exert an excitatory action in immature neurons. GlyRs containing the α2 subunit are highly expressed in the embryonic brain, where they promote cortical interneuron migration and the generation of excitatory projection neurons. We previously identified a rare microdeletion of the X-linked gene GLRA2, encoding the GlyR α2 subunit, in a boy with autism. The microdeletion removes the terminal exons of the gene (GLRA2(Δex8-9)). Here, we sequenced 400 males with ASD and identified one de novo missense mutation, p.R153Q, absent from controls. In vitro functional analysis demonstrated that the GLRA2(Δex8)(-)(9) protein failed to localize to the cell membrane, while the R153Q mutation impaired surface expression and markedly reduced sensitivity to glycine. Very recently, an additional de novo missense mutation (p.N136S) was reported in a boy with ASD, and we show that this mutation also reduced cell-surface expression and glycine sensitivity. Targeted glra2 knockdown in zebrafish induced severe axon-branching defects, rescued by injection of wild type but not GLRA2(Δex8-9) or R153Q transcripts, providing further evidence for their loss-of-function effect. Glra2 knockout mice exhibited deficits in object recognition memory and impaired long-term potentiation in the prefrontal cortex. Taken together, these results implicate GLRA2 in non-syndromic ASD, unveil a novel role for GLRA2 in synaptic plasticity and learning and memory, and link altered glycinergic signaling to social and cognitive

  13. Characterizing genetic diversity of contemporary pacific chickens using mitochondrial DNA analyses.

    Directory of Open Access Journals (Sweden)

    Kelsey Needham Dancause

    Full Text Available BACKGROUND: Mitochondrial DNA (mtDNA hypervariable region (HVR sequences of prehistoric Polynesian chicken samples reflect dispersal of two haplogroups--D and E--by the settlers of the Pacific. The distribution of these chicken haplogroups has been used as an indicator of human movement. Recent analyses suggested similarities between prehistoric Pacific and South American chicken samples, perhaps reflecting prehistoric Polynesian introduction of the chicken into South America. These analyses have been heavily debated. The current distribution of the D and E lineages among contemporary chicken populations in the Western Pacific is unclear, but might ultimately help to inform debates about the movements of humans that carried them. OBJECTIVES: We sought to characterize contemporary mtDNA diversity among chickens in two of the earliest settled archipelagos of Remote Oceania, the Marianas and Vanuatu. METHODS: We generated HVR sequences for 43 chickens from four islands in Vanuatu, and for 5 chickens from Guam in the Marianas. RESULTS: Forty samples from Vanuatu and three from Guam were assigned to haplogroup D, supporting this as a Pacific chicken haplogroup that persists in the Western Pacific. Two haplogroup E lineages were observed in Guam and two in Vanuatu. Of the E lineages in Vanuatu, one was identical to prehistoric Vanuatu and Polynesian samples and the other differed by one polymorphism. Contrary to our expectations, we observed few globally distributed domesticate lineages not associated with Pacific chicken dispersal. This might suggest less European introgression of chickens into Vanuatu than expected. If so, the E lineages might represent lineages maintained from ancient Pacific chicken introductions. The Vanuatu sample might thus provide an opportunity to distinguish between maintained ancestral Pacific chicken lineages and replacement by global domesticates through genomic analyses, which could resolve questions of contemporary

  14. Genome-Wide Association Analyses Highlight the Potential for Different Genetic Mechanisms for Litter Size Among Sheep Breeds

    Science.gov (United States)

    Xu, Song-Song; Gao, Lei; Xie, Xing-Long; Ren, Yan-Ling; Shen, Zhi-Qiang; Wang, Feng; Shen, Min; Eyϸórsdóttir, Emma; Hallsson, Jón H.; Kiseleva, Tatyana; Kantanen, Juha; Li, Meng-Hua

    2018-01-01

    Reproduction is an important trait in sheep breeding as well as in other livestock. However, despite its importance the genetic mechanisms of litter size in domestic sheep (Ovis aries) are still poorly understood. To explore genetic mechanisms underlying the variation in litter size, we conducted multiple independent genome-wide association studies in five sheep breeds of high prolificacy (Wadi, Hu, Icelandic, Finnsheep, and Romanov) and one low prolificacy (Texel) using the Ovine Infinium HD BeadChip, respectively. We identified different sets of candidate genes associated with litter size in different breeds: BMPR1B, FBN1, and MMP2 in Wadi; GRIA2, SMAD1, and CTNNB1 in Hu; NCOA1 in Icelandic; INHBB, NF1, FLT1, PTGS2, and PLCB3 in Finnsheep; ESR2 in Romanov and ESR1, GHR, ETS1, MMP15, FLI1, and SPP1 in Texel. Further annotation of genes and bioinformatics analyses revealed that different biological pathways could be involved in the variation in litter size of females: hormone secretion (FSH and LH) in Wadi and Hu, placenta and embryonic lethality in Icelandic, folliculogenesis and LH signaling in Finnsheep, ovulation and preovulatory follicle maturation in Romanov, and estrogen and follicular growth in Texel. Taken together, our results provide new insights into the genetic mechanisms underlying the prolificacy trait in sheep and other mammals, suggesting targets for selection where the aim is to increase prolificacy in breeding projects.

  15. Cross-disorder genome-wide analyses suggest a complex genetic relationship between Tourette's syndrome and OCD.

    Science.gov (United States)

    Yu, Dongmei; Mathews, Carol A; Scharf, Jeremiah M; Neale, Benjamin M; Davis, Lea K; Gamazon, Eric R; Derks, Eske M; Evans, Patrick; Edlund, Christopher K; Crane, Jacquelyn; Fagerness, Jesen A; Osiecki, Lisa; Gallagher, Patience; Gerber, Gloria; Haddad, Stephen; Illmann, Cornelia; McGrath, Lauren M; Mayerfeld, Catherine; Arepalli, Sampath; Barlassina, Cristina; Barr, Cathy L; Bellodi, Laura; Benarroch, Fortu; Berrió, Gabriel Bedoya; Bienvenu, O Joseph; Black, Donald W; Bloch, Michael H; Brentani, Helena; Bruun, Ruth D; Budman, Cathy L; Camarena, Beatriz; Campbell, Desmond D; Cappi, Carolina; Silgado, Julio C Cardona; Cavallini, Maria C; Chavira, Denise A; Chouinard, Sylvain; Cook, Edwin H; Cookson, M R; Coric, Vladimir; Cullen, Bernadette; Cusi, Daniele; Delorme, Richard; Denys, Damiaan; Dion, Yves; Eapen, Valsama; Egberts, Karin; Falkai, Peter; Fernandez, Thomas; Fournier, Eduardo; Garrido, Helena; Geller, Daniel; Gilbert, Donald L; Girard, Simon L; Grabe, Hans J; Grados, Marco A; Greenberg, Benjamin D; Gross-Tsur, Varda; Grünblatt, Edna; Hardy, John; Heiman, Gary A; Hemmings, Sian M J; Herrera, Luis D; Hezel, Dianne M; Hoekstra, Pieter J; Jankovic, Joseph; Kennedy, James L; King, Robert A; Konkashbaev, Anuar I; Kremeyer, Barbara; Kurlan, Roger; Lanzagorta, Nuria; Leboyer, Marion; Leckman, James F; Lennertz, Leonhard; Liu, Chunyu; Lochner, Christine; Lowe, Thomas L; Lupoli, Sara; Macciardi, Fabio; Maier, Wolfgang; Manunta, Paolo; Marconi, Maurizio; McCracken, James T; Mesa Restrepo, Sandra C; Moessner, Rainald; Moorjani, Priya; Morgan, Jubel; Muller, Heike; Murphy, Dennis L; Naarden, Allan L; Nurmi, Erika; Ochoa, William Cornejo; Ophoff, Roel A; Pakstis, Andrew J; Pato, Michele T; Pato, Carlos N; Piacentini, John; Pittenger, Christopher; Pollak, Yehuda; Rauch, Scott L; Renner, Tobias; Reus, Victor I; Richter, Margaret A; Riddle, Mark A; Robertson, Mary M; Romero, Roxana; Rosário, Maria C; Rosenberg, David; Ruhrmann, Stephan; Sabatti, Chiara; Salvi, Erika; Sampaio, Aline S; Samuels, Jack; Sandor, Paul; Service, Susan K; Sheppard, Brooke; Singer, Harvey S; Smit, Jan H; Stein, Dan J; Strengman, Eric; Tischfield, Jay A; Turiel, Maurizio; Valencia Duarte, Ana V; Vallada, Homero; Veenstra-VanderWeele, Jeremy; Walitza, Susanne; Wang, Ying; Weale, Mike; Weiss, Robert; Wendland, Jens R; Westenberg, Herman G M; Shugart, Yin Yao; Hounie, Ana G; Miguel, Euripedes C; Nicolini, Humberto; Wagner, Michael; Ruiz-Linares, Andres; Cath, Danielle C; McMahon, William; Posthuma, Danielle; Oostra, Ben A; Nestadt, Gerald; Rouleau, Guy A; Purcell, Shaun; Jenike, Michael A; Heutink, Peter; Hanna, Gregory L; Conti, David V; Arnold, Paul D; Freimer, Nelson B; Stewart, S Evelyn; Knowles, James A; Cox, Nancy J; Pauls, David L

    2015-01-01

    Obsessive-compulsive disorder (OCD) and Tourette's syndrome are highly heritable neurodevelopmental disorders that are thought to share genetic risk factors. However, the identification of definitive susceptibility genes for these etiologically complex disorders remains elusive. The authors report a combined genome-wide association study (GWAS) of Tourette's syndrome and OCD. The authors conducted a GWAS in 2,723 cases (1,310 with OCD, 834 with Tourette's syndrome, 579 with OCD plus Tourette's syndrome/chronic tics), 5,667 ancestry-matched controls, and 290 OCD parent-child trios. GWAS summary statistics were examined for enrichment of functional variants associated with gene expression levels in brain regions. Polygenic score analyses were conducted to investigate the genetic architecture within and across the two disorders. Although no individual single-nucleotide polymorphisms (SNPs) achieved genome-wide significance, the GWAS signals were enriched for SNPs strongly associated with variations in brain gene expression levels (expression quantitative loci, or eQTLs), suggesting the presence of true functional variants that contribute to risk of these disorders. Polygenic score analyses identified a significant polygenic component for OCD (p=2×10(-4)), predicting 3.2% of the phenotypic variance in an independent data set. In contrast, Tourette's syndrome had a smaller, nonsignificant polygenic component, predicting only 0.6% of the phenotypic variance (p=0.06). No significant polygenic signal was detected across the two disorders, although the sample is likely underpowered to detect a modest shared signal. Furthermore, the OCD polygenic signal was significantly attenuated when cases with both OCD and co-occurring Tourette's syndrome/chronic tics were included in the analysis (p=0.01). Previous work has shown that Tourette's syndrome and OCD have some degree of shared genetic variation. However, the data from this study suggest that there are also distinct

  16. Pleiotropic Meta-Analyses of Longitudinal Studies Discover Novel Genetic Variants Associated with Age-Related Diseases

    Directory of Open Access Journals (Sweden)

    Liang He

    2016-10-01

    Full Text Available Age-related diseases may result from shared biological mechanisms in intrinsic processes of aging. Genetic effects on age-related diseases are often modulated by environmental factors due to their little contribution to fitness or are mediated through certain endophenotypes. Identification of genetic variants with pleiotropic effects on both common complex diseases and endophenotypes may reveal potential conflicting evolutionary pressures and deliver new insights into shared genetic contribution to healthspan and lifespan. Here, we performed pleiotropic meta-analyses of genetic variants using five NIH-funded datasets by integrating univariate summary statistics for age-related diseases and endophenotypes. We investigated three groups of traits: (1 endophenotypes such as blood glucose, blood pressure, lipids, hematocrit, and body mass index, (2 time-to-event outcomes such as the age-at-onset of diabetes mellitus (DM, cancer, cardiovascular diseases (CVDs and neurodegenerative diseases (NDs, and (3 both combined. In addition to replicating previous findings, we identify seven novel genome-wide significant loci (< 5e-08, out of which five are low-frequency variants. Specifically, from Group 2, we find rs7632505 on 3q21.1 in SEMA5B, rs460976 on 21q22.3 (1 kb from TMPRSS2 and rs12420422 on 11q24.1 predominantly associated with a variety of CVDs, rs4905014 in ITPK1 associated with stroke and heart failure, rs7081476 on 10p12.1 in ANKRD26 associated with multiple diseases including DM, CVDs, and NDs. From Group 3, we find rs8082812 on 18p11.22 and rs1869717 on 4q31.3 associated with both endophenotypes and CVDs. Our follow-up analyses show that rs7632505, rs4905014, and rs8082812 have age-dependent effects on coronary heart disease or stroke. Functional annotation suggests that most of these SNPs are within regulatory regions or DNase clusters and in linkage disequilibrium with expression quantitative trait loci, implying their potential regulatory

  17. Comparative analyses of Legionella species identifies genetic features of strains causing Legionnaires' disease.

    Science.gov (United States)

    Gomez-Valero, Laura; Rusniok, Christophe; Rolando, Monica; Neou, Mario; Dervins-Ravault, Delphine; Demirtas, Jasmin; Rouy, Zoe; Moore, Robert J; Chen, Honglei; Petty, Nicola K; Jarraud, Sophie; Etienne, Jerome; Steinert, Michael; Heuner, Klaus; Gribaldo, Simonetta; Médigue, Claudine; Glöckner, Gernot; Hartland, Elizabeth L; Buchrieser, Carmen

    2014-01-01

    The genus Legionella comprises over 60 species. However, L. pneumophila and L. longbeachae alone cause over 95% of Legionnaires’ disease. To identify the genetic bases underlying the different capacities to cause disease we sequenced and compared the genomes of L. micdadei, L. hackeliae and L. fallonii (LLAP10), which are all rarely isolated from humans. We show that these Legionella species possess different virulence capacities in amoeba and macrophages, correlating with their occurrence in humans. Our comparative analysis of 11 Legionella genomes belonging to five species reveals highly heterogeneous genome content with over 60% representing species-specific genes; these comprise a complete prophage in L. micdadei, the first ever identified in a Legionella genome. Mobile elements are abundant in Legionella genomes; many encode type IV secretion systems for conjugative transfer, pointing to their importance for adaptation of the genus. The Dot/Icm secretion system is conserved, although the core set of substrates is small, as only 24 out of over 300 described Dot/Icm effector genes are present in all Legionella species. We also identified new eukaryotic motifs including thaumatin, synaptobrevin or clathrin/coatomer adaptine like domains. Legionella genomes are highly dynamic due to a large mobilome mainly comprising type IV secretion systems, while a minority of core substrates is shared among the diverse species. Eukaryotic like proteins and motifs remain a hallmark of the genus Legionella. Key factors such as proteins involved in oxygen binding, iron storage, host membrane transport and certain Dot/Icm substrates are specific features of disease-related strains.

  18. A whole genome analyses of genetic variants in two Kelantan Malay individuals.

    Science.gov (United States)

    Wan Juhari, Wan Khairunnisa; Md Tamrin, Nur Aida; Mat Daud, Mohd Hanif Ridzuan; Isa, Hatin Wan; Mohd Nasir, Nurfazreen; Maran, Sathiya; Abdul Rajab, Nur Shafawati; Ahmad Amin Noordin, Khairul Bariah; Nik Hassan, Nik Norliza; Tearle, Rick; Razali, Rozaimi; Merican, Amir Feisal; Zilfalil, Bin Alwi

    2014-12-01

    The sequencing of two members of the Royal Kelantan Malay family genomes will provide insights on the Kelantan Malay whole genome sequences. The two Kelantan Malay genomes were analyzed for the SNP markers associated with thalassemia and Helicobacter pylori infection. Helicobacter pylori infection was reported to be low prevalence in the north-east as compared to the west coast of the Peninsular Malaysia and beta-thalassemia was known to be one of the most common inherited and genetic disorder in Malaysia. By combining SNP information from literatures, GWAS study and NCBI ClinVar, 18 unique SNPs were selected for further analysis. From these 18 SNPs, 10 SNPs came from previous study of Helicobacter pylori infection among Malay patients, 6 SNPs were from NCBI ClinVar and 2 SNPs from GWAS studies. The analysis reveals that both Royal Kelantan Malay genomes shared all the 10 SNPs identified by Maran (Single Nucleotide Polymorphims (SNPs) genotypic profiling of Malay patients with and without Helicobacter pylori infection in Kelantan, 2011) and one SNP from GWAS study. In addition, the analysis also reveals that both Royal Kelantan Malay genomes shared 3 SNP markers; HBG1 (rs1061234), HBB (rs1609812) and BCL11A (rs766432) where all three markers were associated with beta-thalassemia. Our findings suggest that the Royal Kelantan Malays carry the SNPs which are associated with protection to Helicobacter pylori infection. In addition they also carry SNPs which are associated with beta-thalassemia. These findings are in line with the findings by other researchers who conducted studies on thalassemia and Helicobacter pylori infection in the non-royal Malay population.

  19. Cross-Disorder Genome-Wide Analyses Suggest a Complex Genetic Relationship Between Tourette Syndrome and Obsessive-Compulsive Disorder

    Science.gov (United States)

    Yu, Dongmei; Mathews, Carol A.; Scharf, Jeremiah M.; Neale, Benjamin M.; Davis, Lea K.; Gamazon, Eric R.; Derks, Eske M.; Evans, Patrick; Edlund, Christopher K.; Crane, Jacquelyn; Fagerness, Jesen A.; Osiecki, Lisa; Gallagher, Patience; Gerber, Gloria; Haddad, Stephen; Illmann, Cornelia; McGrath, Lauren M.; Mayerfeld, Catherine; Arepalli, Sampath; Barlassina, Cristina; Barr, Cathy L.; Bellodi, Laura; Benarroch, Fortu; Berrió, Gabriel Bedoya; Bienvenu, O. Joseph; Black, Donald; Bloch, Michael H.; Brentani, Helena; Bruun, Ruth D.; Budman, Cathy L.; Camarena, Beatriz; Campbell, Desmond D.; Cappi, Carolina; Cardona Silgado, Julio C.; Cavallini, Maria C.; Chavira, Denise A.; Chouinard, Sylvain; Cook, Edwin H.; Cookson, M. R.; Coric, Vladimir; Cullen, Bernadette; Cusi, Daniele; Delorme, Richard; Denys, Damiaan; Dion, Yves; Eapen, Valsama; Egberts, Karin; Falkai, Peter; Fernandez, Thomas; Fournier, Eduardo; Garrido, Helena; Geller, Daniel; Gilbert, Donald; Girard, Simon L.; Grabe, Hans J.; Grados, Marco A.; Greenberg, Benjamin D.; Gross-Tsur, Varda; Grünblatt, Edna; Hardy, John; Heiman, Gary A.; Hemmings, Sian M.J.; Herrera, Luis D.; Hezel, Dianne M.; Hoekstra, Pieter J.; Jankovic, Joseph; Kennedy, James L.; King, Robert A.; Konkashbaev, Anuar I.; Kremeyer, Barbara; Kurlan, Roger; Lanzagorta, Nuria; Leboyer, Marion; Leckman, James F.; Lennertz, Leonhard; Liu, Chunyu; Lochner, Christine; Lowe, Thomas L.; Lupoli, Sara; Macciardi, Fabio; Maier, Wolfgang; Manunta, Paolo; Marconi, Maurizio; McCracken, James T.; Mesa Restrepo, Sandra C.; Moessner, Rainald; Moorjani, Priya; Morgan, Jubel; Muller, Heike; Murphy, Dennis L.; Naarden, Allan L.; Ochoa, William Cornejo; Ophoff, Roel A.; Pakstis, Andrew J.; Pato, Michele T.; Pato, Carlos N.; Piacentini, John; Pittenger, Christopher; Pollak, Yehuda; Rauch, Scott L.; Renner, Tobias; Reus, Victor I.; Richter, Margaret A.; Riddle, Mark A.; Robertson, Mary M.; Romero, Roxana; Rosário, Maria C.; Rosenberg, David; Ruhrmann, Stephan; Sabatti, Chiara; Salvi, Erika; Sampaio, Aline S.; Samuels, Jack; Sandor, Paul; Service, Susan K.; Sheppard, Brooke; Singer, Harvey S.; Smit, Jan H.; Stein, Dan J.; Strengman, Eric; Tischfield, Jay A.; Turiel, Maurizio; Valencia Duarte, Ana V.; Vallada, Homero; Veenstra-VanderWeele, Jeremy; Walitza, Susanne; Walkup, John; Wang, Ying; Weale, Mike; Weiss, Robert; Wendland, Jens R.; Westenberg, Herman G.M.; Yao, Yin; Hounie, Ana G.; Miguel, Euripedes C.; Nicolini, Humberto; Wagner, Michael; Ruiz-Linares, Andres; Cath, Danielle C.; McMahon, William; Posthuma, Danielle; Oostra, Ben A.; Nestadt, Gerald; Rouleau, Guy A.; Purcell, Shaun; Jenike, Michael A.; Heutink, Peter; Hanna, Gregory L.; Conti, David V.; Arnold, Paul D.; Freimer, Nelson; Stewart, S. Evelyn; Knowles, James A.; Cox, Nancy J.; Pauls, David L.

    2014-01-01

    Obsessive-compulsive disorder (OCD) and Tourette Syndrome (TS) are highly heritable neurodevelopmental disorders that are thought to share genetic risk factors. However, the identification of definitive susceptibility genes for these etiologically complex disorders remains elusive. Here, we report a combined genome-wide association study (GWAS) of TS and OCD in 2723 cases (1310 with OCD, 834 with TS, 579 with OCD plus TS/chronic tics (CT)), 5667 ancestry-matched controls, and 290 OCD parent-child trios. Although no individual single nucleotide polymorphisms (SNPs) achieved genome-wide significance, the GWAS signals were enriched for SNPs strongly associated with variations in brain gene expression levels, i.e. expression quantitative loci (eQTLs), suggesting the presence of true functional variants that contribute to risk of these disorders. Polygenic score analyses identified a significant polygenic component for OCD (p=2×10−4), predicting 3.2% of the phenotypic variance in an independent data set. In contrast, TS had a smaller, non-significant polygenic component, predicting only 0.6% of the phenotypic variance (p=0.06). No significant polygenic signal was detected across the two disorders, although the sample is likely underpowered to detect a modest shared signal. Furthermore, the OCD polygenic signal was significantly attenuated when cases with both OCD and TS/CT were included in the analysis (p=0.01). Previous work has shown that TS and OCD have some degree of shared genetic variation. However, the data from this study suggest that there are also distinct components to the genetic architectures of TS and OCD. Furthermore, OCD with co-occurring TS/CT may have different underlying genetic susceptibility compared to OCD alone. PMID:25158072

  20. Genetic and morphological analyses of Gracilaria firma and G. changii (Gracilariaceae, Rhodophyta), the commercially important agarophytes in western Pacific.

    Science.gov (United States)

    Ng, Poh-Kheng; Lin, Showe-Mei; Lim, Phaik-Eem; Hurtado, Anicia Q; Phang, Siew-Moi; Yow, Yoon-Yen; Sun, Zhongmin

    2017-01-01

    Many studies classifying Gracilaria species for the exploitation of agarophytes and the development of the agar industry were conducted before the prevalence of molecular tools, resulting in the description of many species based solely on their morphology. Gracilaria firma and G. changii are among the commercially important agarophytes from the western Pacific; both feature branches with basal constrictions that taper toward acute apices. In this study, we contrasted the morpho-anatomical circumscriptions of the two traditionally described species with molecular data from samples that included representatives of G. changii collected from its type locality. Concerted molecular analyses using the rbcL and cox1 gene sequences, coupled with morphological observations of the collections from the western Pacific, revealed no inherent differences to support the treatment of the two entities as distinct taxa. We propose merging G. changii (a later synonym) into G. firma and recognize G. firma based on thallus branches with abrupt basal constrictions that gradually taper toward acute (or sometimes broken) apices, cystocarps consisting of small gonimoblast cells and inconspicuous multinucleate tubular nutritive cells issuing from gonimoblasts extending into the inner pericarp at the cystocarp floor, as well as deep spermatangial conceptacles of the verrucosa-type. The validation of specimens under different names as a single genetic species is useful to allow communication and knowledge transfer among groups from different fields. This study also revealed considerably low number of haplotypes and nucleotide diversity with apparent phylogeographic patterns for G. firma in the region. Populations from the Philippines and Taiwan were divergent from each other as well as from the populations from Malaysia, Thailand, Singapore and Vietnam. Establishment of baseline data on the genetic diversity of this commercially important agarophyte is relevant in the context of cultivation

  1. Replicated landscape genetic and network analyses reveal wide variation in functional connectivity for American pikas.

    Science.gov (United States)

    Castillo, Jessica A; Epps, Clinton W; Jeffress, Mackenzie R; Ray, Chris; Rodhouse, Thomas J; Schwalm, Donelle

    2016-09-01

    Landscape connectivity is essential for maintaining viable populations, particularly for species restricted to fragmented habitats or naturally arrayed in metapopulations and facing rapid climate change. The importance of assessing both structural connectivity (physical distribution of favorable habitat patches) and functional connectivity (how species move among habitat patches) for managing such species is well understood. However, the degree to which functional connectivity for a species varies among landscapes, and the resulting implications for conservation, have rarely been assessed. We used a landscape genetics approach to evaluate resistance to gene flow and, thus, to determine how landscape and climate-related variables influence gene flow for American pikas (Ochotona princeps) in eight federally managed sites in the western United States. We used empirically derived, individual-based landscape resistance models in conjunction with predictive occupancy models to generate patch-based network models describing functional landscape connectivity. Metareplication across landscapes enabled identification of limiting factors for dispersal that would not otherwise have been apparent. Despite the cool microclimates characteristic of pika habitat, south-facing aspects consistently represented higher resistance to movement, supporting the previous hypothesis that exposure to relatively high temperatures may limit dispersal in American pikas. We found that other barriers to dispersal included areas with a high degree of topographic relief, such as cliffs and ravines, as well as streams and distances greater than 1-4 km depending on the site. Using the empirically derived network models of habitat patch connectivity, we identified habitat patches that were likely disproportionately important for maintaining functional connectivity, areas in which habitat appeared fragmented, and locations that could be targeted for management actions to improve functional connectivity

  2. Evolutionary genetic analyses of MEF2C gene: implications for learning and memory in Homo sapiens.

    Science.gov (United States)

    Kalmady, Sunil V; Venkatasubramanian, Ganesan; Arasappa, Rashmi; Rao, Naren P

    2013-02-01

    MEF2C facilitates context-dependent fear conditioning (CFC) which is a salient aspect of hippocampus-dependent learning and memory. CFC might have played a crucial role in human evolution because of its advantageous influence on survival of species. In this study, we analyzed 23 orthologous mammalian gene sequences of MEF2C gene to examine the evidence for positive selection on this gene in Homo sapiens using Phylogenetic Analysis by Maximum Likelihood (PAML) and HyPhy software. Both PAML Bayes Empirical Bayes (BEB) and HyPhy Fixed Effects Likelihood (FEL) analyses supported significant positive selection on 4 codon sites in H. sapiens. Also, haplotter analysis revealed significant ongoing positive selection on this gene in Central European population. The study findings suggest that adaptive selective pressure on this gene might have influenced human evolution. Further research on this gene might unravel the potential role of this gene in learning and memory as well as its pathogenetic effect in certain hippocampal disorders with evolutionary basis like schizophrenia. Copyright © 2012 Elsevier B.V. All rights reserved.

  3. Genetic polymorphisms of miR-146a and miR-27a, H. pylori infection, and risk of gastric lesions in a Chinese population.

    Directory of Open Access Journals (Sweden)

    Ming-yang Song

    Full Text Available BACKGROUND: MicroRNAs (miRNAs have been implicated in various human diseases. Single nucleotide polymorphisms (SNPs in inflammation-related miRNA may play an important role in Helicobacter pylori (H. pylori-induced gastric lesions. To evaluate the associations between miRNA SNPs, H. pylori and gastric lesions, a population-based study was conducted in Linqu County, China. METHODOLOGY/PRINCIPAL FINDINGS: Based on serum miRNA array conducted in this population, two SNP loci (miR-146a rs2910164: G>C and miR-27a rs895819: T>C were determined by polymerase chain reaction-restriction fragment length polymorphism in 2,380 participants with diverse gastric lesions. Using participants with superficial gastritis and mild chronic atrophic gastritis as the reference group, we found that rs2910164 CC carriers had a significantly increased risk of intestinal metaplasia [adjusted odds ratio (OR, 1.42; 95% confidence interval (CI, 1.03-1.97] and dysplasia (OR, 1.54; 95% CI, 1.05-2.25 compared to GG carriers, whereas no significant association was observed for rs895819. Stratified analysis by H. pylori infection indicated that rs2910164 C allele was associated with an increased risk of intestinal metaplasia and dysplasia only among individuals infected with H. pylori (CC vs. GG: OR, 1.53; 95% CI, 1.12-2.08, P for trend = 0.004. Participants who simultaneously carried variant alleles and H. pylori infection were more likely to develop intestinal metaplasia and dysplasia, although the interaction between genetic variants and H. pylori infection was not significant (P for interaction = 0.35 for rs2910164 and 0.92 for rs895819. CONCLUSIONS/SIGNIFICANCE: These findings suggest that miR-146a rs2910164 polymorphism may contribute to the evolution of H. pylori-associated gastric lesions in this high-risk population.

  4. Genetic and Cytological Analyses of the Natural Variation of Seed Number per Pod in Rapeseed (Brassica napus L.

    Directory of Open Access Journals (Sweden)

    Yuhua Yang

    2017-11-01

    Full Text Available Seed number is one of the key traits related to plant evolution/domestication and crop improvement/breeding. In rapeseed germplasm, the seed number per pod (SNPP shows a very wide variation from several to nearly 30; however, the underlying causations/mechanisms for this variation are poorly known. In the current study, the genetic and cytological bases for the natural variation of SNPP in rapeseed was firstly and systematically investigated using the representative four high-SNPP and five low-SNPP lines. The results of self- or cross-pollination experiment between the high- and low-SNPP lines showed that the natural variation of SNPP was mainly controlled by maternal effect (mean = 0.79, followed by paternal effect (mean = 0.21. Analysis of the data using diploid seed embryo–cytoplasmic–maternal model further showed that the maternal genotype, embryo, and cytoplasm effects, respectively, explained 47.6, 35.2, and 7.5% of the genetic variance. In addition, the analysis of combining ability showed that for the SNPP of hybrid F1 was mainly determined by the general combining ability of parents (63.0%, followed by special combining ability of parental combination (37.0%. More importantly, the cytological observation showed that the SNPP difference between the high- and low-SNPP lines was attributable to the accumulative differences in its components. Of which, the number of ovules, the proportion of fertile ovules, the proportion of fertile ovules to be fertilized, and the proportion of fertilized ovules to develop into seeds accounted for 30.7, 18.2, 7.1, and 43.9%, respectively. The accordant results of both genetic and cytological analyses provide solid evidences and systematic insights to further understand the mechanisms underlying the natural variation of SNPP, which will facilitate the development of high-yield cultivars in rapeseed.

  5. Genetic variants associated with subjective well-being, depressive symptoms and neuroticism identified through genome-wide analyses

    Science.gov (United States)

    Derringer, Jaime; Gratten, Jacob; Lee, James J; Liu, Jimmy Z; de Vlaming, Ronald; Ahluwalia, Tarunveer S; Buchwald, Jadwiga; Cavadino, Alana; Frazier-Wood, Alexis C; Davies, Gail; Furlotte, Nicholas A; Garfield, Victoria; Geisel, Marie Henrike; Gonzalez, Juan R; Haitjema, Saskia; Karlsson, Robert; van der Laan, Sander W; Ladwig, Karl-Heinz; Lahti, Jari; van der Lee, Sven J; Miller, Michael B; Lind, Penelope A; Liu, Tian; Matteson, Lindsay; Mihailov, Evelin; Minica, Camelia C; Nolte, Ilja M; Mook-Kanamori, Dennis O; van der Most, Peter J; Oldmeadow, Christopher; Qian, Yong; Raitakari, Olli; Rawal, Rajesh; Realo, Anu; Rueedi, Rico; Schmidt, Börge; Smith, Albert V; Stergiakouli, Evie; Tanaka, Toshiko; Taylor, Kent; Thorleifsson, Gudmar; Wedenoja, Juho; Wellmann, Juergen; Westra, Harm-Jan; Willems, Sara M; Zhao, Wei; Amin, Najaf; Bakshi, Andrew; Bergmann, Sven; Bjornsdottir, Gyda; Boyle, Patricia A; Cherney, Samantha; Cox, Simon R; Davis, Oliver S P; Ding, Jun; Direk, Nese; Eibich, Peter; Emeny, Rebecca T; Fatemifar, Ghazaleh; Faul, Jessica D; Ferrucci, Luigi; Forstner, Andreas J; Gieger, Christian; Gupta, Richa; Harris, Tamara B; Harris, Juliette M; Holliday, Elizabeth G; Hottenga, Jouke-Jan; De Jager, Philip L; Kaakinen, Marika A; Kajantie, Eero; Karhunen, Ville; Kolcic, Ivana; Kumari, Meena; Launer, Lenore J; Franke, Lude; Li-Gao, Ruifang; Liewald, David C; Koini, Marisa; Loukola, Anu; Marques-Vidal, Pedro; Montgomery, Grant W; Mosing, Miriam A; Paternoster, Lavinia; Pattie, Alison; Petrovic, Katja E; Pulkki-Råback, Laura; Quaye, Lydia; Räikkönen, Katri; Rudan, Igor; Scott, Rodney J; Smith, Jennifer A; Sutin, Angelina R; Trzaskowski, Maciej; Vinkhuyzen, Anna E; Yu, Lei; Zabaneh, Delilah; Attia, John R; Bennett, David A; Berger, Klaus; Bertram, Lars; Boomsma, Dorret I; Snieder, Harold; Chang, Shun-Chiao; Cucca, Francesco; Deary, Ian J; van Duijn, Cornelia M; Eriksson, Johan G; Bültmann, Ute; de Geus, Eco J C; Groenen, Patrick J F; Gudnason, Vilmundur; Hansen, Torben; Hartman, Catharine A; Haworth, Claire M A; Hayward, Caroline; Heath, Andrew C; Hinds, David A; Hyppönen, Elina; Iacono, William G; Järvelin, Marjo-Riitta; Jöckel, Karl-Heinz; Kaprio, Jaakko; Kardia, Sharon L R; Keltikangas-Järvinen, Liisa; Kraft, Peter; Kubzansky, Laura D; Lehtimäki, Terho; Magnusson, Patrik K E; Martin, Nicholas G; McGue, Matt; Metspalu, Andres; Mills, Melinda; de Mutsert, Renée; Oldehinkel, Albertine J; Pasterkamp, Gerard; Pedersen, Nancy L; Plomin, Robert; Polasek, Ozren; Power, Christine; Rich, Stephen S; Rosendaal, Frits R; den Ruijter, Hester M; Schlessinger, David; Schmidt, Helena; Svento, Rauli; Schmidt, Reinhold; Alizadeh, Behrooz Z; Sørensen, Thorkild I A; Spector, Tim D; Starr, John M; Stefansson, Kari; Steptoe, Andrew; Terracciano, Antonio; Thorsteinsdottir, Unnur; Thurik, A Roy; Timpson, Nicholas J; Tiemeier, Henning; Uitterlinden, André G; Vollenweider, Peter; Wagner, Gert G; Weir, David R; Yang, Jian; Conley, Dalton C; Smith, George Davey; Hofman, Albert; Johannesson, Magnus; Laibson, David I; Medland, Sarah E; Meyer, Michelle N; Pickrell, Joseph K; Esko, Tõnu; Krueger, Robert F; Beauchamp, Jonathan P; Koellinger, Philipp D; Benjamin, Daniel J; Bartels, Meike; Cesarini, David

    2016-01-01

    We conducted genome-wide association studies of three phenotypes: subjective well-being (N = 298,420), depressive symptoms (N = 161,460), and neuroticism (N = 170,910). We identified three variants associated with subjective well-being, two with depressive symptoms, and eleven with neuroticism, including two inversion polymorphisms. The two depressive symptoms loci replicate in an independent depression sample. Joint analyses that exploit the high genetic correlations between the phenotypes (|ρ^| ≈ 0.8) strengthen the overall credibility of the findings, and allow us to identify additional variants. Across our phenotypes, loci regulating expression in central nervous system and adrenal/pancreas tissues are strongly enriched for association. PMID:27089181

  6. On the road to quantitative genetic/genomic analyses of root growth and development components underlying root architecture

    International Nuclear Information System (INIS)

    Draye, X.; Dorlodot, S. de; Lavigne, T.

    2006-01-01

    The quantitative genetic and functional genomic analyses of root development, growth and plasticity will be instrumental in revealing the major regulatory pathways of root architecture. Such knowledge, combined with in-depth consideration of root physiology (e.g. uptake, exsudation), form (space-time dynamics of soil exploration) and ecology (including root environment), will settle the bases for designing root ideotypes for specific environments, for low-input agriculture or for successful agricultural production with minimal impact on the environment. This report summarizes root research initiated in our lab between 2000 and 2004 in the following areas: quantitative analysis of root branching in bananas, high throughput characterisation of root morphology, image analysis, QTL mapping of detailed features of root architecture in rice, and attempts to settle a Crop Root Research Consortium. (author)

  7. Qualitative analysis of mouse specific-locus mutations: information on genetic organization, gene expression, and the chromosomal nature of induced lesions

    International Nuclear Information System (INIS)

    Russell, L.B.

    1982-01-01

    Analysis of mouse specific-locus (SL) mutations at three loci has identified over 33 distinct complementation groups - most of which are probably overlapping deficiencies - and 13 to 14 new functional units. The complementation maps that have been generated for the d-se and c regions include numerous vital functions; however, some of the genes in these regions are non-vital. At such loci, hypomorphic mutants must represent intragenic alterations, and some viable nulls could conceivably be intragenic lesions also. Analysis of SL mutations has provided information on genetic expression. Homozygous deficiencies can be completely viable or can kill at any one of a range of developmental stages. Heterozygonus deficiencies of up to 6 cM or more in genetic length have been recovered and propagated. The time of death of homozygous and the degree of inviability of heterozygous deficiencies are related more to specific content of the missing segment than to its length. Combinations of deficiencies with x-autosome translocations that inactivate the homologous region in a mosaic fashion have shown that organismic lethals are not necessarily cell lethal. The spectrum of mutations induced depends on the nature of the mutagen and the type of germ cell exposed. Radiation of spermatogonia produces intragenic as well as null mutations. Spontaneous mutations have an admixture of types not present in populations of mutations induced in germ cells, and this raises doubts concerning the accuracy of doubling-dose calculations in genetic risk estimation. The analysis of SL mutations has yielded genetic tools for the construction of detailed gene-dosage series, cis-trans comparisons, the mapping of known genes and identification of new genes, genetic rescue of various types, and the identification and isolation of DNA sequences

  8. Genetic polymorphisms of matrix metalloproteinases and their inhibitors in potentially malignant and malignant lesions of the head and neck

    Directory of Open Access Journals (Sweden)

    Asotra Kamlesh

    2010-02-01

    Full Text Available Abstract Matrix metalloproteinases (MMPs are a family of zinc-dependent proteinases that are capable of cleaving all extra cellular matrix (ECM substrates. Degradation of matrix is a key event in progression, invasion and metastasis of potentially malignant and malignant lesions of the head and neck. It might have an important polymorphic association at the promoter regions of several MMPs such as MMP-1 (-1607 1G/2G, MMP-2 (-1306 C/T, MMP-3 (-1171 5A/6A, MMP-9 (-1562 C/T and TIMP-2 (-418 G/C or C/C. Tissue inhibitors of metalloproteinases (TIMPs are naturally occurring inhibitors of MMPs, which inhibit the activity of MMPs and control the breakdown of ECM. Currently, many MMP inhibitors (MMPIs are under development for treating different malignancies. Useful markers associated with molecular aggressiveness might have a role in prognostication of malignancies and to better recognize patient groups that need more antagonistic treatment options. Furthermore, the introduction of novel prognostic markers may also promote exclusively new treatment possibilities, and there is an obvious need to identify markers that could be used as selection criteria for novel therapies. The objective of this review is to discuss the molecular functions and polymorphic association of MMPs and TIMPs and the possible therapeutic aspects of these proteinases in potentially malignant and malignant head and neck lesions. So far, no promising drug target therapy has been developed for MMPs in the lesions of this region. In conclusion, further research is required for the development of their potential diagnostic and therapeutic possibilities.

  9. Gene Set Analyses of Genome-Wide Association Studies on 49 Quantitative Traits Measured in a Single Genetic Epidemiology Dataset

    Directory of Open Access Journals (Sweden)

    Jihye Kim

    2013-09-01

    Full Text Available Gene set analysis is a powerful tool for interpreting a genome-wide association study result and is gaining popularity these days. Comparison of the gene sets obtained for a variety of traits measured from a single genetic epidemiology dataset may give insights into the biological mechanisms underlying these traits. Based on the previously published single nucleotide polymorphism (SNP genotype data on 8,842 individuals enrolled in the Korea Association Resource project, we performed a series of systematic genome-wide association analyses for 49 quantitative traits of basic epidemiological, anthropometric, or blood chemistry parameters. Each analysis result was subjected to subsequent gene set analyses based on Gene Ontology (GO terms using gene set analysis software, GSA-SNP, identifying a set of GO terms significantly associated to each trait (pcorr < 0.05. Pairwise comparison of the traits in terms of the semantic similarity in their GO sets revealed surprising cases where phenotypically uncorrelated traits showed high similarity in terms of biological pathways. For example, the pH level was related to 7 other traits that showed low phenotypic correlations with it. A literature survey implies that these traits may be regulated partly by common pathways that involve neuronal or nerve systems.

  10. Population genetic analyses are consistent with the introduction of Ceramium secundatum (Ceramiaceae, Rhodophyta) to Narragansett Bay, Rhode Island, USA.

    Science.gov (United States)

    Bruce, Meghann R; Saunders, Gary W

    2015-11-01

    During ongoing DNA barcode (COI-5P) surveys of the macroalgal flora along the northwest Atlantic coast, we discovered a population of Ceramium secundatum in Narragansett Bay, Rhode Island, USA. This species is regarded as common and widespread in the northeast Atlantic, ranging from Norway to Morocco, but until now has not been reported from the western Atlantic. Several lines of evidence suggest that C. secundatum may be introduced to Narragansett Bay: (1) despite extensive collecting, specimens have only been obtained from a limited geographic range in the northwest Atlantic; (2) three other nonindigenous seaweed species are reportedly introduced in this region, which is thought to be a consequence of shipping; and (3) this species is introduced to South Africa and New Zealand. To investigate this suspected introduction, we applied population genetic analyses (using the cox2-3 spacer) to compare the Narragansett Bay C. secundatum population to native populations in the Republic of Ireland and the United Kingdom. Collectively, analyses of biogeographical and molecular data indicate that C. secundatum is likely introduced to Narragansett Bay. The implications of this discovery are discussed.

  11. Loss of heterozygosity in fibrocystic change of the breast: genetic relationship between benign proliferative lesions and associated carcinomas.

    Science.gov (United States)

    Washington, C; Dalbègue, F; Abreo, F; Taubenberger, J K; Lichy, J H

    2000-07-01

    Loss of heterozygosity (LOH), a genetic change frequently detected in cancer, can also occur in benign epithelial foci in the breast. To characterize LOH in benign breast tissue, 32 cases containing the various components of fibrocystic change in the absence of malignancy were studied. Microdissected foci of ductal hyperplasia, apocrine metaplasia, sclerosing adenosis, and morphologically normal terminal duct lobular units (TDLUs) were analyzed for LOH at 14 polymorphic loci representing seven chromosomal arms. LOH was detected in 22% of normal TDLUs (6/27), 17% of adenosis (4/23), 19% of hyperplasia (4/21), and 53% of apocrine metaplasia (10/19) specimens. Because of the high percentage of LOH in apocrine metaplasia in nonneoplastic specimens, the genetic relationship between apocrine metaplasia and cancer was studied in a panel of breast cancer cases. Of 14 examples of apocrine metaplasia adjacent to a carcinoma, seven were found to have LOH with at least one marker. In all seven cases, the tumor and apocrine metaplasia shared LOH at one or more markers. The results demonstrate that LOH occurs frequently in the components of fibrocystic change as well as in normal TDLUs and suggest that foci of apocrine metaplasia can share a genetically altered precursor cell with an associated carcinoma.

  12. Characterization of the genome of a phylogenetically distinct tospovirus and its interactions with the local lesion-induced host Chenopodium quinoa by whole-transcriptome analyses.

    Science.gov (United States)

    Chou, Wan-Chen; Lin, Shih-Shun; Yeh, Shyi-Dong; Li, Siang-Ling; Peng, Ying-Che; Fan, Ya-Hsu; Chen, Tsung-Chi

    2017-01-01

    Chenopodium quinoa is a natural local lesion host of numerous plant viruses, including tospoviruses (family Bunyaviridae). Groundnut chlorotic fan-spot tospovirus (GCFSV) has been shown to consistently induce local lesions on the leaves of C. quinoa 4 days post-inoculation (dpi). To reveal the whole genome of GCFSV and its interactions with C. quinoa, RNA-seq was performed to determine the transcriptome profiles of C. quinoa leaves. The high-throughput reads from infected C. quinoa leaves were used to identify the whole genome sequence of GCFSV and its single nucleotide polymorphisms. Our results indicated that GCFSV is a phylogenetically distinct tospovirus. Moreover, 27,170 coding and 29,563 non-coding sequences of C. quinoa were identified through de novo assembly, mixing reads from mock and infected samples. Several key genes involved in the modulation of hypersensitive response (HR) were identified. The expression levels of 4,893 deduced complete genes annotated using the Arabidopsis genome indicated that several HR-related orthologues of pathogenesis-related proteins, transcription factors, mitogen-activated protein kinases, and defense proteins were significantly expressed in leaves that formed local lesions. Here, we also provide new insights into the replication progression of a tospovirus and the molecular regulation of the C. quinoa response to virus infection.

  13. Molecular analyses reveal two geographic and genetic lineages for tapeworms, Taenia solium and Taenia saginata, from Ecuador using mitochondrial DNA.

    Science.gov (United States)

    Solano, Danilo; Navarro, Juan Carlos; León-Reyes, Antonio; Benítez-Ortiz, Washington; Rodríguez-Hidalgo, Richar

    2016-12-01

    Tapeworms Taenia solium and Taenia saginata are the causative agents of taeniasis/cysticercosis. These are diseases with high medical and veterinary importance due to their impact on public health and rural economy in tropical countries. The re-emergence of T. solium as a result of human migration, the economic burden affecting livestock industry, and the large variability of symptoms in several human cysticercosis, encourage studies on genetic diversity, and the identification of these parasites with molecular phylogenetic tools. Samples collected from the Ecuadorian provinces: Loja, Guayas, Manabí, Tungurahua (South), and Imbabura, Pichincha (North) from 2000 to 2012 were performed under Maximum Parsimony analyses and haplotype networks using partial sequences of mitochondrial DNA, cytochrome oxidase subunit I (COI) and NADH subunit I (NDI), from Genbank and own sequences of Taenia solium and Taenia saginata from Ecuador. Both species have shown reciprocal monophyly, which confirms its molecular taxonomic identity. The COI and NDI genes results suggest phylogenetic structure for both parasite species from south and north of Ecuador. In T. solium, both genes gene revealed greater geographic structure, whereas in T. saginata, the variability for both genes was low. In conclusion, COI haplotype networks of T. solium suggest two geographical events in the introduction of this species in Ecuador (African and Asian lineages) and occurring sympatric, probably through the most common routes of maritime trade between the XV-XIX centuries. Moreover, the evidence of two NDI geographical lineages in T. solium from the north (province of Imbabura) and the south (province of Loja) of Ecuador derivate from a common Indian ancestor open new approaches for studies on genetic populations and eco-epidemiology. Copyright © 2016 Elsevier Inc. All rights reserved.

  14. Phenotypic and genetic analyses of the varroa sensitive hygienic trait in Russian honey bee (hymenoptera: apidae) colonies.

    Science.gov (United States)

    Kirrane, Maria J; de Guzman, Lilia I; Holloway, Beth; Frake, Amanda M; Rinderer, Thomas E; Whelan, Pádraig M

    2014-01-01

    Varroa destructor continues to threaten colonies of European honey bees. General hygiene, and more specific Varroa Sensitive Hygiene (VSH), provide resistance towards the Varroa mite in a number of stocks. In this study, 32 Russian (RHB) and 14 Italian honey bee colonies were assessed for the VSH trait using two different assays. Firstly, colonies were assessed using the standard VSH behavioural assay of the change in infestation of a highly infested donor comb after a one-week exposure. Secondly, the same colonies were assessed using an "actual brood removal assay" that measured the removal of brood in a section created within the donor combs as a potential alternative measure of hygiene towards Varroa-infested brood. All colonies were then analysed for the recently discovered VSH quantitative trait locus (QTL) to determine whether the genetic mechanisms were similar across different stocks. Based on the two assays, RHB colonies were consistently more hygienic toward Varroa-infested brood than Italian honey bee colonies. The actual number of brood cells removed in the defined section was negatively correlated with the Varroa infestations of the colonies (r2 = 0.25). Only two (percentages of brood removed and reproductive foundress Varroa) out of nine phenotypic parameters showed significant associations with genotype distributions. However, the allele associated with each parameter was the opposite of that determined by VSH mapping. In this study, RHB colonies showed high levels of hygienic behaviour towards Varroa -infested brood. The genetic mechanisms are similar to those of the VSH stock, though the opposite allele associates in RHB, indicating a stable recombination event before the selection of the VSH stock. The measurement of brood removal is a simple, reliable alternative method of measuring hygienic behaviour towards Varroa mites, at least in RHB stock.

  15. Phenotypic and genetic analyses of the varroa sensitive hygienic trait in Russian honey bee (hymenoptera: apidae colonies.

    Directory of Open Access Journals (Sweden)

    Maria J Kirrane

    Full Text Available Varroa destructor continues to threaten colonies of European honey bees. General hygiene, and more specific Varroa Sensitive Hygiene (VSH, provide resistance towards the Varroa mite in a number of stocks. In this study, 32 Russian (RHB and 14 Italian honey bee colonies were assessed for the VSH trait using two different assays. Firstly, colonies were assessed using the standard VSH behavioural assay of the change in infestation of a highly infested donor comb after a one-week exposure. Secondly, the same colonies were assessed using an "actual brood removal assay" that measured the removal of brood in a section created within the donor combs as a potential alternative measure of hygiene towards Varroa-infested brood. All colonies were then analysed for the recently discovered VSH quantitative trait locus (QTL to determine whether the genetic mechanisms were similar across different stocks. Based on the two assays, RHB colonies were consistently more hygienic toward Varroa-infested brood than Italian honey bee colonies. The actual number of brood cells removed in the defined section was negatively correlated with the Varroa infestations of the colonies (r2 = 0.25. Only two (percentages of brood removed and reproductive foundress Varroa out of nine phenotypic parameters showed significant associations with genotype distributions. However, the allele associated with each parameter was the opposite of that determined by VSH mapping. In this study, RHB colonies showed high levels of hygienic behaviour towards Varroa -infested brood. The genetic mechanisms are similar to those of the VSH stock, though the opposite allele associates in RHB, indicating a stable recombination event before the selection of the VSH stock. The measurement of brood removal is a simple, reliable alternative method of measuring hygienic behaviour towards Varroa mites, at least in RHB stock.

  16. The Limitations of Behavior-Genetic Analyses: Comment on McGue, Elkins, Walden, and Iacono (2005)

    Science.gov (United States)

    Greenberg, Gary

    2005-01-01

    This article takes issue with the behavior-genetic analysis of parenting style presented by M. McGue, I. Elkins, B. Walden, and W. G. Iacono. The author argues that the attribution of their findings to inherited genetic effects was without basis because McGue et al. never indicated how those genetic effects manifested themselves. Instead, McGue et…

  17. Analysis of genetic diversity of Sclerotinia sclerotiorum from eggplant by mycelial compatibility, random amplification of polymorphic DNA (RAPD and simple sequence repeat (SSR analyses

    Directory of Open Access Journals (Sweden)

    Fatih Mehmet Tok

    2016-09-01

    Full Text Available The genetic diversity and pathogenicity/virulence among 60 eggplant Sclerotinia sclerotiorum isolates collected from six different geographic regions of Turkey were analysed using mycelial compatibility groupings (MCGs, random amplified polymorphic DNA (RAPD and simple sequence repeat (SSR polymorphism. By MCG tests, the isolates were classified into 22 groups. Out of 22 MCGs, 36% were represented each by a single isolate. The isolates showed great variability for virulence regardless of MCG and geographic origin. Based on the results of RAPD and SSR analyses, 60 S. sclerotiorum isolates representing 22 MCGs were grouped in 2 and 3 distinct clusters, respectively. Analyses using RAPD and SSR markers illustrated that cluster groupings or genetic distance of S. sclerotiorum populations from eggplant were not distinctly relative to the MCG, geographical origin and virulence diversity. The patterns obtained revealed a high heterogeneity of genetic composition and suggested the occurrence of clonal and sexual reproduction of S. sclerotiorum on eggplant in the areas surveyed.

  18. A DNA microarray-based methylation-sensitive (MS)-AFLP hybridization method for genetic and epigenetic analyses.

    Science.gov (United States)

    Yamamoto, F; Yamamoto, M

    2004-07-01

    We previously developed a PCR-based DNA fingerprinting technique named the Methylation Sensitive (MS)-AFLP method, which permits comparative genome-wide scanning of methylation status with a manageable number of fingerprinting experiments. The technique uses the methylation sensitive restriction enzyme NotI in the context of the existing Amplified Fragment Length Polymorphism (AFLP) method. Here we report the successful conversion of this gel electrophoresis-based DNA fingerprinting technique into a DNA microarray hybridization technique (DNA Microarray MS-AFLP). By performing a total of 30 (15 x 2 reciprocal labeling) DNA Microarray MS-AFLP hybridization experiments on genomic DNA from two breast and three prostate cancer cell lines in all pairwise combinations, and Southern hybridization experiments using more than 100 different probes, we have demonstrated that the DNA Microarray MS-AFLP is a reliable method for genetic and epigenetic analyses. No statistically significant differences were observed in the number of differences between the breast-prostate hybridization experiments and the breast-breast or prostate-prostate comparisons.

  19. Genetic and molecular analyses of UV radiation-induced mutations in the fem-3 gene of Caenorhabditis elegans

    Energy Technology Data Exchange (ETDEWEB)

    Hartman, P S; De Wilde, D; Dwarakanath, V N [Texas Christian Univ., Fort Worth, TX (United States). Dept. of Biology

    1995-06-01

    The utility of a new target gene (fem-3) is described for investigating the molecular nature of mutagenesis in the nematode Caenorhabditis elegans. As a principal attribute, this system allows for the selection, maintenance and molecular analysis of any type of mutation that disrupts the gene, including deletions. In this study, 86 mutant strains were isolated, of which 79 proved to have mutations in fem-3. Twenty of these originally tested as homozygous inviable. Homozygous inviability was expected, as Stewart and coworkers had previously observed that, unlike in other organisms, most UV radiation-induced mutations in C. elegans are chromosomal rearrangements of deficiencies (Mutat. Res 249, 37-54, 1991). However, additional data, including Southern blot analyses on 49 of the strains, indicated that most of the UV radiation-induced fem-3 mutations were not deficiencies, as originally inferred from their homozygous inviability. Instead, the lethals were most likely ``coincident mutations`` in linked, essential genes that were concomitantly induced. As such, they were lost owing to genetic recombination during stock maintenance. As in mammalian cells, yeast and bacteria, the frequency of coincident mutations was much higher than would be predicted by chance. (Author).

  20. Association of physical examination knee effusion with bone marrow lesions: cross-sectional and longitudinal analyses of a population-based cohort.

    Science.gov (United States)

    Cibere, Jolanda; Guermazi, Ali; Nicolaou, Savvas; Esdaile, John M; Thorne, Anona; Singer, Joel; Wong, Hubert; Kopec, Jacek A; Sayre, Eric C

    2018-04-12

    To determine the association of physical examination (PE) effusion with prevalence of bone marrow lesions (BML) on MRI, and incidence/progression of BML over 3 years in knee osteoarthritis (OA). A population-based cohort with knee pain (N=255) was assessed for PE effusion. On MRI, BML was graded 0-3 (none, mild, moderate, severe), incidence/progression defined as a worsening in the sum of BML scores over six surfaces by ≥1 grade. We analyzed the full cohort and mild disease subsample with Kellgren-Lawrence (KL) grade value (PPV) and negative predictive value (NPV) for PE effusion vs. BML (prevalence and incidence/progression). Weighted mean age was 56.7 years, mean BMI 26.5, 56.3% were female, 20.1% had PE effusion and 80.7% had KLrecruitment into clinical trials. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

  1. How Genes Modulate Patterns of Aging-Related Changes on the Way to 100: Biodemographic Models and Methods in Genetic Analyses of Longitudinal Data

    Science.gov (United States)

    Yashin, Anatoliy I.; Arbeev, Konstantin G.; Wu, Deqing; Arbeeva, Liubov; Kulminski, Alexander; Kulminskaya, Irina; Akushevich, Igor; Ukraintseva, Svetlana V.

    2016-01-01

    Background and Objective To clarify mechanisms of genetic regulation of human aging and longevity traits, a number of genome-wide association studies (GWAS) of these traits have been performed. However, the results of these analyses did not meet expectations of the researchers. Most detected genetic associations have not reached a genome-wide level of statistical significance, and suffered from the lack of replication in the studies of independent populations. The reasons for slow progress in this research area include low efficiency of statistical methods used in data analyses, genetic heterogeneity of aging and longevity related traits, possibility of pleiotropic (e.g., age dependent) effects of genetic variants on such traits, underestimation of the effects of (i) mortality selection in genetically heterogeneous cohorts, (ii) external factors and differences in genetic backgrounds of individuals in the populations under study, the weakness of conceptual biological framework that does not fully account for above mentioned factors. One more limitation of conducted studies is that they did not fully realize the potential of longitudinal data that allow for evaluating how genetic influences on life span are mediated by physiological variables and other biomarkers during the life course. The objective of this paper is to address these issues. Data and Methods We performed GWAS of human life span using different subsets of data from the original Framingham Heart Study cohort corresponding to different quality control (QC) procedures and used one subset of selected genetic variants for further analyses. We used simulation study to show that approach to combining data improves the quality of GWAS. We used FHS longitudinal data to compare average age trajectories of physiological variables in carriers and non-carriers of selected genetic variants. We used stochastic process model of human mortality and aging to investigate genetic influence on hidden biomarkers of aging

  2. POST-TRANSPLANT LYMPHOPROLIFERATIVE DISORDERS: ROLE OF VIRAL INFECTION, GENETIC LESIONS AND ANTIGEN STIMULATION IN THE PATHOGENESIS OF THE DISEASE

    Directory of Open Access Journals (Sweden)

    Daniela Capello

    2009-11-01

    Full Text Available Post-transplant lymphoproliferative disorders (PTLD are a life-threatening complication of solid organ transplantation or, more rarely, hematopoietic stem cell transplantation. The majority of PTLD is of B-cell origin and associated with Epstein–Barr virus (EBV infection. PTLD generally display involvement of extranodal sites, aggressive histology and aggressive clinical behavior. The molecular pathogenesis of PTLD involves infection by oncogenic viruses, namely Epstein-Barr virus, as well as genetic or epigenetic alterations of several cellular genes. At variance with lymphoma arising in immunocompetent hosts, whose genome is relatively stable, a fraction of PTLD are characterized by microsatellite instability as a consequence of defects in the DNA mismatch repair mechanism. Apart from microsatellite instability, molecular alterations of cellular genes recognized in PTLD include alterations of cMYC, BCL6, TP53, DNA hypermethylation, and aberrant somatic hypermutation of protooncogenes. The occurrence of IGV mutations in the overwhelming majority of PTLD documents that malignant transformation targets germinal centre (GC B-cells and their descendants both in EBV–positive and EBV–negative cases. Analysis of phenotypic markers of B-cell histogenesis, namely BCL6, MUM1 and CD138, allows further distinction of PTLD histogenetic categories. PTLD expressing the BCL6+/MUM1+/-/CD138- profile reflect B-cells actively experiencing the GC reaction, and comprise diffuse large B-cell lymphoma (DLBCL centroblastic and Burkitt lymphoma. PTLD expressing the BCL6-/MUM1+/CD138- phenotype putatively derive from B-cells that have concluded the GC reaction, and comprise the majority of polymorphic PTLD and a fraction of DLBCL immunoblastic. A third group of PTLD is reminiscent of post-GC and preterminally differentiated B-cells that show the BCL6-/MUM1+/CD138+ phenotype, and are morphologically represented by either polymorphic PTLD or DLBCL immunoblastic.

  3. Mitochondrial DNA Analyses Indicate High Diversity, Expansive Population Growth and High Genetic Connectivity of Vent Copepods (Dirivultidae) across Different Oceans.

    Science.gov (United States)

    Gollner, Sabine; Stuckas, Heiko; Kihara, Terue C; Laurent, Stefan; Kodami, Sahar; Martinez Arbizu, Pedro

    2016-01-01

    Communities in spatially fragmented deep-sea hydrothermal vents rich in polymetallic sulfides could soon face major disturbance events due to deep-sea mineral mining, such that unraveling patterns of gene flow between hydrothermal vent populations will be an important step in the development of conservation policies. Indeed, the time required by deep-sea populations to recover following habitat perturbations depends both on the direction of gene flow and the number of migrants available for re-colonization after disturbance. In this study we compare nine dirivultid copepod species across various geological settings. We analyze partial nucleotide sequences of the mtCOI gene and use divergence estimates (FST) and haplotype networks to infer intraspecific population connectivity between vent sites. Furthermore, we evaluate contrasting scenarios of demographic population expansion/decline versus constant population size (using, for example, Tajima's D). Our results indicate high diversity, population expansion and high connectivity of all copepod populations in all oceans. For example, haplotype diversity values range from 0.89 to 1 and FST values range from 0.001 to 0.11 for Stygiopontius species from the Central Indian Ridge, Mid Atlantic Ridge, East Pacific Rise, and Eastern Lau Spreading Center. We suggest that great abundance and high site occupancy by these species favor high genetic diversity. Two scenarios both showed similarly high connectivity: fast spreading centers with little distance between vent fields and slow spreading centers with greater distance between fields. This unexpected result may be due to some distinct frequency of natural disturbance events, or to aspects of individual life histories that affect realized rates of dispersal. However, our statistical performance analyses showed that at least 100 genomic regions should be sequenced to ensure accurate estimates of migration rate. Our demography parameters demonstrate that dirivultid

  4. Mouse and human genetic analyses associate kalirin with ventral striatal activation during impulsivity and with alcohol misuse

    Directory of Open Access Journals (Sweden)

    Yolanda ePeña-Oliver

    2016-04-01

    Full Text Available Impulsivity is associated with a spectrum of psychiatric disorders including drug addiction. To investigate genetic associations with impulsivity and initiation of drug taking, we took a two-step approach. First, we identified genes whose expression level in prefrontal cortex, striatum and accumbens were associated with impulsive behaviour in the 5-choice serial reaction time task across 10 BXD recombinant inbred (BXD RI mouse strains and their progenitor C57BL/6J and DBA2/J strains. Behavioural data were correlated with regional gene expression using GeneNetwork (www.genenetwork.org, to identify 44 genes whose probability of association with impulsivity exceeded a false discovery rate of <0.05. We then interrogated the IMAGEN database of 1423 adolescents for potential associations of SNPs in human homologues of those genes identified in the mouse study, with brain activation during impulsive performance in the Monetary Incentive Delay task, and with novelty seeking scores from the Temperament and Character Inventory, as well as alcohol-experience. There was a significant overall association between the human homologues of impulsivity-related genes and percentage of premature responses in the MID task and with fMRI BOLD-response in ventral striatum (VS during reward anticipation. In contrast, no significant association was found between the polygenic scores and anterior cingulate cortex activation. Univariate association analyses revealed that the G allele (major of the intronic SNP rs6438839 in the KALRN gene was significantly associated with increased VS activation. Additionally, the A-allele (minor of KALRN intronic SNP rs4634050, belonging to the same haplotype block, was associated with increased frequency of binge drinking.

  5. Genetic variation in growth, carbon isotope discrimination, and foliar N concentration in Picea mariana: analyses from a half-diallel mating design using field-grown trees

    Science.gov (United States)

    Kurt H. Johnsen; Lawrence B. Flanagan; Dudley A. Huber; John E. Major

    1999-01-01

    The authors performed genetic analyses of growth, carbon isotope discrimination (?13C), and foliar N concentration using a half-diallel subset of a 7 × 7 complete diallel planted on three sites ranging in water availability. Trees were 22 years old. Heritabilities; general and...

  6. POST-TRANSPLANT LYMPHOPROLIFERATIVE DISORDERS: ROLE OF VIRAL INFECTION, GENETIC LESIONS AND ANTIGEN STIMULATION IN THE PATHOGENESIS OF THE DISEASE

    Directory of Open Access Journals (Sweden)

    Gianluca Gaidano

    2009-11-01

    Full Text Available

    Post-transplant lymphoproliferative disorders (PTLD are a life-threatening complication of solid organ transplantation or, more rarely, hematopoietic stem cell transplantation. The majority of PTLD is of B-cell origin and associated with Epstein–Barr virus (EBV infection. PTLD generally display involvement of extranodal sites, aggressive histology and aggressive clinical behavior. The molecular pathogenesis of PTLD involves infection by oncogenic viruses, namely Epstein-Barr virus, as well as genetic or epigenetic alterations of several cellular genes. At variance with lymphoma arising in immunocompetent hosts, whose genome is relatively stable, a fraction of PTLD are characterized by microsatellite instability as a consequence of defects in the DNA mismatch repair mechanism. Apart from microsatellite instability, molecular alterations of cellular genes recognized in PTLD include alterations of cMYC, BCL6, TP53, DNA hypermethylation, and aberrant somatic hypermutation of protooncogenes. The occurrence of IGV mutations in the overwhelming majority of PTLD documents that malignant transformation targets germinal centre (GC B-cells and their descendants both in EBV–positive and EBV–negative cases. Analysis of phenotypic markers of B-cell histogenesis, namely BCL6, MUM1 and CD138, allows further distinction of PTLD histogenetic categories. PTLD expressing the BCL6+/MUM1+/-/CD138- profile reflect B-cells actively experiencing the GC reaction, and comprise diffuse large B-cell lymphoma (DLBCL centroblastic and Burkitt lymphoma. PTLD expressing the BCL6-/MUM1+/CD138- phenotype putatively derive from B-cells that have concluded the GC reaction, and comprise the majority of polymorphic PTLD and a fraction of

  7. Genome Analyses of Icelandic Strains of Sulfolobus islandicus, Model Organisms for Genetic and Virus-Host Interaction Studies

    DEFF Research Database (Denmark)

    Guo, Li; Brügger, Kim; Liu, Chao

    2011-01-01

    The genomes of two Sulfolobus islandicus strains obtained from Icelandic solfataras were sequenced and analyzed. Strain REY15A is a host for a versatile genetic toolbox. It exhibits a genome of minimal size, is stable genetically, and is easy to grow and manipulate. Strain HVE10/4 shows a broad h...

  8. Genetic analyses of historic and modern marbled murrelets suggest decoupling of migration and gene flow after habitat fragmentation

    Science.gov (United States)

    M. Zachariah Peery; Laurie A. Hall; Sellas. Anna; Steven R. Beissinger; Craig Moritz; Martine Berube; Martin G. Raphael; S. Kim Nelson; Richard T. Golightly; Laura McFarlane-Tranquilla; Scott H. Newman; Per J. Palsboll

    2009-01-01

    The dispersal of individuals among fragmented populations is generally thought to prevent genetic and demographic isolation, and ultimately reduce extinction risk. In this study, we show that a century of reduction in coastal old-growth forests, as well as a number of other environmental factors, has probably resulted in the genetic divergence of marbled murrelets (...

  9. Genetic variants associated with subjective well-being, depressive symptoms, and neuroticism identified through genome-wide analyses

    NARCIS (Netherlands)

    A. Okbay (Aysu); Baselmans, B.M.L. (Bart M.L.); J.E. de Neve (Jan-Emmanuel); P. Turley (Patrick); M. Nivard (Michel); Fontana, M.A. (Mark Alan); Meddens, S.F.W. (S. Fleur W.); Linnér, R.K. (Richard Karlsson); Rietveld, C.A. (Cornelius A); J. Derringer; J. Gratten (Jacob); J.J. Lee (James J.); Liu, J.Z. (Jimmy Z); R. de Vlaming (Ronald); SAhluwalia, T. (Tarunveer); Buchwald, J. (Jadwiga); A. Cavadino (Alana); A.C. Frazier-Wood (Alexis C.); Furlotte, N.A. (Nicholas A); Garfield, V. (Victoria); Geisel, M.H. (Marie Henrike); J.R. Gonzalez (Juan R.); Haitjema, S. (Saskia); R. Karlsson (Robert); Der Laan, S.W. (Sander Wvan); K.-H. Ladwig (Karl-Heinz); J. Lahti (Jari); S.J. van der Lee (Sven); P.A. Lind (Penelope); Liu, T. (Tian); Matteson, L. (Lindsay); E. Mihailov (Evelin); M. Miller (Mike); CMinica, C. (Camelia); MNolte, I. (Ilja); D.O. Mook-Kanamori (Dennis); P.J. van der Most (Peter); C. Oldmeadow (Christopher); Y. Qian (Yong); O. Raitakari (Olli); R. Rawal (R.); A. Realo; Rueedi, R. (Rico); Schmidt, B. (Börge); A.V. Smith (Albert Vernon); E. Stergiakouli (Evangelia); T. Tanaka (Toshiko); K.D. Taylor (Kent); Wedenoja, J. (Juho); Wellmann, J. (Juergen); H.J. Westra (Harm-Jan); MWillems, S. (Sara); Zhao, W. (Wei); L.C. Study (LifeLines Cohort); N. Amin (Najaf); Bakshi, A. (Andrew); P.A. Boyle (Patricia); Cherney, S. (Samantha); Cox, S.R. (Simon R); G. Davies (Gail); O.S.P. Davis (Oliver S.); J. Ding (Jun); N. Direk (Nese); Eibich, P. (Peter); R. Emeny (Rebecca); Fatemifar, G. (Ghazaleh); J.D. Faul; L. Ferrucci (Luigi); A.J. Forstner (Andreas); C. Gieger (Christian); Gupta, R. (Richa); T.B. Harris (Tamara); J.M. Harris (Juliette); E.G. Holliday (Elizabeth); J.J. Hottenga (Jouke Jan); P.L. de Jager (Philip); M. Kaakinen (Marika); E. Kajantie (Eero); Karhunen, V. (Ville); I. Kolcic (Ivana); M. Kumari (Meena); L.J. Launer (Lenore); L. Franke (Lude); Li-Gao, R. (Ruifang); Koini, M. (Marisa); A. Loukola (Anu); P. Marques-Vidal; G.W. Montgomery (Grant); M. Mosing (Miriam); L. Paternoster (Lavinia); A. Pattie (Alison); K. Petrovic (Katja); Pulkki-R'back, L. (Laura); L. Quaye (Lydia); R'ikkönen, K. (Katri); I. Rudan (Igor); R. Scott (Rodney); J.A. Smith (Jennifer A); A.R. Sutin; Trzaskowski, M. (Maciej); Vinkhuyze, A.E. (Anna E.); L. Yu (Lei); D. Zabaneh (Delilah); J. Attia (John); D.A. Bennett (David A.); Berger, K. (Klaus); L. Bertram (Lars); D.I. Boomsma (Dorret); H. Snieder (Harold); Chang, S.-C. (Shun-Chiao); F. Cucca (Francesco); I.J. Deary (Ian J.); C.M. van Duijn (Cornelia); K. Hagen (Knut); U. Bültmann (Ute); E.J.C. de Geus (Eco); P.J.F. Groenen (Patrick); V. Gudnason (Vilmundur); T. Hansen (T.); Hartman, C.A. (Catharine A); C.M.A. Haworth (Claire M.); C. Hayward (Caroline); A.C. Heath (Andrew C.); D.A. Hinds (David A.); E. Hypponen (Elina); W.G. Iacono (William); M.-R. Jarvelin (Marjo-Riitta); K.-H. JöCkel (Karl-Heinz); J. Kaprio (Jaakko); S.L.R. Kardia (Sharon); Keltikangas-J'rvinen, L. (Liisa); P. Kraft (Peter); Kubzansky, L.D. (Laura D.); Lehtim'ki, T. (Terho); P.K. Magnusson (Patrik); N.G. Martin (Nicholas); M. McGue (Matt); A. Metspalu (Andres); M. Mills (Melinda); R. de Mutsert (Reneé); A.J. Oldehinkel (Albertine); G. Pasterkamp (Gerard); N.L. Pedersen (Nancy); R. Plomin (Robert); O. Polasek (Ozren); C. Power (Christopher); S.S. Rich (Stephen); F.R. Rosendaal (Frits); H.M. den Ruijter (Hester ); Schlessinger, D. (David); R. Schmidt (Reinhold); R. Svento (Rauli); R. Schmidt (Reinhold); B.Z. Alizadeh (Behrooz); T.I.A. Sørensen (Thorkild); DSpector, T. (Tim); Steptoe, A. (Andrew); A. Terracciano; A.R. Thurik (Roy); N.J. Timpson (Nicholas); H.W. Tiemeier (Henning); A.G. Uitterlinden (André); P. Vollenweider (Peter); Wagner, G.G. (Gert G.); D.R. Weir (David); J. Yang (Joanna); Conley, D.C. (Dalton C.); G.D. Smith; Hofman, A. (Albert); M. Johannesson (Magnus); D. Laibson (David); S.E. Medland (Sarah Elizabeth); M.N. Meyer (Michelle N.); Pickrell, J.K. (Joseph K.); Esko, T. (T'nu); R.F. Krueger; J.P. Beauchamp (Jonathan); Ph.D. Koellinger (Philipp); D.J. Benjamin (Daniel J.); M. Bartels (Meike); D. Cesarini (David)

    2016-01-01

    textabstractVery few genetic variants have been associated with depression and neuroticism, likely because of limitations on sample size in previous studies. Subjective well-being, a phenotype that is genetically correlated with both of these traits, has not yet been studied with genome-wide data.

  10. Genetic variants associated with subjective well-being, depressive symptoms, and neuroticism identified through genome-wide analyses

    NARCIS (Netherlands)

    Okbay, Aysu; Baselmans, Bart M L; De Neve, Jan-Emmanuel; Turley, Patrick; Nivard, Michel G; Fontana, Mark Alan; Meddens, S Fleur W; Linnér, Richard Karlsson; Rietveld, Cornelius A; Derringer, Jaime; Gratten, Jacob; Lee, James J; Liu, Jimmy Z; de Vlaming, Ronald; Ahluwalia, Tarunveer S; Buchwald, Jadwiga; Cavadino, Alana; Frazier-Wood, Alexis C; Furlotte, Nicholas A; Garfield, Victoria; Geisel, Marie Henrike; Gonzalez, Juan R; Haitjema, Saskia; Karlsson, Robert; van der Laan, Sander W; Ladwig, Karl-Heinz; Lahti, Jari; van der Lee, Sven J; Lind, Penelope A; Liu, Tian; Matteson, Lindsay; Mihailov, Evelin; Miller, Michael B; Minica, Camelia C; Nolte, Ilja M; Mook-Kanamori, Dennis; van der Most, Peter J; Oldmeadow, Christopher; Qian, Yong; Raitakari, Olli; Rawal, Rajesh; Realo, Anu; Rueedi, Rico; Schmidt, Börge; Smith, Albert V; Stergiakouli, Evie; Tanaka, Toshiko; Taylor, Kent; Wedenoja, Juho; Wellmann, Juergen; Westra, Harm-Jan; Willems, Sara M; Zhao, Wei; Amin, Najaf; Bakshi, Andrew; Boyle, Patricia A; Cherney, Samantha; Cox, Simon R; Davies, Gail; Davis, Oliver S P; Ding, Jun; Direk, Nese; Eibich, Peter; Emeny, Rebecca T; Fatemifar, Ghazaleh; Faul, Jessica D; Ferrucci, Luigi; Forstner, Andreas; Gieger, Christian; Gupta, Richa; Harris, Tamara B; Harris, Juliette M; Holliday, Elizabeth G; Hottenga, Jouke-Jan; De Jager, Philip L; Kaakinen, Marika A; Kajantie, Eero; Karhunen, Ville; Kolcic, Ivana; Kumari, Meena; Launer, Lenore J; Franke, Lude; Li-Gao, Ruifang; Koini, Marisa; Loukola, Anu; Marques-Vidal, Pedro; Montgomery, Grant W; Mosing, Miriam A; Paternoster, Lavinia; Pattie, Alison; Petrovic, Katja E; Pulkki-Råback, Laura; Quaye, Lydia; Räikkönen, Katri; Rudan, Igor; Scott, Rodney J; Smith, Jennifer A; Sutin, Angelina R; Trzaskowski, Maciej; Vinkhuyzen, Anna E; Yu, Lei; Zabaneh, Delilah; Attia, John R; Bennett, David A; Berger, Klaus; Bertram, Lars; Boomsma, Dorret I; Snieder, Harold; Chang, Shun-Chiao; Cucca, Francesco; Deary, Ian J; van Duijn, Cornelia M; Eriksson, Johan G; Bültmann, Ute; de Geus, Eco J C; Groenen, Patrick J F; Gudnason, Vilmundur; Hansen, Torben; Hartman, Catharine A; Haworth, Claire M A; Hayward, Caroline; Heath, Andrew C; Hinds, David A; Hyppönen, Elina; Iacono, William G; Järvelin, Marjo-Riitta; Jöckel, Karl-Heinz; Kaprio, Jaakko; Kardia, Sharon L R; Keltikangas-Järvinen, Liisa; Kraft, Peter; Kubzansky, Laura D; Lehtimäki, Terho; Magnusson, Patrik K E; Martin, Nicholas G; McGue, Matt; Metspalu, Andres; Mills, Melinda; de Mutsert, Renée; Oldehinkel, Albertine J; Pasterkamp, Gerard; Pedersen, Nancy L; Plomin, Robert; Polasek, Ozren; Power, Christine; Rich, Stephen S; Rosendaal, Frits R; den Ruijter, Hester M; Schlessinger, David; Schmidt, Helena; Svento, Rauli; Schmidt, Reinhold; Alizadeh, Behrooz Z; Sørensen, Thorkild I A; Spector, Tim D; Steptoe, Andrew; Terracciano, Antonio; Thurik, A Roy; Timpson, Nicholas J; Tiemeier, Henning; Uitterlinden, André G; Vollenweider, Peter; Wagner, Gert G; Weir, David R; Yang, Jian; Conley, Dalton C; Smith, George Davey; Hofman, Albert; Johannesson, Magnus; Laibson, David I; Medland, Sarah E; Meyer, Michelle N; Pickrell, Joseph K; Esko, Tõnu; Krueger, Robert F; Beauchamp, Jonathan P; Koellinger, Philipp D; Benjamin, Daniel J; Bartels, Meike; Cesarini, David

    Very few genetic variants have been associated with depression and neuroticism, likely because of limitations on sample size in previous studies. Subjective well-being, a phenotype that is genetically correlated with both of these traits, has not yet been studied with genome-wide data. We conducted

  11. Genetic diversity analyses of Lasiodiplodia theobromae on Morus alba and Agave sisalana based on RAPD and ISSR molecular markers

    Directory of Open Access Journals (Sweden)

    Hong-hui Xie

    2016-10-01

    Full Text Available Genetic diversity of 23 Lasiodiplodia theobromae isolates on Morus alba and 6 isolates on Agave sisalana in Guangxi province, China, was studied by using random amplified polymorphic DNA and inter-simple sequence repeat molecular markers. Results of two molecular markers showed that the average percentage of polymorphic loci of all isolates was more than 93%. Both dendrograms of two molecular markers showed obvious relationship between groups and the geographical locations where those strains were collected, among which, the 23 isolates on M. alba were divided into 4 populations and the 6 isolates on A. sisalana were separated as a independent population. The average genetic identity and genetic distance of 5 populations were 0.7215, 0.3284 and 0.7915, 0.2347, respectively, which indicated that the genetic identity was high and the genetic distance was short in the 5 populations. Average value of the gene diversity index (H and the Shannon’s information index (I of 29 isolates were significantly higher than 5 populations which showed that genetic diversity of those isolates was richer than the populations and the degree of genetic differentiation of the isolates was higher. The Gst and Nm of 29 isolates were 0.4411, 0.6335 and 0.4756, 0.5513, respectively, which showed that the genetic diversity was rich in those isolates.

  12. Genetic variants associated with subjective well-being, depressive symptoms, and neuroticism identified through genome-wide analyses.

    NARCIS (Netherlands)

    Okbay, A.; Baselmans, B.M.L.; de Neve, J.E.; Turley, P.; Nivard, M.G.; Fontana, M.A.; Meddens, S.F.W.; Karlsson Linnér, R.; Rietveld, C.A.; Derringer, J.; de Vlaming, R.; Minica, C.C.; Hottenga, J.J.; Vinkhuyzen, A.A.E.; Boomsma, D.I.; de Geus, E.J.C.; Medland, S.E.; Meyer, M.N.; Pickrell, J.K.; Esko, T.; Krueger, R.F.; Beauchamp, J.; Koellinger, P.D.; Benjamin, D.J.; Bartels, M.; Cesarini, D.

    2016-01-01

    Very few genetic variants have been associated with depression and neuroticism, likely because of limitations on sample size in previous studies. Subjective well-being, a phenotype that is genetically correlated with both of these traits, has not yet been studied with genome-wide data. We conducted

  13. Genetic Targets of Acute Toluene Inhalation in Drosophila melanogaster: DGRP activity, overlapping human orthologs, pathway analyses, GWAS results

    Data.gov (United States)

    U.S. Environmental Protection Agency — We used the Drosophila Genetics Reference Panel (DGRP), a collection of ~200 homozygous lines of fruit flies whose genomes have been sequenced. We quantified...

  14. Cross-Disorder Genome-Wide Analyses Suggest a Complex Genetic Relationship Between Tourette's Syndrome and OCD

    NARCIS (Netherlands)

    Yu, Dongmei; Mathews, Carol A.; Scharf, Jeremiah M.; Neale, Benjamin M.; Davis, Lea K.; Gamazon, Eric R.; Derks, Eske M.; Evans, Patrick; Edlund, Christopher K.; Crane, Jacquelyn; Osiecki, Lisa; Gallagher, Patience; Gerber, Gloria; Haddad, Stephen; Illmann, Cornelia; McGrath, Lauren M.; Mayerfeld, Catherine; Arepalli, Sampath; Barlassina, Cristina; Barr, Cathy L.; Bellodi, Laura; Benarroch, Fortu; Berrio, Gabriel Bedoya; Bienvenu, O. Joseph; Black, Donald W.; Bloch, Michael H.; Brentani, Helena; Bruun, Ruth D.; Budman, Cathy L.; Camarena, Beatriz; Campbell, Desmond D.; Cappi, Carolina; Silgado, Julio C. Cardona; Cavallini, Maria C.; Chavira, Denise A.; Chouinard, Sylvain; Cook, Edwin H.; Cookson, M. R.; Coric, Vladimir; Cullen, Bernadette; Cusi, Daniete; Delorme, Richard; Denys, Damiaan; Dion, Yves; Eapen, Valsama; Egberts, Karin; Falkai, Peter; Fernandez, Thomas; Fournier, Eduardo; Garrido, Helena; Geller, Daniel; Gilbert, Donald L.; Girard, Simon L.; Grabe, Hans J.; Grados, Marco A.; Greenberg, Benjamin D.; Gross-Tsur, Varda; Gruenblatt, Edna; Hardy, John; Heiman, Gary A.; Hemmings, Sian M. J.; Herrera, Luis D.; Hezel, Dianne M.; Hoekstra, Pieter J.; Jankovic, Joseph; Kennedy, James L.; King, Robert A.; Konkashbaev, Anuar I.; Kremeyer, Barbara; Kurlan, Roger; Lanzagorta, Nuria; Leboyer, Marion; Leckman, James F.; Lennertz, Leonhard; Liu, Chunyu; Lochner, Christine; Lowe, Thomas L.; Lupoli, Sara; Macciardi, Fabio; Maier, Wolfgang; Manunta, Paolo; Marconi, Maurizio; McCracken, James T.; Restrepo, Sandra C. Mesa; Moessner, Rainald; Moorjani, Priya; Morgan, Jubel; Muller, Heike; Murphy, Dennis L.; Naarden, Allan L.; Nurmi, Erika; Ochoa, William Cornejo; Ophoff, Roel A.; Pakstis, Andrew J.; Pato, Michele T.; Pato, Carlo N.; Piacentini, John; Pittenger, Christopher; Pollak, Yehuda; Rauch, Scott L.; Renner, Tobias; Reus, Victor I.; Richter, Margaret A.; Riddle, Mark A.; Robertson, Mary M.; Romero, Roxana; Rosario, Maria C.; Rosenberg, David; Ruhrmann, Stephan; Sabatti, Chiara; Salvi, Erika; Sampaio, Aline S.; Samuels, Jack; Sandor, Paul; Service, Susan K.; Sheppard, Brooke; Singer, Harvey S.; Smit, Jan H.; Stein, Dan J.; Strengman, Eric; Tischfield, Jay A.; Turiel, Maurizio; Duarte, Ana V. Valencia; Vallada, Homero; Veenstra-VanderWeele, Jeremy; Walitza, Susanne; Wang, Ying; Weale, Mike; Weiss, Robert; Wendland, Jens R.; Westenberg, Herman G. M.; Shugart, Yin Yao; Hounie, Ana G.; Miguel, Euripedes C.; Nicolini, Humberto; Wagner, Michael; Ruiz-Linares, Andres; Cath, Danielle C.; McMahon, William; Posthuma, Danielle; Oostra, Ben A.; Nestadt, Gerald; Routeau, Guy A.; Purcell, Shaun; Jenike, Michael A.; Heutink, Peter; Hanna, Gregory L.; Conti, David V.; Arnold, Paul D.; Freimer, Nelson B.; Stewart, Evelyn; Knowles, James A.; Cox, Nancy J.; Pauls, David L.

    Objective: Obsessive-compulsive disorder (OCD) and Tourette's syndrome are highly heritable neurodevelopmental disorders that are thought to share genetic risk factors. However, the identification of definitive susceptibility genes for these etiologically complex disorders remains elusive. The

  15. Cross-disorder genome-wide analyses suggest a complex genetic relationship between Tourette's syndrome and OCD

    NARCIS (Netherlands)

    Yu, Dongmei; Mathews, Carol A.; Scharf, Jeremiah M.; Neale, Benjamin M.; Davis, Lea K.; Gamazon, Eric R.; Derks, Eske M.; Evans, Patrick; Edlund, Christopher K.; Crane, Jacquelyn; Fagerness, Jesen A.; Osiecki, Lisa; Gallagher, Patience; Gerber, Gloria; Haddad, Stephen; Illmann, Cornelia; McGrath, Lauren M.; Mayerfeld, Catherine; Arepalli, Sampath; Barlassina, Cristina; Barr, Cathy L.; Bellodi, Laura; Benarroch, Fortu; Berrió, Gabriel Bedoya; Bienvenu, O. Joseph; Black, Donald W.; Bloch, Michael H.; Brentani, Helena; Bruun, Ruth D.; Budman, Cathy L.; Camarena, Beatriz; Campbell, Desmond D.; Cappi, Carolina; Silgado, Julio C. Cardona; Cavallini, Maria C.; Chavira, Denise A.; Chouinard, Sylvain; Cook, Edwin H.; Cookson, M. R.; Coric, Vladimir; Cullen, Bernadette; Cusi, Daniele; Delorme, Richard; Denys, Damiaan; Dion, Yves; Eapen, Valsama; Egberts, Karin; Falkai, Peter; Fernandez, Thomas; Fournier, Eduardo; Garrido, Helena; Geller, Daniel; Gilbert, Donald L.; Girard, Simon L.; Grabe, Hans J.; Grados, Marco A.; Greenberg, Benjamin D.; Gross-Tsur, Varda; Grünblatt, Edna; Hardy, John; Heiman, Gary A.; Hemmings, Sian M. J.; Herrera, Luis D.; Hezel, Dianne M.; Hoekstra, Pieter J.; Jankovic, Joseph; Kennedy, James L.; King, Robert A.; Konkashbaev, Anuar I.; Kremeyer, Barbara; Kurlan, Roger; Lanzagorta, Nuria; Leboyer, Marion; Leckman, James F.; Lennertz, Leonhard; Liu, Chunyu; Lochner, Christine; Lowe, Thomas L.; Lupoli, Sara; Macciardi, Fabio; Maier, Wolfgang; Manunta, Paolo; Marconi, Maurizio; McCracken, James T.; Mesa Restrepo, Sandra C.; Moessner, Rainald; Moorjani, Priya; Morgan, Jubel; Muller, Heike; Murphy, Dennis L.; Naarden, Allan L.; Nurmi, Erika; Ochoa, William Cornejo; Ophoff, Roel A.; Pakstis, Andrew J.; Pato, Michele T.; Pato, Carlos N.; Piacentini, John; Pittenger, Christopher; Pollak, Yehuda; Rauch, Scott L.; Renner, Tobias; Reus, Victor I.; Richter, Margaret A.; Riddle, Mark A.; Robertson, Mary M.; Romero, Roxana; Rosário, Maria C.; Rosenberg, David; Ruhrmann, Stephan; Sabatti, Chiara; Salvi, Erika; Sampaio, Aline S.; Samuels, Jack; Sandor, Paul; Service, Susan K.; Sheppard, Brooke; Singer, Harvey S.; Smit, Jan H.; Stein, Dan J.; Strengman, Eric; Tischfield, Jay A.; Turiel, Maurizio; Valencia Duarte, Ana V.; Vallada, Homero; Veenstra-Vanderweele, Jeremy; Walitza, Susanne; Wang, Ying; Weale, Mike; Weiss, Robert; Wendland, Jens R.; Westenberg, Herman G. M.; Shugart, Yin Yao; Hounie, Ana G.; Miguel, Euripedes C.; Nicolini, Humberto; Wagner, Michael; Ruiz-Linares, Andres; Cath, Danielle C.; McMahon, William; Posthuma, Danielle; Oostra, Ben A.; Nestadt, Gerald; Rouleau, Guy A.; Purcell, Shaun; Jenike, Michael A.; Heutink, Peter; Hanna, Gregory L.; Conti, David V.; Arnold, Paul D.; Freimer, Nelson B.; Stewart, S. Evelyn; Knowles, James A.; Cox, Nancy J.; Pauls, David L.

    2015-01-01

    Obsessive-compulsive disorder (OCD) and Tourette's syndrome are highly heritable neurodevelopmental disorders that are thought to share genetic risk factors. However, the identification of definitive susceptibility genes for these etiologically complex disorders remains elusive. The authors report a

  16. Cross-Disorder Genome-Wide Analyses Suggest a Complex Genetic Relationship Between Tourette's Syndrome and OCD

    NARCIS (Netherlands)

    Yu, Dongmei; Mathews, Carol A; Scharf, Jeremiah M; Neale, Benjamin M; Davis, Lea K; Gamazon, Eric R; Derks, Eske M; Evans, Patrick; Edlund, Christopher K; Crane, Jacquelyn; Fagerness, Jesen A; Osiecki, Lisa; Gallagher, Patience; Gerber, Gloria; Haddad, Stephen; Illmann, Cornelia; McGrath, Lauren M; Mayerfeld, Catherine; Arepalli, Sampath; Barlassina, Cristina; Barr, Cathy L; Bellodi, Laura; Benarroch, Fortu; Berrió, Gabriel Bedoya; Bienvenu, O Joseph; Black, Donald W; Bloch, Michael H; Brentani, Helena; Bruun, Ruth D; Budman, Cathy L; Camarena, Beatriz; Campbell, Desmond D; Cappi, Carolina; Silgado, Julio C Cardona; Cavallini, Maria C; Chavira, Denise A; Chouinard, Sylvain; Cook, Edwin H; Cookson, M R; Coric, Vladimir; Cullen, Bernadette; Cusi, Daniele; Delorme, Richard; Denys, Damiaan; Dion, Yves; Eapen, Valsama; Egberts, Karin; Falkai, Peter; Fernandez, Thomas; Fournier, Eduardo; Garrido, Helena; Geller, Daniel; Gilbert, Donald L; Girard, Simon L; Grabe, Hans J; Grados, Marco A; Greenberg, Benjamin D; Gross-Tsur, Varda; Grünblatt, Edna; Hardy, John; Heiman, Gary A; Hemmings, Sian M J; Herrera, Luis D; Hezel, Dianne M; Hoekstra, Pieter J; Jankovic, Joseph; Kennedy, James L; King, Robert A; Konkashbaev, Anuar I; Kremeyer, Barbara; Kurlan, Roger; Lanzagorta, Nuria; Leboyer, Marion; Leckman, James F; Lennertz, Leonhard; Liu, Chunyu; Lochner, Christine; Lowe, Thomas L; Lupoli, Sara; Macciardi, Fabio; Maier, Wolfgang; Manunta, Paolo; Marconi, Maurizio; McCracken, James T; Mesa Restrepo, Sandra C; Moessner, Rainald; Moorjani, Priya; Morgan, Jubel; Muller, Heike; Murphy, Dennis L; Naarden, Allan L; Nurmi, Erika; Ochoa, William Cornejo; Ophoff, Roel A; Pakstis, Andrew J; Pato, Michele T; Pato, Carlos N; Piacentini, John; Pittenger, Christopher; Pollak, Yehuda; Rauch, Scott L; Renner, Tobias; Reus, Victor I; Richter, Margaret A; Riddle, Mark A; Robertson, Mary M; Romero, Roxana; Rosário, Maria C; Rosenberg, David; Ruhrmann, Stephan; Sabatti, Chiara; Salvi, Erika; Sampaio, Aline S; Samuels, Jack; Sandor, Paul; Service, Susan K; Sheppard, Brooke; Singer, Harvey S; Smit, Jan H|info:eu-repo/dai/nl/113700644; Stein, Dan J; Strengman, Eric; Tischfield, Jay A; Turiel, Maurizio; Valencia Duarte, Ana V; Vallada, Homero; Veenstra-VanderWeele, Jeremy; Walitza, Susanne; Wang, Ying; Weale, Mike; Weiss, Robert; Wendland, Jens R; Westenberg, Herman G M; Shugart, Yin Yao; Hounie, Ana G; Miguel, Euripedes C; Nicolini, Humberto; Wagner, Michael; Ruiz-Linares, Andres; Cath, Danielle C|info:eu-repo/dai/nl/194111423; McMahon, William; Posthuma, Danielle; Oostra, Ben A; Nestadt, Gerald; Rouleau, Guy A; Purcell, Shaun; Jenike, Michael A; Heutink, Peter; Hanna, Gregory L; Conti, David V; Arnold, Paul D; Freimer, Nelson B; Stewart, S Evelyn; Knowles, James A; Cox, Nancy J; Pauls, David L

    OBJECTIVE: Obsessive-compulsive disorder (OCD) and Tourette's syndrome are highly heritable neurodevelopmental disorders that are thought to share genetic risk factors. However, the identification of definitive susceptibility genes for these etiologically complex disorders remains elusive. The

  17. Cross-Disorder Genome-Wide Analyses Suggest a Complex Genetic Relationship Between Tourette's Syndrome and OCD

    NARCIS (Netherlands)

    Yu, D.M.; Mathews, C.A.; Scharf, J.M.; Neale, B.M.; Davis, L.K.; Gamazon, E.R.; Derks, E.M.; Evans, P.; Edlund, C.K.; Crane, J.; Osiecki, L.; Gallagher, P.; Gerber, G.; Haddad, S.; Illmann, C.; McGrath, L.M.; Mayerfeld, C.; Arepalli, S.; Barlassina, C.; Barr, C.L.; Bellodi, L.; Benarroch, F.; Berrio, G.B.; Bienvenu, O.J.; Black, D.W.; Bloch, M.H.; Brentani, H.; Bruun, R.D.; Budman, C.L.; Camarena, B.; Campbell, D.D.; Cappi, C.; Silgado, J.C.C.; Cavallini, M.C.; Chavira, D.A.; Chouinard, S.; Cook, E.H.; Cookson, M.R.; Coric, V.; Cullen, B.; Cusi, D.; Delorme, R.; Denys, D.; Dion, Y.; Eapen, V.; Egberts, K.; Falkai, P.; Fernandez, T.; Fournier, E.; Garrido, H.; Geller, D.; Gilbert, D.L.; Girard, S.L.; Grabe, H.J.; Grados, M.A.; Greenberg, B.D.; Gross-Tsur, V.; Grunblatt, E.; Hardy, J.; Heiman, G.A.; Hemmings, S.M.J.; Herrera, L.D.; Hezel, D.M.; Hoekstra, P.J.; Jankovic, J.; Kennedy, J.L.; King, R.A.; Konkashbaev, A.I.; Kremeyer, B.; Kurlan, R.; Lanzagorta, N.; Leboyer, M.; Leckman, J.F.; Lennertz, L.; Liu, C.Y.; Lochner, C.; Lowe, T.L.; Lupoli, S.; Macciardi, F.; Maier, W.; Manunta, P.; Marconi, M.; McCracken, J.T.; Restrepo, S.C.M.; Moessner, R.; Moorjani, P.; Morgan, J.; Muller, H.; Murphy, D.L.; Naarden, A.L.; Nurmi, E.; Ochoa, W.C.; Ophoff, R. A.; Pakstis, A.J.; Pato, M.T.; Pato, C.N.; Piacentini, J.; Pittenger, C.; Pollak, Y.; Smit, J.H.; Posthuma, D.; Cox, N.J.; Pauls, D.L.

    2015-01-01

    Objective: Obsessive-compulsive disorder (OCD) and Tourette's syndrome are highly heritable neurodevelopmental disorders that are thought to share genetic risk factors. However, the identi fication of definitive susceptibility genes for these etiologically complex disorders remains elusive. The

  18. Cross-disorder genome-wide analyses suggest a complex genetic relationship between Tourette's syndrome and OCD

    NARCIS (Netherlands)

    Yu, Dongmei; Cusi, Daniele; Delorme, Richard; Denys, D.; Dion, Yves; Eapen, Valsama; Heutink, Peter; Cox, Nancy J; Pauls, David L

    OBJECTIVE: Obsessive-compulsive disorder (OCD) and Tourette's syndrome are highly heritable neurodevelopmental disorders that are thought to share genetic risk factors. However, the identification of definitive susceptibility genes for these etiologically complex disorders remains elusive. The

  19. Analyses between Reproductive Behavior, Genetic Diversity and Pythium Responsiveness in Zingiber spp. Reveal an Adaptive Significance for Hemiclonality

    Science.gov (United States)

    Thomas, Geethu E.; Geetha, Kiran A.; Augustine, Lesly; Mamiyil, Sabu; Thomas, George

    2016-01-01

    Mode of reproduction is generally considered to have long-range evolutionary implications on population survival. Because sexual reproduction produces genetically diverse genotypes, this mode of reproduction is predicted to positively influence the success potential of offspring in evolutionary arms race with parasites (Red queen) whereas, without segregation and recombination, the obligate asexual multiplication may push a species into extinction due to the steady accumulation of deleterious mutations (Muller’s ratchet). However, the extent of linearity between reproductive strategies, genetic diversity and population fitness, and the contributions of different breeding strategies to population fitness are yet to be understood clearly. Genus Zingiber belonging to the pan-tropic family Zingiberaceae represents a good system to study contributions of different breeding behavior on genetic diversity and population fitness, as this genus comprises species with contrasting breeding systems. In this study, we analyzed breeding behavior, amplified fragment length polymorphism diversity and response to the soft-rot pathogen Pythium aphanidermatum in 18 natural populations of three wild Zingiber spp.: Z. neesanum, Z. nimmonii, and Z. zerumbet, together with the obligately asexual cultivated congener, ginger (Z. officinale). Ginger showed an exceptionally narrow genetic base, and adding to this, all the tested cultivars were uniformly susceptible to soft-rot. Concordant with the postulates of Muller’s ratchet, the background selection may be continuously pushing ginger into the ancestral state, rendering it inefficient in host-pathogen coevolution. Z. neesanum and Z. nimmonii populations were sexual and genetically diverse; however, contrary to Red Queen expectations, the populations were highly susceptible to soft-rot. Z. zerumbet showed a hemiclonal breeding behavior. The populations inhabiting forest understory were large and continuous, sexual and genetically

  20. Genetic variants associated with subjective well-being, depressive symptoms, and neuroticism identified through genome-wide analyses

    OpenAIRE

    Okbay, Aysu; Baselmans, B.M.L. (Bart M.L.); Neve, Jan-Emmanuel; Turley, Patrick; Nivard, Michel; Fontana, M.A. (Mark Alan); Meddens, S.F.W. (S. Fleur W.); Linnér, R.K. (Richard Karlsson); Rietveld, C.A. (Cornelius A); Derringer, J.; Gratten, Jacob; Lee, James J.; Liu, J.Z. (Jimmy Z); Vlaming, Ronald; SAhluwalia, T. (Tarunveer)

    2016-01-01

    textabstractVery few genetic variants have been associated with depression and neuroticism, likely because of limitations on sample size in previous studies. Subjective well-being, a phenotype that is genetically correlated with both of these traits, has not yet been studied with genome-wide data. We conducted genome-wide association studies of three phenotypes: subjective well-being (n = 298,420), depressive symptoms (n = 161,460), and neuroticism (n = 170,911). We identify 3 variants associ...

  1. Genome-wide association analyses identify 44 risk variants and refine the genetic architecture of major depression.

    Science.gov (United States)

    Wray, Naomi R; Ripke, Stephan; Mattheisen, Manuel; Trzaskowski, Maciej; Byrne, Enda M; Abdellaoui, Abdel; Adams, Mark J; Agerbo, Esben; Air, Tracy M; Andlauer, Till M F; Bacanu, Silviu-Alin; Bækvad-Hansen, Marie; Beekman, Aartjan F T; Bigdeli, Tim B; Binder, Elisabeth B; Blackwood, Douglas R H; Bryois, Julien; Buttenschøn, Henriette N; Bybjerg-Grauholm, Jonas; Cai, Na; Castelao, Enrique; Christensen, Jane Hvarregaard; Clarke, Toni-Kim; Coleman, Jonathan I R; Colodro-Conde, Lucía; Couvy-Duchesne, Baptiste; Craddock, Nick; Crawford, Gregory E; Crowley, Cheynna A; Dashti, Hassan S; Davies, Gail; Deary, Ian J; Degenhardt, Franziska; Derks, Eske M; Direk, Nese; Dolan, Conor V; Dunn, Erin C; Eley, Thalia C; Eriksson, Nicholas; Escott-Price, Valentina; Kiadeh, Farnush Hassan Farhadi; Finucane, Hilary K; Forstner, Andreas J; Frank, Josef; Gaspar, Héléna A; Gill, Michael; Giusti-Rodríguez, Paola; Goes, Fernando S; Gordon, Scott D; Grove, Jakob; Hall, Lynsey S; Hannon, Eilis; Hansen, Christine Søholm; Hansen, Thomas F; Herms, Stefan; Hickie, Ian B; Hoffmann, Per; Homuth, Georg; Horn, Carsten; Hottenga, Jouke-Jan; Hougaard, David M; Hu, Ming; Hyde, Craig L; Ising, Marcus; Jansen, Rick; Jin, Fulai; Jorgenson, Eric; Knowles, James A; Kohane, Isaac S; Kraft, Julia; Kretzschmar, Warren W; Krogh, Jesper; Kutalik, Zoltán; Lane, Jacqueline M; Li, Yihan; Li, Yun; Lind, Penelope A; Liu, Xiaoxiao; Lu, Leina; MacIntyre, Donald J; MacKinnon, Dean F; Maier, Robert M; Maier, Wolfgang; Marchini, Jonathan; Mbarek, Hamdi; McGrath, Patrick; McGuffin, Peter; Medland, Sarah E; Mehta, Divya; Middeldorp, Christel M; Mihailov, Evelin; Milaneschi, Yuri; Milani, Lili; Mill, Jonathan; Mondimore, Francis M; Montgomery, Grant W; Mostafavi, Sara; Mullins, Niamh; Nauck, Matthias; Ng, Bernard; Nivard, Michel G; Nyholt, Dale R; O'Reilly, Paul F; Oskarsson, Hogni; Owen, Michael J; Painter, Jodie N; Pedersen, Carsten Bøcker; Pedersen, Marianne Giørtz; Peterson, Roseann E; Pettersson, Erik; Peyrot, Wouter J; Pistis, Giorgio; Posthuma, Danielle; Purcell, Shaun M; Quiroz, Jorge A; Qvist, Per; Rice, John P; Riley, Brien P; Rivera, Margarita; Saeed Mirza, Saira; Saxena, Richa; Schoevers, Robert; Schulte, Eva C; Shen, Ling; Shi, Jianxin; Shyn, Stanley I; Sigurdsson, Engilbert; Sinnamon, Grant B C; Smit, Johannes H; Smith, Daniel J; Stefansson, Hreinn; Steinberg, Stacy; Stockmeier, Craig A; Streit, Fabian; Strohmaier, Jana; Tansey, Katherine E; Teismann, Henning; Teumer, Alexander; Thompson, Wesley; Thomson, Pippa A; Thorgeirsson, Thorgeir E; Tian, Chao; Traylor, Matthew; Treutlein, Jens; Trubetskoy, Vassily; Uitterlinden, André G; Umbricht, Daniel; Van der Auwera, Sandra; van Hemert, Albert M; Viktorin, Alexander; Visscher, Peter M; Wang, Yunpeng; Webb, Bradley T; Weinsheimer, Shantel Marie; Wellmann, Jürgen; Willemsen, Gonneke; Witt, Stephanie H; Wu, Yang; Xi, Hualin S; Yang, Jian; Zhang, Futao; Arolt, Volker; Baune, Bernhard T; Berger, Klaus; Boomsma, Dorret I; Cichon, Sven; Dannlowski, Udo; de Geus, E C J; DePaulo, J Raymond; Domenici, Enrico; Domschke, Katharina; Esko, Tõnu; Grabe, Hans J; Hamilton, Steven P; Hayward, Caroline; Heath, Andrew C; Hinds, David A; Kendler, Kenneth S; Kloiber, Stefan; Lewis, Glyn; Li, Qingqin S; Lucae, Susanne; Madden, Pamela F A; Magnusson, Patrik K; Martin, Nicholas G; McIntosh, Andrew M; Metspalu, Andres; Mors, Ole; Mortensen, Preben Bo; Müller-Myhsok, Bertram; Nordentoft, Merete; Nöthen, Markus M; O'Donovan, Michael C; Paciga, Sara A; Pedersen, Nancy L; Penninx, Brenda W J H; Perlis, Roy H; Porteous, David J; Potash, James B; Preisig, Martin; Rietschel, Marcella; Schaefer, Catherine; Schulze, Thomas G; Smoller, Jordan W; Stefansson, Kari; Tiemeier, Henning; Uher, Rudolf; Völzke, Henry; Weissman, Myrna M; Werge, Thomas; Winslow, Ashley R; Lewis, Cathryn M; Levinson, Douglas F; Breen, Gerome; Børglum, Anders D; Sullivan, Patrick F

    2018-05-01

    Major depressive disorder (MDD) is a common illness accompanied by considerable morbidity, mortality, costs, and heightened risk of suicide. We conducted a genome-wide association meta-analysis based in 135,458 cases and 344,901 controls and identified 44 independent and significant loci. The genetic findings were associated with clinical features of major depression and implicated brain regions exhibiting anatomical differences in cases. Targets of antidepressant medications and genes involved in gene splicing were enriched for smaller association signal. We found important relationships of genetic risk for major depression with educational attainment, body mass, and schizophrenia: lower educational attainment and higher body mass were putatively causal, whereas major depression and schizophrenia reflected a partly shared biological etiology. All humans carry lesser or greater numbers of genetic risk factors for major depression. These findings help refine the basis of major depression and imply that a continuous measure of risk underlies the clinical phenotype.

  2. Genome-Wide Association Meta-Analyses to Identify Common Genetic Variants Associated with Hallux Valgus in Caucasian and African Americans

    Science.gov (United States)

    Hsu, Yi-Hsiang; Liu, Youfang; Hannan, Marian T.; Maixner, William; Smith, Shad B.; Diatchenko, Luda; Golightly, Yvonne M.; Menz, Hylton B.; Kraus, Virginia B.; Doherty, Michael; Wilson, A.G.; Jordan, Joanne M.

    2016-01-01

    Objective Hallux valgus (HV) affects ~36% of Caucasian adults. Although considered highly heritable, the underlying genetic determinants are unclear. We conducted the first genome-wide association study (GWAS) aimed to identify genetic variants associated with HV. Methods HV was assessed in 3 Caucasian cohorts (n=2,263, n=915, and n=1,231 participants, respectively). In each cohort, a GWAS was conducted using 2.5M imputed single nucleotide polymorphisms (SNPs). Mixed-effect regression with the additive genetic model adjusted for age, sex, weight and within-family correlations was used for both sex-specific and combined analyses. To combine GWAS results across cohorts, fixed-effect inverse-variance meta-analyses were used. Following meta-analyses, top-associated findings were also examined in an African American cohort (n=327). Results The proportion of HV variance explained by genome-wide genotyped SNPs was 50% in men and 48% in women. A higher proportion of genetic determinants of HV was sex-specific. The most significantly associated SNP in men was rs9675316 located on chr17q23-a24 near the AXIN2 gene (p=5.46×10−7); the most significantly associated SNP in women was rs7996797 located on chr13q14.1-q14.2 near the ESD gene (p=7.21×10−7). Genome-wide significant SNP-by-sex interaction was found for SNP rs1563374 located on chr11p15.1 near the MRGPRX3 gene (interaction p-value =4.1×10−9). The association signals diminished when combining men and women. Conclusion Findings suggest that the potential pathophysiological mechanisms of HV are complex and strongly underlined by sex-specific interactions. The identified genetic variants imply contribution of biological pathways observed in osteoarthritis as well as new pathways, influencing skeletal development and inflammation. PMID:26337638

  3. Analyses between Reproductive Behaviour, Genetic Diversity and Pythium Responsiveness in Zingiber spp. reveal an adaptive significance for hemiclonality

    Directory of Open Access Journals (Sweden)

    Geethu Elizabath Thomas

    2016-12-01

    Full Text Available AbstractMode of reproduction is generally considered to have long-range evolutionary implications on population survival. Because sexual reproduction produces genetically diverse genotypes, this mode of reproduction is predicted to positively influence the success potential of offspring in evolutionary arms race with parasites (Red queen whereas, without segregation and recombination, the obligate asexual multiplication may push a species into extinction due to the steady accumulation of deleterious mutations (Muller’s ratchet. However, the extent of linearity between reproductive strategies, genetic diversity and population fitness, and the contributions of different breeding strategies to population fitness are yet to be understood clearly. Genus Zingiber belonging to the pan-tropic family Zingiberaceae represents a good system to study contributions of different breeding behaviour on genetic diversity and population fitness, as this genus comprises species with contrasting breeding systems. In this study, we analyzed breeding behaviour, amplified fragment length polymorphism (AFLP diversity and response to the soft-rot pathogen Pythium aphanidermatum in 18 natural populations of three wild Zingiber spp.: Z. neesanum, Z. nimmonii and Z. zerumbet, together with the obligately asexual cultivated congener, ginger (Z. officinale. Ginger showed an exceptionally narrow genetic base, and adding to this, all the tested cultivars were uniformly susceptible to soft-rot. Concordant with the postulates of Muller’s ratchet, the background selection may be continuously pushing ginger into the ancestral state, rendering it inefficient in host-pathogen coevolution. Z. neesanum and Z. nimmonii populations were sexual and genetically diverse; however, contrary to Red Queen expectations, the populations were highly susceptible to soft-rot. Z. zerumbet showed a hemiclonal breeding behaviour. The populations inhabiting forest understory were large and

  4. Genetic characterisation of populations of the critically endangered Goliath grouper ( Epinephelus itajara, Serranidae from the Northern Brazilian coast through analyses of mtDNA

    Directory of Open Access Journals (Sweden)

    Gláucia C. Silva-Oliveira

    2008-01-01

    Full Text Available The Goliath grouper ( Epinephelus itajara is one of the most endangered species of fish of the subfamily Epinephelinae. Slow to develop and mature, and dependent on mangrove habitats for breeding, the species also suffers intense harvesting, which has reduced drastically in numbers in many areas. To contribute to the understanding of the characteristics of E. itajara populations, we conducted a molecular genetics study of the species, focusing on populations from the Northern Brazilian coast. The mtDNA control region (D-loop of 116 individuals from five localities (Bragança, Ajuruteua, Parnaíba, Fortaleza and Natal was analysed, and a sequence of 499 base pairs identified. Analyses of the sequences indicated that genetic variability was generally lower in E. itajara than in other endangered species of the genus. AMOVA found no significant grouping structure among the populations. Nested Clade Analysis revealed a significant association between genetic variability and geographic distribution among only three populations (Ajuruteua, Parnaíba and Natal. Genetic diversity was higher in populations from the Amazon region, which may be related to the better conservation of mangrove habitats in this area. Therefore, the present study could be used for the implementation of conservation and management measures in order to protect and consolidate these populations.

  5. Genome-wide association and longitudinal analyses reveal genetic loci linking pubertal height growth, pubertal timing and childhood adiposity

    NARCIS (Netherlands)

    Cousminer, Diana L.; Berry, Diane J.; Timpson, Nicholas J.; Ang, Wei; Thiering, Elisabeth; Byrne, Enda M.; Taal, H. Rob; Huikari, Ville; Bradfield, Jonathan P.; Kerkhof, Marjan; Groen-Blokhuis, Maria M.; Kreiner-Moller, Eskil; Marinelli, Marcella; Holst, Claus; Leinonen, Jaakko T.; Perry, John R. B.; Surakka, Ida; Pietilainen, Olli; Kettunen, Johannes; Anttila, Verneri; Kaakinen, Marika; Sovio, Ulla; Pouta, Anneli; Das, Shikta; Lagou, Vasiliki; Power, Chris; Prokopenko, Inga; Evans, David M.; Kemp, John P.; St Pourcain, Beate; Ring, Susan; Palotie, Aarno; Kajantie, Eero; Osmond, Clive; Lehtimaki, Terho; Viikari, Jorma S.; Kahonen, Mika; Warrington, Nicole M.; Lye, Stephen J.; Palmer, Lyle J.; Tiesler, Carla M. T.; Flexeder, Claudia; Montgomery, Grant W.; Medland, Sarah E.; Hofman, Albert; Hakonarson, Hakon; Guxens, Monica; Bartels, Meike; Salomaa, Veikko; Koppelman, Gerard H.

    2013-01-01

    The pubertal height growth spurt is a distinctive feature of childhood growth reflecting both the central onset of puberty and local growth factors. Although little is known about the underlying genetics, growth variability during puberty correlates with adult risks for hormone-dependent cancer and

  6. Genome-wide association analyses identify new risk variants and the genetic architecture of amyotrophic lateral sclerosis

    NARCIS (Netherlands)

    van Rheenen, Wouter; Shatunov, Aleksey; Dekker, Annelot M; McLaughlin, Russell L; Diekstra, Frank P; Pulit, Sara L; van der Spek, Rick A A; Võsa, Urmo; de Jong, Simone; Robinson, Matthew R; Yang, Jian; Fogh, Isabella; van Doormaal, Perry Tc; Tazelaar, Gijs H P; Koppers, Max; Blokhuis, Anna M; Sproviero, William; Jones, Ashley R; Kenna, Kevin P; van Eijk, Kristel R; Harschnitz, Oliver; Schellevis, Raymond D; Brands, William J; Medic, Jelena; Menelaou, Androniki; Vajda, Alice; Ticozzi, Nicola; Lin, Kuang; Rogelj, Boris; Vrabec, Katarina; Ravnik-Glavač, Metka; Koritnik, Blaž; Zidar, Janez; Leonardis, Lea; Grošelj, Leja Dolenc; Millecamps, Stéphanie; Salachas, François; Meininger, Vincent; de Carvalho, Mamede; Pinto, Susana; Mora, Jesus S; Rojas-García, Ricardo; Polak, Meraida; Chandran, Siddharthan; Colville, Shuna; Swingler, Robert; Morrison, Karen E; Shaw, Pamela J; Hardy, John; Orrell, Richard W; Pittman, Alan; Sidle, Katie; Fratta, Pietro; Malaspina, Andrea; Topp, Simon; Petri, Susanne; Abdulla, Susanne; Drepper, Carsten; Sendtner, Michael; Meyer, Thomas; Ophoff, Roel A.; Staats, Kim A; Wiedau-Pazos, Martina; Lomen-Hoerth, Catherine; Van Deerlin, Vivianna M; Trojanowski, John Q; Elman, Lauren; McCluskey, Leo; Basak, A Nazli; Tunca, Ceren; Hamzeiy, Hamid; Parman, Yesim; Meitinger, Thomas; Lichtner, Peter; Radivojkov-Blagojevic, Milena; Andres, Christian R; Maurel, Cindy; Bensimon, Gilbert; Landwehrmeyer, Bernhard; Brice, Alexis; Payan, Christine A M; Saker-Delye, Safaa; Dürr, Alexandra; Wood, Nicholas W; Tittmann, Lukas; Lieb, Wolfgang; Franke, Andre; Rietschel, Marcella; Cichon, Sven; Nöthen, Markus M; Amouyel, Philippe; Tzourio, Christophe; Dartigues, Jean-François; Uitterlinden, Andre G; Rivadeneira, Fernando; Estrada, Karol; Hofman, Albert; Curtis, Charles; Blauw, Hylke M; van der Kooi, Anneke J; de Visser, Marianne; Goris, An; Weber, Markus; Shaw, Christopher E; Smith, Bradley N; Pansarasa, Orietta; Cereda, Cristina; Del Bo, Roberto; Comi, Giacomo P; D'Alfonso, Sandra; Bertolin, Cinzia; Sorarù, Gianni; Mazzini, Letizia; Pensato, Viviana; Gellera, Cinzia; Tiloca, Cinzia; Ratti, Antonia; Calvo, Andrea; Moglia, Cristina; Brunetti, Maura; Arcuti, Simona; Capozzo, Rosa; Zecca, Chiara; Lunetta, Christian; Penco, Silvana; Riva, Nilo; Padovani, Alessandro; Filosto, Massimiliano; Muller, Bernard; Stuit, Robbert Jan; Blair, Ian; Zhang, Katharine; McCann, Emily P; Fifita, Jennifer A; Nicholson, Garth A; Rowe, Dominic B; Pamphlett, Roger; Kiernan, Matthew C; Grosskreutz, Julian; Witte, Otto W; Ringer, Thomas; Prell, Tino; Stubendorff, Beatrice; Kurth, Ingo; Hübner, Christian A; Leigh, P Nigel; Casale, Federico; Chio, Adriano; Beghi, Ettore; Pupillo, Elisabetta; Tortelli, Rosanna; Logroscino, Giancarlo; Powell, John; Ludolph, Albert C; Weishaupt, Jochen H; Robberecht, Wim; Van Damme, Philip; Franke, Lude; Pers, Tune H; Brown, Robert H; Glass, Jonathan D; Landers, John E; Hardiman, Orla; Andersen, Peter M; Corcia, Philippe; Vourc'h, Patrick; Silani, Vincenzo; Wray, Naomi R; Visscher, Peter M; de Bakker, Paul I W; van Es, Michael A; Pasterkamp, R Jeroen; Lewis, Cathryn M; Breen, Gerome; Al-Chalabi, Ammar; van den Berg, Leonard H; Veldink, Jan H

    To elucidate the genetic architecture of amyotrophic lateral sclerosis (ALS) and find associated loci, we assembled a custom imputation reference panel from whole-genome-sequenced patients with ALS and matched controls (n = 1,861). Through imputation and mixed-model association analysis in 12,577

  7. Genome-wide association analyses identify new risk variants and the genetic architecture of amyotrophic lateral sclerosis

    NARCIS (Netherlands)

    van Rheenen, Wouter; Shatunov, Aleksey; Dekker, Annelot M.; McLaughlin, Russell L.; Diekstra, Frank P.; Pulit, Sara L.; van der Spek, Rick A. A.; Võsa, Urmo; de Jong, Simone; Robinson, Matthew R.; Yang, Jian; Fogh, Isabella; van Doormaal, Perry Tc; Tazelaar, Gijs H. P.; Koppers, Max; Blokhuis, Anna M.; Sproviero, William; Jones, Ashley R.; Kenna, Kevin P.; van Eijk, Kristel R.; Harschnitz, Oliver; Schellevis, Raymond D.; Brands, William J.; Medic, Jelena; Menelaou, Androniki; Vajda, Alice; Ticozzi, Nicola; Lin, Kuang; Rogelj, Boris; Vrabec, Katarina; Ravnik-Glavač, Metka; Koritnik, Blaž; Zidar, Janez; Leonardis, Lea; Grošelj, Leja Dolenc; Millecamps, Stéphanie; Salachas, François; Meininger, Vincent; de Carvalho, Mamede; Pinto, Susana; Mora, Jesus S.; Rojas-García, Ricardo; Polak, Meraida; Chandran, Siddharthan; Colville, Shuna; Swingler, Robert; Morrison, Karen E.; Shaw, Pamela J.; Hardy, John; Orrell, Richard W.; Pittman, Alan; Sidle, Katie; Fratta, Pietro; Malaspina, Andrea; Topp, Simon; Petri, Susanne; Abdulla, Susanne; Drepper, Carsten; Sendtner, Michael; Meyer, Thomas; Ophoff, Roel A.; Staats, Kim A.; Wiedau-Pazos, Martina; Lomen-Hoerth, Catherine; van Deerlin, Vivianna M.; Trojanowski, John Q.; Elman, Lauren; McCluskey, Leo; Basak, A. Nazli; Tunca, Ceren; Hamzeiy, Hamid; Parman, Yesim; Meitinger, Thomas; Lichtner, Peter; Radivojkov-Blagojevic, Milena; Andres, Christian R.; Maurel, Cindy; Bensimon, Gilbert; Landwehrmeyer, Bernhard; Brice, Alexis; Payan, Christine A. M.; Saker-Delye, Safaa; Dürr, Alexandra; Wood, Nicholas W.; Tittmann, Lukas; Lieb, Wolfgang; Franke, Andre; Rietschel, Marcella; Cichon, Sven; Nöthen, Markus M.; Amouyel, Philippe; Tzourio, Christophe; Dartigues, Jean-François; Uitterlinden, Andre G.; Rivadeneira, Fernando; Estrada, Karol; Hofman, Albert; Curtis, Charles; Blauw, Hylke M.; van der Kooi, Anneke J.; de Visser, Marianne; Goris, An; Weber, Markus; Shaw, Christopher E.; Smith, Bradley N.; Pansarasa, Orietta; Cereda, Cristina; del Bo, Roberto; Comi, Giacomo P.; D'alfonso, Sandra; Bertolin, Cinzia; Sorarù, Gianni; Mazzini, Letizia; Pensato, Viviana; Gellera, Cinzia; Tiloca, Cinzia; Ratti, Antonia; Calvo, Andrea; Moglia, Cristina; Brunetti, Maura; Arcuti, Simona; Capozzo, Rosa; Zecca, Chiara; Lunetta, Christian; Penco, Silvana; Riva, Nilo; Padovani, Alessandro; Filosto, Massimiliano; Muller, Bernard; Stuit, Robbert Jan; Blair, Ian; Zhang, Katharine; McCann, Emily P.; Fifita, Jennifer A.; Nicholson, Garth A.; Rowe, Dominic B.; Pamphlett, Roger; Kiernan, Matthew C.; Grosskreutz, Julian; Witte, Otto W.; Ringer, Thomas; Prell, Tino; Stubendorff, Beatrice; Kurth, Ingo; Hübner, Christian A.; Leigh, P. Nigel; Casale, Federico; Chio, Adriano; Beghi, Ettore; Pupillo, Elisabetta; Tortelli, Rosanna; Logroscino, Giancarlo; Powell, John; Ludolph, Albert C.; Weishaupt, Jochen H.; Robberecht, Wim; van Damme, Philip; Franke, Lude; Pers, Tune H.; Brown, Robert H.; Glass, Jonathan D.; Landers, John E.; Hardiman, Orla; Andersen, Peter M.; Corcia, Philippe; Vourc'h, Patrick; Silani, Vincenzo; Wray, Naomi R.; Visscher, Peter M.; de Bakker, Paul I. W.; van Es, Michael A.; Pasterkamp, R. Jeroen; Lewis, Cathryn M.; Breen, Gerome; Al-Chalabi, Ammar; van den Berg, Leonard H.; Veldink, Jan H.

    2016-01-01

    To elucidate the genetic architecture of amyotrophic lateral sclerosis (ALS) and find associated loci, we assembled a custom imputation reference panel from whole-genome-sequenced patients with ALS and matched controls (n = 1,861). Through imputation and mixed-model association analysis in 12,577

  8. Classical genetic analyses of responses to nicotine and ethanol in crosses derived from long- and short-sleep mice.

    Science.gov (United States)

    de Fiebre, C M; Collins, A C

    1992-04-01

    A classical (Mendelian) genetic analysis of responses to ethanol and nicotine was conducted in crosses derived from mouse lines which were selectively bred for differential duration of loss of the righting response (sleep-time) after ethanol. Dose-response curves for these mice, the long- and short-sleep mouse lines, as well as the derived F1, F2 and backcross (F1 x long-sleep and F1 x short-sleep) generations were generated for several measures of nicotine and ethanol sensitivity. Ethanol sensitivity was assessed using the sleep-time measure. Nicotine sensitivity was tested using a battery of behavioral and physiological tests which included measures of seizure activity, respiration rate, acoustic startle response, Y-maze activities (both crossing and rearing activities), heart rate and body temperature. The inheritance of sensitivities to both of these agents appears to be polygenic and inheritance can be explained primarily by additive genetic effects with some epistasis. Sensitivity to the ethanol sleep-time measure was genetically correlated with sensitivity to both nicotine-induced hypothermia and seizures; the correlation was greater between sleep-time and hypothermia. These data indicate that there is overlap in the genetic regulation of sensitivity to both ethanol and nicotine as measured by some, but not all, tests.

  9. Associations of Fitness, Physical Activity, Strength, and Genetic Risk With Cardiovascular Disease: Longitudinal Analyses in the UK Biobank Study.

    Science.gov (United States)

    Tikkanen, Emmi; Gustafsson, Stefan; Ingelsson, Erik

    2018-04-09

    Background -Observational studies have shown inverse associations among fitness, physical activity, and cardiovascular disease. However, little is known about these associations in individuals with elevated genetic susceptibility for these diseases. Methods -We estimated associations of grip strength, objective and subjective physical activity, and cardiorespiratory fitness with cardiovascular events and all-cause death in a large cohort of 502635 individuals from the UK Biobank (median follow-up, 6.1 years; interquartile range, 5.4-6.8 years). Then we further examined these associations in individuals with different genetic burden by stratifying individuals based on their genetic risk scores for coronary heart disease and atrial fibrillation. We compared disease risk among individuals in different tertiles of fitness, physical activity, and genetic risk using lowest tertiles as reference. Results -Grip strength, physical activity, and cardiorespiratory fitness showed inverse associations with incident cardiovascular events (coronary heart disease: hazard ratio [HR], 0.79; 95% confidence interval [CI], 0.77- 0.81; HR, 0.95; 95% CI, 0.93-0.97; and HR, 0.68; 95% CI, 0.63-0.74, per SD change, respectively; atrial fibrillation: HR, 0.75; 95% CI, 0.73- 0.76; HR, 0.93; 95% CI, 0.91-0.95; and HR, 0.60; 95% CI, 0.56-0.65, per SD change, respectively). Higher grip strength and cardiorespiratory fitness were associated with lower risk of incident coronary heart disease and atrial fibrillation in each genetic risk score group ( P trend fitness were associated with 49% lower risk for coronary heart disease (HR, 0.51; 95% CI, 0.38-0.69) and 60% lower risk for atrial fibrillation (HR, 0.40; 95%, CI 0.30-0.55) among individuals at high genetic risk for these diseases. Conclusions - Fitness and physical activity demonstrated inverse associations with incident cardiovascular disease in the general population, as well as in individuals with elevated genetic risk for these diseases.

  10. Spatial genetic analyses reveal cryptic population structure and migration patterns in a continuously harvested grey wolf (Canis lupus population in north-eastern Europe.

    Directory of Open Access Journals (Sweden)

    Maris Hindrikson

    Full Text Available Spatial genetics is a relatively new field in wildlife and conservation biology that is becoming an essential tool for unravelling the complexities of animal population processes, and for designing effective strategies for conservation and management. Conceptual and methodological developments in this field are therefore critical. Here we present two novel methodological approaches that further the analytical possibilities of STRUCTURE and DResD. Using these approaches we analyse structure and migrations in a grey wolf (Canislupus population in north-eastern Europe. We genotyped 16 microsatellite loci in 166 individuals sampled from the wolf population in Estonia and Latvia that has been under strong and continuous hunting pressure for decades. Our analysis demonstrated that this relatively small wolf population is represented by four genetic groups. We also used a novel methodological approach that uses linear interpolation to statistically test the spatial separation of genetic groups. The new method, which is capable of using program STRUCTURE output, can be applied widely in population genetics to reveal both core areas and areas of low significance for genetic groups. We also used a recently developed spatially explicit individual-based method DResD, and applied it for the first time to microsatellite data, revealing a migration corridor and barriers, and several contact zones.

  11. Genome-Wide Interaction Analyses between Genetic Variants and Alcohol Consumption and Smoking for Risk of Colorectal Cancer.

    Directory of Open Access Journals (Sweden)

    Jian Gong

    2016-10-01

    Full Text Available Genome-wide association studies (GWAS have identified many genetic susceptibility loci for colorectal cancer (CRC. However, variants in these loci explain only a small proportion of familial aggregation, and there are likely additional variants that are associated with CRC susceptibility. Genome-wide studies of gene-environment interactions may identify variants that are not detected in GWAS of marginal gene effects. To study this, we conducted a genome-wide analysis for interaction between genetic variants and alcohol consumption and cigarette smoking using data from the Colon Cancer Family Registry (CCFR and the Genetics and Epidemiology of Colorectal Cancer Consortium (GECCO. Interactions were tested using logistic regression. We identified interaction between CRC risk and alcohol consumption and variants in the 9q22.32/HIATL1 (Pinteraction = 1.76×10-8; permuted p-value 3.51x10-8 region. Compared to non-/occasional drinking light to moderate alcohol consumption was associated with a lower risk of colorectal cancer among individuals with rs9409565 CT genotype (OR, 0.82 [95% CI, 0.74-0.91]; P = 2.1×10-4 and TT genotypes (OR,0.62 [95% CI, 0.51-0.75]; P = 1.3×10-6 but not associated among those with the CC genotype (p = 0.059. No genome-wide statistically significant interactions were observed for smoking. If replicated our suggestive finding of a genome-wide significant interaction between genetic variants and alcohol consumption might contribute to understanding colorectal cancer etiology and identifying subpopulations with differential susceptibility to the effect of alcohol on CRC risk.

  12. Genome-Wide Interaction Analyses between Genetic Variants and Alcohol Consumption and Smoking for Risk of Colorectal Cancer

    Science.gov (United States)

    Newcomb, Polly A.; Campbell, Peter T.; Baron, John A.; Berndt, Sonja I.; Bezieau, Stephane; Brenner, Hermann; Casey, Graham; Chan, Andrew T.; Chang-Claude, Jenny; Du, Mengmeng; Figueiredo, Jane C.; Gallinger, Steven; Giovannucci, Edward L.; Haile, Robert W.; Harrison, Tabitha A.; Hayes, Richard B.; Hoffmeister, Michael; Hopper, John L.; Hudson, Thomas J.; Jeon, Jihyoun; Jenkins, Mark A.; Küry, Sébastien; Le Marchand, Loic; Lin, Yi; Lindor, Noralane M.; Nishihara, Reiko; Ogino, Shuji; Potter, John D.; Rudolph, Anja; Schoen, Robert E.; Seminara, Daniela; Slattery, Martha L.; Thibodeau, Stephen N.; Thornquist, Mark; Toth, Reka; Wallace, Robert; White, Emily; Jiao, Shuo; Lemire, Mathieu; Hsu, Li; Peters, Ulrike

    2016-01-01

    Genome-wide association studies (GWAS) have identified many genetic susceptibility loci for colorectal cancer (CRC). However, variants in these loci explain only a small proportion of familial aggregation, and there are likely additional variants that are associated with CRC susceptibility. Genome-wide studies of gene-environment interactions may identify variants that are not detected in GWAS of marginal gene effects. To study this, we conducted a genome-wide analysis for interaction between genetic variants and alcohol consumption and cigarette smoking using data from the Colon Cancer Family Registry (CCFR) and the Genetics and Epidemiology of Colorectal Cancer Consortium (GECCO). Interactions were tested using logistic regression. We identified interaction between CRC risk and alcohol consumption and variants in the 9q22.32/HIATL1 (Pinteraction = 1.76×10−8; permuted p-value 3.51x10-8) region. Compared to non-/occasional drinking light to moderate alcohol consumption was associated with a lower risk of colorectal cancer among individuals with rs9409565 CT genotype (OR, 0.82 [95% CI, 0.74–0.91]; P = 2.1×10−4) and TT genotypes (OR,0.62 [95% CI, 0.51–0.75]; P = 1.3×10−6) but not associated among those with the CC genotype (p = 0.059). No genome-wide statistically significant interactions were observed for smoking. If replicated our suggestive finding of a genome-wide significant interaction between genetic variants and alcohol consumption might contribute to understanding colorectal cancer etiology and identifying subpopulations with differential susceptibility to the effect of alcohol on CRC risk. PMID:27723779

  13. Bayesian estimation and use of high-throughput remote sensing indices for quantitative genetic analyses of leaf growth.

    Science.gov (United States)

    Baker, Robert L; Leong, Wen Fung; An, Nan; Brock, Marcus T; Rubin, Matthew J; Welch, Stephen; Weinig, Cynthia

    2018-02-01

    We develop Bayesian function-valued trait models that mathematically isolate genetic mechanisms underlying leaf growth trajectories by factoring out genotype-specific differences in photosynthesis. Remote sensing data can be used instead of leaf-level physiological measurements. Characterizing the genetic basis of traits that vary during ontogeny and affect plant performance is a major goal in evolutionary biology and agronomy. Describing genetic programs that specifically regulate morphological traits can be complicated by genotypic differences in physiological traits. We describe the growth trajectories of leaves using novel Bayesian function-valued trait (FVT) modeling approaches in Brassica rapa recombinant inbred lines raised in heterogeneous field settings. While frequentist approaches estimate parameter values by treating each experimental replicate discretely, Bayesian models can utilize information in the global dataset, potentially leading to more robust trait estimation. We illustrate this principle by estimating growth asymptotes in the face of missing data and comparing heritabilities of growth trajectory parameters estimated by Bayesian and frequentist approaches. Using pseudo-Bayes factors, we compare the performance of an initial Bayesian logistic growth model and a model that incorporates carbon assimilation (A max ) as a cofactor, thus statistically accounting for genotypic differences in carbon resources. We further evaluate two remotely sensed spectroradiometric indices, photochemical reflectance (pri2) and MERIS Terrestrial Chlorophyll Index (mtci) as covariates in lieu of A max , because these two indices were genetically correlated with A max across years and treatments yet allow much higher throughput compared to direct leaf-level gas-exchange measurements. For leaf lengths in uncrowded settings, including A max improves model fit over the initial model. The mtci and pri2 indices also outperform direct A max measurements. Of particular

  14. Towards systems genetic analyses in barley: Integration of phenotypic, expression and genotype data into GeneNetwork

    Directory of Open Access Journals (Sweden)

    Druka Arnis

    2008-11-01

    Full Text Available Abstract Background A typical genetical genomics experiment results in four separate data sets; genotype, gene expression, higher-order phenotypic data and metadata that describe the protocols, processing and the array platform. Used in concert, these data sets provide the opportunity to perform genetic analysis at a systems level. Their predictive power is largely determined by the gene expression dataset where tens of millions of data points can be generated using currently available mRNA profiling technologies. Such large, multidimensional data sets often have value beyond that extracted during their initial analysis and interpretation, particularly if conducted on widely distributed reference genetic materials. Besides quality and scale, access to the data is of primary importance as accessibility potentially allows the extraction of considerable added value from the same primary dataset by the wider research community. Although the number of genetical genomics experiments in different plant species is rapidly increasing, none to date has been presented in a form that allows quick and efficient on-line testing for possible associations between genes, loci and traits of interest by an entire research community. Description Using a reference population of 150 recombinant doubled haploid barley lines we generated novel phenotypic, mRNA abundance and SNP-based genotyping data sets, added them to a considerable volume of legacy trait data and entered them into the GeneNetwork http://www.genenetwork.org. GeneNetwork is a unified on-line analytical environment that enables the user to test genetic hypotheses about how component traits, such as mRNA abundance, may interact to condition more complex biological phenotypes (higher-order traits. Here we describe these barley data sets and demonstrate some of the functionalities GeneNetwork provides as an easily accessible and integrated analytical environment for exploring them. Conclusion By

  15. Replication of LDL GWAs hits in PROSPER/PHASE as validation for future (pharmaco)genetic analyses

    LENUS (Irish Health Repository)

    Trompet, Stella

    2011-10-06

    Abstract Background The PHArmacogenetic study of Statins in the Elderly at risk (PHASE) is a genome wide association study in the PROspective Study of Pravastatin in the Elderly at risk for vascular disease (PROSPER) that investigates the genetic variation responsible for the individual variation in drug response to pravastatin. Statins lower LDL-cholesterol in general by 30%, however not in all subjects. Moreover, clinical response is highly variable and adverse effects occur in a minority of patients. In this report we first describe the rationale of the PROSPER\\/PHASE project and second show that the PROSPER\\/PHASE study can be used to study pharmacogenetics in the elderly. Methods The genome wide association study (GWAS) was conducted using the Illumina 660K-Quad beadchips following manufacturer\\'s instructions. After a stringent quality control 557,192 SNPs in 5,244 subjects were available for analysis. To maximize the availability of genetic data and coverage of the genome, imputation up to 2.5 million autosomal CEPH HapMap SNPs was performed with MACH imputation software. The GWAS for LDL-cholesterol is assessed with an additive linear regression model in PROBABEL software, adjusted for age, sex, and country of origin to account for population stratification. Results Forty-two SNPs reached the GWAS significant threshold of p = 5.0e-08 in 5 genomic loci (APOE\\/APOC1; LDLR; FADS2\\/FEN1; HMGCR; PSRC1\\/CELSR5). The top SNP (rs445925, chromosome 19) with a p-value of p = 2.8e-30 is located within the APOC1 gene and near the APOE gene. The second top SNP (rs6511720, chromosome 19) with a p-value of p = 5.22e-15 is located within the LDLR gene. All 5 genomic loci were previously associated with LDL-cholesterol levels, no novel loci were identified. Replication in WOSCOPS and CARE confirmed our results. Conclusion With the GWAS in the PROSPER\\/PHASE study we confirm the previously found genetic associations with LDL-cholesterol levels. With this proof

  16. Phylogenetic and population genetic analyses of diploid Leucaena (Leguminosae; Mimosoideae) reveal cryptic species diversity and patterns of divergent allopatric speciation.

    Science.gov (United States)

    Govindarajulu, Rajanikanth; Hughes, Colin E; Bailey, C Donovan

    2011-12-01

    Leucaena comprises 17 diploid species, five tetraploid species, and a complex series of hybrids whose evolutionary histories have been influenced by human seed translocation, cultivation, and subsequent spontaneous hybridization. Here we investigated patterns of evolutionary divergence among diploid Leucaena through comprehensively sampled multilocus phylogenetic and population genetic approaches to address species delimitation, interspecific relationships, hybridization, and the predominant mode of speciation among diploids. Parsimony- and maximum-likelihood-based phylogenetic approaches were applied to 59 accessions sequenced for six SCAR-based nuclear loci, nrDNA ITS, and four cpDNA regions. Population genetic comparisons included 1215 AFLP loci representing 42 populations and 424 individuals. Phylogenetic results provided a well-resolved hypothesis of divergent species relationships, recovering previously recognized clades of diploids as well as newly resolved relationships. Phylogenetic and population genetic assessments identified two cryptic species that are consistent with geography and morphology. Findings from this study highlight the importance and utility of multilocus data in the recovery of complex evolutionary histories. The results are consistent with allopatric divergence representing the predominant mode of speciation among diploid Leucaena. These findings contrast with the potential hybrid origin of several tetraploid species and highlight the importance of human translocation of seed to the origin of these tetraploids. The recognition of one previously unrecognized species (L. cruziana) and the elevation of another taxon (L. collinsii subsp. zacapana) to specific status (L. zacapana) is consistent with a growing number of newly diagnosed species from neotropical seasonally dry forests, suggesting these communities harbor greater species diversity than previously recognized.

  17. Forensic and population genetic analyses of Danes, Greenlanders and Somalis typed with the Yfiler® Plus PCR amplification kit

    DEFF Research Database (Denmark)

    Olofsson, Jill Katharina; Mogensen, Helle Smidt; Buchard, Anders

    2015-01-01

    (®) in the same individuals. Forensic and population genetic parameters were estimated for Yfiler(®) Plus. Yfiler(®) Plus had a higher power of discrimination than Yfiler(®) in all three populations. Compared to Yfiler(®), Yfiler(®) Plus offers increased power of discrimination, which is obviously an advantage...... in crime case investigations. However, the inclusion of seven RM Y-STRs in Yfiler(®) Plus makes it less attractive for relationship testing because of the relatively high combined mutation rate, approximately 15%....

  18. Lesion progression in post-treatment persistent endodontic lesions.

    Science.gov (United States)

    Yu, Victoria Soo Hoon; Messer, Harold Henry; Shen, Liang; Yee, Robert; Hsu, Chin-ying Stephen

    2012-10-01

    Radiographic lesions related to root-filled teeth may persist for long periods after treatment and are considered to indicate failure of initial treatment. Persistent lesions are found in a proportion of cases, but information on lesion progression is lacking. This study examined the incidence of lesion improvement, remaining unchanged, and deterioration among persistent lesions in a group of patients recruited from a university-based clinic and identified potential predictors for lesion progression. Patients of a university clinic with persistent endodontic lesions at least 4 years since treatment and with original treatment radiographs available were recruited with informed consent. Data were obtained by interview and from dental records and clinical and radiographic examinations. Univariate and multivariate statistical analyses were carried out by using SPSS (version 19). One hundred fifty-one persistent lesions were identified in 114 patients. A majority of the lesions (107, 70.9%) received treatment between 4 and 5 years prior. Eighty-six lesions (57.0%) improved, 18 (11.9%) remained unchanged, and 47 (31.1%) deteriorated since treatment. Potential predictors for lesions that did not improve included recall lesion size, pain on biting at recall examination, history of a postobturation flare-up, and a non-ideal root-filling length (P < .05). Lesions that had persisted for a longer period appeared less likely to be improving (relative risk, 1.038; 95% confidence interval, 1.000-1.077). A specific time interval alone should not be used to conclude that a lesion will not resolve without intervention. This study identified several clinical factors that are associated with deteriorating persistent lesions, which should aid in identifying lesions that require further intervention. Copyright © 2012 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

  19. Minding the gap: Frequency of indels in mtDNA control region sequence data and influence on population genetic analyses

    Science.gov (United States)

    Pearce, J.M.

    2006-01-01

    Insertions and deletions (indels) result in sequences of various lengths when homologous gene regions are compared among individuals or species. Although indels are typically phylogenetically informative, occurrence and incorporation of these characters as gaps in intraspecific population genetic data sets are rarely discussed. Moreover, the impact of gaps on estimates of fixation indices, such as FST, has not been reviewed. Here, I summarize the occurrence and population genetic signal of indels among 60 published studies that involved alignments of multiple sequences from the mitochondrial DNA (mtDNA) control region of vertebrate taxa. Among 30 studies observing indels, an average of 12% of both variable and parsimony-informative sites were composed of these sites. There was no consistent trend between levels of population differentiation and the number of gap characters in a data block. Across all studies, the average influence on estimates of ??ST was small, explaining only an additional 1.8% of among population variance (range 0.0-8.0%). Studies most likely to observe an increase in ??ST with the inclusion of gap characters were those with control region DNA appears small, dependent upon total number of variable sites in the data block, and related to species-specific characteristics and the spatial distribution of mtDNA lineages that contain indels. ?? 2006 Blackwell Publishing Ltd.

  20. Using trajectory analyses to refine phenotype for genetic association: conduct problems and the serotonin transporter (5HTTLPR).

    Science.gov (United States)

    Sakai, Joseph T; Boardman, Jason D; Gelhorn, Heather L; Smolen, Andrew; Corley, Robin P; Huizinga, David; Menard, Scott; Hewitt, John K; Stallings, Michael C

    2010-10-01

    Conduct disorder is a serious, relatively common disorder of childhood and adolescence. Findings from genetic association studies searching for genetic determinants of the liability toward such behaviors have been inconsistent. One possible explanation for differential results is that most studies define phenotype from a single assessment; for many adolescents conduct problems decrease in severity over time, whereas for others such behaviors persist. Therefore, longitudinal datasets offer the opportunity to refine phenotype. We used Caucasians that were first assessed during adolescence from the National Youth Survey Family Study. Nine waves of data were used to create latent growth trajectories and test for associations between trajectory class and 5HTTLPR genotype. For the full sample, 5HTTLPR was not associated with conduct problem phenotypes. However, the short (s) allele was associated with chronic conduct problems in females; a nominally significant sex by 5HTTLPR genotype interaction was noted. Longitudinal studies provide unique opportunities for phenotypic refinement and such techniques, with large samples, may be useful for phenotypic definition with other study designs, such as whole genome association studies.

  1. University Students' Knowledge Structures and Informal Reasoning on the Use of Genetically Modified Foods: Multidimensional Analyses

    Science.gov (United States)

    Wu, Ying-Tien

    2013-01-01

    This study aims to provide insights into the role of learners' knowledge structures about a socio-scientific issue (SSI) in their informal reasoning on the issue. A total of 42 non-science major university students' knowledge structures and informal reasoning were assessed with multidimensional analyses. With both qualitative and…

  2. Analyses of genetic relationships between linear type traits, fat-to-protein ratio, milk production traits, and somatic cell count in first-parity Czech Holstein cows

    DEFF Research Database (Denmark)

    Zink, V; Zavadilová, L; Lassen, Jan

    2014-01-01

    . The number of animals for each linear type trait was 59 454, except for locomotion, for which 53 424 animals were recorded. The numbers of animals with records of milk production data were 43 992 for milk yield, fat percentage, protein percentage, and fat-to-protein percentage ratio and 43 978 for fat yield...... and protein yield. In total, 27 098 somatic cell score records were available. The strongest positive genetic correlation between production traits and linear type traits was estimated between udder width and fat yield (0.51 ± 0.04), while the strongest negative correlation estimated was between body......Genetic and phenotypic correlations between production traits, selected linear type traits, and somatic cell score were estimated. The results could be useful for breeding programs involving Czech Holstein dairy cows or other populations. A series of bivariate analyses was applied whereby (co...

  3. 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

  4. Characterization and mapping of complementary lesion-mimic genes lm1 and lm2 in common wheat.

    Science.gov (United States)

    Yao, Qin; Zhou, Ronghua; Fu, Tihua; Wu, Weiren; Zhu, Zhendong; Li, Aili; Jia, Jizeng

    2009-10-01

    A lesion-mimic phenotype appeared in a segregating population of common wheat cross Yanzhan 1/Zaosui 30. The parents had non-lesion normal phenotypes. Shading treatment and histochemical analyses showed that the lesions were caused by light-dependent cell death and were not associated with pathogens. Studies over two cropping seasons showed that some lines with more highly expressed lesion-mimic phenotypes exhibited significantly lower grain yields than those with the normal phenotype, but there were no significant effects in the lines with weakly expressed lesion-mimic phenotypes. Among yield traits, one-thousand grain weight was the most affected by lesion-mimic phenotypes. Genetic analysis indicated that this was a novel type of lesion mimic, which was caused by interaction of recessive genes derived from each parent. The lm1 (lesion mimic 1) locus from Zaosui 30 was flanked by microsatellite markers Xwmc674 and Xbarc133/Xbarc147 on chromosome 3BS, at genetic distances of 1.2 and 3.8 cM, respectively, whereas lm2 from Yanzhan 1 was mapped between microsatellite markers Xgwm513 and Xksum154 on chromosome 4BL, at genetic distances of 1.5 and 3 cM, respectively. The linked microsatellite makers identified in this study might be useful for evaluating whether potential parents with normal phenotype are carriers of lesion-mimic alleles.

  5. 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...

  6. Genetic influences on political ideologies: twin analyses of 19 measures of political ideologies from five democracies and genome-wide findings from three populations.

    Science.gov (United States)

    Hatemi, Peter K; Medland, Sarah E; Klemmensen, Robert; Oskarsson, Sven; Littvay, Levente; Dawes, Christopher T; Verhulst, Brad; McDermott, Rose; Nørgaard, Asbjørn Sonne; Klofstad, Casey A; Christensen, Kaare; Johannesson, Magnus; Magnusson, Patrik K E; Eaves, Lindon J; Martin, Nicholas G

    2014-05-01

    Almost 40 years ago, evidence from large studies of adult twins and their relatives suggested that between 30 and 60% of the variance in social and political attitudes could be explained by genetic influences. However, these findings have not been widely accepted or incorporated into the dominant paradigms that explain the etiology of political ideology. This has been attributed in part to measurement and sample limitations, as well the relative absence of molecular genetic studies. Here we present results from original analyses of a combined sample of over 12,000 twins pairs, ascertained from nine different studies conducted in five democracies, sampled over the course of four decades. We provide evidence that genetic factors play a role in the formation of political ideology, regardless of how ideology is measured, the era, or the population sampled. The only exception is a question that explicitly uses the phrase "Left-Right". We then present results from one of the first genome-wide association studies on political ideology using data from three samples: a 1990 Australian sample involving 6,894 individuals from 3,516 families; a 2008 Australian sample of 1,160 related individuals from 635 families and a 2010 Swedish sample involving 3,334 individuals from 2,607 families. No polymorphisms reached genome-wide significance in the meta-analysis. The combined evidence suggests that political ideology constitutes a fundamental aspect of one's genetically informed psychological disposition, but as Fisher proposed long ago, genetic influences on complex traits will be composed of thousands of markers of very small effects and it will require extremely large samples to have enough power in order to identify specific polymorphisms related to complex social traits.

  7. Genetic Influences on Political Ideologies: Twin Analyses of 19 Measures of Political Ideologies from Five Democracies and Genome-Wide Findings from Three Populations

    Science.gov (United States)

    Hatemi, Peter K.; Medland, Sarah E.; Klemmensen, Robert; Oskarrson, Sven; Littvay, Levente; Dawes, Chris; Verhulst, Brad; McDermott, Rose; Nørgaard, Asbjørn Sonne; Klofstad, Casey; Christensen, Kaare; Johannesson, Magnus; Magnusson, Patrik K.E.; Eaves, Lindon J.; Martin, Nicholas G.

    2014-01-01

    Almost forty years ago, evidence from large studies of adult twins and their relatives suggested that between 30-60% of the variance in social and political attitudes could be explained by genetic influences. However, these findings have not been widely accepted or incorporated into the dominant paradigms that explain the etiology of political ideology. This has been attributed in part to measurement and sample limitations, as well the relative absence of molecular genetic studies. Here we present results from original analyses of a combined sample of over 12,000 twins pairs, ascertained from nine different studies conducted in five democracies, sampled over the course of four decades. We provide evidence that genetic factors play a role in the formation of political ideology, regardless of how ideology is measured, the era, or the population sampled. The only exception is a question that explicitly uses the phrase “Left-Right”. We then present results from one of the first genome-wide association studies on political ideology using data from three samples: a 1990 Australian sample involving 6,894 individuals from 3,516 families; a 2008 Australian sample of 1,160 related individuals from 635 families and a 2010 Swedish sample involving 3,334 individuals from 2,607 families. No polymorphisms reached genome-wide significance in the meta-analysis. The combined evidence suggests that political ideology constitutes a fundamental aspect of one’s genetically informed psychological disposition, but as Fisher proposed long ago, genetic influences on complex traits will be composed of thousands of markers of very small effects and it will require extremely large samples to have enough power in order to identify specific polymorphisms related to complex social traits. PMID:24569950

  8. Genetic and Functional Analyses of SHANK2 Mutations Suggest a Multiple Hit Model of Autism Spectrum Disorders

    Science.gov (United States)

    Leblond, Claire S.; Heinrich, Jutta; Delorme, Richard; Proepper, Christian; Betancur, Catalina; Huguet, Guillaume; Konyukh, Marina; Chaste, Pauline; Ey, Elodie; Rastam, Maria; Anckarsäter, Henrik; Nygren, Gudrun; Gillberg, I. Carina; Melke, Jonas; Toro, Roberto; Regnault, Beatrice; Fauchereau, Fabien; Mercati, Oriane; Lemière, Nathalie; Skuse, David; Poot, Martin; Holt, Richard; Monaco, Anthony P.; Järvelä, Irma; Kantojärvi, Katri; Vanhala, Raija; Curran, Sarah; Collier, David A.; Bolton, Patrick; Chiocchetti, Andreas; Klauck, Sabine M.; Poustka, Fritz; Freitag, Christine M.; Waltes, Regina; Kopp, Marnie; Duketis, Eftichia; Bacchelli, Elena; Minopoli, Fiorella; Ruta, Liliana; Battaglia, Agatino; Mazzone, Luigi; Maestrini, Elena; Sequeira, Ana F.; Oliveira, Barbara; Vicente, Astrid; Oliveira, Guiomar; Pinto, Dalila; Scherer, Stephen W.; Zelenika, Diana; Delepine, Marc; Lathrop, Mark; Bonneau, Dominique; Guinchat, Vincent; Devillard, Françoise; Assouline, Brigitte; Mouren, Marie-Christine; Leboyer, Marion; Gillberg, Christopher; Boeckers, Tobias M.; Bourgeron, Thomas

    2012-01-01

    Autism spectrum disorders (ASD) are a heterogeneous group of neurodevelopmental disorders with a complex inheritance pattern. While many rare variants in synaptic proteins have been identified in patients with ASD, little is known about their effects at the synapse and their interactions with other genetic variations. Here, following the discovery of two de novo SHANK2 deletions by the Autism Genome Project, we identified a novel 421 kb de novo SHANK2 deletion in a patient with autism. We then sequenced SHANK2 in 455 patients with ASD and 431 controls and integrated these results with those reported by Berkel et al. 2010 (n = 396 patients and n = 659 controls). We observed a significant enrichment of variants affecting conserved amino acids in 29 of 851 (3.4%) patients and in 16 of 1,090 (1.5%) controls (P = 0.004, OR = 2.37, 95% CI = 1.23–4.70). In neuronal cell cultures, the variants identified in patients were associated with a reduced synaptic density at dendrites compared to the variants only detected in controls (P = 0.0013). Interestingly, the three patients with de novo SHANK2 deletions also carried inherited CNVs at 15q11–q13 previously associated with neuropsychiatric disorders. In two cases, the nicotinic receptor CHRNA7 was duplicated and in one case the synaptic translation repressor CYFIP1 was deleted. These results strengthen the role of synaptic gene dysfunction in ASD but also highlight the presence of putative modifier genes, which is in keeping with the “multiple hit model” for ASD. A better knowledge of these genetic interactions will be necessary to understand the complex inheritance pattern of ASD. PMID:22346768

  9. Genetic and functional analyses of SHANK2 mutations suggest a multiple hit model of autism spectrum disorders.

    Directory of Open Access Journals (Sweden)

    Claire S Leblond

    2012-02-01

    Full Text Available Autism spectrum disorders (ASD are a heterogeneous group of neurodevelopmental disorders with a complex inheritance pattern. While many rare variants in synaptic proteins have been identified in patients with ASD, little is known about their effects at the synapse and their interactions with other genetic variations. Here, following the discovery of two de novo SHANK2 deletions by the Autism Genome Project, we identified a novel 421 kb de novo SHANK2 deletion in a patient with autism. We then sequenced SHANK2 in 455 patients with ASD and 431 controls and integrated these results with those reported by Berkel et al. 2010 (n = 396 patients and n = 659 controls. We observed a significant enrichment of variants affecting conserved amino acids in 29 of 851 (3.4% patients and in 16 of 1,090 (1.5% controls (P = 0.004, OR = 2.37, 95% CI = 1.23-4.70. In neuronal cell cultures, the variants identified in patients were associated with a reduced synaptic density at dendrites compared to the variants only detected in controls (P = 0.0013. Interestingly, the three patients with de novo SHANK2 deletions also carried inherited CNVs at 15q11-q13 previously associated with neuropsychiatric disorders. In two cases, the nicotinic receptor CHRNA7 was duplicated and in one case the synaptic translation repressor CYFIP1 was deleted. These results strengthen the role of synaptic gene dysfunction in ASD but also highlight the presence of putative modifier genes, which is in keeping with the "multiple hit model" for ASD. A better knowledge of these genetic interactions will be necessary to understand the complex inheritance pattern of ASD.

  10. Genetic and codon usage bias analyses of polymerase genes of equine influenza virus and its relation to evolution.

    Science.gov (United States)

    Bera, Bidhan Ch; Virmani, Nitin; Kumar, Naveen; Anand, Taruna; Pavulraj, S; Rash, Adam; Elton, Debra; Rash, Nicola; Bhatia, Sandeep; Sood, Richa; Singh, Raj Kumar; Tripathi, Bhupendra Nath

    2017-08-23

    Equine influenza is a major health problem of equines worldwide. The polymerase genes of influenza virus have key roles in virus replication, transcription, transmission between hosts and pathogenesis. Hence, the comprehensive genetic and codon usage bias of polymerase genes of equine influenza virus (EIV) were analyzed to elucidate the genetic and evolutionary relationships in a novel perspective. The group - specific consensus amino acid substitutions were identified in all polymerase genes of EIVs that led to divergence of EIVs into various clades. The consistent amino acid changes were also detected in the Florida clade 2 EIVs circulating in Europe and Asia since 2007. To study the codon usage patterns, a total of 281,324 codons of polymerase genes of EIV H3N8 isolates from 1963 to 2015 were systemically analyzed. The polymerase genes of EIVs exhibit a weak codon usage bias. The ENc-GC3s and Neutrality plots indicated that natural selection is the major influencing factor of codon usage bias, and that the impact of mutation pressure is comparatively minor. The methods for estimating host imposed translation pressure suggested that the polymerase acidic (PA) gene seems to be under less translational pressure compared to polymerase basic 1 (PB1) and polymerase basic 2 (PB2) genes. The multivariate statistical analysis of polymerase genes divided EIVs into four evolutionary diverged clusters - Pre-divergent, Eurasian, Florida sub-lineage 1 and 2. Various lineage specific amino acid substitutions observed in all polymerase genes of EIVs and especially, clade 2 EIVs underwent major variations which led to the emergence of a phylogenetically distinct group of EIVs originating from Richmond/1/07. The codon usage bias was low in all the polymerase genes of EIVs that was influenced by the multiple factors such as the nucleotide compositions, mutation pressure, aromaticity and hydropathicity. However, natural selection was the major influencing factor in defining the

  11. Genetic and evolutionary analyses of the human bone morphogenetic protein receptor 2 (BMPR2 in the pathophysiology of obesity.

    Directory of Open Access Journals (Sweden)

    Dorit Schleinitz

    2011-02-01

    Full Text Available Human bone morphogenetic protein receptor 2 (BMPR2 is essential for BMP signalling and may be involved in the regulation of adipogenesis. The BMPR2 locus has been suggested as target of recent selection in human populations. We hypothesized that BMPR2 might have a role in the pathophysiology of obesity.Evolutionary analyses (dN/dS, Fst, iHS were conducted in vertebrates and human populations. BMPR2 mRNA expression was measured in 190 paired samples of visceral and subcutaneous adipose tissue. The gene was sequenced in 48 DNA samples. Nine representative single nucleotide polymorphisms (SNPs were genotyped for subsequent association studies on quantitative traits related to obesity in 1830 German Caucasians. An independent cohort of 925 Sorbs was used for replication. Finally, relation of genotypes to mRNA in fat was examined.The evolutionary analyses indicated signatures of selection on the BMPR2 locus. BMPR2 mRNA expression was significantly increased both in visceral and subcutaneous adipose tissue of 37 overweight (BMI>25 and 30 kg/m² compared with 44 lean subjects (BMI< 25 kg/m² (P<0.001. In a case-control study including lean and obese subjects, two intronic SNPs (rs6717924, rs13426118 were associated with obesity (adjusted P<0.05. Combined analyses including the initial cohort and the Sorbs confirmed a consistent effect for rs6717924 (combined P = 0.01 on obesity. Moreover, rs6717924 was associated with higher BMPR2 mRNA expression in visceral adipose tissue.Combined BMPR2 genotype-phenotype-mRNA expression data as well as evolutionary aspects suggest a role of BMPR2 in the pathophysiology of obesity.

  12. Genetic analyses using GGE model and a mixed linear model approach, and stability analyses using AMMI bi-plot for late-maturity alpha-amylase activity in bread wheat genotypes.

    Science.gov (United States)

    Rasul, Golam; Glover, Karl D; Krishnan, Padmanaban G; Wu, Jixiang; Berzonsky, William A; Fofana, Bourlaye

    2017-06-01

    Low falling number and discounting grain when it is downgraded in class are the consequences of excessive late-maturity α-amylase activity (LMAA) in bread wheat (Triticum aestivum L.). Grain expressing high LMAA produces poorer quality bread products. To effectively breed for low LMAA, it is necessary to understand what genes control it and how they are expressed, particularly when genotypes are grown in different environments. In this study, an International Collection (IC) of 18 spring wheat genotypes and another set of 15 spring wheat cultivars adapted to South Dakota (SD), USA were assessed to characterize the genetic component of LMAA over 5 and 13 environments, respectively. The data were analysed using a GGE model with a mixed linear model approach and stability analysis was presented using an AMMI bi-plot on R software. All estimated variance components and their proportions to the total phenotypic variance were highly significant for both sets of genotypes, which were validated by the AMMI model analysis. Broad-sense heritability for LMAA was higher in SD adapted cultivars (53%) compared to that in IC (49%). Significant genetic effects and stability analyses showed some genotypes, e.g. 'Lancer', 'Chester' and 'LoSprout' from IC, and 'Alsen', 'Traverse' and 'Forefront' from SD cultivars could be used as parents to develop new cultivars expressing low levels of LMAA. Stability analysis using an AMMI bi-plot revealed that 'Chester', 'Lancer' and 'Advance' were the most stable across environments, while in contrast, 'Kinsman', 'Lerma52' and 'Traverse' exhibited the lowest stability for LMAA across environments.

  13. Identification of Nitrogen Consumption Genetic Variants in Yeast Through QTL Mapping and Bulk Segregant RNA-Seq Analyses.

    Science.gov (United States)

    Cubillos, Francisco A; Brice, Claire; Molinet, Jennifer; Tisné, Sebastién; Abarca, Valentina; Tapia, Sebastián M; Oporto, Christian; García, Verónica; Liti, Gianni; Martínez, Claudio

    2017-06-07

    Saccharomyces cerevisiae is responsible for wine must fermentation. In this process, nitrogen represents a limiting nutrient and its scarcity results in important economic losses for the wine industry. Yeast isolates use different strategies to grow in poor nitrogen environments and their genomic plasticity enables adaptation to multiple habitats through improvements in nitrogen consumption. Here, we used a highly recombinant S. cerevisiae multi-parent population (SGRP-4X) derived from the intercross of four parental strains of different origins to identify new genetic variants responsible for nitrogen consumption differences during wine fermentation. Analysis of 165 fully sequenced F12 segregants allowed us to map 26 QTL in narrow intervals for 14 amino acid sources and ammonium, the majority of which represent genomic regions previously unmapped for these traits. To complement this strategy, we performed Bulk segregant RNA-seq (BSR-seq) analysis in segregants exhibiting extremely high and low ammonium consumption levels. This identified several QTL overlapping differentially expressed genes and refined the gene candidate search. Based on these approaches, we were able to validate ARO1 , PDC1 , CPS1 , ASI2 , LYP1 , and ALP1 allelic variants underlying nitrogen consumption differences between strains, providing evidence of many genes with small phenotypic effects. Altogether, these variants significantly shape yeast nitrogen consumption with important implications for evolution, ecological, and quantitative genomics. Copyright © 2017 Cubillos et al.

  14. Genetic association analyses implicate aberrant regulation of innate and adaptive immunity genes in the pathogenesis of systemic lupus erythematosus

    Science.gov (United States)

    Graham, Deborah S Cunninghame; Pinder, Christopher L; Tombleson, Philip; Behrens, Timothy W; Martín, Javier; Fairfax, Benjamin P; Knight, Julian C; Chen, Lingyan; Replogle, Joseph; Syvänen, Ann-Christine; Rönnblom, Lars; Graham, Robert R; Wither, Joan E; Rioux, John D; Alarcón-Riquelme, Marta E; Vyse, Timothy J

    2015-01-01

    Systemic lupus erythematosus (SLE; OMIM 152700) is a genetically complex autoimmune disease characterized by loss of immune tolerance to nuclear and cell surface antigens. Previous genome-wide association studies (GWAS) had modest sample sizes, reducing their scope and reliability. Our study comprised 7,219 cases and 15,991 controls of European ancestry: a new GWAS, meta-analysis with a published GWAS and a replication study. We have mapped 43 susceptibility loci, including 10 novel associations. Assisted by dense genome coverage, imputation provided evidence for missense variants underpinning associations in eight genes. Other likely causal genes were established by examining associated alleles for cis-acting eQTL effects in a range of ex vivo immune cells. We found an over-representation (n=16) of transcription factors among SLE susceptibility genes. This supports the view that aberrantly regulated gene expression networks in multiple cell types in both the innate and adaptive immune response contribute to the risk of developing SLE. PMID:26502338

  15. Identification of Nitrogen Consumption Genetic Variants in Yeast Through QTL Mapping and Bulk Segregant RNA-Seq Analyses

    Directory of Open Access Journals (Sweden)

    Francisco A. Cubillos

    2017-06-01

    Full Text Available Saccharomyces cerevisiae is responsible for wine must fermentation. In this process, nitrogen represents a limiting nutrient and its scarcity results in important economic losses for the wine industry. Yeast isolates use different strategies to grow in poor nitrogen environments and their genomic plasticity enables adaptation to multiple habitats through improvements in nitrogen consumption. Here, we used a highly recombinant S. cerevisiae multi-parent population (SGRP-4X derived from the intercross of four parental strains of different origins to identify new genetic variants responsible for nitrogen consumption differences during wine fermentation. Analysis of 165 fully sequenced F12 segregants allowed us to map 26 QTL in narrow intervals for 14 amino acid sources and ammonium, the majority of which represent genomic regions previously unmapped for these traits. To complement this strategy, we performed Bulk segregant RNA-seq (BSR-seq analysis in segregants exhibiting extremely high and low ammonium consumption levels. This identified several QTL overlapping differentially expressed genes and refined the gene candidate search. Based on these approaches, we were able to validate ARO1, PDC1, CPS1, ASI2, LYP1, and ALP1 allelic variants underlying nitrogen consumption differences between strains, providing evidence of many genes with small phenotypic effects. Altogether, these variants significantly shape yeast nitrogen consumption with important implications for evolution, ecological, and quantitative genomics.

  16. Mining microsatellites in the peach genome: development of new long-core SSR markers for genetic analyses in five Prunus species.

    Science.gov (United States)

    Dettori, Maria Teresa; Micali, Sabrina; Giovinazzi, Jessica; Scalabrin, Simone; Verde, Ignazio; Cipriani, Guido

    2015-01-01

    A wide inventory of molecular markers is nowadays available for individual fingerprinting. Microsatellites, or simple sequence repeats (SSRs), play a relevant role due to their relatively ease of use, their abundance in the plant genomes, and their co-dominant nature, together with the availability of primer sequences in many important agricultural crops. Microsatellites with long-core motifs are more easily scored and were adopted long ago in human genetics but they were developed only in few crops, and Prunus species are not among them. In the present work the peach whole-genome sequence was used to select 216 SSRs containing long-core motifs with tri-, tetra- and penta-nucleotide repeats. Microsatellite primer pairs were designed and tested for polymorphism in the five diploid Prunus species of economic relevance (almond, apricot, Japanese plum, peach and sweet cherry). A set of 26 microsatellite markers covering all the eight chromosomes, was also selected and used in the molecular characterization, population genetics and structure analyses of a representative sample of the five diploid Prunus species, assessing their transportability and effectiveness. The combined probability of identity between two random individuals for the whole set of 26 SSRs was quite low, ranging from 2.30 × 10(-7) in peach to 9.48 × 10(-10) in almond, confirming the usefulness of the proposed set for fingerprinting analyses in Prunus species.

  17. Genetic and Morphological Analyses Demonstrate That Schizolecis guntheri (Siluriformes: Loricariidae) Is Likely to Be a Species Complex

    Science.gov (United States)

    Souza, Camila S.; Costa-Silva, Guilherme J.; Roxo, Fábio F.; Foresti, Fausto; Oliveira, Claudio

    2018-01-01

    Schizolecis is a monotypic genus of Siluriformes widely distributed throughout isolated coastal drainages of southeastern Brazil. Previous studies have shown that fish groups found in isolated river basins tend to differentiate over time in the absence of gene flow, resulting in allopatric speciation. In this study, we used partial sequences of the mitochondrial gene COI with the analysis of the General Mixed Yule Coalescent model (GMYC) and the Automatic Barcode Gap Discovery (ABGD) for single locus species delimitation, and a Principal Component Analysis (PCA) of external morphology to test the hypothesis that Schizolecis guntheri is a complex of species. We analyzed 94 samples of S. guntheri for GMYC and ABGD, and 82 samples for PCA from 22 coastal rivers draining to the Atlantic in southeastern Brazil from the Paraná State to the north of the Rio de Janeiro State. As a result, the GMYC model and the ABGD delimited five operational taxonomy units (OTUs – a nomenclature referred to in the present study of the possible new species delimited for the genetic analysis), a much higher number compared to the traditional alfa taxonomy that only recognizes S. guntheri across the isolated coastal rivers of Brazil. Furthermore, the PCA analysis suggests that S. guntheri is highly variable in aspects of external body proportions, including dorsal-fin spine length, pectoral-fin spine length, pelvic-fin spine length, lower caudal-fin spine length, caudal peduncle depth, anal width and mandibular ramus length. However, no exclusive character was found among the isolated populations that could be used to describe a new species of Schizolecis. Therefore, we can conclude, based on our results of PCA contrasting with the results of GMYC and ABGD, that S. guntheri represents a complex of species. PMID:29552028

  18. Genetic and Morphological Analyses Demonstrate That Schizolecis guntheri (Siluriformes: Loricariidae) Is Likely to Be a Species Complex.

    Science.gov (United States)

    Souza, Camila S; Costa-Silva, Guilherme J; Roxo, Fábio F; Foresti, Fausto; Oliveira, Claudio

    2018-01-01

    Schizolecis is a monotypic genus of Siluriformes widely distributed throughout isolated coastal drainages of southeastern Brazil. Previous studies have shown that fish groups found in isolated river basins tend to differentiate over time in the absence of gene flow, resulting in allopatric speciation. In this study, we used partial sequences of the mitochondrial gene COI with the analysis of the General Mixed Yule Coalescent model (GMYC) and the Automatic Barcode Gap Discovery (ABGD) for single locus species delimitation, and a Principal Component Analysis (PCA) of external morphology to test the hypothesis that Schizolecis guntheri is a complex of species. We analyzed 94 samples of S. guntheri for GMYC and ABGD, and 82 samples for PCA from 22 coastal rivers draining to the Atlantic in southeastern Brazil from the Paraná State to the north of the Rio de Janeiro State. As a result, the GMYC model and the ABGD delimited five operational taxonomy units (OTUs - a nomenclature referred to in the present study of the possible new species delimited for the genetic analysis), a much higher number compared to the traditional alfa taxonomy that only recognizes S. guntheri across the isolated coastal rivers of Brazil. Furthermore, the PCA analysis suggests that S. guntheri is highly variable in aspects of external body proportions, including dorsal-fin spine length, pectoral-fin spine length, pelvic-fin spine length, lower caudal-fin spine length, caudal peduncle depth, anal width and mandibular ramus length. However, no exclusive character was found among the isolated populations that could be used to describe a new species of Schizolecis . Therefore, we can conclude, based on our results of PCA contrasting with the results of GMYC and ABGD, that S. guntheri represents a complex of species.

  19. Genetic and Morphological Analyses Demonstrate That Schizolecis guntheri (Siluriformes: Loricariidae Is Likely to Be a Species Complex

    Directory of Open Access Journals (Sweden)

    Camila S. Souza

    2018-03-01

    Full Text Available Schizolecis is a monotypic genus of Siluriformes widely distributed throughout isolated coastal drainages of southeastern Brazil. Previous studies have shown that fish groups found in isolated river basins tend to differentiate over time in the absence of gene flow, resulting in allopatric speciation. In this study, we used partial sequences of the mitochondrial gene COI with the analysis of the General Mixed Yule Coalescent model (GMYC and the Automatic Barcode Gap Discovery (ABGD for single locus species delimitation, and a Principal Component Analysis (PCA of external morphology to test the hypothesis that Schizolecis guntheri is a complex of species. We analyzed 94 samples of S. guntheri for GMYC and ABGD, and 82 samples for PCA from 22 coastal rivers draining to the Atlantic in southeastern Brazil from the Paraná State to the north of the Rio de Janeiro State. As a result, the GMYC model and the ABGD delimited five operational taxonomy units (OTUs – a nomenclature referred to in the present study of the possible new species delimited for the genetic analysis, a much higher number compared to the traditional alfa taxonomy that only recognizes S. guntheri across the isolated coastal rivers of Brazil. Furthermore, the PCA analysis suggests that S. guntheri is highly variable in aspects of external body proportions, including dorsal-fin spine length, pectoral-fin spine length, pelvic-fin spine length, lower caudal-fin spine length, caudal peduncle depth, anal width and mandibular ramus length. However, no exclusive character was found among the isolated populations that could be used to describe a new species of Schizolecis. Therefore, we can conclude, based on our results of PCA contrasting with the results of GMYC and ABGD, that S. guntheri represents a complex of species.

  20. Genetic analyses place most Spanish isolates of Beauveria bassiana in a molecular group with word-wide distribution

    Science.gov (United States)

    2011-01-01

    Background The entomopathogenic anamorphic fungus Beauveria bassiana is currently used as a biocontrol agent (BCA) of insects. Fifty-seven Beauveria bassiana isolates -53 from Spain- were characterized, integrating group I intron insertion patterns at the 3'-end of the nuclear large subunit ribosomal gene (LSU rDNA) and elongation factor 1-alpha (EF1-α) phylogenetic information, in order to assess the genetic structure and diversity of this Spanish collection of B. bassiana. Results Group I intron genotype analysis was based on the four highly conserved insertion sites of the LSU (Ec2653, Ec2449, Ec2066, Ec1921). Of the 16 possible combinations/genotypes, only four were detected, two of which were predominant, containing 44 and 9 members out of 57 isolates, respectively. Interestingly, the members of the latter two genotypes showed unique differences in their growth temperatures. In follow, EF1-α phylogeny served to classify most of the strains in the B. bassiana s.s. (sensu stricto) group and separate them into 5 molecular subgroups, all of which contained a group I intron belonging to the IC1 subtype at the Ec1921 position. A number of parameters such as thermal growth or origin (host, geographic location and climatic conditions) were also examined but in general no association could be found. Conclusion Most Spanish B. bassiana isolates (77.2%) are grouped into a major phylogenetic subgroup with word-wide distribution. However, high phylogenetic diversity was also detected among Spanish isolates from close geographic zones with low climatic variation. In general, no correlation was observed between the molecular distribution and geographic origin or climatic characteristics where the Spanish B. bassiana isolates were sampled. PMID:21521527

  1. Sex-biased natal dispersal and inbreeding avoidance in American black bears as revealed by spatial genetic analyses.

    Science.gov (United States)

    Costello, Cecily M; Creel, Scott R; Kalinowski, Steven T; Vu, Ninh V; Quigley, Howard B

    2008-11-01

    We tested the hypothesis that sex-biased natal dispersal reduces close inbreeding in American black bears, a solitary species that exhibits nearly complete male dispersal and female philopatry. Using microsatellite DNA and spatial data from reproductively mature bears (>or= 4 years old), we examined the spatial genetic structure of two distinct populations in New Mexico from 1993 to 2000. As predicted, relatedness (r) and the frequency of close relationships (parent-offspring or full siblings) decreased with distance among female dyads, but little change was observed among male or opposite-sex dyads. Neighbouring females were more closely related than neighbouring males. The potential for inbreeding was low. Most opposite-sex pairs that lived sufficiently close to facilitate mating were unrelated, and few were close relatives. We found no evidence that bears actively avoided inbreeding in their selection of mates from this nearby pool, as mean r and relationship frequencies did not differ between potential and actual mating pairs (determined by parentage analysis). These basic patterns were apparent in both study areas despite a nearly two-fold difference in density. However, the sex bias in dispersal was less pronounced in the lower-density area, based on proportions of bears with male and female relatives residing nearby. This result suggests that male bears may respond to reduced competition by decreasing their rate or distance of dispersal. Evidence supports the hypothesis that inbreeding avoidance is achieved by means of male-biased dispersal but also indicates that competition (for mates or resources) modifies dispersal patterns.

  2. A systemic gene silencing method suitable for high throughput, reverse genetic analyses of gene function in fern gametophytes

    Directory of Open Access Journals (Sweden)

    Tanurdzic Milos

    2004-04-01

    Full Text Available Abstract Background Ceratopteris richardii is a useful experimental system for studying gametophyte development and sexual reproduction in plants. However, few tools for cloning mutant genes or disrupting gene function exist for this species. The feasibility of systemic gene silencing as a reverse genetics tool was examined in this study. Results Several DNA constructs targeting a Ceratopteris protoporphyrin IX magnesium chelatase (CrChlI gene that is required for chlorophyll biosynthesis were each introduced into young gametophytes by biolistic delivery. Their transient expression in individual cells resulted in a colorless cell phenotype that affected most cells of the mature gametophyte, including the meristem and gametangia. The colorless phenotype was associated with a 7-fold decrease in the abundance of the endogenous transcript. While a construct designed to promote the transient expression of a CrChlI double stranded, potentially hairpin-forming RNA was found to be the most efficient in systemically silencing the endogenous gene, a plasmid containing the CrChlI cDNA insert alone was sufficient to induce silencing. Bombarded, colorless hermaphroditic gametophytes produced colorless embryos following self-fertilization, demonstrating that the silencing signal could be transmitted through gametogenesis and fertilization. Bombardment of young gametophytes with constructs targeting the Ceratopteris filamentous temperature sensitive (CrFtsZ and uroporphyrin dehydrogenase (CrUrod genes also produced the expected mutant phenotypes. Conclusion A method that induces the systemic silencing of target genes in the Ceratopteris gametophyte is described. It provides a simple, inexpensive and rapid means to test the functions of genes involved in gametophyte development, especially those involved in cellular processes common to all plants.

  3. ANALYSES OF GENETIC VARIABILITY IN LENTINULA EDODES THROUGH MYCELIA RESPONSES TO DIFFERENT ABIOTIC CONDITIONS AND RAPD MOLECULAR MARKERS

    Directory of Open Access Journals (Sweden)

    Maki Cristina Sayuri

    2001-01-01

    Full Text Available The growth of thirty-four Lentinula edodes strains submitted to different mycelial cultivation conditions (pH and temperature was evaluated and strain variability was assessed by RAPD molecular markers. The growth at three pH values (5, 6 and 7 and four different temperatures (16, 25, 28 and 37ºC was measured using the in vitro mycelial development rate and water retention as parameters. Mycelial cultivation was successful at all pH tested, while the ideal temperature for mycelial cultivation ranged between 25 and 28ºC. The water content was lower in strains grown at 37ºC. Among 20 OPA primers (Operon Technologies, Inc. used for the RAPD analyses, seventeen presented good polymorphism (OPA01 to OPA05, OPA07 to OPA14, OPA17 to OPA20. The clustering based on similarity coefficients allowed the separation of strain in two groups with different geographic origins.

  4. Genetic analyses involving microsatellite ETH10 genotypes on bovine chromosome 5 and performance trait measures in Angus- and Brahman-influenced cattle.

    Science.gov (United States)

    DeAtley, K L; Rincon, G; Farber, C R; Medrano, J F; Luna-Nevarez, P; Enns, R M; VanLeeuwen, D M; Silver, G A; Thomas, M G

    2011-07-01

    ETH10 is a dinucleotide microsatellite within the promoter of signal transducer and activator of transcription 6 (STAT6) gene on bovine chromosome 5. ETH10 is included in the panel of genetic markers used in parentage testing procedures of cattle breed associations. Allelic sizes of ETH10 PCR amplicons range from 199 to 225 bp. Objectives of this study were to use microsatellite data from beef cattle breed associations to investigate genetic distance and population stratification among Angus- and Brahman-influenced cattle and to use ETH10 genotypes and growth and ultrasound carcass data to investigate their statistical relationships. Three series of genotype to phenotype association analyses were conducted with 1) Angus data (n=5,094), 2) Brangus data (3/8 Brahman × 5/8 Angus; n=2,296), and 3) multibreed data (n=4,426) of Angus and Brangus cattle. Thirteen alleles and 38 genotypes were observed, but frequencies varied among breed groups. Tests of genetic identity and distance among 6 breed composition groups increasing in Brahman influence from 0 to 75% revealed that as Brahman-influence increased to ≥50%, genetic distance from Angus ranged from 18.3 to 43.5%. This was accomplished with 10 microsatellite loci. A mixed effects model involving genotype as a fixed effect and sire as a random source of variation suggested that Angus cattle with the 217/219 genotype tended to have 2.1% heavier (P=0.07) 205-d BW than other genotypes. In Brangus cattle, allele combinations were classified as small (≤215 bp) or large (≥217 bp). Brangus cattle with the small/large genotype had 2.0% heavier (PAngus and Brangus cattle. Results from this study provide support for STAT6 as one of the candidate genes underlying cattle growth QTL on chromosome 5. © 2011 American Society of Animal Science. All rights reserved.

  5. Assessing Heterogeneity of Osteolytic Lesions in Multiple Myeloma by 1H HR-MAS NMR Metabolomics

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    Laurette Tavel

    2016-10-01

    Full Text Available Multiple myeloma (MM is a malignancy of plasma cells characterized by multifocal osteolytic bone lesions. Macroscopic and genetic heterogeneity has been documented within MM lesions. Understanding the bases of such heterogeneity may unveil relevant features of MM pathobiology. To this aim, we deployed unbiased 1H high-resolution magic-angle spinning (HR-MAS nuclear magnetic resonance (NMR metabolomics to analyze multiple biopsy specimens of osteolytic lesions from one case of pathological fracture caused by MM. Multivariate analyses on normalized metabolite peak integrals allowed clusterization of samples in accordance with a posteriori histological findings. We investigated the relationship between morphological and NMR features by merging morphological data and metabolite profiling into a single correlation matrix. Data-merging addressed tissue heterogeneity, and greatly facilitated the mapping of lesions and nearby healthy tissues. Our proof-of-principle study reveals integrated metabolomics and histomorphology as a promising approach for the targeted study of osteolytic lesions.

  6. "Contrasting patterns of selection at Pinus pinaster Ait. Drought stress candidate genes as revealed by genetic differentiation analyses".

    Science.gov (United States)

    Eveno, Emmanuelle; Collada, Carmen; Guevara, M Angeles; Léger, Valérie; Soto, Alvaro; Díaz, Luis; Léger, Patrick; González-Martínez, Santiago C; Cervera, M Teresa; Plomion, Christophe; Garnier-Géré, Pauline H

    2008-02-01

    The importance of natural selection for shaping adaptive trait differentiation among natural populations of allogamous tree species has long been recognized. Determining the molecular basis of local adaptation remains largely unresolved, and the respective roles of selection and demography in shaping population structure are actively debated. Using a multilocus scan that aims to detect outliers from simulated neutral expectations, we analyzed patterns of nucleotide diversity and genetic differentiation at 11 polymorphic candidate genes for drought stress tolerance in phenotypically contrasted Pinus pinaster Ait. populations across its geographical range. We compared 3 coalescent-based methods: 2 frequentist-like, including 1 approach specifically developed for biallelic single nucleotide polymorphisms (SNPs) here and 1 Bayesian. Five genes showed outlier patterns that were robust across methods at the haplotype level for 2 of them. Two genes presented higher F(ST) values than expected (PR-AGP4 and erd3), suggesting that they could have been affected by the action of diversifying selection among populations. In contrast, 3 genes presented lower F(ST) values than expected (dhn-1, dhn2, and lp3-1), which could represent signatures of homogenizing selection among populations. A smaller proportion of outliers were detected at the SNP level suggesting the potential functional significance of particular combinations of sites in drought-response candidate genes. The Bayesian method appeared robust to low sample sizes, flexible to assumptions regarding migration rates, and powerful for detecting selection at the haplotype level, but the frequentist-like method adapted to SNPs was more efficient for the identification of outlier SNPs showing low differentiation. Population-specific effects estimated in the Bayesian method also revealed populations with lower immigration rates, which could have led to favorable situations for local adaptation. Outlier patterns are discussed

  7. Genetic linkage analyses and Cx50 mutation detection in a large multiplex Chinese family with hereditary nuclear cataract.

    Science.gov (United States)

    He, Wei; Li, Xin; Chen, Jiajing; Xu, Ling; Zhang, Feng; Dai, Qiushi; Cui, Hao; Wang, Duen-Mei; Yu, Jun; Hu, Songnian; Lu, Shan

    2011-03-01

    The aim of the study was to characterize the underlying mutation in a large multiplex Chinese family with hereditary nuclear cataract. A 6-generation Chinese family having hereditary nuclear cataract was recruited and clinically verified. Blood DNA samples were obtained from 53 available family members. Linkage analyses were performed on the known candidate regions for hereditary cataract with 36 polymorphic microsatellite markers. To identify mutations related to cataract, a direct sequencing approach was applied to a candidate gene residing in our linkage locus. A linkage locus was identified with a maximum 2-point LOD score of 4.31 (recombination fraction = 0) at marker D1S498 and a maximum multipoint LOD score of 5.7 between markers D1S2344 and D1S498 on chromosome 1q21.1, where the candidate gene Cx50 is located. Direct sequencing of Cx50 showed a 139 G to A transition occurred in all affected family members. This transitional mutation resulted in a replacement of aspartic acid by asparagine at residue 47 (D47N) and led to a loss-of-function of the protein. The D47N mutation of Cx50 causes the hereditary nuclear cataract in this family in an autosomal dominant mode of inheritance with incomplete penetrance.

  8. The role of the nucleus basalis of Meynert and reticular thalamic nucleus in pathogenesis of genetically determined absence epilepsy in rats : A lesion study

    NARCIS (Netherlands)

    Berdiev, R. K.; Chepurnov, S. A.; Veening, J. G.; Chepurnova, N. E.; van Luiftelaar, G.

    2007-01-01

    The role of cholinergic nucleus basalis (of Meynert) and the reticular thalamic nucleus in mechanisms of the generation spontaneous spike-and-wave discharges (SWDs) was investigated in the WAG/Rij rat model of absence epilepsy. Selective lesions were affected by local unilateral intraparenchymal

  9. Comprehensive review of genetic association studies and meta-analyses on miRNA polymorphisms and cancer risk.

    Directory of Open Access Journals (Sweden)

    Kshitij Srivastava

    Full Text Available MicroRNAs (miRNAs are small RNA molecules that regulate the expression of corresponding messenger RNAs (mRNAs. Variations in the level of expression of distinct miRNAs have been observed in the genesis, progression and prognosis of multiple human malignancies. The present study was aimed to investigate the association between four highly studied miRNA polymorphisms (mir-146a rs2910164, mir-196a2 rs11614913, mir-149 rs2292832 and mir-499 rs3746444 and cancer risk by using a two-sided meta-analytic approach.An updated meta-analysis based on 53 independent case-control studies consisting of 27573 cancer cases and 34791 controls was performed. Odds ratio (OR and 95% confidence interval (95% CI were used to investigate the strength of the association.Overall, the pooled analysis showed that mir-196a2 rs11614913 was associated with a decreased cancer risk (OR = 0.846, P = 0.004, TT vs. CC while other miRNA SNPs showed no association with overall cancer risk. Subgroup analyses based on type of cancer and ethnicity were also performed, and results indicated that there was a strong association between miR-146a rs2910164 and overall cancer risk in Caucasian population under recessive model (OR = 1.274, 95%CI = 1.096-1.481, P = 0.002. Stratified analysis by cancer type also associated mir-196a2 rs11614913 with lung and colorectal cancer at allelic and genotypic level.The present meta-analysis suggests an important role of mir-196a2 rs11614913 polymorphism with overall cancer risk especially in Asian population. Further studies with large sample size are needed to evaluate and confirm this association.

  10. Insight on trace element detoxification in the Black-tailed Godwit (Limosa limosa) through genetic, enzymatic and metallothionein analyses

    International Nuclear Information System (INIS)

    Lucia, Magali; Bocher, Pierrick; Cosson, Richard P.; Churlaud, Carine; Robin, Frédéric; Bustamante, Paco

    2012-01-01

    Trace element concentrations (Ag, As, Cd, Co, Cr, Cu, Fe, Hg, Mn, Ni, Pb, Se, Zn) were investigated in the liver, kidneys, muscle and feathers of 31 black-tailed godwits (Limosa limosa) accidentally killed during catches by mist net in the Pertuis Charentais, Atlantic coast of France. Analyses of carbon and nitrogen stable isotope ratios were carried out in liver, muscle and feathers in order to elucidate dietary patterns and to determine whether differences in diet explained the variation in elemental uptake. This study also aimed to have a preliminary assessment of sub-lethal effects triggered by trace elements through the investigation of gene expressions by quantitative real-time PCR, antioxidant enzyme activities (catalase, superoxide dismutase, glutathione peroxidase), and metallothionein (MT) levels. The results showed that Cr and Ni concentrations in tissues of adults were lower than in juveniles in part because adults may have eliminated these trace elements through moulting. Except for Cd and Ni, trace element concentrations were negatively correlated to the body mass of godwits. Ag, As, Hg and Se concentrations were positively linked with the trophic position of birds. The diet could be considered as a fundamental route of exposure for these elements demonstrating therefore the qualitative linkage between dietary habits of godwits and their contaminant concentrations. Our results strongly suggest that even though trace element concentrations were mostly below toxicity threshold level, the elevated concentrations of As, Ag, Cd, Cu, Fe and Se may however trigger sub-lethal effects. Trace elements appear to enhance expression of genes involved in oxidative stress defence, which indicates the production of reactive oxygen species. Moreover, birds with the highest concentrations appeared to have an increased mitochondrial metabolism suggesting that the fight against trace element toxicity requires additional energetic needs notably to produce detoxification

  11. Insight on trace element detoxification in the Black-tailed Godwit (Limosa limosa) through genetic, enzymatic and metallothionein analyses

    Energy Technology Data Exchange (ETDEWEB)

    Lucia, Magali, E-mail: m.lucia33@laposte.net [Littoral, Environnement et Societes (LIENSs), UMR 7266 CNRS-Universite de La Rochelle, 2 rue Olympe de Gouges, 17000 La Rochelle (France); Bocher, Pierrick [Littoral, Environnement et Societes (LIENSs), UMR 7266 CNRS-Universite de La Rochelle, 2 rue Olympe de Gouges, 17000 La Rochelle (France); Cosson, Richard P. [Mer Molecules Sante (MMS), Universite de Nantes, EA 2663, 2 rue de la Houssiniere, BP 92208, 44322 Nantes Cedex 3 (France); Churlaud, Carine; Robin, Frederic; Bustamante, Paco [Littoral, Environnement et Societes (LIENSs), UMR 7266 CNRS-Universite de La Rochelle, 2 rue Olympe de Gouges, 17000 La Rochelle (France)

    2012-04-15

    Trace element concentrations (Ag, As, Cd, Co, Cr, Cu, Fe, Hg, Mn, Ni, Pb, Se, Zn) were investigated in the liver, kidneys, muscle and feathers of 31 black-tailed godwits (Limosa limosa) accidentally killed during catches by mist net in the Pertuis Charentais, Atlantic coast of France. Analyses of carbon and nitrogen stable isotope ratios were carried out in liver, muscle and feathers in order to elucidate dietary patterns and to determine whether differences in diet explained the variation in elemental uptake. This study also aimed to have a preliminary assessment of sub-lethal effects triggered by trace elements through the investigation of gene expressions by quantitative real-time PCR, antioxidant enzyme activities (catalase, superoxide dismutase, glutathione peroxidase), and metallothionein (MT) levels. The results showed that Cr and Ni concentrations in tissues of adults were lower than in juveniles in part because adults may have eliminated these trace elements through moulting. Except for Cd and Ni, trace element concentrations were negatively correlated to the body mass of godwits. Ag, As, Hg and Se concentrations were positively linked with the trophic position of birds. The diet could be considered as a fundamental route of exposure for these elements demonstrating therefore the qualitative linkage between dietary habits of godwits and their contaminant concentrations. Our results strongly suggest that even though trace element concentrations were mostly below toxicity threshold level, the elevated concentrations of As, Ag, Cd, Cu, Fe and Se may however trigger sub-lethal effects. Trace elements appear to enhance expression of genes involved in oxidative stress defence, which indicates the production of reactive oxygen species. Moreover, birds with the highest concentrations appeared to have an increased mitochondrial metabolism suggesting that the fight against trace element toxicity requires additional energetic needs notably to produce detoxification

  12. Genetically Predicted Body Mass Index and Breast Cancer Risk: Mendelian Randomization Analyses of Data from 145,000 Women of European Descent.

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    Yan Guo

    2016-08-01

    Full Text Available Observational epidemiological studies have shown that high body mass index (BMI is associated with a reduced risk of breast cancer in premenopausal women but an increased risk in postmenopausal women. It is unclear whether this association is mediated through shared genetic or environmental factors.We applied Mendelian randomization to evaluate the association between BMI and risk of breast cancer occurrence using data from two large breast cancer consortia. We created a weighted BMI genetic score comprising 84 BMI-associated genetic variants to predicted BMI. We evaluated genetically predicted BMI in association with breast cancer risk using individual-level data from the Breast Cancer Association Consortium (BCAC (cases  =  46,325, controls  =  42,482. We further evaluated the association between genetically predicted BMI and breast cancer risk using summary statistics from 16,003 cases and 41,335 controls from the Discovery, Biology, and Risk of Inherited Variants in Breast Cancer (DRIVE Project. Because most studies measured BMI after cancer diagnosis, we could not conduct a parallel analysis to adequately evaluate the association of measured BMI with breast cancer risk prospectively.In the BCAC data, genetically predicted BMI was found to be inversely associated with breast cancer risk (odds ratio [OR]  =  0.65 per 5 kg/m2 increase, 95% confidence interval [CI]: 0.56-0.75, p = 3.32 × 10-10. The associations were similar for both premenopausal (OR   =   0.44, 95% CI:0.31-0.62, p  =  9.91 × 10-8 and postmenopausal breast cancer (OR  =  0.57, 95% CI: 0.46-0.71, p  =  1.88 × 10-8. This association was replicated in the data from the DRIVE consortium (OR  =  0.72, 95% CI: 0.60-0.84, p   =   1.64 × 10-7. Single marker analyses identified 17 of the 84 BMI-associated single nucleotide polymorphisms (SNPs in association with breast cancer risk at p < 0.05; for 16 of them, the

  13. Genetic basis for spontaneous hybrid genome doubling during allopolyploid speciation of common wheat shown by natural variation analyses of the paternal species.

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    Yoshihiro Matsuoka

    Full Text Available The complex process of allopolyploid speciation includes various mechanisms ranging from species crosses and hybrid genome doubling to genome alterations and the establishment of new allopolyploids as persisting natural entities. Currently, little is known about the genetic mechanisms that underlie hybrid genome doubling, despite the fact that natural allopolyploid formation is highly dependent on this phenomenon. We examined the genetic basis for the spontaneous genome doubling of triploid F1 hybrids between the direct ancestors of allohexaploid common wheat (Triticum aestivum L., AABBDD genome, namely Triticumturgidum L. (AABB genome and Aegilopstauschii Coss. (DD genome. An Ae. tauschii intraspecific lineage that is closely related to the D genome of common wheat was identified by population-based analysis. Two representative accessions, one that produces a high-genome-doubling-frequency hybrid when crossed with a T. turgidum cultivar and the other that produces a low-genome-doubling-frequency hybrid with the same cultivar, were chosen from that lineage for further analyses. A series of investigations including fertility analysis, immunostaining, and quantitative trait locus (QTL analysis showed that (1 production of functional unreduced gametes through nonreductional meiosis is an early step key to successful hybrid genome doubling, (2 first division restitution is one of the cytological mechanisms that cause meiotic nonreduction during the production of functional male unreduced gametes, and (3 six QTLs in the Ae. tauschii genome, most of which likely regulate nonreductional meiosis and its subsequent gamete production processes, are involved in hybrid genome doubling. Interlineage comparisons of Ae. tauschii's ability to cause hybrid genome doubling suggested an evolutionary model for the natural variation pattern of the trait in which non-deleterious mutations in six QTLs may have important roles. The findings of this study demonstrated

  14. Range extension for the common dolphin (Delphinus sp. to the Colombian Caribbean, with taxonomic implications from genetic barcoding and phylogenetic analyses.

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    Nohelia Farías-Curtidor

    Full Text Available The nearest known population of common dolphins (Delphinus sp. to the Colombian Caribbean occurs in a fairly restricted range in eastern Venezuela. These dolphins have not been previously reported in the Colombian Caribbean, likely because of a lack of study of the local cetacean fauna. We collected cetacean observations in waters of the Guajira Department, northern Colombia (~11°N, 73°W during two separate efforts: (a a seismic vessel survey (December 2009-March 2010, and (b three coastal surveys from small boats (May-July 2012, May 2013, and May 2014. Here we document ten sightings of common dolphins collected during these surveys, which extend the known range of the species by ~1000 km into the southwestern Caribbean. We also collected nine skin biopsies in 2013 and 2014. In order to determine the taxonomic identity of the specimens, we conducted genetic barcoding and phylogenetic analyses using two mitochondrial markers, the Control Region (mtDNA and Cytochrome b (Cytb. Results indicate that these specimens are genetically closer to the short-beaked common dolphin (Delphinus delphis even though morphologically they resemble a long-beaked form (Delphinus sp.. However, the specific taxonomic status of common dolphins in the Caribbean and in the Western Atlantic remains unresolved. It is also unclear whether the distribution of the species between northern Colombia and eastern Venezuela is continuous or disjoined, or whether they can be considered part of the same stock.

  15. Comprehensive genetic analyses reveal evolutionary distinction of a mouse (Zapus hudsonius preblei) proposed for delisting from the US Endangered Species Act.

    Science.gov (United States)

    King, Tim L; Switzer, John F; Morrison, Cheryl L; Eackles, Michael S; Young, Colleen C; Lubinski, Barbara A; Cryan, Paul

    2006-12-01

    Zapus hudsonius preblei, listed as threatened under the US Endangered Species Act (ESA), is one of 12 recognized subspecies of meadow jumping mice found in North America. Recent morphometric and phylogenetic comparisons among Z. h. preblei and neighbouring conspecifics questioned the taxonomic status of selected subspecies, resulting in a proposal to delist the Z. h. preblei from the ESA. We present additional analyses of the phylogeographic structure within Z. hudsonius that calls into question previously published data (and conclusions) and confirms the original taxonomic designations. A survey of 21 microsatellite DNA loci and 1380 base pairs from two mitochondrial DNA (mtDNA) regions (control region and cytochrome b) revealed that each Z. hudsonius subspecies is genetically distinct. These data do not support the null hypothesis of a homogeneous gene pool among the five subspecies found within the southwestern portion of the species' range. The magnitude of the observed differentiation was considerable and supported by significant findings for nearly every statistical comparison made, regardless of the genome or the taxa under consideration. Structuring of nuclear multilocus genotypes and subspecies-specific mtDNA haplotypes corresponded directly with the disjunct distributions of the subspecies investigated. Given the level of correspondence between the observed genetic population structure and previously proposed taxonomic classification of subspecies (based on the geographic separation and surveys of morphological variation), we conclude that the nominal subspecies surveyed in this study do not warrant synonymy, as has been proposed for Z. h. preblei, Z. h. campestris, and Z. h. intermedius.

  16. White matter lesion progression

    DEFF Research Database (Denmark)

    Hofer, Edith; Cavalieri, Margherita; Bis, Joshua C

    2015-01-01

    10 cohorts. To assess the relative contribution of genetic factors to progression of WML, we compared in 7 cohorts risk models including demographics, vascular risk factors plus single-nucleotide polymorphisms that have been shown to be associated cross-sectionally with WML in the current......BACKGROUND AND PURPOSE: White matter lesion (WML) progression on magnetic resonance imaging is related to cognitive decline and stroke, but its determinants besides baseline WML burden are largely unknown. Here, we estimated heritability of WML progression, and sought common genetic variants...... associated with WML progression in elderly participants from the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) consortium. METHODS: Heritability of WML progression was calculated in the Framingham Heart Study. The genome-wide association study included 7773 elderly participants from...

  17. Giant Galápagos tortoises; molecular genetic analyses identify a trans-island hybrid in a repatriation program of an endangered taxon

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    Caccone Adalgisa

    2007-02-01

    Full Text Available Abstract Background Giant Galápagos tortoises on the island of Española have been the focus of an intensive captive breeding-repatriation programme for over 35 years that saved the taxon from extinction. However, analysis of 118 samples from released individuals indicated that the bias sex ratio and large variance in reproductive success among the 15 breeders has severely reduced the effective population size (Ne. Results We report here that an analysis of an additional 473 captive-bred tortoises released back to the island reveals an individual (E1465 that exhibits nuclear microsatellite alleles not found in any of the 15 breeders. Statistical analyses incorporating genotypes of 304 field-sampled individuals from all populations on the major islands indicate that E1465 is most probably a hybrid between an Española female tortoise and a male from the island of Pinzón, likely present on Española due to human transport. Conclusion Removal of E1465 as well as its father and possible (half-siblings is warranted to prevent further contamination within this taxon of particular conservation significance. Despite this detected single contamination, it is highly noteworthy to emphasize the success of this repatriation program conducted over nearly 40 years and involving release of over 2000 captive-bred tortoises that now reproduce in situ. The incorporation of molecular genetic analysis of the program is providing guidance that will aid in monitoring the genetic integrity of this ambitious effort to restore a unique linage of a spectacular animal.

  18. SDMtoolbox 2.0: the next generation Python-based GIS toolkit for landscape genetic, biogeographic and species distribution model analyses

    Directory of Open Access Journals (Sweden)

    Jason L. Brown

    2017-12-01

    Full Text Available SDMtoolbox 2.0 is a software package for spatial studies of ecology, evolution, and genetics. The release of SDMtoolbox 2.0 allows researchers to use the most current ArcGIS software and MaxEnt software, and reduces the amount of time that would be spent developing common solutions. The central aim of this software is to automate complicated and repetitive spatial analyses in an intuitive graphical user interface. One core tenant facilitates careful parameterization of species distribution models (SDMs to maximize each model’s discriminatory ability and minimize overfitting. This includes carefully processing of occurrence data, environmental data, and model parameterization. This program directly interfaces with MaxEnt, one of the most powerful and widely used species distribution modeling software programs, although SDMtoolbox 2.0 is not limited to species distribution modeling or restricted to modeling in MaxEnt. Many of the SDM pre- and post-processing tools have ‘universal’ analogs for use with any modeling software. The current version contains a total of 79 scripts that harness the power of ArcGIS for macroecology, landscape genetics, and evolutionary studies. For example, these tools allow for biodiversity quantification (such as species richness or corrected weighted endemism, generation of least-cost paths and corridors among shared haplotypes, assessment of the significance of spatial randomizations, and enforcement of dispersal limitations of SDMs projected into future climates—to only name a few functions contained in SDMtoolbox 2.0. Lastly, dozens of generalized tools exists for batch processing and conversion of GIS data types or formats, which are broadly useful to any ArcMap user.

  19. Genetic Structuration, Demography and Evolutionary History of Mycobacterium tuberculosis LAM9 Sublineage in the Americas as Two Distinct Subpopulations Revealed by Bayesian Analyses

    Science.gov (United States)

    Reynaud, Yann; Millet, Julie; Rastogi, Nalin

    2015-01-01

    Tuberculosis (TB) remains broadly present in the Americas despite intense global efforts for its control and elimination. Starting from a large dataset comprising spoligotyping (n = 21183 isolates) and 12-loci MIRU-VNTRs data (n = 4022 isolates) from a total of 31 countries of the Americas (data extracted from the SITVIT2 database), this study aimed to get an overview of lineages circulating in the Americas. A total of 17119 (80.8%) strains belonged to the Euro-American lineage 4, among which the most predominant genotypic family belonged to the Latin American and Mediterranean (LAM) lineage (n = 6386, 30.1% of strains). By combining classical phylogenetic analyses and Bayesian approaches, this study revealed for the first time a clear genetic structuration of LAM9 sublineage into two subpopulations named LAM9C1 and LAM9C2, with distinct genetic characteristics. LAM9C1 was predominant in Chile, Colombia and USA, while LAM9C2 was predominant in Brazil, Dominican Republic, Guadeloupe and French Guiana. Globally, LAM9C2 was characterized by higher allelic richness as compared to LAM9C1 isolates. Moreover, LAM9C2 sublineage appeared to expand close to twenty times more than LAM9C1 and showed older traces of expansion. Interestingly, a significant proportion of LAM9C2 isolates presented typical signature of ancestral LAM-RDRio MIRU-VNTR type (224226153321). Further studies based on Whole Genome Sequencing of LAM strains will provide the needed resolution to decipher the biogeographical structure and evolutionary history of this successful family. PMID:26517715

  20. SDMtoolbox 2.0: the next generation Python-based GIS toolkit for landscape genetic, biogeographic and species distribution model analyses.

    Science.gov (United States)

    Brown, Jason L; Bennett, Joseph R; French, Connor M

    2017-01-01

    SDMtoolbox 2.0 is a software package for spatial studies of ecology, evolution, and genetics. The release of SDMtoolbox 2.0 allows researchers to use the most current ArcGIS software and MaxEnt software, and reduces the amount of time that would be spent developing common solutions. The central aim of this software is to automate complicated and repetitive spatial analyses in an intuitive graphical user interface. One core tenant facilitates careful parameterization of species distribution models (SDMs) to maximize each model's discriminatory ability and minimize overfitting. This includes carefully processing of occurrence data, environmental data, and model parameterization. This program directly interfaces with MaxEnt, one of the most powerful and widely used species distribution modeling software programs, although SDMtoolbox 2.0 is not limited to species distribution modeling or restricted to modeling in MaxEnt. Many of the SDM pre- and post-processing tools have 'universal' analogs for use with any modeling software. The current version contains a total of 79 scripts that harness the power of ArcGIS for macroecology, landscape genetics, and evolutionary studies. For example, these tools allow for biodiversity quantification (such as species richness or corrected weighted endemism), generation of least-cost paths and corridors among shared haplotypes, assessment of the significance of spatial randomizations, and enforcement of dispersal limitations of SDMs projected into future climates-to only name a few functions contained in SDMtoolbox 2.0. Lastly, dozens of generalized tools exists for batch processing and conversion of GIS data types or formats, which are broadly useful to any ArcMap user.

  1. Using genetics to test the causal relationship of total adiposity and periodontitis: Mendelian randomization analyses in the Gene-Lifestyle Interactions and Dental Endpoints (GLIDE) Consortium

    Science.gov (United States)

    Shungin, Dmitry; Cornelis, Marilyn C; Divaris, Kimon; Holtfreter, Birte; Shaffer, John R; Yu, Yau-Hua; Barros, Silvana P; Beck, James D; Biffar, Reiner; Boerwinkle, Eric A; Crout, Richard J.; Ganna, Andrea; Hallmans, Goran; Hindy, George; Hu, Frank B; Kraft, Peter; McNeil, Daniel W; Melander, Olle; Moss, Kevin L; North, Kari E; Orho-Melander, Marju; Pedersen, Nancy L; Ridker, Paul M; Rimm, Eric B; Rose, Lynda M; Rukh, Gull; Teumer, Alexander; Weyant, Robert J; Chasman, Daniel I; Joshipura, Kaumudi; Kocher, Thomas; Magnusson, Patrik KE; Marazita, Mary L; Nilsson, Peter; Offenbacher, Steve; Davey Smith, George; Lundberg, Pernilla; Palmer, Tom M; Timpson, Nicholas J; Johansson, Ingegerd; Franks, Paul W

    2015-01-01

    Background: The observational relationship between obesity and periodontitis is widely known, yet causal evidence is lacking. Our objective was to investigate causal associations between periodontitis and body mass index (BMI). Methods: We performed Mendelian randomization analyses with BMI-associated loci combined in a genetic risk score (GRS) as the instrument for BMI. All analyses were conducted within the Gene-Lifestyle Interactions and Dental Endpoints (GLIDE) Consortium in 13 studies from Europe and the USA, including 49 066 participants with clinically assessed (seven studies, 42.1% of participants) and self-reported (six studies, 57.9% of participants) periodontitis and genotype data (17 672/31 394 with/without periodontitis); 68 761 participants with BMI and genotype data; and 57 871 participants (18 881/38 990 with/without periodontitis) with data on BMI and periodontitis. Results: In the observational meta-analysis of all participants, the pooled crude observational odds ratio (OR) for periodontitis was 1.13 [95% confidence interval (CI): 1.03, 1.24] per standard deviation increase of BMI. Controlling for potential confounders attenuated this estimate (OR = 1.08; 95% CI:1.03, 1.12). For clinically assessed periodontitis, corresponding ORs were 1.25 (95% CI: 1.10, 1.42) and 1.13 (95% CI: 1.10, 1.17), respectively. In the genetic association meta-analysis, the OR for periodontitis was 1.01 (95% CI: 0.99, 1.03) per GRS unit (per one effect allele) in all participants and 1.00 (95% CI: 0.97, 1.03) in participants with clinically assessed periodontitis. The instrumental variable meta-analysis of all participants yielded an OR of 1.05 (95% CI: 0.80, 1.38) per BMI standard deviation, and 0.90 (95% CI: 0.56, 1.46) in participants with clinical data. Conclusions: Our study does not support total adiposity as a causal risk factor for periodontitis, as the point estimate is very close to the null in the causal inference analysis, with wide

  2. Investigation of 305 patients with myelodysplastic syndromes and 20q deletion for associated cytogenetic and molecular genetic lesions and their prognostic impact.

    Science.gov (United States)

    Bacher, Ulrike; Haferlach, Torsten; Schnittger, Susanne; Zenger, Melanie; Meggendorfer, Manja; Jeromin, Sabine; Roller, Andreas; Grossmann, Vera; Krauth, Maria-Theresa; Alpermann, Tamara; Kern, Wolfgang; Haferlach, Claudia

    2014-03-01

    In patients with myelodysplastic syndromes (MDS), sole 20q deletion [del(20q)] is a recurrent favourable abnormality. We studied additional molecular and cytogenetic lesions and their prognostic impact in 305 MDS patients with del(20q) (229 males/76 females; 29-90 years). All patients were investigated by cytomorphology and chromosome banding analysis (CBA), subsets by fluorescence in situ hybridization, molecular mutation screening, and array comparative genomic hybridization (aCGH). By aCGH (n = 30), the minimal common deleted region (CDR) was flanked by PTPRT (20q13·11) and EYA2 (20q13·12). 210 (68·9%) patients had 'early MDS' without blast increase, 95 (31·1%) 'advanced' MDS with blast increase (5-19%). Additional chromosomal abnormalities (ACAs) were detected in 88/305 (28·9%) patients. Patients with advanced MDS more frequently had ACAs (P = 0·003) and had a higher mean number of ACAs (P = 0·020) and of molecular mutations (P = 0·060). Spliceosome mutations were frequent (U2AF1: n = 31/155; 20·0%; SRSF2: n = 31/159; 19·5%; SF3B1mut: n = 8/159; 5·0%). ASXL1mut (25/153; 16·3%) were associated with advanced MDS (P = 0·001). Presence of ≥3 ACAs (P = 0·003) and ASXL1mut (P = 0·002) were associated with worse 2-year survival. In conclusion, the cytogenetic subgroup of MDS with del(20q) has a good prognosis but may be further subclassified by additional cytogenetic and molecular lesions. U2AF1mut is overrepresented in MDS with del(20q), and ASXL1mut is prognostically adverse. © 2013 John Wiley & Sons Ltd.

  3. Population differentiation of the shore crab Carcinus maenas (Brachyura: Portunidae on the southwest English coast based on genetic and morphometric analyses

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    Inês C. Silva

    2010-08-01

    Full Text Available Carcinus maenas has a planktonic larval phase which can potentially disperse over large distances. Consequently, larval transport is expected to play an important role in promoting gene flow and determining population structure. In the present study, population structuring on the southwest coast of England was analysed using molecular and morphometric approaches. Variation at eight microsatellite loci suggested that the individuals sampled within this region comprise a single genetic population and that gene flow among them is not restricted. Nevertheless, the FST values estimated across loci for all populations suggested that the Tamar population was significantly different from the Exe, Camel and Torridge populations. This differentiation is not explained by isolation by distance, and coastal hydrological events that are apparently influencing larval flux might be the cause of this pattern. Morphometric analysis was also performed. Analysis of carapace and chela shape variation using landmark-based geometric morphometrics revealed extensive morphological variability, as the multivariate analysis of variance showed significant morphometric differences among geographic groups for both sexes. Thus, the morphological differentiation found may be a plastic response to habitat-specific selection pressures.

  4. Premalignant Lesions in the Kidney

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    Ziva Kirkali

    2001-01-01

    Full Text Available Renal cell carcinoma (RCC is the most malignant urologic disease. Different lesions, such as dysplasia in the tubules adjacent to RCC, atypical hyperplasia in the cyst epithelium of von Hippel-Lindau syndrome, and adenoma have been described for a number of years as possible premalignant changes or precursor lesions of RCC. In two recent papers, kidneys adjacent to RCC or removed from other causes were analyzed, and dysplastic lesions were identified and defined in detail. Currently renal intraepithelial neoplasia (RIN is the proposed term for classification. The criteria for a lesion to be defined as premalignant are (1 morphological similarity; (2 spatial association; (3 development of microinvasive carcinoma; (4 higher frequency, severity, and extent then invasive carcinoma; (5 progression to invasive cancer; and (6 similar genetic alterations. RIN resembles the neoplastic cells of RCC. There is spatial association. Progression to invasive carcinoma is described in experimental cancer models, and in some human renal tumors. Similar molecular alterations are found in some putative premalignant changes. The treatment for RCC is radical or partial nephrectomy. Preneoplastic lesions may remain in the renal remnant in patients treated by partial nephrectomy and may be the source of local recurrences. RIN seems to be a biologic precursor of some RCCs and warrants further investigation. Interpretation and reporting of these lesions would reveal important resources for the biological nature and clinical significance. The management of RIN diagnosed in a renal biopsy and partial nephrectomy needs to be answered.

  5. [Genetic diversity and subdivision parameters of Colias crocea Fourc. and C. erate Esp. (Lepidoptera, Pieridae) in Crimea according to allozyme and RAPD-PCR analyses].

    Science.gov (United States)

    Milovanov, A E; Simchuk, A P

    2008-01-01

    Some parameters of genetic diversity and subdivision were tested in syntopic Crimean populations of two species of the sulfur butterllies, Colias crocea Fourc. and C. erate Esp. by allozyme and RAPD-PCR analyses. Genetic diversity in each of the species compared appeared to be approximately equal: the portion of polimorphic loci P95 (99) is 67% for C. crocea and is 61% for C. erate. Paratypic forms of both species do not differ from nominative ones by parameters of genetic diversity. The mean expected heterozygosities (H'(e)) in the C. crocea, C. erate and their paratypic forms by the RAPD-PCD data are 24.3 +/- 4.4%, 21.7 +/- 4.2%, 26.4 +/- 4.1%, respectively. The observed heterozygosities by the allozyme data in other samples are considerably less than theoretically expected ones (H(o) = 15.6 +/- 3.3%, H(e) = 50.5 +/- 4.5% for C. crocea; H(o) = 17.95 +/- 6.15%, H(e) = 50.8 +/- 8% for C. erate, and H(o) = 24.2 +/- 7.5%, H(e) = 50.9 +/- 8.7% for paratypic forms, respectively). The mean observed heterozygosity in the paratypic forms of C. erate (f. androconiata, f. chrysodona, f. edusoides) is almost two times higher than that of the f. chlorodona and f. eratoides. Paratypic forms of both species differ from nominative ones (particularly from that of C. crocea) by the level of intrapopulation inbreeding and by the degree of gene flow (F = 0.691 for C. crocea, 0.646 for C. erate, and 0.524 for paratypic forms). One can suppose a significant gene exchange among adjacent populations of C. crocea and C. erate (Wright's F(ST) = 0.155 for 6 allozyme and 18 RAPD loci, Nm = 1.363). Nei's similarity coefficients (S) varies from 0.7554 among nominative C. crocea and C. erate (D(N) = 0.28) to 0.8092 among C. crocea and paratypic forms (D = 0.21) and to 0.8936 among C. erate and paratypic forms of both species (D(N) = 0.11). Paratypic forms with rounded valve margin preliminarily identified as C. crocea revealed a considerable degree of similarity to the paratypic forms of C

  6. Genetic and Informatic Analyses Implicate Kif12 as a Candidate Gene within the Mpkd2 Locus That Modulates Renal Cystic Disease Severity in the Cys1cpk Mouse.

    Directory of Open Access Journals (Sweden)

    Michal Mrug

    Full Text Available We have previously mapped the interval on Chromosome 4 for a major polycystic kidney disease modifier (Mpkd of the B6(Cg-Cys1cpk/J mouse model of recessive polycystic kidney disease (PKD. Informatic analyses predicted that this interval contains at least three individual renal cystic disease severity-modulating loci (Mpkd1-3. In the current study, we provide further validation of these predicted effects using a congenic mouse line carrying the entire CAST/EiJ (CAST-derived Mpkd1-3 interval on the C57BL/6J background. We have also generated a derivative congenic line with a refined CAST-derived Mpkd1-2 interval and demonstrated its dominantly-acting disease-modulating effects (e.g., 4.2-fold increase in total cyst area; p<0.001. The relative strength of these effects allowed the use of recombinants from these crosses to fine map the Mpkd2 effects to a <14 Mbp interval that contains 92 RefSeq sequences. One of them corresponds to the previously described positional Mpkd2 candidate gene, Kif12. Among the positional Mpkd2 candidates, only expression of Kif12 correlates strongly with the expression pattern of Cys1 across multiple anatomical nephron structures and developmental time points. Also, we demonstrate that Kif12 encodes a primary cilium-associated protein. Together, these data provide genetic and informatic validation of the predicted renal cystic disease-modulating effects of Mpkd1-3 loci and implicate Kif12 as the candidate locus for Mpkd2.

  7. X-chromosome SNP analyses in 11 human Mediterranean populations show a high overall genetic homogeneity except in North-west Africans (Moroccans)

    DEFF Research Database (Denmark)

    Tomas Mas, Carmen; Sanchez Sanchez, Juan Jose; Barbaro, Anna

    2008-01-01

    BACKGROUND: Due to its history, with a high number of migration events, the Mediterranean basin represents a challenging area for population genetic studies. A large number of genetic studies have been carried out in the Mediterranean area using different markers but no consensus has been reached...

  8. Fiber tract-specific white matter lesion severity Findings in late-life depression and by AGTR1 A1166C genotype.

    Science.gov (United States)

    Taylor, Warren D; Zhao, Zheen; Ashley-Koch, Allison; Payne, Martha E; Steffens, David C; Krishnan, Ranga R; Hauser, Elizabeth; MacFall, James R

    2013-02-01

    Past work demonstrated that late-life depression is associated with greater severity of ischemic cerebral hyperintense white matter lesions, particularly frontal lesions. However, these lesions are also associated with other neuropsychiatric deficits, so these clinical relationships may depend on which fiber tracts are damaged. We examined the ratio of lesion to nonlesioned white matter tissue within multiple fiber tracts between depressed and nondepressed elders. We also sought to determine if the AGTR1 A1166C and BDNF Val66Met polymorphisms contributed to vulnerability to lesion development in discrete tracts. The 3T structural MR images and blood samples for genetic analyses were acquired on 54 depressed and 37 nondepressed elders. Lesion maps were created through an automated tissue segmentation process and applied to a probabilistic white matter fiber tract atlas allowing for identification of the fraction of the tract occupied by lesion. The depressed cohort exhibited a significantly greater lesion ratio only in the left upper cingulum near the cingulate gyrus (F((1,86)) = 4.62, P = 0.0344), supporting past work implicating cingulate dysfunction in the pathogenesis of depression. In the 62 Caucasian subjects with genetic data, AGTR1 C1166 carriers exhibited greater lesion ratios across multiple tracts including the anterior thalamic radiation and inferior fronto-occipital fasciculus. In contrast, BDNF Met allele carriers exhibited greater lesion ratios only in the frontal corpus callosum. Although these findings did not survive correction for multiple comparisons, this study supports our hypothesis and provides preliminary evidence that genetic differences related to vascular disease may increase lesion vulnerability differentially across fiber tracts. Copyright © 2011 Wiley Periodicals, Inc.

  9. Mitochondrial control region I and microsatellite analyses of endangered Philippine hornbill species (Aves; Bucerotidae) detect gene flow between island populations and genetic diversity loss

    OpenAIRE

    Sammler, Svenja; Ketmaier, Valerio; Havenstein, Katja; Krause, Ulrike; Curio, Eberhard; Tiedemann, Ralph

    2012-01-01

    Abstract Background The Visayan Tarictic Hornbill (Penelopides panini) and the Walden’s Hornbill (Aceros waldeni) are two threatened hornbill species endemic to the western islands of the Visayas that constitute - between Luzon and Mindanao - the central island group of the Philippine archipelago. In order to evaluate their genetic diversity and to support efforts towards their conservation, we analyzed genetic variation in ~ 600 base pairs (bp) of the mitochondrial control region I and at 12...

  10. Mitochondrial control region I and microsatellite analyses of endangered Philippine hornbill species (Aves; Bucerotidae) detect gene flow between island populations and genetic diversity loss.

    Science.gov (United States)

    Sammler, Svenja; Ketmaier, Valerio; Havenstein, Katja; Krause, Ulrike; Curio, Eberhard; Tiedemann, Ralph

    2012-10-12

    The Visayan Tarictic Hornbill (Penelopides panini) and the Walden's Hornbill (Aceros waldeni) are two threatened hornbill species endemic to the western islands of the Visayas that constitute - between Luzon and Mindanao - the central island group of the Philippine archipelago. In order to evaluate their genetic diversity and to support efforts towards their conservation, we analyzed genetic variation in ~ 600 base pairs (bp) of the mitochondrial control region I and at 12-19 nuclear microsatellite loci. The sampling covered extant populations, still occurring only on two islands (P. panini: Panay and Negros, A. waldeni: only Panay), and it was augmented with museum specimens of extinct populations from neighboring islands. For comparison, their less endangered (= more abundant) sister taxa, the Luzon Tarictic Hornbill (P. manillae) from the Luzon and Polillo Islands and the Writhed Hornbill (A. leucocephalus) from Mindanao Island, were also included in the study. We reconstructed the population history of the two Penelopides species and assessed the genetic population structure of the remaining wild populations in all four species. Mitochondrial and nuclear data concordantly show a clear genetic separation according to the island of origin in both Penelopides species, but also unravel sporadic over-water movements between islands. We found evidence that deforestation in the last century influenced these migratory events. Both classes of markers and the comparison to museum specimens reveal a genetic diversity loss in both Visayan hornbill species, P. panini and A. waldeni, as compared to their more abundant relatives. This might have been caused by local extinction of genetically differentiated populations together with the dramatic decline in the abundance of the extant populations. We demonstrated a loss in genetic diversity of P. panini and A. waldeni as compared to their sister taxa P. manillae and A. leucocephalus. Because of the low potential for gene flow

  11. Systems Genetic Analyses Highlight a TGFβ-FOXO3 Dependent Striatal Astrocyte Network Conserved across Species and Associated with Stress, Sleep, and Huntington's Disease.

    Science.gov (United States)

    Scarpa, Joseph R; Jiang, Peng; Losic, Bojan; Readhead, Ben; Gao, Vance D; Dudley, Joel T; Vitaterna, Martha H; Turek, Fred W; Kasarskis, Andrew

    2016-07-01

    Recent systems-based analyses have demonstrated that sleep and stress traits emerge from shared genetic and transcriptional networks, and clinical work has elucidated the emergence of sleep dysfunction and stress susceptibility as early symptoms of Huntington's disease. Understanding the biological bases of these early non-motor symptoms may reveal therapeutic targets that prevent disease onset or slow disease progression, but the molecular mechanisms underlying this complex clinical presentation remain largely unknown. In the present work, we specifically examine the relationship between these psychiatric traits and Huntington's disease (HD) by identifying striatal transcriptional networks shared by HD, stress, and sleep phenotypes. First, we utilize a systems-based approach to examine a large publicly available human transcriptomic dataset for HD (GSE3790 from GEO) in a novel way. We use weighted gene coexpression network analysis and differential connectivity analyses to identify transcriptional networks dysregulated in HD, and we use an unbiased ranking scheme that leverages both gene- and network-level information to identify a novel astrocyte-specific network as most relevant to HD caudate. We validate this result in an independent HD cohort. Next, we computationally predict FOXO3 as a regulator of this network, and use multiple publicly available in vitro and in vivo experimental datasets to validate that this astrocyte HD network is downstream of a signaling pathway important in adult neurogenesis (TGFβ-FOXO3). We also map this HD-relevant caudate subnetwork to striatal transcriptional networks in a large (n = 100) chronically stressed (B6xA/J)F2 mouse population that has been extensively phenotyped (328 stress- and sleep-related measurements), and we show that this striatal astrocyte network is correlated to sleep and stress traits, many of which are known to be altered in HD cohorts. We identify causal regulators of this network through Bayesian network

  12. Comparative analyses of genetic/epigenetic diversities and structures in a wild barley species (Hordeum brevisubulatum) using MSAP, SSAP and AFLP.

    Science.gov (United States)

    Shan, X H; Li, Y D; Liu, X M; Wu, Y; Zhang, M Z; Guo, W L; Liu, B; Yuan, Y P

    2012-08-17

    We analyzed genetic diversity and population genetic structure of four artificial populations of wild barley (Hordeum brevisubulatum); 96 plants collected from the Songnen Prairie in northeastern China were analyzed using amplified fragment length polymorphism (AFLP), specific-sequence amplified polymorphism (SSAP) and methylation-sensitive amplified polymorphism (MSAP) markers. Indices of (epi-)genetic diversity, (epi-)genetic distance, gene flow, genotype frequency, cluster analysis, PCA analysis and AMOVA analysis generated from MSAP, AFLP and SSAP markers had the same trend. We found a high level of correlation in the artificial populations between MSAP, SSAP and AFLP markers by the Mantel test (r > 0.8). This is incongruent with previous findings showing that there is virtually no correlation between DNA methylation polymorphism and classical genetic variation; the high level of genetic polymorphism could be a result of epigenetic regulation. We compared our results with data from natural populations. The population diversity of the artificial populations was lower. However, different from what was found using AFLP and SSAP, based on MSAP results the methylation polymorphism of the artificial populations was not significantly reduced. This leads us to suggest that the DNA methylation pattern change in H. brevisubulatum populations is not only related to DNA sequence variation, but is also regulated by other controlling systems.

  13. FFA STUDY OF MACULAR LESIONS

    Directory of Open Access Journals (Sweden)

    K. Vinayagamurthy

    2017-08-01

    Full Text Available BACKGROUND Macula is an important portion of retina that occupies the posterior pole of retina. Any disease that affects macula results in significant loss of central vision, form vision and colour vision to an extent. Macular lesions can be hereditary as well as acquired. Macular lesions occur in both younger and older individuals. Anatomically, a macular lesions can vary from a simple lesion like an RPF defect to a vision-threatening lesions like choroidal neovascular membrane. Many screening tests that are sensitive and specific are available to assess the functioning of macula called as ‘macular function test’. But, the greater understanding of the retinal vascular led to the usage of fluorescein angiogram in the detection and screening of macular, retinovascular and optic disc lesions. Through fundus fluorescein angiogram is a thirty-year-old procedure; it is still in vogue in almost all parts of the world. It has its own merits. The aim of the study is to study the role of fluorescein angiography in the evaluation of macular lesions. MATERIALS AND METHODS A hospital-based prospective randomised study was done, which included 50 patients. Detailed patient history was taken and thorough ocular and systemic examination was done. All patients were examined by ophthalmoscopy (direct and indirect and slit-lamp examination with 90D followed by fluorescein angiography. Ophthalmoscopic and fluorescein angiography findings were analysed and categorised. Patients were advised proper ocular and systemic treatment and follow up. RESULTS 50 cases with macular lesions were analysed and categorised into conditions like ARMD, CSR, macular oedema, CME, degenerations and dystrophies and miscellaneous conditions. FFA altered the diagnosis in 8% cases and categorised the cases in all cases. 16% patients developed adverse reactions like allergy, vomiting and nausea. On statistical analysis, FFA proved to be cheap and superior diagnostic tool in confirming

  14. A Multi-Faceted Approach to Analyse the Effects of Environmental Variables on Geographic Range and Genetic Structure of a Perennial Psammophilous Geophyte: The Case of the Sea Daffodil Pancratium maritimum L. in the Mediterranean Basin.

    Directory of Open Access Journals (Sweden)

    Olga De Castro

    Full Text Available The Mediterranean coastline is a dynamic and complex system which owes its complexity to its past and present vicissitudes, e.g. complex tectonic history, climatic fluctuations, and prolonged coexistence with human activities. A plant species that is widespread in this habitat is the sea daffodil, Pancratium maritimum (Amaryllidaceae, which is a perennial clonal geophyte of the coastal sands of the Mediterranean and neighbouring areas, well adapted to the stressful conditions of sand dune environments. In this study, an integrated approach was used, combining genetic and environmental data with a niche modelling approach, aimed to investigate: (1 the effect of climate change on the geographic range of this species at different times {past (last inter-glacial, LIG; and last glacial maximum, LGM, present (CURR, near-future (FUT} and (2 the possible influence of environmental variables on the genetic structure of this species in the current period. The genetic results show that 48 sea daffodil populations (867 specimens display a good genetic diversity in which the marginal populations (i.e. Atlantic Sea populations present lower values. Recent genetic signature of bottleneck was detected in few populations (8%. The molecular variation was higher within the populations (77% and two genetic pools were well represented. Comparing the different climatic simulations in time, the global range of this plant increased, and a further extension is foreseen in the near future thanks to projections on the climate of areas currently-more temperate, where our model suggested a forecast for a climate more similar to the Mediterranean coast. A significant positive correlation was observed between the genetic distance and Precipitation of Coldest Quarter variable in current periods. Our analyses support the hypothesis that geomorphology of the Mediterranean coasts, sea currents, and climate have played significant roles in shaping the current genetic structure of

  15. A Multi-Faceted Approach to Analyse the Effects of Environmental Variables on Geographic Range and Genetic Structure of a Perennial Psammophilous Geophyte: The Case of the Sea Daffodil Pancratium maritimum L. in the Mediterranean Basin.

    Science.gov (United States)

    De Castro, Olga; Di Maio, Antonietta; Di Febbraro, Mirko; Imparato, Gennaro; Innangi, Michele; Véla, Errol; Menale, Bruno

    2016-01-01

    The Mediterranean coastline is a dynamic and complex system which owes its complexity to its past and present vicissitudes, e.g. complex tectonic history, climatic fluctuations, and prolonged coexistence with human activities. A plant species that is widespread in this habitat is the sea daffodil, Pancratium maritimum (Amaryllidaceae), which is a perennial clonal geophyte of the coastal sands of the Mediterranean and neighbouring areas, well adapted to the stressful conditions of sand dune environments. In this study, an integrated approach was used, combining genetic and environmental data with a niche modelling approach, aimed to investigate: (1) the effect of climate change on the geographic range of this species at different times {past (last inter-glacial, LIG; and last glacial maximum, LGM), present (CURR), near-future (FUT)} and (2) the possible influence of environmental variables on the genetic structure of this species in the current period. The genetic results show that 48 sea daffodil populations (867 specimens) display a good genetic diversity in which the marginal populations (i.e. Atlantic Sea populations) present lower values. Recent genetic signature of bottleneck was detected in few populations (8%). The molecular variation was higher within the populations (77%) and two genetic pools were well represented. Comparing the different climatic simulations in time, the global range of this plant increased, and a further extension is foreseen in the near future thanks to projections on the climate of areas currently-more temperate, where our model suggested a forecast for a climate more similar to the Mediterranean coast. A significant positive correlation was observed between the genetic distance and Precipitation of Coldest Quarter variable in current periods. Our analyses support the hypothesis that geomorphology of the Mediterranean coasts, sea currents, and climate have played significant roles in shaping the current genetic structure of the sea

  16. Common heritable effects underpin concerns over norm maintenance and in-group favoritism: evidence from genetic analyses of right-wing authoritarianism and traditionalism.

    Science.gov (United States)

    Lewis, Gary J; Bates, Timothy C

    2014-08-01

    Research has shown that in-group favoritism is associated with concerns over the maintenance of social norms. Here we present two studies examining whether genetic factors underpin this association. A classical twin design was used to decompose phenotypic variance into genetic and environmental components in two studies. Study 1 used 812 pairs of adult U.S. twins from the nationally representative MIDUS II sample. Study 2 used 707 pairs of middle-age twins from the Minnesota Twin Registry. In-group favoritism was measured with scales tapping preferences for in-group (vs. out-group) individuals; norm concerns were measured with the Multidimensional Personality Questionnaire-Traditionalism (Study 1) and Right-Wing Authoritarianism (RWA; Study 2) scales. In Study 1, heritable effects underlying traditionalism were moderately (c. 35%) overlapping with the genetic variance underpinning in-group favoritism. In Study 2, heritable influences on RWA were entirely shared with the heritable effects on in-group favoritism. Moreover, we observed that Big Five Openness shared common genetic links to both RWA and in-group favoritism. These results suggest that, at the genetic level, in-group favoritism is linked with a system related to concern over normative social practices, which is, in turn, partially associated with trait Openness. © 2013 Wiley Periodicals, Inc.

  17. Genetic analyses determine connectivity among cave and surface populations of the Jamaican endemic freshwater crab Sesarma fossarum in the Cockpit Country

    Directory of Open Access Journals (Sweden)

    Manuel Stemmer

    2016-01-01

    Full Text Available The Jamaican freshwater crab Sesarma fossarum (Decapoda: Brachyura: Sesarmidae is endemic to western central Jamaica where it occurs in cave and surface streams of karst regions. In the present study, we examine the population genetic structure of the species, providing evidence for intraspecific differentiation and genetic substructure among twelve sampled populations. Interestingly, crabs from caves appear genetically undistinguishable from representatives of nearby surface waters, despite previously observed and described morphometric differentiation. In contrast, genetic isolation takes place among populations from rivers and caves belonging to different watersheds. In one case, even populations from different tributaries of the same river were characterized by different genotypes. Overall, the species shows low haplotype and nucleotide diversities, which indicates a high homogeneity and point towards a relatively recent intraspecific radiation and diversification. Our results on the genetic diversification of S. fossarum helps to reconstruct unknown subterranean water flow and cave connections in its native range, allowing prediction of its further dispersal and differentiation potential. Unfortunately, its natural habitat of Jamaican cockpit karst, which also is home to several other endemic species and is a globally-recognized Key Biodiversity Area, is under imminent threat of intensive bauxite mining.

  18. Mitochondrial control region I and microsatellite analyses of endangered Philippine hornbill species (Aves; Bucerotidae detect gene flow between island populations and genetic diversity loss

    Directory of Open Access Journals (Sweden)

    Sammler Svenja

    2012-10-01

    Full Text Available Abstract Background The Visayan Tarictic Hornbill (Penelopides panini and the Walden’s Hornbill (Aceros waldeni are two threatened hornbill species endemic to the western islands of the Visayas that constitute - between Luzon and Mindanao - the central island group of the Philippine archipelago. In order to evaluate their genetic diversity and to support efforts towards their conservation, we analyzed genetic variation in ~ 600 base pairs (bp of the mitochondrial control region I and at 12–19 nuclear microsatellite loci. The sampling covered extant populations, still occurring only on two islands (P. panini: Panay and Negros, A. waldeni: only Panay, and it was augmented with museum specimens of extinct populations from neighboring islands. For comparison, their less endangered (= more abundant sister taxa, the Luzon Tarictic Hornbill (P. manillae from the Luzon and Polillo Islands and the Writhed Hornbill (A. leucocephalus from Mindanao Island, were also included in the study. We reconstructed the population history of the two Penelopides species and assessed the genetic population structure of the remaining wild populations in all four species. Results Mitochondrial and nuclear data concordantly show a clear genetic separation according to the island of origin in both Penelopides species, but also unravel sporadic over-water movements between islands. We found evidence that deforestation in the last century influenced these migratory events. Both classes of markers and the comparison to museum specimens reveal a genetic diversity loss in both Visayan hornbill species, P. panini and A. waldeni, as compared to their more abundant relatives. This might have been caused by local extinction of genetically differentiated populations together with the dramatic decline in the abundance of the extant populations. Conclusions We demonstrated a loss in genetic diversity of P. panini and A. waldeni as compared to their sister taxa P. manillae and A

  19. Combined use of mark-recapture and genetic analyses reveals response of a black bear population to changes in food productivity

    Science.gov (United States)

    Barbara S. McCall; Michael S. Mitchell; Michael K. Schwartz; Jim Hayden; Samuel A. Cushman; Pete Zager; Wayne F. Kasworm

    2013-01-01

    We used mark-recapture analysis to investigate the dynamics of a black bear (Ursus americanus) population in northern Idaho where food availability varies seasonally and annually. We conducted noninvasive genetic sampling (NGS) during 2003-2006 in the Purcell Mountains of Idaho to collect black bear DNA samples for individual identification of bears. We used a...

  20. Genetically Predicted Body Mass Index and Breast Cancer Risk : Mendelian Randomization Analyses of Data from 145,000 Women of European Descent

    NARCIS (Netherlands)

    Guo, Yan; Warren Andersen, Shaneda; Shu, Xiao-Ou; Michailidou, Kyriaki; Bolla, Manjeet K; Wang, Qin; Garcia-Closas, Montserrat; Milne, Roger L; Schmidt, Marjanka K; Chang-Claude, Jenny; Dunning, Allison; Bojesen, Stig E; Ahsan, Habibul; Aittomäki, Kristiina; Andrulis, Irene L; Anton-Culver, Hoda; Arndt, Volker; Beckmann, Matthias W; Beeghly-Fadiel, Alicia; Benitez, Javier; Bogdanova, Natalia V; Bonanni, Bernardo; Børresen-Dale, Anne-Lise; Brand, Judith; Brauch, Hiltrud; Brenner, Hermann; Brüning, Thomas; Burwinkel, Barbara; Casey, Graham; Chenevix-Trench, Georgia; Couch, Fergus J; Cox, Angela; Cross, Simon S; Czene, Kamila; Devilee, Peter; Dörk, Thilo; Dumont, Martine; Fasching, Peter A; Figueroa, Jonine; Flesch-Janys, Dieter; Fletcher, Olivia; Flyger, Henrik; Fostira, Florentia; Gammon, Marilie; Giles, Graham G; Guénel, Pascal; Haiman, Christopher A; Hamann, Ute; Hooning, Maartje J; Hopper, John L; Jakubowska, Anna; Jasmine, Farzana; Jenkins, Mark; John, Esther M; Johnson, Nichola; Jones, Michael E; Kabisch, Maria; Kibriya, Muhammad; Knight, Julia A; Koppert, Linetta B; Kosma, Veli-Matti; Kristensen, Vessela; Le Marchand, Loic; Lee, Eunjung; Li, Jingmei; Lindblom, Annika; Luben, Robert; Lubinski, Jan; Malone, Kathi E; Mannermaa, Arto; Margolin, Sara; Marme, Frederik; McLean, Catriona; Meijers-Heijboer, Hanne; Meindl, Alfons; Neuhausen, Susan L; Nevanlinna, Heli; Neven, Patrick; Olson, Janet E; Perez, Jose I A; Perkins, Barbara; Peterlongo, Paolo; Phillips, Kelly-Anne; Pylkäs, Katri; Rudolph, Anja; Santella, Regina; Sawyer, Elinor J; Schmutzler, Rita K; Seynaeve, Caroline; Shah, Mitul; Shrubsole, Martha J; Southey, Melissa C; Swerdlow, Anthony J; Toland, Amanda E; Tomlinson, Ian; Torres, Diana; Truong, Thérèse; Ursin, Giske; Van Der Luijt, Rob B; Verhoef, Senno; Whittemore, Alice S; Winqvist, Robert; Zhao, Hui; Zhao, Shilin; Hall, Per; Simard, Jacques; Kraft, Peter; Pharoah, Paul; Hunter, David; Easton, Douglas F; Zheng, Wei

    BACKGROUND: Observational epidemiological studies have shown that high body mass index (BMI) is associated with a reduced risk of breast cancer in premenopausal women but an increased risk in postmenopausal women. It is unclear whether this association is mediated through shared genetic or

  1. Cytogenic and molecular analyses of 46,XX male syndrome with clinical comparison to other groups with testicular azoospermia of genetic origin.

    Science.gov (United States)

    Chiang, Han-Sun; Wu, Yi-No; Wu, Chien-Chih; Hwang, Jiann-Loung

    2013-02-01

    XX male is a rare sex chromosomal disorder in infertile men. The purpose of this study was to distinguish the clinical and genetic features of the 46,XX male syndrome from other more frequent, testicular-origin azoospermic causes of male infertility. To study 46,XX male syndrome, we compared clinical and endocrinological parameters to other groups with testicular-origin azoospermia, and to an age-matched group of healthy males and females as normal control. Fluorescent in situ hybridization for detection and localization of the sex-determining region of the Y gene (SRY), array-based comparative genomic hybridization screening, and real-time qualitative polymerase chain reaction of FGF9, WT1, NR5A1, and SPRY2 genes were performed in this genetic investigation. Our three patients with 46,XX male syndrome had a much higher follicular-stimulating hormone level, lower body height, lower testosterone level, and ambiguous external genitalia. One of the three patients with 46,XX male syndrome was SRY-negative. A further genetic study, including a comparative genomic hybridization array and real-time polymerase chain reaction, showed a gain of FGF9 copy numbers only in the SRY-negative 46,XX male. The genetic copy number of the FGF9 gene was duplicated in that case compared to the normal female control and was significantly lower than that of the normal male control. No such genomic gain was observed in the case of the two SRY-positive 46,XX males. Similar to clinical manifestations of 46,XX male syndrome, genetic evidence in this study suggests that FGF9 may contribute to sex reversal, but additional confirmation with more cases is still needed. Copyright © 2012. Published by Elsevier B.V.

  2. Oropharynx lesion biopsy

    Science.gov (United States)

    ... as papilloma) Fungal infections (such as candida) Histoplasmosis Oral lichen planus Precancerous sore (leukoplakia) Viral infections (such as Herpes simplex) Risks Risks of the procedure may ... Throat lesion biopsy; Biopsy - mouth or throat; Mouth lesion biopsy; Oral cancer - biopsy ...

  3. Genetic variability and bottleneck analyses of Kanni adu goat population using microsatellite markers [Indian Veterinary Journal, 2015, 92(3): 24-27

    International Nuclear Information System (INIS)

    Thiruvenkadan, R.; Jeyakumar, M.; Saravana, R.; Periasamy, K.

    2016-01-01

    Full text: The genetic characterization and bottleneck analysis in Kodi Adu goat was done using 25 FAO recommended microsatellite markers. The mean observed number of alleles and polymorphism information content (PIC) were estimated to be 11.52±-0.95 and 0.817±0.023 respectively. The mean observed and expected equilibrium hyterozygosities were 0.660±0.045 and 0.846±0.018 respectively. The mean expected equilibrium gene diversity across 21 microsatellite loci under TAM, SMM and TPM were 0.793±0.028, 0.854±0.023 and 0.827±0.026 respectively. All the three statistical tests revealed significant deviation of Kodi Adu goats from mutation-drift equilibrium under the IAM and TPM model. The mode shift analysis supported the results under SMM indicating the absence of genetic bottleneck in the recent past in Kodi Adu goats. (author)

  4. Late Quaternary climatic vegetational shifts in an ecological transition zone of northern Madagascar: insights from genetic analyses of two endemic rodent species.

    Science.gov (United States)

    Rakotoarisoa, J-E; Raheriarisena, M; Goodman, S M

    2013-05-01

    The Loky-Manambato region, located in northern Madagascar, is a biotically rich contact zone between different forest biomes. Local current forest cover is composed of both humid and dry formations, which show elevational stratification. A recent phylogeographical study of a regional dry forest rodent, Eliurus carletoni (subfamily Nesomyinae), found genetic evidence of forest contractions between 18 750 and 7500 years BP, which based on extrapolation of the pollen subfossil record, was thought to be associated with an expansion of local humid forests. Herein, we conduct a genetic test of this hypothesis and focused on populations on two neighbouring massifs of forest-dependent rodent species, one associated with low-elevation dry forests (E. carletoni) and the other with higher elevation humid forests (Eliurus tanala). Using mitochondrial markers and a combination of traditional and coalescent-based phylogeographical, historical demographic and population genetic methods, we found evidence of historical connections between populations of E. tanala. Adjacent populations of E. carletoni and E. tanala exhibit opposite historical demographic patterns, and for both, evidence suggests that historical demographic events occurred within the last 25 000 years BP. These findings strongly support the proposed late Quaternary shifts in the floristic composition of the Loky-Manambato region. © 2013 The Authors. Journal of Evolutionary Biology © 2013 European Society For Evolutionary Biology.

  5. Landscape features influence gene flow as measured by cost-distance and genetic analyses: a case study for giant pandas in the Daxiangling and Xiaoxiangling Mountains

    Directory of Open Access Journals (Sweden)

    Wei Fuwen

    2010-07-01

    Full Text Available Abstract Background Gene flow maintains genetic diversity within a species and is influenced by individual behavior and the geographical features of the species' habitat. Here, we have characterized the geographical distribution of genetic patterns in giant pandas (Ailuropoda melanoleuca living in four isolated patches of the Xiaoxiangling and Daxiangling Mountains. Three geographic distance definitions were used with the "isolation by distance theory": Euclidean distance (EUD, least-cost path distance (LCD defined by food resources, and LCD defined by habitat suitability. Results A total of 136 genotypes were obtained from 192 fecal samples and one blood sample, corresponding to 53 unique genotypes. Geographical maps plotted at high resolution using smaller neighborhood radius definitions produced large cost distances, because smaller radii include a finer level of detail in considering each pixel. Mantel tests showed that most correlation indices, particularly bamboo resources defined for different sizes of raster cell, were slightly larger than the correlations calculated for the Euclidean distance, with the exception of Patch C. We found that natural barriers might have decreased gene flow between the Xiaoxiangling and Daxiangling regions. Conclusions Landscape features were found to partially influence gene flow in the giant panda population. This result is closely linked to the biological character and behavior of giant pandas because, as bamboo feeders, individuals spend most of their lives eating bamboo or moving within the bamboo forest. Landscape-based genetic analysis suggests that gene flow will be enhanced if the connectivity between currently fragmented bamboo forests is increased.

  6. Managing Carious Lesions

    DEFF Research Database (Denmark)

    Schwendicke, F; Frencken, J E; Bjørndal, L

    2016-01-01

    should be prioritized, while in shallow or moderately deep lesions, restoration longevity becomes more important. For teeth with shallow or moderately deep cavitated lesions, carious tissue removal is performed according toselective removal to firm dentine.In deep cavitated lesions in primary......The International Caries Consensus Collaboration undertook a consensus process and here presents clinical recommendations for carious tissue removal and managing cavitated carious lesions, including restoration, based on texture of demineralized dentine. Dentists should manage the disease dental...

  7. Periodontal bone lesions

    International Nuclear Information System (INIS)

    Linden, L.W.J. van der.

    1985-01-01

    In the course of life the periodontum is subject to changes which may be physiological or pathological. Intraoral radiographs give insight into the hard structures of the dentomaxillar region and provides information on lesions in the bone of the periodontum in that they show radiopacities and radiolucencies caused by such lesions. In this thesis the relation is investigated between the true shape and dimensions of periodontal bone lesions and their radiographic images. A method is developed and tested of making standardized and reproducible radiographs suitable for longitudinal studies of periodontal lesions. Also the possibility is demonstrated of an objective and reproducible interpretation of radiographic characteristics of periodontal bone lesions. (Auth.)

  8. Clinical-radiological, histological and genetic analyses in a lung transplant recipient with Mounier-Kuhn syndrome and end-stage chronic obstructive pulmonary disease.

    Science.gov (United States)

    Mitterbauer, Andreas; Hoetzenecker, Konrad; Birner, Peter; Mildner, Michael; Prosch, Helmut; Streubel, Berthold; Taghavi, Shahrokh; Klepetko, Walter; Ankersmit, Hendrik Jan

    2015-07-01

    The Mounier-Kuhn syndrome (MKS) is a rare disease characterized by a pathological dilation of the trachea and the bronchial system. The etiology of the disorder remains elusive, but genetic alterations and degradation of elastic fibers are thought to be involved in the pathogenesis. No causative treatment is available although transplantation is an option for end-stage disease. Here, we describe a patient suffering from MKS who received a double lung transplant at our department. Since a familial clustering of MKS is discussed in the literature, we performed a chromosomal analysis and an array-comparative genomic hybridization (CGH) to search for genetic abnormalities. At the time of transplantation, we collected samples from the bronchi and performed hematoxylin and eosin (HE), Elastic von-Gieson (EVG) and immunohistochemical stains of the explanted MKS bronchus, a control bronchus and of the inflammatory infiltrates. Specimens of main bronchi from the donor lung harvested for transplant served as control. Bronchial smears were taken from both main bronchi of the recipient for microbiological cultures. No genetic alterations could be found in chromosomal analysis and in array-CGH. Histological analysis revealed a strong reduction of elastic fibers in the submucosal connective tissue and a diffuse inflammatory infiltrate, mainly comprised of CD4+ cells. In addition, immunohistochemistry showed increased matrix metalloproteinases (MMPs) protein expression of MMP-1, 2, 3 and 9. Based on our findings, we hypothesize that MKS is a chronic inflammatory disease characterized by an MMP-mediated degradation of submucosal elastic fibers. © 2014 John Wiley & Sons Ltd.

  9. Classical genetic analyses of responses to sedative-hypnotic drugs in crosses derived from long-sleep and short-sleep mice.

    Science.gov (United States)

    de Fiebre, C M; Marley, R J; Miner, L L; de Fiebre, N E; Wehner, J M; Collins, A C

    1992-06-01

    A classical (Mendelian) genetic analysis of responses to eight sedative-hypnotic compounds (ethanol, urethane, trifluoroethanol, chloral hydrate, barbital, paraldehyde, methyprylon, pentobarbital) was conducted in crosses derived from mouse lines that were selectively bred for differential duration of anesthesia following ethanol. The sleep-time responses of these mice, the long-sleep (LS) and short-sleep (SS) mouse lines, as well as the F1, F2 and backcross (F1 x LS, F1 x SS) generations were measured. Generally, differences in responses among the generations were greater for water soluble compounds than were differences for more lipid soluble compounds. Also, the inheritance of responses to water soluble compounds could be explained primarily by additive effects of alleles while the inheritance patterns for more lipid soluble compounds were more complex. Genetic correlation with ethanol response decreased with increasing lipophilicity. These results suggest that the selection of the LS-SS mouse lines was specific for water soluble anesthetic agents. Because several of these agents are known to act at GABA receptors, examination of the interactions of compounds which differ in lipid solubility at GABA receptors from LS and SS mice may prove useful in elucidating the mechanism of the anesthetic actions of ethanol and other drugs.

  10. Molecular Comparison and Evolutionary Analyses of VP1 Nucleotide Sequences of New African Human Enterovirus 71 Isolates Reveal a Wide Genetic Diversity

    Science.gov (United States)

    Nougairède, Antoine; Joffret, Marie-Line; Deshpande, Jagadish M.; Dubot-Pérès, Audrey; Héraud, Jean-Michel

    2014-01-01

    Most circulating strains of Human enterovirus 71 (EV-A71) have been classified primarily into three genogroups (A to C) on the basis of genetic divergence between the 1D gene, which encodes the VP1 capsid protein. The aim of the present study was to provide further insights into the diversity of the EV-A71 genogroups following the recent description of highly divergent isolates, in particular those from African countries, including Madagascar. We classified recent EV-A71 isolates by a large comparison of 3,346 VP1 nucleotidic sequences collected from GenBank. Analysis of genetic distances and phylogenetic investigations indicated that some recently-reported isolates did not fall into the genogroups A-C and clustered into three additional genogroups, including one Indian genogroup (genogroup D) and 2 African ones (E and F). Our Bayesian phylogenetic analysis provided consistent data showing that the genogroup D isolates share a recent common ancestor with the members of genogroup E, while the isolates of genogroup F evolved from a recent common ancestor shared with the members of the genogroup B. Our results reveal the wide diversity that exists among EV-A71 isolates and suggest that the number of circulating genogroups is probably underestimated, particularly in developing countries where EV-A71 epidemiology has been poorly studied. PMID:24598878

  11. Myelin basic protein as a novel genetic risk factor in rheumatoid arthritis--a genome-wide study combined with immunological analyses.

    Directory of Open Access Journals (Sweden)

    Chikashi Terao

    Full Text Available Rheumatoid arthritis (RA is a major cause of adult chronic inflammatory arthritis and a typical complex trait. Although several genetic determinants have been identified, they account for only a part of the genetic susceptibility. We conducted a genome-wide association study of RA in Japanese using 225,079 SNPs genotyped in 990 cases and 1,236 controls from two independent collections (658 cases and 934 controls in collection1; 332 cases and 302 controls in collection2, followed by replication studies in two additional collections (874 cases and 855 controls in collection3; 1,264 cases and 948 controls in collection4. SNPs showing p<0.005 in the first two collections and p<10(-4 by meta-analysis were further genotyped in the latter two collections. A novel risk variant, rs2000811, in intron2 of the myelin basic protein (MBP at chromosome 18q23 showed strong association with RA (p = 2.7×10(-8, OR 1.23, 95% CI: 1.14-1.32. The transcription of MBP was significantly elevated with the risk allele compared to the alternative allele (p<0.001. We also established by immunohistochemistry that MBP was expressed in the synovial lining layer of RA patients, the main target of inflammation in the disease. Circulating autoantibody against MBP derived from human brain was quantified by ELISA between patients with RA, other connective tissue diseases and healthy controls. As a result, the titer of anti-MBP antibody was markedly higher in plasma of RA patients compared to healthy controls (p<0.001 and patients with other connective tissue disorders (p<0.001. ELISA experiment using citrullinated recombinant MBP revealed that a large fraction of anti-MBP antibody in RA patients recognized citrullinated MBP. This is the first report of a genetic study in RA implicating MBP as a potential autoantigen and its involvement in pathogenesis of the disease.

  12. Three genetic stocks of frigate tuna Auxis thazard thazard (Lacepede, 1800) along the Indian coast revealed from sequence analyses of mitochondrial DNA D-loop region

    Digital Repository Service at National Institute of Oceanography (India)

    GirishKumar; Kunal, S.P.; Menezes, M.R.; Meena, R.M.

    revealed from sequence analyses of mitochondrial DNA D-loop region Name of authors: 1. Girish Kumar* Biological Oceanography Division (BOD) National Institute of Oceanography (NIO) Dona Paula, Goa 403004, India. Email: girishkumar....nio@gmail.com Tel: +919766548060 2. Swaraj Priyaranjan Kunal Biological Oceanography Division (BOD) National Institute of Oceanography (NIO) Dona Paula, Goa 403004, India. Email: swar.mbt@gmail.com 3. Maria Rosalia Menezes Biological Oceanography...

  13. A cohort study with regard to the risk of haematological malignancies in patients treated with X-ray for benign lesions in the locomotor system. Pt. 1. Epidemiological analyses

    Energy Technology Data Exchange (ETDEWEB)

    Damber, L. [Umeaa Univ. (Sweden). Dept. of Oncology; Larsson, L.G. [Umeaa Univ. (Sweden). Dept. of Oncology; Johansson, L. [Umeaa Univ. (Sweden). Dept. of Radiation Physics; Norin, T. [Gaevle Hospital, Gaevle (Sweden)

    1995-12-31

    Roentgen treatment for painful benign conditions in the locomotor system as arthrosis and spondylosis was in Sweden very common up to the beginning of the 1960s. The mode of treatment differed from the British ankylosing spondylitis series as smaller parts of the red bone marrow were exposed and smaller doses were applied. A cohort of 20024 such patients treated 1950-1964 at two hospitals in northern Sweden was analysed with regard to the risk of haematological malignancies. Average factors for conversion of prescribed skin doses to mean absorbed red bone marrow doses were estimated on random samples of the different treatment sites and then applied on the cohort in its whole. The standard incidence ratio (SIR) for leukaemia was 1.18 (95% CI: 0.98-1.42) and the standard mortality ratio (SMR) 1.25 (0.99-1.45). In the highest dose group (mean absorbed red bone marrow dose > 0.5 Gy) the corresponding values were 1.40 (1.00-1.92) and 1.50 (1.08-2.04). In the mortality analysis also a slightly increased myeloma risk was noted with SMR = 1.20 (0.99-1.56). Extension of the cohort and nested case-control studies are under progress. (orig.).

  14. Ghost cell lesions

    Directory of Open Access Journals (Sweden)

    E Rajesh

    2015-01-01

    Full Text Available Ghost cells have been a controversy for a long time. Ghost cell is a swollen/enlarged epithelial cell with eosnophilic cytoplasm, but without a nucleus. In routine H and E staining these cells give a shadowy appearance. Hence these cells are also called as shadow cells or translucent cells. The appearance of these cells varies from lesion to lesion involving odontogenic and nonodontogenic lesions. This article review about the origin, nature and significance of ghost cells in different neoplasms.

  15. Global genetic analyses reveal strong inter-ethnic variability in the loss of activity of the organic cation transporter OCT1.

    Science.gov (United States)

    Seitz, Tina; Stalmann, Robert; Dalila, Nawar; Chen, Jiayin; Pojar, Sherin; Dos Santos Pereira, Joao N; Krätzner, Ralph; Brockmöller, Jürgen; Tzvetkov, Mladen V

    2015-01-01

    The organic cation transporter OCT1 (SLC22A1) mediates the uptake of vitamin B1, cationic drugs, and xenobiotics into hepatocytes. Nine percent of Caucasians lack or have very low OCT1 activity due to loss-of-function polymorphisms in OCT1 gene. Here we analyzed the global genetic variability in OCT1 to estimate the therapeutic relevance of OCT1 polymorphisms in populations beyond Caucasians and to identify evolutionary patterns of the common loss of OCT1 activity in humans. We applied massively parallel sequencing to screen for coding polymorphisms in 1,079 unrelated individuals from 53 populations worldwide. The obtained data was combined with the existing 1000 Genomes data comprising an additional 1,092 individuals from 14 populations. The identified OCT1 variants were characterized in vitro regarding their cellular localization and their ability to transport 10 known OCT1 substrates. Both the population genetics data and transport data were used in tandem to generate a world map of loss of OCT1 activity. We identified 16 amino acid substitutions potentially causing loss of OCT1 function and analyzed them together with five amino acid substitutions that were not expected to affect OCT1 function. The variants constituted 16 major alleles and 14 sub-alleles. Six major alleles showed improper subcellular localization leading to substrate-wide loss in activity. Five major alleles showed correct subcellular localization, but substrate-specific loss of activity. Striking differences were observed in the frequency of loss of OCT1 activity worldwide. While most East Asian and Oceanian individuals had completely functional OCT1, 80 % of native South American Indians lacked functional OCT1 alleles. In East Asia and Oceania the average nucleotide diversity of the loss-of-function variants was much lower than that of the variants that do not affect OCT1 function (ratio of 0.03) and was significantly lower than the theoretically expected heterozygosity (Tajima's D = -1

  16. The genetic diversity of genus Bacillus and the related genera revealed by 16S rRNA gene sequences and ardra analyses isolated from geothermal regions of turkey

    Directory of Open Access Journals (Sweden)

    Arzu Coleri Cihan

    2012-03-01

    Full Text Available Previously isolated 115 endospore-forming bacilli were basically grouped according to their temperature requirements for growth: the thermophiles (74%, the facultative thermophiles (14% and the mesophiles (12%. These isolates were taken into 16S rRNA gene sequence analyses, and they were clustered among the 7 genera: Anoxybacillus, Aeribacillus, Bacillus, Brevibacillus, Geobacillus, Paenibacillus, and Thermoactinomycetes. Of these bacilli, only the thirty two isolates belonging to genera Bacillus (16, Brevibacillus (13, Paenibacillus (1 and Thermoactinomycetes (2 were selected and presented in this paper. The comparative sequence analyses revealed that the similarity values were ranged as 91.4-100 %, 91.8- 99.2 %, 92.6- 99.8 % and 90.7 - 99.8 % between the isolates and the related type strains from these four genera, respectively. Twenty nine of them were found to be related with the validly published type strains. The most abundant species was B. thermoruber with 9 isolates followed by B. pumilus (6, B. lichenformis (3, B. subtilis (3, B. agri (3, B. smithii (2, T. vulgaris (2 and finally P. barengoltzii (1. In addition, isolates of A391a, B51a and D295 were proposed as novel species as their 16S rRNA gene sequences displayed similarities ≤ 97% to their closely related type strains. The AluI-, HaeIII- and TaqI-ARDRA results were in congruence with the 16S rRNA gene sequence analyses. The ARDRA results allowed us to differentiate these isolates, and their discriminative restriction fragments were able to be determined. Some of their phenotypic characters and their amylase, chitinase and protease production were also studied and biotechnologically valuable enzyme producing isolates were introduced in order to use in further studies.

  17. The optokinetic reflex as a tool for quantitative analyses of nervous system function in mice: application to genetic and drug-induced variation.

    Directory of Open Access Journals (Sweden)

    Hugh Cahill

    2008-04-01

    Full Text Available The optokinetic reflex (OKR, which serves to stabilize a moving image on the retina, is a behavioral response that has many favorable attributes as a test of CNS function. The OKR requires no training, assesses the function of diverse CNS circuits, can be induced repeatedly with minimal fatigue or adaptation, and produces an electronic record that is readily and objectively quantifiable. We describe a new type of OKR test apparatus in which computer-controlled visual stimuli and streamlined data analysis facilitate a relatively high throughput behavioral assay. We used this apparatus, in conjunction with infrared imaging, to quantify basic OKR stimulus-response characteristics for C57BL/6J and 129/SvEv mouse strains and for genetically engineered lines lacking one or more photoreceptor systems or with an alteration in cone spectral sensitivity. A second generation (F2 cross shows that the characteristic difference in OKR frequency between C57BL/6J and 129/SvEv is inherited as a polygenic trait. Finally, we demonstrate the sensitivity and high temporal resolution of the OKR for quantitative analysis of CNS drug action. These experiments show that the mouse OKR is well suited for neurologic testing in the context of drug discovery and large-scale phenotyping programs.

  18. Characterisation of Triticum vavilovii-derived stripe rust resistance using genetic, cytogenetic and molecular analyses and its marker-assisted selection.

    Science.gov (United States)

    Bariana, H. S.; Brown, G. N.; Ahmed, N. U.; Khatkar, S.; Conner, R. L.; Wellings, C. R.; Haley, S.; Sharp, P. J.; Laroche, A.

    2002-02-01

    Stripe rust resistance was identified in Triticum vavilovii( T. vaviloviiAus22498)-derived Russian wheat aphid (RWA)-resistant germplasm. Inheritance studies indicated monogenic control of resistance. The resistance gene was tentatively designated as Yrvav and was located on chromosome 1B by monosomic analysis. A close association (1.5+/-0.9% recombination) of Yrvav with a T. vavilovii-derived gliadin allele ( Gli-B1vav) placed it in chromosome arm 1BS. Yrvavwas allelic with Yr10. Tests with Yr10 avirulent and virulent pathotypes showed that Yrvav and Yr10 possess identical pathogenic specificity. Yrvav and Yr10 showed close genetic associations with alternate alleles at the Xpsp3000(microsatellite marker), Gli-B1 and Rg1 loci. Based on these observations Yrvav was named as Yr10vav. The close association between Xpsp3000 and Gli-B1 was also confirmed. The Yr10vav-linked Xpsp3000 allele (285 bp) was not present in 65 Australian cultivars, whereas seven Australian wheats lacking Yr10 carried the same Xpsp3000 allele (260 bp) as Yr10carrying wheat cultivar Moro. Xpsp3000 and/or Gli-B1 could be used in marker-assisted selection for pyramiding Yr10vavor Yr10 with other stripe rust resistance genes. Yr10vav was inherited independently of the T. vavilovii-derived RWA resistance.

  19. Comparative Genomic Analyses of Multiple Pseudomonas Strains Infecting Corylus avellana Trees Reveal the Occurrence of Two Genetic Clusters with Both Common and Distinctive Virulence and Fitness Traits

    Science.gov (United States)

    Marcelletti, Simone; Scortichini, Marco

    2015-01-01

    The European hazelnut (Corylus avellana) is threatened in Europe by several pseudomonads which cause symptoms ranging from twig dieback to tree death. A comparison of the draft genomes of nine Pseudomonas strains isolated from symptomatic C. avellana trees was performed to identify common and distinctive genomic traits. The thorough assessment of genetic relationships among the strains revealed two clearly distinct clusters: P. avellanae and P. syringae. The latter including the pathovars avellanae, coryli and syringae. Between these two clusters, no recombination event was found. A genomic island of approximately 20 kb, containing the hrp/hrc type III secretion system gene cluster, was found to be present without any genomic difference in all nine pseudomonads. The type III secretion system effector repertoires were remarkably different in the two groups, with P. avellanae showing a higher number of effectors. Homologue genes of the antimetabolite mangotoxin and ice nucleation activity clusters were found solely in all P. syringae pathovar strains, whereas the siderophore yersiniabactin was only present in P. avellanae. All nine strains have genes coding for pectic enzymes and sucrose metabolism. By contrast, they do not have genes coding for indolacetic acid and anti-insect toxin. Collectively, this study reveals that genomically different Pseudomonas can converge on the same host plant by suppressing the host defence mechanisms with the use of different virulence weapons. The integration into their genomes of a horizontally acquired genomic island could play a fundamental role in their evolution, perhaps giving them the ability to exploit new ecological niches. PMID:26147218

  20. Genetic Predisposition to Weight Loss and Regain With Lifestyle Intervention: Analyses From the Diabetes Prevention Program and the Look AHEAD Randomized Controlled Trials.

    Science.gov (United States)

    Papandonatos, George D; Pan, Qing; Pajewski, Nicholas M; Delahanty, Linda M; Peter, Inga; Erar, Bahar; Ahmad, Shafqat; Harden, Maegan; Chen, Ling; Fontanillas, Pierre; Wagenknecht, Lynne E; Kahn, Steven E; Wing, Rena R; Jablonski, Kathleen A; Huggins, Gordon S; Knowler, William C; Florez, Jose C; McCaffery, Jeanne M; Franks, Paul W

    2015-12-01

    Clinically relevant weight loss is achievable through lifestyle modification, but unintentional weight regain is common. We investigated whether recently discovered genetic variants affect weight loss and/or weight regain during behavioral intervention. Participants at high-risk of type 2 diabetes (Diabetes Prevention Program [DPP]; N = 917/907 intervention/comparison) or with type 2 diabetes (Look AHEAD [Action for Health in Diabetes]; N = 2,014/1,892 intervention/comparison) were from two parallel arm (lifestyle vs. comparison) randomized controlled trials. The associations of 91 established obesity-predisposing loci with weight loss across 4 years and with weight regain across years 2-4 after a minimum of 3% weight loss were tested. Each copy of the minor G allele of MTIF3 rs1885988 was consistently associated with greater weight loss following lifestyle intervention over 4 years across the DPP and Look AHEAD. No such effect was observed across comparison arms, leading to a nominally significant single nucleotide polymorphism×treatment interaction (P = 4.3 × 10(-3)). However, this effect was not significant at a study-wise significance level (Bonferroni threshold P lifestyle. © 2015 by the American Diabetes Association. Readers may use this article as long as the work is properly cited, the use is educational and not for profit, and the work is not altered.

  1. Genetic, comparative genomic, and expression analyses of the Mc1r locus in the polychromatic Midas cichlid fish (Teleostei, Cichlidae Amphilophus sp.) species group.

    Science.gov (United States)

    Henning, Frederico; Renz, Adina Josepha; Fukamachi, Shoji; Meyer, Axel

    2010-05-01

    Natural populations of the Midas cichlid species in several different crater lakes in Nicaragua exhibit a conspicuous color polymorphism. Most individuals are dark and the remaining have a gold coloration. The color morphs mate assortatively and sympatric population differentiation has been shown based on neutral molecular data. We investigated the color polymorphism using segregation analysis and a candidate gene approach. The segregation patterns observed in a mapping cross between a gold and a dark individual were consistent with a single dominant gene as a cause of the gold phenotype. This suggests that a simple genetic architecture underlies some of the speciation events in the Midas cichlids. We compared the expression levels of several candidate color genes Mc1r, Ednrb1, Slc45a2, and Tfap1a between the color morphs. Mc1r was found to be up regulated in the gold morph. Given its widespread association in color evolution and role on melanin synthesis, the Mc1r locus was further investigated using sequences derived from a genomic library. Comparative analysis revealed conserved synteny in relation to the majority of teleosts and highlighted several previously unidentified conserved non-coding elements (CNEs) in the upstream and downstream regions in the vicinity of Mc1r. The identification of the CNEs regions allowed the comparison of sequences from gold and dark specimens of natural populations. No polymorphisms were found between in the population sample and Mc1r showed no linkage to the gold phenotype in the mapping cross, demonstrating that it is not causally related to the color polymorphism in the Midas cichlid.

  2. Electroencephalographic precursors of spike-wave discharges in a genetic rat model of absence epilepsy: Power spectrum and coherence EEG analyses.

    Science.gov (United States)

    Sitnikova, Evgenia; van Luijtelaar, Gilles

    2009-04-01

    Periods in the electroencephalogram (EEG) that immediately precede the onset of spontaneous spike-wave discharges (SWD) were examined in WAG/Rij rat model of absence epilepsy. Precursors of SWD (preSWD) were classified based on the distribution of EEG power in delta-theta-alpha frequency bands as measured in the frontal cortex. In 95% of preSWD, an elevation of EEG power was detected in delta band (1-4Hz). 73% of preSWD showed high power in theta frequencies (4.5-8Hz); these preSWD might correspond to 5-9Hz oscillations that were found in GAERS before SWD onset [Pinault, D., Vergnes, M., Marescaux, C., 2001. Medium-voltage 5-9Hz oscillations give rise to spike-and-wave discharges in a genetic model of absence epilepsy: in vivo dual extracellular recording of thalamic relay and reticular neurons. Neuroscience 105, 181-201], however, theta component of preSWD in our WAG/Rij rats was not shaped into a single rhythm. It is concluded that a coalescence of delta and theta in the cortex is favorable for the occurrence of SWD. The onset of SWD was associated with strengthening of intracortical and thalamo-cortical coherence in 9.5-14Hz and in double beta frequencies. No features of EEG coherence can be considered as unique for any of preSWD subtype. Reticular and ventroposteromedial thalamic nuclei were strongly coupled even before the onset of SWD. All this suggests that SWD derive from an intermixed delta-theta EEG background; seizure onset associates with reinforcement of intracortical and cortico-thalamic associations.

  3. Design and rationale for examining neuroimaging genetics in ischemic stroke

    Science.gov (United States)

    Giese, Anne-Katrin; Schirmer, Markus D.; Donahue, Kathleen L.; Cloonan, Lisa; Irie, Robert; Winzeck, Stefan; Bouts, Mark J.R.J.; McIntosh, Elissa C.; Mocking, Steven J.; Dalca, Adrian V.; Sridharan, Ramesh; Xu, Huichun; Frid, Petrea; Giralt-Steinhauer, Eva; Holmegaard, Lukas; Roquer, Jaume; Wasselius, Johan; Cole, John W.; McArdle, Patrick F.; Broderick, Joseph P.; Jimenez-Conde, Jordi; Jern, Christina; Kissela, Brett M.; Kleindorfer, Dawn O.; Lemmens, Robin; Lindgren, Arne; Meschia, James F.; Rundek, Tatjana; Sacco, Ralph L.; Schmidt, Reinhold; Sharma, Pankaj; Slowik, Agnieszka; Thijs, Vincent; Woo, Daniel; Worrall, Bradford B.; Kittner, Steven J.; Mitchell, Braxton D.; Rosand, Jonathan; Golland, Polina; Wu, Ona

    2017-01-01

    Objective: To describe the design and rationale for the genetic analysis of acute and chronic cerebrovascular neuroimaging phenotypes detected on clinical MRI in patients with acute ischemic stroke (AIS) within the scope of the MRI–GENetics Interface Exploration (MRI-GENIE) study. Methods: MRI-GENIE capitalizes on the existing infrastructure of the Stroke Genetics Network (SiGN). In total, 12 international SiGN sites contributed MRIs of 3,301 patients with AIS. Detailed clinical phenotyping with the web-based Causative Classification of Stroke (CCS) system and genome-wide genotyping data were available for all participants. Neuroimaging analyses include the manual and automated assessments of established MRI markers. A high-throughput MRI analysis pipeline for the automated assessment of cerebrovascular lesions on clinical scans will be developed in a subset of scans for both acute and chronic lesions, validated against gold standard, and applied to all available scans. The extracted neuroimaging phenotypes will improve characterization of acute and chronic cerebrovascular lesions in ischemic stroke, including CCS subtypes, and their effect on functional outcomes after stroke. Moreover, genetic testing will uncover variants associated with acute and chronic MRI manifestations of cerebrovascular disease. Conclusions: The MRI-GENIE study aims to develop, validate, and distribute the MRI analysis platform for scans acquired as part of clinical care for patients with AIS, which will lead to (1) novel genetic discoveries in ischemic stroke, (2) strategies for personalized stroke risk assessment, and (3) personalized stroke outcome assessment. PMID:28852707

  4. Lesion activity assessment

    DEFF Research Database (Denmark)

    Ekstrand, K R; Zero, D T; Martignon, S

    2009-01-01

    in response to cariogenic plaque as well as lesion arrest. Based on this understanding, different clinical scoring systems have been developed to assess the severity/depth and activity of lesions. A recent system has been devised by the International Caries Detection and Assessment System Committee...

  5. Impact of diversity of Mycoplasma hyopneumoniae strains on lung lesions in slaughter pigs.

    Science.gov (United States)

    Michiels, Annelies; Vranckx, Katleen; Piepers, Sofie; Del Pozo Sacristán, Rubén; Arsenakis, Ioannis; Boyen, Filip; Haesebrouck, Freddy; Maes, Dominiek

    2017-01-17

    The importance of diversity of Mycoplasma hyopneumoniae (M. hyopneumoniae) strains is not yet fully known. This study investigated the genetic diversity of M. hyopneumoniae strains in ten pig herds, and assessed associations between the presence of different strains of M. hyopneumoniae and lung lesions at slaughter. Within each herd, three batches of slaughter pigs were investigated. At slaughter, from each batch, 20 post mortem bronchoalveolar lavage fluid samples were collected for multiple locus variable-number tandem repeat analysis (MLVA), and lung lesions (Mycoplasma-like lesions, fissures) were examined. Multivariable analyses including potential risk factors for respiratory disease were performed to assess associations between the number of different strains per batch (three categories: one strain, two-six strains, ≥seven strains), and the lung lesions as outcome variables. In total, 135 different M. hyopneumoniae strains were found. The mean (min.-max.) number of different strains per batch were 7 (1-13). Batches with two-six strains or more than six strains had more severe Mycoplasma-like lesions (P = 0.064 and P = 0.012, respectively), a higher prevalence of pneumonia [odds ratio (OR): 1.30, P = 0.33 and OR: 2.08, P = 0.012, respectively], and fissures (OR = 1.35, P = 0.094 and OR = 1.70, P = 0.007, respectively) compared to batches with only one strain. In conclusion, many different M. hyopneumoniae strains were found, and batches of slaughter pigs with different M. hyopneumoniae strains had a higher prevalence and severity of Mycoplasma-like lung lesions at slaughter, implying that reducing the number of different strains may lead to less lung lesions at slaughter and better respiratory health of the pigs.

  6. Comprehensive genetic characterization of CLL: a study on 506 cases analysed with chromosome banding analysis, interphase FISH, IgV(H) status and immunophenotyping.

    Science.gov (United States)

    Haferlach, C; Dicker, F; Schnittger, S; Kern, W; Haferlach, T

    2007-12-01

    In CLL data from chromosome banding analysis (CBA) have been scarce due to the low proliferative activity of CLL cells in vitro. We improved the cultivation technique using an immunostimulatory CpG-oligonucleotide DSP30 and IL-2. A total of 506 CLL samples were analysed with CBA and interphase FISH using probes for the detection of trisomy 12, IgH rearrangements and deletions of 6q21, 11q22.3 (ATM), 13q14 (D13S25 and D13S319) and 17p13 (TP53). A total of 500 of 506 (98.8%) cases were successfully stimulated for metaphase generation and are subject to this study. Aberrations were detected in 415 of 500 (83.0%) cases by CBA and in 392 of 500 (78.4%) cases by FISH. CBA detected 832 abnormalities and FISH only 502. Therefore, CBA offers important information in addition to FISH. (1) CLL is characterized mainly by genomic imbalances and reciprocal translocations are rare. (2) A subgroup with complex aberrant karyotype (16.4%) is identified which is associated with an unmutated IgV(H) status and CD38 expression (P=0.034 and 0.02, respectively). (3) Additional abnormalities are detectable providing new biological insights into different CLL subclasses revealing a much more heterogeneous pattern of cytogenetic abnormalities as assumed so far based on FISH data only. Therefore, prospective clinical trials should evaluate the prognostic impact of newly available CBA data.

  7. Maximum likelihood and Bayesian analyses of a combined nucleotide sequence dataset for genetic characterization of a novel pestivirus, SVA/cont-08.

    Science.gov (United States)

    Liu, Lihong; Xia, Hongyan; Baule, Claudia; Belák, Sándor

    2009-01-01

    Bovine viral diarrhoea virus 1 (BVDV-1) and Bovine viral diarrhoea virus 2 (BVDV-2) are two recognised bovine pestivirus species of the genus Pestivirus. Recently, a pestivirus, termed SVA/cont-08, was detected in a batch of contaminated foetal calf serum originating from South America. Comparative sequence analysis showed that the SVA/cont-08 virus shares 15-28% higher sequence identity to pestivirus D32/00_'HoBi' than to members of BVDV-1 and BVDV-2. In order to reveal the phylogenetic relationship of SVA/cont-08 with other pestiviruses, a molecular dataset of 30 pestiviruses and 1,896 characters, comprising the 5'UTR, N(pro) and E2 gene regions, was analysed by two methods: maximum likelihood and Bayesian approach. An identical, well-supported tree topology was observed, where four pestiviruses (SVA/cont-08, D32/00_'HoBi', CH-KaHo/cont, and Th/04_KhonKaen) formed a monophyletic clade that is closely related to the BVDV-1 and BVDV-2 clades. The strategy applied in this study is useful for classifying novel pestiviruses in the future.

  8. Pathway-based analyses.

    Science.gov (United States)

    Kent, Jack W

    2016-02-03

    New technologies for acquisition of genomic data, while offering unprecedented opportunities for genetic discovery, also impose severe burdens of interpretation and penalties for multiple testing. The Pathway-based Analyses Group of the Genetic Analysis Workshop 19 (GAW19) sought reduction of multiple-testing burden through various approaches to aggregation of highdimensional data in pathways informed by prior biological knowledge. Experimental methods testedincluded the use of "synthetic pathways" (random sets of genes) to estimate power and false-positive error rate of methods applied to simulated data; data reduction via independent components analysis, single-nucleotide polymorphism (SNP)-SNP interaction, and use of gene sets to estimate genetic similarity; and general assessment of the efficacy of prior biological knowledge to reduce the dimensionality of complex genomic data. The work of this group explored several promising approaches to managing high-dimensional data, with the caveat that these methods are necessarily constrained by the quality of external bioinformatic annotation.

  9. Biochemical and genetic analyses of the oomycete Pythium insidiosum provide new insights into clinical identification and urease-based evolution of metabolism-related traits

    Directory of Open Access Journals (Sweden)

    Theerapong Krajaejun

    2018-06-01

    Full Text Available The oomycete microorganism, Pythium insidiosum, causes the life-threatening infectious condition, pythiosis, in humans and animals worldwide. Affected individuals typically endure surgical removal of the infected organ(s. Detection of P. insidiosum by the established microbiological, immunological, or molecular methods is not feasible in non-reference laboratories, resulting in delayed diagnosis. Biochemical assays have been used to characterize P. insidiosum, some of which could aid in the clinical identification of this organism. Although hydrolysis of maltose and sucrose has been proposed as the key biochemical feature useful in discriminating P. insidiosum from other oomycetes and fungi, this technique requires a more rigorous evaluation involving a wider selection of P. insidiosum strains. Here, we evaluated 10 routinely available biochemical assays for characterization of 26 P. insidiosum strains, isolated from different hosts and geographic origins. Initial assessment revealed diverse biochemical characteristics across the P. insidiosum strains tested. Failure to hydrolyze sugars is observed, especially in slow-growing strains. Because hydrolysis of maltose and sucrose varied among different strains, use of the biochemical assays for identification of P. insidiosum should be cautioned. The ability of P. insidiosum to hydrolyze urea is our focus, because this metabolic process relies on the enzyme urease, an important virulence factor of other pathogens. The ability to hydrolyze urea varied among P. insidiosum strains and was not associated with growth rates. Genome analyses demonstrated that urease- and urease accessory protein-encoding genes are present in both urea-hydrolyzing and non-urea-hydrolyzing strains of P. insidiosum. Urease genes are phylogenetically conserved in P. insidiosum and related oomycetes, while the presence of urease accessory protein-encoding genes is markedly diverse in these organisms. In summary, we dissected

  10. Molecular genetics

    International Nuclear Information System (INIS)

    Kubitschek, H.E.

    1975-01-01

    Progress is reported on studies on the nature and action of lethal and mutagenic lesions in DNA and the mechanisms by which these are produced in bacteria by ionizing radiation or by decay of radioisotopes incorporated in DNA. Studies of radioisotope decay provide the advantages that the original lesion is localized in the genetic material and the immediate physical and chemical changes that occur at decay are known. Specific types of DNA damage were related to characteristic decay properties of several radioisotopes. Incorporated 125 I, for example, induces a double-stranded break in DNA with almost every decay, but causes remarkably little damage of any other kind to the DNA. (U.S.)

  11. Intraosseous osteolytic lesions

    Energy Technology Data Exchange (ETDEWEB)

    Adler, C.P.; Wenz, W.

    1981-10-01

    Any pathological damage occurring in a bone will produce either an osteolytic or osteosclerotic lesion which can be seen in the macroscopic specimen as well as in the roentgenogram. Various bone lesions may lead to local destructions of the bone. An osteoma or osteoplastic osteosarcoma produces an osteosclerotic lesion showing a dense mass in the roentgenogram; a chondroblastoma or an osteoclastoma, on the other hand, induces an osteolytic focal lesion. This paper presents examples of different osteolytic lesions of the humerus. An osteolytic lesion seen in the roentgenogram may be either produced by an underlying non-ossifying fibroma of the bone, by fibrous dysplasia, osteomyelitis or Ewing's sarcoma. Differential diagnostic considerations based on the radiological picture include eosinophilic bone granuloma, juvenile or aneurysmal bone cyst, multiple myeloma or bone metastases. Serious differential diagnostic problems may be involved in case of osteolytic lesions occurring in the humerus. Cases of this type involving complications have been reported and include the presence of an teleangiectatic osteosarcoma as well as that of a hemangiosarcoma of the bone.

  12. Factors influencing diagnostic yield of CT-guided percutaneous core needle biopsy for bone lesions

    International Nuclear Information System (INIS)

    Li, Y.; Du, Y.; Luo, T.Y.; Yang, H.F.; Yu, J.H.; Xu, X.X.; Zheng, H.J.; Li, B.

    2014-01-01

    Aim: To evaluate the factors influencing diagnostic yield of computed tomography (CT)-guided percutaneous core needle biopsy (CNB) for bone lesions. Materials and methods: Between September 2005 and July 2011, 162 consecutive CT-guided CNB procedures were performed in 155 patients. The variables analysed were age, sex, lesion location, lesion type, lesion size, specimen size, biopsy needle gauge, and individual radiologist. The factors influencing diagnostic yield of CT-guided percutaneous CNB for bone lesions were determined by multivariate analysis of variables. Results: The diagnostic yield was 81.5%. Diagnostic yield was 89.9% for lytic bone lesions and 48.5% for sclerotic bone lesions (p < 0.001), and 89.2% for lesions ≥3 cm and 73.4% for lesions <3 cm (p = 0.010). The significant factors influencing diagnostic yield of CT-guided percutaneous CNB for bone lesions were lesion type [p < 0.001; odds ratio (OR) for a lytic lesion was approximately 12 times higher than that for a sclerotic lesion; 95% confidence interval (CI): 4.22–34.01], and lesion size (p = 0.012; OR for a lesion size ≥3 cm was about five-times higher than that for a lesion size <3 cm; 95% CI: 1.42–16.71). Conclusion: Lesion type and lesion size are determining factors in diagnostic yield. The higher diagnostic yield is correlated with lytic lesion and lesion size ≥3 cm

  13. The DinB•RecA complex of Escherichia coli mediates an efficient and high-fidelity response to ubiquitous alkylation lesions.

    Science.gov (United States)

    Cafarelli, Tiziana M; Rands, Thomas J; Godoy, Veronica G

    2014-03-01

    Alkylation DNA lesions are ubiquitous, and result from normal cellular metabolism as well as from treatment with methylating agents and chemotherapeutics. DNA damage tolerance by translesion synthesis DNA polymerases has an important role in cellular resistance to alkylating agents. However, it is not yet known whether Escherichia coli (E. coli) DNA Pol IV (DinB) alkylation lesion bypass efficiency and fidelity in vitro are similar to those inferred by genetic analyses. We hypothesized that DinB-mediated bypass of 3-deaza-3-methyladenine, a stable analog of 3-methyladenine, the primary replication fork-stalling alkylation lesion, would be of high fidelity. We performed here the first kinetic analyses of E. coli DinB•RecA binary complexes. Whether alone or in a binary complex, DinB inserted the correct deoxyribonucleoside triphosphate (dNTP) opposite either lesion-containing or undamaged template; the incorporation of other dNTPs was largely inefficient. DinB prefers undamaged DNA, but the DinB•RecA binary complex increases its catalytic efficiency on lesion-containing template, perhaps as part of a regulatory mechanism to better respond to alkylation damage. Notably, we find that a DinB derivative with enhanced affinity for RecA, either alone or in a binary complex, is less efficient and has a lower fidelity than DinB or DinB•RecA. This finding contrasts our previous genetic analyses. Therefore, mutagenesis resulting from alkylation lesions is likely limited in cells by the activity of DinB•RecA. These two highly conserved proteins play an important role in maintaining genomic stability when cells are faced with ubiquitous DNA damage. Kinetic analyses are important to gain insights into the mechanism(s) regulating TLS DNA polymerases. Copyright © 2013 Wiley Periodicals, Inc.

  14. Heritability and prevalence of selected osteochondrosis lesions in yearling Thoroughbred horses.

    Science.gov (United States)

    Russell, J; Matika, O; Russell, T; Reardon, R J M

    2017-05-01

    Osteochondrosis is considered multifactorial in origin, with factors such as nutrition, conformation, body size, trauma and genetics thought to contribute to its pathogenesis. Few studies have investigated the effects of genetic variability of osteochondrosis in Thoroughbreds. To describe the prevalence and genetic variability of a subset of osteochondrosis lesions in a group of Thoroughbred yearlings. Retrospective cohort study. Radiographs of 1962 Thoroughbred yearlings were retrieved from clinical records obtained between 2005 and 2013. Pedigree information was obtained from the Australian Stud Book. Osteochondrosis lesions were documented in selected joints and estimates of heritability were obtained by fitting linear mixed models in ASREML software. The overall prevalence of osteochondrosis was 23%. Osteochondrosis was identified in 10% of stifle joints, 6% of hock joints and 8% of fetlock joints. The heritability estimates ranged from 0 to 0.21. The largest estimates were 0.10, 0.14, 0.16 and 0.21 for lesions of the distal intermediate ridge of the tibia, dorso-proximal proximal phalanx (P1), any stifle osteochondrosis, and lesions of the lateral trochlear ridge of the distal femur, respectively. Although calculated heritability estimates had high standard errors, meta-analyses combining the present results with published estimates were significant at 0.10, 0.17, 0.15 and 0.20 for stifle, tarsal, fetlock and these joints combined, respectively. In addition, there was a permanent environment attributable to the dam effect. Inclusion criteria were based on radiographic findings in specific joints at a specific age range in Thoroughbreds. The present results indicate that only a proportion of osteochondrosis in Thoroughbreds is heritable. The permanent environment effects of the dam were observed to have effects on some categories of osteochondrosis. © 2016 The Authors. Equine Veterinary Journal published by John Wiley & Sons Ltd on behalf of EVJ Ltd.

  15. Diffuse cavitary lung lesions

    Energy Technology Data Exchange (ETDEWEB)

    Grunzke, Mindy; Garrington, Timothy [University of Colorado Denver, Department of Pediatrics, Aurora, CO (United States); The Children' s Hospital, Rick Wilson Center for Cancer and Blood Disorders, Aurora, CO (United States); Hayes, Kari [The Children' s Hospital, Pediatric Radiology, Aurora, CO (United States); Bourland, Wendy [Children' s Hospital at St. Francis, Warren Clinic, Inc., Tulsa, OK (United States)

    2010-02-15

    An 11-year-old girl presented with a 2-month history of progressively worsening cough, daily fevers, and weight loss. A chest radiograph revealed multiple cystic cavitary lung lesions. An extensive infectious work-up was negative. Chest CT verified multiple cavitary lung lesions bilaterally, and [F-18]2-fluoro-2-deoxy-D-glucose ({sup 18}F-FDG) positron emission tomography with CT (PET/CT) showed increased uptake in the lung lesions as well as regional lymph nodes. Subsequent biopsy of an involved lymph node confirmed classical Hodgkin lymphoma, nodular sclerosis type. This case represents an unusual presentation for a child with Hodgkin lymphoma and demonstrates a role for {sup 18}F-FDG PET/CT in evaluating a child with cavitary lung lesions. (orig.)

  16. Diffuse cavitary lung lesions

    International Nuclear Information System (INIS)

    Grunzke, Mindy; Garrington, Timothy; Hayes, Kari; Bourland, Wendy

    2010-01-01

    An 11-year-old girl presented with a 2-month history of progressively worsening cough, daily fevers, and weight loss. A chest radiograph revealed multiple cystic cavitary lung lesions. An extensive infectious work-up was negative. Chest CT verified multiple cavitary lung lesions bilaterally, and [F-18]2-fluoro-2-deoxy-D-glucose ( 18 F-FDG) positron emission tomography with CT (PET/CT) showed increased uptake in the lung lesions as well as regional lymph nodes. Subsequent biopsy of an involved lymph node confirmed classical Hodgkin lymphoma, nodular sclerosis type. This case represents an unusual presentation for a child with Hodgkin lymphoma and demonstrates a role for 18 F-FDG PET/CT in evaluating a child with cavitary lung lesions. (orig.)

  17. Uterine Vascular Lesions

    Science.gov (United States)

    Vijayakumar, Abhishek; Srinivas, Amruthashree; Chandrashekar, Babitha Moogali; Vijayakumar, Avinash

    2013-01-01

    Vascular lesions of the uterus are rare; most reported in the literature are arteriovenous malformations (AVMs). Uterine AVMs can be congenital or acquired. In recent years, there has been an increasing number of reports of acquired vascular lesions of the uterus following pregnancy, abortion, cesarean delivery, and curettage. It can be seen from these reports that there is confusion concerning the terminology of uterine vascular lesions. There is also a lack of diagnostic criteria and management guidelines, which has led to an increased number of unnecessary invasive procedures (eg, angiography, uterine artery embolization, hysterectomy for abnormal vaginal bleeding). This article familiarizes readers with various vascular lesions of the uterus and their management. PMID:24340126

  18. Male breast lesions

    International Nuclear Information System (INIS)

    Matushita, J.P.K.; Andrade, L.G. de; Carregal, E.; Marimatsu, R.I.; Matushita, J.S.

    1989-01-01

    Roentgenographic examination of the male breast is an important aspect of the continued, intensive investigation of the radiologic morphology of the normal and diseased breast conducted in 17 cases examined at the Instituto Nacional do Cancer - RJ. It is purpose of this report to present the Roentgen appearance of various lesions of the male breast as they have been found in our practice and also to stress some of the difficulties in the differential diagnosis of these lesions. (author) [pt

  19. Benign fibroosseous lesions

    Directory of Open Access Journals (Sweden)

    Cansu Köseoğlu Seçgin

    2016-05-01

    Full Text Available Benign fibroosseous lesions represent a group of lesions that share the same basic evolutive mechanism and are characterized by replacement of normal bone with a fibrous connective tissue that gradually undergoes mineralization. These lesions are presented by a variety of diseases including developmental, reactive-dysplastic processes and neoplasms. Depending on the nature and amount of calcified tissue, they can be observed as radiolucent, mixed or radiopaque. Their radiographic features could be well-defined or indistinguishable from the surrounding bone tissue. They can be asymptomatic as in osseous dysplasias and can be detected incidentally on radiographs, or they can lead to expansion in the affected bone as in ossifying fibroma. All fibroosseous lesions seen in the jaws and face are variations of the same histological pattern. Therefore, detailed clinical and radiographic evaluation in differential diagnosis is important. In this review, fibroosseous benign lesions are classified as osseous dysplasia, fibrous dysplasia and fibroosseous tumors; and radiographic features and differential diagnosis of these lesions are reviewed taking into account this classification.

  20. Characteristics of lesional and extra-lesional cortical grey matter in relapsing-remitting and secondary progressive multiple sclerosis: A magnetisation transfer and diffusion tensor imaging study.

    Science.gov (United States)

    Yaldizli, Özgür; Pardini, Matteo; Sethi, Varun; Muhlert, Nils; Liu, Zheng; Tozer, Daniel J; Samson, Rebecca S; Wheeler-Kingshott, Claudia Am; Yousry, Tarek A; Miller, David H; Chard, Declan T

    2016-02-01

    In multiple sclerosis (MS), diffusion tensor and magnetisation transfer imaging are both abnormal in lesional and extra-lesional cortical grey matter, but differences between clinical subtypes and associations with clinical outcomes have only been partly assessed. To compare mean diffusivity, fractional anisotropy and magnetisation transfer ratio (MTR) in cortical grey matter lesions (detected using phase-sensitive inversion recovery (PSIR) imaging) and extra-lesional cortical grey matter, and assess associations with disability in relapse-onset MS. Seventy-two people with MS (46 relapsing-remitting (RR), 26 secondary progressive (SP)) and 36 healthy controls were included in this study. MTR, mean diffusivity and fractional anisotropy were measured in lesional and extra-lesional cortical grey matter. Mean fractional anisotropy was higher and MTR lower in lesional compared with extra-lesional cortical grey matter. In extra-lesional cortical grey matter mean fractional anisotropy and MTR were lower, and mean diffusivity was higher in the MS group compared with controls. Mean MTR was lower and mean diffusivity was higher in lesional and extra-lesional cortical grey matter in SPMS when compared with RRMS. These differences were independent of disease duration. In multivariate analyses, MTR in extra-lesional more so than lesional cortical grey matter was associated with disability. Magnetic resonance abnormalities in lesional and extra-lesional cortical grey matter are greater in SPMS than RRMS. Changes in extra-lesional compared with lesional cortical grey matter are more consistently associated with disability. © The Author(s), 2015.

  1. Coupled biochemical genetic and karyomorphological analyses for ...

    African Journals Online (AJOL)

    S. esocinus showed five bands, S. curvifrons five, S. niger seven, S. labiatus and S. plagiostomus each showed six bands; they also showed species characteristic bands. Karyotypic study of these was carried out. The diploid chromosome numbers recorded were 98 in S. niger (24 m + 32 sm + 22 st + 20 t), 98 in S. esocinus ...

  2. Chemical analyses, antibacterial activity and genetic diversity ...

    African Journals Online (AJOL)

    The phylogenetic tree separated the varieties into discrete clusters according to their respective citrus group. Citrus groups were initially divided into two main clusters at 0.18 level of similarity. Lemon, lime, mandarin and sour orange were grouped in the first cluster, while sweet orange, grapefruit and pummelo were nested ...

  3. Chemical analyses, antibacterial activity and genetic diversity ...

    African Journals Online (AJOL)

    SAM

    2014-06-25

    Jun 25, 2014 ... orange were grouped in the first cluster, while sweet orange, grapefruit and pummelo were nested in the second cluster. ... This information can provide ...... Rekha C, Poornima G, Manasa M, Abhipsa V, Pavithra Devi J, Vijay.

  4. Masticator space lesions: MRI and CT findings

    International Nuclear Information System (INIS)

    Kim, Seung Hoon; Han, Moon Hee; Chang, Kee Kyun; Kim, Kwang Hyun; Song, Jae Uoo; Jo, In Cheol; Yeon, Kyung Mo

    1995-01-01

    We evaluated the MR and CT findings of the masticator space lesions in order to identify the differences among the malignant and benign tumors and infectious conditions. MR and CT findings in 46 cases with proven masticator space lesions were reviewed retrospectively. We analysed the involvement of masticator muscles, adjacent spaces, orbit and intracranium, homogeneity, necrosis, cystic changes, growth patterns, calcifications, enhancement patterns, MR signal intensity, and CT attenuation. Among the 29 cases of malignant tumors, seven cases were mandibular tumors including four chondrosarcomas, and 22 cases were extramandibular tumors. Malignant tumors of mandibular origin showed large masses with severe bone destruction and epicenter of mandible. Extramandibular malignant tumors showed the epicenter out of the mandible and less severe bone destruction than mandibular tumors. Among the nine benign tumors, four cases were ameloblastomas which showed the well-defined masses and the expansion of the mandible, and four cases were extramandibular tumors which showed well-marginated extramandibular masses with no bone destruction. Among the eight infectious conditions, five cases were mandibular osteomyelitis with or without abscess formations, and the other three cases were infections from adjacent soft tissue or limited to the soft tissue. By careful observations of growth patterns, involvement of the masticator and adjacent spaces, bone changes, and epicenter of the lesions, one can discriminate a mandibular lesion from an extramandibular lesion. With this approach, it is thought to be easier to suggest a diagnosis among a wide spectrum of masticator lesions

  5. Precancerous Skin Lesions.

    Science.gov (United States)

    Ferrándiz, C; Malvehy, J; Guillén, C; Ferrándiz-Pulido, C; Fernández-Figueras, M

    Certain clinically and histologically recognizable skin lesions with a degree of risk of progression to squamous cell carcinoma have been traditionally grouped as precancerous skin conditions but now tend to be classified as in situ carcinomas. This consensus statement discusses various aspects of these lesions: their evaluation by means of clinical and histopathologic features, the initial evaluation of the patient, the identification of risk factors for progression, and the diagnostic and treatment strategies available today. Copyright © 2016 AEDV. Publicado por Elsevier España, S.L.U. All rights reserved.

  6. Mitogenomic analyses from ancient DNA

    DEFF Research Database (Denmark)

    Paijmans, Johanna L. A.; Gilbert, Tom; Hofreiter, Michael

    2013-01-01

    The analysis of ancient DNA is playing an increasingly important role in conservation genetic, phylogenetic and population genetic analyses, as it allows incorporating extinct species into DNA sequence trees and adds time depth to population genetics studies. For many years, these types of DNA...... analyses (whether using modern or ancient DNA) were largely restricted to the analysis of short fragments of the mitochondrial genome. However, due to many technological advances during the past decade, a growing number of studies have explored the power of complete mitochondrial genome sequences...... yielded major progress with regard to both the phylogenetic positions of extinct species, as well as resolving population genetics questions in both extinct and extant species....

  7. Common conjunctival lesions

    African Journals Online (AJOL)

    Conjunctival lesions are frequently seen in the eye clinic, because the conjunctiva is readily ... anti-histamine drops and mast cell stabilisers can be used. e more severe cases have to be .... Ehlers J, Shah C . The Wills Eye Manual. Office and.

  8. Skin lesion removal

    Science.gov (United States)

    ... likely to be done when there is a concern about a skin cancer. Most often, an area the shape of an ellipse is removed, as this makes it easier to close with stitches. The entire lesion is removed, going as deep as the fat, if needed, to ...

  9. Genital lesions following bestiality

    Directory of Open Access Journals (Sweden)

    Mittal A

    2000-01-01

    Full Text Available A 48-year-old man presented with painful genital lesions with history of bestiality and abnor-mal sexual behaviour. Examination revealed multiple irregular tender ulcers and erosions, with phimosis and left sided tender inguinal adenopathy. VDRL, TPHA, HIV-ELISA were negative. He was treated with ciprofloxacin 500mg b.d. along with saline compresses with complete resolution.

  10. Morel-Lavallee lesion.

    Science.gov (United States)

    Li, Hui; Zhang, Fangjie; Lei, Guanghua

    2014-01-01

    To review current knowledge of the Morel-Lavallee lesion (MLL) to help clinicians become familiar with this entity. Familiarization may decrease missed diagnoses and misdiagnoses. It could also help steer the clinician to the proper treatment choice. A search was performed via PubMed and EMBASE from 1966 to July 2013 using the following keywords: Morel-Lavallee lesion, closed degloving injury, concealed degloving injury, Morel-Lavallee effusion, Morel-Lavallee hematoma, posttraumatic pseudocyst, posttraumatic soft tissue cyst. Chinese and English language literatures relevant to the subject were collected. Their references were also reviewed. Morel-Lavallee lesion is a relatively rare condition involving a closed degloving injury. It is characterized by a filled cystic cavity created by separation of the subcutaneous tissue from the underlying fascia. Apart from the classic location over the region of the greater trochanter, MLLs have been described in other parts of the body. The natural history of MLL has not yet been established. The lesion may decrease in volume, remain stable, enlarge progressively or show a recurrent pattern. Diagnosis of MLL was often missed or delayed. Ultrasonography, computed tomography, and magnetic resonance imaging have great value in the diagnosis of MLL. Treatment of MLL has included compression, local aspiration, open debridement, and sclerodesis. No standard treatment has been established. A diagnosis of MLL should be suspected when a soft, fluctuant area of skin or chronic recurrent fluid collection is found in a region exposed to a previous shear injury. Clinicians and radiologists should be aware of both the acute and chronic appearances to make the correct diagnosis. Treatment decisions should base on association with fractures, the condition of the lesion, symptom and desire of the patient.

  11. Maxillomandibular giant osteosclerotic lesions

    Directory of Open Access Journals (Sweden)

    Constantino LEDESMA-MONTES

    2018-06-01

    Full Text Available Abstract Giant Osteosclerotic Lesions (GOLs are a group of rarely reported intraosseous lesions. Their precise diagnosis is important since they can be confused with malignant neoplasms. Objective This retrospective study aimed to record and analyze the clinical and radiographic Giant Osteosclerotic Lesions (GOLs detected in the maxillomandibular area of patients attending to our institution. Materials and Methods: Informed consent from the patients was obtained and those cases of 2.5 cm or larger lesions with radiopaque or mixed (radiolucid-radiopaque appearance located in the maxillofacial bones were selected. Assessed parameters were: age, gender, radiographic aspect, shape, borders, size, location and relations to roots. Lesions were classified as radicular, apical, interradicular, interradicular-apical, radicular-apical or located in a previous teeth extraction area. Additionally, several osseous and dental developmental alterations (DDAs were assessed. Results Seventeen radiopacities in 14 patients were found and were located almost exclusively in mandible and were two types: idiopathic osteosclerosis and condensing osteitis. GOLs were more frequent in females, and in the anterior and premolar zones. 94.2% of GOLs were qualified as idiopathic osteosclerosis and one case was condensing osteitis. All studied cases showed different osseous and dental developmental alterations (DDAs. The most common were: Microdontia, hypodontia, pulp stones, macrodontia and variations in the mental foramina. Conclusions GOLs must be differentiated from other radiopaque benign and malignant tumors. Condensing osteitis, was considered an anomalous osseous response induced by a chronic low-grade inflammatory stimulus. For development of idiopathic osteosclerosis, two possible mechanisms could be related. The first is modification of the normal turnover with excessive osseous deposition. The second mechanism will prevent the normal bone resorption, arresting the

  12. Detection of early lung cancer lesions in surgical resections and in bronchial and transbronchial biopsies

    International Nuclear Information System (INIS)

    Rott, T.; Jerse, M.; Tercelj, M.; Erzen, J.

    2006-01-01

    Background. Overall bad prognosis of lung cancer is mostly due to too late detection of early lung cancer, which may be treated with good success. Therefore, different diagnostic methods are developing for more efficient detection of early lung cancer: besides modern radiological, bronchoscopic methods with additional fluorescence techniques, quantitative cytological investigations, also histological and molecular investigations are included. Histology may reveal early preinvasive lung cancer lesions, associated early during multistep lung carcinogenesis with molecular genetic changes. Patients and methods. Preinvasive epithelial lung cancer lesions we searched in two groups of patients. In the first group of 316 patients from the period March 2003 - August 2006, 498 bronchial and transbronchial biopsies were examined for squamous metaplasia and dysplasia, carcinoma in situ, and invasive tumours. In the second group of 238 patients from the period January 2004 - August 2006, resected primary lung tumours were analysed for preinvasive and invasive neuroendocrine tumours and atypical adenomatous hyperplasia. Results. The most frequent changes in bronchial and transbronchial biopsies were squamous metaplasia (46.5%), simple or goblet cell hyperplasia of the bronchial epithelium (44.3%), malignant tumours (20.66%) and squamous dysplasia (16.1%), but rare carcinoma in situ (0.63%). Diffuse idiopathic pulmonary neuroendocrine cell hyperplasia was found in 15 (6.3%) cases in the vicinity of 238 resected lung cancer specimens, carcinoid in 12 patients (5%), and mostly combined large cell neuroendocrine cancer in 21 patients (8.8%). Atypical adenomatous hyperplasia was found in 2 patients. Conclusions. Classical histological analysis should be focused on detection of early preinvasive epithelial lung cancer lesions. Additional available molecular investigations may reveal gradual genetic changes characteristic for a series of the preinvasive epithelial histological changes

  13. Tracing the origin of glomerular extracapillary lesions from parietal epithelial cells.

    Science.gov (United States)

    Smeets, Bart; Uhlig, Sandra; Fuss, Astrid; Mooren, Fieke; Wetzels, Jack F M; Floege, Jürgen; Moeller, Marcus J

    2009-12-01

    Cellular lesions form in Bowman's space in both crescentic glomerulonephritis and collapsing glomerulopathy. The pathomechanism and origin of the proliferating cells in these lesions are unknown. In this study, we examined proliferating cells by lineage tracing of either podocytes or parietal epithelial cells (PECs) in the nephrotoxic nephritis model of inflammatory crescentic glomerulonephritis. In addition, we traced the fate of genetically labeled PECs in the Thy-1.1 transgenic mouse model of collapsing glomerulopathy. In both models, cellular bridges composed of PECs were observed between Bowman's capsule and the glomerular tuft. Genetically labeled PECs also populated larger, more advanced cellular lesions. In these lesions, we detected de novo expression of CD44 in activated PECs. In contrast, we rarely identified genetically labeled podocytes within the cellular lesions of crescentic glomerulonephritis. In conclusion, PECs constitute the majority of cells that compose early extracapillary proliferative lesions in both crescentic glomerulonephritis and collapsing glomerulopathy, suggesting similar pathomechanisms in both diseases.

  14. Semi-automated Robust Quantification of Lesions (SRQL Toolbox

    Directory of Open Access Journals (Sweden)

    Kaori L Ito

    2017-05-01

    Full Text Available Quantifying lesions in a reliable manner is fundamental for studying the effects of neuroanatomical changes related to recovery in the post-stroke brain. However, the wide variability in lesion characteristics across individuals makes manual lesion segmentation a challenging and often subjective process. This often makes it difficult to combine stroke lesion data across multiple research sites, due to subjective differences in how lesions may be defined. Thus, we developed the Semi-automated Robust Quantification of Lesions (SRQL; https://github.com/npnl/SRQL; DOI: 10.5281/zenodo.557114 Toolbox that performs several analysis steps: 1 a white matter intensity correction that removes healthy white matter voxels from the lesion mask, thereby making lesions slightly more robust to subjective errors; 2 an automated report of descriptive statistics on lesions for simplified comparison between or across groups, and 3 an option to perform analyses in both native and standard space to facilitate analyses in either space. Here, we describe the methods implemented in the toolbox.

  15. Semi-automated Robust Quantification of Lesions (SRQL Toolbox

    Directory of Open Access Journals (Sweden)

    Kaori Ito

    2017-02-01

    Full Text Available Quantifying lesions in a robust manner is fundamental for studying the effects of neuroanatomical changes in the post-stroke brain on recovery. However, the wide variability in lesion characteristics across individuals makes manual lesion segmentation a challenging and often subjective process. This makes it difficult to combine stroke lesion data across multiple research sites, due to subjective differences in how lesions may be defined. We developed the Semi-automated Robust Quantification of Lesions (SRQL; https://github.com/npnl/SRQL; DOI: 10.5281/zenodo.267213 Toolbox that performs several analysis steps: 1 a white matter intensity correction that removes healthy white matter voxels from the lesion mask, thereby making lesions slightly more robust to subjective errors; 2 an automated report of descriptive statistics on lesions for simplified comparison between or across groups, and 3 an option to perform analyses in both native and standard space to facilitate analyses in either space, or comparisons between spaces. Here, we describe the methods implemented in the toolbox and demonstrate the outputs of the SRQL toolbox.

  16. Computed tomographic localization of Rt. Juxtadiaphragmatic lesions

    International Nuclear Information System (INIS)

    Lee, Jong Doo; Choe, Kyu Ok; Kim, Ki Whang; Hong, In Soo

    1989-01-01

    Since several reports were published about CT differentiation of peridiaphragmatic fluid collection using 4 useful signs-diaphragm, displaced crus, bare area and interface signs. Transverse CT scans of 20 patients with abnormal diaphragmatic position due to large intrathoracic or intraabdominal lesion were analysed on the basis of those signs. Difficulties were encounted with differentiation when laterally located lesions did not extend to as far medially as crus, and when diaphragmatic stripe could not be distinguished from thickened pleura or adjacent wall of lesions. As a result, limited cases can be adequately assessed by diaphragm or displaced crus sign. Furthermore, bare area and interface signs seemed to be not useful at all. However relationship between caudal tip of lesions and thoracoabdominal wall was always constant in each thoracic or abdominal lesions. All of intrathoracic masses or empyemas were attached to thoracic wall displacing properitoneal and perirenal fat medially or inferiorly. By contraries, all of intraabdominal masses were separated from abdominal wall displacing properitoneal fat or peritoneum laterally. The key to accurate localization seemed to be identification of such relationship

  17. Acute periodontal lesions.

    Science.gov (United States)

    Herrera, David; Alonso, Bettina; de Arriba, Lorenzo; Santa Cruz, Isabel; Serrano, Cristina; Sanz, Mariano

    2014-06-01

    This review provides updates on acute conditions affecting the periodontal tissues, including abscesses in the periodontium, necrotizing periodontal diseases and other acute conditions that cause gingival lesions with acute presentation, such as infectious processes not associated with oral bacterial biofilms, mucocutaneous disorders and traumatic and allergic lesions. A periodontal abscess is clinically important because it is a relatively frequent dental emergency, it can compromise the periodontal prognosis of the affected tooth and bacteria within the abscess can spread and cause infections in other body sites. Different types of abscesses have been identified, mainly classified by their etiology, and there are clear differences between those affecting a pre-existing periodontal pocket and those affecting healthy sites. Therapy for this acute condition consists of drainage and tissue debridement, while an evaluation of the need for systemic antimicrobial therapy will be made for each case, based on local and systemic factors. The definitive treatment of the pre-existing condition should be accomplished after the acute phase is controlled. Necrotizing periodontal diseases present three typical clinical features: papilla necrosis, gingival bleeding and pain. Although the prevalence of these diseases is not high, their importance is clear because they represent the most severe conditions associated with the dental biofilm, with very rapid tissue destruction. In addition to bacteria, the etiology of necrotizing periodontal disease includes numerous factors that alter the host response and predispose to these diseases, namely HIV infection, malnutrition, stress or tobacco smoking. The treatment consists of superficial debridement, careful mechanical oral hygiene, rinsing with chlorhexidine and daily re-evaluation. Systemic antimicrobials may be used adjunctively in severe cases or in nonresponding conditions, being the first option metronidazole. Once the acute

  18. Liposarcoma or lipoma: Does genetics change classic imaging criteria?

    International Nuclear Information System (INIS)

    Bidault, F.; Vanel, D.; Terrier, Ph.; Jalaguier, A.; Bonvalot, S.; Pedeutour, F.; Couturier, J.M.; Dromain, C.

    2009-01-01

    Differentiating benign from malignant fatty tumours has always been very difficult for both radiologists and pathologists. Cytogenetic and molecular genetic analyses provide complementary tools for differentiating soft tissue tumours. Our objective was to compare imaging criteria of malignancy with a new diagnostic gold standard, namely, pathological analysis combined with cytogenetic and molecular genetic analyses. Nineteen patients with a fatty tumour were included. All had computed tomography and/or magnetic resonance imaging examination before any biopsy or surgery. All had histopathological and cytogenetic and/or molecular genetic analyses. The imaging diagnosis of benign or malignant lesions was accurate in 15 cases, with 4 false positives for malignancy. Erroneous criteria were a large size (4 cases), and a mass that was not purely fatty. In conclusion, the main pitfall for a false positive radiological diagnosis of liposarcoma is certainly a large-sized tumour. Cytogenetic and molecular genetic analyses contribute to the diagnosis and can be performed at the same time with a core biopsy.

  19. Design and rationale for examining neuroimaging genetics in ischemic stroke: The MRI-GENIE study.

    Science.gov (United States)

    Giese, Anne-Katrin; Schirmer, Markus D; Donahue, Kathleen L; Cloonan, Lisa; Irie, Robert; Winzeck, Stefan; Bouts, Mark J R J; McIntosh, Elissa C; Mocking, Steven J; Dalca, Adrian V; Sridharan, Ramesh; Xu, Huichun; Frid, Petrea; Giralt-Steinhauer, Eva; Holmegaard, Lukas; Roquer, Jaume; Wasselius, Johan; Cole, John W; McArdle, Patrick F; Broderick, Joseph P; Jimenez-Conde, Jordi; Jern, Christina; Kissela, Brett M; Kleindorfer, Dawn O; Lemmens, Robin; Lindgren, Arne; Meschia, James F; Rundek, Tatjana; Sacco, Ralph L; Schmidt, Reinhold; Sharma, Pankaj; Slowik, Agnieszka; Thijs, Vincent; Woo, Daniel; Worrall, Bradford B; Kittner, Steven J; Mitchell, Braxton D; Rosand, Jonathan; Golland, Polina; Wu, Ona; Rost, Natalia S

    2017-10-01

    To describe the design and rationale for the genetic analysis of acute and chronic cerebrovascular neuroimaging phenotypes detected on clinical MRI in patients with acute ischemic stroke (AIS) within the scope of the MRI-GENetics Interface Exploration (MRI-GENIE) study. MRI-GENIE capitalizes on the existing infrastructure of the Stroke Genetics Network (SiGN). In total, 12 international SiGN sites contributed MRIs of 3,301 patients with AIS. Detailed clinical phenotyping with the web-based Causative Classification of Stroke (CCS) system and genome-wide genotyping data were available for all participants. Neuroimaging analyses include the manual and automated assessments of established MRI markers. A high-throughput MRI analysis pipeline for the automated assessment of cerebrovascular lesions on clinical scans will be developed in a subset of scans for both acute and chronic lesions, validated against gold standard, and applied to all available scans. The extracted neuroimaging phenotypes will improve characterization of acute and chronic cerebrovascular lesions in ischemic stroke, including CCS subtypes, and their effect on functional outcomes after stroke. Moreover, genetic testing will uncover variants associated with acute and chronic MRI manifestations of cerebrovascular disease. The MRI-GENIE study aims to develop, validate, and distribute the MRI analysis platform for scans acquired as part of clinical care for patients with AIS, which will lead to (1) novel genetic discoveries in ischemic stroke, (2) strategies for personalized stroke risk assessment, and (3) personalized stroke outcome assessment.

  20. Genetic effects

    International Nuclear Information System (INIS)

    Abrahamson, S.; Bender, M.; Denniston, C.; Schull, W.

    1985-01-01

    Modeling analyses are used to predict the outcomes for two nuclear power plant accident scenarios, the first in which the population received a chronic dose of 0.1 Gy (10 rad) over a 50 year period, the second in which an equivalent population receives acute dose of 2 Gy. In both cases the analyses are projected over a period of five generations. The risk analysis takes on two major forms: the increase in genetic disease that would be observed in the immediate offspring of the exposed population, and the subsequent transmission of the newly induced mutations through future generations. The classes of genetic diseases studied are: dominant gene mutation, X-linked gene mutation, chromosome disorders and multifactorial disorders which involve the interaction of many mutant genes and environmental factors. 28 references, 3 figures, 5 tables

  1. Localization of lesions in aphasia

    International Nuclear Information System (INIS)

    Hojo, Kei; Watanabe, Shunzo; Tasaki, Hiroichi; Sato, Tokijiro; Metoki, Hirobumi.

    1984-01-01

    Using a microcomputer, the locus and extent of the lesions, as demonstrated by computed tomography for 127 cases with various types of aphasia were superimposed onto standardized marices. The relationship between the foci of the lesions and the types of aphasia was investigated. Broca aphasics (n=39) : Since the accumulated site of the lesions highly involved the deep structures of the lower part of the precentral gyrus as well as the insula and lenticular nucleus, only 60% of the Broca aphasics had lesions on these areas. This finding has proved to have little localizing value. Wernicke aphasics (n=23) : The size of the lesion was significantly smaller than Broca's aphasia. At least 70% of the patients had the superior temporal lesions involving Wernicke's area and subcortical lesions of the superior and middle temporal gyri. Amnestic aphasics (n=18) : The size of the lesion was smaller than any other types. While there was some concentration of the lesions (maximum 40%) in the area of the subcortical region of the anterior temporal gyrus adjacent to Wernicke's area and the lenticular nucleus, the lesions were distributed throughout the left hemisphere. Amnestic aphasia was thought to be the least localizable. Conduction aphasics (n=11) : The lesions were relatively small in size. Many patients had posterior speech area lesions involving at least partially Wernicke's area. In particular, more than 80% of the conduction aphasics had lesions of the supramarginal gyrus and it's adjacent deep structures. Global aphasics (n=36) : In general, the size of the lesion was very large and 70% of the global aphasics had extensive lesions involving both Broca's and Wernicke's areas. However, there were observations showing that the lesions can be small and confined. (J.P.N.)

  2. A disappearing neonatal skin lesion.

    LENUS (Irish Health Repository)

    Hawkes, Colin Patrick

    2012-01-31

    A preterm baby girl was noted at birth to have a firm, raised, non-tender skin lesion located over her right hip. She developed three similar smaller lesions on her ear, buttock and right knee. All lesions had resolved by 2 months of age.

  3. CT-guided transthoracic core needle biopsy for small pulmonary lesions: diagnostic performance and adequacy for molecular testing.

    Science.gov (United States)

    Tian, Panwen; Wang, Ye; Li, Lei; Zhou, Yongzhao; Luo, Wenxin; Li, Weimin

    2017-02-01

    Computed tomography (CT)-guided transthoracic needle biopsy is a well-established, minimally invasive diagnostic tool for pulmonary lesions. Few large studies have been conducted on the diagnostic performance and adequacy for molecular testing of transthoracic core needle biopsy (TCNB) for small pulmonary lesions. This study included CT-guided TCNB with 18-gauge cutting needles in 560 consecutive patients with small (≤3 cm) pulmonary lesions from January 2012 to January 2015. There were 323 males and 237 females, aged 51.8±12.7 years. The size of the pulmonary lesions was 1.8±0.6 cm. The sensitivity, specificity, accuracy and complications of the biopsies were investigated. The risk factors of diagnostic failure were assessed using univariate and multivariate analyses. The sample's adequacy for molecular testing of non-small cell lung cancer (NSCLC) was analyzed. The overall sensitivity, specificity, and accuracy for diagnosis of malignancy were 92.0% (311/338), 98.6% (219/222), and 94.6% (530/560), respectively. The incidence of bleeding complications was 22.9% (128/560), and the incidence of pneumothorax was 10.4% (58/560). Logistic multivariate regression analysis showed that the independent risk factors for diagnostic failure were a lesion size ≤1 cm [odds ratio (OR), 3.95; P=0.007], lower lobe lesions (OR, 2.83; P=0.001), and pneumothorax (OR, 1.98; P=0.004). Genetic analysis was successfully performed on 95.45% (168/176) of specimens diagnosed as NSCLC. At least 96.8% of samples with two or more passes from a lesion were sufficient for molecular testing. The diagnostic yield of small pulmonary lesions by CT-guided TCNB is high, and the procedure is relatively safe. A lesion size ≤1 cm, lower lobe lesions, and pneumothorax are independent risk factors for biopsy diagnostic failure. TCNB specimens could provide adequate tissues for molecular testing.

  4. Lesiones deportivas Sports injuries

    Directory of Open Access Journals (Sweden)

    Isabel Cristina Gallego Ching

    2007-04-01

    Full Text Available El estrés generado por la práctica deportiva ha originado una mayor probabilidad de que los atletas presenten lesiones agudas y crónicas. En el ámbito mundial existen diferentes investigaciones acerca de la incidencia de lesiones deportivas. La comparación de sus resultados es difícil por las diferencias en las características de la población y en la forma de reportar los datos, que varía ampliamente entre los estudios (proporciones o tasas de incidencia o tasas por cada 100 ó 1.000 participantes o tasas por horas de juego o por número de partidos jugados. Las tasas varían entre 1,7 y 53 lesiones por 1.000 horas de práctica deportiva, entre 0,8 y 90,9 por 1.000 horas de entrenamiento, entre 3,1 y 54,8 por 1.000 horas de competición y de 6,1 a 10,9 por 100 juegos. La gran variación entre las tasas de incidencia se explica por las diferencias existentes entre los deportes, los países, el nivel competitivo, las edades y la metodología empleada en los estudios. Se ha definido la lesión deportiva como la que ocurre cuando los atletas están expuestos a la práctica del deporte y se produce alteración o daño de un tejido, afectando el funcionamiento de la estructura. Los deportes de contacto generan mayor riesgo de presentar lesiones; se destacan al respecto los siguientes: fútbol, rugby, baloncesto, balonmano, artes marciales y jockey. Las lesiones ocurren con mayor probabilidad en las competencias que en el entrenamiento. Stress generated by sports practice has increased the probability that athletes suffer from acute and chronic injuries. Worldwide, there have been many different investigations concerning the incidence of sport injuries. The different ways in which results have been presented makes it difficult to compare among them. Rates of sports injuries vary between 1.7 and 53 per 1.000 hours of sports practice; 0.8 and 90.9 per 1.000 hours of training; 3.1 and 54.8 per 1.000 hours of competition, and 6.1 and 10.9 per 100

  5. Analysis of pulmonary coin lesions

    International Nuclear Information System (INIS)

    Kim, O; Kim, K. H.; Oh, K. K.; Park, C. Y.

    1979-01-01

    For A long time the solitary pulmonary nodule has remained a difficult problem to solve and has attracted a great deal of attension in recent years. Circumscribed coin lesions of the lung were generally peripheral in location with respect to the pulmonary hilus. Because of this, important clinical problem in management and diagnosis arise. Such a lesion is discovered through roentgenologic examination. So the roentgenologists is the first be in a position to offer advise. This presentation is an attempt to correlate a useful diagnosis with roentgenologic findings of pulmonary coin lesion which enables us to get differential diagnosis of benign and malignant lesion. Histologically proven 120 cases of the pulmonary coin lesion during the period of 8 years were reviewed through plain film, tomogram, bronchoscopy, variable laboratory findings, and clinical history. The results are as follows: 1. Male to female sex ratio was 3 : 1. In age distribution, most of the malignant pulmonary coin lesion appeared in 6th decade (39%) and 5th decade (27%). In benign lesion, the most cases were in 3 rd decade. 2. Pathological cell type are as follows: Primary bronchogenic cancer 43.3%, tuberculoma 25.8%, inflammatory lesion 17.5%, benign tumor 10%, and bronchial adenoma, harmartoma, A.V. malformation, mesothelioma, are 1 case respectively. As a result benign and malignant lesion showed equal distribution (49.1% : 50.3%). 3. In symptom analysis ; cough is the most common (43.5%) symptom in malignant lesion, next follows hemoptysis (20.9%) and chest pain (14.5%). In benign lesion, most of the patient (32.7%) did not complain any symptom. 4. In malignant lesion, the most common nodular size was 4 cm (32.3%), and in benign lesion 2 cm sized coin was most common (39.3%). 5. In general, margin of nodule was very sharp and well demarcated in benign lesion (83.3%), and in malignant lesion that was less demarcated and poorly defined. 6. Most case of calcification (82.7%) was seen in benign

  6. Managing Carious Lesions

    DEFF Research Database (Denmark)

    Innes, N P T; Frencken, J E; Bjørndal, L

    2016-01-01

    Variation in the terminology used to describe clinical management of carious lesions has contributed to a lack of clarity in the scientific literature and beyond. In this article, the International Caries Consensus Collaboration presents 1) issues around terminology, a scoping review of current...... manifestations to the histopathology, we have based the terminology around the clinical consequences of disease (soft, leathery, firm, and hard dentine). Approaches to carious tissue removal are defined: 1)selective removal of carious tissue-includingselective removal to soft dentineandselective removal to firm...

  7. Study of genital lesions

    Directory of Open Access Journals (Sweden)

    Anand Kumar B

    2003-03-01

    Full Text Available A total of one hundred patients (75 males and 25 females age ranged from 17-65 years with genital lesions attending the STD clinic of Bowring and LC Hospitals Bangalore constituted the study group. Based on clinical features, the study groups were classified as syphilis (39, chancroid (30, herpes genitolis (13, condylomato lato (9, LGV (7t condylomata acuminata (5, genital scabies (3, granuloma inguinole (2 and genital candidiasis (1. In 68% microbiological findings confirmed the clinical diagnosis. Of the 100 cases 13% and 2% were positive for HIV antibodies and HbsAg respectively.

  8. CAROTID ATHEROSCLEROTIC LESION IN YOUNG PATIENTS

    Directory of Open Access Journals (Sweden)

    N. V. Pizova

    2014-01-01

    Full Text Available Objective: to determine the incidence of atherosclerotic lesions in the carotid and vertebral arteries of young patients from Doppler ultrasound data and to compare the quantitatively assessed traditional risk factors of coronary heart disease (CHD with severe extracranial artery atherosclerotic lesion.Subjects and methods. Doppler ultrasound was carried out evaluating structural changes in the aortic arch branches in 1563 railway transport workers less than 45 years of age. A separate sample consisted of 68 young people with carotid atherosclerotic changes, in whom traditional risk factors for CHD were studied, so were in a control group of individuals without atherosclerotic changes (n = 38.Results. Among the examinees, carotid atherosclerotic lesion was detected in 112 (7.1 % cases, the increase in the rate of atherosclerotic plaques in patients aged 35–45 years being 9.08 %; that in the rate of local intima-media thickness in those aged 31–40 years being 5.1 %. Smoking (particularly that along with hypercholesterolemia and a family history of cardiovascular diseases, obesity (along with low activity, and emotional overstrain were defined as important risk factors in the young patients. Moreover, factor analysis has shown that smoking,hypertension, and early cardiovascular pathology in the next of kin makes the greatest contribution to the development of carotid atherosclerotic lesion.Conclusion. Among the patients less than 45 years of age, carotid and vertebral artery atherosclerotic changes were found in 112 (7.1 % cases, which were more pronounced in male patients. Smoking, particularly along with hypercholesterolemia and genetic predisposition to cardiovascular diseases, was a risk factor that had the highest impact on the degree of atherosclerotic lesion in the aortic arch branches of the young patients.

  9. PCR in forensic genetics

    DEFF Research Database (Denmark)

    Morling, Niels

    2009-01-01

    Since the introduction in the mid-1980s of analyses of minisatellites for DNA analyses, a revolution has taken place in forensic genetics. The subsequent invention of the PCR made it possible to develop forensic genetics tools that allow both very informative routine investigations and still more...... and more advanced, special investigations in cases concerning crime, paternity, relationship, disaster victim identification etc. The present review gives an update on the use of DNA investigations in forensic genetics.......Since the introduction in the mid-1980s of analyses of minisatellites for DNA analyses, a revolution has taken place in forensic genetics. The subsequent invention of the PCR made it possible to develop forensic genetics tools that allow both very informative routine investigations and still more...

  10. Diffusion-weighted imaging in characterization of cystic pancreatic lesions

    Energy Technology Data Exchange (ETDEWEB)

    Sandrasegaran, K., E-mail: ksandras@iupui.edu [Department of Radiology, Indiana University School of Medicine, Indianapolis, IN (United States); Akisik, F.M.; Patel, A.A.; Rydberg, M. [Department of Radiology, Indiana University School of Medicine, Indianapolis, IN (United States); Cramer, H.M.; Agaram, N.P. [Department of Pathology, Indiana University School of Medicine, Indianapolis, IN (United States); Schmidt, C.M. [Department of Surgery, Indiana University School of Medicine, Indianapolis, IN (United States)

    2011-09-15

    Aim: To evaluate whether apparent diffusion coefficient (ADC) measurements from diffusion-weighted imaging (DWI) can characterize or predict the malignant potential of cystic pancreatic lesions. Materials and methods: Retrospective review of the magnetic resonance imaging (MRI) database over a 2-year period revealed 136 patients with cystic pancreatic lesions. Patients with DWI studies and histological confirmation of cystic mass were included. In patients with known pancreatitis, lesions with amylase content of >1000 IU/l that resolved on subsequent scans were included as pseudocysts. ADC of cystic lesions was measured by two independent reviewers. These values were then compared to categorize these lesions as benign or malignant using conventional MRI sequences. Results: Seventy lesions were analysed: adenocarcinoma (n = 4), intraductal papillary mucinous neoplasm (IPMN; n = 28), mucinous cystic neoplasm (MCN; n = 9), serous cystadenoma (n = 16), and pseudocysts (n = 13). There was no difference between ADC values of malignant and non-malignant lesions (p = 0.06), between mucinous and serous tumours (p = 0.12), or between IPMN and MCN (p = 0.42). ADC values for low-grade IPMN were significantly higher than those for high-grade or invasive IPMN (p = 0.03). Conclusion: ADC values may be helpful in deciding the malignant potential of IPMN. However, they are not useful in differentiating malignant from benign lesions or for characterizing cystic pancreatic lesions.

  11. Vascular lesions following radiation

    International Nuclear Information System (INIS)

    Fajardo, L.F.; Berthrong, M.

    1988-01-01

    The special radiation sensitivity of the vascular system is mainly linked to that of endothelial cells, which are perhaps the most radiation-vulnerable elements of mesenchymal tissues. Within the vascular tree, radiation injures most often capillaries, sinusoids, and small arteries, in that order. Lesions of veins are observed less often, but in certain tissues the veins are regularly damaged (e.g., intestine) or are the most affected structures (i.e., liver). Large arteries do suffer the least; however, when significant damage does occur in an elastic artery (e.g., thrombosis or rupture), it tends to be clinically significant and even fatal. Although not always demonstrable in human tissues, radiation vasculopathy generally is dose and time dependent. Like other radiation-induced lesions, the morphology in the vessels is not specific, but it is characteristic enough to be often recognizable. Vascular injury, especially by therapeutic radiation is not just a morphologic marker. It is a mediator of tissue damage; perhaps the most consistent pathogenetic mechanism in delayed radiation injury

  12. Genetic effects

    International Nuclear Information System (INIS)

    Bender, M.A.; Abrahamson, S.; Denniston, C.; Schull, W.J.

    1989-01-01

    In this chapter, we present a comprehensive analysis of the major classes of genetic diseases that would be increased as a result of an increased gonadal radiation exposure to a human population. The risk analysis takes on two major forms: the increase in genetic disease that would be observed in the immediate offspring of the exposed population, and the subsequent transmission of the newly induced mutations through future generations. The major classes of genetic disease will be induced at different frequencies, and will also impact differentially in terms of survivability and fertility on the affected individuals and their descendants. Some classes of disease will be expected to persist for only a few generations at most. Other types of genetic disease will persist through a longer period. The classes of genetic diseases studied are: dominant gene mutation, X-linked gene mutation, chromosome disorders and multifactorial disorders which involve the interaction of many mutant genes and environmental factors. For each of these classes we have derived the general equations of mutation induction for the male and female germ cells of critical importance in the mutation process. The frequency of induced mutations will be determined initially by the dose received, the type of radiation and, to some extent at high dose, by the manner in which the dose is received. We have used the modeling analyses to predict the outcomes for two nuclear power plant accident scenarios, the first in which the population receives a chronic dose of 0.1 Gy (10 rad) over a 50-year period, the second in which an equivalent population receives an acute dose of 2 Gy. In both cases the analyses are projected over a period of five generations

  13. Maxillary Bone Regeneration Based on Nanoreservoirs Functionalized ε-Polycaprolactone Biomembranes in a Mouse Model of Jaw Bone Lesion

    Directory of Open Access Journals (Sweden)

    Marion Strub

    2018-01-01

    Full Text Available Current approaches of regenerative therapies constitute strategies for bone tissue reparation and engineering, especially in the context of genetical diseases with skeletal defects. Bone regeneration using electrospun nanofibers’ implant has the following objectives: bone neoformation induction with rapid healing, reduced postoperative complications, and improvement of bone tissue quality. In vivo implantation of polycaprolactone (PCL biomembrane functionalized with BMP-2/Ibuprofen in mouse maxillary defects was followed by bone neoformation kinetics evaluation using microcomputed tomography. Wild-Type (WT and Tabby (Ta mice were used to compare effects on a normal phenotype and on a mutant model of ectodermal dysplasia (ED. After 21 days, no effect on bone neoformation was observed in Ta treated lesion (4% neoformation compared to 13% in the control lesion. Between the 21st and the 30th days, the use of biomembrane functionalized with BMP-2/Ibuprofen in maxillary bone lesions allowed a significant increase in bone neoformation peaks (resp., +8% in mutant Ta and +13% in WT. Histological analyses revealed a neoformed bone with regular trabecular structure, areas of mineralized bone inside the membrane, and an improved neovascularization in the treated lesion with bifunctionalized membrane. In conclusion, PCL functionalized biomembrane promoted bone neoformation, this effect being modulated by the Ta bone phenotype responsible for an alteration of bone response.

  14. Automated segmentation of pigmented skin lesions in multispectral imaging

    International Nuclear Information System (INIS)

    Carrara, Mauro; Tomatis, Stefano; Bono, Aldo; Bartoli, Cesare; Moglia, Daniele; Lualdi, Manuela; Colombo, Ambrogio; Santinami, Mario; Marchesini, Renato

    2005-01-01

    The aim of this study was to develop an algorithm for the automatic segmentation of multispectral images of pigmented skin lesions. The study involved 1700 patients with 1856 cutaneous pigmented lesions, which were analysed in vivo by a novel spectrophotometric system, before excision. The system is able to acquire a set of 15 different multispectral images at equally spaced wavelengths between 483 and 951 nm. An original segmentation algorithm was developed and applied to the whole set of lesions and was able to automatically contour them all. The obtained lesion boundaries were shown to two expert clinicians, who, independently, rejected 54 of them. The 97.1% contour accuracy indicates that the developed algorithm could be a helpful and effective instrument for the automatic segmentation of skin pigmented lesions. (note)

  15. Evidence of a major gene from Bayesian segregation analyses of liability to osteochondral diseases in pigs.

    Science.gov (United States)

    Kadarmideen, Haja N; Janss, Luc L G

    2005-11-01

    Bayesian segregation analyses were used to investigate the mode of inheritance of osteochondral lesions (osteochondrosis, OC) in pigs. Data consisted of 1163 animals with OC and their pedigrees included 2891 animals. Mixed-inheritance threshold models (MITM) and several variants of MITM, in conjunction with Markov chain Monte Carlo methods, were developed for the analysis of these (categorical) data. Results showed major genes with significant and substantially higher variances (range 1.384-37.81), compared to the polygenic variance (sigmau2). Consequently, heritabilities for a mixed inheritance (range 0.65-0.90) were much higher than the heritabilities from the polygenes. Disease allele frequencies range was 0.38-0.88. Additional analyses estimating the transmission probabilities of the major gene showed clear evidence for Mendelian segregation of a major gene affecting osteochondrosis. The variants, MITM with informative prior on sigmau2, showed significant improvement in marginal distributions and accuracy of parameters. MITM with a "reduced polygenic model" for parameterization of polygenic effects avoided convergence problems and poor mixing encountered in an "individual polygenic model." In all cases, "shrinkage estimators" for fixed effects avoided unidentifiability for these parameters. The mixed-inheritance linear model (MILM) was also applied to all OC lesions and compared with the MITM. This is the first study to report evidence of major genes for osteochondral lesions in pigs; these results may also form a basis for underpinning the genetic inheritance of this disease in other animals as well as in humans.

  16. Management of Preinvasive Lesions.

    Science.gov (United States)

    Patrono, Maria G; Corzo, Camila; Iniesta, Maria; Ramirez, Pedro T

    2017-12-01

    Serous tubal intraepithelial carcinoma is considered the precursor lesion of high-grade serous carcinoma, and found in both low-risk and high-risk populations. Isolated serous tubal intraepithelial carcinomas in patients with BRCA1/2 mutations are detected in ∼2% of patients undergoing risk-reducing bilateral salpingo-oophorectomy and even with removal of the tubes and ovaries the rate of developing primary peritoneal carcinoma following remains up to 7.5%. Postoperative recommendations after finding incidental STICs remain unclear and surgical staging, adjuvant chemotherapy, or observation have been proposed. Discovery of STIC should prompt consideration of hereditary cancer program referral for BRCA1/2 mutation screening.

  17. Heterogeneity of mammary lesions represent molecular differences

    International Nuclear Information System (INIS)

    Namba, Ruria; Gregg, Jeffrey P; Maglione, Jeannie E; Davis, Ryan R; Baron, Colin A; Liu, Stephenie; Carmack, Condie E; Young, Lawrence JT; Borowsky, Alexander D; Cardiff, Robert D

    2006-01-01

    Human breast cancer is a heterogeneous disease, histopathologically, molecularly and phenotypically. The molecular basis of this heterogeneity is not well understood. We have used a mouse model of DCIS that consists of unique lines of mammary intraepithelial neoplasia (MIN) outgrowths, the premalignant lesion in the mouse that progress to invasive carcinoma, to understand the molecular changes that are characteristic to certain phenotypes. Each MIN-O line has distinguishable morphologies, metastatic potentials and estrogen dependencies. We utilized oligonucleotide expression arrays and high resolution array comparative genomic hybridization (aCGH) to investigate whole genome expression patterns and whole genome aberrations in both the MIN-O and tumor from four different MIN-O lines that each have different phenotypes. From the whole genome analysis at 35 kb resolution, we found that chromosome 1, 2, 10, and 11 were frequently associated with whole chromosome gains in the MIN-Os. In particular, two MIN-O lines had the majority of the chromosome gains. Although we did not find any whole chromosome loss, we identified 3 recurring chromosome losses (2F1-2, 3E4, 17E2) and two chromosome copy number gains on chromosome 11. These interstitial deletions and duplications were verified with a custom made array designed to interrogate the specific regions at approximately 550 bp resolution. We demonstrated that expression and genomic changes are present in the early premalignant lesions and that these molecular profiles can be correlated to phenotype (metastasis and estrogen responsiveness). We also identified expression changes associated with genomic instability. Progression to invasive carcinoma was associated with few additional changes in gene expression and genomic organization. Therefore, in the MIN-O mice, early premalignant lesions have the major molecular and genetic changes required and these changes have important phenotypic significance. In contrast, the changes

  18. Canine Cutaneous Leishmaniasis: Dissemination and Tissue Tropism of Genetically Distinct Leishmania (Viannia braziliensis Populations

    Directory of Open Access Journals (Sweden)

    Guilherme Marx de Oliveira

    2013-01-01

    Full Text Available Little is known regarding the internal dissemination of initial cutaneous lesions and tissue tropism of Leishmania (Viannia braziliensis populations in naturally infected dogs. The aim of this study was to investigate genetic polymorphisms of L. (V. braziliensis populations in different anatomic sites of naturally infected dogs by using polymerase chain reaction (PCR and low-stringency single specific primer-PCR (LSSP-PCR techniques. The amplified products were analyzed by LSSP-PCR to investigate the genetic variability of the parasite populations present in different anatomical sites. Twenty-three out of the 52 samples gave PCR-positive results. The existence of L. (V. braziliensis strains that remained restricted to cutaneous lesions and others showing characteristics of dissemination to internal organs and healthy skin was observed. LSSP-PCR and numerical analyses revealed that parasite populations that do not disseminate were genetically similar and belonged to a separate phenetic cluster. In contrast, populations that showed spreading to internal organs displayed a more polymorphic genetic profile. Despite the heterogeneity, L. (V. braziliensis populations with identical genetic profiles were observed in popliteal and cervical lymph nodes of the same animal. Our results indicate that infection in dogs can be manifested by dissemination and tissue tropism of genetically distinct populations of L. (V. braziliensis.

  19. MALIGNANCY IN LARGE COLORECTAL LESIONS

    Directory of Open Access Journals (Sweden)

    Carlos Eduardo Oliveira dos SANTOS

    2014-09-01

    Full Text Available Context The size of colorectal lesions, besides a risk factor for malignancy, is a predictor for deeper invasion Objectives To evaluate the malignancy of colorectal lesions ≥20 mm. Methods Between 2007 and 2011, 76 neoplasms ≥20 mm in 70 patients were analyzed Results The mean age of the patients was 67.4 years, and 41 were women. Mean lesion size was 24.7 mm ± 6.2 mm (range: 20 to 50 mm. Half of the neoplasms were polypoid and the other half were non-polypoid. Forty-two (55.3% lesions were located in the left colon, and 34 in the right colon. There was a high prevalence of III L (39.5% and IV (53.9% pit patterns. There were 72 adenomas and 4 adenocarcinomas. Malignancy was observed in 5.3% of the lesions. Thirty-three lesions presented advanced histology (adenomas with high-grade dysplasia or early adenocarcinoma, with no difference in morphology and site. Only one lesion (1.3% invaded the submucosa. Lesions larger than 30 mm had advanced histology (P = 0.001. The primary treatment was endoscopic resection, and invasive carcinoma was referred to surgery. Recurrence rate was 10.6%. Conclusions Large colorectal neoplasms showed a low rate of malignancy. Endoscopic treatment is an effective therapy for these lesions.

  20. Genetics of aggression.

    Science.gov (United States)

    Anholt, Robert R H; Mackay, Trudy F C

    2012-01-01

    Aggression mediates competition for food, mating partners, and habitats and, among social animals, establishes stable dominance hierarchies. In humans, abnormal aggression is a hallmark of neuropsychiatric disorders and can be elicited by environmental factors acting on an underlying genetic susceptibility. Identifying the genetic architecture that predisposes to aggressive behavior in people is challenging because of difficulties in quantifying the phenotype, genetic heterogeneity, and uncontrolled environmental conditions. Studies on mice have identified single-gene mutations that result in hyperaggression, contingent on genetic background. These studies can be complemented by systems genetics approaches in Drosophila melanogaster, in which mutational analyses together with genome-wide transcript analyses, artificial selection studies, and genome-wide analysis of epistasis have revealed that a large segment of the genome contributes to the manifestation of aggressive behavior with widespread epistatic interactions. Comparative genomic analyses based on the principle of evolutionary conservation are needed to enable a complete dissection of the neurogenetic underpinnings of this universal fitness trait.

  1. Predictive features for histology of gastric subepithelial lesions

    Directory of Open Access Journals (Sweden)

    Ricardo Teles SCHULZ

    Full Text Available ABSTRACT BACKGROUND Gastric subepithelial lesion is a relatively common diagnosis after routine upper endoscopy. The diagnostic workup of an undetermined gastric subepithelial lesion should take into consideration clinical and endoscopic features. OBJECTIVE We aimed to investigate the association between patients' characteristics, endoscopic and echographic features with the histologic diagnosis of the gastric subepithelial lesions. METHODS This is a retrospective study with 55 patients, who were consecutively diagnosed with gastric subepithelial lesions, from October 2008 to August 2011. Patients' characteristics, endoscopic and echografic features of each gastric subepithelial lesion were analysed. Histologic diagnosis provided by EUS-guided fine needle aspiration or endoscopic/surgical resection was used as gold standard. RESULTS The probability of gastrointestinal stromal tumors to be located in the cardia was low (4.5%, while for leiomyoma it was high (>95%. In addition, there was a higher risk of gastrointestinal stromal tumors in patients older than 57 years (OR 8.9; 95% CI, with lesions ≥21 mm (OR 7.15; 95% CI, located at 4th layer (OR 18.8; 95% CI, with positive Doppler sign (OR 9; 95% CI, and irregular outer border (OR 7.75; 95% CI. CONCLUSION The location of gastric subepithelial lesions in the gastric cardia lowers the risk of gastrointestinal stromal tumors. While gastric subepithelial lesions occurring in elderly patients, located in the gastric body, with positive Doppler signal and irregular outer border increase the risk of gastrointestinal stromal tumors.

  2. Impairments in proverb interpretation following focal frontal lobe lesions.

    Science.gov (United States)

    Murphy, Patrick; Shallice, Tim; Robinson, Gail; MacPherson, Sarah E; Turner, Martha; Woollett, Katherine; Bozzali, Marco; Cipolotti, Lisa

    2013-09-01

    The proverb interpretation task (PIT) is often used in clinical settings to evaluate frontal "executive" dysfunction. However, only a relatively small number of studies have investigated the relationship between frontal lobe lesions and performance on the PIT. We compared 52 patients with unselected focal frontal lobe lesions with 52 closely matched healthy controls on a proverb interpretation task. Participants also completed a battery of neuropsychological tests, including a fluid intelligence task (Raven's Advanced Progressive Matrices). Lesions were firstly analysed according to a standard left/right sub-division. Secondly, a finer-grained analysis compared the performance of patients with medial, left lateral and right lateral lesions with healthy controls. Thirdly, a contrast of specific frontal subgroups compared the performance of patients with medial lesions with patients with lateral frontal lesions. The results showed that patients with left frontal lesions were significantly impaired on the PIT, while in patients with right frontal lesions the impairments approached significance. Medial frontal patients were the only frontal subgroup impaired on the PIT, relative to healthy controls and lateral frontal patients. Interestingly, an error analysis indicated that a significantly higher number of concrete responses were found in the left lateral subgroup compared to healthy controls. We found no correlation between scores on the PIT and on the fluid intelligence task. Overall our results suggest that specific regions of the frontal lobes contribute to the performance on the PIT. © 2013 The Authors. Published by Elsevier Ltd. All rights reserved.

  3. Claudin-4-targeted optical imaging detects pancreatic cancer and its precursor lesions.

    Science.gov (United States)

    Neesse, Albrecht; Hahnenkamp, Anke; Griesmann, Heidi; Buchholz, Malte; Hahn, Stefan A; Maghnouj, Abdelouahid; Fendrich, Volker; Ring, Janine; Sipos, Bence; Tuveson, David A; Bremer, Christoph; Gress, Thomas M; Michl, Patrick

    2013-07-01

    Novel imaging methods based on specific molecular targets to detect both established neoplasms and their precursor lesions are highly desirable in cancer medicine. Previously, we identified claudin-4, an integral constituent of tight junctions, as highly expressed in various gastrointestinal tumours including pancreatic cancer. Here, we investigate the potential of targeting claudin-4 with a naturally occurring ligand to visualise pancreatic cancer and its precursor lesions in vitro and in vivo by near-infrared imaging approaches. A non-toxic C-terminal fragment of the claudin-4 ligand Clostridium perfringens enterotoxin (C-CPE) was labelled with a cyanine dye (Cy5.5). Binding of the optical tracer was analysed on claudin-4 positive and negative cells in vitro, and tumour xenografts in vivo. In addition, two genetically engineered mouse models for pancreatic intraepithelial neoplasia (PanIN) and pancreatic cancer were used for in vivo validation. Optical imaging studies were conducted using 2D planar fluorescence reflectance imaging (FRI) technology and 3D fluorescence-mediated tomography (FMT). In vitro, the peptide-dye conjugate showed high binding affinity to claudin-4 positive CAPAN1 cells, while claudin-4 negative HT1080 cells revealed little or no fluorescence. In vivo, claudin-4 positive tumour xenografts, endogenous pancreatic tumours, hepatic metastases, as well as preinvasive PanIN lesions, were visualised by FRI and FMT up to 48 h after injection showing a significantly higher average of fluorochrome concentration as compared with claudin-4 negative xenografts and normal pancreatic tissue. C-CPE-Cy5.5 combined with novel optical imaging methods enables non-invasive visualisation of claudin-4 positive murine pancreatic tumours and their precursor lesions, representing a promising modality for early diagnostic imaging.

  4. Enamel lesions in development, classification in Costa Rican families

    International Nuclear Information System (INIS)

    Murillo Knudsen, Gina; Berrocal Salazar, Cristina

    2013-01-01

    Enamel lesions in development were identified and classified in patients of Llano Grande de Cartago, examined at the Facultad de Odontologia of the Universidad de Costa Rica. A guide is provided over the topic. 15 children and 2 Costa Rican adults were selected. Clinical examinations, radiographs and clinical photographs were used as data collection method. Dental defects of the enamel were classified according to the possible genetic causes and without genetic causes. Imperfect Amelogenesis (IA) was diagnosed in 10 of patients. Hypoplastic IA was determined in 3 siblings with autosomal recessive inheritance, for 16% of the total sample. Hypomineralized IA was identified in an adult and two of his sons, with autosomal dominant inheritance. The remaining 4 cases of IA have been sporadic. Lesions of dental fluorosis were determined in the Horowitz index in 4 individuals, from 2 unrelated families. Other defects unspecified of the enamel or hypoplasias were found in 3 individuals. Enamel lesions in development should be classified with precision, for the purpose to inform to patients affected about their condition, origin, prognosis and appropriate treatment. The basis are established to implement reliability in the construction of family genealogy, identification and classification of enamel lesions, as well as the probabilities of future generations to express the lesions in the enamel of temporary or permanent dentition [es

  5. Preoperative nonpalpable breast lesions localization

    Energy Technology Data Exchange (ETDEWEB)

    Gardellin, G; Natale, F; Perin, B

    1986-01-01

    The effectiveness of real time sonography and mammography are examined in localizing with a hookwire (introduced via a straight needle) the nonpalpable breast lesions. The method, used for surgery or biopsy, was successful in a series of 13 patients with nonpalpable breast lesions, 4 affectd by carcinoma. 18 refs.

  6. Fast semi-automated lesion demarcation in stroke

    Directory of Open Access Journals (Sweden)

    Bianca de Haan

    2015-01-01

    Full Text Available Lesion–behaviour mapping analyses require the demarcation of the brain lesion on each (usually transverse slice of the individual stroke patient's brain image. To date, this is generally thought to be most precise when done manually, which is, however, both time-consuming and potentially observer-dependent. Fully automated lesion demarcation methods have been developed to address these issues, but these are often not practicable in acute stroke research where for each patient only a single image modality is available and the available image modality differs over patients. In the current study, we evaluated a semi-automated lesion demarcation approach, the so-called Clusterize algorithm, in acute stroke patients scanned in a range of common image modalities. Our results suggest that, compared to the standard of manual lesion demarcation, the semi-automated Clusterize algorithm is capable of significantly speeding up lesion demarcation in the most commonly used image modalities, without loss of either lesion demarcation precision or lesion demarcation reproducibility. For the three investigated acute datasets (CT, DWI, T2FLAIR, containing a total of 44 patient images obtained in a regular clinical setting at patient admission, the reduction in processing time was on average 17.8 min per patient and this advantage increased with increasing lesion volume (up to 60 min per patient for the largest lesion volumes in our datasets. Additionally, our results suggest that performance of the Clusterize algorithm in a chronic dataset with 11 T1 images was comparable to its performance in the acute datasets. We thus advocate the use of the Clusterize algorithm, integrated into a simple, freely available SPM toolbox, for the precise, reliable and fast preparation of imaging data for lesion–behaviour mapping analyses.

  7. Genetic data for groundfish - Genetics and genomics of northeastern Pacific groundfish

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Conduct genetic analyses of groundfish in the northeastern Pacific, with a focus on population genetics and genomics of rockfishes and sablefish. Genetic data for...

  8. Genetic variability and bottleneck analyses of Kanni adu goat population using microsatellite markers [Also published in The Indian Journal of Small Ruminants, 2015, 21(2): 216-22

    International Nuclear Information System (INIS)

    Jeyakumar, M.; Thiruvenkadan, R.; Saravana, R.; Periasamy, K.

    2016-01-01

    Full text: Microsatellite data on 25 loci were generated and utilized to evaluate the genetic architecture and mutation drift equilibrium of Kanni Adu goats of southern Tamil Nadu. The genetic diversity analysis of Kanni Adu goats displayed higher level of within breed variability in terms of mean number of alleles per locus (11.24±0.87) and heterozygosity values (Ho= 0.677±0.041, He=0.857±0.016). Within population inbreeding estimate (FIS=0.215±0.040) showed moderate level of inbreeding, which warrant adoption of appropriate breeding strategies under field conditions. The polymorphism information content (PIC) value ranged from 0.531 to 0.915 suggested higher polymorphism in this breed. In general, the sign, standardized differences and Wilcoxon rank tests indicated heterozygosity excess in Kanni Adu goat population in infinite alleles and two-phase model and non-significant in stepwise mutation model. Hence, the mode-shift indicator test was utilized and it indicated the absence of genetic bottleneck in the recent past in Kanni Adu goats. It suggests that any unique alleles present in this breed may not have been lost. The study indicated that Kanni adu goats exhibited substantial amount of genetic variation as reflected from the heterozygosity and number of alleles per locus. (author)

  9. Parietal lesion effects on cued recall following pair associate learning.

    Science.gov (United States)

    Ben-Zvi, Shir; Soroker, Nachum; Levy, Daniel A

    2015-07-01

    We investigated the involvement of the posterior parietal cortex in episodic memory in a lesion-effects study of cued recall following pair-associate learning. Groups of patients who had experienced first-incident stroke, generally in middle cerebral artery territory, and exhibited damage that included lateral posterior parietal regions, were tested within an early post-stroke time window. In three experiments, patients and matched healthy comparison groups executed repeated study and cued recall test blocks of pairs of words (Experiment 1), pairs of object pictures (Experiment 2), or pairs of object pictures and environmental sounds (Experiment 3). Patients' brain CT scans were subjected to quantitative analysis of lesion volumes. Behavioral and lesion data were used to compute correlations between area lesion extent and memory deficits, and to conduct voxel-based lesion-symptom mapping. These analyses implicated lateral ventral parietal cortex, especially the angular gyrus, in cued recall deficits, most pronouncedly in the cross-modal picture-sound pairs task, though significant parietal lesion effects were also found in the unimodal word pairs and picture pairs tasks. In contrast to an earlier study in which comparable parietal lesions did not cause deficits in item recognition, these results indicate that lateral posterior parietal areas make a substantive contribution to demanding forms of recollective retrieval as represented by cued recall, especially for complex associative representations. Copyright © 2015 Elsevier Ltd. All rights reserved.

  10. Cryogun cryotherapy for oral leukoplakia and adjacent melanosis lesions.

    Science.gov (United States)

    Chen, Hsin-Ming; Cheng, Shih-Jung; Lin, Hung-Pin; Yu, Chuan-Hang; Wu, Yang-Che; Chiang, Chun-Pin

    2015-09-01

    Our previous study has shown that cryogun cryotherapy is a good and effective treatment modality for oral leukoplakia. In this study, we used cryogun cryotherapy to treat 72 oral leukoplakia and adjacent smoking-induced melanosis (OLM) lesions on the buccal mucosae. Of 72 OLM lesions, 14 had epithelial hyperplasia with parakeratosis, 24 had epithelial hyperplasia with hyperkeratosis, 26 had mild dysplasia, seven had moderate dysplasia, and one had severe dysplasia. Complete regression was achieved in all 72 OLM lesions after a mean of 3.3 ± 1.3 cryogun cryotherapy treatments. We found that OLM lesions in patients without smoking habit, with the greatest diameter cryotherapy treatment to achieve complete regression than those OLM lesions in patients with smoking habit, with the greatest diameter ≥ 2.8 cm, without epithelial dysplasia, or with a surface keratin thickness > 50 μm (all P-values cryotherapy treatment number (all P-values cryotherapy treatment required to achieve complete regression of the OLM lesion by multivariate logistic regression analyses. Cryogun cryotherapy is an effective treatment modality for OLM lesions. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  11. Changing activity in MS lesions

    International Nuclear Information System (INIS)

    Kermode, A.G.; Tofts, P.S.; Thompson, A.J.; Rudge, P.; MacManus, D.G.; Kendall, B.E.; Moseley, I.F.; Kingsley, D.P.E.; McDonald, W.I.

    1989-01-01

    Gd-DTPA enhanced T1 weighted MRI is a discriminating test for a defective blood-brain barrier, with MS lesions showing considerable variation in the pattern of enhancement. Since little is known of the changes in the blood-brain barrier in the active plaque over time, the natural history of blood-brain barrier disturbance in the MS lesion was examined to confirm earlier reports that Gd-DTPA enhancement is a consistent early event in new lesions of relapsing/remitting MS. This knowledge is essential for the use of MRI in monitoring treatment. (author). 9 refs

  12. PHAEOHYPHOMYCOSIS: CUTANEOUS, SUBCUTANEOUS, NASOPHARYNGEAL LESIONS

    Directory of Open Access Journals (Sweden)

    M. Rasoolinejad

    1999-06-01

    Full Text Available Phaeohyphomycosis is an amalgam of clinical diseases caused by a wide variety of dematiaceous fungi. We are reporting on a 16 year-old patient from Amol with subcutaneous cervical nodes and nasopharyngeal lesions of phaeohypho"nmycosis that were confirmed by pathological examination, direct smear, and culture. After treatment with an oral triazole (Itraconazole for 4 months, all nodes and lesions disappeared and treatment was stopped A new lesion appeared on his chest wall 8 months, therapy with itraconazole was restarted and commuted for a long time.

  13. OCT investigation of dental lesions

    Science.gov (United States)

    Osiac, Eugen; Popescu, Sanda Mihaela; Scrieciu, Monica; Mercuţ, Rǎzvan; Mercuţ, Veronica; Vǎtu, Mihaela

    2018-03-01

    There are several important non carious lesions affecting the tooth structure, lesions which may be classified into four clinical forms of dental wear: abfraction, erosion, attrition and abrasion, and different types of root resorption. Search for new, non-invasive and fast methods able to detect and describe such injuries is of utmost importance. Optical coherence tomography (OCT) proved itself as an appropriate investigation method for several medical fields including ophthalmology, dermatology, cardiology etc. Our study reveals OCT preliminary investigations as a promising tool for detecting and evaluating of the mentioned lesions.

  14. Central Lesions With Selective Semicircular Canal Involvement Mimicking Bilateral Vestibulopathy

    Directory of Open Access Journals (Sweden)

    Luke Chen

    2018-04-01

    Full Text Available Bilateral vestibulopathy (BVP, which is due to peripheral lesions, may selectively involve certain semicircular canal (SCC. Recent eye movement recordings with search coil and video head impulse test (HIT have provided insight in central lesions that can cause bilateral and selective SCC deficit mimicking BVP. Since neurological signs or ocular motor deficits maybe subtle or absent, it is critical to recognize central lesions correctly since there is prognostic and treatment implication. Acute floccular lesions cause bilateral horizontal SCC (HC impairment while leaving vertical SCC function unaffected. Vestibular nuclear lesions affect bilateral HC and posterior SCC (PC function, but anterior SCC (AC function is spared. When both eyes are recorded, medial longitudinal fasciculus lesions cause horizontal dysconjugacy in HC function and catch-up saccades, as well as selective deficiency of PC over AC function. Combined peripheral and central lesions may be difficult to distinguish from BVP. Anterior inferior cerebellar artery stroke causes two types of deficits: 1. ipsilateral pan-SCC deficits and contralateral HC deficit and 2. bilateral HC deficit with vertical SCC sparing. Metabolic disorders such as Wernicke encephalopathy characteristically involve HC but not AC or PC function. Gaucher disease causes uniform loss of all SCC function but with minimal horizontal catch-up saccades. Genetic cerebellar ataxias and cerebellar-ataxia neuropathy vestibular areflexia syndrome typically do not spare AC function. While video HIT does not replace the gold-standard, search coil HIT, clinicians are now able to rapidly and accurately identify specific pattern of SCC deficits, which can aid differentiation of central lesions from BVP.

  15. Post-radiotherapeutic heart lesions

    International Nuclear Information System (INIS)

    Testart, F.M.

    1979-05-01

    Heart structures have traditionally been considered radioresistant. In fact all tissues subjected to radiotherapy can develop lesions. Possible damage includes: - pericardiac fibrosis, the commonest and best individualized, associated with a constriction this leads to a stoppage pattern usually occurring late, around the 18th month. Its frequency depends directly on the total radiation dose; - fibrous myocarditis by direct damage to the heart muscle; - stenosis type lesions of the large coronary trunks; - in exceptional cases lesions of the aorta: hyperplastic degenerescence of the intima and adventitia or of the aortic sigmoid valvules and the mitral valves. Three observations are reported, concerning a coronary, a pericardiac and a coronary, myocardiac and pericardiac lesion. Following this account the irradiation techniques and main experimental data are reviewed and the prophylactic and therapeutic consequences to be derived from our observations and those of the literature are examined [fr

  16. Atypical idiopathic inflammatory demyelinating lesions

    DEFF Research Database (Denmark)

    Wallner-Blazek, Mirja; Rovira, Alex; Fillipp, Massimo

    2013-01-01

    Atypical lesions of a presumably idiopathic inflammatory demyelinating origin present quite variably and may pose diagnostic problems. The subsequent clinical course is also uncertain. We, therefore, wanted to clarify if atypical idiopathic inflammatory demyelinating lesions (AIIDLs) can be class......Atypical lesions of a presumably idiopathic inflammatory demyelinating origin present quite variably and may pose diagnostic problems. The subsequent clinical course is also uncertain. We, therefore, wanted to clarify if atypical idiopathic inflammatory demyelinating lesions (AIIDLs) can...... be classified according to previously suggested radiologic characteristics and how this classification relates to prognosis. Searching the databases of eight tertiary referral centres we identified 90 adult patients (61 women, 29 men; mean age 34 years) with ≥1 AIIDL. We collected their demographic, clinical...

  17. Molecular cytogenetic evaluation of gastric cardia adenocarcinoma and precursor lesions

    NARCIS (Netherlands)

    H. van Dekken (Herman); J.C. Alers (Janneke); P.H.J. Riegman (Peter); C. Rosenberg; H.W. Tilanus (Hugo); K.J. Vissers (Kees)

    2001-01-01

    textabstractAnalyses of cancer incidence data in the United States and Western Europe revealed steadily rising rates over the past decades of adenocarcinomas of the esophagus and gastric cardia. Genetic information on gastric cardia adenocarcinoma and its preneoplasias

  18. Analysis of damaged DNA / proteins interactions: Methodological optimizations and applications to DNA lesions induced by platinum anticancer drugs; Analyse des interactions ADN lese / proteines: Optimisations methodologiques et applications aux dommages de l'ADN engendres par les derives du platine

    Energy Technology Data Exchange (ETDEWEB)

    Bounaix Morand du Puch, Ch

    2010-10-15

    DNA lesions contribute to the alteration of DNA structure, thereby inhibiting essential cellular processes. Such alterations may be beneficial for chemotherapies, for example in the case of platinum anticancer agents. They generate bulky adducts that, if not repaired, ultimately cause apoptosis. A better understanding of the biological response to such molecules can be obtained through the study of proteins that directly interact with the damages. These proteins constitute the DNA lesions interactome. This thesis presents the development of tools aiming at increasing the list of platinum adduct-associated proteins. Firstly, we designed a ligand fishing system made of damaged plasmids immobilized onto magnetic beads. Three platinum drugs were selected for our study: cisplatin, oxali-platin and satra-platin. Following exposure of the trap to nuclear extracts from HeLa cancer cells and identification of retained proteins by proteomics, we obtained already known candidates (HMGB1, hUBF, FACT complex) but also 29 new members of the platinated-DNA interactome. Among them, we noted the presence of PNUTS, TOX4 and WDR82, which associate to form the recently-discovered PTW/PP complex. Their capture was then confirmed with a second model, namely breast cancer cell line MDA MB 231, and the biological consequences of such an interaction now need to be elucidated. Secondly, we adapted a SPRi bio-chip to the study of platinum-damaged DNA/proteins interactions. Affinity of HMGB1 and newly characterized TOX4 for adducts generated by our three platinum drugs could be validated thanks to the bio-chip. Finally, we used our tools, as well as analytical chemistry and biochemistry methods, to evaluate the role of DDB2 (a factor involved in the recognition of UV-induced lesions) in the repair of cisplatin adducts. Our experiments using MDA MB 231 cells differentially expressing DDB2 showed that this protein is not responsible for the repair of platinum damages. Instead, it appears to act

  19. MRI atlas of MS lesions

    Energy Technology Data Exchange (ETDEWEB)

    Sahraian, Mohammad Ali [Tehran Univ. of Medical Sciences Sina Hospital (Iran). Dept. of Neurology; Radue, Ernst-Wilhelm [Univ. Hospital Basel (Switzerland). Dept. of Neuroradiology

    2008-07-01

    MRI has become the main paraclinical test in the diagnosis and management of multiple sclerosis. We have demonstrated more than 400 pictures of different typical and atypical MS lesions in this atlas. Each image has a teaching point. New diagnostic criteria and differential diagnosis are discussed and the book is supported by a teaching DVD where the reader can see MS lesions in different slices and sequences. (orig.)

  20. Histomorphological spetrum of breast lesions.

    Science.gov (United States)

    Parajuli, S; Koirala, U; Khatri, R; Acharya, L; Suwal, A

    2011-04-01

    Cancer of the breast is the second most common cause of cancer in women. Mass in the breast, whether benign or malignant is a cause of anxiety to the patients and the family members. All breast lumps are considered to be carcinomas until proved otherwise and are the causes of concern both for the patient and surgeon. This is a retrospective study conducted in Kathmandu Model Hospital for a total duration of three years from August 2007 to August 2010. 114 sample of breast tissue sent for histopathology were studied. Peak incidence of benign lesion was in between 21-30 years and malignant lesions in between 31-50 years. No breast lesions were seen in the first decade of life. Cancer of the breast was seen in 12.28% of cases. Fibroadenoma and fibrocystic disease were the commonest benign lesion and infiltrating ductal carcinoma was the commonest malignant lesion. Specimens from 10 male breasts were received. Gynaecomastia was the most common lesion encountered in males. Infiltrating ductal carcinoma was seen in a 70 year old male. Breast cancer is one of the commonest causes of breast lump particularly in women and is growing public health problem in Nepal.

  1. Pathological criteria and practical issues in papillary lesions of the breast - a review.

    Science.gov (United States)

    Ni, Yun-Bi; Tse, Gary M

    2016-01-01

    Papillary lesions of the breast include a broad spectrum of lesions, ranging from benign papilloma, papilloma with atypical ductal hyperplasia (ADH) or ductal carcinoma in situ (DCIS) to papillary carcinoma. The accurate diagnosis of mammary papillary lesions is a challenge for pathologists, owing to the overlapping features among these lesions. In this review, some of the diagnostic criteria of papillary lesions are discussed, with special emphasis on some key morphological features, namely fibrovascular cores, epithelial proliferation in a solid pattern, intraductal papilloma complicated by ADH or DCIS, and invasion and its mimics. The roles of immunohistochemistry, and the interpretation of myoepithelial cell markers, hormone receptors, and high molecular weight cytokeratin, are addressed. Finally, novel biomarkers and genetic aberrations in papillary lesions are summarized. © 2015 John Wiley & Sons Ltd.

  2. Genetic algorithms

    Science.gov (United States)

    Wang, Lui; Bayer, Steven E.

    1991-01-01

    Genetic algorithms are mathematical, highly parallel, adaptive search procedures (i.e., problem solving methods) based loosely on the processes of natural genetics and Darwinian survival of the fittest. Basic genetic algorithms concepts are introduced, genetic algorithm applications are introduced, and results are presented from a project to develop a software tool that will enable the widespread use of genetic algorithm technology.

  3. Molecular pathology of chondroid neoplasms: part 2, malignant lesions

    International Nuclear Information System (INIS)

    Bell, W.C.; Klein, M.J.; Pitt, M.J.; Siegal, G.P.

    2006-01-01

    This is the second part of a two-part review presenting an overview of the molecular findings associated with both benign and malignant chondroid neoplasms. The first part presented a brief review of modern methods in molecular pathology, along with a review of the cytogenetic and molecular genetic findings in benign chondroid neoplasms. This second part reviews the cytogenetic and molecular genetic findings in malignant chondroid neoplasms. Clinical aspects of the various lesions are briefly discussed, and each tumor is illustrated with representative radiographic and pathologic images. (orig.)

  4. Molecular pathology of chondroid neoplasms: part 2, malignant lesions

    Energy Technology Data Exchange (ETDEWEB)

    Bell, W.C. [University of Alabama at Birmingham, Department of Pathology, Birmingham, AL (United States); University of Alabama at Birmingham, Center for Metabolic Bone Disease, Birmingham, AL (United States); Klein, M.J. [University of Alabama at Birmingham, Center for Metabolic Bone Disease, Birmingham, AL (United States); University of Alabama at Birmingham, Department of Pathology, Birmingham, AL (United States); Pitt, M.J. [University of Alabama at Birmingham, Department of Diagnostic Radiology, Birmingham, AL (United States); University of Alabama at Birmingham, Center for Metabolic Bone Disease, Birmingham, AL (United States); Siegal, G.P. [University of Alabama at Birmingham, Departments of Pathology, Cell Biology, and Surgery, Birmingham, AL (United States); University of Alabama at Birmingham, Center for Metabolic Bone Disease, Birmingham, AL (United States)

    2006-12-15

    This is the second part of a two-part review presenting an overview of the molecular findings associated with both benign and malignant chondroid neoplasms. The first part presented a brief review of modern methods in molecular pathology, along with a review of the cytogenetic and molecular genetic findings in benign chondroid neoplasms. This second part reviews the cytogenetic and molecular genetic findings in malignant chondroid neoplasms. Clinical aspects of the various lesions are briefly discussed, and each tumor is illustrated with representative radiographic and pathologic images. (orig.)

  5. Genetic autonomic disorders.

    Science.gov (United States)

    Axelrod, Felicia B

    2013-03-01

    Genetic disorders affecting the autonomic nervous system can result in abnormal development of the nervous system or they can be caused by neurotransmitter imbalance, an ion-channel disturbance or by storage of deleterious material. The symptoms indicating autonomic dysfunction, however, will depend upon whether the genetic lesion has disrupted peripheral or central autonomic centers or both. Because the autonomic nervous system is pervasive and affects every organ system in the body, autonomic dysfunction will result in impaired homeostasis and symptoms will vary. The possibility of genetic confirmation by molecular testing for specific diagnosis is increasing but treatments tend to remain only supportive and directed toward particular symptoms. Copyright © 2013 Elsevier Inc. All rights reserved.

  6. Molecular pathology of chondroid neoplasms: part 1, benign lesions

    Energy Technology Data Exchange (ETDEWEB)

    Bell, W.C. [University of Alabama at Birmingham, Department of Pathology, Birmingham, AL (United States); University of Alabama at Birmingham, Center for Metabolic Bone Disease, Birmingham, AL (United States); University of Alabama at Birmingham, Department of Diagnostic Radiology, Birmingham, AL (United States); Klein, M.J. [University of Alabama at Birmingham, Center for Metabolic Bone Disease, Birmingham, AL (United States); University of Alabama at Birmingham, Department of Pathology, Birmingham, AL (United States); University of Alabama at Birmingham, Department of Diagnostic Radiology, Birmingham, AL (United States); Pitt, M.J. [University of Alabama at Birmingham, Department of Diagnostic Radiology, Birmingham, AL (United States); University of Alabama at Birmingham, Center for Metabolic Bone Disease, Birmingham, AL (United States); Siegal, G.P. [University of Alabama at Birmingham, Departments of Pathology, Cell Biology, and Surgery, and the Center for Metabolic Bone Disease, Birmingham, AL (United States)

    2006-11-15

    This two-part review presents an overview of the molecular findings associated with both benign and malignant chondroid neoplasms. This first part presents a brief review of methods in molecular pathology along with a review of the cytogenetic and molecular genetic findings in benign chondroid neoplasms. Clinical aspects of the various lesions are briefly discussed, and each tumor is illustrated with representative radiographic and pathologic images. Malignant chondroid neoplasms will be considered in the second part of this review. (orig.)

  7. Molecular pathology of chondroid neoplasms: part 1, benign lesions

    International Nuclear Information System (INIS)

    Bell, W.C.; Klein, M.J.; Pitt, M.J.; Siegal, G.P.

    2006-01-01

    This two-part review presents an overview of the molecular findings associated with both benign and malignant chondroid neoplasms. This first part presents a brief review of methods in molecular pathology along with a review of the cytogenetic and molecular genetic findings in benign chondroid neoplasms. Clinical aspects of the various lesions are briefly discussed, and each tumor is illustrated with representative radiographic and pathologic images. Malignant chondroid neoplasms will be considered in the second part of this review. (orig.)

  8. Apparent genetic difference between hypothyroid patients with blocking-type thyrotropin receptor antibody and those without, as shown by restriction fragement length polymorphism analyses of HLA-DP loci

    Energy Technology Data Exchange (ETDEWEB)

    Inoue, Daisuke; Sugawa, Hideo; Akamizu, Takashi; Mori, Toru (Kyoto Univ. School of Medicine, Kyoto (Japan)); Sato, Kaoru; Inoko, Hidetoshi; Tsuji, Kimiyoshi (Tokai Univ. School of Medicine, Kanagawa (Japan)); Maeda, Masahiro (Nichirei Corp., Tokyo (Japan))

    1993-09-01

    HLA types in Japanese patients with primary hypothyroidism were analyzed to see whether those with blocking-type TSH receptor antibody (TSH-R BAb M) differed genetically from those with idiopathic myxedema (IM). HLA typings of -A, -B, -C, -DR, and -DQ (73 antigens) were performed serologically, and those of -D and -DP (29 antigens) were analyzed by the restriction fragment length polymorphism method. Thirty patients were studied with TSH-R BAb M, and 28 with IM. The data were analyzed and compared with previous results from 88 Graves' patients, 46 Hashimoto patients, and 186 control subjects. Overall, 192 patients with 4 autoimmune thyroid disorders showed a decrease in -Aw19 and an increase in -DQw4 (corrected P < 0.05) and significant associations of -Aw33, -Bw46, -Cw3, -DRw8, -DR9, and -DQw3. In TSH-R BAb M patients, increases in -B35, -Bw60, and -Dw8 and decreases in -DR4 and -DPw2 were seen, whereas IM patients showed increased -DPw2, -Bw61, and -Dw23. In comparisons between TSH-R-BAb M and IM, the difference in -DPw2 was highly significant. HLA-B35 differed significantly in these 2 types of hypothyroidism. In conclusion, TSH-R BAb M patients have decreased frequency of -DPw2 and are genetically similar to Graves' disease, whereas IM patients are characterized by high frequency of -DPw2 and are genetically similar to Hashimoto's thyroiditis. 39 refs., 2 figs., 3 tabs.

  9. Characterization of genetic miscoding lesions caused by postmortem damage

    DEFF Research Database (Denmark)

    Gilbert, M Thomas P; Hansen, Anders J; Willerslev, Eske

    2002-01-01

    The spectrum of postmortem damage in mitochondrial DNA was analyzed in a large data set of cloned sequences from ancient human specimens. The most common forms of damage observed are two complementary groups of transitions, termed "type 1" (adenine-->guanine/thymine-->cytosine) and "type 2...

  10. When Are Circular Lesions Square? A National Clinical Education Skin Lesion Audit and Study

    Directory of Open Access Journals (Sweden)

    Benjamin H Miranda

    2014-09-01

    Full Text Available BackgroundSkin cancer is the most prevalent cancer by organ type and referral accuracy is vital for diagnosis and management. The British Association of Dermatologists (BAD and literature highlight the importance of accurate skin lesion examination, diagnosis and educationally-relevant studies.MethodsWe undertook a review of the relevant literature, a national audit of skin lesion description standards and a study of speciality training influences on these descriptions. Questionnaires (n=200, with pictures of a circular and an oval lesion, were distributed to UK dermatology/plastic surgery consultants and speciality trainees (ST, general practitioners (GP, and medical students (MS. The following variables were analysed against a pre-defined 95% inclusion accuracy standard: site, shape, size, skin/colour, and presence of associated scars.ResultsThere were 250 lesion descriptions provided by 125 consultants, STs, GPs, and MSs. Inclusion accuracy was greatest for consultants over STs (80% vs. 68%; P<0.001, GPs (57% and MSs (46% (P<0.0001, for STs over GPs (P<0.010 and MSs (P<0.0001 and for GPs over MSs (P<0.010, all falling below audit standard. Size description accuracy sub-analysis according to circular/oval dimensions was as follows: consultants (94%, GPs (80%, STs (73%, MSs (37%, with the most common error implying a quadrilateral shape (66%. Addressing BAD guidelines and published requirements for more empirical performance data to improve teaching methods, we performed a national audit and studied skin lesion descriptions. To improve diagnostic and referral accuracy for patients, healthcare professionals must strive towards accuracy (a circle is not a square.ConclusionsWe provide supportive evidence that increased speciality training improves this process and propose that greater focus is placed on such training early on during medical training, and maintained throughout clinical practice.

  11. Genetic Mapping

    Science.gov (United States)

    ... greatly advanced genetics research. The improved quality of genetic data has reduced the time required to identify a ... cases, a matter of months or even weeks. Genetic mapping data generated by the HGP's laboratories is freely accessible ...

  12. Genetics of allergy and allergic sensitization

    DEFF Research Database (Denmark)

    Bønnelykke, Klaus; Sparks, Rachel; Waage, Johannes

    2015-01-01

    information about shared genetics between allergy, related phenotypes and autoimmunity. Studies of monogenic diseases have elucidated critical cellular pathways and protein functions responsible for allergy. These complementary approaches imply genetic mechanisms involved in Th2 immunity, T......Our understanding of the specific genetic lesions in allergy has improved in recent years due to identification of common risk variants from genome-wide association studies (GWAS) and studies of rare, monogenic diseases. Large-scale GWAS have identified novel susceptibility loci and provided...

  13. Genetic privacy.

    Science.gov (United States)

    Sankar, Pamela

    2003-01-01

    During the past 10 years, the number of genetic tests performed more than tripled, and public concern about genetic privacy emerged. The majority of states and the U.S. government have passed regulations protecting genetic information. However, research has shown that concerns about genetic privacy are disproportionate to known instances of information misuse. Beliefs in genetic determinacy explain some of the heightened concern about genetic privacy. Discussion of the debate over genetic testing within families illustrates the most recent response to genetic privacy concerns.

  14. MRI of the stener lesion

    International Nuclear Information System (INIS)

    Haramati, N.; Hiller, N.; Dowdle, J.; Jacobson, M.; Barax, C.N.; Lieberfarb, R.I.; Lester, B.; Kulick, R.G.

    1995-01-01

    Six cadaver thumbs had ulnar collateral ligament (UCL) tears created surgically. MR examinations (2D STIR and 3D GRASS) were performed identically on all specimens both before displacement (non-Stener) and after displacement (Stener lesion) of the UCL. The MR images were then randomly numbered. Each image was evaluated separately in blinded fashion by four musculoskeletal radiologists for the presence or absence of a Stener lesion. Each radiologist reinterpreted the images after an interval of several days. The interpretation was based on previously published criteria for Stener lesion diagnosis by MR. The sensitivity of GRASS ranged from 0.17 to 0.67 with the most experienced reader scoring the lowest. The specificity of GRASS ranged from 0.33 to 1.0 (most experienced reader 0.67, 0.83). STIR had a sensitivity of 0.00-0.17 and a specificity of 0.53-0.83. The K values for inter- and intraobserver agreement were measured. The intraobserver K for GRASS was 0.27-0.75 (most experienced reader 0.75). 2D imaging is probably inadequate for the evaluation of Stener lesions. The most likely reason is that the STIR slice thickness of 3 mm limits resolution of small UCLs. The poor sensitivity and specificity of GRASS as well as poor interobserver agreement suggest that MR may not be sufficiently accurate for Stener lesion evaluation. (orig./MG)

  15. Abfraction lesions reviewed: current concepts

    Directory of Open Access Journals (Sweden)

    Adriana de Fátima Vasconcelos Pereira

    2008-01-01

    Full Text Available Non-carious cervical lesions are characterized by structural loss near the cementoenamel junction, without the presence of caries. Anumber of theories have arisen to explain the etiology of such lesions, although the real causes remain obscure, as is reflected by the contradictory terminology used in the literature. In addition to describing acidic and abrasive processes documented as etiological factors, attention is given to the role of mechanical stress from occlusal load, which is the most accepted theory for the development of abfraction lesions. Considering that tensile stress leads to the failure of restorations in the cervical region and that this is a fruitful area for future research, the present study has highlighted diagnosis, prognosis and the criteria for treatment.

  16. Ultrasonography of chest wall lesion

    Energy Technology Data Exchange (ETDEWEB)

    Park, Cheol Min; Kim, C. H.; Cha, I. H.; Chung, K. B.; Ser, W. H.; Choi, Y. H. [Seoul National University College of Medicine, Seoul (Korea, Republic of)

    1989-12-15

    Thirty-one patients with chest wall diseases were studied with ultrasound to evaluate its role in chest wall lesions. There were eight infectious conditions, 9 benign tumors, 11 malignant lesions and 3 miscellaneous cases. Diffuse chest wall thickening with heterogeneous echogenicity and obliteration of subcutaneous fat layer are findings of acute infection. In cases of tuberculous smpyema necessitates, pleural abnormality extended to the chest wall through intercostal space. Benign tumors were well demarcated, except in 4 cases of lipoma/lipomatosis. Malignant lesions showed irregular soft tissue masses, bone destruction, pleural effusion and subcutaneous invasion. Multiple enlarged lymph nodes were also shown. Ultrasound can demonstrate te internal structure, extent, depth and associated findings such as pleural effusion, bone destruction and peripheral lung involvement. Ultrasound is not only safe, non-invasive and an effective diagnostic imaging modality for chest wall disease, but can also guide aspiration or biopsy for pathologic diagnosis

  17. Ultrasonography of chest wall lesion

    International Nuclear Information System (INIS)

    Park, Cheol Min; Kim, C. H.; Cha, I. H.; Chung, K. B.; Ser, W. H.; Choi, Y. H.

    1989-01-01

    Thirty-one patients with chest wall diseases were studied with ultrasound to evaluate its role in chest wall lesions. There were eight infectious conditions, 9 benign tumors, 11 malignant lesions and 3 miscellaneous cases. Diffuse chest wall thickening with heterogeneous echogenicity and obliteration of subcutaneous fat layer are findings of acute infection. In cases of tuberculous smpyema necessitates, pleural abnormality extended to the chest wall through intercostal space. Benign tumors were well demarcated, except in 4 cases of lipoma/lipomatosis. Malignant lesions showed irregular soft tissue masses, bone destruction, pleural effusion and subcutaneous invasion. Multiple enlarged lymph nodes were also shown. Ultrasound can demonstrate te internal structure, extent, depth and associated findings such as pleural effusion, bone destruction and peripheral lung involvement. Ultrasound is not only safe, non-invasive and an effective diagnostic imaging modality for chest wall disease, but can also guide aspiration or biopsy for pathologic diagnosis

  18. The radiology in the solitary bone lesions

    International Nuclear Information System (INIS)

    Veloso, G.A.; Cardoso, V.M.

    1985-01-01

    Three methods of radiologic analysis of the solitary bone lesions are reviewed. 1. Radiological analysis of the lesions with the objective to suppose the histologic type; 2. To appreciate the velocity of growth and aggressiveness of the lesions. 3. To appreciate the biological behaviour of the bone lesions, making the diagnosis necessary for the treatment. (M.A.C.) [pt

  19. [The treatment of decubitus lesions].

    Science.gov (United States)

    Fugazza, G; Moroni, S; Bona, F

    1995-01-01

    The authors present a plan for pharmacological treatment of pressure sores in patients affected by neurological pathologies: cerebrovascular accidents, head injuries, spinal cord injuries. This plan is easily applicable to all pressure sores included between first and third degree of the Reuler and Cooney classification. Authors identified some drugs specifically usefull in different cutaneous lesion degrees. Skin lesions and employed medicines are described as follows: Erythema: semi occlusive bandage with porous adsorbing membrane. This dressing must be left in for five days at least. Excoriation: bactericidal or bacteriostatic medicines if it's situated in a non pressed area while the same dressing utilized for erythema if it's localized in a pressed area. Pressure sores: if there is local infection cleanse the wound from bacterial defilement using topic antibiotics apply compresses with vitamin C if the cutaneous lesion is larger than deeper, Cadexomero lodico if it's deeper than larger. Fistulas: wadding with tablets of collagen. Necrobiosis: complete or partial surgical removal of eschar preceded by the use of enzymatic drugs when eschar is firmly adherent to subcutaneous tissues. The first group collects 9 patients with stroke and head injury: 8 with sacral and 1 with heel pressure sores. First degree pressure sores heal within 45 days and third degree lesions within 160 days. The second group collects 10 spinal cord injury patients mostly with complete lesion among which: 7 sacral, 1 heel, 1 ischiatic and 1 malleolar lesions. First degree pressure sores heal within 30 days, third degree pressure sores heal within 200 days. Healing time are considered acceptable. Pressure sores recovery swiftness can be related to different factors such as pressure sores sterness, neurological pathology and arising of clinical complication (hyperthermia, infections, low serum albumin values, etc).

  20. Prevalence of ciliated epithelium in apical periodontitis lesions.

    Science.gov (United States)

    Ricucci, Domenico; Loghin, Simona; Siqueira, José F; Abdelsayed, Rafik A

    2014-04-01

    This article reports on the morphologic features and the frequency of ciliated epithelium in apical cysts and discusses its origin. The study material consisted of 167 human apical periodontitis lesions obtained consecutively from patients presenting for treatment during a period of 12 years in a dental practice operated by one of the authors. All of the lesions were obtained still attached to the root apices of teeth with untreated (93 lesions) or treated canals (74 lesions). The former were obtained by extraction and the latter by extraction or apical surgery. Specimens were processed for histopathologic and histobacteriologic analyses. Lesions were classified, and the type of epithelium, if present, was recorded. Of the lesions analyzed, 49 (29%) were diagnosed as cysts. Of these, 26 (53%) were found in untreated teeth, and 23 (47%) related to root canal-treated teeth. Ciliated columnar epithelium was observed partially or completely lining the cyst wall in 4 cysts, and all of them occurred in untreated maxillary molars. Three of these lesions were categorized as pocket cysts, and the other was a true cyst. Ciliated columnar epithelium-lined cysts corresponded to approximately 2% of the apical periodontitis lesions and 8% of the cysts of endodontic origin in the population studied. This epithelium is highly likely to have a sinus origin in the majority of cases. However, the possibility of prosoplasia or upgraded differentiation into ciliated epithelium from the typical cystic lining squamous epithelium may also be considered. Copyright © 2014 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

  1. Hepatic lesions in 90 captive nondomestic felids presented for autopsy.

    Science.gov (United States)

    Bernard, J M; Newkirk, K M; McRee, A E; Whittemore, J C; Ramsay, E C

    2015-03-01

    Hepatic lesions in nondomestic felids are poorly characterized. The purpose of this study was to evaluate hepatic lesions in 90 captive, nondomestic felids including tigers, cougars, and lions. Hepatic lesions were histologically characterized as vacuolar change (lipidosis or glycogenosis), biliary cysts, biliary hyperplasia, hepatitis, necrosis, neoplasia, fibrosis, veno-occlusive disease, cholestasis, hematoma, congestion, or hemorrhage. Stepwise logistic regression analyses were performed for vacuolar change, benign biliary lesions, hepatitis, lipogranulomas, extramedullary hematopoiesis, and hepatic stellate cell hypertrophy and hyperplasia, with species as the outcome variable. Ninety cats met the inclusion criteria. Seventy livers (78%) contained 1 or more lesions. Hepatocellular vacuolar change (41/90 [46%]) was the most common lesion overall. Extramedullary hematopoiesis, lipogranulomas, and hepatic stellate cell hyperplasia were also common. One snow leopard had veno-occlusive disease. Tigers were more likely than other felids to have no significant hepatic histologic lesions (odds ratio [OR], 12.687; P = .002), and lions were more likely to have biliary cysts (OR, 5.97; P = .021). Six animals (7%) died of hepatic disease: cholangiocellular carcinoma (n = 2) and 1 each of hepatic lipidosis, hepatocellular necrosis, pyogranulomatous hepatitis, and suppurative cholecystitis. Hepatocellular iron and copper accumulations were present in 72 of 90 (80%) and 10 of 90 (11%) sections, respectively. Sinusoidal fibrosis was common (74/90 [82%]) and primarily centrilobular (65/74 [88%]). Hepatocellular iron, copper, and fibrosis were not significantly associated with hepatic lesions. Primary hepatic disease was not a common cause of death in nondomestic felids in this study. © The Author(s) 2014.

  2. [Research methods in dentistry. 6. In vivo and in vitro methods for studying caries lesion progression

    NARCIS (Netherlands)

    Huysmans, M.C.; Thomas, R.Z.

    2004-01-01

    This paper describes some of the most used methods for caries lesion progression measurement in in vivo and in vitro research. Clinical measurements are usually limited to visual inspection. Currently available scoring systems and statistical analyses, making use of changes in lesion stage, have the

  3. Lesions of juxtacortical origin (surface lesions of bone)

    International Nuclear Information System (INIS)

    Kenan, S.; Abdelwahab, I.F.; Klein, M.J.; Hermann, G.; Lewis, M.M.

    1993-01-01

    A large variety of tumor and tumor-like conditions have been shown to originate from the surface of bone. Most surface lesions are associated with periosteal reaction. The periosteum is a multipotential membrane. Its cellular composition may give rise to a variety of both neoplasms and tumor-like conditions. To avoid misinterpretation, the orthopedist, radiologist, and pathologist should be familiar with the entire spectrum of surface lesions. A better understanding of the natural history and biological behavior at different lesional maturity stages and correlation of the history with the radiographic and pathological findings is essential to establish the correct diagnosis. A history of injury of blunt trauma is very important. A stress fracture may produce a periosteal reaction acd callus that can be difficult to distinguish from osteosarcoma. In this review article, the authors wish to describe and define each term by its anatomy and radiographic features while discussing the entire spectrum of surface lesions. All the illustrative cases in this review article have been proven histologically. (orig.)

  4. Periapical lesions: diagnosis and treatment

    OpenAIRE

    García-Rubio, A.; Bujaldón-Daza, A.L.; Rodríguez-Archilla, A.

    2015-01-01

    Las lesiones periapicales resultado de la necrosis de la pulpa dental son las patologías que más frecuentemente ocurren encontradas en el hueso alveolar. El tratamiento consiste en la eliminación de los agentes infecciosos mediante el tratamiento del canal radicular, permitiendo la cicatrización de la lesión. Periapical lesions, which are a result of the necrosis of the dental pulp, are the most frequently occurring diseases found in the alveolar bone. The treatment involves the removal of...

  5. Localized lesions in secondary syphillis

    International Nuclear Information System (INIS)

    Rasid, N.; Syphilis, S.

    2008-01-01

    The clinical manifestations of secondary syphilis are variable and can mimic many skin diseases, mostly being generalized and symmetrical in distribution. Localized lesions of secondary syphilis are rarely seen in dermatology clinics. We report an unusual presentation wherein a patient had localized lesions over face and soles only. There is a need for increased awareness on the part of physicians to recognize new patterns of syphilitic infection, together with a willingness to consider the diagnosis of syphilis in patients with unusual clinical features. (author)

  6. Betel quid oral lichenoid lesions: a hospital based cross-sectional study.

    Science.gov (United States)

    Arya, Sugandha; Vengal, Manoj; Raju, Bina; Patil, Neelkant; Sathosker, Sujatha; Bateja, Sumit; David, Jamil

    2017-02-01

    The aim of this study was to assess the prevalence and risk indicators of betel quid oral lichenoid lesions in chewers. A total of 1209 chewers were identified and categorized into three main groups based on the type of lesion: betel quid oral lichenoid lesions only, betel quid oral lichenoid lesions in association with quid-induced other oral mucosal lesions, and no lesions. Multinomial regression analyses were used to determine associations between dependent and independent variables. Betel quid oral lichenoid lesions were more common in individuals who chewed quid comprising both tobacco and areca nut, and in those who chewed it two to three, or greater than three, times a day. Betel quid oral lichenoid lesions + quid-induced other oral mucosal lesions were more likely to occur in females, and in individuals who chewed quid containing both tobacco and areca nut, in their processed and unprocessed forms, and greater than three times a day. The prevalence of betel quid oral lichenoid lesions was higher than that reported in previous studies conducted in India. Increase in the frequency and duration of quid chewing was associated with increased likelihood of developing these oral lichenoid lesions. © 2015 Wiley Publishing Asia Pty Ltd.

  7. Lesion mapping of social problem solving.

    Science.gov (United States)

    Barbey, Aron K; Colom, Roberto; Paul, Erick J; Chau, Aileen; Solomon, Jeffrey; Grafman, Jordan H

    2014-10-01

    Accumulating neuroscience evidence indicates that human intelligence is supported by a distributed network of frontal and parietal regions that enable complex, goal-directed behaviour. However, the contributions of this network to social aspects of intellectual function remain to be well characterized. Here, we report a human lesion study (n = 144) that investigates the neural bases of social problem solving (measured by the Everyday Problem Solving Inventory) and examine the degree to which individual differences in performance are predicted by a broad spectrum of psychological variables, including psychometric intelligence (measured by the Wechsler Adult Intelligence Scale), emotional intelligence (measured by the Mayer, Salovey, Caruso Emotional Intelligence Test), and personality traits (measured by the Neuroticism-Extraversion-Openness Personality Inventory). Scores for each variable were obtained, followed by voxel-based lesion-symptom mapping. Stepwise regression analyses revealed that working memory, processing speed, and emotional intelligence predict individual differences in everyday problem solving. A targeted analysis of specific everyday problem solving domains (involving friends, home management, consumerism, work, information management, and family) revealed psychological variables that selectively contribute to each. Lesion mapping results indicated that social problem solving, psychometric intelligence, and emotional intelligence are supported by a shared network of frontal, temporal, and parietal regions, including white matter association tracts that bind these areas into a coordinated system. The results support an integrative framework for understanding social intelligence and make specific recommendations for the application of the Everyday Problem Solving Inventory to the study of social problem solving in health and disease. © The Author (2014). Published by Oxford University Press on behalf of the Guarantors of Brain. All rights reserved

  8. Disseminated paracoccidioidomycosis diagnosis based on oral lesions

    Directory of Open Access Journals (Sweden)

    Liana Preto Webber

    2014-01-01

    Full Text Available Paracoccidioidomycosis (PCM is a deep mycosis with primary lung manifestations that may present cutaneous and oral lesions. Oral lesions mimic other infectious diseases or even squamous cell carcinoma, clinically and microscopically. Sometimes, the dentist is the first to detect the disease, because lung lesions are asymptomatic, or even misdiagnosed. An unusual case of PCM with 5 months of evolution presenting pulmonary, oral, and cutaneous lesions that was diagnosed by the dentist based on oral lesions is presented and discussed.

  9. Diagnosis of the ulcerous and erosive gastroduodenal lesions with radioisotopes

    International Nuclear Information System (INIS)

    Zuccaro, A.M.; Rocha, A.F.G. da; Palencia, I.I.B.

    1989-01-01

    The use of gastric scintigraphy with technetium 99-m labeled sucralfate is analysed in a study of 25 cases evolving: controls (five), duodenal ulcer (six case), gastric ulcer (four), gastric and duodenal ulcer (two) and gastric mucous acute erosive lesion (eight). All patients were previously submitted to endoscopy and biopsy. Changes in the techniques of other authors were performed. An accurate diagnosis was achieved in 95% of the cases with a specificity of 100%. It is concluded that the method is indicated for the investigation of critical patients, elderly patients, children for the control of lesions identified through endoscopy. (author)

  10. Molecular genetic researches on the radiation genetics of Drosophila in JINR

    International Nuclear Information System (INIS)

    Afanas'eva, K.P.; Aleksandrova, M.V.; Aleksandrov, I.D.

    2016-01-01

    Molecular genetic studies of radiation-induced heritable DNA lesions are carried out by the genetic group of Laboratory of nuclear problem in Joint Institute for Nuclear Research. The first results of molecular analysis of γ –ray- and neutron-induced vestigial mutations using PCR and sequencing will be presented. (authors)

  11. Imaging inflammatory acne: lesion detection and tracking

    Science.gov (United States)

    Cula, Gabriela O.; Bargo, Paulo R.; Kollias, Nikiforos

    2010-02-01

    It is known that effectiveness of acne treatment increases when the lesions are detected earlier, before they could progress into mature wound-like lesions, which lead to scarring and discoloration. However, little is known about the evolution of acne from early signs until after the lesion heals. In this work we computationally characterize the evolution of inflammatory acne lesions, based on analyzing cross-polarized images that document acne-prone facial skin over time. Taking skin images over time, and being able to follow skin features in these images present serious challenges, due to change in the appearance of skin, difficulty in repositioning the subject, involuntary movement such as breathing. A computational technique for automatic detection of lesions by separating the background normal skin from the acne lesions, based on fitting Gaussian distributions to the intensity histograms, is presented. In order to track and quantify the evolution of lesions, in terms of the degree of progress or regress, we designed a study to capture facial skin images from an acne-prone young individual, followed over the course of 3 different time points. Based on the behavior of the lesions between two consecutive time points, the automatically detected lesions are classified in four categories: new lesions, resolved lesions (i.e. lesions that disappear completely), lesions that are progressing, and lesions that are regressing (i.e. lesions in the process of healing). The classification our methods achieve correlates well with visual inspection of a trained human grader.

  12. Cystic Lesions in Autoimmune Pancreatitis

    Directory of Open Access Journals (Sweden)

    Macarena Gompertz

    2015-11-01

    Full Text Available Autoimmune pancreatitis (AIP can be chronic or recurrent, but frequently completely reversible after steroid treatment. A cystic lesion in AIP is a rare finding, and it can mimic a pancreatic cystic neoplasm. Difficulties in an exact diagnosis interfere with treatment, and surgery cannot be avoided in some cases. We report the history of a 63-year-old male presenting with jaundice and pruritus. AIP was confirmed by imaging and elevated IgG4 blood levels, and the patient completely recovered after corticosteroid therapy. One year later, he presented with a recurrent episode of AIP with elevated IgG4 levels, accompanied by the appearance of multiple intrapancreatic cystic lesions. All but 1 of these cysts disappeared after steroid treatment, but the remaining cyst in the pancreatic head was even somewhat larger 1 year later. Pancreatoduodenectomy was finally performed. Histology showed the wall of the cystic lesion to be fibrotic; the surrounding pancreatic tissue presented fibrosis, atrophy and lymphoplasmacytic infiltration by IgG4-positive cells, without malignant elements. Our case illustrates the rare possibility that cystic lesions can be part of AIP. These pseudocysts appear in the pancreatic segments involved in the autoimmune disease and can be a consequence of the local inflammation or related to ductal strictures. Steroid treatment should be initiated, after which these cysts can completely disappear with recovery from AIP. Surgical intervention may be necessary in some exceptional cases.

  13. Stereotactic lesioning for mental illness

    International Nuclear Information System (INIS)

    Kim, M.-C.; Lee, T.-K.

    2008-01-01

    The authors report stereotactically created lesioning by radiofrequency or Cyberknife radiosurgery for patients with mental illness. Since 1993, thirty-eight patients have undergone stereotactic psychosurgery for medically intractable mental illnesses. Two patients had aggressive behavior. Twenty-five patients suffered from Obsessive-Compulsive Disorder (OCD) and ten patients had depression. Another patient suffered from atypical psychosis. Bilateral amygdalotomy and subcaudate tractotomy were done for aggressive behavior. Limbic leucotomy or anterior cingulotomy was done for CCD and subcaudate tractotomy with or without cingulotomy was done for depression. In twenty-three patients, the lesions were made by a radiofrequency (RF) lesion generator. In fifteen cases, the lesions were made with Cyberknife Radiosurgery (CKRS). The Overt Aggression Scale (OAS) declined from 8 to 2 with clinical improvement during follow up period. With long-term follow up (meaning 57 months) in 25 OCDs, the mean Yale Brown Obsessive Compulsive Score (YBOCS) declined from 34 to 13 (n = 25). The Hamilton Depression scale (HAMD) for ten patients with depression declined from 38.5 to 10.5 (n = 10). There was no operative mortality and no significant morbidity except one case with transient urinary incontinence. Authors suggest that stereotactic psychosurgery by RF and CKRS could be a safe and effective means of treating some medically intractable mental illnesses. (author)

  14. Secondary syphilis lesions resembling pityriasis

    International Nuclear Information System (INIS)

    Dar, N.R.; Ali, L.; Nawaz, M.A.

    2007-01-01

    This case report describes a male patient who presented with generalized, centrally-ulcerated papules with crusts and hypopigmented macules. Initially, differential diagnostic considerations included pityriasis lichenoides but the serology for syphilis was positive and there was a rapid response to penicillin with clearing of the lesions at the end of three weeks treatment. (author)

  15. Oral mucosal lesions in denture wearers.

    Science.gov (United States)

    Jainkittivong, Aree; Aneksuk, Vilaiwan; Langlais, Robert P

    2010-03-01

    To determine the prevalence of oral mucosal lesions (OMLs) and denture-related mucosal lesions (DMLs) in denture wearers and to co-relate the prevalence with age, gender, type of denture and any systemic conditions. Dental records of 380 denture wearers were retrospectively reviewed for OMLs and DMLs. We found 45% of the denture wearers had DMLs and 60.8% had OMLs not related to denture wearing. Although the prevalence of DMLs was higher in complete denture wearers than in partial denture wearers (49% vs. 42.2%), this difference was not significant. The most common DMLs were traumatic ulcer (19.5%) and denture-induced stomatitis (18.1%). When analysed by type, traumatic ulcer, denture hyperplasia, frictional keratosis and candidiasis were more common in complete denture wearers, whereas denture-induced stomatitis was more common in partial denture wearers. Frictional keratosis was more common in men than in women. The prevalence of OMLs not related to denture wearing was higher in complete denture wearers than in partial denture wearers, and the most common OML was fissured tongue (27.6%). No association between DMLs and systemic conditions or xerostomic drugs was noted. No differences in the prevalence of DMLs in association with denture type were found. The prevalence of OMLs not related to denture wearing was higher in complete denture wearers than in partial denture wearers. This difference was affected by age, and the data were similar to the findings observed in the elderly.

  16. Novel infectious cDNA clones of hepatitis C virus genotype 3a (strain S52) and 4a (strain ED43): genetic analyses and in vivo pathogenesis studies

    DEFF Research Database (Denmark)

    Gottwein, Judith; Scheel, Troels; Callendret, Benoit

    2010-01-01

    Previously, RNA transcripts of cDNA clones of hepatitis C virus (HCV) genotypes 1a (strains H77, HCV-1, and HC-TN), 1b (HC-J4, Con1, and HCV-N), and 2a (HC-J6 and JFH1) were found to be infectious in chimpanzees. However, only JFH1 was infectious in human hepatoma Huh7 cells. We performed genetic...... analysis of HCV genotype 3a (strain S52) and 4a (strain ED43) prototype strains and generated full-length consensus cDNA clones (pS52 and pED43). Transfection of Huh7.5 cells with RNA transcripts of these clones did not yield cells expressing HCV Core. However, intrahepatic transfection of chimpanzees...... resulted in robust infection with peak HCV RNA titers of approximately 5.5 log(10) international units (IU)/ml. Genomic consensus sequences recovered from serum at the times of peak viral titers were identical to the sequences of the parental plasmids. Both chimpanzees developed acute hepatitis...

  17. How different do visuo-tactile criteria assess caries lesions activity status on occlusal surfaces?

    DEFF Research Database (Denmark)

    Floriano, I; Bonini, G C; Matos, R

    2015-01-01

    the International Caries Detection and Assessment System with an additional criteria--Lesion Activity Assessment (ICDAS + LAA), and a reference examiner classified lesions regarding plaque stagnation, colour, lustre, cavities, depth and texture. Logistic regressions were used to test associations. For analyses, we...... lesions present lustre. CONCLUSION: Most clinical signs associated with active caries lesions were similar, but texture and severity tend to have a greater importance when using ICDAS + LAA for distinguishing caries activity status. Attention should be given to differences due to texture and lustre when...

  18. Diversity of Genetic Resources and Genetic Association Analyses of Green and Dry Chillies of Eastern India Diversidad de Recursos Genéticos y Análisis de Asociación Genética de Ajíes Verdes y Secos del Este de India

    Directory of Open Access Journals (Sweden)

    Arup Chattopadhyay

    2011-09-01

    Full Text Available Chilli (Capsicum annuum L. is regarded as one of the main commercial vegetable and spice crops at the global level. Maximum diversity can be noted among the cultivars/landraces available in India with respect to shape, size, yield, quality, and other traits. The present experiment was conducted to identify the most promising chilli variety suited for green and dry purposes, to study the genetic variability for different traits and to assess the association of different yield attributing traits with the green and dry yield of chilli. Thirty four genotypes were characterized during a 2-yr period. Most of the genotypes possessed the character constellation of C. annuum. Two genotypes, ‘Chaitali Pointed’ and ‘BC CH Sel-4’ were found most promising with respect to green fruit yield (272.79 g, 221.10 g per plant and dry fruit yield (54.56 g, 44.44 g per plant. Phenotypic and Genotypic Coefficient of Variation values for green fruit weight (119.95%, 111.26%, green fruit girth (89.76%, 48.93%, weight of red ripe fruit (112.02%, 111.93%, weight of dry fruit (111.63%, 110.97% and number of fruits per plant (86.05%, 85.02% were recorded to be high. Green fruit yield per plant, ascorbic acid content, and number of fruits per plant also showed very high broad-sense heritability and genetic advance. From the study of correlation and path coefficient analyses, the number of fruits per plant, green fruit length for green chilli, weight of dry fruit and the number of fruits per plant for dry chilli were found to the most important selection indices.El ají (Capsicum annuum L. es considerado como uno de los principales cultivos comerciales de vegetales y especias a nivel mundial. La máxima diversidad puede ser observada entre los cultivares y razas disponibles en India con respecto a forma, tamaño, producción, calidad, y otros rasgos. Este experimento se realizó para identificar la variedad de ají más promisoria y apropiada para fruto verde y seco

  19. Leishmania species identification using FTA card sampling directly from patients' cutaneous lesions in the state of Lara, Venezuela.

    Science.gov (United States)

    Kato, Hirotomo; Watanabe, Junko; Mendoza Nieto, Iraida; Korenaga, Masataka; Hashiguchi, Yoshihisa

    2011-10-01

    A molecular epidemiological study was performed using FTA card materials directly sampled from lesions of patients with cutaneous leishmaniasis (CL) in the state of Lara, Venezuela, where causative agents have been identified as Leishmania (Viannia) braziliensis and L. (Leishmania) venezuelensis in previous studies. Of the 17 patients diagnosed with CL, Leishmania spp. were successfully identified in 16 patients based on analysis of the cytochrome b gene and rRNA internal transcribed spacer sequences. Consistent with previous findings, seven of the patients were infected with L. (V.) braziliensis. However, parasites from the other nine patients were genetically identified as L. (L.) mexicana, which differed from results of previous enzymatic and antigenic analyses. These results strongly suggest that L. (L.) venezuelensis is a variant of L. (L.) mexicana and that the classification of L. (L.) venezuelensis should be reconsidered. Copyright © 2011 Royal Society of Tropical Medicine and Hygiene. Published by Elsevier Ltd. All rights reserved.

  20. Varicose vein therapy and nerve lesions.

    Science.gov (United States)

    Hirsch, Tobias

    2017-03-01

    Treating varicose veins using endovenous thermal techniques - especially laser and radio frequency ablation - has emerged as an effective alternative to open surgery with stripping and high ligation. Even though these methods are very gentle and patient-friendly, they are nevertheless accompanied by risks and side effects. Compared to open surgical therapy, the risk of damage to peripheral and motor nerves is reduced; however, it still exists as a result of heat exposure and tumescent anaesthesia. Non-thermal methods that can be applied without tumescent anaesthesia have been introduced to the market. They pose a considerably lower risk of nerve lesions while proving to be much more effective. This paper investigates data on postoperative nerve damage and paraesthesia using internet research (PubMed). It analyses the current state of knowledge regarding non-thermal treatment methods and takes into account the latest developments in the use of cyanoacrylate to close insufficient saphenous veins.

  1. Petrous apex lesions in the pediatric population

    Energy Technology Data Exchange (ETDEWEB)

    Radhakrishnan, Rupa [University of Cincinnati College of Medicine, Department of Radiology, Cincinnati, OH (United States); Cincinnati Children' s Hospital Medical Center, Department of Radiology, Cincinnati, OH (United States); Son, Hwa Jung [University of Cincinnati College of Medicine, Department of Otolaryngology-Head and Neck Surgery, Cincinnati, OH (United States); Koch, Bernadette L. [Cincinnati Children' s Hospital Medical Center, Department of Radiology, Cincinnati, OH (United States)

    2014-03-15

    A variety of abnormal imaging findings of the petrous apex are encountered in children. Many petrous apex lesions are identified incidentally while images of the brain or head and neck are being obtained for indications unrelated to the temporal bone. Differential considerations of petrous apex lesions in children include ''leave me alone'' lesions, infectious or inflammatory lesions, fibro-osseous lesions, neoplasms and neoplasm-like lesions, as well as a few rare miscellaneous conditions. Some lesions are similar to those encountered in adults, and some are unique to children. Langerhans cell histiocytosis (LCH) and primary and metastatic pediatric malignancies such as neuroblastoma, rhabomyosarcoma and Ewing sarcoma are more likely to be encountered in children. Lesions such as petrous apex cholesterol granuloma, cholesteatoma and chondrosarcoma are more common in adults and are rarely a diagnostic consideration in children. We present a comprehensive pictorial review of CT and MRI appearances of pediatric petrous apex lesions. (orig.)

  2. Acute skin lesions due to localized ''hot particle'' radiation exposures

    International Nuclear Information System (INIS)

    Baum, J.W.; Carsten, A.L.; Kaurin, D.G.L.; Schaefer, C.W.

    1996-01-01

    Purpose of the studies was to determine incidence and severity of lesions resulting from localized deposition of dose to the skin from small ( 2 at 70μm depth) from isotopes having max beta particle energies from about 0.3-3 MeV. Incidence of erythema and scabs (indicating ulceration) were scored routinely for up to 71 days post-irradiation. Responses followed normal probability distributions, and thus, no true threshold could be defined. Ten and 50% incidence rates were deduced using probit analyses. Lowest dose producing 10% incidence was about 1 Gy for exposures to Yb-175 (0.5 MeV max energy) beta particles. Severity of lesions was estimated using diameters and persistence. From preliminary considerations of probability of induction, size, and persistence of acute lesions, a special limit for hot particle exposures in the range of 5-50 Gy may be reasonable, with an action level between about 1 Gy and the limit

  3. Quantification of osteolytic bone lesions in a preclinical rat trial

    Science.gov (United States)

    Fränzle, Andrea; Bretschi, Maren; Bäuerle, Tobias; Giske, Kristina; Hillengass, Jens; Bendl, Rolf

    2013-10-01

    In breast cancer, most of the patients who died, have developed bone metastasis as disease progression. Bone metastases in case of breast cancer are mainly bone destructive (osteolytic). To understand pathogenesis and to analyse response to different treatments, animal models, in our case rats, are examined. For assessment of treatment response to bone remodelling therapies exact segmentations of osteolytic lesions are needed. Manual segmentations are not only time-consuming but lack in reproducibility. Computerized segmentation tools are essential. In this paper we present an approach for the computerized quantification of osteolytic lesion volumes using a comparison to a healthy reference model. The presented qualitative and quantitative evaluation of the reconstructed bone volumes show, that the automatically segmented lesion volumes complete missing bone in a reasonable way.

  4. Imaging review of lipomatous musculoskeletal lesions

    Directory of Open Access Journals (Sweden)

    Burt Ashley M.

    2017-01-01

    Full Text Available Lipomatous lesions are common musculoskeletal lesions that can arise within the soft tissues, bone, neurovascular structures, and synovium. The majority of these lesions are benign, and many of the benign lesions can be diagnosed by radiologic evaluation. However, radiologic differences between benign and malignant lipomatous lesions may be subtle and pathologic correlation is often needed. The use of sonography, computed tomography (CT, and magnetic resonance imaging (MRI is useful not only in portraying fat within the lesion, but also for evaluating the presence and extent of soft tissue components. Lipomas make up most soft tissue lipomatous lesions, but careful evaluation must be performed to distinguish these lesions from a low-grade liposarcoma. In addition to the imaging appearance, the location of the lesion and the patient demographics can be utilized to help diagnose other soft tissue lipomatous lesions, such as elastofibroma dorsi, angiolipoma, lipoblastoma, and hibernoma. Osseous lipomatous lesions such as a parosteal lipoma and intraosseous lipoma occur less commonly as their soft tissue counterpart, but are also benign. Neurovascular and synovial lipomatous lesions are much rarer lesions but demonstrate more classic radiologic findings, particularly on MRI. A review of the clinical, radiologic, and pathologic characteristics of these lesions is presented.

  5. How to approach breast lesions in children and adolescents

    Energy Technology Data Exchange (ETDEWEB)

    Gao, Yiming, E-mail: yiminggao@gmail.com [New York University Langone Medical Center, 221 Lexington Ave., New York, NY 10016 (United States); Massachusetts General Hospital, 55 Fruit Street, Boston, MA 02114 (United States); Saksena, Mansi A.; Brachtel, Elena F.; Meulen, Deborah C. ter; Rafferty, Elizabeth A. [Massachusetts General Hospital, 55 Fruit Street, Boston, MA 02114 (United States)

    2015-07-15

    Highlights: • Recognize why the diagnostic approach to the developing breast differs from that to the adult breast. • Review of embryology, early breast development, and later pubescent breast development. • Learn the spectrum of common and uncommon pediatric breast lesions. • Develop an algorithm for diagnostic evaluation and management of pediatric breast lesions. - Abstract: Assessment of a pediatric breast lesion always starts with clinical evaluation. When imaging of a pediatric breast is indicated, ultrasound is the mainstay. The vast majority of pediatric breast complaints are of benign etiology, therefore the diagnostic/management approach emphasizes “first do no harm”. Correlation with age and clinical history helps to direct diagnosis. It is essential to be familiar with the imaging appearance of the normal developing breast at various Tanner stages, in order to diagnose physiologic breast findings and to minimize unnecessary biopsies in young breasts vulnerable to injury. Normal anatomic structures, developmental conditions, benign neoplastic and non-neoplastic lesions are common causes of breast complaints in children. Uncommon benign masses and rarely, secondary more than primary malignancies may present in a pediatric breast. Chest wall masses such as Ewing's sarcoma or rhabdomyosarcoma occur in children and may involve the breast via contiguous growth or locoregional metastasis. In addition, special attention should be given to any breast lesion in a child with risk factors predisposing to breast cancer, such as known extramammary malignancy, genetic mutations, prior mantle irradiation, or strong family history of breast cancer, which usually requires biopsy to exclude the possibility of malignancy. Conclusion: The developing breast is vulnerable to injury, and because breast malignancy is uncommon in children, diagnostic and management approach emphasizes “first do no harm”. Understanding normal breast development and the

  6. Hock lesions and free-stall design.

    Science.gov (United States)

    Weary, D M; Taszkun, I

    2000-04-01

    We compared the prevalence and severity of skin lesions on the hocks of lactating dairy cows in southern British Columbia, comparing 20 farms using three common bedding surfaces: sawdust, sand, and geotextile mattresses. Skin lesions were scored at five positions on the hock. For each position we noted if the lesion showed inflammatory attributes, and then assigned a severity score. Of the 1752 lactating cows scored, 1267 cows (73%) had at least one hock lesion. Of those cows with lesions, 87% had lesions on both legs, 76% had lesions on more than one location on the hock, and 78% had a lesion of at least moderate severity (i.e., evidence of skin breakage or an area of hair loss >10 cm2). Lesions were most prevalent on farms that used geotextile mattresses (91% of cows) and least common on farms that used sand (24% of cows). Moreover, lesions on cows from farms using mattresses were more numerous and more severe than those on cows from sand-bedded farms. The prevalence and severity of lesions on farms using sawdust was intermediate. Lesions also varied in relation to location on the hock. For farms using geotextile mattresses, lesions were more common and more severe on the lateral surfaces of both the tuber calcis and the tarsal joint. On farms using sawdust, lesions were common on the dorsal surface of the tuber calcis and the lateral surfaces of both the tuber calcis and the tarsal joint. Lesions were rare on all five positions for cows from sand-bedded farms. Among the 10 farms sampled using sawdust, we found a significant negative relationship between the length of the stall and severity of lesions. For cows with lesions, the number and severity of lesions increased with age.

  7. Oral white lesion-histomorhological assessment and associated risk factor

    International Nuclear Information System (INIS)

    Orakzai, G.; Nisa, W.U.; Orakzai, S.H.

    2015-01-01

    Oral white lesions constitute a major clinical problem in Pakistan and South Asian countries. The study was done with the objective to analyse oral white lesions histologically and clinically, and evaluate association between various risk factors in different ages, gender, ethnic groups, sites and sizes of the lesion. Methods: A total of 80 patients presenting with oral white lesions were included in this cross-sectional study conducted at Department of Histopathology, Armed Forces Institute of Pathology (AFIP), Rawalpindi. The biopsy sample was fixed in 10% formalin and after standardized processing, slides were prepared, stained by Hematoxylin and Eosin, with special stains when required. The histo-pathological diagnosis of lesion was recorded. Mean and standard deviation were calculated for quantitative variable. Frequency and percentages were calculated for qualitative variables. Results: Out of total 80 patients 43 were females and 37 males. The mean age of cases was 47.92 years. Majority of the patients were between 30-39 years. Buccal mucosa was affected in majority of the cases (55%), followed by lateral border of tongue 17.5% and lip mucosa (8.8%). No risk factor had been observed in almost half of the patients. Histologically Lichen Planus was the most common lesion (32.5%), followed by chronic nonspecific inflammation in (22.5%), keratosis without dysplasia (10%), keratosis with dysplasia (8.8%), Pemphigus vulgaris (7.5%), fungal infestation (5%) and Squamous cell carcinoma (3.8%). Conclusion: Oral Lichen Planus was the most common oral white lesion in our set up, with buccal mucosa involved in majority of the cases. Association between histo-pathological diagnosis with age and gender was insignificant. However, significant association was observed between histopathological diagnosis and site. Among risk factors significant association was seen between snuff dippers and pan users. (author)

  8. Cell genetic processes under space flight conditions: Analysis of two-factor crosses between spore color mutants of Sordaria macrospora. Final report; Zellgenetische Prozesse unter Weltraumbedingungen: Analyse von Zweifaktorenkreuzungen zwischen Sporenfarbenmutanten von Sordaria macrospora. Abschlussbericht

    Energy Technology Data Exchange (ETDEWEB)

    Hock, B.; Hahn, A.

    2001-07-01

    The purpose of the FUNGUS experiment on S/MM05 was to examine the effects of space flight conditions on the hereditary transmission of the spore color genes. The controls consisted of one further experiment in space with a centrifuge and 1 x g acceleration, and a gravitational reference experiment. A statistical analysis revealed no significant differences attributable to the absence of gravitational effects. A significant increase however was observed in the recombination frequencies, due to the fraction of HZE particles in the cosmic radiation. Gravitational reference experiments showed a dose-dependent effect of heavy-ion particle radiation on the post-reduction frequency and thus on the calculated distances between the genes, higher radiation doses increasing the post-reduction frequency. It was possible to derive dose-response curves for comparison with X-radiation and determination of the RBE of the heavy ion radiation with respect to the calculated distances between the genes 1u and r2. The mycelium of the fungi of the space flight experiment was examined for DNA strand breaks at the molecular level by means of a single cell gel electrophoresis assay. No genetic damage could be detected in the specimens of the experiment in space. Attempts at DNA repair in S. macrospora reveal that most of the damage is healed within a few hours. It was possible to determine the maximum doses of ionizing and non-ionizing radiation up to which DNA repair is possible. (orig./CB) [German] Der Versuch FUNGUS auf S/MM05 hatte zum Ziel, die Auswirkungen der Weltraumbedingungen auf die Vererbung der Farbsporgene zu beobachten. Als Kontrollen dienten eine Zentrifuge, die im Weltraum 1 x g Beschleunigung erzeugte, und ein Bodenreferenzexperiment. Eine statistische Auswertung ergab keine signifikanten Unterschiede, die durch die fehlende Schwerkraft bedingt waren. Eine signifikante Erhoehung der Rekombinationsfrequenzen wird jedoch durch den HZE-Partikelanteil der Weltraumstrahlung

  9. Clinical Significance of Contralateral Reactive Lesion in Vocal Fold Polyp and Cyst.

    Science.gov (United States)

    Cho, Jung-Hae; Choi, Yong-Sug; Joo, Young-Hoon; Park, Young-Hak; Sun, Dong-Il

    2018-01-01

    We investigated the clinical significance of contralateral reactive lesions in patients undergoing laryngeal microsurgery for benign vocal fold lesions such as vocal polyps and cysts. This was a retrospective, single institution cohort study. Patient medical records were reviewed for demographic characteristics; acoustic, aerodynamic, and perceptual analyses; and Voice Handicap Index score before and after laryngeal microsurgery. Definitive diagnoses were made via intraoperative microlaryngoscopic evaluations. Clinical parameters were assessed to identify risk factors for contralateral reactive lesions. We evaluated surgical outcome using voice analysis. We enrolled 268 patients (109 men and 159 women) with benign vocal fold lesions. A total of 195 (72.8%) had a contralateral reactive vocal fold lesion. A multivariable analysis revealed that being a never smoker and having a hoarseness duration ≥6 months, vocal polyps, and small primary lesions were independent risk factors for contralateral reactive lesions (P vocal fold lesions are frequently detected in patients with vocal polyp and cyst. The reactive lesions had an adverse effect on voice quality. Simultaneous excision of primary and contralateral reactive lesions may be an alternative treatment for better voice outcome. Copyright © 2018 The Voice Foundation. Published by Elsevier Inc. All rights reserved.

  10. Morphological and genetic analyses of the first record of the Niger Hind, Cephalopholis nigri (Perciformes: Serranidae, in the Mediterranean Sea and of the African Hind, Cephalopholis taeniops, in Malta

    Directory of Open Access Journals (Sweden)

    Noel Vella

    2016-11-01

    Full Text Available Abstract Background Non-native marine species, including tropical eastern Atlantic fish species are on the increase in Malta, with shipping activities being the main vector for the movement of these alien species from the Atlantic into the Mediterranean Sea. This calls for cooperation and collaboration between various sea-users and researchers to ensure continuous monitoring of coastal biodiversity. Methods Research methods involving local fishermen cooperation in monitoring efforts to identify and track populations of alien species in the Central Mediterranean has led to new records for the genus Cephalopholis (Perciformes: Serranidae in Malta. Morphological characteristics, meristic counts and mitochondrial DNA sequences from specimens of both species sampled from Maltese waters were analysed to confirm their species identify accurately, essential for tracking their respective population expansions in the Mediterranean. Results and conclusion Results from this study have led to confirmation of the first record of the Niger Hind, Cephalopholis nigri (Günther, 1859, in the Mediterranean Sea and of the establishment of the African Hind, Cephalopholis taeniops (Valenciennes, 1828 in Maltese waters.

  11. Eye lesions in pet birds.

    Science.gov (United States)

    Tsai, S S; Park, J H; Hirai, K; Itakura, C

    1993-03-01

    Amongst eye lesions in birds that died in quarantine, cataracts were the most common disorders (37/241, 15.4%), being prevalent in the annular pads of cockatiels (Nymphicus hollandicus), Amazon parrots (Amazona aestiva aestiva) and budgerigars (Melopsittacus undulatus). The incidence in male birds was more than twice that in females. Deposition of crystals, mostly in the cornea, was the second most frequent lesion (21/293, 8.7%), mainly found in cockatiels, parakeets (Psittacula krameri manillensis), Amazon parrots (Amazona aestiva aestiva), budgerigars and finches (Poephila gouldiae gouldiae). These corneal crystals were negative to PAS and Kossa's stains. Six parakeets (Psittacula krameri manillensis) had calcium salts deposited in the inner plexiform layer of the retina and occasionally in the iris and ciliary body. Neither inflammation nor neo-vascularization was observed when cataracts, corneal crystalline deposition, and retinal and ciliary calcification were present. Intranuclear inclusion bodies typical for papovavirus infection were found in the eyelids of six budgerigars (2.5%). Similar inclusions were simultaneously found in the pars ciliaris retinae (4, 1.7%), inner plexiform of retina (1, 0.4%) and anterior epithelium of the cornea (1, 0.4%). Other lesions such as candidial endophthalmitis, conjunctival cryptosporidiosis, corneal dystrophy, keratitis, corneal perforation and iridocyclitis, were occasional findings.

  12. Automatic segmentation of psoriasis lesions

    Science.gov (United States)

    Ning, Yang; Shi, Chenbo; Wang, Li; Shu, Chang

    2014-10-01

    The automatic segmentation of psoriatic lesions is widely researched these years. It is an important step in Computer-aid methods of calculating PASI for estimation of lesions. Currently those algorithms can only handle single erythema or only deal with scaling segmentation. In practice, scaling and erythema are often mixed together. In order to get the segmentation of lesions area - this paper proposes an algorithm based on Random forests with color and texture features. The algorithm has three steps. The first step, the polarized light is applied based on the skin's Tyndall-effect in the imaging to eliminate the reflection and Lab color space are used for fitting the human perception. The second step, sliding window and its sub windows are used to get textural feature and color feature. In this step, a feature of image roughness has been defined, so that scaling can be easily separated from normal skin. In the end, Random forests will be used to ensure the generalization ability of the algorithm. This algorithm can give reliable segmentation results even the image has different lighting conditions, skin types. In the data set offered by Union Hospital, more than 90% images can be segmented accurately.

  13. NEOPLASTIC LESIONS OF THE APPENDIX

    Directory of Open Access Journals (Sweden)

    Piotr Bryk

    2013-11-01

    Full Text Available The aim of the research was to present the clinical observations of neoplastic lesions of the appendix (one carcinoid and two mucous cysts and to discuss various manners of treatment and prognosis. Material and methods: The authors of the following paper present a description of three cases of appendix tumours, two patients with a mucous cyst and a patient with carcinoid, against the background of all the appendectomies performed at the Clinical Department of General, Endocrine and Oncological Surgery of the Provincial Polyclinical Hospital in Kielce in the years 2005–2011. Results : Within the 7-year period, a total of 11 719 surgical operations have been performed, where 834 (7.1% were that of appendectomy. Among all of the removed vermiform appendixes, neoplastic lesions occurred in three cases constituting a mere 0.3% of all of the appendectomies performed within that period. In two of the cases there was a suspicion of mucous cysts before the surgical operation. In none of the above-mentioned cases was is possible to ultimately establish the diagnosis before the operation. The patients were subjected to a simple appendectomy. The patients are in good clinical health, with no signs of relapse. Conclusions : The presented cases of patients with appendix tumours illustrate the difficulty of preoperative detection of a neoplastic lesion. This is mainly due to a scantily symptomatic course or symptoms typical of appendicitis. In light of this, histopathological examination of each appendix should be treated as obligatory.

  14. Genetic modification and genetic determinism

    Science.gov (United States)

    Resnik, David B; Vorhaus, Daniel B

    2006-01-01

    In this article we examine four objections to the genetic modification of human beings: the freedom argument, the giftedness argument, the authenticity argument, and the uniqueness argument. We then demonstrate that each of these arguments against genetic modification assumes a strong version of genetic determinism. Since these strong deterministic assumptions are false, the arguments against genetic modification, which assume and depend upon these assumptions, are therefore unsound. Serious discussion of the morality of genetic modification, and the development of sound science policy, should be driven by arguments that address the actual consequences of genetic modification for individuals and society, not by ones propped up by false or misleading biological assumptions. PMID:16800884

  15. Improved differentiation between MS and vascular brain lesions using FLAIR* at 7 Tesla

    Energy Technology Data Exchange (ETDEWEB)

    Kilsdonk, Iris D.; Wattjes, Mike P.; Lopez-Soriano, Alexandra; Jong, Marcus C. de; Graaf, Wolter L. de; Conijn, Mandy M.A.; Barkhof, Frederik [VU University Medical Center, Department of Radiology, De Boelelaan 1118, HZ, Amsterdam (Netherlands); Kuijer, Joost P.A. [VU University Medical Center, Department of Physics and Medical Technology, Amsterdam (Netherlands); Polman, Chris H. [VU University Medical Center, Department of Neurology, Amsterdam (Netherlands); Luijten, Peter R. [University Medical Center, Department of Radiology, Utrecht (Netherlands); Geurts, Jeroen J.G. [VU University, Department of Anatomy and Neurosciences, Amsterdam (Netherlands); Geerlings, Mirjam I. [University Medical Center, Julius Center for Health Sciences and Primary Care, Utrecht (Netherlands)

    2014-04-15

    To investigate whether a new magnetic resonance image (MRI) technique called T2*-weighted fluid attenuation inversion recovery (FLAIR*) can differentiate between multiple sclerosis (MS) and vascular brain lesions, at 7 Tesla (T). We examined 16 MS patients and 16 age-matched patients with (risk factors for) vascular disease. 3D-FLAIR and T2*-weighted images were combined into FLAIR* images. Lesion type and intensity, perivascular orientation and presence of a hypointense rim were analysed. In total, 433 cerebral lesions were detected in MS patients versus 86 lesions in vascular patients. Lesions in MS patients were significantly more often orientated in a perivascular manner: 74 % vs. 47 % (P < 0.001). Ten MS lesions (2.3 %) were surrounded by a hypointense rim on FLAIR*, and 24 MS lesions (5.5 %) were hypointense on T2*. No lesions in vascular patients showed any rim or hypointensity. Specificity of differentiating MS from vascular lesions on 7-T FLAIR* increased when the presence of a central vessel was taken into account (from 63 % to 88 %), most obviously for deep white matter lesions (from 69 % to 94 %). High sensitivity remained (81 %). 7-T FLAIR* improves differentiation between MS and vascular lesions based on lesion location, perivascular orientation and presence of hypointense (rims around) lesions. circle A new MRI technique T2*-weighted fluid attenuation inversion recovery (FLAIR*) was investigated. circle FLAIR* at 7-T MRI combines FLAIR and T2* images into a single image. circle FLAIR* at 7 T does not require enhancement with contrast agents. (orig.)

  16. Lesion Contrast Enhancement in Medical Ultrasound Imaging

    DEFF Research Database (Denmark)

    Stetson, Paul F.; Sommer, F.G.; Macovski, A.

    1997-01-01

    Methods for improving the contrast-to-noise ratio (CNR) of low-contrast lesions in medical ultrasound imaging are described. Differences in the frequency spectra and amplitude distributions of the lesion and its surroundings can be used to increase the CNR of the lesion relative to the background...

  17. From Genetics to Genetic Algorithms

    Indian Academy of Sciences (India)

    Genetic algorithms (GAs) are computational optimisation schemes with an ... The algorithms solve optimisation problems ..... Genetic Algorithms in Search, Optimisation and Machine. Learning, Addison-Wesley Publishing Company, Inc. 1989.

  18. From Genetics to Genetic Algorithms

    Indian Academy of Sciences (India)

    artificial genetic system) string feature or ... called the genotype whereas it is called a structure in artificial genetic ... assigned a fitness value based on the cost function. Better ..... way it has produced complex, intelligent living organisms capable of ...

  19. About Genetic Counselors

    Science.gov (United States)

    ... clinical care in many areas of medicine. Assisted Reproductive Technology/Infertility Genetics Cancer Genetics Cardiovascular Genetics Cystic Fibrosis Genetics Fetal Intervention and Therapy Genetics Hematology Genetics Metabolic Genetics ...

  20. Theory of pairwise lesion interaction

    International Nuclear Information System (INIS)

    Harder, Dietrich; Virsik-Peuckert, Patricia; Bartels, Ernst

    1992-01-01

    A comparison between repair time constants measured both at the molecular and cellular levels has shown that the DNA double strand break is the molecular change of key importance in the causation of cellular effects such as chromosome aberrations and cell inactivation. Cell fusion experiments provided the evidence that it needs the pairwise interaction between two double strand breaks - or more exactly between the two ''repair sites'' arising from them in the course of enzymatic repair - to provide the faulty chromatin crosslink which leads to cytogenetic and cytolethal effects. These modern experiments have confirmed the classical assumption of pairwise lesion interaction (PLI) on which the models of Lea and Neary were based. It seems worthwhile to continue and complete the mathematical treatment of their proposed mechanism in order to show in quantitative terms that the well-known fractionation, protraction and linear energy transfer (LET) irradiation effects are consequences of or can at least be partly attributed to PLI. Arithmetic treatment of PLI - a second order reaction - has also the advantage of providing a prerequisite for further investigations into the stages of development of misrepair products such as chromatin crosslinks. It has been possible to formulate a completely arithmetic theory of PLI by consequently applying three biophysically permitted approximations - pure first order lesion repair kinetics, dose-independent repair time constants and low yield of the ionization/lesion conversion. The mathematical approach will be summarized here, including several formulae not elaborated at the time of previous publications. We will also study an application which sheds light on the chain of events involved in PLI. (author)

  1. Lesions in the wingless gene of the Apollo butterfly (Parnassius apollo, Lepidoptera: Papilionidae) individuals with deformed or reduced wings, coming from the isolated population in Pieniny (Poland).

    Science.gov (United States)

    Łukasiewicz, Kinga; Sanak, Marek; Węgrzyn, Grzegorz

    2016-02-01

    Parnassius apollo (Lepidoptera: Papilionidae) is a butterfly species which was common in Europe in 19th century, but now it is considered as near threatened. Various programs devoted to protect and save P. apollo have been established, between others the one in Pieniny National Park (Poland). An isolated population of this butterfly has been restored there from a small group of 20-30 individuals in early 1990s. However, deformations or reductions of wings occur in this population in a relatively large number of insects, and the cause of this phenomenon is not known. In this report, the occurrence of lesions in the wingless (wg) gene is demonstrated in most of tested butterflies with deformed or reduced wings, but not in normal insects. Although the analyses indicated that wg lesion(s) cannot be the sole cause of the deformed or reduced wings in the population of P. apollo from Pieniny, the discovery that this genetic defect occurs in most of malformed individuals, can be considered as an important step in understanding this phenomenon. Copyright © 2015 Elsevier B.V. All rights reserved.

  2. Percutaneous acetabuloplasty for metastatic acetabular lesions

    Directory of Open Access Journals (Sweden)

    Logroscino Giandomenico

    2008-05-01

    Full Text Available Abstract Background Osteolytic metastases around the acetabulum are frequent in tumour patients, and may cause intense and drug-resistant pain of the hip. These lesions also cause structural weakening of the pelvis, limping, and poor quality of life. Percutaneous acetabuloplasty is a mini-invasive procedure for the management of metastatic lesions due to carcinoma of the acetabulum performed in patients who cannot tolerate major surgery, or in patients towards whom radiotherapy had already proved ineffective. Methods We report a retrospective study in 25 such patients (30 acetabuli who were evaluated before and after percutaneous acetabuloplasty, with regard to pain, mobility of the hip joint, use of analgesics, by means of evaluation forms: Visual Analog Scale, Harris Hip Score, Western Ontario and McMaster Universities Index of Osteoarthritis (WOMAC, Eastern Cooperative Oncology Group (ECOG. The results obtained were analysed using the χ2 Test and Fisher's exact test. Significance was sent at P Results Marked clinical improvement was observed in all patients during the first six post-operative months, with gradual a worsening thereafter from deterioration of their general condition. Complete pain relief was achieved in 15 of our 25 (59% of patients, and pain reduction was achieved in the remaining 10 (41% patients. The mean duration of pain relief was 7.3 months. Pain recurred in three patients (12% between 2 weeks to 3 months. No major complications occurred. There was transient local pain in most cases, and 2 cases of venous injection of cement without clinical consequences. Conclusion Percutaneous acetabuloplasty is effective in improving the quality of life of patients with osteolytic bone tumours, even though the improvement is observed during the first 6 months only. It can be an effective aid to chemo- and radiotherapy in the management of acetabular metastases.

  3. Benign clavicular lesions that may mimic malignancy

    International Nuclear Information System (INIS)

    Gerscovich, E.G.; Greenspan, A.; Szabo, R.M.

    1991-01-01

    Nontraumatic lesions of the clavicle are infrequent. Of these, malignant tumors are more common than benign lesions. From January 1988 to January 1990, we examined 17 patients with benign lesions of the clavicle; in 8, the morphologic appearance of the lesion raised the possibility of malignancy in the differential diagnosis. The radiologic findings in these patients are presented. We propose that the unique shape and embryologic development of the clavicle may contribute to the atypical, aggressive presentation of some benign lesions in that bone. (orig.)

  4. Quantitative angiography methods for bifurcation lesions

    DEFF Research Database (Denmark)

    Collet, Carlos; Onuma, Yoshinobu; Cavalcante, Rafael

    2017-01-01

    Bifurcation lesions represent one of the most challenging lesion subsets in interventional cardiology. The European Bifurcation Club (EBC) is an academic consortium whose goal has been to assess and recommend the appropriate strategies to manage bifurcation lesions. The quantitative coronary...... angiography (QCA) methods for the evaluation of bifurcation lesions have been subject to extensive research. Single-vessel QCA has been shown to be inaccurate for the assessment of bifurcation lesion dimensions. For this reason, dedicated bifurcation software has been developed and validated. These software...

  5. Solitary lucent epiphyseal lesions in children

    Energy Technology Data Exchange (ETDEWEB)

    Gardner, D.J.; Azouz, E.M.

    1988-10-01

    We evaluated retrospectively the varying radiographic appearances of 15 solitary lucent epiphyseal lesions occurring in children. Imaging modalities used included plain films, conventional tomography, nuclear scintigraphy, and computed tomography. 40% of the lesions (6) were due to osteomyelitis. The remaining lesions included tuberculosis (1), foreign body granuloma (1), chondroblastoma (2), chondromyoxid fibroma (1), enchondroma (1), osteoid osteoma (2), and eosinophilic granuloma (1). Although the radiographic appearances of such lesions may be particularly characteristic, pathologic correlation is frequently necessary. The high incidence of osteomyelitis in our cases emphasizes its importance as a cause for a lucent epiphyseal lesion.

  6. Computerized tomography of orbital lesions

    International Nuclear Information System (INIS)

    Kuroiwa, Mayumi

    1981-01-01

    Two different types of computerized tomography scanners (CT scanner), i.e. a whole-body CT scanner (GE-CT/T8800) and a cerebral CT scanner (EMI-1010), were compared in the assessment and diagnosis of various orbital lesions. The whole-body CT scanner was found to be advantageous over the cerebral CT scanner for the following reasons: (1) CT images were more informative due to thinner slices associated with smaller-sized and larger-numbered matrices; (2) less artifacts derived from motion of the head or eyeball were produced because of the shorter scanning time; (3) with a devised gantry, coronal dissections were available whenever demanded. (author)

  7. Association between selected oral pathogens and gastric precancerous lesions.

    Directory of Open Access Journals (Sweden)

    Christian R Salazar

    Full Text Available We examined whether colonization of selected oral pathogens is associated with gastric precancerous lesions in a cross-sectional study. A total of 119 participants were included, of which 37 were cases of chronic atrophic gastritis, intestinal metaplasia, or dysplasia. An oral examination was performed to measure periodontal indices. Plaque and saliva samples were tested with real-time quantitative PCR for DNA levels of pathogens related to periodontal disease (Porphyromonas gingivalis, Tannerella forsythensis, Treponema denticola, Actinobacillus actinomycetemcomitans and dental caries (Streptococcus mutans and S. sobrinus. There were no consistent associations between DNA levels of selected bacterial species and gastric precancerous lesions, although an elevated but non-significant odds ratio (OR for gastric precancerous lesions was observed in relation to increasing colonization of A. actinomycetemcomitans (OR = 1.36 for one standard deviation increase, 95% Confidence Interval = 0.87-2.12, P. gingivalis (OR = 1.12, 0.67-1.88 and T. denticola (OR = 1.34, 0.83-2.12 measured in plaque. To assess the influence of specific long-term infection, stratified analyses by levels of periodontal indices were conducted. A. actinomycetemcomitans was significantly associated with gastric precancerous lesions (OR = 2.51, 1.13-5.56 among those with ≥ median of percent tooth sites with PD ≥ 3 mm, compared with no association among those below the median (OR = 0.86, 0.43-1.72. A significantly stronger relationship was observed between the cumulative bacterial burden score of periodontal disease-related pathogens and gastric precancerous lesions among those with higher versus lower levels of periodontal disease indices (p-values for interactions: 0.03-0.06. Among individuals with periodontal disease, high levels of colonization of periodontal pathogens are associated with an increased risk of gastric precancerous lesions.

  8. Lesser-known myelin-related disorders: focal tumour-like demyelinating lesions.

    Science.gov (United States)

    Jiménez Arango, J A; Uribe Uribe, C S; Toro González, G

    2015-03-01

    Focal tumour-like demyelinating lesions are defined as solitary demyelinating lesions with a diameter greater than 2 cm. In imaging studies, these lesions may mimic a neoplasm or brain abscess; as a result, invasive diagnostic and therapeutic measures may be performed that will in some cases increase morbidity. Our aim was to analyse and characterise these lesions according to their clinical, radiological, and pathological characteristics, and this data in addition to our literature review will contribute to a better understanding of these lesions. This descriptive study includes 5 cases with pathological diagnoses. We provide subject characteristics gathered through reviewing their clinical, radiology, and pathology reports. Patients' ages ranged from 12 to 60 years; 3 patients were female. The time delay between symptom onset and hospital admission was 3 to 120 days. Clinical manifestations were diverse and dependent on the location of the lesion, pyramidal signs were found in 80% of patients, there were no clinical or radiological signs of spinal cord involvement, and follow-up times ranged from 1 to 15 years. Brain biopsy is the gold standard for the diagnosis of demyelinating tumour-like lesions; however, their clinical features, along with several magnetic resonance imaging features such as open ring enhancement, venular enhancement, the presence of glutamate in spectroscopy, and others, may be sufficient to differentiate neoplastic lesions from focal tumour-like demyelinating lesions. Copyright © 2012 Sociedad Española de Neurología. Published by Elsevier Espana. All rights reserved.

  9. RELATIONSHIP BETWEEN LESION LOCATION AND COGNITIVE DOMAINS IN ACUTE ISCHEMIC STROKE PATIENTS

    Directory of Open Access Journals (Sweden)

    Vojislava Bugarski

    2009-09-01

    Full Text Available Localization of brain lesions in acute ischemic stroke has a significant effect on performance in various cognitive domains. The aim of the study was to determine whether there is association between different locations of ischemic brain lesions and different cognitive domains. The study included 40 acute ischemic stroke pati-ents (26 male and 14 female, aged 45-78 years, with 8-16 years of education. Lesi-on location was visualized using brain computerized tomography, whereas perfor-mance in different cognitive domains was assessed using an extensive neuropsychological test battery. The following domains were evaluated: executive function, language, immediate recall, delayed recall, attention, divergent reasoning, and visual-constructive performance in two dimensions. A series of categorical re-gression analyses were applied. The results showed a significant association between the domains of executive function and language and a set of predictors rela-ted to lesion location. Global brain atrophy was found to be a significant partial pre-dictor of performance in all cognitive domains, with higher degrees of global brain atrophy correlating with poorer performance in each of the studied domains. Combi-ned (cortical-subcortical lesions and unilateral lesions were both found to be signi-ficant partial predictors for language, with a higher lesion load being associated with poorer language performance. Combined lesions were also a significant partial pre-dictor for delayed recall, with a higher lesion load correlating with poorer perfor-mance in the delayed recall domain.

  10. Statistical methods in spatial genetics

    DEFF Research Database (Denmark)

    Guillot, Gilles; Leblois, Raphael; Coulon, Aurelie

    2009-01-01

    The joint analysis of spatial and genetic data is rapidly becoming the norm in population genetics. More and more studies explicitly describe and quantify the spatial organization of genetic variation and try to relate it to underlying ecological processes. As it has become increasingly difficult...... to keep abreast with the latest methodological developments, we review the statistical toolbox available to analyse population genetic data in a spatially explicit framework. We mostly focus on statistical concepts but also discuss practical aspects of the analytical methods, highlighting not only...

  11. Ultrasonographic findings of breast lesions

    International Nuclear Information System (INIS)

    Hwang, In Sung; Kim, Yang Soo; Suh, Hyoung Sim

    1990-01-01

    Authors retrospectively analyzed ultrasonographic findings of 61 cases of breast lesions which were proven pathologically at Daerim St. Mary's Hospital from May 1987 to February 1990. The results were as follows : 1. Of all 61 cases, there were 27 fibroadenomas, 13 fibrocystic diseases, 11 carcinomas, 8 abscesses, 1 sclerosing adenosis, and 1 intraductal papilloma. 2. Findings suggesting benignancy were smooth contour, round or oval shape, homogeneously echolucent internal echo, echogenic boundary echo, and posterior enhancement. In the cases of abscess, the findings were rather irregular contour, strong posterior enhancement, and dirty, inhomogeneous internal echo. While irregular and lobulated shape, inhomogeneous and mixed internal echo and pectoral muscle invasion were suggested for malignancy. 3. The sensitivity was 98% and the specificity 58% in benign mass excluding abscesses, 63% and 98% in abscesses, and 55% and 98% in carcinomas. In conclusion, ultrasonography is one of the excellent imaging modality for detecting breast lesions larger than 5 mm in size, but unfortunately some of the malignant tumors simulated benignancy, thus we considered fine needle aspiration biopsy and adjunctive imaging modalities such as film mammography must be followed for better detection of breast cancer

  12. Ultrasonographic findings of breast lesions

    Energy Technology Data Exchange (ETDEWEB)

    Hwang, In Sung; Kim, Yang Soo; Suh, Hyoung Sim [College of Medicine, Daerim St. Mary' s Hospital, Seoul (Korea, Republic of)

    1990-07-15

    Authors retrospectively analyzed ultrasonographic findings of 61 cases of breast lesions which were proven pathologically at Daerim St. Mary's Hospital from May 1987 to February 1990. The results were as follows : 1. Of all 61 cases, there were 27 fibroadenomas, 13 fibrocystic diseases, 11 carcinomas, 8 abscesses, 1 sclerosing adenosis, and 1 intraductal papilloma. 2. Findings suggesting benignancy were smooth contour, round or oval shape, homogeneously echolucent internal echo, echogenic boundary echo, and posterior enhancement. In the cases of abscess, the findings were rather irregular contour, strong posterior enhancement, and dirty, inhomogeneous internal echo. While irregular and lobulated shape, inhomogeneous and mixed internal echo and pectoral muscle invasion were suggested for malignancy. 3. The sensitivity was 98% and the specificity 58% in benign mass excluding abscesses, 63% and 98% in abscesses, and 55% and 98% in carcinomas. In conclusion, ultrasonography is one of the excellent imaging modality for detecting breast lesions larger than 5 mm in size, but unfortunately some of the malignant tumors simulated benignancy, thus we considered fine needle aspiration biopsy and adjunctive imaging modalities such as film mammography must be followed for better detection of breast cancer.

  13. Imaging in cardiac mass lesions

    International Nuclear Information System (INIS)

    Mundinger, A.; Gruber, H.P.; Dinkel, E.; Geibel, A.; Beck, A.; Wimmer, B.; Schlosser, V.

    1992-01-01

    In 26 patients with cardiac mass lesions confirmed by surgery, diagnostic imaging was performed preoperatively by means of two-dimensional echocardiography (26 patients), angiography (12 patients), correlative computed tomography (CT, 8 patients), and magnetic resonance imaging (MRI, 3 patients). Two-dimensional echocardiography correctly identified the cardiac masses in all patients. Angiography missed two of 12 cardiac masses; CT missed one of eight. MRI identified three of three cardiac masses. Although the sensitivity of two-dimensional echocardiography was high (100%), all methods lacked specificity. None of the methods allowed differentiation between myxoma (n=13) and thrombus (n=7). Malignancy of the lesions was successfully predicted by noninvasive imaging methods in all six patients. However, CT and MRI provided additional information concerning cardiac mural infiltration, pericardial involvement, and extracardiac tumor extension, and should be integrated within a preoperative imaging strategy. Thus two-dimensional echocardiography is the method of choice for primary assessment of patients with suspected cardiac masses. Further preoperative imaging by CT or MRI can be limited to patients with malignancies suspected on the grounds of pericardial effusion or other clinical results. (author)

  14. Magnetic resonance spectroscopy (MRS) of vertebral column – an additional tool for evaluation of aggressiveness of vertebral haemangioma like lesion

    International Nuclear Information System (INIS)

    Jeromel, Miran; Podobnik, Janez

    2014-01-01

    Most vertebral haemangioma are asymptomatic and discovered incidentally. Sometimes the symptomatic lesions present with radiological signs of aggressiveness and their appearance resemble other aggressive lesions (e.g. solitary plasmacytoma). We present a patient with large symptomatic aggressive haemangioma like lesion in 12 th thoracic vertebra in which a magnetic resonance spectroscopy (MRS) was used to analyse fat content within the lesion. The lesion in affected vertebrae showed low fat content with 33% of fat fraction (%FF). The fat content in non-affected (1 st lumbar) vertebra was as expected for patient’s age (68%). Based on MRS data, the lesion was characterized as an aggressive haemangioma. The diagnosis was confirmed with biopsy, performed during the treatment – percutaneous vertebroplasty. The presented case shows that MRS can be used as an additional tool for evaluation of aggressiveness of vertebral haemangioma like lesions

  15. Giant cell lesion of the jaw as a presenting feature of Noonan syndrome.

    Science.gov (United States)

    Sinnott, Bridget P; Patel, Maya

    2018-05-30

    This is a case of a 20-year-old woman who presented with a left jaw mass which was resected and found to be a giant cell granuloma of the mandible. Her history and physical examination were suggestive for Noonan syndrome which was confirmed with genetic testing and the finding of a PTPN11 gene mutation which has rarely been associated with giant cell lesions of the jaw. Given her particular genetic mutation and the presence of a giant cell lesion, we present a case of Noonan-like/multiple giant cell lesion syndrome. © BMJ Publishing Group Ltd (unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

  16. Lesion localization of speech comprehension deficits in chronic aphasia.

    Science.gov (United States)

    Pillay, Sara B; Binder, Jeffrey R; Humphries, Colin; Gross, William L; Book, Diane S

    2017-03-07

    Voxel-based lesion-symptom mapping (VLSM) was used to localize impairments specific to multiword (phrase and sentence) spoken language comprehension. Participants were 51 right-handed patients with chronic left hemisphere stroke. They performed an auditory description naming (ADN) task requiring comprehension of a verbal description, an auditory sentence comprehension (ASC) task, and a picture naming (PN) task. Lesions were mapped using high-resolution MRI. VLSM analyses identified the lesion correlates of ADN and ASC impairment, first with no control measures, then adding PN impairment as a covariate to control for cognitive and language processes not specific to spoken language. ADN and ASC deficits were associated with lesions in a distributed frontal-temporal parietal language network. When PN impairment was included as a covariate, both ADN and ASC deficits were specifically correlated with damage localized to the mid-to-posterior portion of the middle temporal gyrus (MTG). Damage to the mid-to-posterior MTG is associated with an inability to integrate multiword utterances during comprehension of spoken language. Impairment of this integration process likely underlies the speech comprehension deficits characteristic of Wernicke aphasia. © 2017 American Academy of Neurology.

  17. Theory and Practice in Quantitative Genetics

    DEFF Research Database (Denmark)

    Posthuma, Daniëlle; Beem, A Leo; de Geus, Eco J C

    2003-01-01

    With the rapid advances in molecular biology, the near completion of the human genome, the development of appropriate statistical genetic methods and the availability of the necessary computing power, the identification of quantitative trait loci has now become a realistic prospect for quantitative...... geneticists. We briefly describe the theoretical biometrical foundations underlying quantitative genetics. These theoretical underpinnings are translated into mathematical equations that allow the assessment of the contribution of observed (using DNA samples) and unobserved (using known genetic relationships......) genetic variation to population variance in quantitative traits. Several statistical models for quantitative genetic analyses are described, such as models for the classical twin design, multivariate and longitudinal genetic analyses, extended twin analyses, and linkage and association analyses. For each...

  18. Betel nut chewing, oral premalignant lesions, and the oral microbiome.

    Science.gov (United States)

    Hernandez, Brenda Y; Zhu, Xuemei; Goodman, Marc T; Gatewood, Robert; Mendiola, Paul; Quinata, Katrina; Paulino, Yvette C

    2017-01-01

    Oral cancers are attributed to a number of causal agents including tobacco, alcohol, human papillomavirus (HPV), and areca (betel) nut. Although betel nut chewing has been established as an independent cause of oral cancer, the mechanisms of carcinogenesis are poorly understood. An investigation was undertaken to evaluate the influence of betel nut chewing on the oral microbiome and oral premalignant lesions. Study participants were recruited from a dental clinic in Guam. Structured interviews and oral examinations were performed. Oral swabbing and saliva samples were evaluated by 454 pyrosequencing of the V3- V5 region of the 16S rRNA bacterial gene and genotyped for HPV. One hundred twenty-two adults were enrolled including 64 current betel nut chewers, 37 former chewers, and 21 with no history of betel nut use. Oral premalignant lesions, including leukoplakia and submucous fibrosis, were observed in 10 chewers. Within-sample bacterial diversity was significantly lower in long-term (≥10 years) chewers vs. never chewers and in current chewers with oral lesions vs. individuals without lesions. Between-sample bacterial diversity based on Unifrac distances significantly differed by chewing status and oral lesion status. Current chewers had significantly elevated levels of Streptococcus infantis and higher and lower levels of distinct taxa of the Actinomyces and Streptococcus genera. Long-term chewers had reduced levels of Parascardovia and Streptococcus. Chewers with oral lesions had significantly elevated levels of Oribacterium, Actinomyces, and Streptococcus, including Streptococcus anginosus. In multivariate analyses, controlling for smoking, oral HPV, S.anginosus, and S. infantis levels, current betel nut chewing remained the only predictor of oral premalignant lesions. Our study provides evidence that betel nut chewing alters the oral bacterial microbiome including that of chewers who develop oral premalignant lesions. Nonetheless, whether microbial changes

  19. Treatment of metastatic brain lesion

    Directory of Open Access Journals (Sweden)

    A. M. Zaytsev

    2015-01-01

    Full Text Available Objective. Increasing survival in patients with secondary brain damage, and identifying the factors of favorable and adverse prognosis.Material and method. In P. A. Hertsen Moscow Oncology Research Institute from 2007 to 2013 there were treated 268 patients with brain metastases. The mean age was 55.8 years (from 24 to 81 years. Metastases of colorectal cancer identified in 7.8%, cases of lung cancer in 34%, melanoma 9.3 %, breast cancer in 26%, kidney cancer in 11%, with non-identified primary tumor in 4.5%, other tumors accounted for 6.7%. Solitary metastasis was diagnosed in 164 (61,19% patients, oligometastasis (2-3 - 72 (26,87% patients with polymetastasis (more than 3 – 32 (11,94% patients. In 106 (39,55% of patients with brain metastases it was the only manifestation of the generalization process. To control the radical removal of the tumor in 93 (34,7% patients we used the method of fluorescence navigation (FN with the drug Alasens. In 66 (24,6% patients intraoperatively was held a session of photodynamic therapy (PDT. In 212 (79,1% cases, the removal of metastasis performed totally, 55 (20,9% patients stated Subtotal removal.Results. The observation period for the patients ranged from 3 to 79 months. Survival median among the entire group of patients with metastatic brain lesion was 12 months. Overall survival was significantly dependent on RPA class, the volume of postoperative treatment, histological type of primary tumor, number of intracerebral metastases and the timing of the relapse-free period.Conclusions. Factors that affects the overall survival are the features of the histology of the primary lesion, multiplicity of metastatic lesions, RPA class and the synchronous nature of the metastasis. The median of overall survival of patients who did not receive after surgical treatment of a particular type of therapy was only 4 months. If to use the combined treatment (surgical treatment with the irradiation of the whole brain median

  20. Wolf population genetics in Europe

    DEFF Research Database (Denmark)

    Hindrikson, Maris; Remm, Jaanus; Pilot, Malgorzata

    2017-01-01

    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...

  1. MRI of bone and soft tissue tumors and tumorlike lesions. Differential diagnosis and atlas

    Energy Technology Data Exchange (ETDEWEB)

    Meyers, S.P. [Rochester Univ., NY (United States). School of Medicine and Dentistry

    2008-07-01

    The book is devided into three main sections: the introduction presents a detailed overview of magnetic resonance imaging (MRI) of muscoskeletal tumors and tumorlike lesions and includes multiple tables regarding teh WHO classification of bone and soft tissue tumors, their relative frequencies and pertinent immunohistochemical and genetic data. The second part contains 20 tables of differential diagnosis of lesions based on anatomic locations and/or specific MRI features. Pertinent radiographic and CT findings and key clinical data are summarized. The third part contains 77 Atlas chapters organized into a routine format that enables the efficient acquisition of specific information regarding each lesion. For the majority of the Atlas chapters multiple MRI images are provided to demonstrate the range of imaging findings and locations associated with the lesions.

  2. Statistics for Learning Genetics

    Science.gov (United States)

    Charles, Abigail Sheena

    This study investigated the knowledge and skills that biology students may need to help them understand statistics/mathematics as it applies to genetics. The data are based on analyses of current representative genetics texts, practicing genetics professors' perspectives, and more directly, students' perceptions of, and performance in, doing statistically-based genetics problems. This issue is at the emerging edge of modern college-level genetics instruction, and this study attempts to identify key theoretical components for creating a specialized biological statistics curriculum. The goal of this curriculum will be to prepare biology students with the skills for assimilating quantitatively-based genetic processes, increasingly at the forefront of modern genetics. To fulfill this, two college level classes at two universities were surveyed. One university was located in the northeastern US and the other in the West Indies. There was a sample size of 42 students and a supplementary interview was administered to a select 9 students. Interviews were also administered to professors in the field in order to gain insight into the teaching of statistics in genetics. Key findings indicated that students had very little to no background in statistics (55%). Although students did perform well on exams with 60% of the population receiving an A or B grade, 77% of them did not offer good explanations on a probability question associated with the normal distribution provided in the survey. The scope and presentation of the applicable statistics/mathematics in some of the most used textbooks in genetics teaching, as well as genetics syllabi used by instructors do not help the issue. It was found that the text books, often times, either did not give effective explanations for students, or completely left out certain topics. The omission of certain statistical/mathematical oriented topics was seen to be also true with the genetics syllabi reviewed for this study. Nonetheless

  3. Genetic modification and genetic determinism

    Directory of Open Access Journals (Sweden)

    Vorhaus Daniel B

    2006-06-01

    Full Text Available Abstract In this article we examine four objections to the genetic modification of human beings: the freedom argument, the giftedness argument, the authenticity argument, and the uniqueness argument. We then demonstrate that each of these arguments against genetic modification assumes a strong version of genetic determinism. Since these strong deterministic assumptions are false, the arguments against genetic modification, which assume and depend upon these assumptions, are therefore unsound. Serious discussion of the morality of genetic modification, and the development of sound science policy, should be driven by arguments that address the actual consequences of genetic modification for individuals and society, not by ones propped up by false or misleading biological assumptions.

  4. Genetic specificity of face recognition.

    Science.gov (United States)

    Shakeshaft, Nicholas G; Plomin, Robert

    2015-10-13

    Specific cognitive abilities in diverse domains are typically found to be highly heritable and substantially correlated with general cognitive ability (g), both phenotypically and genetically. Recent twin studies have found the ability to memorize and recognize faces to be an exception, being similarly heritable but phenotypically substantially uncorrelated both with g and with general object recognition. However, the genetic relationships between face recognition and other abilities (the extent to which they share a common genetic etiology) cannot be determined from phenotypic associations. In this, to our knowledge, first study of the genetic associations between face recognition and other domains, 2,000 18- and 19-year-old United Kingdom twins completed tests assessing their face recognition, object recognition, and general cognitive abilities. Results confirmed the substantial heritability of face recognition (61%), and multivariate genetic analyses found that most of this genetic influence is unique and not shared with other cognitive abilities.

  5. Genetic and Proteomics Analyses of Space Flown Mice Skin

    Science.gov (United States)

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

    2013-02-01

    Many astronauts stay in the International Space Station (ISS) for a long period of time. Therefore, the development of astronaut health care technologies is very important. Especially, an understanding of the effects of the space environment, such as microgravity and radiation, on protein, gene, and mineral metabolism is important for developing countermeasures against the adverse effects experienced by astronauts who are in space for long periods of time. Since December 2009, the Japan Aerospace Exploration Agency (JAXA) has initiated a human research study to investigate the effects of long-term space flight on gene expression and mineral metabolism by analyzing hair samples from ISS crew members who have been in space (experiment nicknamed “HAIR”). As animal control experiments, we could have an opportunity to analyze rodents samples by participating the tissue sharing program of space-flown mice organized by Italian Space Agency (AGI) and National Aeronautics and Space Administration (NASA). It will reasonably complement human hair experiment because we able to conduct more detailed skin analysis which is enable in human experiment. The purpose of this flown-mice experiment is to study the effects of long-term exposure to space environment. In this experiment, we analyzed mice skin contained hair roots. The samples were taken from space-flown (3-month and 2-week) and 3-month hindlimb suspensioned and 3-month 2G exposed mice, and ground-control mice. For the skin contained hair roots, the extracted and amplified RNA was used to DNA microarray analysis, and was further analyzed with expression on the interesting genes by real time Reverse Transcription Polymerase Chain Reaction (RT-PCR) method. And the extracted protein was used to Mass Spectrometer analysis. Data analysis on the specimen are in progress.

  6. Genetic analyses of the stability of executive functioning during childhood.

    NARCIS (Netherlands)

    Polderman, T.J.C.; Posthuma, D.; de Sonneville, L.M.J.; Stins, J.F.; Verhulst, F.C.; Boomsma, D.I.

    2007-01-01

    Executive functioning is an umbrella term for several related cognitive functions like selective- and sustained attention, working memory, and inhibition. Little is known about the stability of executive functioning during childhood. In this study the longitudinal stability of executive functioning

  7. Genetic and Dynamic Analyses of Murine Peak Bone Density

    Science.gov (United States)

    1999-10-01

    bone density in mice. Femurs from young adult B6, C3H, and CAST females at 4 months of age were measured by pQCT (XCT-960M, Norland Med Sys., Ft...progenitor strains - B6, C3H, and CAST - showed that adult skeletal peak BMD was established at 4 months. Therefore, F2 mice were necropsied at 4...calcium depletion causes hypocalcemia , which leads to secondary hyperparathyroidism, subsequently resulting in increased bone resorption. Conversely

  8. Molecular and genetic analyses of potato cyst nematode resistance loci

    NARCIS (Netherlands)

    Bakker, E.H.

    2003-01-01

    This thesis describes the genomic localisation and organisation of loci that harbour resistance to the potato cyst nematode species Globodera pallida and G. rostochiensis . Resistance to the potato cyst nematodes G. pallida and G. rostochiensis is an important aspect in potato breeding. To gain

  9. Comparative analyses of genetic risk prediction methods reveal ...

    Indian Academy of Sciences (India)

    2015-03-12

    Mar 12, 2015 ... 1National Institute of Biomedical Genomics, Netaji Subhas Sanatorium (T. B. ... 2Institute of Post Graduate Medical Education and Research, J. C. Bose Road, ...... Torres D. M. and Harrison S. A 2008 Diagnosis and therapy of.

  10. Genetic analyses for deciphering the status and role of ...

    Indian Academy of Sciences (India)

    SANJAY GUPTA

    inant alleles at E1, E2, E3, E4, E5, E7 and E8 loci delay time to flowering, recessive alleles at E6, E9 and J loci delay flow- ering time to different extents, interacting with the environ- ment and with ..... 85–90 days. In central India, where cultivar JS 95-60 rules. (35% of total Indian soybean breeder seed requisition), farm-.

  11. Genetic analyses of resistance against Leptopilina victoriae in Drosophila bipectinata.

    Science.gov (United States)

    Takigahira, Tomohiro; Kohyama, Tetsuo I; Suwito, Awit; Kimura, Masahito T

    2015-06-01

    Drosophila bipectinata from Iriomote-jima (IR) is susceptible to the endoparasitoid Leptopilina victoriae from Kota Kinabalu (L. victoriae KK), but D. bipectinata from Kota Kinabalu (KK) and Bogor (BG) is resistant. The cross experiments between the resistant (KK) and susceptible (IR) populations of D. bipectinata suggested that the resistance to this parasitoid is a dominant trait and controlled by a single locus or few linked loci on an autosome. In the AFLP analysis using the IR, KK and BG populations of D. bipectinata and the resistant and susceptible populations derived from a mixed population of these three geographic populations, a DNA fragment almost specific to susceptible flies was detected. It also revealed that genes from the IR population were more frequently maintained in the mixed population compared with those from the KK and BG populations, suggesting that at least a number of genes from the IR population are more advantageous under the laboratory conditions. This explains our previous results that the resistance was lowered in the mixed population although the resistance itself is suggested to incur only low costs; i.e., the resistance gene(s) from the KK and BG populations would have been linked with some genes that are disadvantageous under the laboratory conditions.

  12. Genetic and Dynamic Analyses of Murine Peak Bone Density

    National Research Council Canada - National Science Library

    Beamer, Wesley

    2001-01-01

    .... Locations of the QTLs (LOD scores > 2.9) were established, major effects and modes of inheritance were established, and B6 background congenic strains were established to pursue biological and fine mapping/cloning of genes...

  13. Comparative analyses of genetic risk prediction methods reveal ...

    Indian Academy of Sciences (India)

    0.85. 0.8. 0.95. 0.93. 0.81 rs1227756. 0.5. 0.56. 0.75. 0.55. 0.7. 0.71. 0.58. 0.81. 0.25. 0.5. 0.53. 0.48. 0.64. 0.58. 0.58. 0.8. 0.68. 0.78. 0.48. 0.65. NA. NA. NA. NA rs1501299. 0.64. 0.78. 0.75. 0.83. 0.83. 0.89. 0.83. 0.72. 0.63. 0.73. 0.78. 0.75. 0.84. 0.79. 0.61. 0.78. 0.78. 0.7. 0.73. 0.73. NA. NA. NA. NA rs16944. 0.64. 0.72. 0.68.

  14. Genetic analyses for deciphering the status and role of ...

    Indian Academy of Sciences (India)

    found to encode legume-specific transcription factor that has a putative nuclear ... Presently, India is the fifth largest soybean producing country after US, Brazil, ..... ably the reason for Bragg (MG VII), Lee (MG VI), Clark. 63 (MG IV), improved ...

  15. 'Emotional Intelligence': Lessons from Lesions.

    Science.gov (United States)

    Hogeveen, J; Salvi, C; Grafman, J

    2016-10-01

    'Emotional intelligence' (EI) is one of the most highly used psychological terms in popular nomenclature, yet its construct, divergent, and predictive validities are contentiously debated. Despite this debate, the EI construct is composed of a set of emotional abilities - recognizing emotional states in the self and others, using emotions to guide thought and behavior, understanding how emotions shape behavior, and emotion regulation - that undoubtedly influence important social and personal outcomes. In this review, evidence from human lesion studies is reviewed in order to provide insight into the necessary brain regions for each of these core emotional abilities. Critically, we consider how this neuropsychological evidence might help to guide efforts to define and measure EI. Copyright © 2016 Elsevier Ltd. All rights reserved.

  16. Imaging of extradural spinal lesions

    International Nuclear Information System (INIS)

    Ahlhelm, F.; Schulte-Altedorneburg, G.; Naumann, N.; Reith, W.; Nabhan, A.

    2006-01-01

    There is a wide variety of spinal extradural tumors. In addition to real neoplasms, degenerative diseases, congenital abnormalities and inflammatory disorders can be causes of extradural masses. Due to the bony boundary of the spinal canal, both benign as well as malignant masses can cause progressive neurological deficits including paraplegia. Most of the spinal tumors are benign (hemangioma of the vertebral body, degenerative diseases). In younger patients congenital abnormalities and primary tumors of the spine have to be considered, whereas in adults the list of differential diagnoses should include secondary malignancies such as metastases and lymphomas as well as metabolic disorders such as osteoporotic vertebral compression fracture and Paget's disease. Cross-sectional imaging techniques such as magnetic resonance imaging (MRI) and computed tomography (CT) of the spine often help to make a specific diagnosis of extradural spinal lesions and represent important tools for tumor staging and preoperative evaluation. (orig.) [de

  17. Cutaneous lesions in new born

    Directory of Open Access Journals (Sweden)

    Sachdeva Meenakshi

    2002-11-01

    Full Text Available Five hundred unselected newborn babies delivered in the Department of Obstetrics and Gynaecology, Unit II of SGBT Hospital attached to Government Medical College, Amritsar during April 2000 to October 2000 were examined for cutaneous lesions daily for the first five days after birth. Different cutaneous lesions were seen in 474(94. 8% newborns. The physiological skin changes observed in order of frequency were Epstein pearls in 305(61%, Mongolian spot in 301(60. 2%, superficial cutaneous desquamation in 200(40%, icterus in 128(25. 6%, milia in 119(23. 8%, sebaceous gland hyperplasia in 107 (21. 4%, occipital alopecia in 94(18. 8%, lanugo in 72(14. 4%, peripheral cyanosis in 47(9. 4%, breast hypertrophy in 29(5. 8% and miniature puberty in 28(5. 6% newborns. Of the transient non-infective skin diseases, erythema toxicum neonatorum was observed most commonly in 105(21 %, followed by miliaria rubra in 103(20. 6% and acne neonatorum in 27(5. 4% newborns. The naevi and other developmental defects in the descending order were salmon patch in 69(13. 8%, congenital melanocytic noevi in 10(2%, accessory tragi in 3(0.6%, spina bifida in 2(0.4%, hydrocephalus in 1(0.2% and poliosis in 1(0.2% newborns. Cradle cap was the only dermatitis observed in 50(10% newborns. One (0.2% case each of Harlequin ichthyosis and labial cyst was seen.

  18. Imaging pattern of calvarial lesions in adults

    Energy Technology Data Exchange (ETDEWEB)

    Garfinkle, Jarred; Melancon, Denis; Cortes, Maria; Tampieri, Donatella [Montreal Neurological Institute and Hospital-McGill University Health Center, Department of Diagnostic and Interventional Neuroradiology, Montreal, Quebec (Canada)

    2011-10-15

    Calvarial lesions often present themselves as clinically silent findings on skull radiographs or as palpable masses that may cause localized pain or soreness. This review aims to explore the radiographic, computed tomography (CT), and magnetic resonance imaging (MRI) characteristics of calvarial neoplastic, inflammatory, and congenital lesions that are common in adults in order to facilitate a structured approach to their diagnosis and limit the differential diagnosis. In addition to reviewing the literature, we reviewed the records of 141 patients of the Montreal Neurological Institute and Hospital with radiologically documented calvarial lesions between 2001 and June 2009. CT is ideal for detecting bony lesions and is helpful in precisely localizing a lesion pre-surgically. MRI is best at identifying intradiploic lesions before they affect the cortical tables and is able to establish extraosseous involvement, especially when paramagnetic contrast is employed. (orig.)

  19. Detection of Fundus Lesions Using Classifier Selection

    Science.gov (United States)

    Nagayoshi, Hiroto; Hiramatsu, Yoshitaka; Sako, Hiroshi; Himaga, Mitsutoshi; Kato, Satoshi

    A system for detecting fundus lesions caused by diabetic retinopathy from fundus images is being developed. The system can screen the images in advance in order to reduce the inspection workload on doctors. One of the difficulties that must be addressed in completing this system is how to remove false positives (which tend to arise near blood vessels) without decreasing the detection rate of lesions in other areas. To overcome this difficulty, we developed classifier selection according to the position of a candidate lesion, and we introduced new features that can distinguish true lesions from false positives. A system incorporating classifier selection and these new features was tested in experiments using 55 fundus images with some lesions and 223 images without lesions. The results of the experiments confirm the effectiveness of the proposed system, namely, degrees of sensitivity and specificity of 98% and 81%, respectively.

  20. [Microsatellite instability and human papilloma virus genotypes in preneoplastic and neoplastic uterine cervix lesions].

    Science.gov (United States)

    Roa S, Juan Carlos; Martínez S, Ricardo; Montenegro, Sonia; Roa E, Iván; Capurro V, Italo; Ibacache S, Gilda; Melo A, Angélica

    2007-01-01

    The association between some specific human papilloma virus (HPV) types and cervix cancer is well known. However, the genetic conditions that favor the development of cervical cancer are less well known. To determine the presence of satellite instability (MSI) in preneoplastic and neoplastic lesions of the cervix and correlate these findings with HPV genotypes. Biopsy samples of cervical lesions were studied. Sixteen had low grade lesions, 22 had high grade lesions and 28 had an epidermoid cancer. Viral types were identified with polymerase chain reaction, dot-blot hybridization and restriction fragment length polymorphism. MSI was determined using a panel of eight highly informative microsatellites. Microsatellite instability in at least one locus was observed in 91, 56 and 69% of low grade lesions, high grade lesions and epidermoid carcinomas, respectively. MSI-High grade, MSI-Low grade instability and microsatellite stability were observed in 5, 60 and 46% of samples, respectively. Two of three samples with high grade instability had HPV 52 genotype. Other viral subtypes had frequencies that ranged from 78% to 100%, with the exception of HPV16 that was present in only 53% of samples with low grade instability. Two thirds of biopsy samples from cervical lesions had MSI, mechanism that can be involved in the first stages of cervical carcinogenesis. The low frequency of high grade instability, its association with HPV52 and the low frequency of HPV16 in samples with low grade instability, suggest different coadjutant mechanisms in cervical carcinogenesis.

  1. Genetic Engineering

    Science.gov (United States)

    Phillips, John

    1973-01-01

    Presents a review of genetic engineering, in which the genotypes of plants and animals (including human genotypes) may be manipulated for the benefit of the human species. Discusses associated problems and solutions and provides an extensive bibliography of literature relating to genetic engineering. (JR)

  2. Genetic Romanticism

    DEFF Research Database (Denmark)

    Tupasela, Aaro

    2016-01-01

    inheritance as a way to unify populations within politically and geographically bounded areas. Thus, new genetics have contributed to the development of genetic romanticisms, whereby populations (human, plant, and animal) can be delineated and mobilized through scientific and medical practices to represent...

  3. Challenges of Analysing Gene-Environment Interactions in Mouse Models of Schizophrenia

    Directory of Open Access Journals (Sweden)

    Peter L. Oliver

    2011-01-01

    Full Text Available The modelling of neuropsychiatric disease using the mouse has provided a wealth of information regarding the relationship between specific genetic lesions and behavioural endophenotypes. However, it is becoming increasingly apparent that synergy between genetic and nongenetic factors is a key feature of these disorders that must also be taken into account. With the inherent limitations of retrospective human studies, experiments in mice have begun to tackle this complex association, combining well-established behavioural paradigms and quantitative neuropathology with a range of environmental insults. The conclusions from this work have been varied, due in part to a lack of standardised methodology, although most have illustrated that phenotypes related to disorders such as schizophrenia are consistently modified. Far fewer studies, however, have attempted to generate a “two-hit” model, whereby the consequences of a pathogenic mutation are analysed in combination with environmental manipulation such as prenatal stress. This significant, yet relatively new, approach is beginning to produce valuable new models of neuropsychiatric disease. Focussing on prenatal and perinatal stress models of schizophrenia, this review discusses the current progress in this field, and highlights important issues regarding the interpretation and comparative analysis of such complex behavioural data.

  4. Laser Beam Focus Analyser

    DEFF Research Database (Denmark)

    Nielsen, Peter Carøe; Hansen, Hans Nørgaard; Olsen, Flemming Ove

    2007-01-01

    the obtainable features in direct laser machining as well as heat affected zones in welding processes. This paper describes the development of a measuring unit capable of analysing beam shape and diameter of lasers to be used in manufacturing processes. The analyser is based on the principle of a rotating......The quantitative and qualitative description of laser beam characteristics is important for process implementation and optimisation. In particular, a need for quantitative characterisation of beam diameter was identified when using fibre lasers for micro manufacturing. Here the beam diameter limits...... mechanical wire being swept through the laser beam at varying Z-heights. The reflected signal is analysed and the resulting beam profile determined. The development comprised the design of a flexible fixture capable of providing both rotation and Z-axis movement, control software including data capture...

  5. Hybrid Odontogenic Lesion: A Rare Entity

    Directory of Open Access Journals (Sweden)

    Reza Imani

    2017-03-01

    Full Text Available Hybrid tumors are very rare tumors composed of two different tumor entities, each of which conforms to an exactly defined tumor category. A 14-year-old boy was referred for an intraosseous painless lesion with a histopathological feature of multiple odontogenic lesions including calcifying odontogenic cyst, complex odontoma and ameloblastic fibro-odontoma. The final diagnosis considered to be a hybrid odontogenic lesion.

  6. Space Occupying Lesions in the Liver

    OpenAIRE

    Nasser Ebrahimi Daryani

    2009-01-01

    "nRadiology (imaging) plays a pivotal role for the diagnosis, staging, treatment planning, and follow-up of focal liver lesions. The differential diagnosis in patients presenting with a focal liver lesion is broad. "nThe size of the liver mass is an important consideration in guiding the evaluation. Lesions smaller than approximately 1.0 cm are commonly benign incidental findings on imaging studies, and in most cases represent small cysts, hemangiomas, or biliary hamartomas. Further...

  7. Benign Lesions of The Vocal Fold

    Directory of Open Access Journals (Sweden)

    Ozgur Surmelioglu

    2013-02-01

    Full Text Available Benign lesions of vocal folds are common disorders. Fifty percent of patients who have sound complaints are found to have these lesions after endoscopic and stroboscopic examinations. Benign vocal fold diseases are primarily caused by vibratory trauma. However they may also occur as a result of viral infections and congenital causes. These lesions are often presented with the complaints of dysphonia. [Archives Medical Review Journal 2013; 22(1.000: 86-95

  8. Contesting Citizenship: Comparative Analyses

    DEFF Research Database (Denmark)

    Siim, Birte; Squires, Judith

    2007-01-01

    importance of particularized experiences and multiple ineequality agendas). These developments shape the way citizenship is both practiced and analysed. Mapping neat citizenship modles onto distinct nation-states and evaluating these in relation to formal equality is no longer an adequate approach....... Comparative citizenship analyses need to be considered in relation to multipleinequalities and their intersections and to multiple governance and trans-national organisinf. This, in turn, suggests that comparative citizenship analysis needs to consider new spaces in which struggles for equal citizenship occur...

  9. TH-E-BRF-08: Subpopulations of Similarly-Responding Lesions in Metastatic Prostate Cancer

    International Nuclear Information System (INIS)

    Lin, C; Harmon, S; Perk, T; Jeraj, R

    2014-01-01

    population- and patient-level clustering, indicating that PET-based response features may be used to quantify disease heterogeneity in advanced metastatic disease. This method for categorizing lesion response could help in identifying lesions with similar phenotypic- or genetic-based resistances to therapy. Research Supported by the Prostate Cancer Foundation

  10. Lesion localization in aphasia without hemiparesis

    International Nuclear Information System (INIS)

    Komatsu, Midori; Senoh, Yoko; Okamoto, Koichi; Morimatsu, Mitsunori; Hirai, Shunsaku

    1983-01-01

    The distribution of the lesions responsible for aphasia unassociated with right-sided hemiparesis was evaluated by cranial computed tomography (CT) among stroke patients. In the Broca aphasia group were observed atypical aphasic symptoms, and the lesions were far more localized than in ordinary Broca one. In the Wernicke aphasia group showed relatively large lesions in the left superior temporal gyrus, sometimes extending to supramarginal and angular gyri, which caused such additional symptoms as apraxia without motor paresis in some cases. In the Transcortical motor aphasia group showed the occlusion of the left internal carotid artery, though without obvious abnormality at CT. In another patient a circumscribed low density lesion was disclosed in the area anterior and superior to so-called Broca's area. In the Transcortical sensory aphasia group, the lesion involved the borderzone supplied by the left middle and posterior cerebral arteries. In the Amnestic aphasia group showed a lesion in the left parietal lobe, while in another no remarkable change was demonstrated. In the Global aphasia group, one had multiple isolated lesions in both anterior and posterior speech areas. Another showed a large lesion involving the whole territory of the left middle cerebral artery. In the remaining one a high density area was observed in the left superior temporal, supramarginal and angular gyri, not extending to the frontal lobe beyond with sylvian fissure. Therefore, in interpreting CTs of such aphasic patients we must take account of not only the extent of the lesion but also the severity of destruction. (J.P.N.)

  11. Lesion localization in aphasia without hemiparesis

    Energy Technology Data Exchange (ETDEWEB)

    Komatsu, Midori; Senoh, Yoko; Okamoto, Koichi; Morimatsu, Mitsunori; Hirai, Shunsaku (Gunma Univ., Maebashi (Japan). School of Medicine)

    1983-06-01

    The distribution of the lesions responsible for aphasia unassociated with right-sided hemiparesis was evaluated by cranial computed tomography (CT) among stroke patients. In the Broca aphasia group were observed atypical aphasic symptoms, and the lesions were far more localized than in ordinary Broca one. In the Wernicke aphasia group showed relatively large lesions in the left superior temporal gyrus, sometimes extending to supramarginal and angular gyri, which caused such additional symptoms as apraxia without motor paresis in some cases. In the Transcortical motor aphasia group showed the occlusion of the left internal carotid artery, though without obvious abnormality at CT. In another patient a circumscribed low density lesion was disclosed in the area anterior and superior to so-called Broca's area. In the Transcortical sensory aphasia group, the lesion involved the borderzone supplied by the left middle and posterior cerebral arteries. In the Amnestic aphasia group showed a lesion in the left parietal lobe, while in another no remarkable change was demonstrated. In the Global aphasia group, one had multiple isolated lesions in both anterior and posterior speech areas. Another showed a large lesion involving the whole territory of the left middle cerebral artery. In the remaining one a high density area was observed in the left superior temporal, supramarginal and angular gyri, not extending to the frontal lobe beyond with sylvian fissure. Therefore, in interpreting CTs of such aphasic patients we must take account of not only the extent of the lesion but also the severity of destruction.

  12. Thermophysical lesions caused by HZE particles

    International Nuclear Information System (INIS)

    Tobias, C.A.; Malachowski, M.; Nelson, A.; Philpott, D.E.

    1980-01-01

    This paper deals with a type of damage caused by heavy particles that may occur in subcellular structures. These lesions are called thermophysical radiation injury and are similar to damage produced in solids by HZE particles. This chapter summarizes some of the experimental evidence for the presence of these lesions in certain mammalian tissues including the retina, brain, cornea, lens of mice and seeds of corn. Of all tissues examined, only the cornea exhibited a type of lesion which would fulfill the criteria of thermophysical lesions

  13. MR imaging of sacral and perisacral lesions

    International Nuclear Information System (INIS)

    Wetzel, L.H.; Levine, E.; Murphey, M.D.

    1987-01-01

    This exhibit demonstrates the utility of MR imaging in evaluating sacral and perisacral lesions. Thirty-two lesions were studied using a superconducting 1.0-T MR imager. Eleven primary and 13 metastatic tumors, four congenital lesions, and four arachnoid cysts were evaluated. MR did not usually enable a more specific histologic diagnosis than other imaging techniques. However, extraosseous and proximal spinal extent of tumors was well defined without use of oral or intravenous contrast material. MR imaging is an excellent noninvasive technique for evaluating most sacral and perisacral lesions and is particularly helpful when precise tumor extent must be determined for treatment planning

  14. Visible and occult microscopic lesions of endometriosis

    Directory of Open Access Journals (Sweden)

    Khaleque Newaz Khan

    2014-11-01

    Full Text Available Endometriosis is a multifactorial disease mostly affecting women of reproductive age and is associated with chronic pelvic pain and infertility. Even after 300 years, most of the literature claims that pathogenesis and/or pathophysiology of endometriosis is still elusive. Recurrence of pain and lesion continues to occur after effective medical or surgical therapies. Once generated within the pelvis due to retrograde entry of menstrual debris, peritoneal endometriotic lesions time-dependently change their color appearance resulting from certain biochemical change within lesions. A variable pattern of endometriotic lesions within the pelvis can be detected by laparoscopy as visible peritoneal endometriosis. It is generally believed that besides ovarian steroid hormones, the growth of endometriosis can be regulated by the innate immune system in the pelvic microenvironment by their interaction with endometrial cells and immune cells. Even with the careful eyes of an expert surgeon, we may sometimes miss detecting peritoneal lesion within the peritoneal cavity or deep into the peritoneum. In such a case, random collection of normal peritoneum may carry the possibility to identify some hidden endometriotic lesions by microscopy and these lesions can be named as occult (invisible microscopic endometriosis (OME. Here, we discuss the color appearance of peritoneal lesions and activity of these lesions by analysis of a panel of activity markers. Finally we discuss our recent findings on OME, their biological and clinical significance, and try to make a possible link in the origin between visible endometriosis and OME.

  15. Measuring Cutaneous Lesions: Trends in Clinical Practice.

    Science.gov (United States)

    Zhang, Shali; Blalock, Travis W

    2018-03-01

    Knowing the size of a cutaneous lesion can be important for tracking its progression over time, selecting the proper treatment modality, surgical planning, determining prognosis, and accurate billing. However, providers vary in their consistency, accuracy, and methods of measuring cutaneous lesions. To investigate the clinical practices of US dermatologists and dermatologic surgeons regarding how they determine the size of cutaneous lesions. A survey was electronically distributed to members of the American Society for Dermatologic Surgery. Four hundred twenty-six dermatologists completed the online survey. When a lesion is suspected to be malignant, 85% of respondents obtained exact measurements most, if not all, of the time; however, only 8% did for benign lesions. Most providers determined lesion sizes themselves rather than delegating to staff. When performing visual estimation, approximately three-quarters believed that they were accurate to within 1 to 2 mm. The top reasons for obtaining exact measurements were for tracking atypical pigmented lesions, determining treatment pathways, and accurate billing. The majority of respondents believed that lesion size affected management decisions; however, the need for exact measurement remains controversial, particularly for benign lesions. Future studies may investigate whether taking exact versus estimated measurements has an effect on outcomes.

  16. Genetics of eosinophilic esophagitis.

    Science.gov (United States)

    Kottyan, L C; Rothenberg, M E

    2017-05-01

    Eosinophilic esophagitis (EoE) is a chronic, allergic disease associated with marked mucosal eosinophil accumulation. EoE disease risk is multifactorial and includes environmental and genetic factors. This review will focus on the contribution of genetic variation to EoE risk, as well as the experimental tools and statistical methodology used to identify EoE risk loci. Specific disease-risk loci that are shared between EoE and other allergic diseases (TSLP, LRRC32) or unique to EoE (CAPN14), as well as Mendellian Disorders associated with EoE, will be reviewed in the context of the insight that they provide into the molecular pathoetiology of EoE. We will also discuss the clinical opportunities that genetic analyses provide in the form of decision support tools, molecular diagnostics, and novel therapeutic approaches.

  17. Correlation between model observer and human observer performance in CT imaging when lesion location is uncertain

    Energy Technology Data Exchange (ETDEWEB)

    Leng, Shuai; Yu, Lifeng; Zhang, Yi; McCollough, Cynthia H. [Department of Radiology, Mayo Clinic, 200 First Street Southwest, Rochester, Minnesota 55905 (United States); Carter, Rickey [Department of Biostatistics, Mayo Clinic, 200 First Street Southwest, Rochester, Minnesota 55905 (United States); Toledano, Alicia Y. [Biostatistics Consulting, LLC, 10606 Wheatley Street, Kensington, Maryland 20895 (United States)

    2013-08-15

    Purpose: The purpose of this study was to investigate the correlation between model observer and human observer performance in CT imaging for the task of lesion detection and localization when the lesion location is uncertain.Methods: Two cylindrical rods (3-mm and 5-mm diameters) were placed in a 35 × 26 cm torso-shaped water phantom to simulate lesions with −15 HU contrast at 120 kV. The phantom was scanned 100 times on a 128-slice CT scanner at each of four dose levels (CTDIvol = 5.7, 11.4, 17.1, and 22.8 mGy). Regions of interest (ROIs) around each lesion were extracted to generate images with signal-present, with each ROI containing 128 × 128 pixels. Corresponding ROIs of signal-absent images were generated from images without lesion mimicking rods. The location of the lesion (rod) in each ROI was randomly distributed by moving the ROIs around each lesion. Human observer studies were performed by having three trained observers identify the presence or absence of lesions, indicating the lesion location in each image and scoring confidence for the detection task on a 6-point scale. The same image data were analyzed using a channelized Hotelling model observer (CHO) with Gabor channels. Internal noise was added to the decision variables for the model observer study. Area under the curve (AUC) of ROC and localization ROC (LROC) curves were calculated using a nonparametric approach. The Spearman's rank order correlation between the average performance of the human observers and the model observer performance was calculated for the AUC of both ROC and LROC curves for both the 3- and 5-mm diameter lesions.Results: In both ROC and LROC analyses, AUC values for the model observer agreed well with the average values across the three human observers. The Spearman's rank order correlation values for both ROC and LROC analyses for both the 3- and 5-mm diameter lesions were all 1.0, indicating perfect rank ordering agreement of the figures of merit (AUC

  18. Periapical lesions are not always a sequelae of pulpal necrosis: a retrospective study of 1521 biopsies.

    Science.gov (United States)

    Kontogiannis, T G; Tosios, K I; Kerezoudis, N P; Krithinakis, S; Christopoulos, P; Sklavounou, A

    2015-01-01

    To record the incidence of lesions that were not the sequelae of pulpal necrosis (non-SPN) amongst 1521 biopsies of periapical lesions submitted with a clinical diagnosis of a sequelae of pulpal necrosis (SPN). A retrospective study of 1521 biopsy request forms of specimens submitted for histopathological examination with a clinical diagnosis 'periapical inflammation', 'periapical abscess', 'periapical granuloma' or 'periapical cyst' during an arbitrarily selected 14-year period was undertaken. Gender and age of the patient, site and maximum diameter of the lesion, symptoms, inclusion of the final diagnosis in the differential diagnosis and specialty of the clinician submitting the biopsy material were recorded in each case. The final diagnosis for each case was extracted from the pathology report, and two groups were formed, SPN and non-SPN lesions. Differences between the respective features of SPN and non-SPN cases were analysed with Yate's chi-square test and t-test (significance level P cysts, lateral periodontal cysts, central ossifying fibromas as well as malignancies (metastatic carcinomas and Langerhans cell histiocytosis). Non-SPN lesions appeared in the periapical region mimicking a SPN, although rarely. Most of them were developmental cysts, in particular OKCs, but odontogenic tumours, such as ameloblastoma, or malignant lesions were also diagnosed. Histological examination of tissue harvested from periapical lesions should be performed, in particular when those lesions are large. © 2014 International Endodontic Journal. Published by John Wiley & Sons Ltd.

  19. Using passive cavitation images to classify high-intensity focused ultrasound lesions.

    Science.gov (United States)

    Haworth, Kevin J; Salgaonkar, Vasant A; Corregan, Nicholas M; Holland, Christy K; Mast, T Douglas

    2015-09-01

    Passive cavitation imaging provides spatially resolved monitoring of cavitation emissions. However, the diffraction limit of a linear imaging array results in relatively poor range resolution. Poor range resolution has limited prior analyses of the spatial specificity and sensitivity of passive cavitation imaging in predicting thermal lesion formation. In this study, this limitation is overcome by orienting a linear array orthogonal to the high-intensity focused ultrasound propagation direction and performing passive imaging. Fourteen lesions were formed in ex vivo bovine liver samples as a result of 1.1-MHz continuous-wave ultrasound exposure. The lesions were classified as focal, "tadpole" or pre-focal based on their shape and location. Passive cavitation images were beamformed from emissions at the fundamental, harmonic, ultraharmonic and inharmonic frequencies with an established algorithm. Using the area under a receiver operating characteristic curve (AUROC), fundamental, harmonic and ultraharmonic emissions were found to be significant predictors of lesion formation for all lesion types. For both harmonic and ultraharmonic emissions, pre-focal lesions were classified most successfully (AUROC values of 0.87 and 0.88, respectively), followed by tadpole lesions (AUROC values of 0.77 and 0.64, respectively) and focal lesions (AUROC values of 0.65 and 0.60, respectively). Copyright © 2015 World Federation for Ultrasound in Medicine & Biology. Published by Elsevier Inc. All rights reserved.

  20. Genomic analyses of the CAM plant pineapple.

    Science.gov (United States)

    Zhang, Jisen; Liu, Juan; Ming, Ray

    2014-07-01

    The innovation of crassulacean acid metabolism (CAM) photosynthesis in arid and/or low CO2 conditions is a remarkable case of adaptation in flowering plants. As the most important crop that utilizes CAM photosynthesis, the genetic and genomic resources of pineapple have been developed over many years. Genetic diversity studies using various types of DNA markers led to the reclassification of the two genera Ananas and Pseudananas and nine species into one genus Ananas and two species, A. comosus and A. macrodontes with five botanical varieties in A. comosus. Five genetic maps have been constructed using F1 or F2 populations, and high-density genetic maps generated by genotype sequencing are essential resources for sequencing and assembling the pineapple genome and for marker-assisted selection. There are abundant expression sequence tag resources but limited genomic sequences in pineapple. Genes involved in the CAM pathway has been analysed