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Sample records for microsatellite instability analysis

  1. Quasimonomorphic Mononucleotide Repeats for High-Level Microsatellite Instability Analysis

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    Olivier Buhard

    2004-01-01

    Full Text Available Microsatellite instability (MSI analysis is becoming more and more important to detect sporadic primary tumors of the MSI phenotype as well as in helping to determine Hereditary Non-Polyposis Colorectal Cancer (HNPCC cases. After some years of conflicting data due to the absence of consensus markers for the MSI phenotype, a meeting held in Bethesda to clarify the situation proposed a set of 5 microsatellites (2 mononucleotide repeats and 3 dinucleotide repeats to determine MSI tumors. A second Bethesda consensus meeting was held at the end of 2002. It was discussed here that the 1998 microsatellite panel could underestimate high-level MSI tumors and overestimate low-level MSI tumors. Amongst the suggested changes was the exclusive use of mononucleotide repeats in place of dinucleotide repeats. We have already proposed a pentaplex MSI screening test comprising 5 quasimonomorphic mononucleotide repeats. This article compares the advantages of mono or dinucleotide repeats in determining microsatellite instability.

  2. [Aspirin suppresses microsatellite instability].

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    Wallinger, S; Dietmaier, W; Beyser, K; Bocker, T; Hofstädter, F; Fishel, R; Rüschoff, J

    1999-01-01

    Nonsteroidal anti-inflammatory drugs (NSAIDs) exhibit cancer preventive effects and have been shown to induce regression of adenomas in FAP patients. In order to elucidate the probable underlying mechanism, the effect of NSAIDs on mismatch repair related microsatellite instability was investigated. Six colorectal cancer cell lines all but one deficient for human mismatch repair (MMR) genes were examined for microsatellite instability (MSI) prior and after treatment with Aspirin or Sulindac. For rapid in vitro analysis of MSI a microcloning assay was developed by combining Laser microdissection and random (PEP-) PCR prior to specific MSI-PCR. Effects of NSAIDs on cell cycle and apoptosis were systematically investigated by using flow cytometry and cell-sorting. MSI frequency in cells deficient of MMR genes (hMSH2, hMLH1, hMSH6) was markedly reduced after long-term (> 10 weeks) NSAID treatment. This effect was reversible, time- and concentration dependent. However, in the hPMS2 deficient endometrial cancer cell line (HEC-1-A) the MSI phenotype kept unchanged. According to cell sorting, non-apoptotic cells were stable and apoptotic cells were unstable. These results suggest that aspirin/sulindac induces a genetic selection for microsatellite stability in a subset of MMR-deficient cells and may thus provide an effective prophylactic therapy for HNPCC related colorectal carcinomas.

  3. Microsatellite instability confounds engraftment analysis of hematopoietic stem-cell transplantation.

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    Tseng, Li-Hui; Tang, Jih-Luh; Haley, Lisa; Beierl, Katie; Gocke, Christopher D; Eshleman, James R; Lin, Ming-Tseh

    2014-07-01

    Polymorphic short tandem-repeat, or microsatellite, loci have been widely used to analyze chimerism status after allogeneic hematopoietic stem-cell transplantation. In molecular diagnostic laboratories, it is recommended to calculate mixed chimerism for at least 2 informative loci and to avoid microsatellite loci on chromosomes with copy number changes. In this report, we show that microsatellite instability observed in 2 patients with acute leukemia may confound chimerism analysis. Interpretation errors may occur even if 2 to 3 loci are analyzed because of length variation in multiple microsatellite loci. Although microsatellite loci with length variation should not be selected for chimerism analysis, the presence of microsatellite instability, like copy number alteration because of aberrant chromosomes, provides evidence of recurrent or residual cancer cells after hematopoietic stem-cell transplantation.

  4. Microsatellite instability in bladder cancer

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    Gonzalez-Zulueta, M; Ruppert, J M; Tokino, K;

    1993-01-01

    Somatic instability at microsatellite repeats was detected in 6 of 200 transitional cell carcinomas of the bladder. Instabilities were apparent as changes in (GT)n repeat lengths on human chromosome 9 for four tumors and as alterations in a (CAG)n repeat in the androgen receptor gene on the X...... chromosome for three tumors. Single locus alterations were detected in three tumors, while three other tumors revealed changes in two or more loci. In one tumor we found microsatellite instability in all five loci analyzed on chromosome 9. The alterations detected were either minor 2-base pair changes...

  5. Analysis of microsatellite instability in CRISPR/Cas9 editing mice.

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    Huo, Xueyun; Du, Yating; Lu, Jing; Guo, Meng; Li, Zhenkun; Zhang, Shuangyue; Li, Xiaohong; Chen, Zhenwen; Du, Xiaoyan

    2017-03-01

    Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR- associated (Cas) protein 9 system is a novel and powerful tool which is widely used for genome editing. CRISPR/Cas9 is RNA-guided and can lead to desired genomic modifications. However, whether the CRISPR/Cas9-mediated genome editing causes genomic alterations and genomic instability, such as microsatellite instability (MSI), is still unknown. Here we detected MSI in 21 CRISPR/Cas9 mouse strains using a panel of 42 microsatellite loci which were selected from our previous studies. Surprisingly, MSI occurrence was common in CRISPR/Cas9 modified genome, and most of the strains (19/21, 90.5%) examined showed MSI. Of 42 loci examined, 8 loci (8/42, 19.05%) exhibited MSI in the Cas9 editing mice. The Ttll9 (4/42, 9.5%) were the most unstable strains, and D10Mit3 and D10Mit198 (9/21, 42.9%) were considered to be the most "hot" loci in the Cas9 strains we tested. Through analyzing the mutation of microsatellite loci, we provide new insights into the genomic alterations of CRISPR/Cas9 models and it will help us for a better understanding of this powerful technology. Copyright © 2017 Elsevier B.V. All rights reserved.

  6. Microsatellite Instability Assay — EDRN Public Portal

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    Microsatellite analysis (MSA) is a promising new technique for the surveillance of bladder cancer. The technology, which permits the separation by electrophoresis of polymerase chain reaction (PCR)-amplified sequences from non-malignant and malignant sources, has been applied to the diagnosis of solid tumors arising in colon, lung, oropharynx, kidney and bladder. MSA can detect genetic changes indicative of carcinoma from urothelial cells obtained in voided urine specimens. The genetic profile of DNA purified from urine is compared to that of DNA purified from peripheral lymphocytes that are considered normal. Once the DNA from uroepithelial cells has been obtained, PCR is performed with specific oligonucleotide primers for each chromosomal locus. The PCR products are then examined for evidence of microsatellite instability (MSI) and loss of heterozygosity (LOH), which are genetic characteristics of epithelial tumors. Preliminary work shows that MSA detects 95% of cancers.

  7. Competing risks analysis of microsatellite instability as a prognostic factor in colorectal cancer.

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    Toh, J; Chapuis, P H; Bokey, L; Chan, C; Spring, K J; Dent, O F

    2017-08-01

    Despite an extensive literature suggesting that high microsatellite instability (MSI-H) enhances survival and protects against recurrence after colorectal cancer resection, such effects remain controversial as many studies show only a weak bivariate association or no multivariable association with outcome. This study examined the relationship between MSI status and colorectal cancer outcomes with adjustment for death from other causes as a competing risk. A hospital database of patients following colorectal cancer resection was interrogated for clinical, operative, pathology, adjuvant therapy and follow-up information. MSI-H status was determined by immunohistochemistry for mismatch repair protein deficiency. The cumulative incidence of recurrence and colorectal cancer-specific death was evaluated by competing risks methods. Among 1009 patients who had a resection between August 2002 and December 2008, and were followed to at least December 2013, there were 114 (11·3 per cent) with MSI-H (72·8 per cent aged at least 70 years; 63·2 per cent women). After potentially curative resection, with adjustment for non-colorectal cancer death as a competing risk and adjustment for 22 clinical, operative and pathological variables, there was no association between MSI-H and recurrence (hazard ratio (HR) 0·81, 95 per cent c.i. 0·42 to 1·57) or colorectal cancer-specific death (HR 0·73, 0·39 to 1·35) in this patient population. For palliative resections, there was no association between MSI-H and colorectal cancer-specific death (HR 0·65, 0·21 to 2·04). MSI-H was associated with non-colorectal cancer death after both curative (HR 1·55, 1·04 to 2·30) and palliative (HR 3·80, 1·32 to 11·00) resections. Microsatellite instability status was not an independent prognostic variable in these patients. © 2017 BJS Society Ltd Published by John Wiley & Sons Ltd.

  8. The pathological phenotype of colon cancer with microsatellite instability

    DEFF Research Database (Denmark)

    Andersen, Helene Schou; Bertelsen, Claus Anders; Henriksen, Rikke;

    2016-01-01

    clinicopathological features of microsatellite unstable tumours with stable ones. METHODS: Data were collected retrospectively, but the pathological analyses were all made prospectively. The study included a total of 833 patients undergoing resection of their colon tumour at Nordsjællands Hospital - Hillerød......, with mismatch repair analysis from 1 January 2007 to 30 November 2012. The study was performed in a setting with complete mesocolic excision surgery and post-operative expert pathological examination of the tumours. Mismatch repair analysis was done by immuno-histochemical staining for the mismatch repair...... proteins: pMLH1, pMSH2, pMSH6 and pPMS2 for the determination of microsatellite instability. Microsatellite instability was defined as deficient expression of one or more of these proteins. RESULTS: Of the 833 patients, 177 had microsatellite instable tumours (21%). Using multivariable logistic regression...

  9. Analysis of microsatellite instability in stool DNA of patients with colorectal cancer using denaturing high performance liquid chromatography

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    Seok-Byung Lim; Yong Shin; Sang-Geun Jang; Jae-Hyun Park; Jae-Gahb Park; Seung-Yong Jeong; Il-Jin Kim; Dae Yong Kim; Kyung Hae Jung; Hee Jin Chang; Hyo Seong Choi; Dae Kyung Sohn; Hio Chung Kang

    2006-01-01

    AIM: To evaluate the usefulness of denaturing high performance liquid chromatography (DHPLC) for analyzing microsatellite instability (MSI) status in stool DNA of patients with colorectal cancer.METHODS: A total of 80 cancer tissues from patients with primary sporadic colorectal tumor (proximal cancer:27, distal cancer: 53) and matched stool (which were employed for comparison with the tissues) were analyzed for MSI status in BAT 26. DNA samples extracted from stool were evaluated by nested polymerase chain reaction (PCR) and DHPLC for MSI analysis.RESULTS: Six cases (7.5%) of MSI were identified in BAT 26 from 80 cancer tissues. All the stool DNA samples from patients whose cancer tissue showed MSI also displayed MSI in BAT 26.CONCLUSION: As MSI is one of the established fecal DNA markers to screen colorectal cancer, we propose to use DHPLC for the MSI analysis in fecal DNA.

  10. Microsatellite instability analysis in hereditary non-polyposis colon cancer using the Bethesda consensus panel of microsatellite markers in the absence of proband normal tissue

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    Dourisboure Ricardo J

    2006-01-01

    Full Text Available Abstract Background Hereditary non-polyposis colon cancer (HNPCC is an autosomal dominant syndrome predisposing to the early development of various cancers including those of colon, rectum, endometrium, ovarium, small bowel, stomach and urinary tract. HNPCC is caused by germline mutations in the DNA mismatch repair genes, mostly hMSH2 or hMLH1. In this study, we report the analysis for genetic counseling of three first-degree relatives (the mother and two sisters of a male who died of colorectal adenocarcinoma at the age of 23. The family fulfilled strict Amsterdam-I criteria (AC-I with the presence of extracolonic tumors in the extended pedigree. We overcame the difficulty of having a proband post-mortem non-tumor tissue sample for MSI testing by studying the alleles carried by his progenitors. Methods Tumor MSI testing is described as initial screening in both primary and metastasis tumor tissue blocks, using the reference panel of 5 microsatellite markers standardized by the National Cancer Institute (NCI for the screening of HNPCC (BAT-25, BAT-26, D2S123, D5S346 and D17S250. Subsequent mutation analysis of the hMLH1 and hMSH2 genes was performed. Results Three of five microsatellite markers (BAT-25, BAT-26 and D5S346 presented different alleles in the proband's tumor as compared to those inherited from his parents. The tumor was classified as high frequency microsatellite instability (MSI-H. We identified in the HNPCC family a novel germline missense (c.1864C>A mutation in exon 12 of hMSH2 gene, leading to a proline 622 to threonine (p.Pro622Thr amino acid substitution. Conclusion This approach allowed us to establish the tumor MSI status using the NCI recommended panel in the absence of proband's non-tumor tissue and before sequencing the obligate carrier. According to the Human Gene Mutation Database (HGMD and the International Society for Gastrointestinal Hereditary Tumors (InSiGHT Database this is the first report of this mutation.

  11. Evidence for heterozygote instability in microsatellite loci in house wrens.

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    Masters, Brian S; Johnson, L Scott; Johnson, Bonnie G P; Brubaker, Jessica L; Sakaluk, Scott K; Thompson, Charles F

    2011-02-23

    Microsatellite loci have high mutation rates and high levels of allelic variation, but the factors influencing their mutation rate are not well understood. The proposal that heterozygosity may increase mutation rates has profound implications for understanding the evolution of microsatellite loci, but currently has limited empirical support. We examined 20 microsatellite mutations identified in an analysis of 12 260 meiotic events across three loci in two populations of a songbird, the house wren (Troglodytes aedon). We found that for an allele of a given length, mutation was significantly more likely when there was a relatively large difference in size between the allele and its homologue (i.e. a large 'allele span'). Our results support the proposal of heterozygote instability at microsatellite loci.

  12. Microsatellite instability analysis using BAT-26 marker in patients with gastric or colorectal cancer diagnosed at Hospital Universitario de Santander.

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    Wilmer Cárdenas

    2009-11-01

    Full Text Available Introduction: The path of microsatellite instability has mainly been found in cancers of digestive tracts, of which 90% of cases are hereditary cancer patients and 15% are patients with sporadic cancer. That instability produces a phenotype called Microsatellite instability (IMI+ or phenotype by replication mistake (RER+ that leads to the accumulation of mutations in higher rates to normal. Objectives: To identify the presence of IMI+ phenotype in patients analyzed and evaluated its relationship with the differentiation histopathologic tumor, because which together have been associated with a better prognosis and improved response to treatment given to the patient. Methodology: DNA was extracted from blood samples (normal cells and biopsy of the tumor (tumor cells of the 23 patients who were included in the study and through the amplification by PCR and subsequent capillary electrophoresis was typified the microsatellite mononucleotidic BAT-26, who was employed by his sensitivity to detect IMI+ phenotype (95%. Finally, we made a statistical correlation between the microsatellite instability phenotype, the presence (IMI+ or the absence (IMI-, with histopathological findings using Fisher’s exact test. Results: In 17% of cases (4 patients had IMI+: 3 of them with colorectal cancer (CRC -2 cases possibly with hereditary cancer- and one with gastric cancer (GC. There was no association between phenotype IMI+ with the pathological diagnosis, age, sex and differentiation histopathologic tumor. Conclusion: We found the phenotype IMI + in 17% of cases without association with the degree of differentiation histopathologic tumor, possibly by the reduced number of samples analyzed, making it essential to review the methods of fixation, paraffin and storage tissue because current techniques hinder digestion of proteinase k and PCR.

  13. Microsatellite instability and cytogenetic survey in myeloid leukemias

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    E.M.S.F. Ribeiro

    2002-02-01

    Full Text Available Microsatellites are short tandem repeat sequences dispersed throughout the genome. Their instability at multiple genetic loci may result from mismatch repair errors and it occurs in hereditary nonpolyposis colorectal cancer. This instability is also found in many sporadic cancers. In order to evaluate the importance of this process in myeloid leukemias, we studied five loci in different chromosomes of 43 patients, 22 with chronic myelocytic leukemia (CML in the chronic phase, 7 with CML in blast crisis, and 14 with acute myeloid leukemia (AML, by comparing leukemic DNA extracted from bone marrow and constitutional DNA obtained from buccal epithelial cells. Only one of the 43 patients (2.1%, with relapsed AML, showed an alteration in the allele length at a single locus. Cytogenetic analysis was performed in order to improve the characterization of leukemic subtypes and to determine if specific chromosome aberrations were associated with the presence of microsatellite instability. Several chromosome aberrations were observed, most of them detected at diagnosis and during follow-up of the patients, according to current literature. These findings suggest that microsatellite instability is an infrequent genetic event in myeloid leukemias, adding support to the current view that the mechanisms of genomic instability in solid tumors differ from those observed in leukemias, where specific chromosome aberrations seem to play a major role.

  14. The pathological phenotype of colon cancer with microsatellite instability

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    Andersen, Helene Schou; Bertelsen, Claus Anders; Henriksen, Rikke;

    2016-01-01

    INTRODUCTION: Colorectal cancer is a common malignant disease, caused by different aetiologies and molecular pathways. Heterogeneous results have been published regarding the association of microsatellite instability and clinicopathological features. The aim of this study was to compare clinicopa......INTRODUCTION: Colorectal cancer is a common malignant disease, caused by different aetiologies and molecular pathways. Heterogeneous results have been published regarding the association of microsatellite instability and clinicopathological features. The aim of this study was to compare...... clinicopathological features of microsatellite unstable tumours with stable ones. METHODS: Data were collected retrospectively, but the pathological analyses were all made prospectively. The study included a total of 833 patients undergoing resection of their colon tumour at Nordsjællands Hospital - Hillerød...... analysis, we demonstrated that microsatellite unstable cancers were significantly associated with a lower degree of lymph node metastases (odds ratio (OR) = 0.92), distant metastases (OR = 0.33) and tumour budding (OR = 0.41). CONCLUSIONS: We found that microsatellite unstable tumours show a pathological...

  15. Discrimination of patients with microsatellite instability colon cancer using 1H HR MAS MR spectroscopy and chemometric analysis.

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    Tessem, May-Britt; Selnaes, Kirsten M; Sjursen, Wenche; Tranø, Gerd; Giskeødegård, Guro F; Bathen, Tone F; Gribbestad, Ingrid S; Hofsli, Eva

    2010-07-02

    The primary aim of this study was to analyze human colon cancer and normal adjacent tissue using (1)H HR MAS MR spectroscopy and chemometric analyses, evaluating possible biomarkers for colon cancer. The secondary aim was to investigate metabolic profiles of tissue samples (n = 63, 31 patients) with microsatellite instability (MSI-H) compared to microsatellite stable (MSS) colon tissue. Our hypothesis was that this method may provide an alternative to MSI genotyping. Cancer samples were clearly separated from normal adjacent mucosa by 100% accuracy. Several metabolites such as lactate, taurine, glycine, myo-inositol, scyllo-inositol, phosphocholine (PC), glycerophosphocholine (GPC), creatine, and glucose were identified as potential biomarkers for cancer detection. Adenomas (n = 4) were also separated from cancer and normal samples mainly based on higher GPC and PC levels. Interestingly, metabolic differences in normal colon mucosa between MSI-H and MSS patients were observed. MSI status was validated with 80% accuracy with a sensitivity and specificity of 79% and 82%, respectively, including both cancer and normal samples The metabolic differences between MSI-H and MSS may be very interesting in the early detection of cancer development and of high clinical importance in the work of improving diagnosis and characterization of colon cancer.

  16. Mitochondrial microsatellite instability in patients with metastatic colorectal cancer

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    Venderbosch, S.; van Vliet, S.; Craenmehr, M. H C; Simmer, F.; de Haan, A. F J; Punt, C. J A; Koopman, M.; Nagtegaal, I. D.

    2015-01-01

    Mitochondrial microsatellite instability (mtMSI), a change in length in mtDNA microsatellite sequences between normal and tumor tissue, has been described as a frequent occurrence in colorectal cancer (CRC). We evaluated the prevalence and prognostic value of mtMSI and its relation to nuclear

  17. Analysis of Inactivation of hMLH1 by Promoter Hypermethylation and Microsatellite Instability in Gastric Carcinogenesis

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    Dong Wang; Yao Xu; Xin Geng; Weiming Zhang

    2006-01-01

    BJECTIVE To study the microsatellite instability (MSI) and methylation state of the hMLH1 gene promoter and their mechanisms underlying the development of gastric cancer.METHODS Forty-one gastric cancer samples were obtained from patients undergoing surgery and 46 chronic atrophic gastritis tissues with dysplasia or intestinal metaplasia (IM) were obtained from patients undergoing gastro-endoscopy. Fourteen normal gastric mucosal samples were used as controls. Genomic DNA was extracted from the samples and 5 microsatellite markers were used to measure MSI. Methylationspecific PCR (MSP) was used to screen the methylation state of the samples. DNA sequencing and immunohistochemistry were performed to verify the results.RESULTS MSI was identified in 22 out of the 41 (53.7%) gastric cancers,of which 8 cases showed high-level MSI (2 or more loci altered) and 14showed low-level MSI (1 locus altered). MSI was also detected in 12 out of 46 (26.1%) pre-cancerous lesions of the stomach, whereas it was not seen in the normal tissue. Moreover, hMLH1 hypermethylation was detected in 17 out of the 41 (41.5%) gastric cancers, 9 out of the 46 (19.6%)pre-cancerous lesions and O out of the 14 normal tissue. Significant differences in frequency of MSI and hMLH1 promoter methylation were observed among gastric cancers, precancerous lesions and normal gastric tissue. Gastric samples with MSI had a tendency to be hypermethylated in the hMLH1 promoter. DNA sequencing and immunohistochemistry results also confirmed that hMLH1 promoter methylation could lead to loss of the hMLH1 protein and gene silence which sequentely resulted in gene mismatch and MSI.CONCLUSION Accumulation of MSI and hMLH1 promoter methylation may be important early molecular events during gastric carcinogenesis and may contribute to the acquisition of a transformed cell phenotype and the development of gastric cancer.

  18. Microsatellite Instability in Young Women with Endometrioid type Endometrial Cancer

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    MR Abbaszadegan

    2009-09-01

    Full Text Available "nBackground: This study was designed to determine the frequency of Microsatellite Instability (MSI in young Iranian pa­tients with endometrial carcinoma and to evaluate its association with histopathologic and clinical features of disease."nMethods: Microsatellite status was analyzed in 23 patients with endometrioid type endometrial cancer who were less than 55 years. Clinicopathologic characteristics such as age, International Federation of Gynecology and Obstetric (FIGO grad­ing and staging of tumor, family history of Hereditary Non-polyposis Colorectal Cancer (HNPCC, oral conception (OC consump­tion, number of pregnancies, fertility, menstrual cycles and underlying disease were considered. Chi-square and Fisher exact tests were used to find the significant relationships."nResults: MSI analysis showed 8 patients (34.8% were MSS (Microsatellite Stable, 15 patients (62.5% were MSI positive. Among cases with MSI phenotype, 4 cases (17.4% had low instability (MSI-L and 11 cases (47.8% had high instability (MSI-H. Three cases with MSI-H had family history of HNPCC related cancers. Five cases (21.7% had infertility in which 4 of them (80% had MSI phenotype. There was no statistically significant relationship between MSI phenotype and tumor grade and stage."nConclusion: Few studies reported high frequency of MSI among young patients. Some studies mentioned similar results in endo­metrioid type of tumor. This study showed even higher frequency (65% when MSI analyzed in young endometrioid type endometrial patients. Most cases with infertility had MSI-H phenotype. It may suggest that beside women with family his­tory of HNPCC, EC screening using MSI would be beneficial in infertile women too.  

  19. Frequent allelic imbalance but infrequent microsatellite instability in gastric lymphoma

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    Hoeve, M A; Ferreira Mota, S C; Schuuring, E; de Leeuw, W J; Chott, A; Meijerink, J P; Kluin, P M; van Krieken, J H

    1999-01-01

    Specific defects in DNA repair pathways are reflected by DNA microsatellite instability (MSI) and play an important role in carcinogenesis. Reported frequencies in gastric non-Hodgkin's lymphomas (NHL) vary from 14% to as high as 90%. Another form of genetic instability in tumours is allelic imbalan

  20. Fragile X gene instability: Anchoring AGGs and linked microsatellites

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    Zhong, Nan; Yang, Weihong; Dobkin, C. [Institute for Basic Research in Developmental Disabilities, Staten Island, NY (United States)] [and others

    1995-08-01

    Interspersed AGGs within the FMR1 gene CGG repeat region may anchor the sequence and prevent slippage during replication. In order to detect the AGG position variations, we developed a method employing partial MnlI restriction analysis and analyzed X chromosomes from 187 males, including 133 normal controls (17 with 20-34 and 16 with 35-52 repeats), plus 54 fragile X premutations with 56-180 repeats. Among controls, the interspersed AGG positions were highly polymorphic, with heterozygosity of 91%. Among the control samples, 1.5% had no AGG positions, 25% had one, 71% had two, and 3% had three. Among the fragile X premutation samples, 63% had no AGG, while 37% had only one AGG. Analysis of premutation samples within fragile X families showed that variation occurred only within the 3{prime} end of the region. Thus, the instability was polar. Controls with {ge}15 pure CGG repeats were associated with the longest alleles of two nearby microsatellites, FRAXAC1 with 20-21 repeats and DXS548 with 202-206 bp and with increased microsatellite heterzygosity. The association of long pure CGG regions, as with fragile X chromosomes, with the longer and more heterozygous microsatellite alleles suggests they may be related mechanistically. Further, our results do not support a recent suggestion that the frequency of fragile X alleles may be increasing. Finally, analysis of a set of nonhuman primate samples showed that long pure CGG tracks are variable in size and are located within the 3{prime} region, which suggests that polar instability within FMR1 is evolutionarily quite old. 55 refs., 3 figs., 4 tabs.

  1. Microsatellite Instability Is Common in Colorectal Cancer in Native Nigerians.

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    Irabor, David O; Oluwasola, Olayiwola A; Ogunbiyi, Olufemi J; Ogun, Olabiyi G; Okolo, Clement A; Melas, Marilena; Gruber, Stephen B; Shi, Chanjuan; Raskin, Leon

    2017-05-01

    Colorectal cancer (CRC) is the fifth most common cancer in Africa, with significant differences in incidence, biology and clinical behavior from other populations. We studied prevalence and clinicopathological features of microsatellite instability (MSI) and young onset CRC in 83 archival samples from the University of Ibadan, Nigeria. Nigerian cases of CRC were MSI-high in 43% and MSI-high CRC had significantly lower histological heterogeneity than microsatellite-stable CRC (20% vs. 55% respectively, p=0.046). Presence of signet ring cell differentiation (10-50% of tumor) was significantly higher in younger patients with CRC (prevalence of mucinous (10%) and signet ring cell adenocarcinomas (4%) were among distinct features of Nigerian patients with CRC. MSI-high CRC is more common in West Africa and more detailed molecular and genetic analysis is warranted as CRC incidence and mortality continue to increase in the Sub-Saharan Africa. Copyright© 2017, International Institute of Anticancer Research (Dr. George J. Delinasios), All rights reserved.

  2. Microsatellite instability and MLH1 promoter hypermethylation in colorectal cancer

    Institute of Scientific and Technical Information of China (English)

    Yaron Niv

    2007-01-01

    Colorectal cancer (CRC) is caused by a series of genetic or epigenetic changes, and in the last decade there has been an increased awareness that there are multiple forms of colorectal cancer that develop through different pathways. Microsatellite instability is involved in the genesis of about 15% of sporadic colorectal cancers and most of hereditary nonpolyposis cancers. Tumors with a high frequency of microsatellite instability tend to be diploid, to possess a mucinous histology, and to have a surrounding lymphoid reaction. They are more prevalent in the proximal colon and have a fast pass from polyp to cancer. Nevertheless, they are associated with longer survival than stage-matched tumors with microsatellite stability. Resistance of colorectal cancers with a high frequency of microsatellite instability to 5-fluorouracil-based chemotherapy is well established. Silencing the MLH1 gene expression by its promoter methylation stops the formation of MLH1 protein, and prevents the normal activation of the DMA repair gene. This is an important cause for genomic instability and cell proliferation to the point of colorectal cancer formation. Better knowledge of this process will have a huge impact on colorectal cancer management, prevention, treatment and prognosis.

  3. Integrative Analyses of Colorectal Cancer Show Immunoscore Is a Stronger Predictor of Patient Survival Than Microsatellite Instability.

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    Mlecnik, Bernhard; Bindea, Gabriela; Angell, Helen K; Maby, Pauline; Angelova, Mihaela; Tougeron, David; Church, Sarah E; Lafontaine, Lucie; Fischer, Maria; Fredriksen, Tessa; Sasso, Maristella; Bilocq, Amélie M; Kirilovsky, Amos; Obenauf, Anna C; Hamieh, Mohamad; Berger, Anne; Bruneval, Patrick; Tuech, Jean-Jacques; Sabourin, Jean-Christophe; Le Pessot, Florence; Mauillon, Jacques; Rafii, Arash; Laurent-Puig, Pierre; Speicher, Michael R; Trajanoski, Zlatko; Michel, Pierre; Sesboüe, Richard; Frebourg, Thierry; Pagès, Franck; Valge-Archer, Viia; Latouche, Jean-Baptiste; Galon, Jérôme

    2016-03-15

    Microsatellite instability in colorectal cancer predicts favorable outcomes. However, the mechanistic relationship between microsatellite instability, tumor-infiltrating immune cells, Immunoscore, and their impact on patient survival remains to be elucidated. We found significant differences in mutational patterns, chromosomal instability, and gene expression that correlated with patient microsatellite instability status. A prominent immune gene expression was observed in microsatellite-instable (MSI) tumors, as well as in a subgroup of microsatellite-stable (MSS) tumors. MSI tumors had increased frameshift mutations, showed genetic evidence of immunoediting, had higher densities of Th1, effector-memory T cells, in situ proliferating T cells, and inhibitory PD1-PDL1 cells, had high Immunoscores, and were infiltrated with mutation-specific cytotoxic T cells. Multivariate analysis revealed that Immunoscore was superior to microsatellite instability in predicting patients' disease-specific recurrence and survival. These findings indicate that assessment of the immune status via Immunoscore provides a potent indicator of tumor recurrence beyond microsatellite-instability staging that could be an important guide for immunotherapy strategies.

  4. A novel approach for characterizing microsatellite instability in cancer cells.

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    Yuheng Lu

    Full Text Available Microsatellite instability (MSI is characterized by the expansion or contraction of DNA repeat tracts as a consequence of DNA mismatch repair deficiency (MMRD. Accurate detection of MSI in cancer cells is important since MSI is associated with several cancer subtypes and can help inform therapeutic decisions. Although experimental assays have been developed to detect MSI, they typically depend on a small number of known microsatellite loci or mismatch repair genes and have limited reliability. Here, we report a novel genome-wide approach for MSI detection based on the global detection of insertions and deletions (indels in microsatellites found in expressed genes. Our large-scale analyses of 20 cancer cell lines and 123 normal individuals revealed striking indel features associated with MSI: there is a significant increase of short microsatellite deletions in MSI samples compared to microsatellite stable (MSS ones, suggesting a mechanistic bias of repair efficiency between insertions and deletions in normal human cells. By incorporating this observation into our MSI scoring metric, we show that our approach can correctly distinguish between MSI and MSS cancer cell lines. Moreover, when we applied this approach to primal tumor samples, our metric is also well consistent with diagnosed MSI status. Thus, our study offers new insight into DNA mismatch repair system, and also provides a novel MSI diagnosis method for clinical oncology with better reliability.

  5. Microsatellite instability in cancer of the proximal colon

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    Thibodeau, S.N.; Bren, G.; Schaid, D. (Mayo Clinic and Foundation, Rochester, MN (United States))

    1993-05-07

    Colorectal tumor DNA was examined for somatic instability at (CA)[sub n] repeats on human chromosomes 5q, 15q, 17p, and 18q. Differences between tumor and normal DNA were detected in 25 of the 90 (28 percent) tumors examined. This instability appeared as either a substantial change in repeat length (often heterogeneous in nature) or a minor change (typically two base pairs). Microsatellite instability was significantly correlated with the tumor's location in the proximal colon (P = 0.003), with increased patient survival (P = 0.02), and, inversely, with loss of heterozygosity for chromosomes 5q, 17p, and 18q. These data suggest that some colorectal cancers may arise through a mechanism that does not necessarily involve loss of heterozygosity. 23 refs., 2 figs., 3 tabs.

  6. Colorectal cancer among young native Indonesians: A clinicopathological and molecular assessment on microsatellite instability

    Directory of Open Access Journals (Sweden)

    Aru W. Sudoyo

    2010-11-01

    Full Text Available Aim: To obtain clinicopathological characteristics of colorectal cancer among young native Indonesians and to assess MLH1, MSH2, and SMAD4 protein expressions, comparing them with a matched population of colorectal cancer patients aged 60 years old and older.Methods: Medical records of colorectal cancer patients aged 40 years or younger and 60 years or older from several hospitals in three Indonesian cities – Jakarta, Makassar, and Bandung - were reviewed. The “native” ethnic groups were selected from those originating from Java, Makassar (South Celebes,  Minangkabau (West Sumatra. Ethnicity of 121 colorectal  carcinoma patients was confirmed by fulfilling requirements in a questionnaire. Tumor specimens of those patients underwent evaluation for histopathology, tumor grading as well as  immunohistochemical analysis to assess MLH1, MSH2 protein expressions to detect microsatellite instability mutation pathway and SMAD4 protein expression to reconfirm that the specimens were not microsatellite instability origin.Results: There were 121 colorectal carcinoma cases of Sundanese, Javanese, Macassarese and Minangkabau ethnic group. This study indicated that colorectal cancer has statistically different grade (p = 0.001 between the young and the older patients. Immunohistochemical staining for MSH2 protein and MLH1 were done for 92 and 97 specimens respectively. There was no significant difference between the expressions of MLH1 and MSH2 on tumor grading, indicated there was no correlation between microsatellite instability and tumor grading in this study.Conclusion: Colorectal cancer in young native Indonesian patients (40 years old or less was not different in clinicopathological characteristics compared to older patients (60 years old or more in similar ethnic groups. There was also no difference in MSH2 and MLH1 protein expressions, important indicators of microsatellite instability and. (Med J Indones 2010; 19:245-51Keywords: colorectal

  7. Microsatellite instability and the association with plasma homocysteine and thymidylate synthase in colorectal cancer

    DEFF Research Database (Denmark)

    Jensen, Lars Henrik; Lindebjerg, Jan; Crüger, Dorthe G.;

    2008-01-01

    The possible associations between microsatellite instability, homocysteine and thymidylate synthase were investigated in tumors and plasma from 130 patients with colorectal cancer. Other analyses included thymidylate synthase and 5,10-methylene-tetrahydrofolate reductase gene polymorphisms......, carcinoembryonic antigen, vitamin B12, and folate. Microsatellite instability of tumors was associated with higher levels of plasma homocysteine (p = 0.008) and higher protein expression of thymidylate synthase (p ... factors. CEA was not associated with neither homocysteine nor microsatellite instability. The data suggests that there is a more pronounced methyl unit deficiency in microsatellite instable tumors....

  8. Pb2+ exposure induced microsatellite instability in Pisum sativum in a locus related with glutamine metabolism.

    Science.gov (United States)

    Rodriguez, E; Azevedo, R; Moreira, H; Souto, L; Santos, Conceição

    2013-01-01

    Lead (Pb) is a toxic element, but its putative mutagenic effects in plant cells, using molecular markers, remain to unveil. To evaluate if Pb induces mutagenicity, Pisum sativum L. seedlings were exposed to Pb(2+) (up to 2000 mg L(-1)) for 28 days and the instability of microsatellites (or Simple Sequence Repeats, SSR) was analyzed in leaves and roots. The analysis of eight selected microsatellites (SSR1-SSR8) demonstrated that only at the highest dosage microsatellite instability (MSI) occurred, at a frequency of 4.2%. Changes were detected in one microsatellite (SSR6) that is inserted in the locus for glutamine synthetase. SSR6 products of roots exposed to the highest concentration of Pb were 3 bp larger than those of the control. Our data demonstrate that: (a) SSR technique is sensitive to detect Pb-induced mutagenicity in plants. MSI instability is Pb dose dependent and organ dependent (roots are more sensitive); (b) the Pb-sensitive SSR6 is inserted in the glutamine synthetase locus, with still unknown relation with functional changes of this enzyme; (c) Pb levels inducing MSI are much above the maximum admitted levels in some European Union countries for agricultural purpose waters. In conclusion, we propose here the potential use of SSR to evaluate Pb(2+)-induced mutagenicity, in combination with other genetic markers.

  9. Immunotherapy and patients treated for cancer with microsatellite instability.

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    Colle, Raphaël; Cohen, Romain; Cochereau, Delphine; Duval, Alex; Lascols, Olivier; Lopez-Trabada, Daniel; Afchain, Pauline; Trouilloud, Isabelle; Parc, Yann; Lefevre, Jérémie H; Fléjou, Jean-François; Svrcek, Magali; André, Thierry

    2017-01-01

    Microsatellite instability (MSI) is a tumor phenotype linked to somatic or germline (Lynch syndrome) inactivating alterations of DNA mismatch repair genes. A broad spectrum of neoplasms exhibits MSI phenotype, mainly colorectal cancer, endometrial cancer, and gastric cancer. MSI tumors are characterized by dense immune infiltration and high load of tumor neo-antigens. Growing evidence is accumulating on the efficacy of immune checkpoint inhibition for patients treated for MSI solid tumors. We present a comprehensive overview of MSI phenotype, its biological landscape and current diagnostic methods. Then we focus on MSI as a predictive biomarker of response to immune checkpoint inhibition in the context of colorectal cancer and non-colorectal tumors.

  10. Improved Detection of Microsatellite Instability in Early Colorectal Lesions.

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    Jeffery W Bacher

    Full Text Available Microsatellite instability (MSI occurs in over 90% of Lynch syndrome cancers and is considered a hallmark of the disease. MSI is an early event in colon tumor development, but screening polyps for MSI remains controversial because of reduced sensitivity compared to more advanced neoplasms. To increase sensitivity, we investigated the use of a novel type of marker consisting of long mononucleotide repeat (LMR tracts. Adenomas from 160 patients, ranging in age from 29-55 years old, were screened for MSI using the new markers and compared with current marker panels and immunohistochemistry standards. Overall, 15 tumors were scored as MSI-High using the LMRs compared to 9 for the NCI panel and 8 for the MSI Analysis System (Promega. This difference represents at least a 1.7-fold increase in detection of MSI-High lesions over currently available markers. Moreover, the number of MSI-positive markers per sample and the size of allelic changes were significantly greater with the LMRs (p = 0.001, which increased confidence in MSI classification. The overall sensitivity and specificity of the LMR panel for detection of mismatch repair deficient lesions were 100% and 96%, respectively. In comparison, the sensitivity and specificity of the MSI Analysis System were 67% and 100%; and for the NCI panel, 75% and 97%. The difference in sensitivity between the LMR panel and the other panels was statistically significant (p<0.001. The increased sensitivity for detection of MSI-High phenotype in early colorectal lesions with the new LMR markers indicates that MSI screening for the early detection of Lynch syndrome might be feasible.

  11. LINE-1 hypomethylation in cancer is highly variable and inversely correlated with microsatellite instability.

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    Marcos R H Estécio

    Full Text Available BACKGROUND: Alterations in DNA methylation in cancer include global hypomethylation and gene-specific hypermethylation. It is not clear whether these two epigenetic errors are mechanistically linked or occur independently. This study was performed to determine the relationship between DNA hypomethylation, hypermethylation and microsatellite instability in cancer. METHODOLOGY/PRINCIPAL FINDINGS: We examined 61 cancer cell lines and 60 colorectal carcinomas and their adjacent tissues using LINE-1 bisulfite-PCR as a surrogate for global demethylation. Colorectal carcinomas with sporadic microsatellite instability (MSI, most of which are due to a CpG island methylation phenotype (CIMP and associated MLH1 promoter methylation, showed in average no difference in LINE-1 methylation between normal adjacent and cancer tissues. Interestingly, some tumor samples in this group showed increase in LINE-1 methylation. In contrast, MSI-showed a significant decrease in LINE-1 methylation between normal adjacent and cancer tissues (P<0.001. Microarray analysis of repetitive element methylation confirmed this observation and showed a high degree of variability in hypomethylation between samples. Additionally, unsupervised hierarchical clustering identified a group of highly hypomethylated tumors, composed mostly of tumors without microsatellite instability. We extended LINE-1 analysis to cancer cell lines from different tissues and found that 50/61 were hypomethylated compared to peripheral blood lymphocytes and normal colon mucosa. Interestingly, these cancer cell lines also exhibited a large variation in demethylation, which was tissue-specific and thus unlikely to be resultant from a stochastic process. CONCLUSION/SIGNIFICANCE: Global hypomethylation is partially reversed in cancers with microsatellite instability and also shows high variability in cancer, which may reflect alternative progression pathways in cancer.

  12. Clinicopathological significance of loss of heterozygosity and microsatellite instability in hepatocellular carcinoma in China

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    Shu-Hui Zhang; Wen-Ming Cong; Zhi-Hong Xian; Meng-Chao Wu

    2005-01-01

    AIM: To determine the features of microsatellite alterations and their association with clinicopathological characteristics of hepatocellular carcinoma (HCC). METHODS: Loss of heterozygosity (LOH) and microsatellite instability (MSI) of 55 microsatellite loci were detected with PCR-based microsatellite polymorphism analyses in tumors and corresponding noncancerous liver tissues of 56 surgically resected HCCs using the MegaBACE 500 automatic DNA analysis system.RESULTS: LOH was found in 44 of 56 HCCs (78.6%) at one or several loci. Frequencies of LOH on 1p, 4q, 8p,16q, and 17p were 69.6% (39/56), 71.4% (40/56), 66.1% (37/56), 66.1% (37/56), and 64.3% (36/56), respectively. MSI was found in 18 of 56 HCCs (32.1%) at one or several loci. Ten of fifty-six (17.9%) HCCs had MSI-H. Serum HBV infection, alpha-fetoprotein concentration, tumor size, cirrhosis, histological grade, tumor capsule, as well as tumor intrahepatic metastasis, might be correlated with LOH on certain chromosome regions. CONCLUSION: Frequent microsatellite alterations exist in HCC. LOH, which represents a tumor suppressor gene pathway, plays a more important role in hepatocarcinogenesis. MSI, which represents a mismatch repair genepathway, is a rare event during liver carcinogenesis. Furthermore, LOH on certain chromosome regions may be correlated with clinicopathological characteristics in HCC.

  13. Colon and rectal cancer survival by tumor location and microsatellite instability: the Colon Cancer Family Registry.

    Science.gov (United States)

    Phipps, Amanda I; Lindor, Noralane M; Jenkins, Mark A; Baron, John A; Win, Aung Ko; Gallinger, Steven; Gryfe, Robert; Newcomb, Polly A

    2013-08-01

    Cancers in the proximal colon, distal colon, and rectum are frequently studied together; however, there are biological differences in cancers across these sites, particularly in the prevalence of microsatellite instability. We assessed the differences in survival by colon or rectal cancer site, considering the contribution of microsatellite instability to such differences. This is a population-based prospective cohort study for cancer survival. This study was conducted within the Colon Cancer Family Registry, an international consortium. Participants were identified from population-based cancer registries in the United States, Canada, and Australia. Information on tumor site, microsatellite instability, and survival after diagnosis was available for 3284 men and women diagnosed with incident invasive colon or rectal cancer between 1997 and 2002, with ages at diagnosis ranging from 18 to 74. Cox regression was used to calculate hazard ratios for the association between all-cause mortality and tumor location, overall and by microsatellite instability status. Distal colon (HR, 0.59; 95% CI, 0.49-0.71) and rectal cancers (HR, 0.68; 95% CI, 0.57-0.81) were associated with lower mortality than proximal colon cancer overall. Compared specifically with patients with proximal colon cancer exhibiting no/low microsatellite instability, patients with distal colon and rectal cancers experienced lower mortality, regardless of microsatellite instability status; patients with proximal colon cancer exhibiting high microsatellite instability had the lowest mortality. Study limitations include the absence of stage at diagnosis and cause-of-death information for all but a subset of study participants. Some patient groups defined jointly by tumor site and microsatellite instability status are subject to small numbers. Proximal colon cancer survival differs from survival for distal colon and rectal cancer in a manner apparently dependent on microsatellite instability status. These

  14. Imbalanced adaptive responses associated with microsatellite instability in cholangiocarcinoma

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    Loilome, Watcharin; Kadsanit, Sasithorn; Muisook, Kanha; Yongvanit, Puangrat; Namwat, Nisana; Techasen, Anchalee; Puapairoj, Anucha; Khuntikeo, Narong; Phonjit, Pichai

    2017-01-01

    The adaptive response of the genome protection mechanism occurs in cells when exposed to genotoxic stress due to the overproduction of free radicals via inflammation and infection. In such circumstances, cells attempt to maintain health via several genome protection mechanisms. However, evidence is increasing that this adaptive response may have deleterious effect; a reduction of antioxidant enzymes and/or imbalance in the DNA repair system generates microsatellite instability (MSI), which has procarcinogenic implications. Therefore, the present study hypothesized that MSI caused by imbalanced responses of antioxidant enzymes and/or DNA repair enzymes as a result of oxidative/nitrative stress arising from the inflammatory response is involved in liver fluke-associated cholangiocarcinogenesis. The present study investigated this hypothesis by identifying the expression patterns of antioxidant enzymes, including superoxide dismutase 2 (SOD2) and catalase (CAT), and DNA repair enzymes, including alkyladenine DNA glycosylase (AAG), apurinic endonuclease (APE) and DNA polymerase β (DNA pol β). In addition, the activities of the antioxidant enzymes, SOD2 and CAT, were examined in human cholangiocarcinoma (CCA) tissues using immunohistochemical staining. MSI was also analyzed in human CCA tissues. The resulting data demonstrated that the expression levels of the SOD2 and CAT enzymes decreased. The activities of SOD2 and CAT decreased significantly in the CCA tissues, compared with the hepatic tissue of cadaveric donors. In the DNA repairing enzymes, it was found that the expression levels of AAG and DNA pol β enzymes increased, whereas the expression of APE decreased. In addition, it was found that MSI-high was present in 69% of patients, whereas MSI-low was present in 31% of patients, with no patients classified as having microsatellite stability. In the patients, a MSI-high was correlated with poor prognosis, indicated by a shorter survival rate. These results

  15. Laser microdissection and microsatellite analysis of colorectal adenocarcinomas

    DEFF Research Database (Denmark)

    Jensen, Lars Henrik; Cruger, Dorthe G; Lindebjerg, Jan;

    2006-01-01

    BACKGROUND: Microsatellite instability (MSI) is an important marker in colorectal cancer. The analysis may be difficult if the tumour is heterogeneous or only scarce material is available. The aim of this study was to apply laser microdissection (LMD) to MSI analysis in an attempt to allow...... the MSI status. RESULTS: The method proved efficient in as little as 4,000 microm3 formalin-treated and paraffin-embedded tumour tissue. The result of microsatellite analysis was independent of sample location in the primary tumour and its metastasis. CONCLUSION: LMD followed by a multiplex PCR...

  16. Helicobacter pylori and EBV in gastric carcinomas:Methylation status and microsatellite instability

    Institute of Scientific and Technical Information of China (English)

    Adriana; Camargo; Ferrasi; Nídia; Alice; Pinheiro; Silvia; Helena; Barem; Rabenhorst; Otávia; Luisa; Caballero; Maria; Aparecida; Marchesan; Rodrigues; Fabrício; de; Carvalho; Celso; Vieira; de; Souza; Leite; Marcia; Valéria; Pitombeira; Ferreira; Marcos; Aurélio; Pessoa; Barros; Maria; Inês; de; Moura; Campos; Pardini

    2010-01-01

    AIM:To verify the methylation status of CDH1, DAPK, COX2, hMLH1 and CDKN2A genes and to evaluate their association with Helicobacter pylori (H. pylori)-cagA+ and Epstein Barr virus (EBV) infections in gastric adenocarcinomas.METHODS: Methylation-specific PCR (MSP) assay was performed in 89 primary gastric carcinomas (intestinal and diffuse types). Microsatellite instability (MSI) analysis was performed using the BAT26 primer set and PCR products were analyzed with the ABI PRISM 3100 Genetic Analyzer using G...

  17. Infrequent microsatellite instability mutator phenotype in Chinese hepatocellular carcinomas

    Institute of Scientific and Technical Information of China (English)

    方丽; 房殿春; 汪荣泉; 杨仕明; 吴凯

    2003-01-01

    Objective:In order to elucidate the molecular mechanisms that might be responsible for hepatocarcinogenesis,we examined microsatellite instability(MSI),mismatch repair gene hMLH1 mutation and methylation in hepatocellular carcinoma.Methods:Fifty-two cases of surgically resected sporadic hepatocellular carcinoma(HCC)were studied.hMLH1 mutation was examined by two-dimensional electrophoresis and DNA sequencing; hMLH1 methylation was determined by methylation-specific PCR(MSP); and MSI at BAT26 was analyzed by PCR-based methods.Results:MSI at BAT26 was found in 3 of 52 cases(5.8%)of the tumors analyzed.No hMLH1 mutation or hypermethylation was found in these 52 cancerous tissues.No correlation existed between MSI and clinico-pathological characteristics of the patients.Conclusion:Our results suggest that MSI at BAT26 is rarely associated with carcinogenesis of chinese HCC.The genesis of sporadic HCC may occur in an alternative pathway that is probably different from MSI pathway.

  18. Microsatellite Instability in Intestinal Metaplasia and Gastric Cancer

    Institute of Scientific and Technical Information of China (English)

    SHAOYun; ZHANGXiao-yong; LIUPing

    2004-01-01

    To investigate the changeable patterns of microsatellite instability(MSI)in intestinal metaplasia(IM)and gastric cancer(GC)and the role of MSI in gastric carcinogenesis. Methods: Silver staining single strand confornmtion polymorphism-polymeriase chain reaction(PCR-SSCP)wus used to screen MSI nmrkers at 5 loci in formalin-fixed, paraffin-embedded tissues of GC ( n = 30), IM ( n = 40) and corresponding normal gastric tissues. Resu/ts: The abnormal shifting of the single-strand DNA was identified in 7 (23.3%) out of GC and in 8 (20%) out of IM samples. Three ( 10 % ) tumors and one ( 2.5 % ) IM displayed high- frequency MSI ( two or more loci altered ). Low- frequencySI(one loci altered) was detected in 4( 13.3% )of the tmnors and in 7( 17.5% ) IM samples. GC with MSI was associated with distal location of the tumors but age,sex, differenl~ation, lymph nodes metastasis and TNM stage( P = 0.044).MSI was more likely detected in moderate-grade IM than in mild, grade IM tissues(34.8% versus 0; P = 0.013) ; and MSI had a tendency to be easily detected in female with IM. Conc/u,6~ : The progressive accmnulation of MSI in areas ofIM may contribute to GC development, represen~_g an importmlt molecular event in the multistep gastric ~~.

  19. Microsatellite instability in gastric cancer and pre-cancerous lesions

    Institute of Scientific and Technical Information of China (English)

    Ping Liu; Xiao-Yong Zhang; Yun Shao; Dao-Fu Zhang

    2005-01-01

    AIM: To investigate the microsatellite instability (MSI) in cancer and pre-cancerous lesions of the stomach and its mechanisms underlying the development of gastric cancer.METHODS: Thirty-six gastric cancer samples were obtained from patients undergoing surgery. Forty-one gastric mucosa samples with dysplasia and 51 with intestinal metaplasia (IM) were obtained from patients with chronic gastritis undergoing gastro-endoscopy. Genomic DNA was extracted from the samples. Silver staining single strand conformation polymorphis-polymerize chain reaction (SSCP-PCR) was used to screen MSI markers at 5 loci (Bat-25, Bat-26, D5S346, D17S250, and D2S123)in fresh tissues and formalin-fixed, paraffin-embedded samples and their corresponding normal gastric mucosa.RESULTS: The abnormal shifting of the single-strand DNA (MSI) was identified in 21 out of 36 (58.3%) gastric cancers.Seven cases showed high-level MSI (two or more loci altered) and 14 showed low-level MSI (one locus altered).Gastric cancer with MSI had a tendency to be located in the distal stomach. MSI was also detected in 11 out of 41(26.8%) dysplasia samples and in 9 of 51 (17.6%) IM samples respectively. Three cases of dysplasia and one case of IM showed high-level MSI. Eight cases of dysplasia and 8 cases of IM displayed low-level MSI. MIS in IM was found only in moderate or severe-grade IM. No association was detected between MSI and dysplasia grade.CONCLUSION: Accumulation of MSI in dysplasia and intestinal metaplasia of gastric mucosa may be an early molecular event during gastric carcinogenesis and may contribute to the acquisition of transformed cell phenotype and the development of gastric cancer.

  20. Colorectal Tumour Microsatellite Instability Test Results: Perspectives from Patients

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    Lindor Noralane M

    2004-05-01

    Full Text Available Abstract Purpose To determine which individuals with colorectal cancer (CRC were interested in knowing the results of their tumour microsatellite instability (MSI and immunohistochemistry (IHC testing. We were also interested in the patients' reasons for choosing to learn their results and in the impact of those results on overall self-assessed quality of life. Patients and Methods CRCs from 414 individuals were assayed for MSI and IHC for DNA mismatch repair gene products (MLH1, MSH2, MSH6. Individuals were invited to learn their MSI/IHC results. They randomly received either brief or extended educational materials about the testing and a pretest survey to learn reasons for their interest and to assess their pretest quality of life. Results Of the 414 individuals, 307 (74% chose to learn their results. There was no significant difference in interest in knowing test results according to gender, age, educational level, or family history of colon cancer. The level of detail in the information piece received by the patients did not influence their desire to know their test results. Self-assessed quality of life was not altered by receiving results and was not correlated with the test outcome. Conclusions Individuals with colorectal cancer had a high level of interest in learning their individual MSI/IHC test results and did not seem deterred by the inherent complexity or ambiguity of this information. Regardless of test outcome, results did not significantly affect self-assessed quality of life. Further studies are needed to assess comprehension of results and behavioural changes resulting from the learning of MSI/IHC results.

  1. Utility of immunohistochemistry in predicting microsatellite instability in endometrial carcinoma.

    Science.gov (United States)

    Modica, Ippolito; Soslow, Robert A; Black, Destin; Tornos, Carmen; Kauff, Noah; Shia, Jinru

    2007-05-01

    Identification of the microsatellite instability (MSI) phenotype in endometrial carcinoma is important given that such tumors are the most common noncolorectal tumors to occur in hereditary nonpolyposis colorectal cancer syndrome, and may bear prognostic relevance. The objective of this study was to assess the utility of immunohistochemistry (IHC), a simple and fast technique, in detecting MSI in endometrial carcinoma. The study subjects consisted of 90 endometrial carcinoma patients with equal representation of MSI-high (MSI-H) and non-MSI-H tumors. MSI was tested using the standard polymerase chain reaction-based method and the 5 NCI-recommended markers. Overall, IHC with MLH1 and MSH2 antibodies detected 69% of MSI-H tumors with a specificity of 100%. Adding PMS2 and MSH6 to the antibody panel increased the sensitivity to 91% but decreased the specificity to 83%. The most common IHC abnormality in MSI tumors was concurrent loss of MLH1/PMS2. Assessment of staining was straightforward in most cases but not in all. Staining inadequacies existed. Five stains (4 MLH1 and 1 MSH6) were not interpretable because of the lack of any internal positive control. Two percent to 10% of the cases (depending on the antibody assessed) had only focal weak staining; the highest frequency (10%) occurred with MLH1 antibody. PMS2 staining detected 7 MLH1-staining present MSI-H cases, thus partly accounting for the increased sensitivity with the 4-antibody panel. MSH6 staining identified 9 cases with loss of MSH6 alone, 6 of 9 were non-MSI-H, thus partly accounting for the decreased specificity with the 4-antibody panel. In conclusion, our results suggest that IHC is useful in detecting MSI in endometrial carcinoma. Although IHC has a lower sensitivity with more apparent staining inadequacies in detecting MSI in endometrial carcinoma than it does in colorectal carcinoma, its use in endometrial carcinoma may be an important adjunct when screening for hereditary cases. In the future, as

  2. High-level microsatellite instability in appendiceal carcinomas.

    Science.gov (United States)

    Taggart, Melissa W; Galbincea, John; Mansfield, Paul F; Fournier, Keith F; Royal, Richard E; Overman, Michael J; Rashid, Asif; Abraham, Susan C

    2013-08-01

    High-level microsatellite instability (MSI-high) is found in approximately 15% of all colorectal adenocarcinomas (CRCs) and in at least 20% of right-sided cancers. It is most commonly due to somatic hypermethylation of the MLH1 gene promoter region, with familial cases (Lynch syndrome) representing only 2% to 3% of CRCs overall. In contrast to CRC, MSI-high in appendiceal adenocarcinomas is rare. Only 4 MSI-high appendiceal carcinomas and 1 MSI-high appendiceal serrated adenoma have been previously reported, and the prevalence of MSI in the appendix is unknown. We identified 108 appendiceal carcinomas from MD Anderson Cancer Center in which MSI status had been assessed by immunohistochemistry for the DNA mismatch-repair proteins MLH1, MSH2, MSH6, and PMS2 (n=83), polymerase chain reaction (n=7), or both (n=18). Three cases (2.8%) were MSI-high, and 1 was MSI-low. The 3 MSI-high cases included: (1) a poorly differentiated nonmucinous adenocarcinoma with loss of MLH1/PMS2 expression, lack of MLH1 promoter methylation, and lack of BRAF gene mutation, but no detected germline mutation in MLH1 from a 39-year-old man; (2) an undifferentiated carcinoma with loss of MSH2/MSH6, but no detected germline mutation in MSH2 or TACSTD1, from a 59-year-old woman; and (3) a moderately differentiated mucinous adenocarcinoma arising in a villous adenoma with loss of MSH2/MSH6 expression, in a 38-year-old man with a strong family history of CRC who declined germline testing. When the overall group of appendiceal carcinomas was classified according to histologic features and precursor lesions, the frequencies of MSI-high were: 3 of 108 (2.8%) invasive carcinomas, 3 of 96 (3.1%) invasive carcinomas that did not arise from a background of goblet cell carcinoid tumors, and 0 of 12 (0%) signet ring and mucinous carcinomas arising in goblet cell carcinoid tumors. These findings, in conjunction with the previously reported MSI-high appendiceal carcinomas, highlight the low prevalence of MSI

  3. Familial colorectal cancer, can it be identified by microsatellite instability and chromosomal instability? - A case-control study

    DEFF Research Database (Denmark)

    Sunde, Lone; Bisgaard, Marie Luise; Soll-Johanning, Helle

    2009-01-01

    Colonoscopy is recommended for persons with a familial risk of colorectal cancer (CRC). A familial risk is identified by a family history with CRC and/or predisposing mutation(s). However, such information may not be available. We analysed whether MSI (MicroSatellite Instability) and/or CIN...

  4. Study of microsatellite instability in epithelial ovarian tumors%上皮性卵巢癌中微卫星不稳定的研究

    Institute of Scientific and Technical Information of China (English)

    卢媛; 刘惜时; 王跃祥; 宋后燕; Nanbert ZHONG

    2006-01-01

    Objective: To evaluate the frequency of MSI in epithelial ovarian tumors and its relationship with clinicopathologic features. Methods: Ninety fresh specimens of epithelial ovarian tumors, including 74 primary and 16 secondary tumors, were collected. Microsatellite analysis was carried out using 5 mono- and dinucleotide markers from the National Cancer Institute Consensus Panel by fluorescence-labeled polymerase chain reaction. Results: Of 90 epithelial ovarian tumors analyzed, 18 demonstrated a high level of microsatellite instability (MSI-H), 30 demonstrated a low level of microsatellite instability (MSI-L), and the remaining 42 exhibited microsatellite stability (MSS). Frequency of microsatellite instability (MSI) at loci BAT-25 was higher than that at any other loci. No correlation was found between MSI level and patient age, tumor type, tumor differentiation (P>0.05). But the microsatellite instability-high phenotype correlates with clinical stage.It tended to occur more frequently in early-stage tumors (P=0.03). Conclusion: The frequent MSI in epithelial ovarian tumors suggests that it is an early event to involve in the development of epithelial ovarian tumors.

  5. Microsatellite instability in tumor and nonneoplastic colorectal cells from hereditary non-polyposis colorectal cancer and sporadic high microsatellite-instable tumor patients.

    Science.gov (United States)

    Dietmaier, W; Gänsbauer, S; Beyser, K; Renke, B; Hartmann, A; Rümmele, P; Jauch, K W; Hofstädter, F; Rüschoff, J

    2000-01-01

    Genetic alterations such as loss of heterozygosity (LOH) and microsatellite instability (MSI) have been frequently studied in various tumor types. Genetic heterogeneity of nonneoplastic cells has not yet been sufficiently investigated. However, genomic instability in normal cells could be a potentially important issue, in particular when these cells are used as reference in LOH and MSI analyses of tumor samples. In order to investigate possible genetic abnormalities in normal colorectal cells of tumor patients, MSI analyses of normal colonic mucosa were performed. Up to 15 different laser-microdissected normal regions containing 50-150 cells were investigated in each of 15 individual microsatellite-stable, sporadic high microsatellite-instable (MSI-H) and hereditary non-polyposis coli cancer (HNPCC) colorectal cancer patients. Frequent MSI and heterogeneity in the MSI pattern were found both in normal and tumor cells from 10 HNPCC and sporadic MSI-H tumor patients whose tumors had defect mismatch repair protein expressions. This observation shows that MSI can also occur in nonneoplastic cells which has to be considered in MSI analyses for molecular HNPCC screening. In addition, considerable genetic heterogeneity was detected in all MSI-H (sporadic and HNPCC) tumors when analyzing five different regions with less than 150 cells, respectively. These differences were not detectable in larger tumor regions containing about 10,000 cells. Thus, heterogeneity of the MSI pattern (e.g. intratumoral MSI) is an important feature of tumors with the MSI-H phenotype.

  6. EMAST is associated with a poor prognosis in microsatellite instable metastatic colorectal cancer.

    Directory of Open Access Journals (Sweden)

    Sabine Venderbosch

    Full Text Available To determine the frequency and prognostic value of elevated microsatellite alterations at selected tetranucleotide repeats (EMAST in metastatic colorectal cancer (mCRC patients in relation to microsatellite instability (MSI status and MSH3 protein expression.The frequency of EMAST was evaluated in mCRC patients with MSI tumors and microsatellite stable (MSS tumors. A literature overview was performed to compare the frequency of EMAST in our study with existing data. Immunohistochemistry for MSH3 was compared with EMAST status. Outcome was studied in terms of overall survival (OS of mCRC patients with MSI and MSS tumors.EMAST was evaluated in 89 patients with MSI tumors (including 39 patients with Lynch syndrome and 94 patients with MSS tumors. EMAST was observed in 45.9% (84 out of 183 of patients, with an increased frequency in MSI tumors (79.8% versus 13.8%, p < 0.001. We found no correlation between EMAST and MSH3 protein expression. There was no effect of EMAST on prognosis in patients with MSS tumors, but patients with MSI / non-EMAST tumors had a significantly better prognosis than patients with MSI / EMAST tumors (OS: HR 3.22, 95% CI 1.25-8.30.Frequency of EMAST was increased in mCRC patients with MSI tumors, compared to MSS tumors. Our data suggest that the presence of EMAST correlates with worse OS in these patients. There was no effect of EMAST on the prognosis of patients with MSS tumors. A limitation of our study is the small number of patients in our subgroup analysis.

  7. Detection of microsatellite instability but not truncating APC mutations in gastric adenocarcinomas in Brazilian patients

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    Bevilacqua Roberta A.U.

    2000-01-01

    Full Text Available A crucial role for the adenomatous polyposis colonic (APC gene in colorectal carcinogenesis has been conclusively established, but, the role of APC in gastric tumors remains controversial. APC mutations have been detected at a relatively high frequency in gastric tumors of Japanese patients, yet such mutations have been reported to be extremely rare in British patients and patients from north-central-Italy. We here report the analysis of 40 primary sporadic gastric adenocarcinomas and 35 primary sporadic colon adenocarcinomas (from patients resident in São Paulo, Brazil, for mutations in the APC gene between codons 686 and 1693 using the protein truncation test. Although 19 truncating mutations were detected in 35 colon adenocarcinomas (54.2% none were found in any of the gastric adenocarcinomas. As an internal control the tumor samples were also evaluated for microsatellite alterations, which are also common features of both tumor types. Microsatellite instability was present in 1 colon and 7 gastric tumor samples. This suggests that in relation to APC mutations gastric adenocarcinomas from Brazilian patients are similar to those that occur in Europe, and support a fundamental difference both between gastric carcinomas that occur in different geographical regions and between the molecular etiology of gastric and colorectal adenocarcinomas occurring in São Paulo, Brazil.

  8. CpG Island Methylation, Microsatellite Instability, and BRAF Mutations and Their Clinical Application in the Treatment of Colon Cancer

    Directory of Open Access Journals (Sweden)

    Christina Wu

    2012-01-01

    Full Text Available There have been significant developments in colon cancer research over the last few years, enabling us to better characterize tumors individually and classifying them according to certain molecular or genetic features. Currently, we are able to use KRAS mutational status as a guide to therapy with anti-epidermal growth factor receptor antibodies. Other molecular features under research include BRAF mutation, microsatellite instability, and CpG island methylation. These three molecular features are often associated with tumors that have overlapping phenotypes and can be present simultaneously in the same tumor. However, they carry different prognostic and predictive qualities, making analysis of their interaction relatively complex. Much research thus far has examined the clinical relevance of microsatellite instability in helping determine prognosis and the predictive value of adjuvant 5-fluorouracil chemotherapy in stages II and III colon cancers. BRAF mutation appears to be a biomarker for poor prognosis. CpG island methylation is tightly associated with microsatellite instable tumors and BRAF mutation, but its clinical utility remains uncertain. Hereby, we examine preclinical and clinical data that supports the utilization of all three phenotypes in future research applied to clinical practice.

  9. The relationship between serum vascular endothelial growth factor A and microsatellite instability in colorectal cancer

    DEFF Research Database (Denmark)

    Hansen, T F; Jensen, L H; Spindler, K-L G;

    2011-01-01

    AIM: It has been suggested that colorectal neoplasms with or without microsatellite instability (MSI) can stimulate angiogenesis in different ways. The vascular endothelial growth factor (VEGF) system is essential for the angiogenetic process and the growth of malignant tumours. The aim of this s......AIM: It has been suggested that colorectal neoplasms with or without microsatellite instability (MSI) can stimulate angiogenesis in different ways. The vascular endothelial growth factor (VEGF) system is essential for the angiogenetic process and the growth of malignant tumours. The aim...... lacking protein expression of any of the four mismatch repair genes (MLH1, PMS2, MSH2 or MSH6) were labelled as high MSI. The rest were considered to be microsatellite stable (MSS). The serum VEGF-A analyses were performed by ELISA. RESULTS: The tumours of 15 patients in the test cohort and 27...

  10. Current Hypotheses on How Microsatellite Instability Leads to Enhanced Survival of Lynch Syndrome Patients

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    Kristen M. Drescher

    2010-01-01

    Full Text Available High levels of microsatellite instability (MSI-high are a cardinal feature of colorectal tumors from patients with Lynch Syndrome. Other key characteristics of Lynch Syndrome are that these patients experience fewer metastases and have enhanced survival when compared to patients diagnosed with microsatellite stable (MSS colorectal cancer. Many of the characteristics associated with Lynch Syndrome including enhanced survival are also observed in patients with sporadic MSI-high colorectal cancer. In this review we will present the current state of knowledge regarding the mechanisms that are utilized by the host to control colorectal cancer in Lynch Syndrome and why these same mechanisms fail in MSS colorectal cancers.

  11. MICROSATELLITE ANALYSIS OF INTRA CULTIVAR DIVERSITY IN ...

    African Journals Online (AJOL)

    ACSS

    were sampled to study intracultivar diversity following microsatellite analysis. The dendrogram ... composition are available on the Indian market. Notable local juicy ..... management and genetic identification of ... the application of the SSR technique allows to discriminate all .... and multivariate analysis system, version 2.1.

  12. TP53 Codon 72 Heterozygosity May Promote MicrosatelliteInstability in Sporadic Colorectal Cancer

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    Mehdi Nikbahkt Dastjerdi

    2010-01-01

    Full Text Available Objective: The polymorphic variants at codon 72 of the p53 gene, encoding prolineor arginine at residue 72, produce marked changes in the p53 structure. From theevidence that the DNA mismatch repair system and p53 interact to maintain genomicintegrity, we hypothesized that codon 72 variations may influence the prevalence ofmicrosatellite instability (MSI, a feature of malignancies associated with mismatchrepair deficiency in sporadic colorectal cancer.Materials and Methods: We investigated the frequency of MSI in three P53 codon72 genotypes using genomic DNAs from 144 paraffin blocks of sporadic colorectaladenocarcinomas by testing the BAT-26 poly(A marker. We used PCR-SSCP analysisto detect tumor sample MSI for the nonisotopic detection of deletions in the BAT-26 poly (A mononucleotide repeat. Associations between qualitative variables wereevaluated using the χ2-test. Statistical significance level was set to p ≤ 0.05.Results: MSI analysis revealed that 24.3% of the tumors (n=35 were MSI-positiveand 75.7% (n=109 were MSI-negative. The frequency of microsatellite instability inthe arginine/arginine, arginine/proline and proline/proline genotypes were 11 (16.9%,22 (36.1% and 2 (11.1% respectively. A significant difference in distribution of MSIwas found for the arginine/proline genotype compared with the grouped arginine/arginineand proline/proline genotypes (p=0.05.Conclusion: Our findings suggested that colorectal adenocarcinomas arising in individualswith the p53 codon 72 arginine/proline heterozygosity are more prone tomicrosatellite instability than those with other p53 genotypes. In our study, MSI wasimportant in the carcinogenesis of sporadic colorectal cancer arising in pro/arg heterozygotes.

  13. Prognostic value of BRAF and KRAS mutation status in stage II and III microsatellite instable colon cancers

    NARCIS (Netherlands)

    de Cuba, E. M. V.; Snaebjornsson, P.; Heideman, D. A. M.; van Grieken, N. C. T.; Bosch, L.J.W.; Fijneman, R. J. A.; Belt, E.; Bril, H.; Stockmann, H. B. A. C.; Hooijberg, E.; Punt, C. J. A.; Koopman, M.; Nagtegaal, I. D.; Coupe, V. H. M.; Carvalho, B.; Meijer, G. A.

    2016-01-01

    Microsatellite instability (MSI) has been associated with favourable survival in early stage colorectal cancer (CRC) compared to microsatellite stable (MSS) CRC. The BRAF V600E mutation has been associated with worse survival in MSS CRC. This mutation occurs in 40% of MSI CRC and it is unclear wheth

  14. Interactions between microsatellite instability and human gut colonization by Escherichia coli in colorectal cancer.

    Science.gov (United States)

    Gagnière, Johan; Bonnin, Virginie; Jarrousse, Anne-Sophie; Cardamone, Emilie; Agus, Allison; Uhrhammer, Nancy; Sauvanet, Pierre; Déchelotte, Pierre; Barnich, Nicolas; Bonnet, Richard; Pezet, Denis; Bonnet, Mathilde

    2017-01-16

    Recent studies suggest that colonization of colonic mucosa by pathogenic Escherichia coli (E. coli) could be involved in the development of colorectal cancer (CRC), especially through the production of genotoxins such as colibactin and/or by interfering with the DNA mismatch repair (MMR) pathway which leads to microsatellite instability (MSI). This work, performed on 88 CRC patients, revealed a significant increase in E. coli colonization in the MSI CRC phenotype. In the same way, E. coli persistence and internalization were increased in vitro in MMR-deficient cells. Moreover, we demonstrated that colibactin-producing E. coli induce inhibition of the MLH1 MMR proteins, which could lead to genomic instability. However, colibactin-producing E. coli were more frequently identified in microsatellite stable (MSS) CRC. This work suggests differences in the involvement of colibactin-producing E. coli in colorectal carcinogenesis according to the CRC phenotype. Further host/pathogens interactions studies should take into account CRC phenotypes.

  15. Microsatellite instability at tetranucleotide repeats in sporadic colorectal cancer in Japan.

    Science.gov (United States)

    Yamada, Kanae; Kanazawa, Shinsaku; Koike, Junichi; Sugiyama, Hisahiko; Xu, Can; Funahashi, Kimihiko; Boland, C Richard; Koi, Minoru; Hemmi, Hiromichi

    2010-02-01

    Most tumors of patients with Lynch syndrome and a fraction of sporadic colorectal cancers (CRCs) exhibit high levels of microsatellite instability (MSI) at mono- and dinucleotide repeat loci. A different type of instability, elevated microsatellite alterations at selected tetranucleotide repeats (EMAST) has been found in non-colonic cancers. Our previous study demonstrated that EMAST is common in sporadic CRC. Here, we focused on the relationships between EMAST and other genomic instability parameters or clinicopathological features in an unselected series of 88 sporadic CRCs. Of the tumors in the sample, 4 (4.5%) were MSI-high (MSI-H), 9 (10.2%) were MSI-low (MSI-L) and 75 (85.2%) were microsatellite stable. EMAST status was determined using 7 EMAST markers. Fifty-three (60.2%) tumors without MSI-H showed instability at >or=1 EMAST loci. All 4 MSI-H tumors showed instability at several EMAST loci. Instability profiles of MSI-H tumors at EMAST loci were more complex than those of non-MSI-H tumors. A tendency of positive association was observed between MSI-L and EMAST (P=0.023). The frequency of loss of heterozygosity (LOH) for the 14 loci in EMAST-positive tumors was significantly higher than negative tumors (P=0.048). Among the clinicopathological parameters, only tumor location at the distal colon was associated with EMAST-negative tumors (P=0.0084, one-tailed). A relatively higher frequency of well-differentiated adenocarcinomas was observed in EMAST tumors as opposed to non-EMAST tumors, though the survival rate was similar. These results suggest that overlapping mechanisms that cause MSI-L, EMAST and LOH in CRCs may exist.

  16. The immunogenicity of colorectal cancers with high-degree microsatellite instability

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    Dorudi Sina

    2005-05-01

    Full Text Available Abstract Background High-degree microsatellite instability (MSI-H is a feature of approximately 15% of sporadic colorectal cancers. Patients with MSI-H cancers have been reported to have a better prognosis than those with non-MSI-H cancers. The MSI-H subset is also characterised by a dense infiltrate of intra-epithelial lymphocytes and the hypothesis that the latter represents an efficacious immune response contributing to improved outcome is very attractive. Methods Data for this review were identified by searches of MEDLINE, PubMed, and cross references from relevant articles using the search terms 'microsatellite instability', 'colorectal cancer' and 'immunology', 'immune response' or 'immunogenicity'. Results A total of 38 articles were identified by the search criteria and a further 95 articles by cross-referencing. The relevance of the articles to be interviewed was established by hand searching. Out of a total of 133 articles identified, 47 articles were rejected due to lack of relevance. A total of 86 articles were included in the review, pertaining to microsatellite instability in colorectal cancer, and immune mechanisms in colorectal cancer. Conclusion It is suggested that this distinct group of colorectal cancers may have inherent immunogenic properties and that further elucidation of these may be invaluable to the development of successful immunotherapy.

  17. Microsatellite instability in colorectal cancer and association with thymidylate synthase and dihydropyrimidine dehydrogenase expression

    Directory of Open Access Journals (Sweden)

    Kruhøffer Mogens

    2009-01-01

    Full Text Available Abstract Background Microsatellite instability (MSI refers to mutations in short motifs of tandemly repeated nucleotides resulting from replication errors and deficient mismatch repair (MMR. Colorectal cancer with MSI has characteristic biology and chemosensitivity, however the molecular basis remains unclarified. The association of MSI and MMR status with outcome and with thymidylate synthase (TS and dihydropyrimidine dehydrogenase (DPD expression in colorectal cancer were evaluated. Methods MSI in five reference loci, MMR enzymes (hMSH2, hMSH6, hMLH1 and hPMS2, thymidylate synthase (TS and dihydropyrimidine dehydrogenase (DPD expression were assessed in paraffin embedded tumor specimens, and associated with outcome in 340 consecutive patients completely resected for colorectal cancer stages II-IV and subsequently receiving adjuvant 5-fluorouracil therapy. Results MSI was found in 43 (13.8% tumors. Absence of repair protein expression was assessed in 52 (17.0% tumors, which had primarily lost hMLH1 in 39 (12.7%, hMSH2 in 5 (1.6%, and hMSH6 in 8 (2.6% tumors. In multivariate analysis MSI (instable compared to MSS (stable tumors were significantly associated with lower risk of recurrence (hazard ratio (HR = 0.3; 95% CI: 0.2–0.7; P = 0.0007 and death (HR = 0.4; 95% CI: 0.2–0.9; P = 0.02 independently of the TS and DPD expressions. A direct relationship between MSI and TS intensity (P = 0.001 was found, while there was no significant association with DPD intensity (P = 0.1. Conclusion The favourable outcome of MSI colorectal carcinomas is ascribed mainly to the tumor biology and to a lesser extent to antitumor response to 5-fluorouracil therapy. There is no evidence that differential TS or DPD expression may account for these outcome characteristics.

  18. Telomerase activity in colorectal cancer, prognostic factor and implications in the microsatellite instability pathway

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    AIM: To determine whether the telomerase activity is related to the Microsatellite instability (MSI) genetic pathway and whether it means a difference in the survival.METHODS: The population consisted of 97 colorectal cancer patients. MSI determination was performed in accordance with the NCI criteria using PCR and Genescan. Telomerase activity was determined by the TRAP-assay, an ELISA procedure based on the amplification of telomeric repeat sequences.RESULTS: 6.2% showed high MSI (MSI-H), 10.3% showed low MSI (MSI-L) and 83.5% did not show this alteration (MSS). Positive telomerase activity was detected in 92.8% of the patients. 83.3% of MSI-H tumors showed positive telomerase against 93.8% of MSS tumors. In the overall survival analysis the absence of telomerase activity conferred a better prognosis.CONCLUSION: Previous works have shown that tumors which develop via the MSI pathway present a better prognosis. No link between telomerase activity and MSI status is observed, although sample sizes are small.Patients with telomerase negative tumors had better overall survival than patients with telomerase positive tumors.

  19. [Molecular Pathology of Colorectal Cancer, Microsatellite Instability - the Detection, the Relationship to the Pathophysiology and Prognosis].

    Science.gov (United States)

    Brychtová, V; Šefr, R; Hrstka, R; Vídeňská, P; Bencsiková, B; Hanáková, B; Zdražilová Dubská, L; Nenutil, R; Budinská, E

    2017-01-01

    Colorectal carcinoma (CRC) is third most common cancer worldwide with very heterogenous character. In most cases, it is caused by sporadic events leading to disruption of epithelial cells of the colon. The minority evolves from germline mutations associated with hereditary cancer syndromes. Mechanisms leading to mutations of oncogenes, tumour suppressors and genes of DNA repair mechanisms include: 1. chromosomal instability, 2. microsatellite instability and 3. CpG island methylator phenotype. Microsatellite instability (MSI) usually arises from a germline mutation of the component of mismatch repair machinery (MMR) or somatic hypermethylation of the MLH1 promoter. The diagnostic approaches include PCR methods and immunohistochemistry for the detection of the loss of MMR part. The aim of our study was to characterise the cohort of ongoing study of gut microbiome in CRC patients considering MSI. The consecutive study group consisted of 103 patients diagnosed with CRC. The cohort consisted of 45 women (43.7%) and 58 men (56.3%). Patient age at the time of diagnosis was within the range of 31-83 years (median 66 years). The expression of MLH1, MSH2, MSH6 and PMS2 proteins was detected by immunohistochemical method and the positivity was correlated with the stage and the localization of the primary tumour. The MMR status was determined by immunohistochemical method in 43 (41.7%) from the existing total of 103 patients. MSI was detected in 11 (25.6%) cases while 32 (74.4%) were microsatellite stabile. With the respect to cancer clasification the most cases of MSI was detected in stage II (8 cases; 22.2%). In regard to localization of primary tumour, MSI rather correlates to right site CRC, while microsatellite stable tumours do not show any site preferences. Considering low number of MMR status determination in study group, statistic evaluation is inaccurate so far. However there is a trend in our cohort in relation to determination of the portion of MSI in CRC

  20. A substantial proportion of microsatellite-unstable colon tumors carry TP53 mutations while not showing chromosomal instability

    NARCIS (Netherlands)

    Westra, JL; Boven, LG; van der Wes, P; Faber, H; Sikkema, B; Schaapveld, M; Dijkhuizen, T; Hollema, H; Buys, CHCM; Plukker, JTM; Kok, K; Hofstra, RMW

    2005-01-01

    Chromosomal instability in colon tumors implies the presence of numerical and structural chromosome aberrations and is further characterized by the absence of microsatellite instability and the occurrence of KRAS and/or TP53 mutations. In a previous screening of 194 colon tumors for both microsatell

  1. A substantial proportion of microsatellite-unstable colon tumors carry TP53 mutations while not showing chromosomal instability

    NARCIS (Netherlands)

    Westra, JL; Boven, LG; van der Wes, P; Faber, H; Sikkema, B; Schaapveld, M; Dijkhuizen, T; Hollema, H; Buys, CHCM; Plukker, JTM; Kok, K; Hofstra, RMW

    2005-01-01

    Chromosomal instability in colon tumors implies the presence of numerical and structural chromosome aberrations and is further characterized by the absence of microsatellite instability and the occurrence of KRAS and/or TP53 mutations. In a previous screening of 194 colon tumors for both microsatell

  2. Microsatellite data analysis for population genetics.

    Science.gov (United States)

    Kim, Kyung Seok; Sappington, Thomas W

    2013-01-01

    Theories and analytical tools of population genetics have been widely applied for addressing various questions in the fields of ecological genetics, conservation biology, and any context where the role of dispersal or gene flow is important. Underlying much of population genetics is the analysis of variation at selectively neutral marker loci, and microsatellites continue to be a popular choice of marker. In recent decades, software programs to estimate population genetics parameters have been developed at an increasing pace as computational science and theoretical knowledge advance. Numerous population genetics software programs are presently available to analyze microsatellite genotype data, but only a handful are commonly employed for calculating parameters such as genetic variation, genetic structure, patterns of spatial and temporal gene flow, population demography, individual population assignment, and genetic relationships within and between populations. In this chapter, we introduce statistical analyses and relevant population genetic software programs that are commonly employed in the field of population genetics and molecular ecology.

  3. Regional bias of intratumoral genetic heterogeneity of nucleotide repeats in colon cancers with microsatellite instability.

    Science.gov (United States)

    Choi, Youn Jin; Kim, Min Sung; An, Chang Hyeok; Yoo, Nam Jin; Lee, Sug Hyung

    2014-10-01

    Intratumoral heterogeneity (ITH) may produce regional biases in genotype and phenotype evaluation in a single tumor and may impede proper cancer diagnosis. To evaluate the extent of ITH in colorectal cancer (CRC) with microsatellite instability (MSI), we obtained 4-7 biopsies from 39 CRCs followed by MSI analysis either using the Bethesda MSI evaluation system or Promega system with 5 mononucleotide markers. We found decreased prevalence of MSI (+) by the Promega system compared to the Bethesda system. The overall discordance between the two systems was 54 %. In contrast to the previous studies that had shown discordance only in low MSI (MSI-L), our results showed the discordance not only in MSI-L, but also in high MSI (MSI-H) cases. Among the MSI (+) CRCs, ITH of MSI status was identified in 41.7 % of CRC by the Bethesda system and 22.2 % by the Promega system. In terms of MSI markers, the ITH originated from dinucleotide markers in most cases (69 %), but it originated from mononucleotide markers (31 %) as well. Pooling of DNA from a regional biopsy with MSI (+) with additional biopsies from stable MSI (MSS) showed that this approach was beneficial to increase the sensitivity of MSI detection. Our results indicate that ITH of MSI phenotype by the Bethesda system is more overestimated than previously identified. However, because there was considerable ITH of MSI subtypes and markers even by the Promega system, our data suggest that analysis of MSI status in multiple regional biopsies is needed for a better evaluation of MSI status in CRC.

  4. Role of microsatellites instability in carcinogenesis of postcricoid carcinoma on top of plummer-vinson syndrome.

    Science.gov (United States)

    Badawy, Badawy Shahat; Ahmad, Mohamed Abdel-Kader; Sayed, Ramadan Hashem; Habib, Tito Naeem

    2010-10-01

    To develop a molecular pattern that might help in understanding carcinogenesis of postcricoid carcinoma (PCC) on top of Plummer-Vinson syndrome (PVS) in a prospective controlled study. Twenty-four patients with PVS were diagnosed and followed up over a 4 year period, during which eight of them showed malignant change to PCC. Twenty volunteers free of neoplastic diseases were included as a control group. In the two groups, DNA extraction from mononuclear peripheral blood cells, and analysis of loss of heterozygosity (LOH) and microsatellite instability (MSI) using six paired simple tandem repeats (STRs) primers were done. The molecular weight of each STRs locus was scored and statistical correlations were performed. LOH occurred in 55.6 and 72.9% of PVS and PCC cases compared to 25% of control group. At loci D17S695, D9S753 and D9S171, LOH occurred in 54.2, 66.7, and 70.8% of PVS cases; and in 62.5% of PCC cases for each locus compared to 15, 25 and 45% of control cases. D3S1286 and CFS1-R displayed the highest frequency of LOH in PCC (100% for each) while recorded in 58.3 and 33.3% in PVS compared to 30 and 0% in control cases. Certain genetic events tend to occur as early and late events in malignant change of PVS to PCC. Detection of these events may help in understanding carcinogenesis and in early detection of malignancy. CFS1-R is the most informative marker of tumor progression.

  5. Microsatellite instability in pulmonary adenocarcinomas: a comprehensive study of 480 cases.

    Science.gov (United States)

    Warth, Arne; Körner, Sandrina; Penzel, Roland; Muley, Thomas; Dienemann, Hendrik; Schirmacher, Peter; von Knebel-Doeberitz, Magnus; Weichert, Wilko; Kloor, Matthias

    2016-03-01

    A major molecular pathway of genetic instability in cancer is DNA mismatch repair deficiency, leading to accumulation of numerous mutations at repetitive DNA sequence stretches (microsatellites), known as high-level microsatellite instability (MSI-H). In colorectal cancer, MSI-H tumors show a clinical behavior different from microsatellite-stable (MSS) tumors. Data about the prevalence of MSI among non-small cell lung cancer (NSCLC) are conflicting, and clinical relevance of MSI is largely unknown. We analyzed a series of 480 pulmonary adenocarcinomas (ADC) for MSI using a sensitive mononucleotide marker panel (BAT25, BAT26, and CAT25). Positive cases were further analyzed by immunohistochemical staining for DNA mismatch repair proteins. Results were correlated with clinicopathological variables. MSI-H was detected in 4/480 (0.8 %) cases. In none of these, a background of Lynch syndrome was found. Three of the patients developed a metachronous carcinoma (esophagus, pancreas, and kidney). All MSI-H cases were stage I and occurred in smokers/ex-smokers. Mutations were found in EGFR (n = 2), KRAS (n = 1), or BRAF (n = 1). MSI-H neoplasms had a higher proliferative activity (38.7 %) than MSS neoplasms (28.3 %). Mean overall survival for MSS and MSI-H cases was 64.8 (CI 60.4-69.1) and 47.1 (CI 21-73.2) months, respectively. When specific mononucleotide marker panels are applied, the MSI-H phenotype is rare and predominantly found in early stage ADC of smokers. However, the frequency of MSI-H is in the range of other relevant molecular alterations. In the era of precision therapy, associations with distinct clinicopathological variables merit further investigation.

  6. Telomere erosion is independent of microsatellite instability but related to loss of heterozygosity in gastric cancer

    Institute of Scientific and Technical Information of China (English)

    Dian-Chun Fang; Shi-Ming Yang; Xiao-Dong Zhou; Dong-Xu Wang; Yuan-Hui Luo

    2001-01-01

    AIM To correlate the length of the telomere to microsatellite instability (MSI) and loss of heterozygosity (LOH) of APC, MCC and DCC genes in gastric carcinomas. METHODS Telomeric restriction fragment (TRF) length of gastric cancer was measured with Southern blot. LOH of APC, MCC and DCC genes, microsatellite instability (MSI) and frameshift mutation of hMSH6, TGF-βR Ⅱ and BAX genes were analyzed by PCR-based methods. RESULTS Sixty-eight cases of sporadic gastric carcinoma were studied for MSI using five microsatellite markers. MSI in at least one locus was detected in 17 (25%) of 68 tumors analyzed. Frameshift mutations of hMSH6, TGF-βR Ⅱ and BAX were detected in 2,6 and 3 of gastric carcinomas respectively showing high MSI (≥ 2 loci, n = 8), but none was found in those showing Iow MSI (only one locus, n = 9) or MSS (tumor lacking MSI or stable, n = 51). Thirty-five cases, including all high MSI and Iow MSl, were studied for TRF. The mean TRF length was not correlated with clinicopathological parameters.No association was observed between TRF length and MSI or frameshift mutation. On the contrary, LOH at the DCC locus was related to telomere shortening (P< 0.01). This tendency was also observed in APC and MCC genes,although there was no statistical significance. CONCLUSION The development of gastric cancer can arise through two different genetic pathways. In high MSI gastric cancers, defective mismatch repair allows mutations to accumulate and generate the high MSI phenotype. In gastric cancers showing either Iow MSI or MSS, multiple deletions may represent the LOH pathway.Telomere erosion is independent of high MSI phenotype but related to the LOH pathway in gastric cancer.

  7. Mutations in the WTX - gene are found in some high-grade microsatellite instable (MSI-H colorectal cancers

    Directory of Open Access Journals (Sweden)

    Scheel Silvio K

    2010-08-01

    Full Text Available Abstract Background Genetically, colorectal cancers (CRCs can be subdivided into tumors with chromosomal instability (CIN or microsatellite instability (MSI. In both types of CRCs genes that are involved in the degradation of β-CATENIN are frequently mutated. Whereas in CIN CRCs APC (Adenomatous Polyposis Coli is affected in most cases, high grade MSI (MSI-H CRCs frequently display mutations in various genes, like the APC-, AXIN2- or CTNNBI (β-CATENIN gene itself. Recently in Wilms tumors, WTX (Wilms tumor gene on the X-chromosome was discovered as another gene involved in the destruction of β-CATENIN. As the WTX-gene harbors a short T6-microsatellite in its N-terminal coding region, we hypothesized that frameshift-mutations might occur in MSI-H CRCs in the WTX gene, thus additionally contributing to the stabilization of β-CATENIN in human CRCs. Methods DNA was extracted from 632 formalin-fixed, paraffin-embedded metastatic CRCs (UICCIV and analyzed for MSI-H by investigating the stability of the highly sensitive microsatellite markers BAT25 and BAT26 applying fluorescence capillary electrophoresis (FCE. Then, in the MSI-H cases, well described mutational hot spot regions from the APC-, AXIN2- and CTNNBI genes were analyzed for genomic alterations by didesoxy-sequencing while the WTX T6-microsatellite was analyzed by fragment analysis. Additionally, the PCR products of T5-repeats were subcloned and mutations were validated using didesoxy-sequencing. Furthermore, the KRAS and the BRAF proto-oncogenes were analyzed for the most common activating mutations applying pyro-sequencing. mRNA expression of WTX from MSI-H and MSS cases and a panel of colorectal cancer cell lines was investigated using reverse transcription (RT- PCR and FCE. Results In our cohort of 632 metastatic CRCs (UICCIV we identified 41 MSI-H cases (6.5%. Two of the 41 MSI-H cases (4.8% displayed a frameshift mutation in the T6-repeat resulting in a T5 sequence. Only one case, a

  8. Cadmium-induced microsatellite instability in the kidneys and leukocytes of C57BL/6J mice.

    Science.gov (United States)

    Du, Xiaoyan; Lan, Tianfeng; Yuan, Bao; Chen, Jian; Hu, Jinping; Ren, Wenzhi; Chen, Zhenwen

    2015-01-01

    Cadmium is a cytotoxic, carcinogenic, and mutagenic industrial product or byproduct. The correlation between metal exposure and microsatellite instability (MSI) has been reported by several groups. In the present study, 50 C57BL/6J mice at 6 weeks of age were divided into five groups and intraperitoneally injected with 0, 0.25, 0.5, 1, or 2 mg/kg cadmium chloride quaque die alterna for 4 weeks. Then, the liver, kidney, testis, leukocytes, bone marrow, and small intestine were collected from the treated mice and weighed. Portions of these tissues were fixed for further histological analysis, and the remaining tissues were subjected to genomic DNA extraction for the analysis of a panel of 42 microsatellite markers. The liver and testis weight coefficients were significantly changed in the 1 and 2 mg/kg cadmium chloride-treated groups compared with the control group. Simultaneously, severe histopathologic changes in the liver and kidneys, along with a complete disorganization of testicular structure and obvious severe necrosis in the testes were observed in the cadmium-treated group. The cadmium accumulated in the liver and kidneys of the mice in all cadmium-treated groups; the tissue cadmium concentrations were significantly higher than those in the control group. After STR scanning, MSI was found at three loci (D15Mit5, D10Mit266, and DxMit172) in the kidneys and leukocytes of mice in the lower dose groups (0.25 and 0.5 mg/kg). In summary, we have successfully established a sub-chronic cadmium exposure model and confirmed that cadmium exposure can induce MSI in mice. We also identified two loci that could be regarded as "hotspots" of microsatellite mutation in mice.

  9. Detection of frameshift mutations of RIZin gastric cancers with microsatellite instability

    Institute of Scientific and Technical Information of China (English)

    Kai-Feng Pan; You-Yong Lu; Wan-Guo Liu; Lian Zhang; Wei-Cheng You

    2004-01-01

    AIM: To study the frameshift mutations of the retinoblastomaprotein-interacting zinc finger gene RIZ in gastric cancer with microsatellite instability, and to identify two coding polyadenosine tracts of RIZ.METHODS: Frameshift mutations at (A)8 and (A)9 tracts of RIZwere detected in 70 human gastric cancer (HGC) specimens by DHPLC and DNA sequencing. Microsatelliteinstability (MSI) status was assessed by two mononucleotide markers, BAT26 and BAT25, by means of denaturing highperformance liquid chromatography (DHPLC).RESULTS: In 70 HGC samples, 8 (11.4%) were found positivefor instabilities at BAT26 and BAT25. In 7 of the 8 cases with instabilities at both BAT26 and BAT25 (MSI-H), 1 was unstable at BAT26 but stable at BAT25. Frameshift mutations were identified in 4 (57.1%) of the 7 samples with MSI-Hin the (A)9 tract of RIZ without mutations in the (A)8 tract.In contrast, frameshift mutations were found in neither of the polyadenosine tracts in 63 samples of MSI-L or MSI stable tumors. Pro704 LOH detection in 4 cases with frameshift mutations did not find LOH in these cases.CONCLUSION: Frameshift mutations of RIZ may play an important role in gastric cancers with MSI.

  10. Influence of race on microsatellite instability and CD8+ T cell infiltration in colon cancer.

    Directory of Open Access Journals (Sweden)

    John M Carethers

    Full Text Available African American patients with colorectal cancer show higher mortality than their Caucasian counterparts. Biology might play a partial role, and prior studies suggest a higher prevalence for microsatellite instability (MSI among cancers from African Americans, albeit patients with MSI cancers have improved survival over patients with non-MSI cancers, counter to the outcome observed for African American patients. CD8+ T cell infiltration of colon cancer is postively correlated with MSI tumors, and is also related to improved outcome. Here, we utilized a 503-person, population-based colon cancer cohort comprising 45% African Americans to determine, under blinded conditions from all epidemiological data, the prevalence of MSI and associated CD8+ T cell infiltration within the cancers. Among Caucasian cancers, 14% were MSI, whereas African American cancers demonstrated 7% MSI (P = 0.009. Clinically, MSI cancers between races were similar; among microsatellite stable cancers, African American patients were younger, female, and with proximal cancers. CD8+ T cells were higher in MSI cancers (88.0 vs 30.4/hpf, P<0.0001, but was not different between races. Utilizing this population-based cohort, African American cancers show half the MSI prevalence of Caucasians without change in CD8+ T cell infiltration which may contribute towards their higher mortality from colon cancer.

  11. Clinical Significance and Prognostic Relevance of Microsatellite Instability in Sporadic Colorectal Cancer Patients

    Directory of Open Access Journals (Sweden)

    Angelika Copija

    2017-01-01

    Full Text Available Microsatellite instability (MSI is a marker of the replication error phenotype. It is caused by impaired DNA mismatch repair processes (MMR, resulting in ineffectiveness of the mechanisms responsible for the DNA replication precision and postreplicative DNA repair. MSI underlies the pathogenesis of 10%–20% of colorectal cancer (CRC cases. The data about the potential value of MMR status as a predictive factor for 5-fluorouracil (FU-based chemotherapy remain unclear. According to National Comprehensive Cancer Network updated guidelines, MSI testing is recommended for all patients with stage II CRC because patients with MSI-H (high-frequency MSI tumour may have a good prognosis and obtain no benefit from 5-FU-based adjuvant chemotherapy. The significance of the MSI status as a predictive factor for patients with metastatic disease was not confirmed. The association between the MSI status and the efficacy of the therapy based on anti-programmed death-1 receptor inhibitors requires further studies.

  12. Inhibitory Effect of Sodium Selenite on Microsatellite Instability of RER+ Colorectal Cancer Cells

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Objective Investigation of the effects of sodium selenite on genetic instability of human tumor cells via its role in alteration of microsatellite sequence(MS) of RER+ (replication error) colon cancer cell line. Methods RER+ and RER- human colon cancer cell lines, RKO or SW480, were used as hosts for lipofection with pcmv-car in which a foreign(CA)14 repeat was inserted in the coding sequence of LacZ reporter gene, resulting in misreading LacZ frame. Any mutation which makes the base number of (CA)14 tract to be 3-fold will resume the normal reading frame of the reporter gene, and thus lead to expression and production of bioactive β-galactosidase. To test the effect of selenite on MI(microsatellite instability) of tumor cells, a series of concentrations of selenite were administered in cell culture in vitro. Variable expression of bioactive β-galactosidase of transfectant cells resulted from selenite administration was measured by A reading at λ410 after X-gal staining; Results Mutations of the exogenous(CA)14 developed and maintained in pcmv-car transfectant RKO cells but not in SW480 cells. It was found that blue cell frequency of RKO transfectant cells was markedly reduced after incubation of cells with 5 μmol/L of selenite for 5 days, at which concentration it was not toxic to cell growth. However, selenite at lower concentration of 1μmol/L didn′t exhibit suppression of blue cell rate until cell′s exposure to it for a longer period up to 5 weeks or more. Conclusion Our data showed that selenite displayed inhibitory effect on MI of human cancer cells and thus demonstrated its beneficial role in stabilization of human genomic DNA.

  13. Nuclear and mitochondrial DNA microsatellite instability in hepatocellular carcinoma in Chinese

    Institute of Scientific and Technical Information of China (English)

    Dian-Chun Fang; Li Fang; Rong-Quan Wang; Shi-Ming Yang

    2004-01-01

    AIM: To study the nuclear microsatellite instability (nMSI)at BAT26 and mitochondral microsalellite instability (mtMSI)in the occurrence and development of hepatocellular carcinoma and the relationship between nMSI and mtMSI.METHODS: nMSI was observed with PCR and mtMSI with PCR-SSCP in 52 cases of hepatocellular carcinoma.RESULTS: mtMSI was detected in 11 out of the 52 cases of hepatocellular carcinoma (21.2%). Among the 11 cases of hepatocellular carcinoma with mtMSI, 7 occured in one locus and 4 in 2 loci. The frequency of mtMSI in the 52 cases of hepatocellular careinoma showed no correlation to sex, age,infection of hepatitis B, liver cirrhosis as well as positive AFP of the patients (P>0.05). In addition, nMSI was detected in 3 out of 52 cases of hepatocellular carcinoma (5.8%) and there was no correlation of the incidence of mtMSI to that CONCLUSION: mtMSI may be involved in the coccurrence and development of hepatocellular carcinoma and it is independent of nMSI.

  14. Microsatellite analysis of medfly bioinfestations in California.

    Science.gov (United States)

    Bonizzoni, M; Zheng, L; Guglielmino, C R; Haymer, D S; Gasperi, G; Gomulski, L M; Malacrida, A R

    2001-10-01

    The Mediterranean fruit fly, Ceratitis capitata, is a destructive agricultural pest with a long history of invasion success. This pest has been affecting different regions of the United States for the past 30 years, but a number of studies of medfly bioinfestations has focused on the situation in California. Although some progress has been made in terms of establishing the origin of infestations, the overall status of this pest in this area remains controversial. Specifically, do flies captured over the years represent independent infestations or the persistence of a resident population? We present an effort to answer this question based on the use of multilocus genotyping. Ten microsatellite loci were used to analyse 109 medflies captured in several infestations within California between 1992 and 1998. Using these same markers, 242 medflies from regions of the world having 'established' populations of this pest including Hawaii, Guatemala, El Salvador, Ecuador, Brazil, Argentina and Peru, were also analysed. Although phylogenetic analysis, amova analysis, the IMMANC assignment test and geneclass exclusion test analysis suggest that some of the medflies captured in California are derived from independent invasion events, analysis of specimens from the Los Angeles basin provides support for the hypothesis that an endemic population, probably derived from Guatemala, has been established.

  15. Mutation rate analysis at 19 autosomal microsatellites.

    Science.gov (United States)

    Qian, Xiao-Qin; Yin, Cai-Yong; Ji, Qiang; Li, Kai; Fan, Han-Ting; Yu, Yan-Fang; Bu, Fan-Li; Hu, Ling-Li; Wang, Jian-Wen; Mu, Hao-Fang; Haigh, Steven; Chen, Feng

    2015-07-01

    Previous studies have demonstrated that a large sample size is needed to reliably estimate population- and locus-specific microsatellite mutation rates. Therefore, we conducted a long-term collaboration study and performed a comprehensive analysis on the mutation characteristics of 19 autosomal short tandem repeat (STR) loci. The STR loci located on 15 of 22 autosomal chromosomes were analyzed in a total of 21,106 samples (11,468 parent-child meioses) in a Chinese population. This provided 217,892 allele transfers at 19 STR loci. An overall mutation rate of 1.20 × 10(-3) (95% CI, 1.06-1.36 × 10(-3) ) was observed in the populations across 18 of 19 STR loci, except for the TH01 locus with no mutation found. Most STR mutations (97.7%) were single-step mutations, and only a few mutations (2.30%) comprised two and multiple steps. Interestingly, approximately 93% of mutation events occur in the male germline. The mutation ratios increased with the paternal age at child birth (r = 0.99, ptesting, kinship analysis, and population genetics.

  16. Microsatellite instability as prognostic marker in bladder tumors: a clinical significance

    Directory of Open Access Journals (Sweden)

    Mittal RD

    2005-01-01

    Full Text Available Abstract Background Carcinoma of urinary bladder is one of the leading causes of death in India. Successful treatment of bladder cancer depends on the early detection & specific diagnostic approaches. In the present study, microsatellite instability (MSI has been evaluated as a prognostic marker in patients with superficial urinary bladder cancer in lower urinary tract for determining risk of recurrence. Methods A total of 44 patients with bladder tumors diagnosed with Transitional Cell Carcinomas [TCC] from lower urinary tract were selected for the study. Tumors were staged and graded according to AJCC-UICC (1997 classification and patients were followed with cystoscopy as per the protocol. Polymerase chain reaction (PCR was done to amplify microsatellite sequences at mononucleotide BAT – 26, BAT – 40, TGFβ RII, IGFIIR, hMSH3, BAX and dinucleotide D2S123, D9S283, D9S1851 and D18S58 loci in blood (control and tumor DNA. PCR products were separated on 8% denaturing polyacrylamide gel and visualized by autoradiography. Results MSI was observed in 72.7% of tumors at BAT – 26, BAT – 40, D2S123, D9S283, D9S1851 and D18S58 loci. Good association of MSI was seen with tumor stage and grade. MSI – High (instability at > 30% of loci was frequently observed in high stage (40.6% and high grade (59.4% tumors. Of 24 tumors of Ta-T1 stage with different grades, 11 (9/18 high grade and 2/6 low grade tumors recurred in the mean duration of 36 months. MSI positivity was significantly high in patients who had one or more recurrences (p = 0.02 for high grade and 0.04 for low grade tumors. Conclusions MSI may be an independent prognostic marker for assessing risk of recurrence in superficial tumors irrespective of the grade. Further studies on progression would help in stratifying the patients of T1G3 for early cystectomy vs bladder preservation protocol.

  17. Low Level of Microsatellite Instability Correlates with Poor Clinical Prognosis in Stage II Colorectal Cancer Patients

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    Ehsan Nazemalhosseini Mojarad

    2016-01-01

    Full Text Available The influence of microsatellite instability (MSI on the prognosis of colorectal cancer (CRC requires more investigation. We assessed the role of MSI status in survival of individuals diagnosed with primary colorectal cancer. In this retrospective cross-sectional study the MSI status was determined in 158 formalin-fixed paraffin-embedded tumors and their matched normal tissues from patients who underwent curative surgery. Cox proportional hazard modeling was performed to assess the clinical prognostic significance. In this study we found that MSI-H tumors were predominantly located in the colon versus rectum (p=0.03, associated with poorer differentiation (p=0.003 and TNM stage II/III of tumors (p=0.02. In CRC patients with stage II, MSI-L cases showed significantly poorer survival compared with patients who had MSI-H or MSS tumors (p=0.04. This study indicates that MSI-L tumors correlate with poorer clinical outcome in patients with stage II tumors (p=0.04 or in tumors located in the colon (p=0.02. MSI-L characterizes a distinct subgroup of CRC patients who have a poorer outcome. This study suggests that MSI status in CRC, as a clinical prognostic marker, is dependent on other factors, such as tumor stage and location.

  18. PAI-1 4G/5G repeat is a target in gastric carcinomas with microsatellite instability.

    Science.gov (United States)

    Palmirotta, Raffaele; Guadagni, Fiorella; Savonarola, Annalisa; Ludovici, Giorgia; Nesi, Gabriella; Palli, Domenico; Falchetti, Mario; Ottini, Laura

    2011-06-01

    The plasminogen activator inhibitor-1 (PAI-1) plays an important role in the pathogenesis of cancer. The 4G/5G promoter polymorphism of PAI-1 is potentially involved in regulating gene transcription. To explore the role of the PAI-1 4G/5G repeat as target of microsatellite instability (MSI), 50 gastric carcinomas (GCs), characterized for MSI, were screened. PAI-1 4G/5G was analysed by direct sequencing. Allelic imbalance was observed in 5 of the 50 (10%) GCs. Specifically, 2 cases (40%) harboured a G deletion and 3 (60%) a G insertion in tumour compared to normal DNA. These five cases were included in the subgroup of 20 GCs (25%) with high level of MSI (MSI-H). A statistically significant association emerged between PAI-1 mutations and MSI-H status (p=0.0073). The frequency of PAI-1 mutations was also evaluated, together with other known target genes, by analysing MSI-H GCs for mutations at selected coding repeats within genes controlling cell growth, apoptosis and DNA repair. Overall, mutation frequency ranged from 56.3% to 5.3%. The frequency of PAI-1 mutations here reported in MSI-H GCs is, accordingly, comparable with values obtained for real targets. The relatively high incidence of PAI-1 mutations is suggestive of a positive pressure towards selection in MSI-H GCs. Copyright © 2010 Editrice Gastroenterologica Italiana S.r.l. Published by Elsevier Ltd. All rights reserved.

  19. Eguchipsammia fistula Microsatellite Development and Population Analysis

    KAUST Repository

    Mughal, Mehreen

    2012-12-01

    Deep water corals are an understudied yet biologically important and fragile ecosystem under threat from recent increasing temperatures and high carbon dioxide emissions. Using 454 sequencing, we develop 14 new microsatellite markers for the deep water coral Eguchipsammia fistula, collected from the Red Sea but found in deep water coral ecosystems globally. We tested these microsatellite primers on 26 samples of this coral collected from a single population. Results show that these corals are highly clonal within this population stemming from a high level of asexual reproduction. Mitochondrial studies back up microsatellite findings of high levels of genetic similarity. CO1, ND1 and ATP6 mitochondrial sequences of E. fistula and 11 other coral species were used to build phylogenetic trees which grouped E. fistula with shallow water coral Porites rather than deep sea L. Petusa.

  20. The vigorous immune microenvironment of microsatellite instable colon cancer is balanced by multiple counter-inhibitory checkpoints.

    Science.gov (United States)

    Llosa, Nicolas J; Cruise, Michael; Tam, Ada; Wicks, Elizabeth C; Hechenbleikner, Elizabeth M; Taube, Janis M; Blosser, Richard L; Fan, Hongni; Wang, Hao; Luber, Brandon S; Zhang, Ming; Papadopoulos, Nickolas; Kinzler, Kenneth W; Vogelstein, Bert; Sears, Cynthia L; Anders, Robert A; Pardoll, Drew M; Housseau, Franck

    2015-01-01

    We examined the immune microenvironment of primary colorectal cancer using immunohistochemistry, laser capture microdissection/qRT-PCR, flow cytometry, and functional analysis of tumor-infiltrating lymphocytes. A subset of colorectal cancer displayed high infiltration with activated CD8(+) cytotoxic T lymphocyte (CTL) as well as activated Th1 cells characterized by IFNγ production and the Th1 transcription factor TBET. Parallel analysis of tumor genotypes revealed that virtually all of the tumors with this active Th1/CTL microenvironment had defects in mismatch repair, as evidenced by microsatellite instability (MSI). Counterbalancing this active Th1/CTL microenvironment, MSI tumors selectively demonstrated highly upregulated expression of multiple immune checkpoints, including five-PD-1, PD-L1, CTLA-4, LAG-3, and IDO-currently being targeted clinically with inhibitors. These findings link tumor genotype with the immune microenvironment, and explain why MSI tumors are not naturally eliminated despite a hostile Th1/CTL microenvironment. They further suggest that blockade of specific checkpoints may be selectively efficacious in the MSI subset of colorectal cancer. The findings reported in this article are the first to demonstrate a link between a genetically defined subtype of cancer and its corresponding expression of immune checkpoints in the tumor microenvironment. The mismatch repair-defective subset of colorectal cancer selectively upregulates at least five checkpoint molecules that are targets of inhibitors currently being clinically tested. ©2014 American Association for Cancer Research.

  1. Interrelationship between microsatellite instability and microRNA in gastrointestinal cancer

    Institute of Scientific and Technical Information of China (English)

    Hiroyuki Yamamoto; Yasushi Adachi; Hiroaki Taniguchi; Hiroaki Kunimoto; Katsuhiko Nosho; Hiromu Suzuki; Yasuhisa Shinomura

    2012-01-01

    There is an increasing understanding of the roles that microsatellite instability (MSI) plays in Lynch syndrome (by mutations) and sporadic (by mainly epigenetic changes) gastrointestinal (GI) and other cancers.Deficient DNA mismatch repair (MMR) results in the strong mutator phenotype known as MSI,which is the hallmark of cancers arising within Lynch syndrome.MSI is characterized by length alterations within simple repeated sequences called microsatellites.Lynch syndrome occurs primarily because of germline mutations in one of the MMR genes,mainly MLH1 or MSH2,less frequently MSH6,and rarely PMS2.MSI is also observed in about 15% of sporadic colorectal,gastric,and endometrial cancers and in lower frequencies in a minority of other cancers where it is often associated with the hypermethylation of the MLH1 gene.miRNAs are small noncoding RNAs that regulate gene expression at the posttranscriptional level and are critical in many biological processes and cellular pathways.There is accumulating evidence to support the notion that theinterrelationship between MSI and miRNA plays a key role in the pathogenesis of GI cancer.As a possible new mechanism underlying MSI,overexpression of miR-155 has been shown to downregulate expression of MLH1,MSH2,and MSH6.Thus,a subset of MSI-positive (MSI+)cancers without known MMR defects may result from miR-155 overexpression.Target genes of frameshift mutation for MSI are involved in various cellular functions,such as DNA repair,cell signaling,and apoptosis.A novel class of target genes that included not only epigenetic modifier genes,such as HDAC2,but also miRNA processing machinery genes,including TARBP2 and XPO5,were found to be mutated in MSI+ GI cancers.Thus,a subset of MSI+ colorectal cancers (CRCs) has been proposed to exhibit a mutated miRNA machinery phenotype.Genetic,epigenetic,and transcriptomic differences exist between MSI+ and MSI-cancers.Molecular signatures of miRNA expression apparently have the potential to

  2. DNA microsatellite analysis for tomato genetic differentiation

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    Miskoska-Milevska Elizabeta

    2015-01-01

    Full Text Available Commonly used method for determination of the genetic diversity among the populations is the test for genetic differentiation. DNA microsatellite markers are usually used to investigate the genetic structure of natural populations. The aim of this study was to evaluate the applicability of eight DNA microsatellite loci (LECH13, LE21085, LEMDDNa, LEEF1Aa, LELEUZIP, LE20592, TMS9 and LE2A11 in genetic differentiation of six morphologically different tomato varieties (var. grandifolium from subsp. cultum; var. cerasiforme - red and yellow, var. pruniforme and var. pyriforme from subsp. subspontaneum; and var. racemigerum from subsp. spontaneum. The fragment analyses was performed using Applied Biosystems DNA analyzer (ABI 3130 and GeneMapper® Software program. The data were analysed using the specific program Power Marker Software. The average number of detected alleles was 3,625. Also, the average PIC value for all 8 DNA microsatellites loci was 0,3571. The genetic differentiation test in the researched tomato subspecies showed minor differentiation for locus LELEUZIP (- 0,0009, modest differentiation for locus LECH13 (0,0896, locus LEMDDNa (0,0896 and locus LE21085 (0,0551 and major differentiation for locus LE2A11 (0,7633, locus LEEF1Aa (0,6167, locus TMS9 (0.4967 and locus LE20592 (0,4263. On the other hand, in the estimated tomato varieties, locus LE21085 (0,0297, locus LECH13 (0,0256 and locus LELEUZIP (0,0005 showed minor differentiation, locus LEMDDNa (0,1333 showed modest differentiation, while locus TMS9 (0,5929, locus LEEF1Aa (0,5006, locus LE2A11 (0,4013 and locus LE20592 (0,2606 showed major differentiation. The eight DNA microsatellite loci can be applicable solution for tomato genetic differentiation. The overall results suggest that these microsatellite loci could be used in further population genetic studies of tomatoes.

  3. Mutation and methylation of hMLH1 in gastric carcinomas with microsatellite instability

    Institute of Scientific and Technical Information of China (English)

    Dian-Chun Fang; Rong-Quan Wang; Shi-Ming Yang; Jian-Ming Yang; Hai-Feng Liu; Gui-Yong Peng; Tian-Li Xiao; Yuan-Hui Luo

    2003-01-01

    AIM: To appraise the correlation of mutation and methylation of hMSH1 with microsatellite instability (MSI) in gastric cancers.METHODS: Mutation of hMLH1 was detected by Twodimensional electrophoresis (Two-D) and DNA sequencing;Methylation of hMLH1 promoter was measured with methylation-specific PCR; MST was analyzed by PCR-basecl methods.RESULTS: Sixty-eight cases of sporadic gastric carcinoma were studied for mutation and methylation of hMLH1 promoter and MSI. Three mutations were found, two of them were caused by a single bp substitution and one was caused by a 2 bp substitution, which displayed similar Two-D band pattern.Methylation of hMLH1 promoter was detected in 11(16.2%)gastric cancer. By using five MSI markers, MSI in at least one locus was detected in 17/68(25 %) of the tumors analyzed.Three hMLH1 mutations were all detected in MSI-H (≥2 loci,n=8), but no mutation was found in MSI-L (only one locus,n=9) or MSS (tumor lacking MSI or stable, n=51). Methylation frequency of hMLH1 in MSI-H (87.5 %, 7/8) was significantly higher than that in MSI-L (11.1%, 1/9) or MSS (5.9%, 3/51)(P<0.01-0.001), but no difference was found between MSI-L and MSS (P>0.05).CONCLUSION: Both mutation and methylation of hMLH1are involved in the MSI pathway but not related to the LOH pathway in gastric carcinogenesis.

  4. Loss of heterozygosity and microsatellite instabilities of fragile histidine triad gene in gastric carcinoma

    Institute of Scientific and Technical Information of China (English)

    Yu-Ping Xiao; Dong-Ying Wu; Lei Xu; Yan Xin

    2006-01-01

    AIM: To detect the loss of heterozygosity (LOH) and microsatellite instabilities (MSI) of fragile histidine triad (FHIT) gene in gastric carcinoma and to study their association with the clinical pathological characteristics of gastric carcinoma.METHODS: LOH and MSI of FHIT gene were detected at four microsaterllite loci D3S13H, D3S4103, D3S1481 and D3S1234 using PCR in matched normal and cancerous tissues from 50 patients with primary gastric cancer.RESULTS: The average frequency of LOH and MSI of FHIT gene in gastric cancer was 32.4% and 26.4%respectively. LOH and MSI of FHIT gene in gastric cancer had no association with histological, Borrmann,and Lauren's classification. LOH of FHIT gene in gastric cancer was related to invasive depth. The frequency of FHIT LOH in gastric cancer with serosa-penetration was obviously higher than that in gastric cancer without serosa-penetration (73.5% vs 37.5%, P<0.05). MSI of FHIT gene in gastric cancer was associated with the lymph node metastasis. The frequency of MSI in gastric cancer without lymph node metastasis was significantly higher than that in gastric cancer with lymph node metastasis (66.7% vs 34.3%, P<0.05).CONCLUSION: LOH of FHIT gene is correlated with invasive depth of gastric carcinoma. MSI of FHIT gene is correlated with lymph node metastases. LOH and MSI of FHIT gene play an important role in carcinogenesis of gastric cancer.

  5. Very low prevalence of germline MSH6 mutations in hereditary non-polyposis colorectal cancer suspected patients with colorectal cancer without microsatellite instability.

    NARCIS (Netherlands)

    Kets, M.; Krieken, J.H.J.M. van; Hebeda, K.M.; Wezenberg, S.J.; Goossens, M.; Brunner, H.G.; Ligtenberg, M.J.L.; Hoogerbrugge-van der Linden, N.

    2006-01-01

    Hereditary non-polyposis colorectal cancer (HNPCC) is caused by mutations in one of the mismatch repair genes MLH1, MSH2, MSH6, or PMS2 and results in high-level microsatellite instability (MSI-high) in tumours of HNPCC patients. The MSI test is considered reliable for indicating mutations in MLH1

  6. Detection of Frameshift Mutations of the Transforming Growth Factor Receptor Ⅱ in Gastric Cancers with Microsatellite Instability

    Institute of Scientific and Technical Information of China (English)

    Dong Wang; Xin Geng; Yanyun Li; Yuchuan Wang; Yanni Li; Linsheng Zhao; Weiming Zhang

    2006-01-01

    OBJECTIVE To study the relationship among microsatellite instability (MSI), frameshift mutations (FM) of the transforming growth factor β receptor Ⅱ (TGFβR Ⅱ), methylation state of the hMLH1 promoter and hMLH1 protein expression level in gastric cancers, and to explore their relationship to gastric carcinogenesis.METHODS DNA was isolated from 101 gastric specimens and 5 microsatellite loci were detected. PCR, electrophoresis on denatured polyacrylamide gels and silver staining were performed to detect the MSI. The FMs of TGFβR Ⅱ were also screened with the same method. HMLH1 methylation was analyzed by methylation specific PCR (MSP) and sequencing. HMLH1 protein expression was detected using immunohistochemistry.RESULTS The incidence of MSIs was 53.7% and 0% in the cancers and normal tissues, respectively, with the frequency of MSIs being significantly higher in the gastric cancers compared to the normal gastric tissues (P<0.05). The frequency of hMLH1 methylation was 41.5%(17/41) in the gastric cancers and 0%(0/60) in the normal group. Decreased hMLH1 expression was observed in 94.1%(16/17) of cases exhibiting methylation. FMs of TGFβR Ⅱ were identified in 5 (62.5%) of the 8 samples with MSIH. In contrast, FMs were not found in MSI-L or microsatellite stable (MSS) cases.CONCLUSION MSIs and FMs of TGFβR Ⅱ may play an important role in gastric carcinogenesis. HMLH1 methylation is an important modification of the DNA which results in inactivation of hMLH1 and mismatch repair defects which lead to MSIs and FMs of TGFβR Ⅱ.

  7. 结直肠癌线粒体基因组的微卫星不稳定性%Mitochondrial DNA microsatellite instability in colorectal cancer

    Institute of Scientific and Technical Information of China (English)

    崔海宏; 黄平; 赵婷; 张振华; 徐伟; 王小鹏; 韩英

    2012-01-01

    目的:探讨结直肠癌(colorectal cancer,CRC)线粒体DNA(mitochondrial DNA,mtDNA)非编码区及编码区的微卫星不稳定.方法:选取50例新鲜CRC及相应癌旁组织标本,提取基因组DNA.利用荧光标记聚合酶链反应及短重复序列位点扫描的方法,对线粒体DNA编码区及非编码区微卫星不稳定进行比较分析.结果:共检出19例线粒体微卫星不稳定(mitochondrial microsatellite instability,mtMSl),发生率为38%(19/50),线粒体非编码区微卫星与编码区微卫星不稳定有显著相关性(重要数据列出来P<0.05).结论:结直肠癌患者肠黏膜细胞mtDNA中存在较高频率的微卫星不稳定,在一些结直肠癌的发生中可能起一定作用.%AIM: To investigate microsatellite instability in the non-coding region and coding regions of mitochondrial DNA in colorectal cancer. METHODS: Mitochondrial DNA was extracted from 50 cases of fresh CRC samples and matched tumor-adjacent noncancerous tissue. Fluorescence polymerase chain reaction and short tandem repeat locus scanning were conducted to analyze microsatellite instability. RESULTS: Mitochondrial DNA microsatellite instability was detected in 19 of 50 (38%) patients with CRC. The microsatellite instability in the non-coding region and coding region of mitochondrial DNA had a significant correlation (X2 = 4.929, P = 0.026). CONCLUSION: There is a high frequency of microsatellite instability in mitochondrial DNA of CRC patients, and mitochondrial DNA micro-satellite instability may play a role in the occurrence of colorectal cancer.

  8. Genetic and Epigenetic Changes of Components Affecting the WNT Pathway in Colorectal Carcinomas Stratified by Microsatellite Instability

    Directory of Open Access Journals (Sweden)

    Lin Thorstensen

    2005-02-01

    Full Text Available An unselected series of 310 colorectal carcinomas, stratified according to microsatellite instability (MSI and DNA ploidy, was examined for mutations and/or promoter hypermethylation of five components of the WNT signaling cascade [APC, CTNNB1 (encoding Rcatenin, AXIN2, TCF4, and WISP3] and three genes indirectly affecting this pathway [CDH1 (encoding β-cadherin, PTEN, and TP53]. APC and TP53 mutations were each present more often in microsatellite-stable (MSS tumors than in those with MSI (P < .001 for both. We confirmed that the aneuploid MSS tumors frequently contained TP53 mutations (P < .001, whereas tumors with APC mutations and/or promoter hypermethylation revealed no associations to ploidy. Mutations in APC upstream of codons 1020 to 1169, encoding the β-catenin binding site, were found in 15/144 mutated tumors and these patients seemed to have poor clinical outcome (P = .096. Frameshift mutations in AXIN2, PTEN, TCF4, and WISP3 were found in 20%, 17%, 46%, and 28% of the MSI tumors, respectively. More than half of the tumors with heterozygote mutations in AXIN2 were concurrently mutated in APC. The present study showed that more than 90% of all samples had alteration in one or more of the genes investigated, adding further evidence to the vital importance of activated WNT signaling in colorectal carcinogenesis.

  9. Role of detection of microsatellite instability in Chinese with hereditary nonpolyposis colorectal cancer or ordinary hereditary colorectal cancer

    Institute of Scientific and Technical Information of China (English)

    Wen-Zhi Liu; Feng Jin; Zhen-Hai Zhang; Shu-Bao Wang

    2006-01-01

    AIM: To detect microsatellite instability (MSI) in patients with hereditary nonpolyposis colorectal cancer or ordinary hereditary colorectal cancer and to provide criteria for screening the kindreds with hereditary nonpolyposis colorectal cancer at molecular level.METHODS: MSI was detected in the specimens from 20 cases with HNPCC, 20 cases with ordinary hereditary colorectal cancer and 20 cases with sporadic colorectal cancer by means of polymerase chain reaction-single strand conformation polymorphism.RESULTS: The positive rate of MSI was 85% (17/20) in HNPCC group, 40% (8/20) in ordinary hereditary colorectal cancer group and 10% (2/20) in the sporadic colorectal cancer group respectively. The differences were significant. The mean ages of the three groups were 43.6, 52.2, and 61.8 years respectively, which increased gradually. The incidence of right hemicolon cancer was 64.7%, 37.5%, and 0% respectively, which decreased gradually and had significant difference. The expression ratio of BAT26 and BAT25 was 94.1% respectively, which was highest in the 5 gene sites studied. The incidence of poorly differentiated adenocarcinoma was 70.6% in HNPCC group among high frequency microsatellite instability (MSI-H), which was higher than the other two groups, which had 50% and 50% respectively.CONCLUSION: The incidence of MSI-H is higher in HNPCC group. The detection of MSI is simple and economical and has high correlation with the clinicopathologic feature of HNPCC and can be used as a screening method to detect the germ line mutation of the mismatch repair gene.

  10. Large proportion of low frequency microsatellite-instability and loss of heterozygosity in pheochromocytoma and endocrine tumors detected with an extended marker panel.

    Science.gov (United States)

    Kupka, Susan; Haack, Birgit; Zdichavsky, Marty; Mlinar, Tanja; Kienzle, Christine; Bock, Thomas; Kandolf, Reinhard; Kroeber, Stefan-Martin; Königsrainer, Alfred

    2008-04-01

    Pheochromocytoma (PCC) is a usually benign tumor originated in the majority of patients from the adrenal medulla. Regarding sporadic forms of PCC, mechanisms of pathogenesis are largely unknown. Recently, microsatellite-instability (MSI) was discussed as genetic factor contributing to PCC development. Since microsatellite markers used for MSI detection have only been recommended for colorectal carcinoma (CRC), we established an extended marker set for MSI detection in PCC. Twenty-two PCC patients were analyzed applying 11 microsatellite markers. Our marker set comprised the reference panel for CRC and six additional markers, which have already been described to detect MSI in tumors other than CRC. Moreover, 23 endocrine tumors with gastrointestinal origin were examined in order to test the applicability of this marker panel. Microsatellite-instability was detected in 41% of PCCs. Twenty-seven percent showed loss of heterozygosity (LOH) events affecting different chromosomal regions. Among the 23 patients with endocrine tumors, only three (one pancreatic endocrine tumor, one duodenal neuro-endocrine tumor, one hepatic metastasis of a primary tumor with unknown origin) demonstrated MSI. The extended microsatellite panel is qualified to detect MSI in PCC. Nine percent of MSI-positive cases would have not been noticed by the use of the reference panel alone. PCCs are characterized by low frequency MSI pointing to failures in factors involved in DNA replication.

  11. Microsatellite repeat instability fuels evolution of embryonic enhancers in Hawaiian Drosophila.

    Science.gov (United States)

    Brittain, Andrew; Stroebele, Elizabeth; Erives, Albert

    2014-01-01

    For ∼30 million years, the eggs of Hawaiian Drosophila were laid in ever-changing environments caused by high rates of island formation. The associated diversification of the size and developmental rate of the syncytial fly embryo would have altered morphogenic gradients, thus necessitating frequent evolutionary compensation of transcriptional responses. We investigate the consequences these radiations had on transcriptional enhancers patterning the embryo to see whether their pattern of molecular evolution is different from non-Hawaiian species. We identify and functionally assay in transgenic D. melanogaster the Neurogenic Ectoderm Enhancers from two different Hawaiian Drosophila groups: (i) the picture wing group, and (ii) the modified mouthparts group. We find that the binding sites in this set of well-characterized enhancers are footprinted by diverse microsatellite repeat (MSR) sequences. We further show that Hawaiian embryonic enhancers in general are enriched in MSR relative to both Hawaiian non-embryonic enhancers and non-Hawaiian embryonic enhancers. We propose embryonic enhancers are sensitive to Activator spacing because they often serve as assembly scaffolds for the aggregation of transcription factor activator complexes. Furthermore, as most indels are produced by microsatellite repeat slippage, enhancers from Hawaiian Drosophila lineages, which experience dynamic evolutionary pressures, would become grossly enriched in MSR content.

  12. Effect of zinc and polyphenols supplementation on antioxidative defense mechanisms and the frequency of microsatellite instability in chemically-induced mammary carcinogenesis in the rat.

    Science.gov (United States)

    Bobrowska-Korczak, Barbara; Skrajnowska, Dorota; Tokarz, Andrzej; Bialek, Slawomir; Jezierska, Ewelina

    2015-01-01

    The aim of the present study was to assess the effect of dietary supplementation (with zinc or zinc and polyphenolic compounds - resveratrol or genistein) on antioxidant enzymes (glutathione peroxidase - GPx, catalase - CAT and superoxide dismutase - SOD) and the frequency of microsatellite instability (MSI) in a widely used model of mammary carcinogenesis induced in the rat by treatment with 7,12-dimethyl-1,2-benz[a]anthracene (DMBA). The impact of selected compounds on the intensity of DMBA-induced carcinogenesis was also assessed. Sixty four Sprague-Dawley female rats were divided into study groups which, apart from the standard diet and DMBA, were treated with zinc, zinc and resveratrol or zinc and genistein via gavage for a period ranging from 40 days to 20 weeks of age. On the basis of the obtained results it can be said that synergistic reaction between Zn(II) and genistein causes a delay in cancer development as compared with the animals treated with DMBA but with no food supplementation. Supplementation with Zn(II) and polyphenolic compounds resulted in the occurrence of microsatellite instabilities in tumors. LOH (loss of heterozygosity) was found in tumor samples at microsatellite D1Mgh6 and D3Mgh9. DMBA treatment increased significantly the glutathione peroxidase activity whereas it had no effect on the SOD and CAT activities, as compared with control rats. Diet supplementation has an effect on the activity of selected antioxidant enzymes. Diet supplementation has an effect on the occurrence of microsatellite instabilities as well as on the intensity of the neoplastic process. The intensity of occurrence of microsatellite instabilities does not depend on the activity of selected antioxidant enzymes.

  13. Microsatellite data analysis for population genetics

    Science.gov (United States)

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

  14. Microsatellite instability typing in serum and tissue of patients with colorectal cancer: comparing real time PCR with hybridization probe and high-performance liquid chromatography.

    Science.gov (United States)

    Mokarram, P; Rismanchi, M; Alizadeh Naeeni, M; Mirab Samiee, S; Paryan, M; Alipour, A; Honardar, Z; Kavousipour, S; Naghibalhossaini, F; Mostafavi-Pour, Z; Monabati, A; Hosseni, S V; Shamsdin, S A

    2014-05-01

    Allelic variation of BAT-25 (a 25-repeat quasimonomorphic poly T) and BAT-26 (a 26-repeat quasimonomorphic polyA) loci as two mononucleotide microsatellite markers, were analyzed with high-performance liquid chromatography (HPLC) compared with Real-Time PCR using hybridization probes. BAT-26 and BAT-25 markers were used to determine an appropriate screening technique with high sensitivity and specificity to diagnose microsatellite instability (MSI) status in patients with colorectal cancer (CRC). One of the pathways in colorectal tumor genesis is microsatellite instability (MSI+). MSI is detected in about 15% of all CRCs; 3% are of these are associated with Lynch syndrome and the other 12% are caused by sporadic. Colorectal tumors with MSI have distinctive features compared with microsatellite stable tumors. Due to the high percentage of MSI+ CRC in Iran, screening of this type of CRC is imperative. Two markers were analyzed in tissues and sera of 44 normal volunteers and tumor and matched normal mucosal tissues as well as sera of 44 patients with sporadic CRC. The sensitivity and specificity of BAT-26 with real time PCR method (Hybridization probe) were 100% in comparison with sequencing method as the gold standard, while HPLC had a lower sensitivity and specificity. According to HPLC data, BAT-26 was more sensitive than BAT-25 in identifying MSI tumors. Therefore, MSI typing using the BAT-26 hybridization probe method compared to HPLC could be considered as an accurate method for diagnosing MSI in CRC tumors but not in serum circulating DNAs.

  15. Correlation of chromosomal instability, telomere length and telomere maintenance in microsatellite stable rectal cancer: a molecular subclass of rectal cancer.

    Directory of Open Access Journals (Sweden)

    Lisa A Boardman

    Full Text Available INTRODUCTION: Colorectal cancer (CRC tumor DNA is characterized by chromosomal damage termed chromosomal instability (CIN and excessively shortened telomeres. Up to 80% of CRC is microsatellite stable (MSS and is historically considered to be chromosomally unstable (CIN+. However, tumor phenotyping depicts some MSS CRC with little or no genetic changes, thus being chromosomally stable (CIN-. MSS CIN- tumors have not been assessed for telomere attrition. EXPERIMENTAL DESIGN: MSS rectal cancers from patients ≤50 years old with Stage II (B2 or higher or Stage III disease were assessed for CIN, telomere length and telomere maintenance mechanism (telomerase activation [TA]; alternative lengthening of telomeres [ALT]. Relative telomere length was measured by qPCR in somatic epithelial and cancer DNA. TA was measured with the TRAPeze assay, and tumors were evaluated for the presence of C-circles indicative of ALT. p53 mutation status was assessed in all available samples. DNA copy number changes were evaluated with Spectral Genomics aCGH. RESULTS: Tumors were classified as chromosomally stable (CIN- and chromosomally instable (CIN+ by degree of DNA copy number changes. CIN- tumors (35%; n=6 had fewer copy number changes (<17% of their clones with DNA copy number changes than CIN+ tumors (65%; n=13 which had high levels of copy number changes in 20% to 49% of clones. Telomere lengths were longer in CIN- compared to CIN+ tumors (p=0.0066 and in those in which telomerase was not activated (p=0.004. Tumors exhibiting activation of telomerase had shorter tumor telomeres (p=0.0040; and tended to be CIN+ (p=0.0949. CONCLUSIONS: MSS rectal cancer appears to represent a heterogeneous group of tumors that may be categorized both on the basis of CIN status and telomere maintenance mechanism. MSS CIN- rectal cancers appear to have longer telomeres than those of MSS CIN+ rectal cancers and to utilize ALT rather than activation of telomerase.

  16. Rectal Cancer Diagnosed after Cesarean Section in Which High Microsatellite Instability Indicated the Presence of Lynch Syndrome

    Directory of Open Access Journals (Sweden)

    Tomohiro Okuda

    2015-01-01

    Full Text Available We report a case of rectal cancer with microsatellite instability (MSI that probably resulted from Lynch syndrome and that was diagnosed after Cesarean section. The patient was a 28-year-old woman (gravid 1, para 1 without a significant medical history. At 35 gestational weeks, vaginal ultrasonography revealed a 5 cm tumor behind the uterine cervix, which was diagnosed as a uterine myoma. The tumor gradually increased in size and blocked the birth canal, resulting in the patient undergoing an emergency Cesarean section. Postoperatively, the tumor was diagnosed as rectal cancer with MSI. After concurrent chemoradiation therapy, a lower anterior resection was performed. The patient’s family history revealed she met the criteria of the revised Bethesda guidelines for testing the colorectal tumor for MSI. Testing revealed that the tumor did indeed show high MSI and, combined with the family history, suggested this could be a case of Lynch syndrome. Our findings emphasize the importance of considering the possibility of Lynch syndrome in pregnant women with colorectal cancer, particularly those with a family history of this condition. We suggest that the presence of Lynch syndrome should also be considered for any young woman with endometrial, ovarian, or colorectal cancer.

  17. Potential of Microsatellites Markers for the Genetic Analysis of Bryophytes

    Directory of Open Access Journals (Sweden)

    Saumy PANDEY

    2016-03-01

    Full Text Available Microsatellites have increasingly being used to study genetic diversity, phylogeny, population genetics, population ecology and genetic mapping of bryophytes. Due to co-dominant and highly reproducible features, microsatellites became markers of choice for several genetic analyses of bryophytes. However, the major limitation is de novo isolation of microsatellites from the interest species which were studied and gave genomic libraries. Initially, traditional methods of microsatellite development were tedious and time consuming, but due to the sequencing of several bryophytes available in public databases, advancement in PCR technologies and computer software, have cumulatively facilitated the development of microsatellites for bryophytes study. This review examines the features, strategies for the development of microsatellites and their utilization in many aspects of genetic and ecological studies of bryophytes.

  18. Nonsense mediated decay resistant mutations are a source of expressed mutant proteins in colon cancer cell lines with microsatellite instability.

    Directory of Open Access Journals (Sweden)

    David S Williams

    Full Text Available BACKGROUND: Frameshift mutations in microsatellite instability high (MSI-High colorectal cancers are a potential source of targetable neo-antigens. Many nonsense transcripts are subject to rapid degradation due to nonsense-mediated decay (NMD, but nonsense transcripts with a cMS in the last exon or near the last exon-exon junction have intrinsic resistance to nonsense-mediated decay (NMD. NMD-resistant transcripts are therefore a likely source of expressed mutant proteins in MSI-High tumours. METHODS: Using antibodies to the conserved N-termini of predicted mutant proteins, we analysed MSI-High colorectal cancer cell lines for examples of naturally expressed mutant proteins arising from frameshift mutations in coding microsatellites (cMS by immunoprecipitation and Western Blot experiments. Detected mutant protein bands from NMD-resistant transcripts were further validated by gene-specific short-interfering RNA (siRNA knockdown. A genome-wide search was performed to identify cMS-containing genes likely to generate NMD-resistant transcripts that could encode for antigenic expressed mutant proteins in MSI-High colon cancers. These genes were screened for cMS mutations in the MSI-High colon cancer cell lines. RESULTS: Mutant protein bands of expected molecular weight were detected in mutated MSI-High cell lines for NMD-resistant transcripts (CREBBP, EP300, TTK, but not NMD-sensitive transcripts (BAX, CASP5, MSH3. Expression of the mutant CREBBP and EP300 proteins was confirmed by siRNA knockdown. Five cMS-bearing genes identified from the genome-wide search and without existing mutation data (SFRS12IP1, MED8, ASXL1, FBXL3 and RGS12 were found to be mutated in at least 5 of 11 (45% of the MSI-High cell lines tested. CONCLUSION: NMD-resistant transcripts can give rise to expressed mutant proteins in MSI-High colon cancer cells. If commonly expressed in primary MSI-High colon cancers, MSI-derived mutant proteins could be useful as cancer specific

  19. Analysis of microsatellite markers in the genome of the plant pathogen Ceratocystis fimbriata.

    Science.gov (United States)

    Simpson, Melissa C; Wilken, P Markus; Coetzee, Martin P A; Wingfield, Michael J; Wingfield, Brenda D

    2013-01-01

    Ceratocystis fimbriata sensu lato represents a complex of cryptic and commonly plant pathogenic species that are morphologically similar. Species in this complex have been described using morphological characteristics, intersterility tests and phylogenetics. Microsatellite markers have been useful to study the population structure and origin of some species in the complex. In this study we sequenced the genome of C. fimbriata. This provided an opportunity to mine the genome for microsatellites, to develop new microsatellite markers, and map previously developed markers onto the genome. Over 6000 microsatellites were identified in the genome and their abundance and distribution was determined. Ceratocystis fimbriata has a medium level of microsatellite density and slightly smaller genome when compared with other fungi for which similar microsatellite analyses have been performed. This is the first report of a microsatellite analysis conducted on a genome sequence of a fungal species in the order Microascales. Forty-seven microsatellite markers have been published for population genetic studies, of which 35 could be mapped onto the C. fimbriata genome sequence. We developed an additional ten microsatellite markers within putative genes to differentiate between species in the C. fimbriata s.l. complex. These markers were used to distinguish between 12 species in the complex.

  20. IGFBP3 Promoter Methylation in Colorectal Cancer: Relationship with Microsatellite Instability, CpG Island Methylator Phenotype, p53

    Directory of Open Access Journals (Sweden)

    Takako Kawasaki

    2007-12-01

    Full Text Available Insulin-like growth factor binding protein 3 (IGFBP3, which is induced by wild-type p53, regulates IGF and interacts with the TGF-β pathway. IGFBP3 promoter methylation may occur in colorectal cancer with or without the CpG island methylator phenotype (CIMP, which is associated with microsatellite instability (MSI and TGFBR2 mutation. We examined the relationship between IGFBP3 methylation, p53 expression, CIMP and MSI in 902 population-based colorectal cancers. Utilizing real-time PCR (MethyLight, we quantified promoter methylation in IGFBP3 and eight other CIMP-high-specific promoters (CACNA1G, CDKN2A, CRABP1, IGF2, MLH1, NEUROG1, RUNX3, and SOCS1. IGFBP3 methylation was far more frequent in non-MSI-high CIMP-high tumors (85% = 35/41 than in MSI-high CIMPhigh (49% = 44/90, P < .0001, MSI-high non-CIMP-high (17% = 6/36, P < .0001, non-MSI-high non-CIMP-high tumors (22% = 152/680, P < .0001. Among CIMPhigh tumors, the inverse relationship between MSI and IGFBP3 methylation persisted in p53-negative tumors (P < .0001, but not in p53-positive tumors. IGFBP3 methylation was associated inversely with TGFBR2 mutation in MSI-high non-CIMP-high tumors (P = .02. In conclusion, IGFBP3 methylation is inversely associated with MSI in CIMP-high colorectal cancers, this relationship is limited to p53-negative tumors. Our data suggest complex relationship between global genomic/epigenomic phenomena (such as MSI/ CIMP, single molecular events (e.g., IGFBP3 methylation, TP53 mutation, TGFBR2 mutation, the related pathways.

  1. The differential impact of microsatellite instability as a marker of prognosis and tumour response between colon cancer and rectal cancer.

    Science.gov (United States)

    Hong, Sung Pil; Min, Byung So; Kim, Tae Il; Cheon, Jae Hee; Kim, Nam Kyu; Kim, Hoguen; Kim, Won Ho

    2012-05-01

    Microsatellite instability (MSI) is a distinct molecular phenotype of colorectal cancer related to prognosis and tumour response to 5-fluorouracil (5-FU)-based chemotherapy. We investigated the differential impact of MSI between colon and rectal cancers as a marker of prognosis and chemotherapeutic response. PCR-based MSI assay was performed on 1125 patients. Six hundred and sixty patients (58.7%) had colon cancer and 465 patients (41.3%) had rectal cancer. Among 1125 patients, 106 (9.4%) had high-frequency MSI (MSI-H) tumours. MSI-H colon cancers (13%) had distinct phenotypes including young age at diagnosis, family history of colorectal cancer, early Tumor, Node, Metastasis (TNM) stage, proximal location, poor differentiation, and high level of baseline carcinoembryonic antigen (CEA), while MSI-H rectal cancers (4.3%) showed similar clinicopathological characteristics to MSS/MSI-L tumours except for family history of colorectal cancer. MSI-H tumours were strongly correlated with longer disease free survival (DFS) (P=0.005) and overall survival (OS) (P=0.009) than MSS/MSI-L tumours in colon cancer, while these positive correlations were not observed in rectal cancers. The patients with MSS/MSI-L tumours receiving 5-FU-based chemotherapy showed good prognosis (P=0.013), but this positive association was not observed in MSI-H (P=0.104). These results support the use of MSI status as a marker of prognosis and response to 5-FU-based chemotherapy in patients with colon cancers. Further study is mandatory to evaluate the precise role of MSI in patients with rectal cancers and the effect of 5-FU-based chemotherapy in MSI-H tumours. Copyright © 2011 Elsevier Ltd. All rights reserved.

  2. Psychological distress in newly diagnosed colorectal cancer patients following microsatellite instability testing for Lynch syndrome on the pathologist's initiative.

    Science.gov (United States)

    Landsbergen, K M; Prins, J B; Brunner, H G; van Duijvendijk, P; Nagengast, F M; van Krieken, J H; Ligtenberg, M; Hoogerbrugge, N

    2012-06-01

    According to the Dutch Guideline on Hereditary Colorectal Cancer published in 2008, patients with recently diagnosed colorectal cancer (CRC) should undergo microsatellite instability (MSI) testing by a pathologist immediately after tumour resection if they are younger than 50 years, or if a second CRC has been diagnosed before the age of 70 years, owing to the high risk of Lynch syndrome (MIPA). The aim of the present MIPAPS study was to investigate general distress and cancer-specific distress following MSI testing. From March 2007 to September 2009, 400 patients who had been tested for MSI after newly diagnosed CRC were recruited from 30 Dutch hospitals. Levels of general distress (SCL-90) and cancer-specific distress (IES) were assessed immediately after MSI result disclosure (T1) and 6 months later (T2). Response rates were 23/77 (30%) in the MSI-positive patients and 58/323 (18%) in the MSI-negative patients. Levels of general distress and cancer-specific distress were moderate. In the MSI-positive group, 27% of the patients had high general distress at T1 versus 18% at T2 (p = 0.5), whereas in the MSI-negative group, these percentage were 14 and 18% (p = 0.6), respectively. At T1 and T2, cancer-specific distress rates in the MSI-positive group and MSI-negative group were 39 versus 27% (p = 0.3) and 38 versus 36% (p = 1.0), respectively. High levels of general distress were correlated with female gender, low social support and high perceived cancer risk. Moderate levels of distress were observed after MSI testing, similar to those found in other patients diagnosed with CRC. Immediately after result disclosure, high cancer-specific distress was observed in 40% of the MSI-positive patients.

  3. Development of Pineapple Microsatellite Markers and Germplasm Genetic Diversity Analysis

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    Suping Feng

    2013-01-01

    Full Text Available Two methods were used to develop pineapple microsatellite markers. Genomic library-based SSR development: using selectively amplified microsatellite assay, 86 sequences were generated from pineapple genomic library. 91 (96.8% of the 94 Simple Sequence Repeat (SSR loci were dinucleotide repeats (39 AC/GT repeats and 52 GA/TC repeats, accounting for 42.9% and 57.1%, resp., and the other three were mononucleotide repeats. Thirty-six pairs of SSR primers were designed; 24 of them generated clear bands of expected sizes, and 13 of them showed polymorphism. EST-based SSR development: 5659 pineapple EST sequences obtained from NCBI were analyzed; among 1397 nonredundant EST sequences, 843 were found containing 1110 SSR loci (217 of them contained more than one SSR locus. Frequency of SSRs in pineapple EST sequences is 1SSR/3.73 kb, and 44 types were found. Mononucleotide, dinucleotide, and trinucleotide repeats dominate, accounting for 95.6% in total. AG/CT and AGC/GCT were the dominant type of dinucleotide and trinucleotide repeats, accounting for 83.5% and 24.1%, respectively. Thirty pairs of primers were designed for each of randomly selected 30 sequences; 26 of them generated clear and reproducible bands, and 22 of them showed polymorphism. Eighteen pairs of primers obtained by the one or the other of the two methods above that showed polymorphism were selected to carry out germplasm genetic diversity analysis for 48 breeds of pineapple; similarity coefficients of these breeds were between 0.59 and 1.00, and they can be divided into four groups accordingly. Amplification products of five SSR markers were extracted and sequenced, corresponding repeat loci were found and locus mutations are mainly in copy number of repeats and base mutations in the flanking region.

  4. Combustion instability modeling and analysis

    Energy Technology Data Exchange (ETDEWEB)

    Santoro, R.J.; Yang, V.; Santavicca, D.A. [Pennsylvania State Univ., University Park, PA (United States)] [and others

    1995-10-01

    It is well known that the two key elements for achieving low emissions and high performance in a gas turbine combustor are to simultaneously establish (1) a lean combustion zone for maintaining low NO{sub x} emissions and (2) rapid mixing for good ignition and flame stability. However, these requirements, when coupled with the short combustor lengths used to limit the residence time for NO formation typical of advanced gas turbine combustors, can lead to problems regarding unburned hydrocarbons (UHC) and carbon monoxide (CO) emissions, as well as the occurrence of combustion instabilities. Clearly, the key to successful gas turbine development is based on understanding the effects of geometry and operating conditions on combustion instability, emissions (including UHC, CO and NO{sub x}) and performance. The concurrent development of suitable analytical and numerical models that are validated with experimental studies is important for achieving this objective. A major benefit of the present research will be to provide for the first time an experimentally verified model of emissions and performance of gas turbine combustors.

  5. Molecular Detection of Bladder Cancer by Fluorescence Microsatellite Analysis and an Automated Genetic Analyzing System

    Directory of Open Access Journals (Sweden)

    Sarel Halachmi

    2007-01-01

    Full Text Available To investigate the ability of an automated fluorescent analyzing system to detect microsatellite alterations, in patients with bladder cancer. We investigated 11 with pathology proven bladder Transitional Cell Carcinoma (TCC for microsatellite alterations in blood, urine, and tumor biopsies. DNA was prepared by standard methods from blood, urine and resected tumor specimens, and was used for microsatellite analysis. After the primers were fluorescent labeled, amplification of the DNA was performed with PCR. The PCR products were placed into the automated genetic analyser (ABI Prism 310, Perkin Elmer, USA and were subjected to fluorescent scanning with argon ion laser beams. The fluorescent signal intensity measured by the genetic analyzer measured the product size in terms of base pairs. We found loss of heterozygocity (LOH or microsatellite alterations (a loss or gain of nucleotides, which alter the original normal locus size in all the patients by using fluorescent microsatellite analysis and an automated analyzing system. In each case the genetic changes found in urine samples were identical to those found in the resected tumor sample. The studies demonstrated the ability to detect bladder tumor non-invasively by fluorescent microsatellite analysis of urine samples. Our study supports the worldwide trend for the search of non-invasive methods to detect bladder cancer. We have overcome major obstacles that prevented the clinical use of an experimental system. With our new tested system microsatellite analysis can be done cheaper, faster, easier and with higher scientific accuracy.

  6. Detection of Bladder CA by Microsatellite Analysis (MSA) — EDRN Public Portal

    Science.gov (United States)

    Goal 1: To determine sensitivity and specificity of microsatellite analysis (MSA) of urine sediment, using a panel of 15 microsatellite markers, in detecting bladder cancer in participants requiring cystoscopy. This technique will be compared to the diagnostic standard of cystoscopy, as well as to urine cytology. Goal 2: To determine the temporal performance characteristics of microsatellite analysis of urine sediment. Goal 3: To determine which of the 15 individual markers or combination of markers that make up the MSA test are most predictive of the presence of bladder cancer.

  7. T-cell factor-4 frameshift mutations occur frequently in human microsatellite instability-high colorectal carcinomas but do not contribute to carcinogenesis.

    Science.gov (United States)

    Ruckert, Stefan; Hiendlmeyer, Elke; Brueckl, Wolfgang M; Oswald, Ursula; Beyser, Kurt; Dietmaier, Wolfgang; Haynl, Angela; Koch, Claudia; Rüschoff, Josef; Brabletz, Thomas; Kirchner, Thomas; Jung, Andreas

    2002-06-01

    Colorectal carcinomas with microsatellite instability accumulate errors in short repetitive DNA repeats, especially mono and dinucleotide repeats. One such error-prone A(9) monorepeat is found in exon 17 of the TCF-4 gene. TCF-4 and beta-catenin form a transcription complex, which is important for both maintenance of normal epithelium and development of colorectal tumors. To elucidate the relevance of frameshift mutations in the TCF-4 in colorectal carcinogenesis, a variety of investigations in human tumors and cell lines was performed. It was found that mutations in the TCF-4 A(9) repeat do not contribute to tumorigenesis and seem to be passenger mutations.

  8. Informativeness of minisatellite and microsatellite markers for genetic analysis in papaya.

    Science.gov (United States)

    Oliveira, G A F; Dantas, J L L; Oliveira, E J

    2015-10-01

    The objective of this study was to evaluate information on minisatellite and microsatellite markers in papaya (Carica papaya L.). Forty minisatellites and 91 microsatellites were used for genotyping 24 papaya accessions. Estimates of genetic diversity, genetic linkage and analyses of population structure were compared. A lower average number of alleles per locus was observed in minisatellites (3.10) compared with microsatellites (3.57), although the minisatellites showed rarer alleles (18.54 %) compared with microsatellite (13.85 %). Greater expected (He = 0.52) and observed (Ho = 0.16) heterozygosity was observed in the microsatellites compared with minisatellites (He = 0.42 and Ho = 0.11), possibly due to the high number of hermaphroditic accessions, resulting in high rates of self-fertilization. The polymorphic information content and Shannon-Wiener diversity were also higher for microsatellites (from 0.47 to 1.10, respectively) compared with minisatellite (0.38 and 0.85, respectively). The probability of paternity exclusion was high for both markers (>0.999), and the combined probability of identity was from 1.65(-13) to 4.33(-38) for mini- and micro-satellites, respectively, which indicates that both types of markers are ideal for genetic analysis. The Bayesian analysis indicated the formation of two groups (K = 2) for both markers, although the minisatellites indicated a substructure (K = 4). A greater number of accessions with a low probability of assignment to specific groups were observed for microsatellites. Collectively, the results indicated higher informativeness of microsatellites. However, the lower informative power of minisatellites may be offset by the use of larger number of loci. Furthermore, minisatellites are subject to less error in genotyping because there is greater power to detect genotyping systems when larger motifs are used.

  9. The "Fas counterattack" is not an active mode of tumor immune evasion in colorectal cancer with high-level microsatellite instability.

    LENUS (Irish Health Repository)

    Houston, Aileen M

    2012-02-03

    Microsatellite instability (MSI) is an alternative pathway of colorectal carcinogenesis. It is found in 10% to 15% of sporadic colorectal neoplasms and is characterized by failure of the DNA mismatch-repair system. High-level MSI (MSI-H) is associated with tumor-infiltrating lymphocytes (TILs) and a favorable prognosis. Expression of Fas ligand (FasL\\/CD95L) by cancer cells may mediate tumor immune privilege by inducing apoptosis of antitumor immune cells. The aim of this study was to investigate the relationship between FasL expression and MSI status in primary colon tumors. Using immunohistochemistry, we detected FasL expression in 91 colorectal carcinoma specimens, previously classified according to the level of MSI as MSI-H (n = 26), MSI-low (MSI-L) (n = 29), and microsatellite stable (n = 36). Tumor-infiltrating lymphocyte density was quantified by immunohistochemical staining for CD3. MSI-H tumors were significantly associated with reduced frequency (P = .04) and intensity (P = .066) of FasL expression relative to non-MSI-H (ie, microsatellite stable and MSI-L) tumors. Higher FasL staining intensity correlated with reduced TIL density (P = .059). Together, these findings suggest that the abundance of TILs found in MSI-H tumors may be due to the failure of these tumor cells to up-regulate FasL and may explain, in part, the improved prognosis associated with these tumors.

  10. Screening for microsatellite instability identifies frequent 3'-untranslated region mutation of the RB1-inducible coiled-coil 1 gene in colon tumors.

    Directory of Open Access Journals (Sweden)

    Bogdan C Paun

    Full Text Available BACKGROUND: Coding region microsatellite instability (MSI results in loss of gene products and promotion of microsatellite-unstable (MSI-H carcinogenesis. Recent studies have indicated that MSI within 3'-untranslated regions (3'UTRs may post-transcriptionally dysregulate gene products. Within this context, we conducted a broad mutational survey of 42 short 3'UTR microsatellites (MSs in 45 MSI-H colorectal tumors and their corresponding normal colonic mucosae. METHODOLOGY/PRINCIPAL FINDINGS: In order to estimate the overall susceptibility of MSs to MSI in MSI-H tumors, the observed MSI frequency of each MS was correlated with its length, interspecies sequence conservation level, and distance from some genetic elements (i.e., stop codon, polyA signal, and microRNA binding sites. All MSs were stable in normal colonic mucosae. The MSI frequency at each MS in MSI-H tumors was independent of sequence conservation level and distance from other genetic elements. In contrast, MS length correlated significantly with MSI frequency in MSI-H tumors (r=0.86, p=7.2x10(-13. 3'UTR MSs demonstrated MSI frequencies in MSI-H tumors higher than the 99% upper limit predicted by MS length for RB1-inducible coiled-coil 1(RB1CC1, mutation frequency 68.4%, NUAK family SNF1-like kinase 1(NUAK1, 31.0%, and Rtf1, Paf1/RNA polymerase II complex component, homolog (RTF1, 25.0%. An in silico prediction of RNA structure alterations was conducted for these MSI events to gauge their likelihood of affecting post-transcriptional regulation. RB1CC1 mutant was predicted to lose a microRNA-accessible loop structure at a putative binding site for the tumor-suppressive microRNA, miR-138. In contrast, the predicted 3'UTR structural change was minimal for NUAK1- and RTF1 mutants. Notably, real-time quantitative RT-PCR analysis revealed significant RB1CC1 mRNA overexpression vs. normal colonic mucosae in MSI-H cancers manifesting RB1CC1 3'UTR MSI (9.0-fold; p = 3.6x10(-4. CONCLUSIONS: This

  11. Immunohistochemical staining for p16 and BRAFV600E is useful to distinguish between sporadic and hereditary (Lynch syndrome-related) microsatellite instable colorectal carcinomas.

    Science.gov (United States)

    Boissière-Michot, Florence; Frugier, Hélène; Ho-Pun-Cheung, Alexandre; Lopez-Crapez, Evelyne; Duffour, Jacqueline; Bibeau, Frédéric

    2016-08-01

    DNA mismatch repair (MMR) protein analysis by immunohistochemistry (IHC) can identify colorectal cancer (CRC) with microsatellite instability (MSI). As MLH1-deficient CRC can be hereditary or sporadic, markers to distinguish between them are needed. MLH1 promoter methylation assay is the reference method; however, sometimes, it is challenging on formalin-fixed paraffin-embedded tissue samples. We assessed by IHC the expression of BRAFV600E, p16, MGMT, and CDX2 in 55 MLH1-deficient MSI CRC samples (of which 8 had a germline MLH1 mutation) to determine whether this panel differentiates between sporadic and hereditary CRCs. We also analyzed MLH1 promoter methylation by methylation-specific PCR and pyrosequencing and BRAF status by genotyping. None of the hereditary CRCs showed MLH1 methylation, BRAF mutation, BRAFV600E-positive immunostaining, or loss of p16 expression. We detected MLH1 promoter methylation in 67 % and a BRAF mutation in 42 % of CRC, all showing MLH1 promoter methylation. BRAFV600E IHC and BRAF genotyping gave concordant results in all but two samples. Loss of expression of p16 was found in 30 % of CRC with methylation of the MLH1 promoter, but its expression was retained in all non-methylated and part of MLH1-methylated tumors (100 % specificity, 30 % sensitivity). CDX2 and MGMT expression was not associated with MLH1 status. Thus, BRAFV600E and p16 IHC may help in differentiating sporadic from hereditary MLH1-deficient CRC with MSI. Specifically, p16 IHC might be used as a surrogate marker for MLH1 promoter methylation, because all p16-negative CRCs displayed MLH1 methylation, whereas hereditary CRCs were all p16-positive.

  12. Frameshift mutation of a histone methylation-related gene SETD1B and its regional heterogeneity in gastric and colorectal cancers with high microsatellite instability.

    Science.gov (United States)

    Choi, Youn Jin; Oh, Hye Rim; Choi, Mi Ryoung; Gwak, Min; An, Chang Hyeok; Chung, Yeun Jun; Yoo, Nam Jin; Lee, Sug Hyung

    2014-08-01

    Histone methyltransferase (HMT), which catalyzes a histone methylation, is frequently altered in cancers at mutation and expression levels. The aims of this study were to explore whether SETD1B, SETDB2, and SETD2, SET domain-containing HMT genes, are mutated and expressionally altered in gastric (GC) and colorectal cancers (CRC). In a public database, we found that SETD1B, SETDB2, and SETD2 had mononucleotide repeats in coding sequences that might be mutation targets in cancers with microsatellite instability (MSI). We analyzed the mutations in 76 GCs and 93 CRCs and found SETD1B (38.7% of GC and 35.6% of CRC with high MSI [MSI-H]), SETDB2 (11.1% of CRC with MSI-H), and SETD2 frameshift mutations (6.7% of CRC with MSI-H). These mutations were not found in stable MSI/low MSI. In addition, we analyzed intratumoral heterogeneity (ITH) of SETD1B mutation in 6 CRCs and found that 2 CRCs harbored regional ITH of SETD1B. We also analyzed SETD1B expression in GC and CRC by immunohistochemistry. Loss of SETD1B expression was identified in 15% to 55% of the GC and CRC with respect to the MSI status. Of note, the loss of expression was more common in those with SETD1B mutations than those with wild-type SETD1B. We identified alterations of SET domain-containing HMT at various levels (frameshift mutations, genetic ITH, and expression loss), which together might play a role in tumorigenesis of GC and CRC with MSI-H. Our data suggest that mutation analysis in multiple regions is needed for a better evaluation of mutation status in CRC with MSI-H.

  13. Analysis of microsatellite polymorphism in inbred knockout mice.

    Science.gov (United States)

    Zuo, Baofen; Du, Xiaoyan; Zhao, Jing; Yang, Huixin; Wang, Chao; Wu, Yanhua; Lu, Jing; Wang, Ying; Chen, Zhenwen

    2012-01-01

    Previously, we found that the genotype of 42 out of 198 mouse microsatellite loci, which are distributed among all chromosomes except the Y chromosome, changed from monomorphism to polymorphism (CMP) in a genetically modified inbred mouse strain. In this study, we further examined whether CMP also relates to the homologous recombination in gene knockout (KO) mouse strains. The same 42 microsatellite loci were analyzed by polymerase chain reaction (PCR) in 29 KO inbred mouse strains via short tandem sequence repeat (STR) scanning and direct sequence cloning to justify microsatellite polymorphisms. The C57BL/6J and 129 mouse strains, from which these 29 KO mice were derived, were chosen as the background controls. The results indicated that 10 out of 42 (23.8%) loci showed CMP in some of these mouse strains. Except for the trinucleotide repeat locus of D3Mit22, which had microsatellite CMP in strain number 9, the core sequences of the remaining 41 loci were dinucleotide repeats, and 9 out of 41 (21.95%) showed CMPs among detected mouse strains. However, 11 out of 29 (37.9%) KO mice strains were recognized as having CMPs. The popular dinucleotide motifs in CMP were (TG)(n) (50%, 2/4), followed by (GT)(n) (27.27%, 3/11) and (CA)(n) (23.08%, 3/13). The microsatellite CMP in (CT)(n) and (AG)(n) repeats were 20% (1/5). According to cloning sequencing results, 6 KO mouse strains showed insertions of nucleotides whereas 1 showed a deletion. Furthermore, 2 loci (D13Mit3 and D14Mit102) revealed CMP in 2 strains, and mouse strain number 9 showed CMPs in two loci (D3Mit22 and D13Mit3) simultaneously. Collectively, these results indicated that microsatellite polymorphisms were present in the examined inbred KO mice.

  14. Analysis of microsatellite polymorphism in inbred knockout mice.

    Directory of Open Access Journals (Sweden)

    Baofen Zuo

    Full Text Available Previously, we found that the genotype of 42 out of 198 mouse microsatellite loci, which are distributed among all chromosomes except the Y chromosome, changed from monomorphism to polymorphism (CMP in a genetically modified inbred mouse strain. In this study, we further examined whether CMP also relates to the homologous recombination in gene knockout (KO mouse strains. The same 42 microsatellite loci were analyzed by polymerase chain reaction (PCR in 29 KO inbred mouse strains via short tandem sequence repeat (STR scanning and direct sequence cloning to justify microsatellite polymorphisms. The C57BL/6J and 129 mouse strains, from which these 29 KO mice were derived, were chosen as the background controls. The results indicated that 10 out of 42 (23.8% loci showed CMP in some of these mouse strains. Except for the trinucleotide repeat locus of D3Mit22, which had microsatellite CMP in strain number 9, the core sequences of the remaining 41 loci were dinucleotide repeats, and 9 out of 41 (21.95% showed CMPs among detected mouse strains. However, 11 out of 29 (37.9% KO mice strains were recognized as having CMPs. The popular dinucleotide motifs in CMP were (TG(n (50%, 2/4, followed by (GT(n (27.27%, 3/11 and (CA(n (23.08%, 3/13. The microsatellite CMP in (CT(n and (AG(n repeats were 20% (1/5. According to cloning sequencing results, 6 KO mouse strains showed insertions of nucleotides whereas 1 showed a deletion. Furthermore, 2 loci (D13Mit3 and D14Mit102 revealed CMP in 2 strains, and mouse strain number 9 showed CMPs in two loci (D3Mit22 and D13Mit3 simultaneously. Collectively, these results indicated that microsatellite polymorphisms were present in the examined inbred KO mice.

  15. Geographic structure of Plasmodium vivax: microsatellite analysis of parasite populations from Sri Lanka, Myanmar, and Ethiopia

    DEFF Research Database (Denmark)

    Gunawardena, Sharmini; Karunaweera, Nadira D; Ferreira, Marcelo U;

    2010-01-01

    , Myanmar, and Ethiopia using 12 trinucleotide and tetranucleotide microsatellite markers. All three parasite populations were highly polymorphic with 3-44 alleles per locus. Approximately 65% were multiple-clone infections. Mean genetic diversity (H(E)) was 0.7517 in Ethiopia, 0.8450 in Myanmar, and 0...... as a model identified 78.2% of isolates accurately as being African or Asian. Microsatellite analysis is a useful tool for mapping short-term outbreaks of malaria and for predicting ancestry....

  16. High Resolution Microsatellite Marker Analysis of Some Rice Landraces Using Metaphor Agarose Gel Electrophoresis

    OpenAIRE

    K. Kristamtini; T. Taryono; Panjisakti Basunanda; Rudi Hari Murti

    2016-01-01

    Microsatellite markers or simple sequences repeats are DNA - based molecular techniques that are used to see the different among accessions and inbred lines. There are three methods to analysis the results of the polymerase chain reaction of microsatellite markers namely polyacrylamide gel electrophoresis (PAGE), capillary electroforesis, and Metaphor Agarose Gel Electroforesis (MAGE), and the Use of MAGE assessed more easily and economically the polymorphic pattern of DNA markers...

  17. Analysis of genetic diversity in Bolivian llama populations using microsatellites.

    Science.gov (United States)

    Barreta, J; Gutiérrez-Gil, B; Iñiguez, V; Romero, F; Saavedra, V; Chiri, R; Rodríguez, T; Arranz, J J

    2013-08-01

    South American camelids (SACs) have a major role in the maintenance and potential future of rural Andean human populations. More than 60% of the 3.7 million llamas living worldwide are found in Bolivia. Due to the lack of studies focusing on genetic diversity in Bolivian llamas, this analysis investigates both the genetic diversity and structure of 12 regional groups of llamas that span the greater part of the range of distribution for this species in Bolivia. The analysis of 42 microsatellite markers in the considered regional groups showed that, in general, there were high levels of polymorphism (a total of 506 detected alleles; average PIC across per marker: 0.66), which are comparable with those reported for other populations of domestic SACs. The estimated diversity parameters indicated that there was high intrapopulational genetic variation (average number of alleles and average expected heterozygosity per marker: 12.04 and 0.68, respectively) and weak genetic differentiation among populations (FST range: 0.003-0.052). In agreement with these estimates, Bolivian llamas showed a weak genetic structure and an intense gene flow between all the studied regional groups, which is due to the exchange of reproductive males between the different flocks. Interestingly, the groups for which the largest pairwise FST estimates were observed, Sud Lípez and Nor Lípez, showed a certain level of genetic differentiation that is probably due to the pattern of geographic isolation and limited communication infrastructures of these southern localities. Overall, the population parameters reported here may serve as a reference when establishing conservation policies that address Bolivian llama populations.

  18. Whole-genome linkage analysis in mapping alcoholism genes using single-nucleotide polymorphisms and microsatellites.

    Science.gov (United States)

    Wang, Shuang; Huang, Song; Liu, Nianjun; Chen, Liang; Oh, Cheongeun; Zhao, Hongyu

    2005-12-30

    There is currently a great interest in using single-nucleotide polymorphisms (SNPs) in genetic linkage and association studies because of the abundance of SNPs as well as the availability of high-throughput genotyping technologies. In this study, we compared the performance of whole-genome scans using SNPs with microsatellites on 143 pedigrees from the Collaborative Studies on Genetics of Alcoholism provided by Genetic Analysis Workshop 14. A total of 315 microsatellites and 10,081 SNPs from Affymetrix on 22 autosomal chromosomes were used in our analyses. We found that the results from the two scans had good overall concordance. One region on chromosome 2 and two regions on chromosome 7 showed significant linkage signals (i.e., NPL >or= 2) for alcoholism from both the SNP and microsatellite scans. The different results observed between the two scans may be explained by the difference observed in information content between the SNPs and the microsatellites.

  19. Microsatellite analysis in two populations of Kunming mice

    DEFF Research Database (Denmark)

    Shang, Haitao; Wei, Hong; Yue, Bingfei;

    2009-01-01

    populations are unclear. Fifteen microsatellite markers were screened by a fluorescence-based semi-automated genotyping method for the two main populations of Kunming mice from Beijing (BJ) and Shanghai (SH) in China. The observed number of alleles, effective number of alleles, observed heterozygosity...

  20. p53 and H-ras mutations and microsatellite instability in renal pelvic carcinomas of NON / Shi mice treated with N-butyl-N-(4-hydroxybutyl)-nitrosamine: different genetic alteration from urinary bladder carcinoma.

    Science.gov (United States)

    Gen, H; Yamamoto, S; Morimura, K; Min, W; Mitsuhashi, M; Murai, T; Mori, S; Hosono, M; Oohara, T; Makino, S; Wanibuchi, H; Fukushima, S

    2001-12-01

    We previously reported p53 mutations to be frequent (greater than 70%), whereas both H-ras mutations and microsatellite instability (MSI) were infrequent (about 10%), in urinary bladder carcinomas (UBCs) and their metastatic foci in the N-butyl-N-(4-hydroxybutyl)nitrosamine (BBN)-induced mouse urothelial carcinogenesis model. In the present study, an analysis of p53 and H-ras mutations as well as MSI was performed on 12 renal pelvic carcinomas (RPCs) and 8 metastatic or invading foci produced by the same experimental procedure. Histologically, 10 of the RPCs were transitional cell carcinomas and the remaining 2 were squamous cell carcinomas. p53 mutations were infrequent and only found in one primary RPC (8%), its metastatic foci and an invading lesion in another animal (in a total 2 of 12; 17%). H-ras mutations were slightly more frequent (found in 3 of 12 animals; 25%), 4 of 5 involving codon 44, GTG to GCG, not a hot-spot reported for human cancers. In two cases, H-ras mutations were confined to lung metastasis and not detectable in their primary RPCs. MSI analysis was available for 6 pairs of primary RPCs and their metastatic foci, and 4 animals (67%) had MSI at one or more microsatellite loci. Overall, the distribution of genetic alterations differed from that in UBCs produced by the same experimental protocol. The results thus suggest that different genetic pathways may participate in carcinogenesis of the upper and lower urinary tract due to BBN.

  1. Heterogenous MSH6 loss is a result of microsatellite instability within MSH6 and occurs in sporadic and hereditary colorectal and endometrial carcinomas.

    Science.gov (United States)

    Graham, Rondell P; Kerr, Sarah E; Butz, Malinda L; Thibodeau, Stephen N; Halling, Kevin C; Smyrk, Thomas C; Dina, Michelle A; Waugh, Victoria M; Rumilla, Kandelaria M

    2015-10-01

    Mismatch-repair (MMR) immunohistochemistry is used to detect tumor MMR deficiency associated with high-level microsatellite instability (MSI). Rare tumors show heterogenous loss of mutS homolog 6 (MSH6) with immunohistochemistry, defined by areas of retained staining and separate areas of complete loss of staining. To investigate the clinical interpretation of this phenomenon, we identified 22 cases of heterogenous MSH6 loss interpreted at Mayo Clinic from January 2001 through December 2012 and reviewed histologic features, MSH6 and other MMR immunohistochemistry, and accompanying MSI testing results (n=20). Heterogenous MSH6 loss was seen in colorectal carcinoma (n=18), endometrial carcinoma (n=3), and sebaceous neoplasm (n=1). In the 18 colorectal carcinoma cases, it accompanied complete loss of mutL homolog 1 (MLH1) or PMS2, or both. Heterogenous MSH6 loss was characterized by MSI and MSH6 C8 tract instability in treatment-naive cases and showed mucinous or signet-ring zones in one quarter of cases. Two cases status post neoadjuvant chemoradiation showed heterogenous MSH6 loss but were microsatellite and C8 tract stable. C8 tracts were unstable in 2 of 4 MSH6-associated Lynch syndrome (LS) tumors, but all 4 showed complete MSH6 loss on immunohistochemistry. Further, 12 such MSH6-associated LS cases showed complete MSH6 loss. In conclusion, heterogenous MSH6 loss is uncommon, usually caused by instability in MSH6 exon 5 polycytosine tract, and not associated with germline MSH6 mutation. Although heterogenous MSH6 loss provides evidence against germline MSH6 mutation, patients whose tumors exhibit this immunolabeling pattern may have LS due to a defect in a different MMR gene.

  2. Microsatellite instability derived JAK1 frameshift mutations are associated with tumor immune evasion in endometrioid endometrial cancer

    NARCIS (Netherlands)

    Stelloo, Ellen; Versluis, Marco A; Nijman, Hans W; de Bruyn, Marco; Plat, Annechien; Osse, Elisabeth M; van Dijk, Reinhardt H; Nout, Remi A; Creutzberg, Carien L; de Bock, Geertruida H; Smit, Vincent T; Bosse, Tjalling; Hollema, Harry

    2016-01-01

    JAK1 frameshift mutations may promote cancer cell immune evasion by impeding upregulation of the antigen presentation pathway in microsatellite unstable endometrial cancers (ECs). This study investigated the JAK1 mutation frequency, its functional implication in immune evasion and its prognostic sig

  3. Microsatellite analysis of paternity and reproduction in Arctic grizzly bears.

    Science.gov (United States)

    Craighead, L; Paetkau, D; Reynolds, H V; Vyse, E R; Strobeck, C

    1995-01-01

    We report data from analyses of microsatellite loci of 30 grizzly bear family groups which demonstrate that each cub in a litter can be sired independently, and we derive estimates of maximum reproductive success for males, from an Arctic population in northwestern Alaska that is minimally affected by human activities. These analyses were made possible by the use of single-locus primers that amplified both of an individual's alleles at eight microsatellite loci and by detailed knowledge of maternal/offspring relationships that allowed the identification of paternal alleles. No single male was responsible for more than approximately 11% of known offspring, and no more than 49% of breeding-age males successfully bred. These data contribute to an understanding of the genetic and demographic basis of male reproductive success, which is of vital importance in the maintenance of small, isolated grizzly bear populations.

  4. Genetic changes of p53, K-ras, and microsatellite instability in gallbladder carcinoma in high-incidence areas of Japan and Hungary

    Institute of Scientific and Technical Information of China (English)

    Masayuki Nagahashi; Toshifumi Wakai; Yoshio Shirai; Katsuyoshi Hatakeyama; Masaharu Yamamoto; Yoichi Ajioka; Istvan Lang; Zoltan Szentirmay; Miklos Kasler; Hiroto Nakadaira; Naoyuki Yokoyama; Gen Watanabe; Ken Nishikura

    2008-01-01

    AIM:To disclose geographic differences in genetic changes involved in gallbladder carcinogenesis between two distinct high-incidence areas of Japan and Hungary. METHODS: We examined 42 cases of gallbladder carcinoma: 22 Japanese and 20 Hungarian cases, p53 mutations at exons 5 to 8 and K-ras mutations at codon 12 were tested by direct sequencing. Microsatellite instability was determined from fluorescent dye-labeled PCR amplifications of five-microsatellite markers (BAT-25, BAT-25, D2S123, D5S346, and D17S250).RESULTS: Mutations of p53 were detected in 11 of 22 Japanese cases and 6 of 18 Hungarian cases (11/22 vs 6/18, P = 0.348). Transition at CpG sites was found in none of 11 Japanese cases and 2 of 6 Hungarian cases; the difference was marginally significant (0/11 vs 2/6,P = 0.110). K-ras mutations were detected in only one of the Hungarian cases. Eight of 19 (42.1%) Japanese cases were MSI-high (presence of novel peaks in more than one of the five loci analyzed), whereas only 1 of 15 (6.7%) Hungarian cases was HSI-high (P = 0.047). CONCLUSION: It appears that the p53 mutations and MSI differ in patients with gallbladder carcinoma between two distinct high-incidence areas. Geographic variation might exist in the process of gallbladder carcinogenesis.

  5. Historical metal pollution in natural gudgeon populations: Inferences from allozyme, microsatellite and condition factor analysis

    Energy Technology Data Exchange (ETDEWEB)

    Knapen, Dries, E-mail: dries.knapen@ua.ac.be [University of Antwerp, Department of Biology, Ecophysiology, Biochemistry and Toxicology Research Group, Groenenborgerlaan 171, 2020 Antwerpen (Belgium); De Wolf, Hans [University of Antwerp, Department of Biology, Ecophysiology, Biochemistry and Toxicology Research Group, Groenenborgerlaan 171, 2020 Antwerpen (Belgium); Knaepkens, Guy [University of Antwerp, Department of Biology, Ethology Research Group, Universiteitsplein 1, 2610 Wilrijk (Belgium); Bervoets, Lieven [University of Antwerp, Department of Biology, Ecophysiology, Biochemistry and Toxicology Research Group, Groenenborgerlaan 171, 2020 Antwerpen (Belgium); Eens, Marcel [University of Antwerp, Department of Biology, Ethology Research Group, Universiteitsplein 1, 2610 Wilrijk (Belgium); Blust, Ronny [University of Antwerp, Department of Biology, Ecophysiology, Biochemistry and Toxicology Research Group, Groenenborgerlaan 171, 2020 Antwerpen (Belgium); Verheyen, Erik [Royal Belgian Institute of Natural Sciences, Department of Vertebrates, Molecular Laboratory, Vautierstraat 29, 1000 Brussel (Belgium)

    2009-10-19

    This study presents the results of a microsatellite and allozyme analysis on natural populations of the gudgeon (Gobio gobio) located in a pollution gradient of cadmium and zinc. Differences among contaminated and reference populations were observed at 2 allozyme loci, as well as a relationship between the fish condition factor and glucose-6-phosphate dehydrogenase genotypes, the locus that showed the largest difference in allele frequencies. The microsatellite data partly confirmed the differentiation pattern that was revealed by the allozyme survey. Our data further suggest that at least 2 microsatellite loci may be affected by natural selection. We thus illustrate that both microsatellite and allozyme loci do not necessarily behave as selectively neutral markers in polluted populations. Estimates of population differentiation can therefore be significantly different depending on which loci are being studied. Finally, these results are discussed in the light of the conservation unit concept, because microsatellites are often used to assess genetic variation in endangered natural populations and to propose measures for conservation or management.

  6. Microsatellite analysis in the genome of Acanthaceae: An in silico approach

    Directory of Open Access Journals (Sweden)

    Priyadharsini Kaliswamy

    2015-01-01

    Full Text Available Background: Acanthaceae is one of the advanced and specialized families with conventionally used medicinal plants. Simple sequence repeats (SSRs play a major role as molecular markers for genome analysis and plant breeding. The microsatellites existing in the complete genome sequences would help to attain a direct role in the genome organization, recombination, gene regulation, quantitative genetic variation, and evolution of genes. Objective: The current study reports the frequency of microsatellites and appropriate markers for the Acanthaceae family genome sequences. Materials and Methods: The whole nucleotide sequences of Acanthaceae species were obtained from National Center for Biotechnology Information database and screened for the presence of SSRs. SSR Locator tool was used to predict the microsatellites and inbuilt Primer3 module was used for primer designing. Results: Totally 110 repeats from 108 sequences of Acanthaceae family plant genomes were identified, and the occurrence of dinucleotide repeats was found to be abundant in the genome sequences. The essential amino acid isoleucine was found rich in all the sequences. We also designed the SSR-based primers/markers for 59 sequences of this family that contains microsatellite repeats in their genome. Conclusion: The identified microsatellites and primers might be useful for breeding and genetic studies of plants that belong to Acanthaceae family in the future.

  7. The same but different: monomorphic microsatellite markers as a new tool for genetic analysis.

    Science.gov (United States)

    Nazareno, Alison G; dos Reis, Mauricio S

    2011-10-01

    The nucleotide variation at a microsatellite locus lacking length polymorphisms among its alleles was assessed to generate an informative tool for genetic analysis. From a set of microsatellite markers, a monomorphic microsatellite locus developed for the palm species Butia eriospatha was used to elucidate whether there are polymorphic sites in its flanking regions. DNA sequences ≈133 bp long were obtained. Aligned sequences show variation at 17 polymorphic sites with both insertions and nucleotide substitutions. Fourteen distinct sequences (alleles) among 22 individuals were identified. The percent sequence difference varied from 0.0 to 5%, indicating that there is significant variation among sequences. Due to significant levels of information and sequence diversity on a simple sequence repeat (SSR) locus of identical size, our study highlights that this molecular marker class can be a useful tool for population genetics and evolutionary studies for many plant species.

  8. Comparative Analysis of the Korean Population of Magnaporthe oryzae by Multilocus Microsatellite Typing

    Directory of Open Access Journals (Sweden)

    Jaehyuk Choi

    2013-12-01

    Full Text Available Rice blast fungus, Magnaporthe oryzae, inflicts serious damage to global rice production. Due to high variability of this fungal pathogen, resistance of newly-released rice cultivars is easily broken down. To understand the population structure of M. oryzae, we analyzed the genetic diversity of the Korean population using multilocus microsatellite typing. Eleven microsatellite markers were applied to the population of 190 rice isolates which had been collected in Korea for two decades since the 1980’s. Average values of gene diversity and allele frequency were 0.412 and 6.5, respectively. Comparative analysis of the digitized allele information revealed that the Korean population exhibited a similar level of allele diversity to the integrated diversity of the world populations, suggesting a particularly high diversity of the Korean population. Therefore, these microsatellite markers and the comprehensive collection of field isolates will be useful genetic resources to identify the genetic diversity of M. oryzae population.

  9. Oligodeoxynucleotide binding to (CTG) · (CAG) microsatellite repeats inhibits replication fork stalling, hairpin formation, and genome instability.

    Science.gov (United States)

    Liu, Guoqi; Chen, Xiaomi; Leffak, Michael

    2013-02-01

    (CTG)(n) · (CAG)(n) trinucleotide repeat (TNR) expansion in the 3' untranslated region of the dystrophia myotonica protein kinase (DMPK) gene causes myotonic dystrophy type 1. However, a direct link between TNR instability, the formation of noncanonical (CTG)(n) · (CAG)(n) structures, and replication stress has not been demonstrated. In a human cell model, we found that (CTG)(45) · (CAG)(45) causes local replication fork stalling, DNA hairpin formation, and TNR instability. Oligodeoxynucleotides (ODNs) complementary to the (CTG)(45) · (CAG)(45) lagging-strand template eliminated DNA hairpin formation on leading- and lagging-strand templates and relieved fork stalling. Prolonged cell culture, emetine inhibition of lagging-strand synthesis, or slowing of DNA synthesis by low-dose aphidicolin induced (CTG)(45) · (CAG)(45) expansions and contractions. ODNs targeting the lagging-strand template blocked the time-dependent or emetine-induced instability but did not eliminate aphidicolin-induced instability. These results show directly that TNR replication stalling, replication stress, hairpin formation, and instability are mechanistically linked in vivo.

  10. Complementary analysis of microsatellite tumor profile and mismatch repair defects in colorectal carcinomas

    Institute of Scientific and Technical Information of China (English)

    Alfredo Blanes; Salvador J Diaz-Cano

    2006-01-01

    Microsatellite instability (MSI) is a prognostic factor and a marker of deficient mismatch repair (MMR) in colorectal adenocarcinomas (CRC). However, a proper application of this marker requires understanding the following: (1)The MSI concept: The PCR approach must amplify the correct locus and accurately identify the microsatellite pattern in the patient's normal tissue. MSI is demonstrated when the length of DNA sequences in a tumor differs from that of nontumor tissue. Any anomalous expansion or reduction of tandem repeats results in extra-bands normally located in the expected size range (100 bp,above or below the expected product), differ from the germline pattern by some multiple of the repeating unit,and must show appropriate stutter. (2) MSI mechanisms:MMR gene inactivation (by either mutation or protein down-regulation as frequently present in deep CRC compartments) leads to mutation accumulation in a cell with every cellular division, resulting in malignant transformation. These mechanisms can express tumor progression and result in a decreased prevalence of aneuploid cells and loss of the physiologic cell kinetic correlations in the deep CRC compartments. MSI molecular mechanisms are not necessarily independent from chromosomal instability and may coexist in a given CRC. (3) Because of intratumoural heterogeneity, at least two samples from each CRC should be screened, preferably from the superficial (tumor cells above the muscularis propria) and deep (tumor cells infiltrating the muscularis propria) CRC compartments to cover the topographic tumor heterogeneity. (4) Pathologists play a critical role in identifying microsatellite-unstable CRC, such as occur in young patients with synchronous or metachronous tumors or with tumors showing classic histologic features. In these cases, MSI testing and/or MMR immunohistochemistry are advisable, along with gene sequencing and genetic counseling if appropriate. MSI is an excellent functional and prognostically

  11. T cell responses against microsatellite instability-induced frameshift peptides and influence of regulatory T cells in colorectal cancer.

    Science.gov (United States)

    Bauer, Kathrin; Nelius, Nina; Reuschenbach, Miriam; Koch, Moritz; Weitz, Jürgen; Steinert, Gunnar; Kopitz, Jürgen; Beckhove, Philipp; Tariverdian, Mirjam; von Knebel Doeberitz, Magnus; Kloor, Matthias

    2013-01-01

    High-level microsatellite-unstable (MSI-H) colorectal carcinomas (CRC) represent a distinct subtype of tumors commonly characterized by dense infiltration with cytotoxic T cells, most likely due to expression of MSI-H-related frameshift peptides (FSP). The contribution of FSP and classical antigens like MUC1 and CEA to the cellular immune response against MSI-H CRC had not been analyzed so far. We analyzed tumor-infiltrating and peripheral T cells from MSI-H (n = 4 and n = 14, respectively) and microsatellite-stable (MSS) tumor patients (n = 26 and n = 17) using interferon gamma ELISpot assays. Responses against 4 FSP antigens and peptides derived from MUC1 to CEA were compared with and without depletion of regulatory T cells, and the results were related to the presence of the respective antigens in tumor tissue. Preexisting FSP-specific T cell responses were detected in all (4 out of 4) tumor-infiltrating and in the majority (10 out of 14) of peripheral T cell samples from MSI-H CRC patients, but rarely observed in MSS CRC patients. Preexisting T cell responses in MSI-H CRC patients were significantly more frequently directed against FSP tested in the present study than against peptides derived from classical antigens MUC1 or CEA (p = 0.049). Depletion of regulatory T cells increased the frequency of effector T cell responses specific for MUC1/CEA-derived peptides and, to a lesser extent, T cell responses specific for FSP. Our data suggest that the analyzed FSP may represent an immunologically relevant pool of antigens capable of eliciting antitumoral effector T cell responses.

  12. Identification and Characterization of Microsatellite Markers Derived from the Whole Genome Analysis of Taenia solium

    Science.gov (United States)

    Pajuelo, Mónica J.; Eguiluz, María; Dahlstrom, Eric; Requena, David; Guzmán, Frank; Ramirez, Manuel; Sheen, Patricia; Frace, Michael; Sammons, Scott; Cama, Vitaliano; Anzick, Sarah; Bruno, Dan; Mahanty, Siddhartha; Wilkins, Patricia; Nash, Theodore; Gonzalez, Armando; García, Héctor H.; Gilman, Robert H.; Porcella, Steve; Zimic, Mirko

    2015-01-01

    Background Infections with Taenia solium are the most common cause of adult acquired seizures worldwide, and are the leading cause of epilepsy in developing countries. A better understanding of the genetic diversity of T. solium will improve parasite diagnostics and transmission pathways in endemic areas thereby facilitating the design of future control measures and interventions. Microsatellite markers are useful genome features, which enable strain typing and identification in complex pathogen genomes. Here we describe microsatellite identification and characterization in T. solium, providing information that will assist in global efforts to control this important pathogen. Methods For genome sequencing, T. solium cysts and proglottids were collected from Huancayo and Puno in Peru, respectively. Using next generation sequencing (NGS) and de novo assembly, we assembled two draft genomes and one hybrid genome. Microsatellite sequences were identified and 36 of them were selected for further analysis. Twenty T. solium isolates were collected from Tumbes in the northern region, and twenty from Puno in the southern region of Peru. The size-polymorphism of the selected microsatellites was determined with multi-capillary electrophoresis. We analyzed the association between microsatellite polymorphism and the geographic origin of the samples. Results The predicted size of the hybrid (proglottid genome combined with cyst genome) T. solium genome was 111 MB with a GC content of 42.54%. A total of 7,979 contigs (>1,000 nt) were obtained. We identified 9,129 microsatellites in the Puno-proglottid genome and 9,936 in the Huancayo-cyst genome, with 5 or more repeats, ranging from mono- to hexa-nucleotide. Seven microsatellites were polymorphic and 29 were monomorphic within the analyzed isolates. T. solium tapeworms were classified into two genetic groups that correlated with the North/South geographic origin of the parasites. Conclusions/Significance The availability of draft

  13. Identification and Characterization of Microsatellite Markers Derived from the Whole Genome Analysis of Taenia solium.

    Directory of Open Access Journals (Sweden)

    Mónica J Pajuelo

    2015-12-01

    Full Text Available Infections with Taenia solium are the most common cause of adult acquired seizures worldwide, and are the leading cause of epilepsy in developing countries. A better understanding of the genetic diversity of T. solium will improve parasite diagnostics and transmission pathways in endemic areas thereby facilitating the design of future control measures and interventions. Microsatellite markers are useful genome features, which enable strain typing and identification in complex pathogen genomes. Here we describe microsatellite identification and characterization in T. solium, providing information that will assist in global efforts to control this important pathogen.For genome sequencing, T. solium cysts and proglottids were collected from Huancayo and Puno in Peru, respectively. Using next generation sequencing (NGS and de novo assembly, we assembled two draft genomes and one hybrid genome. Microsatellite sequences were identified and 36 of them were selected for further analysis. Twenty T. solium isolates were collected from Tumbes in the northern region, and twenty from Puno in the southern region of Peru. The size-polymorphism of the selected microsatellites was determined with multi-capillary electrophoresis. We analyzed the association between microsatellite polymorphism and the geographic origin of the samples.The predicted size of the hybrid (proglottid genome combined with cyst genome T. solium genome was 111 MB with a GC content of 42.54%. A total of 7,979 contigs (>1,000 nt were obtained. We identified 9,129 microsatellites in the Puno-proglottid genome and 9,936 in the Huancayo-cyst genome, with 5 or more repeats, ranging from mono- to hexa-nucleotide. Seven microsatellites were polymorphic and 29 were monomorphic within the analyzed isolates. T. solium tapeworms were classified into two genetic groups that correlated with the North/South geographic origin of the parasites.The availability of draft genomes for T. solium represents a

  14. STAMP: Extensions to the STADEN sequence analysis package for high throughput interactive microsatellite marker design.

    Science.gov (United States)

    Kraemer, Lars; Beszteri, Bánk; Gäbler-Schwarz, Steffi; Held, Christoph; Leese, Florian; Mayer, Christoph; Pöhlmann, Kevin; Frickenhaus, Stephan

    2009-01-30

    Microsatellites (MSs) are DNA markers with high analytical power, which are widely used in population genetics, genetic mapping, and forensic studies. Currently available software solutions for high-throughput MS design (i) have shortcomings in detecting and distinguishing imperfect and perfect MSs, (ii) lack often necessary interactive design steps, and (iii) do not allow for the development of primers for multiplex amplifications. We present a set of new tools implemented as extensions to the STADEN package, which provides the backbone functionality for flexible sequence analysis workflows. The possibility to assemble overlapping reads into unique contigs (provided by the base functionality of the STADEN package) is important to avoid developing redundant markers, a feature missing from most other similar tools. Our extensions to the STADEN package provide the following functionality to facilitate microsatellite (and also minisatellite) marker design: The new modules (i) integrate the state-of-the-art tandem repeat detection and analysis software PHOBOS into workflows, (ii) provide two separate repeat detection steps - with different search criteria - one for masking repetitive regions during assembly of sequencing reads and the other for designing repeat-flanking primers for MS candidate loci, (iii) incorporate the widely used primer design program PRIMER3 into STADEN workflows, enabling the interactive design and visualization of flanking primers for microsatellites, and (iv) provide the functionality to find optimal locus- and primer pair combinations for multiplex primer design. Furthermore, our extensions include a module for storing analysis results in an SQLite database, providing a transparent solution for data access from within as well as from outside of the STADEN Package. The STADEN package is enhanced by our modules into a highly flexible, high-throughput, interactive tool for conventional and multiplex microsatellite marker design. It gives the user

  15. Microsatellite instability in solitary and sporadic gastric cancer Instabilidade de microsatelites no cancer gástrico solitário e esporádico

    Directory of Open Access Journals (Sweden)

    Rodrigo Oliva Perez

    2004-01-01

    Full Text Available Recently, the presence of microsatellite instability (MSI has been reported in gastric cancer and associated with older age of presentation, distal tumor location, early disease staging, and better overall prognosis. Different characteristics in presentation and in tumor behavior may be explained by different genetic alterations during carcinogenesis of gastric cancer. Identification of specific genetic pathways in gastric cancer may have direct impact on prognosis and selection of treatment strategies. PATIENTS AND METHODS: All 24 patients were treated by radical surgery. Fragments of normal and tumor tissues were extracted from the specimen and stored at -80ºC before DNA purification and extraction. PCR amplification utilizing microsatellite markers was performed. Tumors presenting PCR products of abnormal sizes were considered positive for microsatellite instability (MSI+. RESULTS: Five patients (21% had tumors that were MSI+ in at least 1 marker. In the group of patients with Lauren's intestinal-type gastric carcinoma, 3 had tumors that were MSI+ (23%, while in the group of diffuse-type gastric cancer, 2 patients had tumors that were MSI+ (19%. The mean age of presentation and the male:female ratio was similar in both groups. Tumors that were MSI+ were more frequently located in proximal portion of the stomach compared to microsatellite-stable (MSS tumors (40% vs. 16%. Although there was a trend of patients with MSI+ tumors towards a proximal gastric tumor location, early staging, and negative lymph node metastasis, there was no statistical significance compared to those with MSS tumors (P >.1. Comparison of overall and disease-free survival between gastric tumors that were MSI+ and those that were MSS found no statistically significant differences (P >.1. CONCLUSIONS: Microsatellite instability is a frequent event in gastric carcinogenesis and shows a trend towards distinct clinical and pathological characteristics of gastric cancer

  16. Comparative analysis of microsatellites in chloroplast genomes of lower and higher plants.

    Science.gov (United States)

    George, Biju; Bhatt, Bhavin S; Awasthi, Mayur; George, Binu; Singh, Achuit K

    2015-11-01

    Microsatellites, or simple sequence repeats (SSRs), contain repetitive DNA sequence where tandem repeats of one to six base pairs are present number of times. Chloroplast genome sequences have been  shown to possess extensive variations in the length, number and distribution of SSRs. However, a comparative analysis of chloroplast microsatellites is not available. Considering their potential importance in generating genomic diversity, we have systematically analysed the abundance and distribution of simple and compound microsatellites in 164 sequenced chloroplast genomes from wide range of plants. The key findings of these studies are (1) a large number of mononucleotide repeats as compared to SSR(2-6)(di-, tri-, tetra-, penta-, hexanucleotide repeats) are present in all chloroplast genomes investigated, (2) lower plants such as algae show wide variation in relative abundance, density and distribution of microsatellite repeats as compared to flowering plants, (3) longer SSRs are excluded from coding regions of most chloroplast genomes, (4) GC content has a weak influence on number, relative abundance and relative density of mononucleotide as well as SSR(2-6). However, GC content strongly showed negative correlation with relative density (R (2) = 0.5, P plants possesses relatively more genomic diversity compared to higher plants.

  17. Microsatellite analysis of serum DNA in patients with oral squamous cell carcinoma.

    Science.gov (United States)

    Kakimoto, Yoshidou; Yamamoto, Nobuharu; Shibahara, Takahiko

    2008-11-01

    The purpose of this study was to assess the possibility of prognosis of oral squamous cell carcinoma by microsatellite blood assay. Altered microsatellite DNA in the blood of cancer patients may provide a novel method for tumor detection. DNA from normal and tumor tissues and serum obtained at two time-points (preoperatively and postoperatively) in 20 patients with oral squamous cell carcinoma was examined at 9 microsatellite loci on chromosomes 2, 3, and 21 by polymerase chain reaction (PCR)-based analysis of loss of heterozygosity (LOH). Eighteen patients (90%) showed microsatellite alterations in serum DNA identical to those in the corresponding tumor DNA. Among those showing allelic imbalance preoperatively (18 patients, 90%), 8 patients (44%) showed no evidence of allelic imbalance in serum postoperatively, and these showed no recurrence or distant metastasis. In 10 patients, allelic imbalance was detected postoperatively in serum. Seven (70%) out of these 10 patients showed an allelic imbalance at both time-points (preoperatively and postoperatively), and these patients had a poor prognosis. In conclusion, this study suggests that blood testing for circulating tumor genetic markers may provide valuable prognostic information and a guide for future therapy.

  18. Influence of anatomical subsite on the incidence of microsatellite instability, and KRAS and BRAF mutation rates in patients with colon carcinoma.

    Science.gov (United States)

    Benedix, Frank; Meyer, Frank; Kube, Rainer; Kropf, Siegfried; Kuester, Doerthe; Lippert, Hans; Roessner, Albert; Krüger, Sabine

    2012-10-15

    There is a growing amount of data supporting the concept that cancers originating from the proximal and distal colon are distinct clinicopathological entities. The incidence of MSI and BRAF mutation is strongly associated with right sided tumor location, whereas there are conflicting results for KRAS mutation rates. However, to date, no data exist whether and to what extent defined colonic subsites influence MSI status, KRAS and BRAF mutation rates. We selected primary colon cancer from 171 patients operated on at our institution between 2007 and 2010. BRAF, KRAS mutation rates and microsatellite instability were determined and correlated with clinicopathological features and tumor location. MSI-h cancers were significantly associated with poor histological grade but a lower rate of distant metastases. KRAS-mutated tumors were linked to lower T-stage and better differentiation. Colon carcinomas with BRAF mutation were significantly associated with distant metastatic spread and poor histological grade. Furthermore, we found that MSI-h status, KRAS and BRAF mutation rates varied remarkably among the colonic subsites irrespective of right- and left-sided origin, respectively. The results of the current study provide further evidence that a simple classification into right- and left-sided colon carcinoma does not represent the complexity of this tumor entity.

  19. Waves and Instabilities in Accretion Disks MHD Spectroscopic Analysis

    CERN Document Server

    Keppens, R; Goedbloed, J P

    2002-01-01

    A complete analytical and numerical treatment of all magnetohydrodynamic waves and instabilities for radially stratified, magnetized accretion disks is presented. The instabilities are a possible source of anomalous transport. While recovering results on known hydrodynamicand both weak- and strong-field magnetohydrodynamic perturbations, the full magnetohydrodynamic spectra for a realistic accretion disk model demonstrates a much richer variety of instabilities accessible to the plasma than previously realized. We show that both weakly and strongly magnetized accretion disks are prone to strong non-axisymmetric instabilities.The ability to characterize all waves arising in accretion disks holds great promise for magnetohydrodynamic spectroscopic analysis.

  20. Analysis of microsatellites from the transcriptome of downy mildew pathogens and their application for characterization of Pseudoperonospora populations

    Directory of Open Access Journals (Sweden)

    Emma C. Wallace

    2017-05-01

    Full Text Available Downy mildew pathogens affect several economically important crops worldwide but, due to their obligate nature, few genetic resources are available for genomic and population analyses. Draft genomes for emergent downy mildew pathogens such as the oomycete Pseudoperonospora cubensis, causal agent of cucurbit downy mildew, have been published and can be used to perform comparative genomic analysis and develop tools such as microsatellites to characterize pathogen population structure. We used bioinformatics to identify 2,738 microsatellites in the P. cubensis predicted transcriptome and evaluate them for transferability to the hop downy mildew pathogen, Pseudoperonospora humuli, since no draft genome is available for this species. We also compared the microsatellite repertoire of P. cubensis to that of the model organism Hyaloperonospora arabidopsidis, which causes downy mildew in Arabidopsis. Although trends in frequency of motif-type were similar, the percentage of SSRs identified from P. cubensis transcripts differed significantly from H. arabidopsidis. The majority of a subset of microsatellites selected for laboratory validation (92% produced a product in P. cubensis isolates, and 83 microsatellites demonstrated transferability to P. humuli. Eleven microsatellites were found to be polymorphic and consistently amplified in P. cubensis isolates. Analysis of Pseudoperonospora isolates from diverse hosts and locations revealed higher diversity in P. cubensis compared to P. humuli isolates. These microsatellites will be useful in efforts to better understand relationships within Pseudoperonospora species and P. cubensis on a population level.

  1. [Analysis of genetic variations in different goose breeds using microsatellite markers].

    Science.gov (United States)

    Liu, Shuang; Li, Peng; Song, Yi; Li, Shi-Ze; Wei, Chun-Bo; Yang, Huan-Min

    2006-11-01

    The genetic diversity of six goose breeds (White Goose, Zi Goose, Huoyan Goose, Wanxi Goose, Rhin, Landoise) was analyzed using microsatellite markers. Heterozygosity(H), polymorphism information content (PIC) and genetic distances were calculated for each breed based on the allele frequency. Results showed that 7 microsatellite sites were highly polymorphic, and could be used as effective markers for analysis of genetic relationship among different goose breeds. The mean heterozygosityies of were between 0.6617 (Rhin) and 0.8814 (Zi goose), among six goose breeds, the lowest was Rhin goose (0.6617) and the highest was Zi goose (0.8814). The range of mean PIC was between 0.6145 and 0.7814, which was in the similar range as the mean heterozygosities. Based on the UPGMA cluster analysis results, six goose breeds were grouped into classes, White, Zi, Huoyan and Wanxi Goose in one class, and the foreign breeds of Rhin and Landoise goose in another class. These results indicated that the dendrogram obtain from genetic distance could be used to correctly reflect the phylogenetic relationship among the six goose breeds, suggesting that microsatellite DNA marker is a useful tool to determine the genetic diversity in closely related breeds.

  2. Comparative genomic analysis reveals species-dependent complexities that explain difficulties with microsatellite marker development in molluscs

    OpenAIRE

    2010-01-01

    Reliable population DNA molecular markers are difficult to develop for molluscs, the reasons for which are largely unknown. Identical protocols for microsatellite marker development were implemented in three gastropods. Success rates were lower for Gibbula cineraria compared to Littorina littorea and L. saxatilis. Comparative genomic analysis of 47.2 kb of microsatellite containing sequences (MCS) revealed a high incidence of cryptic repetitive DNA in their flanking regions. The majority of t...

  3. Coding Microsatellite Frameshift Mutations Accumulate in Atherosclerotic Carotid Artery Lesions: Evaluation of 26 Cases and Literature Review.

    Science.gov (United States)

    Kurz, Carolin; Hakimi, Maani; Kloor, Matthias; Grond-Ginsbach, Caspar; Gross-Weissmann, Marie-Luise; Böckler, Dittmar; von Knebel Doeberitz, Magnus; Dihlmann, Susanne

    2015-06-09

    Somatic DNA alterations are known to occur in atherosclerotic carotid artery lesions; however, their significance is unknown. The accumulation of microsatellite mutations in coding DNA regions may reflect a deficiency of the DNA mismatch repair (MMR) system. Alternatively, accumulation of these coding microsatellite mutations may indicate that they contribute to the pathology. To discriminate between these two possibilities, we compared the mutation frequencies in coding microsatellites (likely functionally relevant) with those in noncoding microsatellites (likely neutral). Genomic DNA was isolated from carotid endarterectomy (CEA) specimens of 26 patients undergoing carotid surgery and from 15 nonatherosclerotic control arteries. Samples were analyzed by DNA fragment analysis for instability at three noncoding (BAT25, BAT26, CAT25) and five coding (AIM2, ACVR2, BAX, CASP5, TGFBR2) microsatellite loci, with proven validity for detection of microsatellite instability in neoplasms. We found an increased frequency of coding microsatellite mutations in CEA specimens compared with control specimens (34.6 versus 0%; p = 0.0013). Five CEA specimens exhibited more than one frameshift mutation, and ACVR2 and CASP5 were affected most frequently (5/26 and 6/26). Moreover, the rate of coding microsatellite alterations (15/130) differed significantly from that of noncoding alterations (0/78) in CEA specimens (p = 0.0013). In control arteries, no microsatellite alterations were observed, neither in coding nor in noncoding microsatellite loci. In conclusion, the specific accumulation of coding mutations suggests that these mutations play a role in the pathogenesis of atherosclerotic carotid lesions, since the absence of mutations in noncoding microsatellites argues against general microsatellite instability, reflecting MMR deficiency.

  4. Microsatellite Analysis of Genetic Diversity Between Loach with Different Levels of Ploidy

    Institute of Scientific and Technical Information of China (English)

    Li Ya-juan; Qi Hong-rui; Ma Hai-yan; Zhou He; Xu Wen; Sui Yi; Li Jia-qi

    2014-01-01

    We used microsatellite markers to investigate the genetic parameters of three different polyploidy populations ofMisgurnus anguillicaudatus from Honghu City, Hubei Province. Polyacrylamide gel electrophoresis banding patterns of diploid (2n), triploid (3n) and tetraploid loaches (4n) were analyzed with PopGen software. A total of 68 alleles were obtained from seven microsatellite loci and the polymorphism information content (PIC) indices were all above 0.5. The average expected mean heterozygosity values (He) were 0.8420, 0.7186 and 0.8521; the average observed mean heterozygosity values (Ho) were 0.9674, 0.9785 and 0.8928; and the Hardy-WeinbergP values were 0.3078, 0.3151 and 0.3762, for diploid, triploid and tetraploid individuals, respectively. The results indicated that the three populations were highly polymorphic, with no deviations from Hardy-Weinberg equilibrium observed at all the seven microsatellite loci. This indicated a high level of genetic diversity within the populations. A cluster analysis diagram showed that the shortest genetic distance was between diploid and tetraploid loaches and they shared a close phylogenetic relationship. The triploid and tetraploid individuals had the most distant phylogenetic relationship.

  5. Identification of geographically distributed sub-populations of Leishmania (Leishmania major by microsatellite analysis

    Directory of Open Access Journals (Sweden)

    Schwenkenbecher Jan

    2008-06-01

    Full Text Available Abstract Background Leishmania (Leishmania major, one of the agents causing cutaneous leishmaniasis (CL in humans, is widely distributed in the Old World where different species of wild rodent and phlebotomine sand fly serve as animal reservoir hosts and vectors, respectively. Despite this, strains of L. (L. major isolated from many different sources over many years have proved to be relatively uniform. To investigate the population structure of the species highly polymorphic microsatellite markers were employed for greater discrimination among it's otherwise closely related strains, an approach applied successfully to other species of Leishmania. Results Multilocus Microsatellite Typing (MLMT based on 10 different microsatellite markers was applied to 106 strains of L. (L. major from different regions where it is endemic. On applying a Bayesian model-based approach, three main populations were identified, corresponding to three separate geographical regions: Central Asia (CA; the Middle East (ME; and Africa (AF. This was congruent with phylogenetic reconstructions based on genetic distances. Re-analysis separated each of the populations into two sub-populations. The two African sub-populations did not correlate well with strains' geographical origin. Strains falling into the sub-populations CA and ME did mostly group according to their place of isolation although some anomalies were seen, probably, owing to human migration. Conclusion The model- and distance-based analyses of the microsatellite data exposed three main populations of L. (L. major, Central Asia, the Middle East and Africa, each of which separated into two sub-populations. This probably correlates with the different species of rodent host.

  6. Dynamic Radiographic Analysis of Sympathetic Cervical Spondylosis Instability

    Institute of Scientific and Technical Information of China (English)

    Jun Qian; Ye Tian; Gui-xing Qiu; Jian-hua Hu

    2009-01-01

    Objective To investigate the correlation between subaxial cervical spine instability and cervical spondylotic sympathetic symptoms as well as the difference of cervical spondylotic subaxial instability between male and female patients. Methods We analyzed retrospectively 318 surgical cases of cervical spondylosis treated at Department of Orthopedic Surgery of Peking Union Medical College Hospital between July 2003 and December 2007. All cases were divided into group A without sympathetic symptoms (n=284) and group B with sympathetic symptoms (n=34). Angular and horizontal translation values between two adjacent vertebral bodies from C2 to C7 were measured separately on hyperflexion and hyperextension lateral cervical spine radiographs. Fisher's exact test was used to evaluate the correlation between subaxial cervical instability and sympathetic symptoms. Intragroup correlation between patient gender and subaxial cervical instability was also evaluated. Results Subaxial instability incidences in groups A and B were 21.8% (62/284) and 55.9% (19/34), respectively. Statistical analysis indicated a definite correlation between subaxial cervical instability and sympathetic symptoms (P=0.000). Among patients without sympathetic symptoms, subaxial instability incidences were 21.4% (37/173) in males and 22.5% (25/111) in females, respectively (P=0.883). While among patients with sympathetic symptoms, subaxial instability incidences were 27.3% (3/11) in males and 69.6% (16/23) in females, respectively, indicating significant difference (P=0.030). Subaxial instability was most commonly seen at C4-C5 intervertebral space in sympathetic cervical spondylosis patients. Conclusions High correlation exists between subaxial cervical spine instability and cervical spondylotic sympathetic symptoms, especially in female patients. Hyperextension and hyperflexion radiographs of cervical spine are important to assess sympathetic cervical spondylotic subaxial instability.

  7. Population-Based Lynch Syndrome Screening by Microsatellite Instability in Patients ≤50: Prevalence, Testing Determinants, and Result Availability Prior to Colon Surgery.

    Science.gov (United States)

    Karlitz, Jordan J; Hsieh, Mei-Chin; Liu, Yong; Blanton, Christine; Schmidt, Beth; Jessup, J Milburn; Wu, Xiao-Cheng; Chen, Vivien W

    2015-07-01

    As there are no US population-based studies examining Lynch syndrome (LS) screening frequency by microsatellite instability (MSI) and immunohistochemistry (IHC), we seek to quantitate statewide rates in patients aged ≤50 years using data from a Centers for Disease Control and Prevention-funded Comparative Effectiveness Research (CER) project and identify factors associated with testing. Screening rates in this young, high-risk population may provide a best-case scenario as older patients, potentially deemed lower risk, may undergo testing less frequently. We also seek to determine how frequently MSI/IHC results are available preoperatively, as this may assist with decisions regarding colonic resection extent. Data from all Louisiana colorectal cancer (CRC) patients aged ≤50 years diagnosed in 2011 were obtained from the Louisiana Tumor Registry CER project. Registry researchers and physicians analyzed data, including pathology and MSI/IHC. Of the 2,427 statewide all-age CRC patients, there were 274 patients aged ≤50 years, representing health care at 61 distinct facilities. MSI and/or IHC were performed in 23.0% of patients. Testing-associated factors included CRC family history (Plocation (P<0.0370), and care at comprehensive cancer centers (P<0.0020) but not synchronous/metachronous CRC or MSI-like histology. Public hospital screening was disproportionately low (P<0.0217). Of those tested, MSI and/or IHC was abnormal in 21.7%. Of those with abnormal IHC, staining patterns were consistent with LS in 87.5%. MSI/IHC results were available preoperatively in 16.9% of cases. Despite frequently abnormal MSI/IHC results, LS screening in young, high-risk patients is low. Provider education and disparities in access to specialized services, particularly in underserved populations, are possible contributors. MSI/IHC results are infrequently available preoperatively.

  8. Nonmodal analysis of helical and azimuthal magnetorotational instabilities

    CERN Document Server

    Mamatsashvili, G

    2016-01-01

    The helical and the azimuthal magnetorotational instabilities operate in rotating magnetized flows with relatively steep negative or extremely steep positive shear. The corresponding lower and upper Liu limits of the shear, which determine the threshold of modal growth of these instabilities, are continuously connected when some axial electrical current is allowed to pass through the rotating fluid. We investigate the nonmodal dynamics of these instabilities arising from the nonnormality of shear flow in the local approximation, generalizing the results of the modal approach. It is demonstrated that moderate transient/nonmodal amplification of both types of magnetorotational instability occurs within the Liu limits, where the system is stable according to modal analysis. We show that for the helical magnetorotational instability this magnetohydrodynamic behavior is closely connected with the nonmodal growth of the underlying purely hydrodynamic problem.

  9. Parentage Reconstruction in Eucalyptus nitens Using SNPs and Microsatellite Markers: A Comparative Analysis of Marker Data Power and Robustness.

    Science.gov (United States)

    Telfer, Emily J; Stovold, Grahame T; Li, Yongjun; Silva-Junior, Orzenil B; Grattapaglia, Dario G; Dungey, Heidi S

    2015-01-01

    Pedigree reconstruction using molecular markers enables efficient management of inbreeding in open-pollinated breeding strategies, replacing expensive and time-consuming controlled pollination. This is particularly useful in preferentially outcrossed, insect pollinated Eucalypts known to suffer considerable inbreeding depression from related matings. A single nucleotide polymorphism (SNP) marker panel consisting of 106 markers was selected for pedigree reconstruction from the recently developed high-density Eucalyptus Infinium SNP chip (EuCHIP60K). The performance of this SNP panel for pedigree reconstruction in open-pollinated progenies of two Eucalyptus nitens seed orchards was compared with that of two microsatellite panels with 13 and 16 markers respectively. The SNP marker panel out-performed one of the microsatellite panels in the resolution power to reconstruct pedigrees and out-performed both panels with respect to data quality. Parentage of all but one offspring in each clonal seed orchard was correctly matched to the expected seed parent using the SNP marker panel, whereas parentage assignment to less than a third of the expected seed parents were supported using the 13-microsatellite panel. The 16-microsatellite panel supported all but one of the recorded seed parents, one better than the SNP panel, although there was still a considerable level of missing and inconsistent data. SNP marker data was considerably superior to microsatellite data in accuracy, reproducibility and robustness. Although microsatellites and SNPs data provide equivalent resolution for pedigree reconstruction, microsatellite analysis requires more time and experience to deal with the uncertainties of allele calling and faces challenges for data transferability across labs and over time. While microsatellite analysis will continue to be useful for some breeding tasks due to the high information content, existing infrastructure and low operating costs, the multi-species SNP resource

  10. The same but different: monomorphic microsatellite markers as a new tool for genetic analysis

    National Research Council Canada - National Science Library

    Nazareno, Alison G; dos Reis, Mauricio S

    2011-01-01

    .... From a set of microsatellite markers, a monomorphic microsatellite locus developed for the palm species Butia eriospatha was used to elucidate whether there are polymorphic sites in its flanking regions. DNA sequences...

  11. Lattice Boltzmann methods for global linear instability analysis

    Science.gov (United States)

    Pérez, José Miguel; Aguilar, Alfonso; Theofilis, Vassilis

    2016-11-01

    Modal global linear instability analysis is performed using, for the first time ever, the lattice Boltzmann method (LBM) to analyze incompressible flows with two and three inhomogeneous spatial directions. Four linearization models have been implemented in order to recover the linearized Navier-Stokes equations in the incompressible limit. Two of those models employ the single relaxation time and have been proposed previously in the literature as linearization of the collision operator of the lattice Boltzmann equation. Two additional models are derived herein for the first time by linearizing the local equilibrium probability distribution function. Instability analysis results are obtained in three benchmark problems, two in closed geometries and one in open flow, namely the square and cubic lid-driven cavity flow and flow in the wake of the circular cylinder. Comparisons with results delivered by classic spectral element methods verify the accuracy of the proposed new methodologies and point potential limitations particular to the LBM approach. The known issue of appearance of numerical instabilities when the SRT model is used in direct numerical simulations employing the LBM is shown to be reflected in a spurious global eigenmode when the SRT model is used in the instability analysis. Although this mode is absent in the multiple relaxation times model, other spurious instabilities can also arise and are documented herein. Areas of potential improvements in order to make the proposed methodology competitive with established approaches for global instability analysis are discussed.

  12. Analysis of flow instabilities in forced-convection steam generator

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    Because of the practical importance of two-phase instabilities, substantial efforts have been made to date to understand the physical phenomena governing such instabilities and to develop computational tools to model the dynamics. The purpose of this study is to present a numerical model for the analysis of flow-induced instabilities in forced-convection steam generator. The model is based on the assumption of homogeneous two-phase flow and thermodynamic equilibrium of the phases. The thermal capacity of the heater wall has been included in the analysis. The model is used to analyze the flow instabilities in the steam generator and to study the effects of system pressure, mass flux, inlet temperature and inlet/outlet restriction, gap size, the ratio of do /di, and the ratio of qi/qo on the system behavior.

  13. Analytical analysis of modulation instability in fiber optics

    Directory of Open Access Journals (Sweden)

    M. Saeed Aslam

    2012-06-01

    Full Text Available In this paper, an improved analysis for modulation instability, which results from interaction between optical wave and noise, is presented. It is shown that Nonlinear Schrodinger equation (NLSE, which governs this process, leads to the coupled wave equations that result to Riccati's differential equations. A completely analytical solution of Riccati's equation is obtained for small fiber length that results in efficient computation of the modulation instability effect.

  14. Microsatellite DNA analysis proves nucleus of interspecies reconstructed blastocyst coming from that of donor giant panda

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    A method for DNA isolation from early development of blastocyst and further analysis of nuclear and mitochondrial DNA was developed in present study. Total DNA was prepared from interspecies reconstructed blastocyst and a giant panda specific microsatellite locus g010 was successfully amplified. DNA sequencing of the PCR product showed that two sequences of reconstructed blastocysts are the same as that of positive control giant panda. Our results prove that the nucleus of interspecies reconstructed blastocyst comes from somatic nucleus of donor giant panda.

  15. Independent clonal origin of multiple uterine leiomyomas that was determined by X chromosome inactivation and microsatellite analysis

    DEFF Research Database (Denmark)

    Canevari, Renata A; Pontes, Anaglória; Rosa, Fabíola E;

    2005-01-01

    OBJECTIVE: In an attempt to clarify the clonality and genetic relationships that are involved in the tumorigenesis of uterine leiomyomas, we used a total of 43 multiple leiomyomas from 14 patients and analyzed the allelic status with 15 microsatellite markers and X chromosome inactivation analysis....... STUDY DESIGN: We have used a set of 15 microsatellite polymorphism markers mapped on 3q, 7p, 11, and 15q by automated analysis. The X chromosome inactivation was evaluated by the methylation status of the X-linked androgen receptor gene. RESULTS: Loss of heterozygosity analysis showed a different...... pattern in 7 of the 8 cases with allelic loss for at least 1 of 15 microsatellite markers that were analyzed. A similar loss of heterozygosity findings at 7p22-15 was detected in 3 samples from the same patient. X chromosome inactivation analysis demonstrated the same inactivated allele in all tumors...

  16. Local potential analysis of MHD instability

    Science.gov (United States)

    Sen, K. K.; Wilson, S. J.

    1985-02-01

    The use of the local potential method for studying instabilities of MHD fluids is examined. The mathematical method is similar to that developed by the authors for studying the time-dependent radiative transfer problem and the radiative stability of interstellar masers. The scheme is based on the universal evolution criterion proposed by Glansdorff and Prigogine (1964) as demonstrated by Hays (1965) for the heat equation and Schechter and Himmelblau (1965) for the Benard problem in hydrodynamics. The scheme for securing stability criteria is demonstrated for two particular cases.

  17. 微卫星不稳定性与脊柱裂发生的关联性研究%Study on the Relationship of Microsatellite Instability and the Occurrence of Spina Bifida

    Institute of Scientific and Technical Information of China (English)

    王志刚; 李媛媛; 刘卓; 欧阳胜荣; 常会波; 吴建新

    2011-01-01

    目的:通过对脊柱裂(spina bifida)胚胎脑组织中微卫星不稳定性(microsatellite instability,MSI)的分析,探讨遗传不稳定性是否为此疾病的特征之一,进而研究错配修复系统(mismatch repair,MMR)与脊柱裂发病的分子机制.方法:19例脊柱裂和19例非神经管畸形对照脑组织中提取DNA;尿素变性凝胶电泳法检测标本中MSI发生情况.结果:在19例脊柱裂脑组织中9例MSI阳性,阳性率47.4%.其中2例为高度微卫星不稳定(high frequency microsatellite instability,MSI-H),7例为低度微卫星不稳定(lowfrequency microsatellite instability,MSI-L),其余10例为微卫星稳定(microsatellite stable,MSS),对照组中未出现MSI.选择的5个微卫星位点MSI的阳性率分别为Bat34C4(10.5%)、Bat26(26.5%)、D2S123(10.5%)、D3S1611(5.3%),D2S119(5.3%).结论:脊柱裂中存在MSI现象,提示MSI、错配修复系统可能与脊柱裂的发生有一定关系.%Objective: To investigate microsatellite instability(MSI) in fetuses with spina bifida and explore whether genetic instability is a feature of this disease, and to study the molecular mechanism between mismatch repair(MMR) and the occurrence of spina bifida. Methods: DNA was extracted from 19 cases of spina bifida and the control group. PCR-urea denaturing polyacrylamide gel elec-trophoresis was used to analyze MSI. Results: Of 19 cases of spina bifida, 9 with MSI (47.4%),2 with MSI-H, 7 with MSI-L and 10 with MSS. Positive cases of five microsatellite loci were 2 for Bat34C4 (10.5%), 5 for Bat26 (26.5%), 2 for D2S123 (10.5%), 1 for D3S1611 (5.3%) and 1 for D2S119 (5.3%) respectively. No MSI was found in normal group. Conclusion: The high incidence of MSI was found in fetuses with spina bifida, which indicated that MSI and MMR may be correlated with the occurrence of spina bifida.

  18. Microsatellite Instability in Intestinal Metaplasia and Gastric Cancer%胃癌及肠化组织的微卫星不稳定性

    Institute of Scientific and Technical Information of China (English)

    邵耘; 张小勇; 刘平

    2004-01-01

    目的:探讨微卫星不稳定性(MSI)在胃癌及肠化组织中的发生规律及其在胃癌发生过程中的作用.方法:对30例胃癌、40例肠上皮化生的石蜡标本分别提取病变及相应正常组织的DNA,应用银染PCR-SSCP技术检测5个微卫星位点的不稳定性.结果:胃癌组织MSI的发生率为23.3%,胃窦癌MSI的发生率显著高于贲门癌(P=0.044).肠化组织MSI发生率20%,MSI全部出现在中度以上肠化组织中(P=0.013),且更多见于女性(P=0.044).结论:MSI是胃癌多步骤发生过程中的早期分子事件,在胃癌的发生中可能具有重要作用.%Objectiye: To investigate the changeable patterns of microsatellite instability (MSI)in intestinal metaplasia(IM)and gastric cancer(CC)and the role of MSI in gastric carcinogenesis. Methods: Silver staining single strand conformation polymorphism-polymeriase chain reaction(PCR-SSCP)was used to screen MSI markers at 5 loci in formalin-fixed, paraffin-embedded tissues of GC ( n = 30), IM ( n 40) and corresponding normal gastric tissues. Results: The abnormal shifting of the single-strand DNA was identified in 7(23.3%)out of GC and in 8(20%)out of IM samples. Three( 10% )tumors and one(2.5% ) IM displayed high-frequency MSI( two or more loci altered) .Low-frequency MSI(one loci altered)was detected in 4 (13.3 % )of the tumors and in 7 (17.5%)IM samples. GC with MSI was associated with distal locaton of the tumors but age, sex, differentiation, lymph nodes metastasis and TNM stage( P = 0.044). MSI was more likely detected in moderate-grade IM than in mild-grade IM tssues(34.8% versus 0; P = 0.013); and MSI had a tendency to be easily detected in female with IM. Conclusion: The progressive accumulation of MSI in areas of IM may contribute to GC development, representing an important molecular event in the multistep gastric carcinogenesis.

  19. Microsatellite-centromere mapping in Japanese scallop ( Patinopecten yessoensis) through half-tetrad analysis in gynogenetic diploid families

    Science.gov (United States)

    Li, Qi; Qi, Mingjun; Nie, Hongtao; Kong, Lingfeng; Yu, Hong

    2016-06-01

    Gene-centromere mapping is an essential prerequisite for understanding the composition and structure of genomes. Half-tetrad analysis is a powerful tool for mapping genes and understanding chromosomal behavior during meiosis. The Japanese scallop ( Patinopecten yessoensis), a cold-tolerant species inhabiting the northwestern Pacific coast, is a commercially important marine bivalve in Asian countries. In this study, inheritance of 32 informative microsatellite loci was examined in 70-h D-shaped larvae of three induced meiogynogenetic diploid families of P. yessoensis for centromere mapping using half-tetrad analysis. The ratio of gynogenetic diploids was proven to be 100%, 100% and 96% in the three families, respectively. Inheritance analysis in the control crosses showed that 51 of the 53 genotypic ratios observed were in accordance with Mendelian expectations at the 5% level after Bonferroni correction. Seven of the 32 microsatellite loci showed the existence of null alleles in control crosses. The second division segregation frequency ( y) of the microsatellite loci ranged from 0.07 to 0.85 with a mean of 0.38, suggesting the existence of positive interference after a single chiasma formation in some chromosomes in the scallop. Microsatellite-centromere distances ranged from 4 cM to 42 cM under the assumption of complete interference. Information on the positions of centromeres in relation to the microsatellite loci will represent a contribution towards the assembly of genetic maps in the commercially important scallop species.

  20. Development and characterization of highly polymorphic long TC repeat microsatellite markers for genetic analysis of peanut

    Directory of Open Access Journals (Sweden)

    Macedo Selma E

    2012-02-01

    Full Text Available Abstract Background Peanut (Arachis hypogaea L. is a crop of economic and social importance, mainly in tropical areas, and developing countries. Its molecular breeding has been hindered by a shortage of polymorphic genetic markers due to a very narrow genetic base. Microsatellites (SSRs are markers of choice in peanut because they are co-dominant, highly transferrable between species and easily applicable in the allotetraploid genome. In spite of substantial effort over the last few years by a number of research groups, the number of SSRs that are polymorphic for A. hypogaea is still limiting for routine application, creating the demand for the discovery of more markers polymorphic within cultivated germplasm. Findings A plasmid genomic library enriched for TC/AG repeats was constructed and 1401 clones sequenced. From the sequences obtained 146 primer pairs flanking mostly TC microsatellites were developed. The average number of repeat motifs amplified was 23. These 146 markers were characterized on 22 genotypes of cultivated peanut. In total 78 of the markers were polymorphic within cultivated germplasm. Most of those 78 markers were highly informative with an average of 5.4 alleles per locus being amplified. Average gene diversity index (GD was 0.6, and 66 markers showed a GD of more than 0.5. Genetic relationship analysis was performed and corroborated the current taxonomical classification of A. hypogaea subspecies and varieties. Conclusions The microsatellite markers described here are a useful resource for genetics and genomics in Arachis. In particular, the 66 markers that are highly polymorphic in cultivated peanut are a significant step towards routine genetic mapping and marker-assisted selection for the crop.

  1. Analysis of genital Candida albicans infection by rapid microsatellite markers genotyping

    Institute of Scientific and Technical Information of China (English)

    SHI Wei-min; MEI Xing-yu; GAO Fei; HUO Ke-ke; SHEN Liang-liang; QIN Hai-hong; WU Zhou-wei; ZHENG Jie

    2007-01-01

    Background Candida albicans (C. albicans) infection, often occurring in genital candidiasis, has increased dramatically recently. Developing an efficient C. albicans typing method may contribute to understanding its epidemiological characteristics and guiding efficient treatment. We used rapid microsatellite genotyping assay for interstrain differentiation of C. albicans isolates and explored some characteristics of its spread.Methods DNA was extracted from C. albicans isolates from gentalia, recta and mouths of 39 female cases and 27 male cases of genital candidiasis. Three fluorescent primers for the microsatellite markers in conserved genes (CDC3, EF3and HIS3) of C. albicans were used to amplify the isolates DNA by PCR. Fluorescent signals were read with an automatic sequencer and analyzed with GeneScan software.Results Analysis of the three microsatellites markers showed 18 gene allelic associations in genital C. albicans infected patients: 10 allelic associations in female and 11 allelic associations in male, of which 3 allelic associations shared by both genders covered 71% of infections. The most dominant allele association of pathogenic strains for both genders was 116:124, 122:131,160:200 that covered about 50% of infection. Gentalia and recta shared the same strains in 80%of female patients, but in only 3.8% of male patients. There were 2.7% female patients, but no males, with same strain in both gentalia and mouths. Five of seven genital C. albicans infected couples had the same allelic associations of which 4were the dominant pathogenic C. albicans susceptible for both genders.Conclusions The predominant allelic association of the pathogenic strain in genital C. albicans infection is 116:124,122:131, 160:200. Vaginal pathogenic strains are probably maintained from the rectal reservoir. Pathogenic strains of male patients are probably from frequent sexual intercourse. The aggressiveness of some strains varies with gender.

  2. Genetic diversity in four populations of Nguni (Zulu sheep assessed by microsatellite analysis

    Directory of Open Access Journals (Sweden)

    Nokuthula W. Kunene

    2014-02-01

    Full Text Available Zulu sheep are found mainly in the rural KwaZulu-Natal province and the numbers are declining due to indiscriminate inbreeding. There is thus a need for phenotypic and genetic characterisation as a first phase for planning conservation strategies. Zulu sheep populations sampled were from Makhathini research station (MS (n=33, University of Zululand (UZ (n=21, a community at KwaMthethwa (KM (n=32 and from Msinga (EM (n=33. One European breed Appen - ninica (AP was used as out group. Microsatellite analysis using 29 microsatellite loci was used in this study. Among the Zulu sheep, the mean number of alleles per locus was the lowest (3.86 in UZ and the highest (6.24 was realised in EM. The mean values of observed and expected heterozygosity were 0.57 and 0.61, respectively. Neighbour-joining tree showed two main Zulu sheep clusters: the UZ, KM and MS sheep populations clustered together and the second cluster included only representatives from the EM population. The STRUCTURE analysis showed that KM, AP and EM were founded in separate clusters, whereas UZ and MS clustered together. The study demonstrated that there was a common origin of the population from the research stations (MS and UZ populations. It also demonstrated that the EM had a different history for the other three populations. This work suggests that exchange of rams could be useful in reducing inbreeding when considering conservation breeding programmes.

  3. Multilocus microsatellite analysis of 'Candidatus Liberibacter asiaticus' associated with citrus Huanglongbing worldwide

    Directory of Open Access Journals (Sweden)

    Islam Md-Sajedul

    2012-03-01

    Full Text Available Abstract Background Huanglongbing (HLB is one of the most destructive citrus diseases in the world. The disease is associated with the presence of a fastidious, phloem-limited α- proteobacterium, 'Candidatus Liberibacter asiaticus', 'Ca. Liberibacter africanus' or 'Ca. Liberibacter americanus'. HLB-associated Liberibacters have spread to North America and South America in recent years. While the causal agents of HLB have been putatively identified, information regarding the worldwide population structure and epidemiological relationships for 'Ca. L. asiaticus' is limited. The availability of the 'Ca. L. asiaticus' genome sequence has facilitated development of molecular markers from this bacterium. The objectives of this study were to develop microsatellite markers and conduct genetic analyses of 'Ca. L. asiaticus' from a worldwide collection. Two hundred eighty seven isolates from USA (Florida, Brazil, China, India, Cambodia, Vietnam, Taiwan, Thailand, and Japan were analyzed. Results A panel of seven polymorphic microsatellite markers was developed for 'Ca. L. asiaticus'. Microsatellite analyses across the samples showed that the genetic diversity of 'Ca. L. asiaticus' is higher in Asia than Americas. UPGMA and STRUCTURE analyses identified three major genetic groups worldwide. Isolates from India were genetically distinct. East-southeast Asian and Brazilian isolates were generally included in the same group; a few members of this group were found in Florida, but the majority of the isolates from Florida were clustered separately. eBURST analysis predicted three founder haplotypes, which may have given rise to three groups worldwide. Conclusions Our results identified three major genetic groups of 'Ca. L. asiaticus' worldwide. Isolates from Brazil showed similar genetic makeup with east-southeast Asian dominant group, suggesting the possibility of a common origin. However, most of the isolates recovered from Florida were clustered in a

  4. Multilocus microsatellite analysis of 'Candidatus Liberibacter asiaticus' associated with citrus Huanglongbing worldwide

    Science.gov (United States)

    2012-01-01

    Background Huanglongbing (HLB) is one of the most destructive citrus diseases in the world. The disease is associated with the presence of a fastidious, phloem-limited α- proteobacterium, 'Candidatus Liberibacter asiaticus', 'Ca. Liberibacter africanus' or 'Ca. Liberibacter americanus'. HLB-associated Liberibacters have spread to North America and South America in recent years. While the causal agents of HLB have been putatively identified, information regarding the worldwide population structure and epidemiological relationships for 'Ca. L. asiaticus' is limited. The availability of the 'Ca. L. asiaticus' genome sequence has facilitated development of molecular markers from this bacterium. The objectives of this study were to develop microsatellite markers and conduct genetic analyses of 'Ca. L. asiaticus' from a worldwide collection. Two hundred eighty seven isolates from USA (Florida), Brazil, China, India, Cambodia, Vietnam, Taiwan, Thailand, and Japan were analyzed. Results A panel of seven polymorphic microsatellite markers was developed for 'Ca. L. asiaticus'. Microsatellite analyses across the samples showed that the genetic diversity of 'Ca. L. asiaticus' is higher in Asia than Americas. UPGMA and STRUCTURE analyses identified three major genetic groups worldwide. Isolates from India were genetically distinct. East-southeast Asian and Brazilian isolates were generally included in the same group; a few members of this group were found in Florida, but the majority of the isolates from Florida were clustered separately. eBURST analysis predicted three founder haplotypes, which may have given rise to three groups worldwide. Conclusions Our results identified three major genetic groups of 'Ca. L. asiaticus' worldwide. Isolates from Brazil showed similar genetic makeup with east-southeast Asian dominant group, suggesting the possibility of a common origin. However, most of the isolates recovered from Florida were clustered in a separate group. While the sources

  5. Multilocus microsatellite analysis of 'Candidatus Liberibacter asiaticus' associated with citrus Huanglongbing worldwide.

    Science.gov (United States)

    Islam, Md-Sajedul; Glynn, Jonathan M; Bai, Yang; Duan, Yong-Ping; Coletta-Filho, Helvecio D; Kuruba, Gopal; Civerolo, Edwin L; Lin, Hong

    2012-03-20

    Huanglongbing (HLB) is one of the most destructive citrus diseases in the world. The disease is associated with the presence of a fastidious, phloem-limited α- proteobacterium, 'Candidatus Liberibacter asiaticus', 'Ca. Liberibacter africanus' or 'Ca. Liberibacter americanus'. HLB-associated Liberibacters have spread to North America and South America in recent years. While the causal agents of HLB have been putatively identified, information regarding the worldwide population structure and epidemiological relationships for 'Ca. L. asiaticus' is limited. The availability of the 'Ca. L. asiaticus' genome sequence has facilitated development of molecular markers from this bacterium. The objectives of this study were to develop microsatellite markers and conduct genetic analyses of 'Ca. L. asiaticus' from a worldwide collection. Two hundred eighty seven isolates from USA (Florida), Brazil, China, India, Cambodia, Vietnam, Taiwan, Thailand, and Japan were analyzed. A panel of seven polymorphic microsatellite markers was developed for 'Ca. L. asiaticus'. Microsatellite analyses across the samples showed that the genetic diversity of 'Ca. L. asiaticus' is higher in Asia than Americas. UPGMA and STRUCTURE analyses identified three major genetic groups worldwide. Isolates from India were genetically distinct. East-southeast Asian and Brazilian isolates were generally included in the same group; a few members of this group were found in Florida, but the majority of the isolates from Florida were clustered separately. eBURST analysis predicted three founder haplotypes, which may have given rise to three groups worldwide. Our results identified three major genetic groups of 'Ca. L. asiaticus' worldwide. Isolates from Brazil showed similar genetic makeup with east-southeast Asian dominant group, suggesting the possibility of a common origin. However, most of the isolates recovered from Florida were clustered in a separate group. While the sources of the dominant 'Ca. L

  6. Microsatellite genotyping reveals a signature in breast cancer exomes.

    Science.gov (United States)

    McIver, L J; Fonville, N C; Karunasena, E; Garner, H R

    2014-06-01

    Genomic instability at microsatellite loci is a hallmark of many cancers, including breast cancer. However, much of the genomic variation and many of the hereditary components responsible for breast cancer remain undetected. We hypothesized that variation at microsatellites could provide additional genomic markers for breast cancer risk assessment. A total of 1,345 germline and tumor DNA samples from individuals diagnosed with breast cancer, exome sequenced as part of The Cancer Genome Atlas, were analyzed for microsatellite variation. The comparison group for our analysis, representing healthy individuals, consisted of 249 females which were exome sequenced as part of the 1,000 Genomes Project. We applied our microsatellite-based genotyping pipeline to identify 55 microsatellite loci that can distinguish between the germline of individuals diagnosed with breast cancer and healthy individuals with a sensitivity of 88.4 % and a specificity of 77.1 %. Further, we identified additional microsatellite loci that are potentially useful for distinguishing between breast cancer subtypes, revealing a possible fifth subtype. These findings are of clinical interest as possible risk diagnostics and reveal genes that may be of potential therapeutic value, including genes previously not associated with breast cancer.

  7. Microsatellite marker-based genetic analysis of relatedness between commercial and heritage turkeys (Meleagris gallopavo).

    Science.gov (United States)

    Kamara, D; Gyenai, K B; Geng, T; Hammade, H; Smith, E J

    2007-01-01

    The turkey is second only to the chicken in importance as an agriculturally important poultry species. Unlike the chicken, however, genetic studies of the turkey continue to be limited. For example, to date, many genomic investigations have been conducted to characterize genetic relationships between commercial (CO) and non-CO chicken breeds, whereas the nature of the genetic relatedness between CO and heritage turkeys remains unknown. The objective of the current research was to use microsatellites to analyze the genetic relatedness between CO and heritage domestic turkeys including Narragansett, Bourbon Red, Blue Slate, Spanish Black, and Royal Palm. Primer pairs specific for 10 previously described turkey microsatellite markers were used. The phylogenetic analysis showed that the Blue Slate, Bourbon Red, and Narragansett were genetically closely related to the CO strain, with a Nei distance of 0.30, and the Royal Palm and Spanish Black were the least related to the CO strain, with Nei distances of 0.41 and 0.40, respectively. The present work provides a foundation for the basis of using heritage turkeys to genetically improve CO populations by introgression.

  8. Parentage assignment and parental contribution analysis in large yellow croaker Larimichthys crocea using microsatellite markers

    Institute of Scientific and Technical Information of China (English)

    Xiande LIU; Guangtai ZHAO; Zhiyong WANG; Mingyi CAI; Hua YE; Qiurong WANG

    2012-01-01

    The large yellow croaker Larimichthys crocea is one of the most important fish species in China.To estimate the reproductive success of breeders,three independent full-factorial crosses were created and the fins of breeders and progenies were sampled for microsatellite analysis.Out of 959 offspring from three sets,99.6% were assigned to their parents using 6-7 microsatellite markers.In all crosses,some parent pairs produced a large number of offspring and some parent pairs did not produce any offspring.The contributions of male or female parents were unequal,ranging from 1.0-89.3% across the three sets.The loss of putative Ne was 69.6% in set 1,31.2% in set 2 and 57.6% in set 3.These results suggest that the unequal contribution of parents is universal in artificial breeding ofL.crocea,especially in a small population,and this should be taken into account in hatcheries or when releasing animals for resource enhancement [Current Zoology 58 (2):244-249,2012].

  9. Outcrossing and paternity analysis of Pinus densiflora (Japanese red pine) by microsatellite polymorphism.

    Science.gov (United States)

    Lian, C; Miwa, M; Hogetsu, T

    2001-07-01

    This study employed microsatellite loci to analyse outcrossing rate and pollen dispersal in Japanese red pine (Pinus densiflora) in an isolated stand. The average offspring outcrossing rate for 29 cones was 0.955. Significant differences in outcrossing rates between offspring groups on individual branches that extended in different directions at different heights were not detected. Male parents of 874 offspring collected from the maternal tree were assessed by exclusion using polymorphisms at three microsatellite loci. Paternity analysis indicated that at least 31% of the offspring were fertilized by pollen from trees outside the stand. The average distance of pollen migration within the study stand was 68 m, with a maximum value of 325 m. There was excess mating with nearby P. densiflora trees, of which only a few were predominant pollen donors. In addition, a weakly directional bias in P. densiflora pollination was also detected in the study stand, suggesting that female strobili on a branch of the maternal tree were more easily fertilized by pollen from trees in that direction.

  10. Analysis of genetic diversity and differentiation of seven stocks of Litopenaeus vannamei using microsatellite markers

    Science.gov (United States)

    Zhang, Kai; Wang, Weiji; Li, Weiya; Zhang, Quanqi; Kong, Jie

    2014-08-01

    Seven microsatellite markers were used to evaluate the genetic diversity and differentiation of seven stocks of Litopenaeus vannamei, which were introduced from Central and South America to China. All seven microsatellite loci were polymorphic, with polymorphism information content ( PIC) values ranging from 0.593 to 0.952. Totally 92 alleles were identified, and the number of alleles ( Na) and effective alleles ( Ne) varied between 4 and 21 and 2.7 and 14.6, respectively. Observed heterozygosity ( H o) values were lower than the expected heterozygosity ( H e) values (0.526-0.754), which indicated that the seven stocks possessed a rich genetic diversity. Thirty-seven tests were detected for reasonable significant deviation from Hardy-Weinberg equilibrium. F is values were positive at five loci, suggesting that there was a relatively high degree of inbreeding within stocks. Pairwise F st values ranged from 0.0225 to 0.151, and most of the stock pairs were moderately differentiated. Genetic distance and cluster analysis using UPGMA revealed a close genetic relationship of L. vannamei between Pop2 and Pop3. AMOVA indicated that the genetic variation among stocks (11.3%) was much lower than that within stocks (88.7%). Although the seven stocks had a certain degree of genetic differentiation and a rich genetic diversity, there is an increasing risk of decreased performance due to inbreeding in subsequent generations.

  11. Microsatellite-based parentage analysis of Aedes aegypti (Diptera: Culicidae) using nonlethal DNA sampling.

    Science.gov (United States)

    Wong, Jacklyn; Chu, Yui Yin; Stoddard, Steven T; Lee, Yoosook; Morrison, Amy C; Scott, Thomas W

    2012-01-01

    To track Aedes aegypti (L.) egg-laying behavior in the field in Iquitos, Peru, we developed methods for 1) sampling DNA from live mosquitoes and 2) high through-put parentage analysis using microsatellite markers. We were able to amplify DNA extracted from a single hind leg, but not from the pupal exuvia. Removal of a leg from teneral females caused no significant changes in female behavioral or life history traits (e.g., longevity, blood feeding frequency, fecundity, egg hatch rate, gonotrophic cycle length, or oviposition behavior). Using a panel of nine microsatellite markers and an exclusion-based software program, we matched offspring to parental pairs in 10 Ae. aegypti test families in which parents originated from natural development sites in Iquitos. By mating known individuals in the laboratory, retaining the male, sampling the female's DNA before release, and collecting offspring in the field, the technique we developed can be used to genotype large numbers of Ae. aegypti, reconstruct family relationships, and track the egg-laying behavior of individual Ae. aegypti in nature.

  12. Analysis of olive fly invasion in California based on microsatellite markers.

    Science.gov (United States)

    Zygouridis, N E; Augustinos, A A; Zalom, F G; Mathiopoulos, K D

    2009-04-01

    The olive fruit fly, Bactrocera oleae, is the main pest of the olive fruit and its expansion is exclusively restricted to the cultivation zone of the olive tree. Even though olive production has a century-old history in California, the olive fly was first detected in the Los Angeles area in 1998. Within 5 years of the first observation, the insect was reported from all olive cultivation areas of the state. Field-collected flies from five locations in California and another from Israel were analyzed on the basis of microsatellite polymorphisms in 10 microsatellite loci. These results were integrated with those of a previous study of olive fly populations around the European part of the Mediterranean basin. The analysis pointed to the eastern part of the Mediterranean as the putative source of the observed invasion. Moreover, samples from California were quite different from Mediterranean samples implying the participation of phenomena such as genetic drift during the invasion and expansion of the olive fly in California.

  13. Analysis of genetic diversity and population structure of Chinese yak breeds (Bos grunniens) using microsatellite markers

    Institute of Scientific and Technical Information of China (English)

    Guixiang Zhang; Weisheng Chen; Ming Xue; Zhigang Wang; Hong Chang; Xu Han; Xinjun Liao; Donglei Wang

    2008-01-01

    Nine Chinese yak breeds (Maiwa,Tianzhu White,Qinghai Plateau,Sibu,Zhongdian,Pall,Tibetan High Mountain,Jiulong,and Xin-jiang) and Gayal were analyzed by means of 16 microsatellite markers to determine the level of genetic variation within populations,genetic relationship between populations,and population structure for each breed.A total of 206 microsatellite alleles were observed.Mean F-statistics (0.056) for 9 yak breeds indicated that 94.4% of the genetic variation was observed within yak breeds and 5.6% of the genetic variation existed amongst breeds.The Neighbor-Joining phylogenetic free was constructed based on Nei's standard genetic dis-tances and two clusters were obtained.The Gayal separated from the yaks far away and formed one cluster and 9 yak breeds were grouped together.The analysis of population structure for 9 yak breeds and the Gayal showed that they resulted in four clusters; one clus-ter includes yaks from Tibet Autonomous Region and Qinghai Province,one cluster combines Zhongdian,Maiwa,and Tianzhu White,and Jiulong and Xinjiang come into the third cluster.Pali was mainly in the first cluster (90%),Jiulong was mainly in the second cluster (87.1%),Zhongdian was primarily in the third cluster (83%),and the other yak breeds were distributed in two to three clusters.The Gayal was positively left in the fourth cluster (99.3%).

  14. Geographic Structure of Plasmodium vivax: Microsatellite Analysis of Parasite Populations from Sri Lanka, Myanmar, and Ethiopia

    Science.gov (United States)

    Gunawardena, Sharmini; Karunaweera, Nadira D.; Ferreira, Marcelo U.; Phone-Kyaw, Myatt; Pollack, Richard J.; Alifrangis, Michael; Rajakaruna, Rupika S.; Konradsen, Flemming; Amerasinghe, Priyanie H.; Schousboe, Mette L.; Galappaththy, Gawrie N. L.; Abeyasinghe, Rabindra R.; Hartl, Daniel L.; Wirth, Dyann F.

    2010-01-01

    Genetic diversity and population structure of Plasmodium vivax parasites can predict the origin and spread of novel variants within a population enabling population specific malaria control measures. We analyzed the genetic diversity and population structure of 425 P. vivax isolates from Sri Lanka, Myanmar, and Ethiopia using 12 trinucleotide and tetranucleotide microsatellite markers. All three parasite populations were highly polymorphic with 3–44 alleles per locus. Approximately 65% were multiple-clone infections. Mean genetic diversity (HE) was 0.7517 in Ethiopia, 0.8450 in Myanmar, and 0.8610 in Sri Lanka. Significant linkage disequilibrium was maintained. Population structure showed two clusters (Asian and African) according to geography and ancestry. Strong clustering of outbreak isolates from Sri Lanka and Ethiopia was observed. Predictive power of ancestry using two-thirds of the isolates as a model identified 78.2% of isolates accurately as being African or Asian. Microsatellite analysis is a useful tool for mapping short-term outbreaks of malaria and for predicting ancestry. PMID:20133999

  15. [Analysis of Microsatellite DNA in Rodents from Eastern Urals Radioactive Trace Zone and Contiguous Territories].

    Science.gov (United States)

    Rakitin, S B; Grigorkina, E B; Olenev, G V

    2016-04-01

    The variability of four microsatellite loci of rodents, caught from the head part of Eastern Urals Radioactive Trace (EURT), along with the rodents inhabiting contiguous zone with background radiation level and distant-reference territory, was analyzed forthe first time. Differences in the parameters of genetic diversity between northern red-backed voles from the EURT zone and from the reference population were detected. An increase in some indices of genetic diversity in animals from a contiguous to the EURT zone was found; this is probably associated with animal migration and configuration of the area of pollution. A transfer of radiation-induced effects to the contiguous territories and a decrease in the possibility of fixation of adaptations in a series of generations of mobile rodent species in the area of local radioactive pollution are consequences of migrations. The results of the study make it possible to recommend microsatellite markers for the analysis of radiation-induced effects in rodents as model objects of radioecological monitoring.

  16. Polymorphic microsatellite loci from two enriched genomic libraries for the genetic analysis of the miiuy croaker, Miichthys miiuy (Sciaenidae).

    Science.gov (United States)

    Wang, R X; Xu, T J; Sun, Y N; He, G Y

    2010-05-18

    Twelve polymorphic microsatellites from the (AG)(13) and (CA)(13) enriched genomic libraries of Miichthys miiuy were isolated and characterized in a test population; the number of alleles ranged from two to nine. The observed and expected heterozygosities ranged from 0.1923 to 1.0000 and from 0.2633 to 0.8337, respectively. Three loci deviated from Hardy-Weinberg equilibrium, and linkage disequilibrium between five pairs of loci was significant. These polymorphic microsatellite loci can be used for genetic diversity analysis and molecular-assisted breeding of M. miiuy.

  17. Combined microsatellite and FGFR3 mutation analysis enables a highly sensitive detection of urothelial cell carcinoma in voided urine

    NARCIS (Netherlands)

    B.W. van Rhijn (Bas); I. Lurkin (Irene); D.K. Chopin; W.J. Kirkels (Wim); J.P. Thiery (Joachim); Th.H. van der Kwast (Theo); F. Radvanyi (Franois); E.C. Zwarthoff (Ellen)

    2003-01-01

    textabstractPURPOSE: Fibroblast growth factor receptor 3 (FGFR3) mutations were reported recently at a high frequency in low-grade urothelial cell carcinoma (UCC). We investigated the feasibility of combining microsatellite analysis (MA) and the FGFR3 status for the detection of UC

  18. Instability analysis of unsymmetrical rotor-bearing systems

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    This paper presents the instability analysis of unsymmetricalrotor-bearing system in accordance with the Campbell diagrams of the system, and concludes that the unstable regions stay in high speed regions with the increase of supporting stiffness and they decrease or disappear with the decrease of the inequality diametrical moments of the inertia and stiffness of shaft.

  19. 冬凌草甲素对微卫星不稳定结直肠癌的作用在体研究%The study of anticancer values of Oridonin for microsatellite instability colorectal cancer

    Institute of Scientific and Technical Information of China (English)

    戴功建; 金黑鹰

    2011-01-01

    目的 探索冬凌草甲素对微卫星不稳定的结直肠癌的作用并对其机理进行研究.方法 使用 Lovo细胞(MSH2缺失结肠癌细胞株)建立裸鼠皮下接种模型,4周后使用该模型生长的肿瘤建立结肠造口的结肠癌原位移植模型,使用不同剂量的冬凌草甲素处理动物模型,观察肿瘤的生长曲线、肿瘤微卫星不稳定和TGFβ1、TGFβ2和IGF片段的大小变化.结果 使用5 mg/kg、7.5 mg/kg和10 mg/kg3个治疗组在注射冬凌草甲素后,在1、2、3、4、5周末,治疗组和对照组肿瘤抑制率差异有统计学意义(p<0.01),而3个治疗组之间蔗异无统计学意义,使用冬凌草甲素治疗后肿瘤微卫星标志仍呈不稳定状态.结论 冬凌草甲素对错配修复基因缺失的结直肠癌有明显抑制作用,但LOVO细胞微卫星不稳定状态并未改变,发生的作用机理与抑制微卫星不稳定无关.%Objective To study the anticancer effects of Oridonin on colorectal cancer with microsatellite instability (MSI) in nude mice and to explore its mechanism. Methods A colostomy was performed on caecum of nude mice. Tumor fragments collected from the subcutaneous tumor of hMSH2 - absence colon carcinoma Lovo cell Line were surgically implanted onto the submucosa of the caecum during colostomy to establish the model after 4 weeks. Various concentrations of Oridonin were applied for observing the growth curve of the tumors and the changes of microsatellite instability. Results The mice in Oridonin - treated groups were given intra - abdominal injection of 5.0, 7.5 and 10.0 mg/kg Oridonin respectively. The tumor volumes of the three groups began to decrease at the 1st week and decreased most greatly from 2 to 3 weeks after treatment. The tumor inhibition rates in the three groups were significantly higher than those in untreated group 1, 2, 3, 4 and 5 weeks after treatment (P<0.01). After using Oridonin, the microsatellite remained unstable. Conclusion Oridonin can

  20. Validation of microsatellite multiplexes for parentage analysis in a coral reef fish (Lutjanus carponotatus, Lutjanidae)

    KAUST Repository

    Harrison, Hugo B.

    2014-05-25

    Parentage analysis is an important tool for identifying connectivity patterns in coral reef fishes, but often requires numerous highly polymorphic markers. We isolated 21 polymorphic microsatellite markers from the stripey snapper, Lutjanus carponotatus and describe their integration into three multiplex PCRs. All markers were highly polymorphic with a mean of 24.9 ± 1.8 SE alleles per locus and an average observed heterozygosity of 0.797 ± 0.038 SE across 285 genotyped individuals. Using a simulated dataset, we conclude that the complete marker set provides sufficient resolution to resolve parent–offspring relationships in natural populations with 99.6 ± 0.1 % accuracy in parentage assignments. This multiplex assay provides an effective means of investigating larval dispersal and population connectivity in this fishery-targeted coral reef fish species and informing the design of marine protected area networks for biodiversity conservation and fisheries management.

  1. Species diversity and geographic distribution of Gymnotus (Pisces: Gymnotiformes by nuclear (GGACn microsatellite analysis

    Directory of Open Access Journals (Sweden)

    Fernandes-Matioli F.M.C.

    2000-01-01

    Full Text Available Patterns of amplified DNA fragments flanked by (GGACn microsatellites, obtained by single primer amplification reaction (SPAR, from 198 Gymnotus specimens (Pisces: Gymnotiformes sampled from 8 southeastern Brazilian river basins were analyzed. The species studied were Gymnotus carapo, G. pantherinus, G. inaequilabiatus, and G. sylvius. The indirectly obtained patterns reflected the distribution of simple sequence repeats in the nuclear genome of the specimens. Species-specific patterns of DNA amplification were found and were useful for the analysis of the geographic distribution of Gymnotus species. Monomorphic patterns were found in G. carapo, G. pantherinus, and G. inaequilabiatus. Three polymorphic patterns were found in G. sylvius populations. The SPAR technique could be a useful molecular tool in conservation programs involving communities of neotropical freshwater fish.

  2. Assessing Spontaneous Combustion Instability with Nonlinear Time Series Analysis

    Science.gov (United States)

    Eberhart, C. J.; Casiano, M. J.

    2015-01-01

    Considerable interest lies in the ability to characterize the onset of spontaneous instabilities within liquid propellant rocket engine (LPRE) combustion devices. Linear techniques, such as fast Fourier transforms, various correlation parameters, and critical damping parameters, have been used at great length for over fifty years. Recently, nonlinear time series methods have been applied to deduce information pertaining to instability incipiency hidden in seemingly stochastic combustion noise. A technique commonly used in biological sciences known as the Multifractal Detrended Fluctuation Analysis has been extended to the combustion dynamics field, and is introduced here as a data analysis approach complementary to linear ones. Advancing, a modified technique is leveraged to extract artifacts of impending combustion instability that present themselves a priori growth to limit cycle amplitudes. Analysis is demonstrated on data from J-2X gas generator testing during which a distinct spontaneous instability was observed. Comparisons are made to previous work wherein the data were characterized using linear approaches. Verification of the technique is performed by examining idealized signals and comparing two separate, independently developed tools.

  3. Genetic linkage analysis of familial amyotrophic lateral sclerosis using human chromosome 21 microsatellite DNA markers

    Energy Technology Data Exchange (ETDEWEB)

    Rosen, D.R.; Sapp, P.; O`Regan, J.; McKenna-Yasek, D.; Schlumpf, K.S.; Haines, J.L.; Gusella, J.F.; Horvitz, H.R.; Brown, R.H. Jr. [Massachusetts Institute of Technology, Cambridge, MA (United States)

    1994-05-15

    Amyotrophic lateral sclerosis (ALS; Lou Gehrig`s Disease) is a lethal neurodegenerative disease of upper and lower motorneurons in the brain and spinal cord. We previously reported linkage of a gene for familial ALS (FALS) to human chromosome 21 using 4 restriction fragment length polymorphism DNA markers and identified disease-associated mutations in the superoxide dismutase (SOD)-1 gene in some ALS families. We report here the genetic linkage data that led us to examine the SOD-1 gene for mutations. We also report a new microsatellite DNA marker for D21S63, derived from the cosmid PW517. Ten microsatellite DNA markers, including the new marker D21S63, were used to reinvestigate linkage of FALS to chromosome 21. Genetic linkage analysis performed with 13 ALS familes for these 10 DNA markers confirmed the presence of a FALS gene on chromosome 21. The highest total 2-point LOD score for all families was 4.33, obtained at a distance of 10 cM from the marker D21S223. For 5 ALS families linked to chromosome 21, a peak 2-point LOD score of 5.94 was obtained at the DNA marker D21S223. A multipoint score of 6.50 was obtained with the markers D21S213, D21S223, D21S167, and FALS for 5 chromosome 21-linked ALS families. The haplotypes of these families for the 10 DNA markers reveal recombination events that further refined the location of the FALS gene to a segment of approximately 5 megabases (Mb) between D21S213 and D21S219. The only characterized gene within this segment was SOD-1, the structural gene for Cu, Zn SOD. 30 refs., 4 figs., 4 tabs.

  4. Microsatellite analysis of Damask rose (Rosa damascena Mill. accessions from various regions in Iran reveals multiple genotypes

    Directory of Open Access Journals (Sweden)

    Naghavi Mohammad

    2007-03-01

    Full Text Available Abstract Background Damask roses (Rosa damascena Mill. are mainly used for essential oil production. Previous studies have indicated that all production material in Bulgaria and Turkey consists of only one genotype. Nine polymorphic microsatellite markers were used to analyze the genetic diversity of 40 accessions of R. damascena collected across major and minor rose oil production areas in Iran. Results All microsatellite markers showed a high level of polymorphism (5–15 alleles per microsatellite marker, with an average of 9.11 alleles per locus. Cluster analysis of genetic similarities revealed that these microsatellites identified a total of nine different genotypes. The genotype from Isfahan province, which is the major production area, was by far the most common genotype (27/40 accessions. It was identical to the Bulgarian genotype. Other genotypes (each represented by 1–4 accessions were collected from minor production areas in several provinces, notably in the mountainous Northwest of Iran. Conclusion This is the first study that uncovered genetic diversity within Damask rose. Our results will guide new collection activities to establish larger collections and manage the Iranian Damask rose genetic resources. The genotypes identified here may be directly useful for breeding.

  5. Somatic deletions of the polyA tract in the 3' untranslated region of epidermal growth factor receptor are common in microsatellite instability-high endometrial and colorectal carcinomas.

    Science.gov (United States)

    Deqin, Ma; Chen, Zhao; Nero, Christopher; Patel, Keyur P; Daoud, Emad M; Cheng, Hanyin; Djordjevic, Bojana; Broaddus, Russell R; Medeiros, L Jeffrey; Rashid, Asif; Luthra, Rajyalakshmi

    2012-05-01

    Epidermal growth factor receptor (EGFR) is overexpressed in up to 80% of colorectal and endometrial carcinomas. Deletions of the polyA tract in the 3' untranslated region (3' UTR) have been reported in microsatellite instability-high (MSI-H) colonic carcinomas, but their impacts on EGFR expression and downstream pathways are unclear. This phenomenon has not been reported in other MSI-H tumors. To assess the 3' UTR polyA tract of EGFR in both endometrial and colorectal carcinomas and the mutational status of EGFR downstream pathways. Ninety-eight colorectal carcinomas and 47 endometrial carcinomas were included. EGFR 3' UTR polyA status was detected by capillary electrophoresis and Sanger sequencing. EGFR gene expression, EGFR copy numbers, and KRAS and BRAF mutation status were analyzed accordingly. The 3' UTR polyA tract was deleted in 18 of 23 (78%) MSI-H versus 0 of 24 microsatellite-stable endometrial carcinomas (P polyA deletions versus those with wild-type polyA tract. Amplification of the EGFR gene was not observed. Deletions in polyA tract do not seem to affect the frequency of KRAS and BRAF mutations. Deletions of EGFR 3' UTR polyA are frequent in endometrial and colorectal carcinomas, are confined almost exclusively to MSI-H tumors, and do not affect KRAS and BRAF mutations.

  6. Analysis of beam plasma instability effects on incoherent scatter spectra

    Directory of Open Access Journals (Sweden)

    M. A. Diaz

    2010-12-01

    Full Text Available Naturally Enhanced Ion Acoustic Lines (NEIALs detected with Incoherent Scatter Radars (ISRs can be produced by a Langmuir decay mechanism, triggered by a bump on tail instability. A recent model of the beam-plasma instability suggests that weak-warm beams, such those associated with NEIAL events, might produce Langmuir harmonics which could be detected by a properly configured ISR. The analysis performed in this work shows that such a beam-driven wave may be simultaneously detected with NEIALs within the baseband signal of a single ISR. The analysis shows that simultaneous detection of NEIALs and the first Langmuir harmonic is more likely than simultaneous detection of NEIALs and enhanced plasma line. This detection not only would help to discriminate between current NEIAL models, but could also aid in the parameter estimation of soft precipitating electrons.

  7. Genetic diversity analysis in blackgram (Vigna mungo (L.) Hepper) using AFLP and transferable microsatellite markers from azuki bean (Vigna angularis (Willd.) Ohwi & Ohashi).

    Science.gov (United States)

    Gupta, S K; Gopalakrishna, T

    2009-02-01

    Genetic diversity in 20 elite blackgram (Vigna mungo (L.) Hepper) genotypes was studied using microsatellite and AFLP markers. Thirty-six microsatellite markers from azuki bean (Vigna angularis (Willd.) Ohwi & Ohashi) were successfully amplified across the 20 blackgram genotypes and 33 microsatellite markers showed polymorphism. A total of 137 microsatellite alleles were generated with an average of 4.1 alleles per locus. The number of alleles ranged from two to nine and the polymorphic information content value for the microsatellite markers varied from 0.10 to 0.87 with an average of 0.49. Microsatellite markers were highly informative and a combination of only three microsatellite markers (CEDG264, CEDG173, and CEDG044) was sufficient to discriminate all 20 blackgram genotypes. In the case of AFLP, 11 primer pairs generated 324 polymorphic marker fragments. The polymorphic information content values for AFLP primer combinations ranged from 0.21 to 0.34 with an average of 0.29. Similarity measures and clustering analyses were made using microsatellite and AFLP data separately. The resulting dendrograms distributed the 20 blackgram genotypes into five main clusters. The dendrograms were comparable with each other with the Mantel test between the cophenetic matrices of microsatellite data and AFLP data showing moderate correlation (r = 0.64). The results of the principal components analysis were well congruent with the dendrograms. In the dendrograms as well as in the principal components analyses, genotype Trombay wild (Vigna mungo var. silvestris) was placed separately from rest of the genotypes. This study demonstrated that the azuki bean microsatellite markers are highly polymorphic and informative and can be successfully used for genome analysis in blackgram. Results indicate that sufficient variability is present in the blackgram genotypes and would be helpful in the selection of suitable parents for breeding purposes and gene mapping studies.

  8. Numerical Analysis of Modal Instability Onset in Fiber Amplifiers

    Science.gov (United States)

    2014-03-11

    Evolution of the logarithmic frequency spectrum of the off-center optical intensity probe along the length of the co-pumped amplifier for the case of...Evolution of the logarithmic frequency spectrum of the off-center optical intensity probe along the length of the counter-pumped amplifier for the...ABSTRACT 16. SECURITY CLASSIFICATION OF: Numerical analysis of the onset of modal instability in fiber amplifiers is presented. Specifically calculations

  9. Microsatellite analysis of genetic diversity and population structure of Arabian horse populations.

    Science.gov (United States)

    Khanshour, Anas; Conant, Eleanore; Juras, Rytis; Cothran, Ernest Gus

    2013-01-01

    The Arabian horse ignites imagination throughout the world. Populations of this breed exist in many countries, and recent genetic work has examined the diversity and ancestry of a few of these populations in isolation. Here, we explore 7 different populations of Arabians represented by 682 horses. Three of these are Middle Eastern populations from near the historical origin of the breed, including Syrian, Persian, and Saudi Arabian. The remaining Western populations are found in Europe (the Shagya Arabian and Polish Arabian) and in America (American Arabian). Analysis of genetic structure was carried out using 15 microsatellite loci. Genetic distances, analysis of molecular variance, factorial correspondence analysis, and a Bayesian method were applied. The results consistently show higher level of diversity within the Middle Eastern populations than the Western populations. The Western Arabian populations were the main source among population variation. Genetic differentiation was not strong among all Middle Eastern populations, but all American Arabians showed differentiation from Middle Eastern populations and were somewhat uniform among themselves. Here, we explore the diversities of many different populations of Arabian horses and find that populations not from the Middle East have noticeably lower levels of diversity, which may adversely affect the health of these populations.

  10. Sequence analysis of trinucleotide repeat microsatellites from an enrichment library of the equine genome.

    Science.gov (United States)

    Tozaki, T; Inoue, S; Mashima, S; Ohta, M; Miura, N; Tomita, M

    2000-04-01

    Microsatellites are useful tools for the construction of a linkage map and parentage testing of equines, but only a limited number of equine microsatellites have been elucidated. Thus, we constructed the equine genomic library enriched for DNA fragments containing (CAG)n repeats. The enriched method includes hybridization-capture of repeat regions using biotin-conjugated oligonucleotides, nucleotide substrate-biased polymerase reaction with the oligonucleotides and subsequent PCR amplification, because these procedures are useful for the cloning of less abundant trinucleotide microsatellites. Microsatellites containing (CAG)n repeats were obtained at the ratio of one per 3-4 clones, indicating an enrichment value about 10(4)-fold, resulting in less time consumption and less cost for cloning. In this study, 66 different microsatellites, (CAG)n repeats, were identified. The number of complete simple CAG repeats in our clones ranged 4-33, with an average repeat length of 8.8 units. The microsatellites were useful as sequence-tagged site (STS) markers. In addition, some clones containing (CAG)n repeats showed homology to human (CAG)n-containing genes, which have been previously mapped. These results indicate that the clones might be a useful tool for chromosome comparison between equines and humans.

  11. Monomorphic Analysis of Microsatellite Loci at BAT-26%微卫星BAT-26位点单态性的分析

    Institute of Scientific and Technical Information of China (English)

    狄金明; 张一楚; 陈蕾; 顾琴龙

    2001-01-01

    Objective MSI plays an important role in carainogenesis of manttumors.Most MS loci show polymorphism in normal tissues.It has been reported that BAT-26 was quasi-monomorphic,showing only minor size variathions.To analysis monomorphism at BAT-26 loci,60 normal colorectal tissues were examined.Methods Genomic DNA extracted from tissues was PCR amplified.PCR products were run on 6% denaturing polyacrylamide gel and stained with silver.Results All specimens showed no variation in the length of MS DNA at BAT-26 loci.Conclusion BAT-26 has much monomorphism in human genome.%目的 微卫星不稳定性(MicrosatelliteInstability,MSI)在许多肿瘤的发生中具很重要的作用,大多数微卫星(Microsatellite,MS)位点在正常人群中多态性明显,有报道表明BAT-26位点单态性很好,据此我们分析了60例正常肠粘膜标本中BAT-26位点MSDNA的情况,以便了解BAT-26位点单态性情况。方法 组织DNA提取后PCR扩增,扩增产物行6%变性聚丙烯酰胺凝胶电泳,最后银染。结果 所有标本在BAT-26位点MSDNA长度无明显改变。结论 BAT-26具有较好的单态性。

  12. Genetic Diversity Analysis of South and East Asian Duck Populations Using Highly Polymorphic Microsatellite Markers.

    Science.gov (United States)

    Seo, Dongwon; Bhuiyan, Md Shamsul Alam; Sultana, Hasina; Heo, Jung Min; Lee, Jun Heon

    2016-04-01

    Native duck populations have lower productivity, and have not been developed as much as commercials duck breeds. However, native ducks have more importance in terms of genetic diversity and potentially valuable economic traits. For this reason, population discriminable genetic markers are needed for conservation and development of native ducks. In this study, 24 highly polymorphic microsatellite (MS) markers were investigated using commercial ducks and native East and South Asian ducks. The average polymorphic information content (PIC) value for all MS markers was 0.584, indicating high discrimination power. All populations were discriminated using 14 highly polymorphic MS markers by genetic distance and phylogenetic analysis. The results indicated that there were close genetic relationships among populations. In the structure analysis, East Asian ducks shared more haplotypes with commercial ducks than South Asian ducks, and they had more independent haplotypes than others did. These results will provide useful information for genetic diversity studies in ducks and for the development of duck traceability systems in the market.

  13. Genetic Diversity Analysis of South and East Asian Duck Populations Using Highly Polymorphic Microsatellite Markers

    Directory of Open Access Journals (Sweden)

    Dongwon Seo

    2016-04-01

    Full Text Available Native duck populations have lower productivity, and have not been developed as much as commercials duck breeds. However, native ducks have more importance in terms of genetic diversity and potentially valuable economic traits. For this reason, population discriminable genetic markers are needed for conservation and development of native ducks. In this study, 24 highly polymorphic microsatellite (MS markers were investigated using commercial ducks and native East and South Asian ducks. The average polymorphic information content (PIC value for all MS markers was 0.584, indicating high discrimination power. All populations were discriminated using 14 highly polymorphic MS markers by genetic distance and phylogenetic analysis. The results indicated that there were close genetic relationships among populations. In the structure analysis, East Asian ducks shared more haplotypes with commercial ducks than South Asian ducks, and they had more independent haplotypes than others did. These results will provide useful information for genetic diversity studies in ducks and for the development of duck traceability systems in the market.

  14. An Extensive Analysis of Y-Chromosomal Microsatellite Haplotypes in Globally Dispersed Human Populations

    Science.gov (United States)

    Kayser, Manfred; Krawczak, Michael; Excoffier, Laurent; Dieltjes, Patrick; Corach, Daniel; Pascali, Vincente; Gehrig, Christian; Bernini, Luigi F.; Jespersen, Jørgen; Bakker, Egbert; Roewer, Lutz; de Knijff, Peter

    2001-01-01

    The genetic variance at seven Y-chromosomal microsatellite loci (or short tandem repeats [STRs]) was studied among 986 male individuals from 20 globally dispersed human populations. A total of 598 different haplotypes were observed, of which 437 (73.1%) were each found in a single male only. Population-specific haplotype-diversity values were .86–.99. Analyses of haplotype diversity and population-specific haplotypes revealed marked population-structure differences between more-isolated indigenous populations (e.g., Central African Pygmies or Greenland Inuit) and more-admixed populations (e.g., Europeans or Surinamese). Furthermore, male individuals from isolated indigenous populations shared haplotypes mainly with male individuals from their own population. By analysis of molecular variance, we found that 76.8% of the total genetic variance present among these male individuals could be attributed to genetic differences between male individuals who were members of the same population. Haplotype sharing between populations, ΦST statistics, and phylogenetic analysis identified close genetic affinities among European populations and among New Guinean populations. Our data illustrate that Y-chromosomal STR haplotypes are an ideal tool for the study of the genetic affinities between groups of male subjects and for detection of population structure. PMID:11254455

  15. Analysis of once-through steam generator instability

    Energy Technology Data Exchange (ETDEWEB)

    Kang, Han Ok; Kang, Hyung Suk; Cho, Bong Hyun; Yoon, Ju Hyeon [Korea Atomic Energy Research Institute, Taejon (Korea)

    1998-03-01

    KAERI is carrying out a development of the design for a new type of integral reactor named SMART (System-integrated Modular Advanced Reactor). Two models, the frequency domain-linear model and the time domain-nonlinear model, are developed for the analysis of once-through helical steam generator flow instability. The linear model is used for easy determination of critical point with constant heat flux condition. The nonlinear model is for the analysis of oscillation characteristics beyond the critical point as well as determination of the point with real primary boundary conditions. The developed linear model is utilized to evaluate the effect of several nondimensional parameters on flow stability for the wide range of input conditions. The results from the developed nonlinear model are compared with the existing experimental data including steady state values and critical conditions. The calculated lengths of each region and pressure drops in the steady show almost same trends with Nariai's experimental results. Two developed models can be utilized to analyze the steam generator flow instabilities and to design the inlet orifices are to prevent flow instabilities. (author). 118 refs., 32 figs., 1 tab.

  16. Linear stability analysis of capillary instabilities for concentric cylindrical shells

    CERN Document Server

    Liang, X; Nave, J -C; Johnson, S G

    2010-01-01

    Motivated by complex multi-fluid geometries currently being explored in fibre-device manufacturing, we study capillary instabilities in concentric cylindrical flows of N fluids with arbitrary viscosities, thicknesses, densities, and surface tensions in both the Stokes regime and for the full Navier--Stokes problem. Generalising previous work by Tomotika (N=2), Stone & Brenner (N=3, equal viscosities) and others, we present a full linear stability analysis of the growth modes and rates, reducing the system to a linear generalised eigenproblem in the Stokes case. Furthermore, we demonstrate by Plateau-style geometrical arguments that only axisymmetric instabilities need be considered. We show that the N=3 case is already sufficient to obtain several interesting phenomena: limiting cases of thin shells or low shell viscosity that reduce to N=2 problems, and a system with competing breakup processes at very different length scales. The latter is demonstrated with full 3-dimensional simulations. Many $N > 3$ c...

  17. Numerical analysis of anisotropic diffusion effect on ICF hydrodynamic instabilities

    Directory of Open Access Journals (Sweden)

    Olazabal-Loumé M.

    2013-11-01

    Full Text Available The effect of anisotropic diffusion on hydrodynamic instabilities in the context of Inertial Confinement Fusion (ICF flows is numerically assessed. This anisotropy occurs in indirect-drive when laminated ablators are used to modify the lateral transport [1,2]. In direct-drive, non-local transport mechanisms and magnetic fields may modify the lateral conduction [3]. In this work, numerical simulations obtained with the code PERLE [4], dedicated to linear stability analysis, are compared with previous theoretical results [5]. In these approaches, the diffusion anisotropy can be controlled by a characteristic coefficient which enables a comprehensive study. This work provides new results on the ablative Rayleigh-Taylor (RT, ablative Richtmyer-Meshkov (RM and Darrieus-Landau (DL instabilities.

  18. Laplace-Fourier analysis and instabilities of a gainy slab

    CERN Document Server

    Hågenvik, Hans Olaf

    2015-01-01

    The idealization of monochromatic plane waves leads to considerable simplifications in the analysis of electromagnetic systems. However, for active systems this idealization may be dangerous due to the presence of growing waves. Here we consider a gainy slab, and use a realistic incident beam, which is both causal and has finite width. This clarifies some apparent paradoxes arising from earlier analyses of this setup. In general it turns out to be necessary to involve complex frequencies $\\omega$ and/or complex transversal wavenumbers $k_x$. Simultaneously real $\\omega$ and $k_x$ cannot describe amplified waves in a slab which is infinite in the transversal direction. We also show that the only possibility to have an absolute instability for a finite width beam, is if a normally incident plane wave would experience an instability.

  19. [The diagnostic value of microsatellite LOH analysis and the prognostic relevance of angiogenic gene expression in urinary bladder cancer].

    Science.gov (United States)

    Szarvas, Tibor

    2009-12-01

    Bladder cancer is the second most common malignancy affecting the urinary system. Currently, histology is the only tool that determines therapy and patients' prognosis. As the treatment of non-invasive (Ta/T1) and muscle invasive (T2-T4) bladder tumors are completely different, correct staging is important, although it is often hampered by disturbing factors. Molecular methods offer new prospects for early disease detection, confirmation of unclear histological findings and prognostication. Applying molecular biological methods, the present study is searching for answers to current diagnostic and prognostic problems in bladder carcinoma. We analyzed tumor, blood and/or urine samples of 334 bladder cancer patients and 117 control individuals. Genetic alterations were analyzed in urine samples of patients and controls, both by PCR-based microsatellite loss of heterozigosity (LOH) analysis using 12 fluorescently labeled primers and by DNA hybridization based UroVysion FISH technique using 4 probes, to assess the diagnostic values of these methods. Whole genome microsatellite analysis (with 400 markers) was performed in tumor and blood specimens of bladder cancer patients to find chromosomal regions, the loss of which may be associated with tumor stage. Furthermore, we assessed the prognostic value of Tie2, VEGF, Angiopoietin-1 and -2. We concluded that DNA analysis of voided urine samples by microsatellite analysis and FISH are sensitive and non-invasive methods to detect bladder cancer. Furthermore, we established a panel of microsatellite markers that could differentiate between non-invasive and invasive bladder cancer. However, further analyses in a larger cohort of patients are needed to assess their specificity and sensitivity. Finally, we identified high Ang-2 and low Tie2 gene expression as significant and independent risk factors of tumor recurrence and cancer related survival.

  20. Linkage analysis of five Chinese families with arrhythmogenic right ventricular cardiomyopathy using microsatellite genetic markers

    Institute of Scientific and Technical Information of China (English)

    黄峻; 杨春梅; 马立隽; 单其俊; 许迪; 华子春; 曹克将

    2003-01-01

    Objective To explore the linkage relationship between specific genetic markers and arrhythmogenic right ventricular cardiomyopathy (ARVC) in Chinese pedigrees.Methods The microsatellite genetic markers D2S152, D14S252, and D10S1664 were studied for their linkages to ARVC in five Chinese ARVC pedigrees and a normal population of 121 Chinese individuals. Genomic DNA of the pedigrees and normal population was amplified using PCR techniques. Denaturing polyacrylamide sequencing gel (4%) electrophoresis was used to detect microsatellite repeat polymorphisms. Gels were silver-stained. A classical linkage analysis program was used assuming models of autosomal dominance and recession. Results The logarithm of the odds (LOD) scores of D2S152 with ARVC in LW, WD, DS, LC and TY pedigrees were 2.174, -0.589, -∞, - (indicating that linkage is not supported in this mode), and -∞ respectively in autosomal dominant model (recombination fraction=0.000 respectively)and were -∞, -∞, -∞, -∞, and 0.182 respectively in the autosomal recessive model. The LOD scores of D14S252 with ARVC in LW, WD, DS, LC and TY pedigrees were -, -, -∞, -, and 0 respectively in autosomal dominant model, and were -∞, -0.812, -∞, -∞, and 0.087 respectively in autosomal recessive model. The LOD scores of D2S152 with ARVC in LW, WD, DS, LC and TY pedigrees were -, -0.539, -, and 0.602 respectively in autosomal dominant model and were -, -∞, -∞, -∞, and -∞ respectively in autosomal recessive model. Conclusions The LOD score for D2S152 in the LW pedigree was 2.174, indicating that the chance of linkage is about 150∶ 1. This suggests that there is a possible ARVC-related gene near this marker. There were no clear linkage relationships between ARVC and D10S1664 and D14S252 in this family, and no linkages between ARVC and any of the three genetic markers in the other four families. These results also suggest that there is genetic heterogeneity in LW and in the other pedigrees.

  1. Microsatellite Analysis of the Population Genetic Structure of Anolis carolinensis Introduced to the Ogasawara Islands.

    Science.gov (United States)

    Sugawara, Hirotaka; Takahashi, Hiroo; Hayashi, Fumio

    2015-01-01

    DNA analysis can reveal the origins and dispersal patterns of invasive species. The green anole Anolis carolinensis is one such alien animal, which has been dispersed widely by humans from its native North America to many Pacific Ocean islands. In the Ogasawara (Bonin) Islands, this anole was recorded from Chichi-jima at the end of the 1960s, and then from Haha-jima in the early 1980s. These two islands are inhabited. In 2013, it was also found on the uninhabited Ani-jima, close to Chichi-jima. Humans are thought to have introduced the anole to Haha-jima, while the mode of introduction to Ani-jima is unknown. To clarify its dispersal patterns within and among these three islands, we assessed the fine-scale population genetic structure using five microsatellite loci. The results show a homogeneous genetic structure within islands, but different genetic structures among islands, suggesting that limited gene flow occurs between islands. The recently established Ani-jima population may have originated from several individuals simultaneously, or by repeated immigration from Chichi-jima. We must consider frequent incursions among these islands to control these invasive lizard populations and prevent their negative impact on native biodiversity.

  2. Microsatellite analysis reveals strong but differential impact of a social parasite on its two host species.

    Science.gov (United States)

    Fischer-Blass, Birgit; Heinze, Jürgen; Foitzik, Susanne

    2006-03-01

    The speed and the dynamics of the co-evolutionary process strongly depend on the relative strengths of reciprocal selection pressures exerted by the interacting species. Here, we investigate the influence of an obligate social parasite, the slave-making ant Harpagoxenus sublaevis, on populations of the two main host species Leptothorax acervorum and Leptothorax muscorum from a German ant community. A combination of genetic and demographic data allowed us to analyse the consequences of raiding pressure on the hosts' life history and possible host preferences of the parasite. We can demonstrate that slave raids during which the social parasite pillages brood from neighbouring host colonies are both frequent and extremely destructive for both host species. Microsatellite analysis showed that, on average, a single slave-maker colony conducts more than three raids per year and that host colonies mostly perish in the aftermath of these parasite attacks. Only in few cases, surviving nests of previously raided host colonies were found in the surroundings of slave-maker colonies. As a consequence of the high prevalence of parasites and their recurrent and devastating slave raids on host colonies, the life expectancy of host colonies was severely reduced. Combining our results on host-specific parasitic colony founding and raiding frequencies with the post-raid survival rate, we can demonstrate an overall higher mortality rate for the smaller host species L. muscorum. This might be caused by a preference of H. sublaevis for this secondary host species as demographic data on host species usage indicate.

  3. Analysis of thermodiffusive cellular instabilities in continuum combustion fronts

    Science.gov (United States)

    Azizi, Hossein; Gurevich, Sebastian; Provatas, Nikolas

    2017-01-01

    We explore numerically the morphological patterns of thermodiffusive instabilities in combustion fronts with a continuum fuel source, within a range of Lewis numbers and ignition temperatures, focusing on the cellular regime. For this purpose, we generalize the recent model of Brailovsky et al. to include distinct process kinetics and reactant heterogeneity. The generalized model is derived analytically and validated with other established models in the limit of infinite Lewis number for zero-order and first-order kinetics. Cellular and dendritic instabilities are found at low Lewis numbers. These are studied using a dynamic adaptive mesh refinement technique that allows very large computational domains, thus allowing us to reduce finite-size effects that can affect or even preclude the emergence of these patterns. Our numerical linear stability analysis is consistent with the analytical results of Brailovsky et al. The distinct types of dynamics found in the vicinity of the critical Lewis number, ranging from steady-state cells to continued tip splitting and cell merging, are well described within the framework of thermodiffusive instabilities and are consistent with previous numerical studies. These types of dynamics are classified as "quasilinear" and characterized by low-amplitude cells that may be strongly affected by the mode selection mechanism and growth prescribed by the linear theory. Below this range of Lewis number, highly nonlinear effects become prominent and large-amplitude, complex cellular and seaweed dendritic morphologies emerge.

  4. Map and analysis of microsatellites in the genome of Populus: The first sequenced perennial plant

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    We mapped and analyzed the microsatellites throughout 284295605 base pairs of the unambiguously assembled sequence scaffolds along 19 chromosomes of the haploid poplar genome. Totally, we found 150985 SSRs with repeat unit lengths between 2 and 5 bp. The established microsatellite physical map demonstrated trat SSRs were distributed relatively evenly across the genome of Populus. On average, These SSRs occurred every 1883 bp within the poplar genome and the SSR densities in intergenic regions, introns, exons and UTRs were 85.4%, 10.7%, 2.7% and 1.2%, respectively. We took di-, tri-, tetra-and pentamers as the four classes of repeat units and found that the density of each class of SSRs decreased with the repeat unit lengths except for the tetranucleotide repeats. It was noteworthy that the length diversification of microsatellite sequences was negatively correlated with their repeat unit length and the SSRs with shorter repeat units gained repeats faster than the SSRs with longer repeat units. We also found that the GC content of poplar sequence significantly correlated with densities of SSRs with uneven repeat unit lengths (tri- and penta-), but had no significant correlation with densities of SSRs with even repeat unit lengths (di- and tetra-). In poplar genome, there were evidences that the occurrence of different microsatellites was under selection and the GC content in SSR sequences was found to significantly relate to the functional importance of microsatellites.

  5. Phenetic analysis of Trifolium resupinatum L. (Persian clover and Trifolium fragiferum L. (strawberry clover using new microsatellite loci

    Directory of Open Access Journals (Sweden)

    Maryam Haerinasab

    2013-06-01

    Full Text Available Trifolium resupinatum and T. fragiferum are two important crop species among the legumes. T. fragiferum is considered as one of the gene pools of T. resupinatum. In this study, the transferability of SSR markers from T. pratense and T. repens to genotypes of these two species was evaluated and new microsatellite loci for these species were obtained. Their genomic similarity was studied using the SSR markers and phenetic analysis. The results of this study indicated a high level of transferability and polymorphism for microsatellites from T. pratense and T. repens to genotype of T. resupinatum and T. fragiferum. Studies also showed that the genetic diversity was high among the populations and the studied populations were grouped in the low levels of similarity. Also, T. resupinatum and T. fragiferum were grouped in clusters with very low similarity that indicated genomic differences between them in tested SSR loci. This study showed that microsatellites can be useful tools to evaluate genetic variation in these species. The results suggested that as long as specific SSR primers for these two species were not designed, SSR primers of T. pratense and T. repens could be used with high reliability for genomic analysis of these species.

  6. Genetic instability in Gynecological Cancer

    Institute of Scientific and Technical Information of China (English)

    ZHAO Qing-hua; ZHOU Hong-lin

    2003-01-01

    Defects of mismatch repair (MMR) genes also have beenidentified in many kinds of tumors. Loss of MMR functionhas been linked to genetic instability especially microsatelliteinstability that results in high mutation rate. In this review, wediscussed the microsatellite instability observed in thegynecological tumors. We also discussed defects in the DNAmismatch repair in these tumors and their correlation to themicrosatellite instability, as well as the gene mutations due tothe microsatellite instability in these tumors. From thesediscussion, we tried to understand the mechanism ofcarcinogenesis in gynecological tumors from the aspect ofgenetic instability due to mismatch repair defects.

  7. Microsatellite markers for identification and parentage analysis in the European wild boar (Sus scrofa

    Directory of Open Access Journals (Sweden)

    Costa Vânia

    2012-09-01

    Full Text Available Abstract Background The wild boar (Sus scrofa is among the most widespread mammal species throughout the old world. Presently, studies concerning microsatellites in domestic pigs and wild boars have been carried out in order to investigate domestication, social behavior and general diversity patterns among either populations or breeds. The purpose of the current study is to develop a robust set of microsatellites markers for parentage analyses and individual identification. Findings A set of 14 previously reported microsatellites markers have been optimized and tested in three populations from Hungary, Portugal and Spain, in a total of 167 samples. The results indicate high probabilities of exclusion (0.99999, low probability of identity (2.0E-13 – 2.5E-9 and a parentage assignment of 100%. Conclusions Our results demonstrate that this set of markers is a useful and efficient tool for the individual identification and parentage assignment in wild boars.

  8. Analysis of beam loss induced abort kicker instability

    Energy Technology Data Exchange (ETDEWEB)

    Zhang W.; Sandberg, J.; Ahrens, L.; Fischer, W.; Hahn, H.; Mi, J.; Pai, C.; Tan, Y.

    2012-05-20

    Through more than a decade of operation, we have noticed the phenomena of beam loss induced kicker instability in the RHIC beam abort systems. In this study, we analyze the short term beam loss before abort kicker pre-fire events and operation conditions before capacitor failures. Beam loss has caused capacitor failures and elevated radiation level concentrated at failed end of capacitor has been observed. We are interested in beam loss induced radiation and heat dissipation in large oil filled capacitors and beam triggered thyratron conduction. We hope the analysis result would lead to better protection of the abort systems and improved stability of the RHIC operation.

  9. Beam instability in 980-nm power lasers: Experiment and analysis

    Science.gov (United States)

    Guthrie, James; Tan, G. L.; Ohkubo, M.; Fukushima, T.; Ikegami, Y.; Ijichi, T.; Irikawa, M.; Mand, R. S.; Xu, J. M.

    1994-12-01

    A theoretical analysis of beam instability (steering), commonly observed in high power ridge waveguide laser diodes is presented. A physical model of multiple interfering lateral modes is proposed and implemented in a two-dimensional self-consistent numerical code. It is shown that the dynamic evolution of the effective waveguide and the coherent lasing of emergent multiple lateral modes of the waveguide under high injection could lead to beam steering and knees in the fiber coupled L-I characteristics. The theory of simultaneous lasing and interaction between several lateral modes is found to be consistent with the observed back-plane radiation image.

  10. Studies on microsatellite instability in p16 gene and expression of hMSH2 mRNA in human gastric cancer tissues

    Institute of Scientific and Technical Information of China (English)

    Qin-Xian Zhang; Yi Ding; Xiao-Ping Le; Peng Du

    2003-01-01

    AIM: To detect the loss of heterozygosity (LOH) frequency of microsatellite sites D9s171, D9s1604 of p16 gene and expression of hMSH2 mRNA in various differentiated types of gastric cancer, adjacent cancer tissues and normal gastric mucosa.METHODS: LOH was detected by polymerase chain reaction (PCR)-denaturing polyacrylamide gel electrophoresis-silver staining. The expression of hMSH2 mRNA was examined with in situ hybridization.RESULTS: The frequency rate of LOH was significantly higher in gastric cancers than that in adjacent cancer tissues (P=0.032). No significant difference was noted among various differentiated types and various clinical stages of gastric cancers. The significantly reduced expression of hMSH2mRNA positive signal cells exhibited in gastric cancers, in comparison with that in the adjacent cancer tissues and normal gastric mucosa, respectively (P=0.001). No significant difference was noted among various clinical stages of gastric cancers (P>0.05). The difference of positive signal cells in poorly differentiated cancers and those in well and moderately differentiated cancers were significant (P<0.001).CONCLUSION: The frequencies of LOH in two microsatellite sites, D9s171 and D9s1604, in p16 genome were associated with development of gastric cancer and no significant correlation was demonstrated between the LOH frequency and the cell differentiated types of tumor cells or clinical stages. There was a positive relationship between the expression of hMSH2 mRNA and the differentiated types of gastric cancer.

  11. DVI Film Flow Instability Based on the Normal Mode Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Jae Young; Euh, Dong Jin [Handong Global Univ., Pohang (Korea, Republic of)

    2013-10-15

    In the present paper, as the first step of nonlinear studies, the appearance of the third order spatial differentiation of the film thickness in the wave propagation equation is to be derived. The two-fluid model in the adiabatic condition is employed and normal mode analysis. Interfacial pressure forces between steam and water need to be modeled for this purpose. n the present study, we developed a theoretical basis to study nonlinear wave phenomena on the DVI film flow which highly affect the DVI penetration and liquid droplets entrainment out. We set the hyperbolicity breaking condition by providing the interfacial pressure difference considering the curvature of the reactor vessel. The interfacial pressure difference could generate nonlinear wave such as the horseshoe wave which has been believed as a main source of film break up to produce huge amount of droplets to be entrained out. As a safety injection method, the direct vessel injection has been intensively developed in Korea and employed in the APR1400. The developing efforts were made from the determination of the number, location and size of DVI nozzles to the experimental demonstrations. Experimental facilities with various scales have shown its complicated phenomena due to highly nonlinear interaction between the steam and injected water flow. The injected DVI water forms a film type flow but very unstable due to the unsteady energetic steam flow which find the exits around the shell of the downcomer of the reactor vessel. This steam and liquid film interaction leads to the instability on the surface of the film flow and the waves are highly nonlinear to form undercutting, roll over, and finally droplet releasing. The entrained droplets causes a difficulty in the analysis to estimate the water penetrated into the reactor core to cool the nuclear fuels heated up. Unfortunately, these instabilities on the interface of the DVI liquid film have not been studied appropriately and the conservative

  12. Target genes of microsatellite sequences in head and neck squamous cell carcinoma: mononucleotide repeats are not detected.

    Science.gov (United States)

    Wang, Yimin; Liu, Xuejuan; Li, Yulin

    2012-09-10

    Microsatellite instability (MSI) is detected in a wide variety of tumors. It is thought that mismatch repair gene mutation or inactivation is the major cause of MSI. Microsatellite sequences are predominantly distributed in intergenic or intronic DNA. However, MSI is found in the exonic sequences of some genes, causing their inactivation. In this report, we searched GenBank for candidate genes containing potential MSI sequences in exonic regions. Twenty seven target genes were selected for MSI analysis. Instability was found in 70% of these genes (14/20) with head and neck squamous cell carcinoma (HNSCC). Interestingly, no instability was detected in mononucleotide repeats in genes or in intergenic sequences. We conclude that instability of mononucleotide repeats is a rare event in HNSCC. High MSI phenotype in young HNSCC patients is limited to noncoding regions only. MSI percentage in HNSCC tumor is closely related to the repeat type, repeat location and patient's age.

  13. Temporal genetic variation as revealed by a microsatellite analysis of European sardine ( Sardina pilchardus) archived samples

    DEFF Research Database (Denmark)

    Ruggeri, Paolo; Splendiani, Andrea; Bonanomi, Sara;

    2012-01-01

    The Adriatic stock of European sardine ( Sardina pilchardus) has experienced large interannual demographic fluctuations over the last 30 years, with a severe decline beginning in 1991 and continuing until 1997. In the present study, six microsatellite loci were used on a time series collection of...

  14. Analysis of Instabilities in Non-Equilibrium Plasmas

    Institute of Scientific and Technical Information of China (English)

    LIN Lie; WU Bin; ZHANG Peng; WANG Yong-Qing

    2004-01-01

    Plasma instabilities with charged particle production processes in non-equilibrium plasma are analysed. A criterion on plasma instabilities is deduced by first-order perturbation theory. The relationship between plasma instabilities and certain factors (degree of non-equilibrium in plasma, the electron attachment rate coefficient and electron temperature) are described.

  15. Modeling and analysis of thermoacoustic instabilities in an annular combustor

    Science.gov (United States)

    Murthy, Sandeep; Sayadi, Taraneh; Le Chenadec, Vincent; Schmid, Peter

    2015-11-01

    A simplified model is introduced to study thermo-acoustic instabilities in axisymmetric combustion chambers. Such instabilities can be triggered when correlations between heat-release and pressure oscillations exist, leading to undesirable effects. Gas turbine designs typically consist of a periodic assembly of N identical units; as evidenced by documented studies, the coupling across sectors may give rise to unstable modes, which are the highlight of this study. In the proposed model, the governing equations are linearized in the acoustic limit, with each burner modeled as a one-dimensional system, featuring acoustic damping and a compact heat source. The coupling between the burners is accounted for by solving the two-dimensional wave equation over an annular region, perpendicular to the burners, representing the chamber's geometry. The discretization of these equations results in a set of coupled delay-differential equations, that depends on a finite set of parameters. The system's periodicity is leveraged using a recently developed root-of-unity formalism (Schmid et al., 2015). This results in a linear system, which is then subjected to modal and non-modal analysis to explore the influence of the coupled behavior of the burners on the system's stability and receptivity.

  16. Qualitative and quantitative analysis of stability and instability dynamics of positive lattice solitons.

    Science.gov (United States)

    Sivan, Y; Fibich, G; Ilan, B; Weinstein, M I

    2008-10-01

    We present a unified approach for qualitative and quantitative analysis of stability and instability dynamics of positive bright solitons in multidimensional focusing nonlinear media with a potential (lattice), which can be periodic, periodic with defects, quasiperiodic, single waveguide, etc. We show that when the soliton is unstable, the type of instability dynamic that develops depends on which of two stability conditions is violated. Specifically, violation of the slope condition leads to a focusing instability, whereas violation of the spectral condition leads to a drift instability. We also present a quantitative approach that allows one to predict the stability and instability strength.

  17. Analysis on secondary instability of shear layer based on the concept of phase synchronization

    Directory of Open Access Journals (Sweden)

    Wubing Yang

    2014-01-01

    Full Text Available A concept of phase synchronization point is proposed, and then a model is built using this concept to explain secondary instabilities. This model has been used to determine the conditions of K- and H-type secondary instabilities, which are coincident with the conditions published in literatures. It also can be used to analyze other secondary instability phenomena. For example, the numerical results validate the analysis results in the case of 1/3rd subharmonic mode secondary instability. Furthermore, the numerical results indicate that the spanwise wave number of 3D disturbance has significant effect on the secondary instability.

  18. Comparative analysis of the within-population genetic structure in wild cherry (Prunus avium L.) at the self-incompatibility locus and nuclear microsatellites.

    Science.gov (United States)

    Schueler, Silvio; Tusch, Alexandra; Scholz, Florian

    2006-10-01

    Gametophytic self-incompatibility (SI) systems in plants exhibit high polymorphism at the SI controlling S-locus because individuals with rare alleles have a higher probability to successfully pollinate other plants than individuals with more frequent alleles. This process, referred to as frequency-dependent selection, is expected to shape number, frequency distribution, and spatial distribution of self-incompatibility alleles in natural populations. We investigated the genetic diversity and the spatial genetic structure within a Prunus avium population at two contrasting gene loci: nuclear microsatellites and the S-locus. The S-locus revealed a higher diversity (15 alleles) than the eight microsatellites (4-12 alleles). Although the frequency distribution of S-alleles differed significantly from the expected equal distribution, the S-locus showed a higher evenness than the microsatellites (Shannon's evenness index for the S-locus: E = 0.91; for the microsatellites: E = 0.48-0.83). Also, highly significant deviations from neutrality were found for the S-locus whereas only minor deviations were found for two of eight microsatellites. A comparison of the frequency distribution of S-alleles in three age-cohorts revealed no significant differences, suggesting that different levels of selection acting on the S-locus or on S-linked sites might also affect the distribution and dynamics of S-alleles. Autocorrelation analysis revealed a weak but significant spatial genetic structure for the multilocus average of the microsatellites and for the S-locus, but could not ascertain differences in the extent of spatial genetic structure between these locus types. An indirect estimate of gene dispersal, which was obtained to explain this spatial genetic pattern, indicated high levels of gene dispersal within our population (sigma(g) = 106 m). This high gene dispersal, which may be partly due to the self-incompatibility system itself, aids the effective gene flow of the

  19. Genetic diversity analysis in the section Caulorrhizae (genus Arachis) using microsatellite markers

    Science.gov (United States)

    2010-01-01

    Diversity in 26 microsatellite loci from section Caulorrhizae germplasm was evaluated by using 33 accessions of A. pintoi Krapov. & W.C. Gregory and ten accessions of Arachis repens Handro. Twenty loci proved to be polymorphic and a total of 196 alleles were detected with an average of 9.8 alleles per locus. The variability found in those loci was greater than the variability found using morphological characters, seed storage proteins and RAPD markers previously used in this germplasm. The high potential of these markers to detect species-specific alleles and discriminate among accessions was demonstrated. The set of microsatellite primer pairs developed by our group for A. pintoi are useful molecular tools for evaluating Section Caulorrhizae germplasm, as well as that of species belonging to other Arachis sections. PMID:21637613

  20. Analysis of Two Chinese Yak(Bos grunniens) Population Using Bovine Microsatellite Primers

    Institute of Scientific and Technical Information of China (English)

    Wang Minqiang; S.Weigend; A.Barre-Dirie; J.W.Carnwath; Lou Zhonglin; H.Niemann

    2005-01-01

    Two Chinese domestic yak populations representing the Plateau type and the Huanhu Alpine type were analysed with 12 bovine microsatellite primers. All primer pairs functioned in the yak genome and polymorphism was found at all loci. The allele size ranges and frequencies of the two yak populations were similar and there was considerable overlap with the allele size ranges observed in cattle. Data for European cattle breeds was obtained from the Cattle Diversity Database(CaDBase)to interpret the heterozygosity and genetic distance estimates in yak populations. Heterozygosity estimated for the two yak populations was comparable to that of European cattle while Nei's Genetic Distance DA between the two yak populations was less than distances between the most closely related German cattle breeds. Bovine microsatellite primers proved to be a valuable tool for characterization of yak populations.

  1. Genetic diversity analysis in the section Caulorrhizae (genus Arachis using microsatellite markers

    Directory of Open Access Journals (Sweden)

    Darío A. Palmieri

    2010-01-01

    Full Text Available Diversity in 26 microsatellite loci from section Caulorrhizae germplasm was evaluated by using 33 accessions of A. pintoi Krapov. & W.C. Gregory and ten accessions of Arachis repens Handro. Twenty loci proved to be polymorphic and a total of 196 alleles were detected with an average of 9.8 alleles per locus. The variability found in those loci was greater than the variability found using morphological characters, seed storage proteins and RAPD markers previously used in this germplasm. The high potential of these markers to detect species-specific alleles and discriminate among accessions was demonstrated. The set of microsatellite primer pairs developed by our group for A. pintoi are useful molecular tools for evaluating Section Caulorrhizae germplasm, as well as that of species belonging to other Arachis sections.

  2. Identification and Characterization of Microsatellite Markers Derived from the Whole Genome Analysis of Taenia solium

    OpenAIRE

    Mónica J Pajuelo; María Eguiluz; Eric Dahlstrom; David Requena; Frank Guzmán; Manuel Ramirez; Patricia Sheen; Michael Frace; Scott Sammons; Vitaliano Cama; Sarah Anzick; Dan Bruno; Siddhartha Mahanty; Patricia Wilkins; Theodore Nash

    2015-01-01

    Background Infections with Taenia solium are the most common cause of adult acquired seizures worldwide, and are the leading cause of epilepsy in developing countries. A better understanding of the genetic diversity of T. solium will improve parasite diagnostics and transmission pathways in endemic areas thereby facilitating the design of future control measures and interventions. Microsatellite markers are useful genome features, which enable strain typing and identification in complex patho...

  3. Analysis on Frequency and Density of Microsatellites in Coding Sequences of Several Eukaryotic Genomes

    Institute of Scientific and Technical Information of China (English)

    Bin Li; Qingyou Xia; Cheng Lu; Zeyang Zhou; Zhonghuai Xiang

    2004-01-01

    Microsatellites or simple sequence repeats (SSRs) have been found in most organisms during the last decade. Since large-scale sequences are being generated, especially those that can be used to search for microsatellites, the development of these markers is getting more convenient. Keeping SSRs in viewing the importance of the application, available CDS (coding sequences) or ESTs (expressed sequence tags) of some eukaryotic species were used to study the frequency and density of various types of microsatellites. On the basis of surveying CDS or EST sequences amounting to 66.6 Mb in silkworm, 37.2 Mb in fly, 20.8 Mb in mosquito, 60.0 Mb in mouse, 34.9 Mb in zebrafish and 33.5 Mb in Caenorhabditis elegans, the frequency of SSRs was 1/1.00 Kb in silkworm, 1/0.77 Kb in fly, 1/1.03 Kb in mosquito, 1/1.21 Kb in mousey 1/1.25 Kb in zebrafish and 1/1.38 Kb in C. Elegans. The overall average SSR frequency of these species is 1/1.07 Kb. Hexanucleotide repeats (64.5%-76.6%) are the most abundant class of SSR in the investigated species, followed by trimeric, dimeric, tetrameric, monomeric and pentameric repeats. Furthermore, the A-rich repeats are predominant in each type of SSRs, whereas G-rich repeats are rare in the coding regions.

  4. Establishment of microsatellite-based triplex PCR for parentage analysis of Chinese shrimp Fenneropenaeus chinensis

    Institute of Scientific and Technical Information of China (English)

    GAO Huan; KONG Jie; LIU Ping; MENG Xianhong; LUAN Sheng; ZHANG Tianshi

    2007-01-01

    Through exploring the microsatellite primers from the random genome sequences of Chinese shrimp (Fenneropenaeus chinensis), some microsatellite primers were obtained with rich polymorphic genetic information, and a triplex PCR was established using three primers (RS1101, RS0683 and H081 primers). By adjusting the final concentration of Mg2+, dNTP and primers, and using a touch-town PCR program, the optimum amplification parameters of PCR system were obtained, which could successfully amplify the three primers in a PCR reaction. In the denatured PAGE gel, the amplified DNA fragments of three primers RS1 101,RS0683 and H081 could be easily identified each other. For the triplex PCR system, the PPE (probabilities of paternity exclusion) is 0.967 9,and the DP (discrimination power) is 0.999 327.Using the triplex PCR to test ten individuals of a parentage and their parents, an individual was excluded from the parentage in all of the three microsatellite loci, which might be mixed into the parentage for some unknown reason such as factitious misplay. The triplex PCR will be of great practical value in identifying the parentages of F. chinensis.

  5. Microsatellite analysis of the genetic relationships between wild and cultivated giant grouper in the South China Sea

    Indian Academy of Sciences (India)

    QING WANG; XIANG WANG; ZHENZHEN XIE; YIQ ILI; LING XIAO; CHENG PENG; HAIFA ZHANG; SHUISHENG LI; YONG ZHANG; HAORAN LIN

    2016-06-01

    The giant grouper (Epinephelus lanceolatus) is a coral fish with high commercial value in Southeast Asia. In the present study, we isolated 11 microsatellite DNA markers, and analysed the genetic diversity and differentiation between cultured stocks and wild populations of the giant grouper originating from the South China Sea. A total of 390 alleles at 11 microsatellite loci were detected in 130 individuals from five different populations. The expected heterozygosity varied from 0.131 to 0.855 with a mean value of 0.623 and the observed heterozygosity varied from 0.145 to 0.869 with a mean value of 0.379. The allelic richness and heterozygosity studies revealed that the genetic diversity of the cultured population was significantly reduced when compared with that of the wild population. The Fis,pairwise Fst values, analysis of molecular variance (AMOVA), three- dimensional factorial correspondence analysis and structure analysis revealed significant population differentiation between the cultured stocks and the wild populations, among the three cultured populations and between the two wild populations. These differences may be caused by random genetic drift, the effects of artificial selection and founder effects. Our results will be useful in the management of cultured stocks and conservation of wild populations of the giant group

  6. Candidate driver genes in microsatellite-unstable colorectal cancer

    NARCIS (Netherlands)

    Alhopuro, Pia; Sammalkorpi, Heli; Niittymaki, Iina; Bistrom, Mia; Raitila, Anniina; Saharinen, Juha; Nousiainen, Kari; Lehtonen, Heli J.; Heliovaara, Elina; Puhakka, Jani; Tuupanen, Sari; Sousa, Sonia; Seruca, Raquel; Ferreira, Ana M.; Hofstra, Robert M. W.; Mecklin, Jukka-Pekka; Jarvinen, Heikki; Ristimaki, Ari; Orntoft, Torben F.; Hautaniemi, Sampsa; Arango, Diego; Karhu, Auli; Aaltonen, Lauri A.

    2012-01-01

    Defects in the mismatch repair system lead to microsatellite instability (MSI), a feature observed in similar to 15% of all colorectal cancers (CRCs). Microsatellite mutations that drive tumourigenesis, typically inactivation of tumour suppressors, are selected for and are frequently detected in MSI

  7. Overturning instability in the mesosphere and lower thermosphere: analysis of instability conditions in lidar data

    Directory of Open Access Journals (Sweden)

    L. Hurd

    2009-07-01

    Full Text Available Resonant sodium lidar measurements from the transition region between the mesosphere and lower thermosphere have revealed frequently-occurring overturning events characterized by vertical scales of ~3–6 km and timescales of several hours. Larsen et al. (2004 proposed that a convective roll instability, similar to that found in the planetary boundary layer, is the likely mechanism responsible for the events. This type of instability requires an inflection point in the background winds near the center of the vortex roll with a low static stability region capped by an inversion. The earlier paper argued that the conditions required to support the instability are common in the altitude range where the features are found. In this paper, we use data from the University of Illinois sodium lidar that was located at the Starfire Optical Range near Albuquerque, New Mexico, and from the Maui/MALT Lidar Facility in Hawaii and present several cases that are used to examine the behavior of the inflection point in detail as a function of time during the evolution of the overturning event. In addition, we examine the background static stability conditions using the temperature data from the lidar.

  8. Vlasov analysis of microbunching instability for magnetized beams

    Directory of Open Access Journals (Sweden)

    C.-Y. Tsai

    2017-05-01

    Full Text Available For a high-brightness electron beam with high bunch charge traversing a recirculation beam line, coherent synchrotron radiation and space charge effects may result in microbunching instability (MBI. Both tracking simulation and Vlasov analysis for an early design of a circulator cooler ring (CCR for the Jefferson Lab Electron Ion Collider (JLEIC reveal significant MBI [Ya. Derbenev and Y. Zhang, Proceedings of the Workshop on Beam Cooling and Related Topics, COOL’09, Lanzhou, China, 2009 (2009, FRM2MCCO01]. It is envisioned that the MBI could be substantially suppressed by using a magnetized beam. In this paper we have generalized the existing Vlasov analysis, originally developed for a nonmagnetized beam (or transversely uncoupled beam, to the description of transport of a magnetized beam including relevant collective effects. The new formulation is then employed to confirm prediction of microbunching suppression for a magnetized beam transport in the recirculation arc of a recent JLEIC energy recovery linac (ERL based cooler design for electron cooling. It is found that the smearing effect in the longitudinal beam phase space originates from the large transverse beam size as a nature of the magnetized beams and becomes effective through the x-z correlation when the correlated distance is larger than the microbunched scale. As a comparison, MBI analysis of the early design of JLEIC CCR is also presented in this paper.

  9. Pulsatile instability in rapid directional solidification - Strongly-nonlinear analysis

    Science.gov (United States)

    Merchant, G. J.; Braun, R. J.; Brattkus, K.; Davis, S. H.

    1992-01-01

    In the rapid directional solidification of a dilute binary alloy, analysis reveals that, in addition to the cellular mode of Mullins and Sekerka (1964), there is an oscillatory instability. For the model analyzed by Merchant and Davis (1990), the preferred wavenumber is zero; the mode is one of pulsation. Two strongly nonlinear analyses are performed that describe this pulsatile mode. In the first case, nonequilibrium effects that alter solute rejection at the interface are taken asymptotically small. A nonlinear oscillator equation governs the position of the solid-liquid interface at leading order, and amplitude and phase evolution equations are derived for the uniformly pulsating interface. The analysis provides a uniform description of both subcritical and supercritical bifurcation and the transition between the two. In the second case, nonequilibrium effects that alter solute rejection are taken asymptotically large, and a different nonlinear oscillator equation governs the location of the interface to leading order. A similar analysis allows for the derivation of an amplitude evolution equation for the uniformly pulsating interface. In this case, the bifurcation is always supercritical. The results are used to make predictions about the characteristics of solute bands that would be frozen into the solid.

  10. MICROSATELLITE ANALYSIS OF THE SLOVAK CARNIOLAN HONEY BEE (APIS MELLIFERA CARNICA

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    Dušan Paál

    2013-02-01

    Full Text Available The aim of this study was the selection and testing of suitable microsatellite markers for evaluation of the Slovak carniolan honey bee, particularly the population structure, genetic diversity, breed assignment and paternity testing of honey bee queens in Slovakia. Fourteen microsatellite markers running in two multiplex PCR reactions have been tested on 40 randomly selected workers and queens and further verified by PIC index, expected heterozygosity (HE and observed heterozygosity (HO. Chi-squared test of goodness of fit (α = 0,05 was used to check the Hardy-Weinberg equilibrium (HWE of genotype for each marker. For the comparison tests the workers of A. mellifera mellifera x ligurica, A. mellifera macedonica and A. mellifera iberica were analyzed, using the same set of markers. We identified a total of 123 alleles in the Slovak carniolan honey bee samples, with the mean value of 8,78 allele per locus. Eleven markers showed the PIC value greater than 0,5 and thus were highly informative. The mean value of expected heterozygosity HE for all loci was 0,705 ± 0,15, the mean value of observed heterozygosity HO was 0,704 ± 0,18. The frequencies of genotypes for most tested markers were in The aim of this study was the selection and testing of suitable microsatellite markers for evaluation of the Slovak carniolan honey bee, particularly the population structure, genetic diversity, breed assignment and paternity testing of honey bee queens in Slovakia. Fourteen microsatellite markers running in two multiplex PCR reactions have been tested on 40 randomly selected workers and queens and further verified by PIC index, expected heterozygosity (HE and observed heterozygosity (HO. Chi-squared test of goodness of fit (α = 0,05 was used to check the Hardy-Weinberg equilibrium (HWE of genotype for each marker. For the comparison tests the workers of A. mellifera mellifera x ligurica, A. mellifera macedonica and A. mellifera iberica were analyzed, using

  11. A SUBLOCUS OF THE MULTICOPY MICROSATELLITE MARKER CMS1 MAPS PROXIMAL TO SPINAL MUSCULAR-ATROPHY (SMA) AS SHOWN BY RECOMBINANT ANALYSIS

    NARCIS (Netherlands)

    VANDERSTEEGE, G; COBBEN, JM; OSINGA, J; SCHEFFER, H; VANOMMEN, GJB; BUYS, CHCM

    1995-01-01

    The critical region containing the spinal muscular atrophy (SMA) gene is flanked by the 5q11-q13 markers, D5S435 and D5S557, as determined by linkage analysis. Here we present the results of an analysis of a Dutch SMA family with the multicopy microsatellite marker CMS1. A crossover is revealed in

  12. Polymorphism analysis of microsatellites and construction of linkage map in part regions of four chromosomes in chicken

    Institute of Scientific and Technical Information of China (English)

    WANG Shouzhi; LI Hui; LI Ning; GAO Yu; DU Zhiqiang; GU Zhiliang; WANG Qigui; LI Zhihui; WANG Ying

    2007-01-01

    Based on chicken' consensus map issued in 2000, 17 microsatellites near 4 candidate genes such as IGF2, OBR, GDFS and APOA1 in 4 chromosomes (chromosome 5, 7, 8 and 24) were chosen for polymorphism analysis and construction of linkage map. Combining the technique of PCR and the fluorescent semi-automated detection, genome scanning was performed for 440 chickens, which was derived from China Agricultural University chicken resource families within three generations. The individuals of this resource families were genotyped. The results showed that the number of alleles ranged from 4 to 14; heterozygosity (H) of markers was between 0.3116 and 0.9148. Polymorphic information content (PIC) varied from 0.2672 to 0.8679. Microsatellites along with above-mentioned 4 candidate genes doing as general markers were used to construct linkage map. The spans of 4 linkage maps constructed in the part region of chromosome 5, 7, 8 and 24 were 263.5, 79.9, 206.2 and 104.2 cM, respectively. The order of markers was consistent with that of counterpart of reported consensus map. However, The spans of linkage map were larger than that of consensus map. The constructed linkage maps laid the foundation for mapping quantitative trait loci (QTL) responsible for economically important traits in chicken.

  13. The population structure of Trypanosoma cruzi: expanded analysis of 54 strains using eight polymorphic CA-repeat microsatellites

    Directory of Open Access Journals (Sweden)

    Riva P Oliveira

    1999-09-01

    Full Text Available Recently we cloned and sequenced the first eight Trypanosoma cruzi polymorphic microsatellite loci and studied 31 clones and strains to obtain valuable information about the population structure of the parasite. We have now studied 23 further strains, increasing from 11 to 31 the number of strains obtained from patients with chronic Chagas disease. This expanded set of 54 strains and clones analyzed with the eight microsatellites markers confirmed the previously observed diploidy, clonal population organization and very high polymorphism of T. cruzi. Moreover, this new study disclosed two new features of the population genetic structure of T. cruzi. The first was the discovery that, similarly to what we had previously shown for strains isolated from insect vectors, mammals and humans with acute disease, isolates from patients in the chronic phase of Chagas disease could also be multiclonal, albeit at a reduced proportion. Second, when we used parsimony to display the genetic relationship among the clonal lineages in an unrooted Wagner network we observed, like before, a good correlation of the tree topography with the classification in three clusters on the basis of single locus analysis of the ribosomal RNA genes. However, a significant new finding was that now the strains belonging to cluster 2 split in two distant sub-clusters. This observation suggests that the evolutionary history of T. cruzi may be more complex than we previously thought.

  14. Paternity Analysis of the Olive Variety “Istrska Belica” and Identification of Pollen Donors by Microsatellite Markers

    Directory of Open Access Journals (Sweden)

    Alenka Baruca Arbeiter

    2014-01-01

    Full Text Available The leading olive variety in Slovenia is “Istrska belica” (Olea europaea L., which currently represents 70% of all olive trees in productive orchards. Paternity analysis based on microsatellite markers was used for genotyping and identification of the potential pollen donors of “Istrska belica” and for assessing the proportion of self-fertilization in monovarietal olive orchards in the Slovene Istria. Seven microsatellite loci were used for genotyping thirty-one olive embryos from “Istrska belica” trees and for all potential pollen donor varieties, which are grown in the region and could participate as pollinators. Genotyping results and allele identification were performed using the FaMoz software. The most probable pollen donor was assigned to 39% of all analyzed embryos. Among all analyzed embryos no single case of self-fertilization was confirmed. According to the present results, the variety “Istrska belica” was in all cases fertilized by foreign pollen. The results will contribute to defining the new guidelines for farmers regarding the proper management and growing practice in monovarietal olive groves.

  15. Preliminary study of microsatellite instability and loss of heterozygosity in thymic squamous cell carcinoma%胸腺鳞癌微卫星不稳定和杂合性缺失的初步探讨

    Institute of Scientific and Technical Information of China (English)

    邵明海; 胡炜; 王建华; 卢洪胜; 陈仕林

    2010-01-01

    Objective To investigate the frequency of micresatellite instability (MSI) and loss of heterozygosity (LOH) and select sensitive loci for studying microsatellite DNA imbalance in thymic squamous cell carcinoma. Methods 5 microsat-ellitc polymorphism markers and extrated DNA were selected from 9 specmiens of paired thymie squamous cell carcinoma/nor-real tissues. MSI and LOH in the specmiens of thymic carcinoma and relevant pericancerou tissues were detected by polymerase chain reaction (PCR) followed by 6% polyacrylamide gel electrophoresis(PAGE) with silver staining. Results MSI or LOH was detected in 9 thymic carcinoma tissues. The frequency of MSI or LOH was 66.7% (6/9) at loci of D6S1708, 33.3% (3/9) at TP53, 33.3% (3/9)at DM, 33.3% (3/9)at D11S988 and 0% (0/9)at D8S136, LOH at D6S1708 (5/6) was a common genetic alteration. DI1S988 had only LOH alteration. Conclusion D6S1708, TP53, DM, and D11S988 are sensi-tive loci for studying microsatellite DNA imbalance in thymic squamous cell carcinoma. Microsatellite DNA imbalance may play a certain role in occurrence and development of thymic squamous cell carcinoma, and the relationship between MSi or LOH.The linicopathological features of thymic squamous cell carcinoma needs further investigation.%目的 检测胸腺鳞癌微卫星不稳定(MSI)和杂合性缺失(LOH)发生频率,以探讨胸腺鳞癌MSI现象的合适微卫星(MS)位点.方法 选择5个微卫星多态性标记,从石蜡包埋的存档标本中选取9例肿瘤组织和其对应的自身正常组织,提取DNA后用PCR扩增,6%聚丙稀酰胺凝胶电泳,银染显色后进行MSI和LOH分析.结果 9例胸腺鳞癌均出现MSI或LOH.在所检5个位点中D6S1708、TP53、DM、D11S988和D8S136微卫星不平衡发生率分别为66.7%(6/9)、33.3%(3/9)、33.3%(3/9)、33.3%(3/9)和0%(0/9).D6S1708遗传学改变多为LOH(5/6),D11S988位点仅见于LOH.结论 D6S1708、TP53、DM和D11S988可以作为研究胸腺鳞癌微卫星的位点;微卫星不平衡可

  16. The analysis of genetic diversity and differentiation of six Chinese cattle populations using microsatellite markers

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    A total of 321 individuals from six cattle populations of four species in a bovine subfamily in China were studied using 12 pairs of microsatellite markers. The genetic diversities within and between populations were calculated. The phylogenetic trees were constructed by(δμ)2 and DA distances, and the divergence times between populations were estimated by (δμ)2. Altogether, 144 microsatellite alleles were detected including 24 private alleles and nine shared alleles. Chinese Holstein had the largest number of private alleles (10), whereas,Bohai black and Buffalo had the smallest number of private alleles (2). Chinese Holstein showed the highest genetic variability. Its observed number of alleles (Na), mean effective number of alleles (MNA), and mean heterozygosity (He) were 7.7500, 4.9722, and 0.7719,respectively, whereas, the Buffalo and Yak showed low genetic variability. In the phylogenetic trees, Luxi and Holstein grouped first,followed by Bohai and Minnan. Yak branched next and buffalo emerged as the most divergent population from other cattle populations.Luxi and Bohai were estimated to have diverged 0.039-0.105 million years ago (MYA), however, buffalo and Holstein diverged 0.501-1.337 MYA. The divergence time of Yak versus Minnan, Holstein and buffalo was 0.136-0.363, 0.273-0.729, and 0.326-0.600MYA, respectively.

  17. Comparative analysis of microsatellite variability in five macaw species (Psittaciformes, Psittacidae: application for conservation

    Directory of Open Access Journals (Sweden)

    Flavia T. Presti

    2011-01-01

    Full Text Available Cross-amplification was tested and variability in microsatellite primers (designed for Neotropical parrots compared, in five macaw species, viz., three endangered blue macaws (Cyanopsitta spixii [extinct in the wild], Anodorhynchus leari [endangered] and Anodorhynchus hyacinthinus [vulnerable], and two unthreatened red macaws (Ara chloropterus and Ara macao. Among the primers tested, 84.6% successfully amplified products in C. spixii, 83.3% in A. leari, 76.4% in A. hyacinthinus, 78.6% in A. chloropterus and 71.4% in A. macao. The mean expected heterozygosity estimated for each species, and based on loci analyzed in all the five, ranged from 0.33 (A. hyacinthinus to 0.85 (A. macao. As expected, the results revealed lower levels of genetic variability in threatened macaw species than in unthreatened. The low combined probability of genetic identity and the moderate to high potential for paternity exclusion, indicate the utility of the microsatellite loci set selected for each macaw species in kinship and population studies, thus constituting an aid in planning in-situ and ex-situ conservation.

  18. Genetic diversity analysis among pigeonpea genotypes adapted to South American regions based on microsatellite markers

    Directory of Open Access Journals (Sweden)

    Adna Cristina Barbosa de Sousa

    2011-08-01

    Full Text Available The pigeonpea [Cajanus cajan (L Millspaugh] is one of the most important perennial legume crops utilized in the food, fodder, soil conservation, crop-livestock integrated systems, reclaiming of degraded pastures and symbiotic nitrogen fixation. Microsatellite markers were used to estimate the genetic diversity of 77 pigeonpea genotypes selected from the germplasm collections at Embrapa Cattle-Southeast and, to evaluate their transferability to Phaseolus vulgaris and Vigna unguiculata species. The number of alleles per locus ranged from 2 to12, with an average of 5.1 alleles. The PIC values ranged from 0.11 to 0.80 (average 0.49 and the D values from 0.23 to 0.91 (average 0.58. The averages of observed and expected heterozygosity were 0.25 and 0.47, respectively, showing a deficit in heterozygosity. A model-based Bayesian approach implemented in the software STRUCTURE was used to assign genotypes into clusters. A dendrogram was constructed based on the modified Roger's genetic distances using a neighbor-joining method (NJ. A total of four clusters were assembled by STRUCTURE and a strong tendency of correspondence between the Bayesian clusters in the NJ tree was observed. The genetic distance ranged from 0.09 to 0.62 (average 0.37, showing a low genetic diversity in the pigeonpea genotypes. Transferability of pigeonpea-specific microsatellites revealed a cross-amplification and the presence of polymorphic alleles in P. vulgaris and V. unguiculata.

  19. Use of microsatellite markers in molecular analysis of segregating populations of papaya (Carica papaya L.) derived from backcrossing.

    Science.gov (United States)

    Pinto, F O; Pereira, M G; Luz, L N; Cardozo, D L; Ramos, H C C; Macedo, C M P

    2013-07-08

    Brazil is the world leader in papaya production. However, only a small number of cultivars are registered for commercial planting, mainly owing to delays in obtaining cultivars and the high costs of the field phase of breeding programs. These costs can be reduced when molecular tools are combined with conventional breeding methods. In the present study, we conducted a molecular analysis of a self-fertilized population of a first backcrossing generation of BC1S1 papaya plants via microsatellite markers both to monitor the level of homozygosity and the gene/allele transfer that confers the Golden trait (fruit color) and to assess the parental genomic proportion in the genotypes studied. Based on the analysis of 20 polymorphic microsatellite loci, 19 genotypes with the Golden trait belonging to BC1S1 were evaluated in addition to the parental genotypes. Genetic distance was estimated through weighted index. The genotypes were then grouped using the hierarchical nearest neighbor method, and the analysis of principal coordinates was used to measure the proportion of parental genomes in the segregating genotypes. The mean value of the inbreeding coefficient was 0.36. The analysis of the principal coordinates revealed that on average, 64% of the recurrent parent genome was present in the population. Together, the analyses allowed the selection of 3 individuals for the next backcross cycle (33BC1S1-18, 34BC1S1-16, and 37BC1S1-10). These individuals had a higher proportion of the recurrent parent and were grouped close to the recurrent parent in the cluster analysis.

  20. Genome-wide survey and analysis of microsatellites in nematodes, with a focus on the plant-parasitic species Meloidogyne incognita

    Directory of Open Access Journals (Sweden)

    Guillemaud Thomas

    2010-10-01

    Full Text Available Abstract Background Microsatellites are the most popular source of molecular markers for studying population genetic variation in eukaryotes. However, few data are currently available about their genomic distribution and abundance across the phylum Nematoda. The recent completion of the genomes of several nematode species, including Meloidogyne incognita, a major agricultural pest worldwide, now opens the way for a comparative survey and analysis of microsatellites in these organisms. Results Using MsatFinder, the total numbers of 1-6 bp perfect microsatellites detected in the complete genomes of five nematode species (Brugia malayi, Caenorhabditis elegans, M. hapla, M. incognita, Pristionchus pacificus ranged from 2,842 to 61,547, and covered from 0.09 to 1.20% of the nematode genomes. Under our search criteria, the most common repeat motifs for each length class varied according to the different nematode species considered, with no obvious relation to the AT-richness of their genomes. Overall, (ATn, (AGn and (CTn were the three most frequent dinucleotide microsatellite motifs found in the five genomes considered. Except for two motifs in P. pacificus, all the most frequent trinucleotide motifs were AT-rich, with (AATn and (ATTn being the only common to the five nematode species. A particular attention was paid to the microsatellite content of the plant-parasitic species M. incognita. In this species, a repertoire of 4,880 microsatellite loci was identified, from which 2,183 appeared suitable to design markers for population genetic studies. Interestingly, 1,094 microsatellites were identified in 801 predicted protein-coding regions, 99% of them being trinucleotides. When compared against the InterPro domain database, 497 of these CDS were successfully annotated, and further assigned to Gene Ontology terms. Conclusions Contrasted patterns of microsatellite abundance and diversity were characterized in five nematode genomes, even in the case of

  1. Gene expression signatures for colorectal cancer microsatellite status and HNPCC

    DEFF Research Database (Denmark)

    Kruhøffer, M; Jensen, J L; Laiho, P;

    2005-01-01

    The majority of microsatellite instable (MSI) colorectal cancers are sporadic, but a subset belongs to the syndrome hereditary non-polyposis colorectal cancer (HNPCC). Microsatellite instability is caused by dysfunction of the mismatch repair (MMR) system that leads to a mutator phenotype, and MSI...... of 101 stage II and III colorectal cancers (34 MSI, 67 microsatellite stable (MSS)) using high-density oligonucleotide microarrays. From these data, we constructed a nine-gene signature capable of separating the mismatch repair proficient and deficient tumours. Subsequently, we demonstrated...

  2. Analysis of Kelvin Helmholtz Instabilities of Plasma Jets

    Science.gov (United States)

    Friedman, Mark J.; Hollingsworth, Blane J.

    1999-01-01

    Ulysses data indicates density fluctuations which are theorized to be the result of shear between a solar jet and its ambient. The MHD Kelvin-Helmholtz ("KH") instability causes such fluctuations as observed by Ulysses. A new dispersion relationship which accounts for this KH instability is derived via the linearization of the MHD equations. This generalizes an earlier result by Hardee. This dispersion relationship has the form of eight non-linear equations with nine unknowns.

  3. Microsatellite loci for population and parentage analysis in the Amazon River dolphin (Inia geoffrensis de Blainville, 1817).

    Science.gov (United States)

    Gravena, Waleska; Hrbek, Tomas; DA Silva, Vera M S; Astolfi-Filho, Spartaco; Farias, Izeni P

    2009-03-01

    We developed specific primers for microsatellite DNA regions for the Amazon River dolphin or boto Inia geoffrensis, for use in population and conservation genetic studies. We also tested their transferability for two other species, Pontoporia blainvillei (sister taxon of I. geoffrensis) and Sotalia guianensis. A total of 12 microsatellite loci were polymorphic for the boto. An additional 25 microsatellite loci previously isolated from other cetacean species were also tested in the boto. The 26 polymorphic microsatellite loci indicate they will be excellent markers for studies of population structure and kinship relations of the boto.

  4. Inheritance of 15 microsatellites in the Pacific oyster Crassostrea gigas: segregation and null allele identification for linkage analysis

    Institute of Scientific and Technical Information of China (English)

    LI Li; GUO Ximing; ZHANG Guofan

    2009-01-01

    Microsatellites were screened in a backcross family of the Pacific oyster, Crassostrea gigas. Fifteen microsatellite loci were distinguishable and polymorphic with 6 types of allele-combinations. Null alleles were detected in 46.7% of loci, accounting for 11.7% of the total alleles. Four loci did not segregate in Mendelian Ratios. Three linkage groups were identified among 7 of the 15 segregating loci. Fluorescence-based automated capillary electrophoresis (ABI 310 Genetic Analyzer) that used to detect the microsatellite loci, has been proved a fast, precise, and reliable method in microsatellite genotyping.

  5. Generation and analysis of ESTs from the eastern oyster, Crassostrea virginica Gmelin and identification of microsatellite and SNP markers

    Directory of Open Access Journals (Sweden)

    Wallace Richard

    2007-06-01

    Full Text Available Abstract Background The eastern oyster, Crassostrea virginica (Gmelin 1791, is an economically important species cultured in many areas in North America. It is also ecologically important because of the impact of its filter feeding behaviour on water quality. Populations of C. virginica have been threatened by overfishing, habitat degradation, and diseases. Through genome research, strategies are being developed to reverse its population decline. However, large-scale expressed sequence tag (EST resources have been lacking for this species. Efficient generation of EST resources from this species has been hindered by a high redundancy of transcripts. The objectives of this study were to construct a normalized cDNA library for efficient EST analysis, to generate thousands of ESTs, and to analyze the ESTs for microsatellites and potential single nucleotide polymorphisms (SNPs. Results A normalized and subtracted C. virginica cDNA library was constructed from pooled RNA isolated from hemocytes, mantle, gill, gonad and digestive tract, muscle, and a whole juvenile oyster. A total of 6,528 clones were sequenced from this library generating 5,542 high-quality EST sequences. Cluster analysis indicated the presence of 635 contigs and 4,053 singletons, generating a total of 4,688 unique sequences. About 46% (2,174 of the unique ESTs had significant hits (E-value ≤ 1e-05 to the non-redundant protein database; 1,104 of which were annotated using Gene Ontology (GO terms. A total of 35 microsatellites were identified from the ESTs, with 18 having sufficient flanking sequences for primer design. A total of 6,533 putative SNPs were also identified using all existing and the newly generated EST resources of the eastern oysters. Conclusion A high quality normalized cDNA library was constructed. A total of 5,542 ESTs were generated representing 4,688 unique sequences. Putative microsatellite and SNP markers were identified. These genome resources provide the

  6. Demographic estimates from Y chromosome microsatellite polymorphisms: Analysis of a worldwide sample

    Directory of Open Access Journals (Sweden)

    Macpherson J

    2004-08-01

    Full Text Available Abstract Polymorphisms in microsatellites on the human Y chromosome have been used to estimate important demographic parameters of human history. We compare two coalescent-based statistical methods that give estimates for a number of demographic parameters using the seven Y chromosome polymorphisms in the HGDP-CEPH Cell Line Panel, a collection of samples from 52 worldwide populations. The estimates for the time to the most recent common ancestor vary according to the method used and the assumptions about the prior distributions of model parameters, but are generally consistent with other global Y chromosome studies. We explore the sensitivity of these results to assumptions about the prior distributions and the evolutionary models themselves.

  7. Sequence Divergence of Microsatellites and Phylogeny Analysis in Tetraploid Cotton Species and Their Putative Diploid Ancestors

    Institute of Scientific and Technical Information of China (English)

    Wang-Zhen GUO; Dong FANG; Wen-Duo YU; Tian-Zhen ZHANG

    2005-01-01

    To determine the level of microsatellite sequence differences and to use the information to construct a phylogenetic relationship for cultivated tetraploid cotton (Gossypium spp.) species and their putative diploid ancestors, 10 genome-derived microsatellite primer pairs were used to amplify eight species,including two tetraploid and six diploid species, in Gossypium. A total of 92 unique amplicons were resolved using polyacrylamide gel electrophoresis. Each amplicon was cloned, sequenced, and analyzed using standard phylogenetic software. Allelic diversities were caused mostly by changes in the number of simple sequence repeat (SSR) motif repeats and only a small proportion resulted from interruption of the SSR motif within the locus for the same genome. The frequency of base substitutions was 0.5%-1.0% in different genomes, with only few indels found. Based on the combined 10 SSR flanking sequence data, the homology of A-genome diploid species averaged 98.9%, even though most of the amplicons were of the same size, and the sequence homology between G. gossypioides (Ulbr.) Standl. and three other D-genome species (G.raimondii Ulbr., G. davidsonii Kell., and G. thurberi Tod.) was 98.5%, 98.6%, and 98.5%, respectively.Phylogenetic trees of the two allotetraploid species and their putative diploid progenitors showed that homoelogous sequences from the A- and D-subgenome were still present in the polyploid subgenomes and they evolved independently. Meanwhile, homoelogous sequence interaction that duplicated loci in the polyploid subgenomes became phylogenetic sisters was also found in the evolutionary history of tetraploid cotton species. The results of the present study suggest that evaluation of SSR variation at the sequence level can be effective in exploring the evolutionary relationships among Gossypuim species.

  8. Multi-Dimensional Combustion Instability Analysis of Solid Propellant Rocket Motors.

    Science.gov (United States)

    2014-09-26

    RI D-R159 314 MULTI-DIMENSIONAL COMBUSTION INSTABLITY ANALYSIS OF 1/1 I SOLID PROPELLANT ROCK.. (U) ALABAMA UNIY IN HUNTSVILLE I DEPT OF MECHANICAL...STANDARDS MlICROCOPY RESOLUTION TEST CHART 0 0 0 03 V.%% f iSR.TR. 85-0567 NULTI-DIMNSIONAL COMBUSTION INSTABILITY ANALYSIS OF SOLID PROPELLANT ROCKET...analysis of solid propellant rocket motors. This research was motivated by the need for im- provement of the current practice in combustion instability

  9. A comparative analysis of distribution and conservation of microsatellites in the transcripts of sequenced Fusarium species and development of genic-SSR markers for polymorphism analysis.

    Science.gov (United States)

    Mahfooz, Sahil; Srivastava, Arpita; Srivastava, Alok K; Arora, Dilip K

    2015-09-01

    We used an in silico approach to survey and compare microsatellites in transcript sequences of four sequenced members of genus Fusarium. G + C content of transcripts was found to be positively correlated with the frequency of SSRs. Our analysis revealed that, in all the four transcript sequences studied, the occurrence, relative abundance and density of microsatellites varied and was not influenced by transcript sizes. No correlation between relative abundance and transcript sizes was observed. The relative abundance and density of microsatellites were highest in the transcripts of Fusarium solani when compared with F. graminearum, F. verticillioides and F. oxysporum. The maximum frequency of SSRs among all four sequence sets was of trinucleotide repeats (67.8%), whereas the dinucleotide repeat represents Fusarium species. In order to study polymorphism within Fusarium isolates, 11 polymorphic genic-SSR markers were developed. Of the 11 markers, 5 were from F. oxysporum and remaining 6 belongs to F. solani. SSR markers from F. oxysporum were found to be more polymorphic (38%) as compared to F. solani (26%). Eleven polymorphic markers obtained in this study clearly demonstrate the utility of newly developed SSR markers in establishing genetic relationships among different isolates of Fusarium. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  10. Catastrophe analysis on pillar instability considered mining effect

    Institute of Scientific and Technical Information of China (English)

    LI Jiang-teng; CAO Ping

    2005-01-01

    The instability of the pillar was discussed based on the potential energy principle and the cusp catastrophe theory, and a simplified mechanical model of the pillar was established considering the mining effect. The necessary-sufficient conditions, the jump value of displacement of pillar and the released energy expressions were deduced. The results show that the instability of the pillar is related to the properties of the rock, the external force and the relative stiffness of the elastic area to the plastic area. The instability of system is like to occur with the enlarging of the softening area or the decreasing of E/λ. The calculation done shows that the estimated results correspond to practical experience.

  11. Numerical Analysis for Dynamic Instability of Electrodynamic Maglev Systems

    Directory of Open Access Journals (Sweden)

    Y. Cai

    1995-01-01

    Full Text Available Suspension instabilities in an electrodynamic maglev system with three- and five-degrees-of-freedom DOF vehicles traveling on a double L-shaped set of guideway conductors were investigated with various experimentally measured magnetic force data incorporated into theoretical models. Divergence and flutter were obtained from both analytical and numerical solutions for coupled vibration of the three-DOF maglev vehicle model. Instabilities of five direction motion (heave, slip, roll, pitch, and yaw were observed for the five-DOF vehicle model. The results demonstrate that system parameters such as system damping, vehicle geometry, and coupling effects among five different motions play very important roles in the occurrence of dynamic instabilities of maglev vehicles.

  12. Instability analysis on drainage flow over a complex terrain

    Science.gov (United States)

    Yi, C.

    2007-12-01

    The turbulent transport processes that occur within canopies are extremely complex and have not been accurately represented in past models, especially for ecosystems with hilly or mountainous terrain. The stability analysis on the terrain-induced canopy flows is the key to understanding the introduction of pollutants into the atmosphere and the transfer of water from soil and vegetation to the atmosphere. We applied the Computational Fluid Dynamics (CFD) approach to forest environments to simulate airflows within and above canopy. The results of the CFD experiments show three different dynamic regimes of topographic drainage flow that were simulated under different thermal-dynamic conditions: (1) Cold inflow induces drainage flow in the lower part of canopy and strong stratification of airflows within entire canopy; additionally, the model predicts that there is a super stable layer around the maximum LAD level, which is consistent with our canopy flow theory. This super stable layer minimizes vertical land-atmosphere exchange around the middle level of canopy. (2) Warm inflow causes the rapid flushing of land-atmosphere exchange at the location where two opposite air motions meet, this is called the 'chimney phenomenon'. (3) The oscillation of canopy flow occurs as the inflow temperature is close to the environmental temperature. These CFD simulations are based on fully derived thermal and fluid dynamic equations. In order to clearly understand the physical mechanisms for the transfer between the different dynamic regimes, I utilized the nonlinear dynamics approach to derive the analytical instability conditions of terrain-induced flows from the simplified thermal-hydro-mechanical equations. The analytical derivations are tested against the CFD simulations. These analytical conditions provide a better understanding of transport problem in ecosystem- atmosphere exchanges of water, carbon dioxide, and energy over complex terrain.

  13. Finite Element Analysis of Patella Alta: A Patellofemoral Instability Model

    Science.gov (United States)

    Duchman, Kyle R.; Grosland, Nicole M.; Bollier, Matthew J.

    2017-01-01

    Abstract Background: This study aims to provide biomechanical data on the effect of patella height in the setting of medial patellofemoral ligament (MPFL) reconstruction using finite element analysis. The study will also examine patellofemoral joint biomechanics using variable femoral insertion sites for MPFL reconstruction. Methods: A previously validated finite element knee model was modified to study patella alta and baja by translating the patella a given distance to achieve each patella height ratio. Additionally, the models were modified to study various femoral insertion sites of the MPFL (anatomic, anterior, proximal, and distal) for each patella height model, resulting in 32 unique scenarios available for investigation. Results: In the setting of patella alta, the patellofemoral contact area decreased, resulting in a subsequent increase in maximum patellofemoral contact pressures as compared to the scenarios with normal patellar height. Additionally, patella alta resulted in decreased lateral restraining forces in the native knee scenario as well as following MPFL reconstruction. Changing femoral insertion sites had a variable effect on patellofemoral contact pressures; however, distal and anterior femoral tunnel malpositioning in the setting of patella alta resulted in grossly elevated maximum patellofemoral contact pressures as compared to other scenarios. Conclusions: Patella alta after MPFL reconstruction results in decreased lateral restraining forces and patellofemoral contact area and increased maximum patellofemoral contact pressures. When the femoral MPFL tunnel is malpositioned anteriorly or distally on the femur, the maximum patellofemoral contact pressures increase with severity of patella alta. Clinical Relevance: When evaluating patients with patellofemoral instability, it is important to recognize patella alta as a potential aggravating factor. Failure to address patella alta in the setting of MPFL femoral tunnel malposition may result in

  14. Development of genomic microsatellite multiplex PCR using dye-labeled universal primer and its validation in pedigree analysis of Pacific oyster ( Crassostrea gigas)

    Science.gov (United States)

    Liu, Ting; Li, Qi; Song, Junlin; Yu, Hong

    2017-02-01

    There is an increasing requirement for traceability of aquaculture products, both for consumer protection and for food safety. There are high error rates in the conventional traceability systems depending on physical labels. Genetic traceability technique depending on DNA-based tracking system can overcome this problem. Genealogy information is essential for genetic traceability, and microsatellite DNA marker is a good choice for pedigree analysis. As increasing genotyping throughput of microsatellites, microsatellite multiplex PCR has become a fast and cost-effective technique. As a commercially important cultured aquatic species, Pacific oyster Crassostrea gigas has the highest global production. The objective of this study was to develop microsatellite multiplex PCR panels with dye-labeled universal primer for pedigree analysis in C. gigas, and these multiplex PCRs were validated using 12 full-sib families with known pedigrees. Here we developed six informative multiplex PCRs using 18 genomic microsatellites in C. gigas. Each multiplex panel contained a single universal primer M13(-21) used as a tail on each locus-specific forward primer and a single universal primer M13(-21) labeled with fluorophores. The polymorphisms of the markers were moderate, with an average of 10.3 alleles per locus and average polymorphic information content of 0.740. The observed heterozygosity per locus ranged from 0.492 to 0.822. Cervus simulations revealed that the six panels would still be of great value when massive families were analysed. Pedigree analysis of real offspring demonstrated that 100% of the offspring were unambiguously allocated to their parents when two multiplex PCRs were used. The six sets of multiplex PCRs can be an important tool for tracing cultured individuals, population genetic analysis, and selective breeding program in C. gigas.

  15. Relationship between microsatellite instability and deficiency of DNA mismatch repair system in lung carcinoma%肺癌微卫星不稳定性与错配修复基因缺陷的相关性研究

    Institute of Scientific and Technical Information of China (English)

    李曼; 喻喆; 李英华; 张晶

    2011-01-01

    Objectiye To investigate the relationship between microsatellite instability (MSI) and mismatch repair gene (MMR) in lung carcinoma,and to analyze its action in lung carcinogenesis.Methods DNA was extracted from 50 cases of lung carcinoma and adjacent normal tissue.SSCP was used to detect MSI.Immunohistochemistry was performed to measure the expression of hMLH1 and hMSH2 protein in lung carcinoma.Results Of the 50 cases of lung carcinoma,14 with high MSI,21 with low MSI,and 15 with microsatellite stability,0 with MSI in normal group (P = 0.000).Lack of hMLH1 and hMLH2 staining was found in 37 of 50 (74 %) and 16 of 50 (32 %) lung carcinoma tissues with MSI,respectively; but both of hMLH1 and hMSH2 positive staining was found in the lung carcinoma tissues with MSS.Conclusion MSI appears to be associated with lung carcinogenesis,and inactivation of either hMLH1 or hMSH2 may be responsible for MSI,suggesting that MSI may become one of diagnosis indexes of lung carcinoma.%目的 通过对肺癌微卫星不稳定性(MSI)的分析与错配修复基因蛋白表达的检测,探讨肺癌发病的分子机制.方法 从50例肺癌患者的正常肺组织、癌组织中提取DNA;SSCP法检测标本中MSI发生情况;免疫组织化学法检测错配修复基因hMLH1及hMSH2在肺癌中的表达情况.结果 50例肺癌中微卫星高度不稳定(MSI-H)14例,低度不稳定(MSI-I)21例,稳定(MSS)15例,正常组织中未出现MSI,两者之间差异有统计学意义(P=0.000);免疫组化结果显示hMLH1在MSI肺癌组织中常为缺失表达,表达率为74%(37/50);hMSH2在MSI肺癌组织中也呈缺失表达,表达率为32%(16/50);而在MSS肺癌组织中均显示hMLH1、hMSH2基因蛋白表达阳性.结论 肺癌的发生可能存在MSI途径,而hMLH1、hMSH2的表达失活则可能导致MSI的发生,因此,MSI可作为肺癌诊断的指标之一.

  16. MICROSATELLITE ALTERATION AND ITS CHARACTERISTICS IN COLORECTAL CARCINOMA

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Objective: To determine the role of microsatellite alterations incarcinogenesis of colorectal carcinoma (CRC). Methods: Alterations of 10 microsatellite loci from 5 different chromosomes were detected in 92 colorectal cancers and their paired normal mucosa by PCR, denatured polyacrylamide gel electrophoresis and silver staining. Associations of microsatellite alterations with clinopathologic parameters were statistically clarified.Results: Alterations of microsatellite were classified into microsatellite instability type I, type II and loss of heterozygosity (LOH). The carcinoma with ≥30% loci microsatellite alterations was defined as replication error(RER) positive tumors. Of 92 cases, 14 were RER+. Microsatellite alterations of P53(1) and D18S363 loci (64.29% ) was most commonly identified in the RER+ tumors. RER+ were more commonly seen in poorly differentiated carcinomas and tended to occur in mucoid carcinomas. The type of microsatellite alterations varied in different histological types of CRC. Conclusions: Microsatellite alteration is a common molecular event in CRC. Different microsatellite loci showed various biologic significance. P53(1) and D18S363 should be essentially detected loci that can show the RER status of tumors.

  17. Radiation induced genome instability: multiscale modelling and data analysis

    Science.gov (United States)

    Andreev, Sergey; Eidelman, Yuri

    2012-07-01

    Genome instability (GI) is thought to be an important step in cancer induction and progression. Radiation induced GI is usually defined as genome alterations in the progeny of irradiated cells. The aim of this report is to demonstrate an opportunity for integrative analysis of radiation induced GI on the basis of multiscale modelling. Integrative, systems level modelling is necessary to assess different pathways resulting in GI in which a variety of genetic and epigenetic processes are involved. The multilevel modelling includes the Monte Carlo based simulation of several key processes involved in GI: DNA double strand breaks (DSBs) generation in cells initially irradiated as well as in descendants of irradiated cells, damage transmission through mitosis. Taking the cell-cycle-dependent generation of DNA/chromosome breakage into account ensures an advantage in estimating the contribution of different DNA damage response pathways to GI, as to nonhomologous vs homologous recombination repair mechanisms, the role of DSBs at telomeres or interstitial chromosomal sites, etc. The preliminary estimates show that both telomeric and non-telomeric DSB interactions are involved in delayed effects of radiation although differentially for different cell types. The computational experiments provide the data on the wide spectrum of GI endpoints (dicentrics, micronuclei, nonclonal translocations, chromatid exchanges, chromosome fragments) similar to those obtained experimentally for various cell lines under various experimental conditions. The modelling based analysis of experimental data demonstrates that radiation induced GI may be viewed as processes of delayed DSB induction/interaction/transmission being a key for quantification of GI. On the other hand, this conclusion is not sufficient to understand GI as a whole because factors of DNA non-damaging origin can also induce GI. Additionally, new data on induced pluripotent stem cells reveal that GI is acquired in normal mature

  18. High frequency of submicroscopic chromosomal imbalances in patients with syndromic craniosynostosis detected by a combined approach of microsatellite segregation analysis, multiplex ligation-dependent probe amplification and array-based comparative genome hybridisation.

    NARCIS (Netherlands)

    Jehee, F.S.; Krepischi-Santos, A.C.; Rocha, K.M.; Cavalcanti, D.P.; Kim, C.A.; Bertola, D.R.; Alonso, L.G.; D'Angelo, C.S.; Mazzeu, J.F.; Froyen, G.; Lugtenberg, D.; Vianna-Morgante, A.M.; Rosenberg, C.; Passos-Bueno, M.R.

    2008-01-01

    We present the first comprehensive study, to our knowledge, on genomic chromosomal analysis in syndromic craniosynostosis. In total, 45 patients with craniosynostotic disorders were screened with a variety of methods including conventional karyotype, microsatellite segregation analysis, subtelomeric

  19. Population genetic analysis of the Brahman cattle (Bos indicus) in Colombia with microsatellite markers.

    Science.gov (United States)

    Novoa, M A; Usaquén, W

    2010-04-01

    The Brahman is one of the most popular breeds for meat production in the Neotropics. However, genetic studies of the breed in Latin American countries have only recently begun. In total, 178 animals of the Brahman breed from 20 Colombian provinces were genotyped at 11 microsatellite markers with the aim of studying the genetic diversity of this population and its genetic relationships with zebuine and taurine breeds. The outcomes of multivariate analyses, Bayesian inferences and inter-individual genetic distances suggested that there is no genetic sub-structure in the population, because of the high rate of animal migration among provinces. The population shows a high degree of heterozygosity and allelic diversity compared with other breeds, reflecting its multibreed origin. The study of the genetic relationships among the breeds reveals that the Brahman breed belongs to the zebuine group. However, it is the population nearest to taurine breeds with high frequencies of taurine alleles. Intensive artificial selection may have favoured the taurine alleles after the breed was formed. There has also been some degree of mixture with local taurine breeds while the Brahman breed has evolved in Colombia.

  20. Comparative analysis of microsatellites in five different antagonistic Trichoderma species for diversity assessment.

    Science.gov (United States)

    Rai, Shalini; Kashyap, Prem Lal; Kumar, Sudheer; Srivastava, Alok Kumar; Ramteke, Pramod W

    2016-01-01

    Microsatellites provide an ideal molecular markers system to screen, characterize and evaluate genetic diversity of several fungal species. Currently, there is very limited information on the genetic diversity of antagonistic Trichoderma species as determined using a range of molecular markers. In this study, expressed and whole genome sequences available in public database were used to investigate the occurrence, relative abundance and relative density of SSRs in five different antagonistic Trichoderma species: Trichoderma atroviride, T. harzianum, T. reesei, T. virens and T. asperellum. Fifteen SSRs loci were used to evaluate genetic diversity of twenty isolates of Trichoderma spp. from different geographical regions of India. Results indicated that relative abundance and relative density of SSRs were higher in T. asperellum followed by T. reesei and T. atroviride. Tri-nucleotide repeats (80.2%) were invariably the most abundant in all species. The abundance and relative density of SSRs were not influenced by the genome sizes and GC content. Out of eighteen primer sets, only 15 primer pairs showed successful amplification in all the test species. A total of 24 alleles were detected and five loci were highly informative with polymorphism information content values greater than 0.40, these markers provide useful information on genetic diversity and population genetic structure, which, in turn, can exploit for establishing conservation strategy for antagonistic Trichoderma isolates.

  1. Population genetic analysis and conservation strategies for redtail shrimp Fenneropenaeus penicillatus using ten microsatellite markers.

    Science.gov (United States)

    Cao, Y Y; Shangguan, J B; Li, Z B

    2017-03-15

    Fenneropenaeus penicillatus, which is on the Red List of Endangered Species for China, is an important shrimp species. However, there is not enough genetic information on F. penicillatus for conservation and management purposes. Ten microsatellite markers were used to analyze the genetic diversity, genetic differentiation, and population structure of F. penicillatus to provide scientific information for the conservation of the species. Low genetic diversity and moderate genetic differentiation were found among 12 putative populations [Beihai, Dongshan (DS), Hainan (HN), Lianjiang, Nanao (NA), Ningde (ND), Putian, Quanzhou (QZ), Xiamen (XM), Shenzhen, Zhanjiang, and Zhangpu] along the southeast coast of China. QZ, XM, and DS exhibited the highest genetic diversity, while NA and ND had the lowest genetic diversity. Genetic differentiation among all populations, except HN, was low compared to the genetic differentiation between HN and the other 11 putative populations. These 12 putative populations were divided into two subgroups. One group consisted of XM, DS, and QZ. The other group consisted of the other eight putative populations with the exception of HN. The HN Island population requires further study due to its large genetic distance from the other 11 putative populations. Problems with the current conservation strategy are pointed out and suggestions given based on genetic information.

  2. A microsatellite analysis of five Colonial Spanish horse populations of the southeastern United States.

    Science.gov (United States)

    Conant, E K; Juras, R; Cothran, E G

    2012-02-01

    The domestic horse (Equus caballus) was re-introduced to the Americas by Spanish explorers. Although horses from other parts of Europe were subsequently introduced, some New World populations maintain characteristics ascribed to their Spanish heritage. The southeastern United States has a history of Spanish invasion and settlement, and this influence on local feral horse populations includes two feral-recaptured breeds: the Florida Cracker and the Marsh Tacky, both of which are classified as Colonial Spanish horses. The feral Banker horses found on islands off the coast of North Carolina, which include, among others, the Shackleford Banks, the Corolla and the Ocracoke, are also Colonial Spanish horses. Herein we analyse 15 microsatellite loci from 532 feral and 2583 domestic horses in order to compare the genetic variation of these five Colonial Spanish Horse populations to 40 modern horse breeds. We find that the Corolla horse has very low heterozygosity and that both the Corolla and Ocracoke populations have a low mean number of alleles. We also find that the Florida Cracker population has a heterozygosity deficit. In addition, we find evidence of similarity of the Shackleford Banks, Marsh Tacky and Florida Cracker populations to New World Iberian horse breeds, while the origins of the other two populations are less clear.

  3. Population genetic analysis among five Indian population groups using six microsatellite markers.

    Science.gov (United States)

    Ghosh, Anu; Das, Birajalaxmi; Seshadri, M

    2003-04-01

    Genetic variation at six tetranucleotide microsatellites (HUMTHO1, HUMVWA, F13A01, D3S1359, D12S66, and D12S67) has heen determined in five endogamous ethnic population groups of India belonging to two major linguistic families. The populations analyzed were Konkanastha Brahmins and Marathas (Maharashtra state) from the Indo-Aryan linguistic family and Nairs, Ezhavas, and Muslims (Kerala state) from the Dravidian family. All six loci show high gene diversity, ranging from 0.63 +/- 0.04 to 0.84 +/- 0.02. The average GST value observed was 1.7%, indicating that the differences between the populations account for less than 2% of the diversity, while the genetic variation is high within the five population groups studied (>98%). The phylogenetic tree fails to show any clear cluster. The absence of any cluster along with low average GST is suggestive of substantial genetic similarity among the studied populations, in spite of clear geographical, linguistic, and cultural barriers. This similarity indicates either a greater gene flow between these groups or, alternatively, may reflect a recent evolution for them, considering that the Indian caste system evolved only about 3000 years ago.

  4. DNA fingerprinting and diversity analysis in Aus genotypes using microsatellite markers

    Directory of Open Access Journals (Sweden)

    MD. MONIRUL ISLAM

    2015-08-01

    Full Text Available DNA fingerprinting and genetic diversity of 94 Aus (6 BRRI released Aus variety and 88 local Aus landraces genotypes were carried out to protect the Aus landraces from biopiracy. A total of 91 microsatellite markers were tested for screening the genotypes. Among 91 amplified products, 56% have polymorphic bands giving 195 alleles. The number of alleles per locus ranged from four (RM25 and RM147 to twenty seven (RM519, where average allele number was 9.76. The Polymorphism Information Contents (PIC lied between 0.455 (RM5 to 0.934 (RM519. Most robust marker was found RM519 since it provided the highest PIC value (0.934. Pair-wise genetic dissimilarity co-efficient showed the lowest genetic dissimilarity was found BRRI dhan42 and BRRI dhan43 and the highest genetic dissimilarity was found local landraces each other. Here it is shown that most Aus landraces is recognized to have broad genetic base. Thus it is recommended to use these landraces for future breeding program or include new and untouched local landraces to incorporate new genes and broaden genetic base.

  5. Post-bottleneck genetic diversity of elephant populations in South Africa, revealed using microsatellite analysis.

    Science.gov (United States)

    Whitehouse, A M; Harley, E H

    2001-09-01

    Widespread hunting had fragmented and severely reduced elephant populations in South Africa by 1900. Elephant numbers increased during the 1900s, although rates of recovery of individual populations varied. The Kruger National Park elephant population increased rapidly, to more than 6000 by 1967, with recruitment boosted by immigration from Mozambique. The Addo Elephant National Park population was reduced to 11 elephants in 1931 and remains relatively small (n = 325). Loss of genetic variation is expected to occur whenever a population goes through a bottleneck, especially when post-bottleneck recovery is slow. Variation at nine polymorphic microsatellite loci was analysed for Kruger and Addo elephants, as well as museum specimens of Addo elephants shot prior to the population bottleneck. Significantly reduced genetic variation and heterozygosity were observed in Addo in comparison to Kruger (mean alleles/locus and H(E): Addo 1.89, 0.18; Kruger 3.89, 0.44). Two alleles not present in the current Addo population were observed in the museum specimens. Addo elephants represent a genetic subset of the Kruger population, with high levels of genetic differentiation resulting from rapid genetic drift. The Kruger population is low in genetic diversity in comparison to East African elephants, confirming this population also suffered an appreciable bottleneck.

  6. Microsatellite DNA Analysis on the Polyandry of Green Sea Turtle Chelonia mydas

    Directory of Open Access Journals (Sweden)

    Dewi Purnama

    2013-12-01

    Full Text Available Green turtle (Cheloniamydas; Testudines is included in the group of polyandryanimals, which is single female mated with many male. DNA polymorphism method generally considered to have a high degree of accuracy as compared to other methods to elucidate polyandry phenomena on many animals. In this research, three microsatellite loci were used to identify the number and frequency of genotypes per locus, the number and frequency alleles per locus, and genotypes and number of alleles in the nest. The purpose of this research was to study the reproductive pattern of Cheloniamydas and compensation eggs of males from hatchling’s population in turtle conservation area of Pangumbahan Coastal Park, West Java. The result showed that from 10 nests, we could find 37 genotypes with 11 alleles for D108 locus, 21 genotypes with 9 alleles for B103 locus, and 27 genotypes with 9 alleles for C102 locus. The alleles number of each nest was more than 5 alleles for 5 nests, and more than 4 alleles for the remaining nests. Based on the probabilities of alleles contribution of each parent, the green turtle was polyandry animals.

  7. Validation of microsatellite multiplexes for parentage analysis and species discrimination in two hybridizing species of coral reef fish (Plectropomus spp., Serranidae).

    Science.gov (United States)

    Harrison, Hugo B; Feldheim, Kevin A; Jones, Geoffrey P; Ma, Kayan; Mansour, Hicham; Perumal, Sadhasivam; Williamson, David H; Berumen, Michael L

    2014-06-01

    Microsatellites are often considered ideal markers to investigate ecological processes in animal populations. They are regularly used as genetic barcodes to identify species, individuals, and infer familial relationships. However, such applications are highly sensitive the number and diversity of microsatellite markers, which are also prone to error. Here, we propose a novel framework to assess the suitability of microsatellite datasets for parentage analysis and species discrimination in two closely related species of coral reef fish, Plectropomus leopardus and P. maculatus (Serranidae). Coral trout are important fisheries species throughout the Indo-Pacific region and have been shown to hybridize in parts of the Great Barrier Reef, Australia. We first describe the development of 25 microsatellite loci and their integration to three multiplex PCRs that co-amplify in both species. Using simulations, we demonstrate that the complete suite of markers provides appropriate power to discriminate between species, detect hybrid individuals, and resolve parent-offspring relationships in natural populations, with over 99.6% accuracy in parent-offspring assignments. The markers were also tested on seven additional species within the Plectropomus genus with polymorphism in 28-96% of loci. The multiplex PCRs developed here provide a reliable and cost-effective strategy to investigate evolutionary and ecological dynamics and will be broadly applicable in studies of wild populations and aquaculture brood stocks for these closely related fish species.

  8. Validation of microsatellite multiplexes for parentage analysis and species discrimination in two hybridizing species of coral reef fish (Plectropomus spp., Serranidae)

    KAUST Repository

    Harrison, H.B.

    2014-04-24

    Microsatellites are often considered ideal markers to investigate ecological processes in animal populations. They are regularly used as genetic barcodes to identify species, individuals, and infer familial relationships. However, such applications are highly sensitive the number and diversity of microsatellite markers, which are also prone to error. Here, we propose a novel framework to assess the suitability of microsatellite datasets for parentage analysis and species discrimination in two closely related species of coral reef fish, Plectropomus leopardus and P. maculatus (Serranidae). Coral trout are important fisheries species throughout the Indo-Pacific region and have been shown to hybridize in parts of the Great Barrier Reef, Australia. We first describe the development of 25 microsatellite loci and their integration to three multiplex PCRs that co-amplify in both species. Using simulations, we demonstrate that the complete suite of markers provides appropriate power to discriminate between species, detect hybrid individuals, and resolve parent-offspring relationships in natural populations, with over 99.6% accuracy in parent-offspring assignments. The markers were also tested on seven additional species within the Plectropomus genus with polymorphism in 28-96% of loci. The multiplex PCRs developed here provide a reliable and cost-effective strategy to investigate evolutionary and ecological dynamics and will be broadly applicable in studies of wild populations and aquaculture brood stocks for these closely related fish species. 2014 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.

  9. Genetic potential analysis of German mirror carp (Cyprinus carpio L.) using microsatellite markers

    Institute of Scientific and Technical Information of China (English)

    Ning HOU; Xiaoshu HOU; Yong LI; Dayu LI; Fujun LIU; Ruixin MAO; Xiaowen SUN

    2008-01-01

    Using 30 microsatellite markers and combin-ing quantifiable characteristics such as body weight, body length and body width, we evaluated the genetic potential of 3 German mirror carp (Cyprinus carpio L.) popula-tions. Number of effective alleles (Ae), observed (Ho) and expected (He) heterozygosity values and polymorphic information contents (PIC) were all calculated. Two hun-dred and eighty-seven alleles and 559 genotypes were detected. The DNA fragment length was 109-400 bp. The Hardy-Weinberg Equilibrium was checked and the phenomenon of some disequilibrium was studied accord-ing to the χ2test. The results showed that the level of genetic variability was moderate, but genetic potential of Shuanglai population was much lower than that of Huanxin and Songpu breeding populations. PIC of the three populations of German mirror carp were between 0.08787 and 0.5377, both highly and moderately poly-morphic markers were 13. The number of the Ae was between 1.1014 and 6.4665. The Ho and He heterozygos-ity values were 0.0968-0.9892 and 0.0926-0.8554, respect-ively. The linkage correlation was analyzed using the data of body weight, body length and body width, and 30 loci. The result showed that there existed 2 loci, HLJ319 and HLJ693, associated with body length. The HLJ693 locus was significantly correlated with body weight trait. The HLJ677 locus was linked with body width. And then the result was verified in Recombinant Inbred Lines (RIL) of common carp. It showed that the HLJ319 locus was sig-nificantly linked with body length, the same as the result of quantitative trait loci (QTL) location for common carp.

  10. Analysis of fast ion induced instabilities in tokamak plasmas

    CERN Document Server

    Horváth, László

    2015-01-01

    In magnetic confinement fusion devices like tokamaks, it is crucial to confine the high energy fusion-born helium nuclei ($\\alpha$-particles) to maintain the energy equilibrium of the plasma. However, energetic ions can excite various instabilities which can lead to their enhanced radial transport. Consequently, these instabilities may degrade the heating efficiency and they can also cause harmful power loads on the plasma-facing components of the device. Therefore, the understanding of these modes is a key issue regarding future burning plasma experiments. One of the main open questions concerning energetic particle (EP) driven instabilities is the non-linear evolution of the mode structure. In this thesis, I present my results on the investigation of $\\beta$-induced Alfv\\'{e}n eigenmodes (BAEs) and EP-driven geodesic acoustic modes (EGAMs) observed in the ramp-up phase of off-axis NBI heated plasmas in the ASDEX Upgrade tokamak. These modes were well visible on several line-of-sights (LOSs) of the soft X-ra...

  11. Haplotype analysis of DNA microsatellites tightly linked to the locus of Usher syndrome type I on chromosome 11q

    Energy Technology Data Exchange (ETDEWEB)

    Korostishevsky, M.; Kalinsky, H.; Seroussi, E. [Sackler Faculty of Medicine, Ramat-Aviv (Israel)] [and other

    1994-09-01

    Usher syndrome type I (USHI), an autosomal recessive disorder associated with congenital sensorineural deafness and progressive visual loss, is closely linked to the D11S533 locus. The availability of 7 other polymorphic markers within few centimorgans spanning the disease locus allowed us to identify a unique and single haplotype among all carriers of USHI gene in the Samaritan kindred. Occurrence of recombination in this small chromosomal interval is rare, hindering the detection of the mitotic recombination events needed for analysis by traditional linkage methods. Attempts to order the eight loci by linkage disequilibrium models proved to be problematic. However, our haplotype analysis implied that recombinations which had arisen in past generations may be utilized in fine mapping of the USHI gene and in resolving the conflicting linkage maps previously obtained for this region. We have developed a simple algorithm for predicting the order of the microsatellites on the basis of haplotype resemblance. The following chromosomal map in which the USHI gene is closest to D11S533 (location score of 31.0 by multipoint analysis) is suggested: D11S916, GARP, D11S527, D11S533, OMP, D11S906, D11S911, D11S937. Physical mapping efforts are currently directed to verify and to detail the map of this chromosomal region.

  12. Analysis of the genetic relationships and diversity among 11 populations of Xanthoceras sorbifolia using phenotypic and microsatellite marker data

    Directory of Open Access Journals (Sweden)

    Zhan Shen

    2017-03-01

    Conclusions: Microsatellite markers can be used to efficiently distinguish X. sorbifolia populations and assess their genetic diversity. The information we have provided will contribute to the conservation and management of this important plant genetic resource.

  13. Identification of genic moss SSR markers and a comparative analysis of twenty-four algal and plant gene indices reveal species-specific rather than group-specific characteristics of microsatellites

    Directory of Open Access Journals (Sweden)

    Rensing Stefan A

    2006-05-01

    Full Text Available Abstract Background The moss Physcomitrella patens is an emerging model in comparative plant science. At present, the Physcomitrella genome is sequenced at the Joint Genome Institute (USA. In this study we present our results on the development of expressed sequence tag-derived microsatellite markers for Physcomitrella patens, their classification and applicability as genetic markers on the intra- as well as on the interspecies level. We experienced severe restrictions to compare our results on Physcomitrella with earlier studies for other plant species due to varying microsatellite search criteria and a limited selection of analysed species. As a consequence, we performed a side by side analysis of expressed sequence tag-derived microsatellites among 24 plant species covering a broad phylogenetic range and present our results on the observed frequencies. Results We identified 3,723 microsatellites using the software MISA in a non-redundant Physcomitrella expressed sequence tag database comprising more than 37 megabases of nucleotide information. For 2,951 microsatellites appendant primer sequences have been derived. PCR of 376 microsatellites yielded 88 % successful amplicons and over 30 % polymorphisms between two Physcomitrella accessions. The polymorphism information content of 64 microsatellites based on 21 different Physcomitrella accessions was comparably high with a mean of 0.47 +/- 0.17. Of the 64 Physcomitrella microsatellite markers, 34 % respectively 79.7 % revealed cross-species applicability in two closely related moss species. In our survey of two green algae, two mosses, a fern, a fern palm, the ginkgo tree, two conifers, ten dicots and five monocots we detected an up to sevenfold variation in the overall frequency with a minimum of 37 up to maximal 258 microsatellites per megabase and a high variability among the different microsatellite class and motif frequencies. Numerous species-specific microsatellite frequencies became

  14. An imprecise probability approach for squeal instability analysis based on evidence theory

    Science.gov (United States)

    Lü, Hui; Shangguan, Wen-Bin; Yu, Dejie

    2017-01-01

    An imprecise probability approach based on evidence theory is proposed for squeal instability analysis of uncertain disc brakes in this paper. First, the squeal instability of the finite element (FE) model of a disc brake is investigated and its dominant unstable eigenvalue is detected by running two typical numerical simulations, i.e., complex eigenvalue analysis (CEA) and transient dynamical analysis. Next, the uncertainty mainly caused by contact and friction is taken into account and some key parameters of the brake are described as uncertain parameters. All these uncertain parameters are usually involved with imprecise data such as incomplete information and conflict information. Finally, a squeal instability analysis model considering imprecise uncertainty is established by integrating evidence theory, Taylor expansion, subinterval analysis and surrogate model. In the proposed analysis model, the uncertain parameters with imprecise data are treated as evidence variables, and the belief measure and plausibility measure are employed to evaluate system squeal instability. The effectiveness of the proposed approach is demonstrated by numerical examples and some interesting observations and conclusions are summarized from the analyses and discussions. The proposed approach is generally limited to the squeal problems without too many investigated parameters. It can be considered as a potential method for squeal instability analysis, which will act as the first step to reduce squeal noise of uncertain brakes with imprecise information.

  15. Multiple harmonic ULF waves in the plasma sheet boundary layer: Instability analysis

    Science.gov (United States)

    Denton, R. E.; Engebretson, M. J.; Keiling, A.; Walsh, A. P.; Gary, S. P.; DéCréAu, P. M. E.; Cattell, C. A.; RèMe, H.

    2010-12-01

    Multiple-harmonic electromagnetic waves in the ULF band have occasionally been observed in Earth's magnetosphere, both near the magnetic equator in the outer plasmasphere and in the plasma sheet boundary layer (PSBL) in Earth's magnetotail. Observations by the Cluster spacecraft of multiple-harmonic electromagnetic waves with fundamental frequency near the local proton cyclotron frequency, Ωcp, were recently reported in the plasma sheet boundary layer by Broughton et al. (2008). A companion paper surveys the entire magnetotail passage of Cluster during 2003, and reports 35 such events, all in the PSBL, and all associated with elevated fluxes of counterstreaming ions and electrons. In this study we use observed pitch angle distributions of ions and electrons during a wave event observed by Cluster on 9 September 2003 to perform an instability analysis. We use a semiautomatic procedure for developing model distributions composed of bi-Maxwellian components that minimizes the difference between modeled and observed distribution functions. Analysis of wave instability using the WHAMP electromagnetic plasma wave dispersion code and these model distributions reveals an instability near Ωcp and its harmonics. The observed and model ion distributions exhibit both beam-like and ring-like features which might lead to instability. Further instability analysis with simple beam-like and ring-like model distribution functions indicates that the instability is due to the ring-like feature. Our analysis indicates that this instability persists over an enormous range in the effective ion beta (based on a best fit for the observed distribution function using a single Maxwellian distribution), β', but that the character of the instability changes with β'. For β' of order unity (for instance, the observed case with β' ˜ 0.4), the instability is predominantly electromagnetic; the fluctuating magnetic field has components in both the perpendicular and parallel directions, but the

  16. Analysis of shear band instabilities in sintered metals

    DEFF Research Database (Denmark)

    Redanz, Pia; Tvergaard, Viggo

    1999-01-01

    of a material instability. The elastic plastic behaviour of the material is represented by a material model, which combines the Gurson model, relevant to rather low porosities, with the FKM model, developed for high porosity powder compacts. Predictions are shown for various levels of initial porosity...... and for various levels of initial material:imperfections, considering both plane strain and axisymmetric conditions outside the shear band. Also a comparison of localization predictions by the Gurson model, the FKM model and the combined model is presented. (C) 1999 Elsevier Science Ltd. All rights reserved....

  17. Transcriptome-Derived Tetranucleotide Microsatellites and Their Associated Genes from the Giant Panda (Ailuropoda melanoleuca).

    Science.gov (United States)

    Song, Xuhao; Shen, Fujun; Huang, Jie; Huang, Yan; Du, Lianming; Wang, Chengdong; Fan, Zhenxin; Hou, Rong; Yue, Bisong; Zhang, Xiuyue

    2016-09-01

    Recently, an increasing number of microsatellites or simple sequence repeats (SSRs) have been found and characterized from transcriptomes. Such SSRs can be employed as putative functional markers to easily tag corresponding genes, which play an important role in biomedical studies and genetic analysis. However, the transcriptome-derived SSRs for giant panda (Ailuropoda melanoleuca) are not yet available. In this work, we identified and characterized 20 tetranucleotide microsatellite loci from a transcript database generated from the blood of giant panda. Furthermore, we assigned their predicted transcriptome locations: 16 loci were assigned to untranslated regions (UTRs) and 4 loci were assigned to coding regions (CDSs). Gene identities of 14 transcripts contained corresponding microsatellites were determined, which provide useful information to study the potential contribution of SSRs to gene regulation in giant panda. The polymorphic information content (PIC) values ranged from 0.293 to 0.789 with an average of 0.603 for the 16 UTRs-derived SSRs. Interestingly, 4 CDS-derived microsatellites developed in our study were also polymorphic, and the instability of these 4 CDS-derived SSRs was further validated by re-genotyping and sequencing. The genes containing these 4 CDS-derived SSRs were embedded with various types of repeat motifs. The interaction of all the length-changing SSRs might provide a way against coding region frameshift caused by microsatellite instability. We hope these newly gene-associated biomarkers will pave the way for genetic and biomedical studies for giant panda in the future. In sum, this set of transcriptome-derived markers complements the genetic resources available for giant panda.

  18. Analysis of strange-mode instability with time-dependent convection in hot massive stars

    CERN Document Server

    Sonoi, Takafumi

    2013-01-01

    We carry out nonadiabatic analysis of strange-modes in hot massive stars with time-dependent convection (TDC) for the first time. Although convective luminosity in envelopes of hot massive stars is not as dominative as in stars near the red edge of the classical Cepheid instability strip in the Hertzsprung-Russell (H-R) diagram, we have found that the strange-mode instability can be affected by the treatment of convection. However, existence of the instability around and over the Humphreys-Davidson (H-D) limit is independent of the treatment. This implies that the strange-mode instability could be responsible for the lack of observed stars over the H-D limit regardless of uncertainties on convection theories.

  19. Liquid rocket combustion instability analysis by CFD methods

    Science.gov (United States)

    Grenda, J. M.; Venkateswaran, S.; Merkle, C. L.

    1991-01-01

    Combustion instability in liquid rocket engines is simulated computationally by using a simple two-parameter model for the combustion response function. The objectives of the study are to assess the capabilities of CFD algorithms for instability studies and to investigate the response to parametric effects such as bombs and distributed combustion. Results indicate that numerical solutions of high accuracy can be obtained if a sufficient number of grid points are used per wavelength of the disturbance. The short-term response to bombs or pulses triggers a large number of modes in the combustor whose faithful resolution requires highly dense grids, although there is evidence that correct long-term solutions can be obtained even if all the short-term frequencies are not resolved. Long-term responses to pulses are shown to decay to the most unstable mode in small amplitude cases, and to exhibit limit cycles in large amplitude cases. Comparison of distributed with concentrated heat release indicates the former is more stable for given values of the combustion response parameters, and that the distributed heat release gives rise to higher frequency disturbances. Wave steepening is observed in the solutions, but its effect is less pronounced in multidimensional waves than in one-dimensional waves.

  20. Active Control Analysis for Aeroelastic Instabilities in Turbomachines

    Science.gov (United States)

    Keith, Theo G., Jr.; Srivastava, Rakesh

    2002-01-01

    Turbomachines onboard aircraft operate in a highly complex and harsh environment. The unsteady flowfield inherent to turbomachines leads to several problems associated with safety, stability, performance and noise. In-flight surge or flutter incidents could be catastrophic and impact the safety and reliability of the aircraft. High-Cycle-Fatigue (HCF), on the other hand, can significantly impact safety, readiness and maintenance costs. To avoid or minimize these problems generally a more conservative design method must be initiated which results in thicker blades and a loss of performance. Actively controlled turbomachines have the potential to reduce or even eliminate the instabilities by impacting the unsteady aerodynamic characteristics. By modifying the unsteady aerodynamics, active control may significantly improve the safety and performance especially at off-design conditions, reduce noise, and increase the range of operation of the turbomachine. Active control can also help improve reliability for mission critical applications such as the Mars Flyer. In recent years, HCF has become one of the major issues concerning the cost of operation for current turbomachines. HCF alone accounts for roughly 30% of maintenance cost for the United States Air-Force. Other instabilities (flutter, surge, rotating-stall, etc.) are generally identified during the design and testing phase. Usually a redesign overcomes these problems, often reducing performance and range of operation, and resulting in an increase in the development cost and time. Despite a redesign, the engines do not have the capabilities or means to cope with in-flight unforeseen vibration, stall, flutter or surge related instabilities. This could require the entire fleet worldwide to be stood down for expensive modifications. These problems can be largely overcome by incorporating active control within the turbomachine and its design. Active control can help in maintaining the integrity of the system in

  1. Heterozygosity analysis of Bionda Piemontese and Bianca di Saluzzo chicken breeds by microsatellites markers: a preliminary study

    Directory of Open Access Journals (Sweden)

    M. Longeri

    2010-04-01

    Full Text Available Conservation of genetic variability is one of the main goals in animal production science and the analysis of breeds genetic asset can supply objective basis for effective conservation programs and selection strategies. Bionda Piemontese (PIB and Bianca di Saluzzo (SAB chicken breeds originated in Piemonte region. Breeds conservation programmes started in 1999 in Verzuolo (CN aiming to preserve the breeds and to improve their diffusion being particularly adapted to free range rearing systems thanks to their resistance. PIB and SAB are both suggested for traditional recipes and production (e.g. Morozzo capon and are Slow Food presidia. A total of 76 birds were analysed: PIB (n=36, SAB (n=40. Genomic DNA was extracted from blood samples. All birds were genotyped at eight microsatellite loci. Each marker was subjected to PCR and the products were separated by electrophoresis in 4.2% denaturing polyacrylamide gels on ABI Prism 377 DNA Sequencer equipped with Genescan and Genotyper software. The results of this preliminary study highlight the genetic differences occurring between PIB and SAB populations

  2. Microsatellite alterations in phenotypically normal esophageal squamous epithelium and metaplasia-dysplasia-adenocarcinoma sequence

    Institute of Scientific and Technical Information of China (English)

    Jian-Chun Cai; Di Liu; Kai-Hua Liu; Hai-Ping Zhang; Shan Zhong; Ning-Sao Xia

    2008-01-01

    AIM: To investigate the microsatellite alterations in phenotypically normal esophageal squamous epithelium and metaplasia-dysplasia-adenocarcinoma sequence.METHODS: Forty-one specimens were obtained from esophageal cancer (EC) patients. Histopathological assessment identified 23 squamous cell carcinomas (SCC) and 18 adenocarcinomas (ADC), including only 8 ADC with Barrett esophageal columnar epithelium (metaplasia) and dysplasia adjacent to ADC. Paraffinembedded normal squamous epithelium, Barrett esophageal columnar epithelium (metaplasia), dysplasia and esophageal tumor tissues were dissected from the surrounding tissues under microscopic guidance. DNA was extracted using proteinase K digestion buffer, and DNA was diluted at 1:100, 1:1000, 1:5000, 1:10000 and 1:50000, respectively. Seven microsatellite markers (D2S123, D3S1616, D3S1300, D5S346, D17S787, D18S58 and BATRII loci) were used in this study. Un-dilution and dilution polymerase chain reactions (PCR) were performed, and microsatellite analysis was carried out.RESULTS: No statistically significant difference was found in microsatellite instability (MSI) and loss of heterozygosity (LOH) of un-diluted DNA between SCC and ADC. The levels of MSI and LOH were high in the metaplasia-dysplasia-adenocarcinoma sequence of diluted DNA. The more the diluted DNA was, the higher the rates of MSI and LOH were at the above 7 loci, especially at D3S1616, D5S346, D2S123, D3S1300 and D18S58 loci.CONCLUSION: The sequence of metaplasia-dysplasia-adenocarcinoma is associated with microsatellite alterations, including MSI and LOH. The MSI and LOH may be the early genetic events during esophageal carcinogenesis, and genetic alterations at the D3S1616, D5S346 and D3S123 loci may play a role in the progress of microsatellite alterations.

  3. Analysis of Jeans instability from the Boltzmann equation

    Science.gov (United States)

    Kremer, Gilberto M.

    2016-11-01

    The dynamics of self-gravitating fluids is analyzed within the framework of a collisionless Boltzmann equation in the presence of gravitational fields and Poisson equation. Two cases are analyzed: a system with baryonic and dark matter in a static universe and a single system in an expanding universe. The amplitudes of the perturbed distribution functions are considered as a linear combination of the collision invariants of the Boltzmann equation. For the system of baryonic and dark matter, the Jeans mass of the combined system is smaller than the one of the single system indicating that a smaller mass is needed to initiate the collapse. For the single system in an expanding universe it is not necessary to make use of Jeans "swindle"and it shown that for small wavelengths the density contrast oscillates while for large wavelengths it grows with time and the Jeans instability emerges.

  4. Instability and pattern formation in reaction-diffusion systems: a higher order analysis.

    Science.gov (United States)

    Riaz, Syed Shahed; Sharma, Rahul; Bhattacharyya, S P; Ray, D S

    2007-08-14

    We analyze the condition for instability and pattern formation in reaction-diffusion systems beyond the usual linear regime. The approach is based on taking into account perturbations of higher orders. Our analysis reveals that nonlinearity present in the system can be instrumental in determining the stability of a system, even to the extent of destabilizing one in a linearly stable parameter regime. The analysis is also successful to account for the observed effect of additive noise in modifying the instability threshold of a system. The analytical study is corroborated by numerical simulation in a standard reaction-diffusion system.

  5. Microsatellite flanking region similarities among different loci within insect species.

    Science.gov (United States)

    Meglécz, E; Anderson, S J; Bourguet, D; Butcher, R; Caldas, A; Cassel-Lundhagen, A; d'Acier, A C; Dawson, D A; Faure, N; Fauvelot, C; Franck, P; Harper, G; Keyghobadi, N; Kluetsch, C; Muthulakshmi, M; Nagaraju, J; Patt, A; Péténian, F; Silvain, J-F; Wilcock, H R

    2007-04-01

    Although microsatellites are ubiquitous in eukaryota, the number of available markers varies strongly among taxa. This meta-analysis was conducted on 32 insect species. Sequences were obtained from two assembled whole genomes, whole genome shotgun (WGS) sequences from 10 species and screening partial genomic libraries for microsatellites from 23 species. We have demonstrated: (1) strong differences in the abundance of microsatellites among species; (2) that microsatellites within species are often grouped into families based on similarities in their flanking sequences; (3) that the proportion of microsatellites grouped into families varies strongly among taxa; and (4) that microsatellite families were significantly more often associated with transposable elements - or their remnants - than unique microsatellite sequences.

  6. Analysis of microsatellite markers D18S70 and d20S116 in DNA isolated from dentin: Use in forensic medicine

    Directory of Open Access Journals (Sweden)

    Puzović Dragana

    2009-01-01

    Full Text Available Introduction. Short tandem repeats and more specifically microsatellites represent a powerful tool in forensic medicine. In the past years, they have been extensively used in human identification and paternity testing. Objective The aim of the present study was to analyze two microsatellite markers in the Serbian population, i.e. to determine the number of alleles and the relevant forensic parameters. Methods. DNA was isolated from teeth samples using standard proteinase K digestion and phenol/chloroform alcohol extraction. PCR products were analyzed on polyacrilamide gels and visualized by AgNO3 staining. Forensic parameters were calculated using the Cervus software. Results. The loci D18S70 and D20S116 were analyzed on a sample of 70 unrelated, healthy adult individuals from Serbia. The number of alleles was determined and Hardy Weinberg equilibrium was confirmed for both loci. D18S70 and D20S116 demonstrated 6 and 8 alleles, respectively. The power of discrimination (PD and the power of exclusion (PE for the tested STR loci, D18S70 and D20S116 were 0.92 (PD, 0.41 (PE and 0.95 (PD, 0.480 (PE, respectively. Conclusion. According to the presented data, D18S70 and D20S116 are most informative markers. Based on allelic frequencies and statistical parameters for forensic testing, it may be suggested that these two microsatellites represent useful markers for individual identification and parentage analysis in the Serbian population.

  7. Analysis of genetic relationships of pearl millet (Pennisetum glaucum L.) landraces from Zimbabwe, using microsatellites

    CSIR Research Space (South Africa)

    Chakauya, E

    2008-01-01

    Full Text Available and indigenous farmer given names. Analysis was done by PAGE stained with ethidium bromide. Simple matching coefficients were compared and the genetic relationships between genotypes were clarified on dendrograms by unweighted pair-group averages (UPGMA). Two...

  8. DNA copy-number alterations underlie gene expression differences between microsatellite stable and unstable colorectal cancers

    DEFF Research Database (Denmark)

    Jorissen, Robert N; Lipton, Lara; Gibbs, Peter

    2008-01-01

    Purpose: About 15% of colorectal cancers harbor microsatellite instability (MSI). MSI-associated gene expression changes have been identified in colorectal cancers, but little overlap exists between signatures hindering an assessment of overall consistency. Little is known about the causes...... and downstream effects of differential gene expression. Experimental Design: DNA microarray data on 89 MSI and 140 microsatellite-stable (MSS) colorectal cancers from this study and 58 MSI and 77 MSS cases from three published reports were randomly divided into test and training sets. MSI-associated gene...... expression changes were assessed for cross-study consistency using training samples and validated as MSI classifier using test samples. Differences in biological pathways were identified by functional category analysis. Causation of differential gene expression was investigated by comparison to DNA copy...

  9. Analysis of simple sequence repeats in the Gaeumannomyces graminis var. tritici genome and the development of microsatellite markers.

    Science.gov (United States)

    Li, Wei; Feng, Yanxia; Sun, Haiyan; Deng, Yuanyu; Yu, Hanshou; Chen, Huaigu

    2014-11-01

    Understanding the genetic structure of Gaeumannomyces graminis var. tritici is essential for the establishment of efficient disease control strategies. It is becoming clear that microsatellites, or simple sequence repeats (SSRs), play an important role in genome organization and phenotypic diversity, and are a large source of genetic markers for population genetics and meiotic maps. In this study, we examined the G. graminis var. tritici genome (1) to analyze its pattern of SSRs, (2) to compare it with other plant pathogenic filamentous fungi, such as Magnaporthe oryzae and M. poae, and (3) to identify new polymorphic SSR markers for genetic diversity. The G. graminis var. tritici genome was rich in SSRs; a total 13,650 SSRs have been identified with mononucleotides being the most common motifs. In coding regions, the densities of tri- and hexanucleotides were significantly higher than in noncoding regions. The di-, tri-, tetra, penta, and hexanucleotide repeats in the G. graminis var. tritici genome were more abundant than the same repeats in M. oryzae and M. poae. From 115 devised primers, 39 SSRs are polymorphic with G. graminis var. tritici isolates, and 8 primers were randomly selected to analyze 116 isolates from China. The number of alleles varied from 2 to 7 and the expected heterozygosity (He) from 0.499 to 0.837. In conclusion, SSRs developed in this study were highly polymorphic, and our analysis indicated that G. graminis var. tritici is a species with high genetic diversity. The results provide a pioneering report for several applications, such as the assessment of population structure and genetic diversity of G. graminis var. tritici.

  10. The complete chloroplast genome sequence of an endemic monotypic genus Hagenia (Rosaceae): structural comparative analysis, gene content and microsatellite detection.

    Science.gov (United States)

    Gichira, Andrew W; Li, Zhizhong; Saina, Josphat K; Long, Zhicheng; Hu, Guangwan; Gituru, Robert W; Wang, Qingfeng; Chen, Jinming

    2017-01-01

    Hagenia is an endangered monotypic genus endemic to the topical mountains of Africa. The only species, Hagenia abyssinica (Bruce) J.F. Gmel, is an important medicinal plant producing bioactive compounds that have been traditionally used by African communities as a remedy for gastrointestinal ailments in both humans and animals. Complete chloroplast genomes have been applied in resolving phylogenetic relationships within plant families. We employed high-throughput sequencing technologies to determine the complete chloroplast genome sequence of H. abyssinica. The genome is a circular molecule of 154,961 base pairs (bp), with a pair of Inverted Repeats (IR) 25,971 bp each, separated by two single copies; a large (LSC, 84,320 bp) and a small single copy (SSC, 18,696). H. abyssinica's chloroplast genome has a 37.1% GC content and encodes 112 unique genes, 78 of which code for proteins, 30 are tRNA genes and four are rRNA genes. A comparative analysis with twenty other species, sequenced to-date from the family Rosaceae, revealed similarities in structural organization, gene content and arrangement. The observed size differences are attributed to the contraction/expansion of the inverted repeats. The translational initiation factor gene (infA) which had been previously reported in other chloroplast genomes was conspicuously missing in H. abyssinica. A total of 172 microsatellites and 49 large repeat sequences were detected in the chloroplast genome. A Maximum Likelihood analyses of 71 protein-coding genes placed Hagenia in Rosoideae. The availability of a complete chloroplast genome, the first in the Sanguisorbeae tribe, is beneficial for further molecular studies on taxonomic and phylogenomic resolution within the Rosaceae family.

  11. The complete chloroplast genome sequence of an endemic monotypic genus Hagenia (Rosaceae: structural comparative analysis, gene content and microsatellite detection

    Directory of Open Access Journals (Sweden)

    Andrew W. Gichira

    2017-01-01

    Full Text Available Hagenia is an endangered monotypic genus endemic to the topical mountains of Africa. The only species, Hagenia abyssinica (Bruce J.F. Gmel, is an important medicinal plant producing bioactive compounds that have been traditionally used by African communities as a remedy for gastrointestinal ailments in both humans and animals. Complete chloroplast genomes have been applied in resolving phylogenetic relationships within plant families. We employed high-throughput sequencing technologies to determine the complete chloroplast genome sequence of H. abyssinica. The genome is a circular molecule of 154,961 base pairs (bp, with a pair of Inverted Repeats (IR 25,971 bp each, separated by two single copies; a large (LSC, 84,320 bp and a small single copy (SSC, 18,696. H. abyssinica’s chloroplast genome has a 37.1% GC content and encodes 112 unique genes, 78 of which code for proteins, 30 are tRNA genes and four are rRNA genes. A comparative analysis with twenty other species, sequenced to-date from the family Rosaceae, revealed similarities in structural organization, gene content and arrangement. The observed size differences are attributed to the contraction/expansion of the inverted repeats. The translational initiation factor gene (infA which had been previously reported in other chloroplast genomes was conspicuously missing in H. abyssinica. A total of 172 microsatellites and 49 large repeat sequences were detected in the chloroplast genome. A Maximum Likelihood analyses of 71 protein-coding genes placed Hagenia in Rosoideae. The availability of a complete chloroplast genome, the first in the Sanguisorbeae tribe, is beneficial for further molecular studies on taxonomic and phylogenomic resolution within the Rosaceae family.

  12. High genetic diversity in gametophyte clones of Undaria pinnatifida from Vladivostok, Dalian and Qingdao revealed using microsatellite analysis

    Institute of Scientific and Technical Information of China (English)

    SHAN Tifeng; PANG Shaojun; LIU Feng; XU Na; ZHAO Xiaobo; GAO Suqin

    2012-01-01

    Breeding practice for Undaria pinnatifida (Harvey) Suringar requires the screening of a large number of offspring from gametophyte crossings to obtain an elite variety for large-scale cultivation.To better understand the genetic relationships of different gametophyte cultures isolated from different sources,20 microsatellite loci were screened and 53 gametophyte clone cultures analyzed for U.pinnatifida isolated from wild sporophytes in Vladivostok,Russia and from cultivated sporophytes from Dalian and Qingdao,China.One locus was abandoned because of poor amplification.At the sex-linked locus of Up-AC-2A8,3 alleles were detected in 25 female gametophyte clones,with sizes ranging from 307 to 316 bp.At other loci,3 to 7 alleles were detected with an average of 4.5 alleles per locus.The average number of alleles at each locus was 1.3 and 3.7 for Russian and Chinese gametophyte clones,respectively.The average gene diversity for Russian,Chinese,and for the combined total of gametophyte clones was 0.1,0.4,and 0.5,respectively.Russian gametophyte clones had unique alleles at 7 out of the 19 loci.In cluster analysis,Russian and Chinese gametophyte clones were separated into two different groups according to genetic distance.Overall,high genetic diversity was detected in gametophyte clones isolated from the two countries.These gametophyte cultures were believed to be appropriate parental materials for conducting breeding programs in the future.

  13. Trypanosoma cruzi IIc: Phylogenetic and Phylogeographic Insights from Sequence and Microsatellite Analysis and Potential Impact on Emergent Chagas Disease

    Science.gov (United States)

    Llewellyn, Martin S.; Lewis, Michael D.; Acosta, Nidia; Yeo, Matthew; Carrasco, Hernan J.; Segovia, Maikell; Vargas, Jorge; Torrico, Faustino; Miles, Michael A.; Gaunt, Michael W.

    2009-01-01

    Trypanosoma cruzi, the etiological agent of Chagas disease, is highly genetically diverse. Numerous lines of evidence point to the existence of six stable genetic lineages or DTUs: TcI, TcIIa, TcIIb, TcIIc, TcIId, and TcIIe. Molecular dating suggests that T. cruzi is likely to have been an endemic infection of neotropical mammalian fauna for many millions of years. Here we have applied a panel of 49 polymorphic microsatellite markers developed from the online T. cruzi genome to document genetic diversity among 53 isolates belonging to TcIIc, a lineage so far recorded almost exclusively in silvatic transmission cycles but increasingly a potential source of human infection. These data are complemented by parallel analysis of sequence variation in a fragment of the glucose-6-phosphate isomerase gene. New isolates confirm that TcIIc is associated with terrestrial transmission cycles and armadillo reservoir hosts, and demonstrate that TcIIc is far more widespread than previously thought, with a distribution at least from Western Venezuela to the Argentine Chaco. We show that TcIIc is truly a discrete T. cruzi lineage, that it could have an ancient origin and that diversity occurs within the terrestrial niche independently of the host species. We also show that spatial structure among TcIIc isolates from its principal host, the armadillo Dasypus novemcinctus, is greater than that among TcI from Didelphis spp. opossums and link this observation to differences in ecology of their respective niches. Homozygosity in TcIIc populations and some linkage indices indicate the possibility of recombination but cannot yet be effectively discriminated from a high genome-wide frequency of gene conversion. Finally, we suggest that the derived TcIIc population genetic data have a vital role in determining the origin of the epidemiologically important hybrid lineages TcIId and TcIIe. PMID:19721699

  14. Trypanosoma cruzi IIc: phylogenetic and phylogeographic insights from sequence and microsatellite analysis and potential impact on emergent Chagas disease.

    Directory of Open Access Journals (Sweden)

    Martin S Llewellyn

    Full Text Available Trypanosoma cruzi, the etiological agent of Chagas disease, is highly genetically diverse. Numerous lines of evidence point to the existence of six stable genetic lineages or DTUs: TcI, TcIIa, TcIIb, TcIIc, TcIId, and TcIIe. Molecular dating suggests that T. cruzi is likely to have been an endemic infection of neotropical mammalian fauna for many millions of years. Here we have applied a panel of 49 polymorphic microsatellite markers developed from the online T. cruzi genome to document genetic diversity among 53 isolates belonging to TcIIc, a lineage so far recorded almost exclusively in silvatic transmission cycles but increasingly a potential source of human infection. These data are complemented by parallel analysis of sequence variation in a fragment of the glucose-6-phosphate isomerase gene. New isolates confirm that TcIIc is associated with terrestrial transmission cycles and armadillo reservoir hosts, and demonstrate that TcIIc is far more widespread than previously thought, with a distribution at least from Western Venezuela to the Argentine Chaco. We show that TcIIc is truly a discrete T. cruzi lineage, that it could have an ancient origin and that diversity occurs within the terrestrial niche independently of the host species. We also show that spatial structure among TcIIc isolates from its principal host, the armadillo Dasypus novemcinctus, is greater than that among TcI from Didelphis spp. opossums and link this observation to differences in ecology of their respective niches. Homozygosity in TcIIc populations and some linkage indices indicate the possibility of recombination but cannot yet be effectively discriminated from a high genome-wide frequency of gene conversion. Finally, we suggest that the derived TcIIc population genetic data have a vital role in determining the origin of the epidemiologically important hybrid lineages TcIId and TcIIe.

  15. The complete chloroplast genome sequence of an endemic monotypic genus Hagenia (Rosaceae): structural comparative analysis, gene content and microsatellite detection

    Science.gov (United States)

    Saina, Josphat K.; Long, Zhicheng; Hu, Guangwan; Gituru, Robert W.

    2017-01-01

    Hagenia is an endangered monotypic genus endemic to the topical mountains of Africa. The only species, Hagenia abyssinica (Bruce) J.F. Gmel, is an important medicinal plant producing bioactive compounds that have been traditionally used by African communities as a remedy for gastrointestinal ailments in both humans and animals. Complete chloroplast genomes have been applied in resolving phylogenetic relationships within plant families. We employed high-throughput sequencing technologies to determine the complete chloroplast genome sequence of H. abyssinica. The genome is a circular molecule of 154,961 base pairs (bp), with a pair of Inverted Repeats (IR) 25,971 bp each, separated by two single copies; a large (LSC, 84,320 bp) and a small single copy (SSC, 18,696). H. abyssinica’s chloroplast genome has a 37.1% GC content and encodes 112 unique genes, 78 of which code for proteins, 30 are tRNA genes and four are rRNA genes. A comparative analysis with twenty other species, sequenced to-date from the family Rosaceae, revealed similarities in structural organization, gene content and arrangement. The observed size differences are attributed to the contraction/expansion of the inverted repeats. The translational initiation factor gene (infA) which had been previously reported in other chloroplast genomes was conspicuously missing in H. abyssinica. A total of 172 microsatellites and 49 large repeat sequences were detected in the chloroplast genome. A Maximum Likelihood analyses of 71 protein-coding genes placed Hagenia in Rosoideae. The availability of a complete chloroplast genome, the first in the Sanguisorbeae tribe, is beneficial for further molecular studies on taxonomic and phylogenomic resolution within the Rosaceae family.

  16. Inheritance mode of microsatellite loci and their use for kinship analysis in the Pacific oyster (Crassostrea gigas)

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    Five full-sib families of the Pacific oyster (Crassostrea gigas) larvae were used to study the mode of inheritance at eight microsatellite loci, and the feasibility of these markers for kinship estimate was also examined. All eight microsatellite loci were compatible with Mendelian inheritance. Neither evidence of sex-linked barriers to transmission nor evidence of major barriers to fertilization between gametes from the parents was shown. Three of the eight loci showed the presence of null alleles in four families, demonstrating the need to conduct comprehensive species-specific inheritance studies for microsatellite loci used in population genetic studies. Although the null allele heterozygotes were considered as homozygotes in the calculation of genetic distance, offspring from five full-sib families were unambiguously discriminated in the neighbor-joining dendrogram. This result indicates that the microsatellite markers may be capable of discriminating between related and unrelated oyster larvae in the absence of pedigree information, and is applicable to the investigation of the effective number of parents contributing to the hatchery population of the Pacific oyster.

  17. Microsatellite markers from the 'South American fruit fly' Anastrepha fraterculus: a valuable tool for population genetic analysis and SIT applications

    Science.gov (United States)

    2014-01-01

    Background Anastrepha fraterculus Wiedemann is a horticultural pest which causes significant economic losses in the fruit-producing areas of the American continent and limits the access of products to international markets. The use of environmentally friendly control strategies against this pest is constrained due to the limited knowledge of its population structure. Results We developed microsatellite markers for A. fraterculus from four genomic libraries, which were enriched in CA, CAA, GA and CAT microsatellite motifs. Fifty microsatellite regions were evaluated and 14 loci were selected for population genetics studies. Genotypes of 122 individuals sampled from four A. fraterculus populations were analyzed. The level of polymorphism ranged from three to 13 alleles per locus and the mean expected heterozygosity ranged from 0.60 to 0.64. Comparison between allelic and genotypic frequencies showed significant differences among all pairs of populations. Conclusions This novel set of microsatellite markers provides valuable information for the description of genetic variability and population structure of wild populations and laboratory strains of A. fraterculus. This information will be used to identify and characterize candidate strains suitable to implement effective pest control strategies and might represent a first step towards having a more comprehensive knowledge about the genetics of this pest. PMID:25471285

  18. Microsatellite analysis of Damask rose (Rosa damascena Mill.) accessions from various regions in Iran reveals multiple genotypes

    NARCIS (Netherlands)

    Babaei, A.; Tabaei-Aghdaei, S.R.; Khosh-Khui, M.; Omidbaigi, R.; Naghavi, M.R.; Esselink, G.D.; Smulders, M.J.M.

    2007-01-01

    Background - Damask roses (Rosa damascena Mill.) are mainly used for essential oil production. Previous studies have indicated that all production material in Bulgaria and Turkey consists of only one genotype. Nine polymorphic microsatellite markers were used to analyze the genetic diversity of 40 a

  19. Inheritance Pattern of Microsatellite Loci and Their Use for Kinship Analysis m the Japanese Scallop Patinopecten yessoensis

    Institute of Scientific and Technical Information of China (English)

    XU Kefeng; LI Qi

    2009-01-01

    The inheritance mode of seven microsatellite markers was investigated in Patinopecten yessoensis larvae from four con-trolled crosses, and the feasibility of using these markers for kinship estimation was also examined. All the seven microsatellite loci were compatible with Mendelian inheritance. Neither sex-linked barriers to transmission nor major barriers to fertilization between gametes from the parents were evident. Two of the seven loci showed the presence of null alleles in two families, suggesting the need to conduct comprehensive species-specific inheritance studies for microsatellite loci used in population genetic studies. However, even if the null allele heterozygotes were considered as homozygotes in the calculation of genetic distance, offspring from four fami-lies were all unambiguously discriminated in the neighbor-joining dendrogram. This result indicates that the microsatellite markers used may be capable of discriminating between related and unrelated scallop larvae in the absence of pedigree information, and of investigating the effective number of parents contributing to the hatchery population of the Japanese scallop.

  20. Viscous Potential Flow Analysis of Electroaerodynamic Instability of a Liquid Sheet Sprayed with an Air Stream

    Directory of Open Access Journals (Sweden)

    Mukesh Kumar Awasthi

    2013-01-01

    Full Text Available The instability of a thin sheet of viscous and dielectric liquid moving in the same direction as an air stream in the presence of a uniform horizontal electric field has been carried out using viscous potential flow theory. It is observed that aerodynamic-enhanced instability occurs if the Weber number is much less than a critical value related to the ratio of the air and liquid stream velocities, viscosity ratio of two fluids, the electric field, and the dielectric constant values. Liquid viscosity has stabilizing effect in the stability analysis, while air viscosity has destabilizing effect.

  1. Three-dimensional Rayleigh-Taylor instability analysis of implosion system with scientific animation

    Energy Technology Data Exchange (ETDEWEB)

    Sakagami, Hitoshi [Himeji Inst. of Tech., Hyogo (Japan)

    1999-05-01

    A fully three-dimensional Rayleigh-Taylor instability taking place at the pusher-fuel contact surface in spherically stagnating systems has been investigated. Scientific color animations were rendered and constructed from the simulation results. At first, the rendering algorithm for an isovalue surface is discussed, and then the construction methods for scientific color animation are summarized by comparing analog based animation systems and digital ones. It is showed that the nonlinear dynamics of the Rayleigh-Taylor instability are characterized by vortex rings that are induced in bubble-spike structures with the use of scientific animation analysis. (author)

  2. Parametric Instability Analysis of Deepwater Top-Tensioned Risers Considering Variable Tension Along the Length

    Institute of Scientific and Technical Information of China (English)

    ZHANG Jie; TANG Yougang

    2015-01-01

    Parametric instability of a riser is caused by fluctuation of its tension in time due to the heave motion of floating plat-form. Many studies have tackled the problem of parametric instability of a riser with constant tension. However, tension in the riser actually varies linearly from the top to the bottom due to the effect of gravity. This paper presents the parametric instability analysis of deepwater top-tensioned risers (TTR) considering the linearly varying tension along the length. Firstly, the governing equation of transverse motion of TTR under parametric excitation is established. This equation is reduced to a system of ordinary differential equations by using the Galerkin method. Then the parametric instability of TTR for three calculation models are investigated by ap-plying the Floquet theory. The results show that the natural frequencies of TTR with variable tension are evidently reduced, the pa-rametric instability zones are significantly increased and the maximum allowable amplitude of platform heave is much smaller under the same damping; The nodes and antinodes of mode shape are no longer uniformly distributed along the axial direction and the am-plitude also changes with depth, which leads to coupling between the modes. The combination resonance phenomenon occurs as a result of mode coupling, which causes more serious damage.

  3. On the multistream approach of relativistic Weibel instability. I. Linear analysis and specific illustrations

    Energy Technology Data Exchange (ETDEWEB)

    Ghizzo, A.; Bertrand, P. [Institut Jean Lamour-UMR 7168, University of Lorraine, BP 239 F-54506 Vandoeuvre les Nancy (France)

    2013-08-15

    A one-dimensional multistream formalism is extended for the study of temperature anisotropy driven Weibel-type instabilities in collisionless and relativistic plasma. The formulation is based on a Hamiltonian reduction technique using the invariance of generalized canonical momentum in transverse direction. The Vlasov-Maxwell model is expressed in terms of an ensemble of one-dimensional Vlasov-type equations, coupled together with the Maxwell equations in a self-consistent way. Although the model is fundamentally nonlinear, this first of three companion papers focuses on the linear aspect. Dispersion relations of the Weibel instability are derived in the linear regime for different kinds of polarization of the electromagnetic potential vector. The model allows new unexpected insights on the instability: enhanced growth rates for the Weibel instability are predicted when a dissymmetric distribution is considered in p{sub ⊥}. In the case of a circular polarization, a simplification of the linear analysis can be obtained by the introduction of the “multiring” approach allowing to extend the analytical model of Yoon and Davidson [Phys. Rev. A 35, 2718 (1987)]. Applications of this model are left to the other two papers of the series where specific problems are addressed pertaining to the nonlinear and relativistic dynamics of magnetically trapped particles met in the saturation regime of the Weibel instability.

  4. Secure and robust cloud computing for high-throughput forensic microsatellite sequence analysis and databasing.

    Science.gov (United States)

    Bailey, Sarah F; Scheible, Melissa K; Williams, Christopher; Silva, Deborah S B S; Hoggan, Marina; Eichman, Christopher; Faith, Seth A

    2017-08-08

    Next-generation Sequencing (NGS) is a rapidly evolving technology with demonstrated benefits for forensic genetic applications, and the strategies to analyze and manage the massive NGS datasets are currently in development. Here, the computing, data storage, connectivity, and security resources of the Cloud were evaluated as a model for forensic laboratory systems that produce NGS data. A complete front-to-end Cloud system was developed to upload, process, and interpret raw NGS data using a web browser dashboard. The system was extensible, demonstrating analysis capabilities of autosomal and Y-STRs from a variety of NGS instrumentation (Illumina MiniSeq and MiSeq, and Oxford Nanopore MinION). NGS data for STRs were concordant with standard reference materials previously characterized with capillary electrophoresis and Sanger sequencing. The computing power of the Cloud was implemented with on-demand auto-scaling to allow multiple file analysis in tandem. The system was designed to store resulting data in a relational database, amenable to downstream sample interpretations and databasing applications following the most recent guidelines in nomenclature for sequenced alleles. Lastly, a multi-layered Cloud security architecture was tested and showed that industry standards for securing data and computing resources were readily applied to the NGS system without disadvantageous effects for bioinformatic analysis, connectivity or data storage/retrieval. The results of this study demonstrate the feasibility of using Cloud-based systems for secured NGS data analysis, storage, databasing, and multi-user distributed connectivity. Copyright © 2017 Elsevier B.V. All rights reserved.

  5. Molecular characterization and genetic diversity analysis of different rice cultivars by microsatellite markers

    Directory of Open Access Journals (Sweden)

    Allhgholipour Mehrzad

    2014-01-01

    Full Text Available A total of 52 rice SSR markers well distributed on 12 chromosomes were used to characterize and assess the genetic diversity among ninety four rice genotypes. The total number of polymorphic alleles was 361 alleles with the average of 5.86 alleles per SSR locus. The study revealed that some markers such as RM276 and RM5642 on chromosome 6 and RM14 and RM1 on chromosome 1 have more than 9 observed alleles compared to other primers like RM16, RM207, RM208 and RM317 with 3-4 alleles. The highest and lowest PIC values were observed for primers RM276 (0.892 and RM208 (0.423 respectively. Using Shannon´s diversity index, a mean genetic diversity of 1.641 was obtained from the analysis, indicating a high level of genetic variation among these cultivars. Cluster analysis using the complete linkage method based on jaccard similarity coefficient revealed that all genotypes were classified to nine clusters at genetic similarity level of 0.010.75, which contained 12, 16, 2, 18, 3, 6, 16, 10 and 11 varieties, respectively. Results of discriminant analysis showed that the nine cluster groups were confirmed at high levels of correct percent (96.8 and revealed true differences among these clusters. As a final result from this study, we selected eight cultivars from different cluster including Daylamani, Tarom mohali (landrace rice cultivars, RI1843046, Back cross line, RI184472, RI184421 (promising cultivars, Line 23 and IR50 (IRRI lines as parents. All of the selected cultivars will be arranged in complete diallel design to obtain combining abilities, gene effects and heterosis for each important morphology and physico-chemical characters.

  6. Identification and Analysis of Genetic Diversity Structure Within Pisum Genus Based on Microsatellite Markers

    Institute of Scientific and Technical Information of China (English)

    ZONG Xu-xiao; Rebecca Ford; Robert R Redden; GUAN Jian-ping; WANG Shu-min

    2009-01-01

    To assesse the genetic diversity among wild and cultivated accessions of 8 taxonomic groups in 2 species, and 5 subspecies under Pisum genus, and to analyze population structure and their genetic relationships among various groups of taxonomy,the study tried to verify the fitness of traditionally botanical taxonomic system under Pisum genus and to provide essential information for the exploration and utilization of wild relatives of pea genetic resources. 197 Pisum accessions from 62 counties of 5 continents were employed for SSR analysis using 21 polymorphic primer pairs in this study. Except for cultivated field pea Pisum sativum ssp. sativum vat. sativum (94 genotypes), also included were wild relative genotypes that were classified as belonging to P. fulvum, P. sativum ssp.abyssinicum, P. sativum ssp. asiaticum, P. sativum ssp. transcaucasicum, P. sativum ssp. elatius vat. elatius, P. sativum ssp. elatius vat. pumilio and P. sativum ssp.sativum vat. arvense (103 genotypes). The PCA analyses and 3-dimension PCA graphs were conducted and drawn by NTSYSpe 2.2d statistical package. Nei78 genetic distances among groups of genetic resources were calculated, and cluster analysis using UPGMA method was carried out by using Popgene V1.32 statistical package, the dendrogram was drawn by MEGA3.1 statistical package. Allelie statistics were carried out by Popgene V1.32. The significance test between groups of genotypes was carried out by Fstat V2.9.3.2 statistical package. 104 polymorphic bands were amplified using 21 SSR primer pairs with unambiguous unique polymorphic bands. 4.95 alleles were detected by each SSR primer pair in average, of which 65.56% were effective alleles for diversity. PSAD270, PSAC58, PSAA18, PSAC75, PSAA175 and PSAB72 were the most effective SSR pairs. SSR alleles were uniformly distributed among botanical taxon units under Pisum genus, but significant difference appeared in most pairwise comparisons for genetic diversity between taxon unit based

  7. Forensic analysis of polymorphism and regional stratification of Y-chromosomal microsatellites in Belarus.

    Science.gov (United States)

    Rebała, Krzysztof; Tsybovsky, Iosif S; Bogacheva, Anna V; Kotova, Svetlana A; Mikulich, Alexei I; Szczerkowska, Zofia

    2011-01-01

    Nine loci defining minimal haplotypes and four other Y-chromosomal short tandem repeats (Y-STRs) DYS437, DYS438, DYS439 and GATA H4.1 were analysed in 414 unrelated males residing in four regions of Belarus. Haplotypes of 328 males were further extended by 7 additional Y-STRs: DYS388, DYS426, DYS448, DYS456, DYS458, DYS460 and DYS635. The 13-locus haplotype diversity was 0.9978 and discrimination capacity was 78.7%, indicating presence of identical haplotypes among unrelated males. Seven additional Y-STRs enabled almost complete discrimination of undifferentiated 13-locus haplotypes, increasing haplotype diversity to 0.9998 and discrimination capacity to 97.9%. Analysis of molecular variance of minimal haplotypes excluded the use of a Y-STR database for Belarusians residing in northeastern Poland as representative for the Belarusian population in forensic practice, and revealed regional stratification within the country. However, four additional markers (DYS437, DYS438, DYS439 and GATA H4.1) were shown to eliminate the observed geographical substructure among Belarusian males. The results imply that in case of minimal and PowerPlex Y haplotypes, a separate frequency database should be used for northern Belarus to estimate Y-STR profile frequencies in forensic casework. In case of Yfiler haplotypes, regional stratification within Belarus may be neglected.

  8. Application of maximum entropy method for droplet size distribution prediction using instability analysis of liquid sheet

    Science.gov (United States)

    Movahednejad, E.; Ommi, F.; Hosseinalipour, S. M.; Chen, C. P.; Mahdavi, S. A.

    2011-12-01

    This paper describes the implementation of the instability analysis of wave growth on liquid jet surface, and maximum entropy principle (MEP) for prediction of droplet diameter distribution in primary breakup region. The early stage of the primary breakup, which contains the growth of wave on liquid-gas interface, is deterministic; whereas the droplet formation stage at the end of primary breakup is random and stochastic. The stage of droplet formation after the liquid bulk breakup can be modeled by statistical means based on the maximum entropy principle. The MEP provides a formulation that predicts the atomization process while satisfying constraint equations based on conservations of mass, momentum and energy. The deterministic aspect considers the instability of wave motion on jet surface before the liquid bulk breakup using the linear instability analysis, which provides information of the maximum growth rate and corresponding wavelength of instabilities in breakup zone. The two sub-models are coupled together using momentum source term and mean diameter of droplets. This model is also capable of considering drag force on droplets through gas-liquid interaction. The predicted results compared favorably with the experimentally measured droplet size distributions for hollow-cone sprays.

  9. Analysis of multi-bunch instabilities at the diamond storage ring

    CERN Document Server

    Bartolini, Riccardo; Rehm, Guenther; Smaluk, Victor

    2017-01-01

    We present the result of the analytical, numerical and experimental analysis of multi-bunch instabilities at the Diamond storage ring. This work compares the impedance estimates with CST with the analysis of the growth rates of the excited multi-bunch modes in different machine configurations. The contribution of a number of wakefield sources has been identified with very high precision thanks to high quality data provided by the existing TMBF diagnostics.

  10. A combined DNA-microsatellite and isozyme analysis of the population structure of the harbour porpoise in Danish waters and west Greenland

    DEFF Research Database (Denmark)

    Andersen, L W; Holm, L E; Siegismund, Hans Redlef;

    1997-01-01

    One hundred and twenty-four specimens of the harbour porpoise, Phocoena phocoena, occurring in inner Danish waters (IDW), the North Sea and West Greenland were analysed to study subdivision into genetically differentiated subpopulations using PCR-amplified DNA-microsatellites and isozyme markers...... or nonrandom mating. The analysis of the genetical population structure showed that harbour porpoises from West Greenland, the North Sea and IDW were three geographically, genetically differentiated populations even though connected through some degree of gene flow. A tendency for females to be more stationary...... than males was suggested. Furthermore, the population structure suggested a closer relationship between IDW and the North Sea....

  11. System dynamic instabilities induced by sliding contact: A numerical analysis with experimental validation

    Science.gov (United States)

    Brunetti, J.; Massi, F.; Saulot, A.; Renouf, M.; D`Ambrogio, W.

    2015-06-01

    Mechanical systems present several contact surfaces between deformable bodies. The contact interface can be either static (joints) or in sliding (active interfaces). The sliding interfaces can have several roles and according to their application they can be developed either for maximizing the friction coefficient and the energy dissipation (e.g. brakes) or rather to allow the relative displacement at joints with a maximum efficiency. In both cases the coupling between system and local contact dynamics can bring to system dynamics instabilities (e.g. brake squeal or squeaking of hip prostheses). This results in unstable vibrations of the system, induced by the oscillation of the contact forces. In the literature, a large number of works deal with such kind of instabilities and are mainly focused on applied problems such as brake squeal noise. This paper shows a more general numerical analysis of a simple system constituted by two bodies in sliding contact: a rigid cylinder rotating inside a deformable one. The parametrical Complex Eigenvalue Analysis and the transient numerical simulations show how the friction forces can give rise to in-plane dynamic instabilities due to the interaction between two system modes, even for such a simple system characterized by one deformable body. Results from transient simulations highlight the key role of realistic values of the material damping to have convergence of the model and, consequently, reliable physical results. To this aim an experimental estimation of the material damping has been carried out. Moreover, the simplicity of the system allows for a deeper analysis of the contact instability and a balance of the energy flux among friction, system vibrations and damping. The numerical results have been validated by comparison with experimental ones, obtained by a specific test bench developed to reproduce and analyze the contact friction instabilities.

  12. Analysis of Self-Excited Combustion Instabilities Using Decomposition Techniques

    Science.gov (United States)

    2016-07-05

    SVD ), while for DMD, the data are reduced using the Arnoldi algorithm. POD decomposes data based on optimality to obtain a set of best representations...analysis is performed with the same domains that were used for the POD analysis. The DMD frequency spectra of pressure and heat-release fluctuations are...temporal data andm columns of spatial data, the POD matrix will be of size N ×m. Once we obtain the POD matrix A, the SVD of A is A UΣVT (A4) where U is an

  13. Development of novel microsatellite DNA markers by cross-amplification and analysis of genetic variation in gerbils.

    Science.gov (United States)

    Du, Xiaoyan; Chen, Zhenwen; Li, Wei; Tan, Yuanqing; Lu, Jing; Zhu, Xiangdong; Zhao, Taiyun; Dong, Gang; Zeng, Lin

    2010-01-01

    The objectives of this study are to establish microsatellite loci for the Mongolian gerbil based on mouse microsatellite DNA sequences and to investigate genetic variation in the laboratory gerbil (Capital Medical University, CMU) and 2 wild gerbil populations (from Yin Chuan city [YIN] and the Hohehot Municipality [HOH]). In total, 536 mouse microsatellite markers were chosen to identify polymorphic dinucleotide repeat loci in the gerbil by cross-amplification. Of these markers, 313 (58.39%) have been discretely amplified from the CMU laboratory gerbil and been sequenced. Of the 313 sequenced markers, 130 were confirmed as simple sequence repeat (SSR) loci in the gerbil. In total, 6 of those newly identified loci plus 6 identified in previous reports were used to estimate the genetic polymorphism for 30 laboratory gerbils and 54 wild gerbils (27 each of the HOH and YIN groups). A total of 29 alleles were observed in the 3 populations, and 11 of 12 loci (91.67%) are polymorphic markers. Nei's standard genetic distances of 0.0592 (CMU vs. HOH) and 0.1033 (CMU vs. YIN) were observed. The averages of observed versus expected heterozygosity are 0.5231/0.4008, 0.5051/0.3882, and 0.4825/0.3665 for the YIN, HOH, and CMU populations, respectively. These results show that cross-amplification using mouse microsatellite primers is an efficient way to identify gerbil SSR loci. By using these 12 selected markers, we have demonstrated that genetic variation level within the CMU population is higher than that has been reported previously and are comparable with the levels found in 2 wild populations.

  14. Genome-Wide Analysis of Microsatellite Markers Based on Sequenced Database in Chinese Spring Wheat (Triticum aestivum L..

    Directory of Open Access Journals (Sweden)

    Bin Han

    Full Text Available Microsatellites or simple sequence repeats (SSRs are distributed across both prokaryotic and eukaryotic genomes and have been widely used for genetic studies and molecular marker-assisted breeding in crops. Though an ordered draft sequence of hexaploid bread wheat have been announced, the researches about systemic analysis of SSRs for wheat still have not been reported so far. In the present study, we identified 364,347 SSRs from among 10,603,760 sequences of the Chinese spring wheat (CSW genome, which were present at a density of 36.68 SSR/Mb. In total, we detected 488 types of motifs ranging from di- to hexanucleotides, among which dinucleotide repeats dominated, accounting for approximately 42.52% of the genome. The density of tri- to hexanucleotide repeats was 24.97%, 4.62%, 3.25% and 24.65%, respectively. AG/CT, AAG/CTT, AGAT/ATCT, AAAAG/CTTTT and AAAATT/AATTTT were the most frequent repeats among di- to hexanucleotide repeats. Among the 21 chromosomes of CSW, the density of repeats was highest on chromosome 2D and lowest on chromosome 3A. The proportions of di-, tri-, tetra-, penta- and hexanucleotide repeats on each chromosome, and even on the whole genome, were almost identical. In addition, 295,267 SSR markers were successfully developed from the 21 chromosomes of CSW, which cover the entire genome at a density of 29.73 per Mb. All of the SSR markers were validated by reverse electronic-Polymerase Chain Reaction (re-PCR; 70,564 (23.9% were found to be monomorphic and 224,703 (76.1% were found to be polymorphic. A total of 45 monomorphic markers were selected randomly for validation purposes; 24 (53.3% amplified one locus, 8 (17.8% amplified multiple identical loci, and 13 (28.9% did not amplify any fragments from the genomic DNA of CSW. Then a dendrogram was generated based on the 24 monomorphic SSR markers among 20 wheat cultivars and three species of its diploid ancestors showing that monomorphic SSR markers represented a promising

  15. Thermoacoustic instability - a dynamical system and time domain analysis

    CERN Document Server

    Sayadi, Taraneh; Schmid, Peter; Richecoeur, Franck; Massot, Marc

    2013-01-01

    This study focuses on the Rijke tube problem, which includes features relevant to the modeling of thermoacoustic coupling in reactive flows: a compact acoustic source, an empirical model for the heat source, and nonlinearities. This system features both linear and nonlinear flow regimes with complex dynamical behavior. In order to synthesize accurate time-series, we tackle this problem from a numerical point-of-view, and start by proposing a dedicated solver designed for dealing with the underlying stiffness, in particular, the retarded time and the discontinuity at the location of the heat source. Stability analysis is performed on the limit of the low amplitude perturbations by means of the projection method proposed by Jarlebring (2008), which alleviates the linearization of the retarded term. The results are then compared to the analytical solution of the undamped system, in addition to the analysis based on Galerkin projection. The method provides insight into the consequence of the simplification due to...

  16. A polymorphic microsatellite from the Squalius alburnoides complex (Osteichthyes, Cyprinidae cloned by serendipity can be useful in genetic analysis of polyploids

    Directory of Open Access Journals (Sweden)

    Luis Boto

    2011-01-01

    Full Text Available A new microsatellite locus (SAS1 for Squalius alburnoides was obtained through cloning by serendipity. The possible usefulness of this new species-specific microsatellite in genetic studies of this hybrid-species complex, was explored. The polymorphism exhibited by SAS1 microsatellite is an important addition to the set of microsatellites previously used in genetic studies in S. alburnoides complex, that mostly relied in markers described for other species. Moreover, the SAS1 microsatellite could be used to identify the parental genomes of the complex, complementing other methods recently described for the same purpose.

  17. A polymorphic microsatellite from the Squalius alburnoides complex (Osteichthyes, Cyprinidae) cloned by serendipity can be useful in genetic analysis of polyploids.

    Science.gov (United States)

    Boto, Luis; Cunha, Carina; Doadrio, Ignacio

    2011-07-01

    A new microsatellite locus (SAS1) for Squalius alburnoides was obtained through cloning by serendipity. The possible usefulness of this new species-specific microsatellite in genetic studies of this hybrid-species complex, was explored. The polymorphism exhibited by SAS1 microsatellite is an important addition to the set of microsatellites previously used in genetic studies in S. alburnoides complex, that mostly relied in markers described for other species. Moreover, the SAS1 microsatellite could be used to identify the parental genomes of the complex, complementing other methods recently described for the same purpose..

  18. Linear analysis of the vertical shear instability: outstanding issues and improved solutions (Research Note)

    CERN Document Server

    Umurhan, O M; Gressel, O

    2015-01-01

    The Vertical Shear Instability is one of two known mechanisms potentially active in the so-called dead zones of protoplanetary accretion disks. A recent analysis indicates that a subset of unstable modes shows unbounded growth - both as resolution is increased and when the nominal lid of the atmosphere is extended, possibly indicating ill-posedness in previous attempts of linear analysis. The reduced equations governing the instability are revisited and the generated solutions are examined using both the previously assumed separable forms and an improved non-separable solution form that is herewith introduced. Analyzing the reduced equations using the separable form shows that, while the low-order body modes have converged eigenvalues and eigenfunctions (as both the vertical boundaries of the atmosphere are extended and with increased radial resolution), it is also confirmed that the corresponding high-order body modes and the surface modes do indeed show unbounded growth rates. However, the energy contained ...

  19. Genetic Diversity and Differentiation of the Orange-Spotted Grouper (Epinephelus coioides Between and Within Cultured Stocks and Wild Populations Inferred from Microsatellite DNA Analysis

    Directory of Open Access Journals (Sweden)

    Haoran Lin

    2011-07-01

    Full Text Available In the present study, we employed microsatellite DNA markers to analyze the genetic diversity and differentiation between and within cultured stocks and wild populations of the orange-spotted grouper originating from the South China Sea and Southeast Asia. Compared to wild populations, genetic changes including reduced genetic diversity and significant differentiation have taken place in cultured grouper stocks, as shown by allele richness and heterozygosity studies, pairwise Fst, structure, molecular variance analysis, as well as multidimensional scaling analysis. Although two geographically adjacent orange-spotted grouper populations in China showed negligible genetic divergence, significant population differentiation was observed in wild grouper populations distributed in a wide geographical area from China, through Malaysia to Indonesia. However, the Mantel test rejected the isolation-by-distance model of genetic structure, which indicated the genetic differentiation among the populations could result from the co-effects of various factors, such as historical dispersal, local environment, ocean currents, river flows and island blocks. Our results demonstrated that microsatellite markers could be suitable not only for genetic monitoring cultured stocks but also for revealing the population structuring of wild orange-spotted grouper populations. Meanwhile, our study provided important information for breeding programs, management of cultured stocks and conservation of wild populations of the orange-spotted grouper.

  20. Loss of genetic variation in Greek hatchery populations of the European sea bass (Dicentrarchus labrax L. as revealed by microsatellite DNA analysis

    Directory of Open Access Journals (Sweden)

    D. LOUKOVITIS

    2015-01-01

    Full Text Available Genetic variation in four reared stocks of European sea bass Dicentrarchus labrax L., originating from Greek commercial farms, was assessed using five polymorphic microsatellite markers and was compared with that of three natural populations from Greece and France. The total number of alleles per marker ranged from 8 to 22 alleles, and hatchery samples showed the same levels of observed heterozygosity with samples from the wild but substantially smaller allelic richness and expected heterozygosity. The genetic differentiation of cultivated samples between them as well as from the wild origin fish was significant as indicated by Fst analysis. All population pairwise comparisons were statistically significant, except for the pair of the two natural Greek populations. Results of microsatellite DNA analysis herein showed a 37 % reduction of the mean allele number in the hatchery samples compared to the wild ones, suggesting random genetic drift and inbreeding events operating in the hatcheries. Knowledge of the genetic variation in D. labrax cultured populations compared with that in the wild ones is essential for setting up appropriate guidelines for proper monitoring and management of the stocks either under traditional practices or for the implementation of selective breeding programmes.

  1. Three-dimensional instability analysis of boundary layers perturbed by streamwise vortices

    Science.gov (United States)

    Martín, Juan A.; Paredes, Pedro

    2016-08-01

    A parametric study is presented for the incompressible, zero-pressure-gradient flat-plate boundary layer perturbed by streamwise vortices. The vortices are placed near the leading edge and model the vortices induced by miniature vortex generators (MVGs), which consist in a spanwise-periodic array of small winglet pairs. The introduction of MVGs has been experimentally proved to be a successful passive flow control strategy for delaying laminar-turbulent transition caused by Tollmien-Schlichting (TS) waves. The counter-rotating vortex pairs induce non-modal, transient growth that leads to a streaky boundary layer flow. The initial intensity of the vortices and their wall-normal distances to the plate wall are varied with the aim of finding the most effective location for streak generation and the effect on the instability characteristics of the perturbed flow. The study includes the solution of the three-dimensional, stationary, streaky boundary layer flows by using the boundary region equations, and the three-dimensional instability analysis of the resulting basic flows by using the plane-marching parabolized stability equations. Depending on the initial circulation and positioning of the vortices, planar TS waves are stabilized by the presence of the streaks, resulting in a reduction in the region of instability and shrink of the neutral stability curve. For a fixed maximum streak amplitude below the threshold for secondary instability (SI), the most effective wall-normal distance for the formation of the streaks is found to also offer the most stabilization of TS waves. By setting a maximum streak amplitude above the threshold for SI, sinuous shear layer modes become unstable, as well as another instability mode that is amplified in a narrow region near the vortex inlet position.

  2. MISA-web: a web server for microsatellite prediction.

    Science.gov (United States)

    Beier, Sebastian; Thiel, Thomas; Münch, Thomas; Scholz, Uwe; Mascher, Martin

    2017-08-15

    Microsatellites are a widely-used marker system in plant genetics and forensics. The development of reliable microsatellite markers from resequencing data is challenging. We extended MISA, a computational tool assisting the development of microsatellite markers, and reimplemented it as a web-based application. We improved compound microsatellite detection and added the possibility to display and export MISA results in GFF3 format for downstream analysis. MISA-web can be accessed under http://misaweb.ipk-gatersleben.de/. The website provides tutorials, usage note as well as download links to the source code. scholz@ipk-gatersleben.de.

  3. Detecting microsatellites within genomes: significant variation among algorithms

    Directory of Open Access Journals (Sweden)

    Rivals Eric

    2007-04-01

    Full Text Available Abstract Background Microsatellites are short, tandemly-repeated DNA sequences which are widely distributed among genomes. Their structure, role and evolution can be analyzed based on exhaustive extraction from sequenced genomes. Several dedicated algorithms have been developed for this purpose. Here, we compared the detection efficiency of five of them (TRF, Mreps, Sputnik, STAR, and RepeatMasker. Results Our analysis was first conducted on the human X chromosome, and microsatellite distributions were characterized by microsatellite number, length, and divergence from a pure motif. The algorithms work with user-defined parameters, and we demonstrate that the parameter values chosen can strongly influence microsatellite distributions. The five algorithms were then compared by fixing parameters settings, and the analysis was extended to three other genomes (Saccharomyces cerevisiae, Neurospora crassa and Drosophila melanogaster spanning a wide range of size and structure. Significant differences for all characteristics of microsatellites were observed among algorithms, but not among genomes, for both perfect and imperfect microsatellites. Striking differences were detected for short microsatellites (below 20 bp, regardless of motif. Conclusion Since the algorithm used strongly influences empirical distributions, studies analyzing microsatellite evolution based on a comparison between empirical and theoretical size distributions should therefore be considered with caution. We also discuss why a typological definition of microsatellites limits our capacity to capture their genomic distributions.

  4. Initiation, ablation, precursor formation, and instability analysis of thin foil liner Z-pinches

    Science.gov (United States)

    Blesener, Isaac Curtis

    This dissertation presents the results of mostly experimental work studying the early-time behavior of thin foil liners as compared to wire-array Z-pinches. It involves three studies, covering initiation, ablation and precursor formation, and instability analysis. Initiation was studied by observing the optical emission of various thickness (0.6-23.5 μm Cu) liners using a streak camera. It was found that thinner liners initiated sooner, more quickly, and more uniformly than thicker liners. This correlated well with both an increase in instantaneous dJ/dt at the time of first emission as well as the inductive voltage at the time of first emission. The threshold for uniform initiation was dJ/dt>3.5×1016Acm -2s-1. Uniform initiation is important for liners because nonuniformities could lead to enhanced instabilities and poor liner performance (compression, x-ray production, etc.). Ablation and precursor formation of wire-arrays (16x75 μm Cu) and liners (6 μm Cu) were studied using r-θ density maps and radial mass profiles created by an axial X pinch radiography diagnostic. These images show very strong differences in this stage of the Z-pinch. Wire-arrays develop complex, azimuthally varying ablation structures that lead to dense precursors. Liners, however, show significantly reduced and azimuthally uniform ablation leading to an order of magnitude less dense precursor on axis. This is likely due to the discrete versus continuous nature of wire-arrays versus liners. With wire-arrays, plasma that is created on the outside of the wires can reach the array axis by being swept through the gaps between the stationary wire cores. In contrast, liners have no “gaps” for plasma to flow through. Therefore, any plasma that is created on the outside of the liner is trapped there until the bulk of the liner moves with the implosion. Consequently, only the plasma that is created on the inside of the liner is able to contribute to precursor formation. This is an important

  5. Inbreeding and genetic diversity analysis in a hatchery release population and clones of Rhopilema esculentum based on microsatellite markers

    Science.gov (United States)

    Tian, Tao; Chen, Zaizhong; Wang, Mosang; Hu, Yulong; Wang, Weiji

    2017-05-01

    Ten microsatellite markers were used to analyze the levels of genetic diversity and inbreeding in a hatchery release population of Rhopilema esculentum Kishinouye (Scyphozoa: Rhizostomatidae). A total of 85 alleles were detected in 600 individuals. Within-population levels of observed ( H o) and expected ( H e) heterozygosity ranged from 0.152 to 0.839 (mean=0.464) and from 0.235 to 0.821 (mean=0.618), respectively. The polymorphism information content (PIC) of each marker ranged from 0.207 to 0.795 with an average of 0.580, indicating that the hatchery population maintained a high level of genetic diversity. Inbreeding levels were estimated in the hatchery population and the inbreeding coefficient was 0.203. This result revealed that a certain level of inbreeding occurred within the population. Meanwhile, we also determined genetic diversity at the clone level. Several polyps from the same scyphistomae were genotyped at the ten microsatellite loci and there was virtually no difference in their genotypes. Furthermore, we calculated the probabilities of exclusion. When both parents were known, the average exclusion probability of ten loci was 99.99%. Our data suggest that the ten microsatellite markers can not only be used to analyze the identity of individuals but they can also be applied to parentage identification. Our research provides a theoretical basis and technical support for genetic diversity detection and reasonable selection of R. esculentum hatchery populations. These findings support the use of releasing studies and conservation of R. esculentum germplasm resources.

  6. Inbreeding and genetic diversity analysis in a hatchery release population and clones of Rhopilema esculentum based on microsatellite markers

    Science.gov (United States)

    Tian, Tao; Chen, Zaizhong; Wang, Mosang; Hu, Yulong; Wang, Weiji

    2016-07-01

    Ten microsatellite markers were used to analyze the levels of genetic diversity and inbreeding in a hatchery release population of Rhopilema esculentum Kishinouye (Scyphozoa: Rhizostomatidae). A total of 85 alleles were detected in 600 individuals. Within-population levels of observed (H o) and expected (H e) heterozygosity ranged from 0.152 to 0.839 (mean=0.464) and from 0.235 to 0.821 (mean=0.618), respectively. The polymorphism information content (PIC) of each marker ranged from 0.207 to 0.795 with an average of 0.580, indicating that the hatchery population maintained a high level of genetic diversity. Inbreeding levels were estimated in the hatchery population and the inbreeding coefficient was 0.203. This result revealed that a certain level of inbreeding occurred within the population. Meanwhile, we also determined genetic diversity at the clone level. Several polyps from the same scyphistomae were genotyped at the ten microsatellite loci and there was virtually no difference in their genotypes. Furthermore, we calculated the probabilities of exclusion. When both parents were known, the average exclusion probability of ten loci was 99.99%. Our data suggest that the ten microsatellite markers can not only be used to analyze the identity of individuals but they can also be applied to parentage identification. Our research provides a theoretical basis and technical support for genetic diversity detection and reasonable selection of R. esculentum hatchery populations. These findings support the use of releasing studies and conservation of R. esculentum germplasm resources.

  7. Instability analysis procedure for 3-level multi-bearing rotor-foundation systems

    Science.gov (United States)

    Zhou, S.; Rieger, N. F.

    1985-01-01

    A procedure for the instability analysis of a three-level multispan rotor systems is described. This procedure is based on a distributed mass elastic representation of the rotor system in several eight-coefficient bearings. Each bearing is supported from an elastic foundation on damped, elastic pedestals. The foundation is represented as a general distributed mass elastic structure on discrete supports, which may have different stiffness and damping properties in the horizontal and vertical directions. This system model is suited to studies of instability threshold conditions for multirotor turbomachines on either massive or flexible foundations. The instability conditions is found by obtaining the eigenvalues of the system determinant, which is obtained by the transfer matrix method from the three-level system model. The stability determinant is solved for the lowest rotational speed at which the system damping becomes zero in the complex eigenvalue, and for the whirl frequency corresponding to the natural frequency of the unstable mode. An efficient algorithm for achieving this is described. Application of this procedure to a rigid rotor in two damped-elastic bearings and flexible supports is described. A second example discusses a flexible rotor with four damped-elastic bearings. The third case compares the stability of a six-bearing 300 Mw turbine generator unit, using two different bearing types. These applications validate the computer program and various aspects of the analysis.

  8. Analysis of Combustion Instability in Liquid Fuel Rocket Motors. Ph.D. Thesis

    Science.gov (United States)

    Wong, K. W.; Ventrice, M.

    1979-01-01

    The development of a technique to be used in the solution of nonlinear velocity-sensitive combustion instability problems is described. The orthogonal collocation method was investigated. It found that the results are heavily dependent on the location of the collocation points and characteristics of the equations, so the method was rejected as unreliabile. The Galerkin method, which has proved to be very successful in analysis of the pressure sensitive combustion instability was found to work very well. It was found that the pressure wave forms exhibit a strong second harmonic distortion and a variety of behaviors are possible depending on the nature of the combustion process and the parametric values involved. A one-dimensional model provides further insight into the problem by allowing a comparison of Galerkin solutions with more exact finite-difference computations.

  9. Multifractal analysis and instability index of prior-to-crash market situations

    CERN Document Server

    Piacquadio, M

    2009-01-01

    We take prior-to-crash market prices (NASDAQ, Dow Jones Industrial Average) as a signal, a function of time, we project these discrete values onto a vertical axis, thus obtaining a Cantordust. We study said cantordust with the tools of multifractal analysis, obtaining spectra by definition and by lagrangian coordinates. These spectra have properties that typify the prior-to-crash market situation. Any of these spectra entail elaborate processing of the raw signal data. With the unprocessed raw data we obtain an instability index, also with properties that typify the prior-to-crisis market situation. Both spectra and the instability index agree in characterizing such crashes, and in giving an early warning of them.

  10. FOKKER-PLANCK ANALYSIS OF TRANSVERSE COLLECTIVE INSTABILITIES IN ELECTRON STORAGE RINGS

    Energy Technology Data Exchange (ETDEWEB)

    Lindberg, R. R.

    2017-06-25

    We analyze single bunch transverse instabilities due to wakefields using a Fokker-Planck model. We expand on the work of Suzuki [1], writing out the linear matrix equation including chromaticity, both dipolar and quadrupolar transverse wakefields, and the effects of damping and diffusion due to the synchrotron radiation. The eigenvalues and eigenvectors determine the collective stability of the beam, and we show that the predicted threshold current for transverse instability and the profile of the unstable agree well with tracking simulations. In particular, we find that predicting collective stability for high energy electron beams at moderate to large values of chromaticity requires the full Fokker-Planck analysis to properly account for the effects of damping and diffusion due to synchrotron radiation.

  11. High-Speed Linear Raman Spectroscopy for Instability Analysis of a Bluff Body Flame

    Science.gov (United States)

    Kojima, Jun; Fischer, David

    2013-01-01

    We report a high-speed laser diagnostics technique based on point-wise linear Raman spectroscopy for measuring the frequency content of a CH4-air premixed flame stabilized behind a circular bluff body. The technique, which primarily employs a Nd:YLF pulsed laser and a fast image-intensified CCD camera, successfully measures the time evolution of scalar parameters (N2, O2, CH4, and H2O) in the vortex-induced flame instability at a data rate of 1 kHz. Oscillation of the V-shaped flame front is quantified through frequency analysis of the combustion species data and their correlations. This technique promises to be a useful diagnostics tool for combustion instability studies.

  12. Fokker-Planck analysis of transverse collective instabilities in electron storage rings

    Science.gov (United States)

    Lindberg, Ryan R.

    2016-12-01

    We analyze single bunch transverse instabilities due to wakefields using a Fokker-Planck model. We first expand on the work of T. Suzuki, Part. Accel. 12, 237 (1982) to derive the theoretical model including chromaticity, both dipolar and quadrupolar transverse wakefields, and the effects of damping and diffusion due to the synchrotron radiation. We reduce the problem to a linear matrix equation, whose eigenvalues and eigenvectors determine the collective stability of the beam. We then show that various predictions of the theory agree quite well with results from particle tracking simulations, including the threshold current for transverse instability and the profile of the unstable mode. In particular, we find that predicting collective stability for high energy electron beams at moderate to large values of chromaticity requires the full Fokker-Planck analysis to properly account for the effects of damping and diffusion due to synchrotron radiation.

  13. Analysis of Thermo-Diffusive Cellular Instabilities in Continuum Combustion Fronts

    CERN Document Server

    Azizi, Hossein; Provatas, Nikolas

    2016-01-01

    We explore numerically the morphological patterns of thermo-diffusive instabilities in combustion fronts with a continuum fuel source, within a range of Lewis numbers and ignition temperatures, focusing on the cellular regime. For this purpose, we generalize the model of Brailovsky et al. to include distinct process kinetics and reactant heterogeneity. The generalized model is derived analytically and validated with other established models in the limit of infinite Lewis number for zero-order and first-order kinetics. Cellular and dendritic instabilities are found at low Lewis numbers thanks to a dynamic adaptive mesh refinement technique that reduces finite size effects, which can affect or even preclude the emergence of these patterns. This technique also allows achieving very large computational domains, enabling the study of system-size effects. Our numerical linear stability analysis is consistent with the analytical results of Brailovsky et al. The distinct types of dynamics found in the vicinity of the...

  14. Industrial Growth Rates and Instability: An Historical Analysis of the Former Centrally Planned Economies of Eastern Europe

    Directory of Open Access Journals (Sweden)

    Evan E. ANDERSON

    2011-11-01

    Full Text Available One of the central tenets of socialism and central planning economics, as practiced by the East European countries, was that this organization of employment, production and activity could achieve higher growth rates than market economies. This paper presents an historical analysis of economic performance of seven countries: Bulgaria, Czechoslovakia, GDR, Hungary, Poland, Romania and Yugoslavia during the crucial period of socialism (1960-80. It studies the relationship between industry output growth rates and output instabilities in approximately twenty-five industries. Using empirically estimated models it was found that the instability (volatility of industry output increased with growth rates and at an increasing rate. Since instability creates substantial costs, these findings imply that the true value of income and product streams in East European countries, after discounting for instability, was lower than otherwise believed. A decomposition of instability into two sources, systemic structure versus operational implementation is suggested.

  15. Extrapair paternity and maternity in the three-toed woodpecker, Picoides tridactylus: insights from microsatellite-based parentage analysis.

    Directory of Open Access Journals (Sweden)

    Meng-Hua Li

    Full Text Available Molecular techniques have revealed that avian mating systems are more diverse and complex than previously thought. We used microsatellite markers to determine genetic parentage, the prevalence of extrapair paternity and quasi-parasitism (i.e. situations where a male's extrapair mate lay in his nest in a socially monogamous population of three-toed woodpeckers (Picoides tridactylus in southern Finland. A total of 129 adults and nestlings, representing 5-9 families annually from 2004-2007, were genotyped at up to ten microsatellite loci. The results of genetic assignment tests confirmed that monogamous parentage characterized the majority (84.6%, 22/26 of broods, and that most (93.8%, 75/80 nestlings were the offspring of their social parents. Two of 80 nestlings (2.5% in two of 26 broods (7.7% were sired by extrapair males and quasi-parasitism occurred in 3.8% (3/80 of nestlings and 7.7% (2/26 of broods. Hence, the levels of extrapair parentage were low, possibly because both genetic polygyny and polyandry are constrained by the high paternal effort required for parental care. The co-occurrence of low levels of extrapair paternity and quasi-parasitism are discussed in light of ecological and behavioural factors characterizing the species biology.

  16. Multiplexed microsatellite recovery using massively parallel sequencing.

    Science.gov (United States)

    Jennings, T N; Knaus, B J; Mullins, T D; Haig, S M; Cronn, R C

    2011-11-01

    Conservation and management of natural populations requires accurate and inexpensive genotyping methods. Traditional microsatellite, or simple sequence repeat (SSR), marker analysis remains a popular genotyping method because of the comparatively low cost of marker development, ease of analysis and high power of genotype discrimination. With the availability of massively parallel sequencing (MPS), it is now possible to sequence microsatellite-enriched genomic libraries in multiplex pools. To test this approach, we prepared seven microsatellite-enriched, barcoded genomic libraries from diverse taxa (two conifer trees, five birds) and sequenced these on one lane of the Illumina Genome Analyzer using paired-end 80-bp reads. In this experiment, we screened 6.1 million sequences and identified 356,958 unique microreads that contained di- or trinucleotide microsatellites. Examination of four species shows that our conversion rate from raw sequences to polymorphic markers compares favourably to Sanger- and 454-based methods. The advantage of multiplexed MPS is that the staggering capacity of modern microread sequencing is spread across many libraries; this reduces sample preparation and sequencing costs to less than $400 (USD) per species. This price is sufficiently low that microsatellite libraries could be prepared and sequenced for all 1373 organisms listed as 'threatened' and 'endangered' in the United States for under $0.5 M (USD).

  17. Analysis of microsatellite markers and single nucleotide polymorphisms in candidate genes for susceptibility to bipolar affective disorder in the chromosome 12Q24.31 region.

    Science.gov (United States)

    Shink, Eric; Harvey, Mario; Tremblay, Monique; Gagné, Bernard; Belleau, Pascal; Raymond, Catherine; Labbé, Michel; Dubé, Marie-Pierre; Lafrenière, Ronald G; Barden, Nicholas

    2005-05-05

    Previous results from our genetic analyses using pedigrees from a French Canadian population suggested that the interval delimited by markers D12S86 and D12S378 on chromosome 12 was the most probable genomic region to contain a susceptibility gene for affective disorders. Here we present a more detailed genetic analysis of a 7.7 Mb genomic region located on 12q24.31. This region was saturated with 20 microsatellite markers to refine the candidate region and linkage analysis performed in 41 families from the Saguenay-Lac-St-Jean (SLSJ) region of Quebec. The results of two point parametric analysis using MFLINK supported the presence of a susceptibility locus on chromosome 12q24.31. Association studies with microsatellite markers using a case/control sample from the same population (n = 401) and analyzed with CLUMP revealed significant allelic associations between the bipolar phenotype and markers NBG6 (P = 0.008) and NBG12 (P < 10(-3)). According to these results, we investigated candidate genes in the NBG12 area. We analyzed 32 genes for the presence of polymorphisms in coding sequences and intron/exon junctions and genotyped 22 non-synonymous SNPs in the SLSJ case/control sample. Two uncommon polymorphisms (minor allele frequency < or = 0.03) found in KIAA1595 and FLJ22471 genes, gave P-values below 0.05 with the T1 statistic. Moreover, using haplotype analysis, a nearly significant haplotypic association was observed at the HM74 gene. These results do not give strong support for a role in the susceptibility to bipolar disorder of any of these genes analyzed. However, the significance of rare polymorphisms should be explored by further analyses. Copyright 2005 Wiley-Liss, Inc.

  18. Thermomagnetic instabilities in a vertical layer of ferrofluid: nonlinear analysis away from a critical point

    Science.gov (United States)

    Dey, Pinkee; Suslov, Sergey A.

    2016-12-01

    A finite amplitude instability has been analysed to discover the exact mechanism leading to the appearance of stationary magnetoconvection patterns in a vertical layer of a non-conducting ferrofluid heated from the side and placed in an external magnetic field perpendicular to the walls. The physical results have been obtained using a version of a weakly nonlinear analysis that is based on the disturbance amplitude expansion. It enables a low-dimensional reduction of a full nonlinear problem in supercritical regimes away from a bifurcation point. The details of the reduction are given in comparison with traditional small-parameter expansions. It is also demonstrated that Squire’s transformation can be introduced for higher-order nonlinear terms thus reducing the full three-dimensional problem to its equivalent two-dimensional counterpart and enabling significant computational savings. The full three-dimensional instability patterns are subsequently recovered using the inverse transforms The analysed stationary thermomagnetic instability is shown to occur as a result of a supercritical pitchfork bifurcation.

  19. Combining US and Brazilian microsatellite data for a meta-analysis of sheep (Ovis aries) breed diversity: facilitating the FAO Global Plan of Action for Conserving Animal Genetic Resources.

    Science.gov (United States)

    Paiva, Samuel Rezende; Mariante, Arthur da Silva; Blackburn, Harvey D

    2011-01-01

    Microsatellites are commonly used to understand genetic diversity among livestock populations. Nevertheless, most studies have involved the processing of samples in one laboratory or with common standards across laboratories. Our objective was to identify an approach to facilitate the merger of microsatellite data for cross-country comparison of genetic resources when samples were not evaluated in a single laboratory. Eleven microsatellites were included in the analysis of 13 US and 9 Brazilian sheep breeds (N = 706). A Bayesian approach was selected and evaluated with and without a shared set of samples analyzed by each country. All markers had a posterior probability of greater than 0.5, which was higher than predicted as reasonable by the software used. Sensitivity analysis indicated no difference between results with or without shared samples. Cluster analysis showed breeds to be partitioned by functional groups of hair, meat, or wool types (K = 7 and 12 of STRUCTURE). Cross-country comparison of hair breeds indicated substantial genetic distances and within breed variability. The selected approach can facilitate the merger and analysis of microsatellite data for cross-country comparison and extend the utility of previously collected molecular markers. In addition, the result of this type of analysis can be used in new and existing conservation programs.

  20. Covariant Lyapunov Vectors of a Quasi-geostrophic Baroclinic Model: Analysis of Instabilities and Feedbacks

    Science.gov (United States)

    Schubert, Sebastian; Lucarini, Valerio

    2016-04-01

    The classical approach for studying atmospheric variability is based on defining a background state and studying the linear stability of the small fluctuations around such a state. Weakly non-linear theories can be constructed using higher order expansions terms. While these methods have undoubtedly great value for elucidating the relevant physical processes, they are unable to follow the dynamics of a turbulent atmosphere. We provide a first example of extension of the classical stability analysis to a non-linearly evolving quasi-geostrophic flow. The so-called covariant Lyapunov vectors (CLVs) provide a covariant basis describing the directions of exponential expansion and decay of perturbations to the non-linear trajectory of the flow. We use such a formalism to re-examine the basic barotropic and baroclinic processes of the atmosphere with a quasi-geostrophic beta-plane two-layer model in a periodic channel driven by a forced meridional temperature gradient ΔT . We explore three settings of ΔT , representative of relatively weak turbulence, well-developed turbulence, and intermediate conditions. We construct the Lorenz energy cycle for each CLV describing the energy exchanges with the background state. A positive baroclinic conversion rate is a necessary but not sufficient condition of instability. Barotropic instability is present only for few very unstable CLVs for large values of ΔT. Slowly growing and decaying hydrodynamic Lyapunov modes closely mirror the properties of the background flow. Following classical necessary conditions for barotropic/baroclinic instability, we find a clear relationship between the properties of the eddy fluxes of a CLV and its instability. CLVs with positive baroclinic conversion seem to form a set of modes for constructing a reduced model of the atmosphere dynamics.

  1. Analysis of Genomic Microsatellite Sequence and Development of SSR Markers in Metasequoia glyptostroboides%水杉基因组微卫星分析及标记开发

    Institute of Scientific and Technical Information of China (English)

    张新叶; 张亚东; 彭婵; 宋丛文; 杨彦伶

    2013-01-01

    In this paper, the partial genome of Metasequoia glyptostroboides, a rare plant, was sequenced by using the ROCHE-454 GLX high-throughput sequencing platform. Through sequence assembly and microsatellite finding, 1 965 microsatellite loci were obtained in the sequence and the repeat unit length was 2 - 5 base pairs, by which 921 pairs of primer were designed with the Primer 3 Plus software. Analysis of these microsatellite sequences showed that tetranucleotide microsatellite was the most abundant, accounting for 38.8% of the total repeat sequences, followed by dinucleotide (31.8%), trinucleotide (22%) and pentanucleotide (7.4%) in the M. glyptostroboides genome. Among the dinucleotide repeat types, AG type was the most, accounting for 13.9% of total repeats and 43.8% of dinucleotide repeats. In the eight trinucleotide repeat types, AAG type accounted for 8.3% of total repeats and 37.7% of trinucleotide repeats, followed by ATG (23.1%), AAC (16.%) and AAT (13.0%). The analysis of different lengths of the microsatellite repeat unit showed that the most abundant variants were dinucleotide microsatellite and there were 23 different types of repeat lengths, followed by the tetranucleotide repeat (10 types), trinucleotide repeat (8 types) and pentanucleotide repeat (3 types). The validation of SSR markers showed that, 87 pairs brought about clear products and 46 pairs had polymorphic products, accounting for 62. 14% and 32.86% out of the 140 primer pairs,respectively.

  2. Helicobacter pylori infection generates genetic instability in gastric cells

    DEFF Research Database (Denmark)

    Machado, Ana Manuel; Figueiredo, C.; Seruca, R.

    2010-01-01

    The discovery that Helicobacter pylori is associated with gastric cancer has led to numerous studies that investigate the mechanisms by which H. pylori induces carcinogenesis. Gastric cancer shows genetic instability both in nuclear and mitochondrial DNA, besides impairment of important DNA repair...... of the host, such as oxidative damage, methylation, chromosomal instability, microsatellite instability, and mutations. Interestingly, H. pylori infection generates genetic instability in nuclear and mitochondrial DNA. Based on the reviewed literature we conclude that H. pylori infection promotes gastric...

  3. Microsatellite isolation and marker development in carrot - genomic distribution, linkage mapping, genetic diversity analysis and marker transferability across Apiaceae

    Directory of Open Access Journals (Sweden)

    Yildiz Mehtap

    2011-08-01

    Full Text Available Abstract Background The Apiaceae family includes several vegetable and spice crop species among which carrot is the most economically important member, with ~21 million tons produced yearly worldwide. Despite its importance, molecular resources in this species are relatively underdeveloped. The availability of informative, polymorphic, and robust PCR-based markers, such as microsatellites (or SSRs, will facilitate genetics and breeding of carrot and other Apiaceae, including integration of linkage maps, tagging of phenotypic traits and assisting positional gene cloning. Thus, with the purpose of isolating carrot microsatellites, two different strategies were used; a hybridization-based library enrichment for SSRs, and bioinformatic mining of SSRs in BAC-end sequence and EST sequence databases. This work reports on the development of 300 carrot SSR markers and their characterization at various levels. Results Evaluation of microsatellites isolated from both DNA sources in subsets of 7 carrot F2 mapping populations revealed that SSRs from the hybridization-based method were longer, had more repeat units and were more polymorphic than SSRs isolated by sequence search. Overall, 196 SSRs (65.1% were polymorphic in at least one mapping population, and the percentage of polymophic SSRs across F2 populations ranged from 17.8 to 24.7. Polymorphic markers in one family were evaluated in the entire F2, allowing the genetic mapping of 55 SSRs (38 codominant onto the carrot reference map. The SSR loci were distributed throughout all 9 carrot linkage groups (LGs, with 2 to 9 SSRs/LG. In addition, SSR evaluations in carrot-related taxa indicated that a significant fraction of the carrot SSRs transfer successfully across Apiaceae, with heterologous amplification success rate decreasing with the target-species evolutionary distance from carrot. SSR diversity evaluated in a collection of 65 D. carota accessions revealed a high level of polymorphism for these

  4. Gastric cancers of Western European and African patients show different patterns of genomic instability

    Directory of Open Access Journals (Sweden)

    Mulder Chris JJ

    2011-01-01

    Full Text Available Abstract Background Infection with H. pylori is important in the etiology of gastric cancer. Gastric cancer is infrequent in Africa, despite high frequencies of H. pylori infection, referred to as the African enigma. Variation in environmental and host factors influencing gastric cancer risk between different populations have been reported but little is known about the biological differences between gastric cancers from different geographic locations. We aim to study genomic instability patterns of gastric cancers obtained from patients from United Kingdom (UK and South Africa (SA, in an attempt to support the African enigma hypothesis at the biological level. Methods DNA was isolated from 67 gastric adenocarcinomas, 33 UK patients, 9 Caucasian SA patients and 25 native SA patients. Microsatellite instability and chromosomal instability were analyzed by PCR and microarray comparative genomic hybridization, respectively. Data was analyzed by supervised univariate and multivariate analyses as well as unsupervised hierarchical cluster analysis. Results Tumors from Caucasian and native SA patients showed significantly more microsatellite instable tumors (p Conclusions Gastric cancers from SA and UK patients show differences in genetic instability patterns, indicating possible different biological mechanisms in patients from different geographical origin. This is of future clinical relevance for stratification of gastric cancer therapy.

  5. Genetic restoration of a stocked brown trout Salmo trutta population using microsatellite DNA analysis of historical and contemporary samples

    DEFF Research Database (Denmark)

    Hansen, Michael Møller; Bekkevold, Dorte; Jensen, L.F.;

    2006-01-01

    -admixed individuals nevertheless remained in the wild-caught samples. In addition, two resident populations in isolated tributaries were found to be indigenous. The indigenous anadromous individuals from the Skjern River were unlikely to have been recruited from either the isolated tributary populations......1. Gene flow from domesticated to wild populations is a major threat to wild salmonid fish. However, few studies have addressed how populations could be restored after admixture has occurred. We analysed the prospects for restoring the previously intensively stocked brown trout population...... of the Skjern River, Denmark, by identifying remaining non-admixed individuals to be used for supportive breeding. 2. We analysed microsatellite DNA markers in historical (1940-50s) and contemporary (1992-2004) samples from the Skjern River system, from the strain of domesticated trout previously used...

  6. Performance Analysis of Anti-Interference Wireless Packet Networks for LEO Micro-Satellite with Adaptive Nulling Antenna Array

    Institute of Scientific and Technical Information of China (English)

    LIU Hai-tao; HAN Fang-jing; WAN Jian-wei

    2006-01-01

    Information integrity is key to successful operations in intricacy environments in the future, especially when strong interferences exist. This paper presents the design of a novel wireless packet network receiver system for Low Earth Orbit (LEO) micro-satellites with adaptive nulling antenna arrays. It uses three types of interference suppression in cascade: namely spread spectrum, adaptive array nulling, and transform domain filtering. This paper proposes a pilot channel-aided method in order to make full advantage of this arrangement, and analyzes its throughput and delay performance using the Markov chain model. Our results show that this method can achieve excellent delay and throughput performance: When the number of array antenna is 8, its throughput increase relative to the standard Slot-ALOHA protocol is 125 %.

  7. Analysis of Genetic Diversity and Relationships in a Tunisian Fig (Ficus carica) Germplasm Collection by Random Amplified Microsatellite Polymorphisms

    Institute of Scientific and Technical Information of China (English)

    Khaled Chatti; Olfa Saddoud; Amel Salhi-Hannachi; Messaoud Mars; Mohamed Marrakchi; Mokhtar Trifi

    2007-01-01

    The random amplified mirosatellite polymorphism method was performed in a set of Tunisian fig landraces using eighteen primer combinations. Atotal of sixty three random amplified microsatellite polymorphism (RAMPO) markers were scored and used either to assess the genetic diversity in these cultivars or to detect cases of mislabeling. Opportunely, data proved that the designed procedure constitutes an attractive and fast method with low costs and prevents radio exposure. As a result, we have identified the primer combinations that are the most efficient to detect genetic polymorphism in this crop. Therefore, the derived unweighted pair-group method with arithmetic averages (UPGMA) dendrogram illustrates the genetic divergence among the landraces studied and exhibits a typically continuous variation. Moreover, no evident correlation between the sexes of trees was observed. In addition, using these markers, discrimination between landraces has been achieved. Thus, random amplified mirosatellite polymorphism is proved to be powerful for characterizing the local fig germplasm.

  8. Analysis of microsatellite polymorphisms within the GLC1F locus in Japanese patients with normal tension glaucoma

    Science.gov (United States)

    Murakami, Kaori; Ota, Masao; Shiota, Tomoko; Nomura, Naoko; Kashiwagi, Kenji; Mabuchi, Fumihiko; Iijima, Hiroyuki; Kawase, Kazuhide; Yamamoto, Tetsuya; Nakamura, Makoto; Negi, Akira; Sagara, Takeshi; Nishida, Teruo; Inatani, Masaru; Tanihara, Hidenobu; Aihara, Makoto; Araie, Makoto; Fukuchi, Takeo; Abe, Haruki; Higashide, Tomomi; Sugiyama, Kazuhisa; Kanamoto, Takashi; Kiuchi, Yoshiaki; Iwase, Aiko; Ohno, Shigeaki; Inoko, Hidetoshi; Mizuki, Nobuhisa

    2010-01-01

    Purpose To investigate whether the GLC1F locus is associated with normal tension glaucoma (NTG) in Japanese patients. Methods We recruited 242 unrelated Japanese subjects, including, 141 NTG patients and 101 healthy controls. The patients exhibiting a comparatively early onset were selected as they suggest that genetic factors may show stronger involvement. Genotyping and assessment of allelic diversity was performed on 11 highly polymorphic microsatellite markers in and around the GLC1F locus. Results Individuals carrying the 163 allele of D7S1277i had a statistically significant increased risk of NTG (p=0.0013, pc=0.016, OR=2.47, 95%CI=1.42–4.30). None of the other markers identified significant loci (pc>0.05) after Bonferroni’s correction. Conclusions These findings suggested that the genes in the GLC1F locus may be associated with the pathogenesis of NTG. PMID:20309402

  9. Genetic analysis of QTL for eye cross and eye diameter in common carp (Cyprinus carpio L.) using microsatellites and SNPs.

    Science.gov (United States)

    Jin, S B; Zhang, X F; Lu, J G; Fu, H T; Jia, Z Y; Sun, X W

    2015-04-17

    A group of 107 F1 hybrid common carp was used to construct a linkage map using JoinMap 4.0. A total of 4877 microsatellite and single nucleotide polymorphism (SNP) markers isolated from a genomic library (978 microsatellite and 3899 SNP markers) were assigned to construct the genetic map, which comprised 50 linkage groups. The total length of the linkage map for the common carp was 4775.90 cM with an average distance between markers of 0.98 cM. Ten quantitative trait loci (QTL) were associated with eye diameter, corresponding to 10.5-57.2% of the total phenotypic variation. Twenty QTL were related to eye cross, contributing to 10.8-36.9% of the total phenotypic variation. Two QTL for eye diameter and four QTL for eye cross each accounted for more than 20% of the total phenotypic variation and were considered to be major QTL. One growth factor related to eye diameter was observed on LG10 of the common carp genome, and three growth factors related to eye cross were observed on LG10, LG35, and LG44 of the common carp genome. The significant positive relationship of eye cross and eye diameter with other commercial traits suggests that eye diameter and eye cross can be used to assist in indirect selection for many commercial traits, particularly body weight. Thus, the growth factor for eye cross may also contribute to the growth of body weight, implying that aggregate breeding could have multiple effects. These findings provide information for future genetic studies and breeding of common carp.

  10. Gas Evolution Dynamics in Godunov-Type Schemes and Analysis of Numerical Shock Instability

    Science.gov (United States)

    Xu, Kun

    1999-01-01

    In this paper we are going to study the gas evolution dynamics of the exact and approximate Riemann solvers, e.g., the Flux Vector Splitting (FVS) and the Flux Difference Splitting (FDS) schemes. Since the FVS scheme and the Kinetic Flux Vector Splitting (KFVS) scheme have the same physical mechanism and similar flux function, based on the analysis of the discretized KFVS scheme the weakness and advantage of the FVS scheme are closely observed. The subtle dissipative mechanism of the Godunov method in the 2D case is also analyzed, and the physical reason for shock instability, i.e., carbuncle phenomena and odd-even decoupling, is presented.

  11. Further analysis of the effects of baffles on combustion instability. [computer techniques

    Science.gov (United States)

    Oberg, C. L.; Schuman, M. D.

    1975-01-01

    A computerized analytical model, developed to predict the effects of baffles on combustion instability, was modified in an effort to improve the ability to properly predict stability effects. The model was modified: (1) to replace a single spatially-averaged response factor by separate values for each baffle compartment; (2) to calculate the axial component of the acoustic energy flux, and (3) to permit analysis of traveling waves in a thin annular chamber. Allowance for separate average response factors in each baffle compartment was found to significantly affect the predicted results. With this modification, an optimum baffle length was predicted which gave maximum stability.

  12. Magnetohydrodynamic instabilities in rotating and precessing sheared flows: an asymptotic analysis.

    Science.gov (United States)

    Salhi, A; Lehner, T; Cambon, C

    2010-07-01

    Linear magnetohydrodynamic instabilities are studied analytically in the case of unbounded inviscid and electrically conducting flows that are submitted to both rotation and precession with shear in an external magnetic field. For given rotation and precession the possible configurations of the shear and of the magnetic field and their interplay are imposed by the "admissibility" condition (i.e., the base flow must be a solution of the magnetohydrodynamic Euler equations): we show that an "admissible" basic magnetic field must align with the basic absolute vorticity. For these flows with elliptical streamlines due to precession we undertake an analytical stability analysis for the corresponding Floquet system, by using an asymptotic expansion into the small parameter ε (ratio of precession to rotation frequencies) by a method first developed in the magnetoelliptical instabilities study by Lebovitz and Zweibel [Astrophys. J. 609, 301 (2004)]10.1086/420972. The present stability analysis is performed into a suitable frame that is obtained by a systematic change of variables guided by symmetry and the existence of invariants of motion. The obtained Floquet system depends on three parameters: ε , η (ratio of the cyclotron frequency to the rotation frequency) and χ=cos α, with α being a characteristic angle which, for circular streamlines, ε=0, identifies with the angle between the wave vector and the axis of the solid body rotation. We look at the various (centrifugal or precessional) resonant couplings between the three present modes: hydrodynamical (inertial), magnetic (Alfvén), and mixed (magnetoinertial) modes by computing analytically to leading order in ε the instabilities by estimating their threshold, growth rate, and maximum growth rate and their bandwidths as functions of ε, η, and χ. We show that the subharmonic "magnetic" mode appears only for η>square root of 5/2 and at large η (>1) the maximal growth rate of both the "hydrodynamic" and

  13. Genetic Monitoring of PLCε Knockout Mice by Microsatellite DNA Analysis%PLCε基因敲除小鼠微卫星DNA遗传监测分析

    Institute of Scientific and Technical Information of China (English)

    崔智; 李晓娟; 白云峰; 侯俊; 戴广海; 李瑞生

    2012-01-01

    Objective To determine the genetic characteristics of PLCe knockout mice by polymorphic microsatellite DNA loci analysis. Methods Genome DNA of 28 PLCe gene knockout mice were amplified by PCR using screening 15 microsatellite DNA loci, and population genetic diversity was identified by gene fragments. Results Among 13 microsatellite DNA loci (DlMit365, D3Mit51 , D4Mit235 , D6MM02, D7Mit281 , D8Mitll3, D9Mit23 , D10MM80, D13Mit88,D16Mitl45,D17Mit36,D18Mit94,D19Mit97),each locus of electrophoresis distance of DNA fragments in the 28 PLCe gene knockout mice kept consistent and presented monomorphism , indicating the genetic stability. However the two loci Dq (knock genotype) and Dy (wild-type) were used to discriminate 28 PLCe gene knockout mice by PCR amplification. Among them, 6 mice were of gene knock mice, 7 mice were of wild-type mice, and 15 mice were of heterozygous type. Conclusions The method of microsatellite marker analysis can be used to monitor population genetic quality and accurately distinguish different genotypes of mice , providing a feasible method for the detection of genetic quality%目的 利用多态性微卫星DNA位点分析PLCε基因敲除小鼠的遗传特性.方法 用所筛选的15个微卫星DNA位点对28只PLCε基因敲除小鼠的DNA进行了PCR扩增,通过基因片段大小来分析群体的遗传多样性.结果 13个微卫星DNA位点中(D1Mit365、D3Mit51、D4Mit235、D6Mit102、D7Mit281、D8Mit113、D9Mit23、D10Mit180、D13Mit88、D16Mit145、D17Mit36、D18Mit94、D19Mit97)每个位点的28只小鼠DNA片段泳动距离一致,呈现单态性,表明该群体符合近交系的遗传特性;而利用Dq(敲基因型)和Dy(野生型)两个位点对28只小鼠的PCR扩增结果进行了鉴别分析,其中敲除基因型小鼠为6只;野生型为7只;杂合型为15只.结论 利用微卫星标记技术可以对群体进行遗传质量监测,并能有效地鉴别不同的基因型,为小鼠的遗传质量监测提供了一种可行的方法.

  14. Investigation of the association between the GLC3A locus and normal tension glaucoma in Japanese patients by microsatellite analysis

    Directory of Open Access Journals (Sweden)

    M Kamio

    2009-01-01

    (NTG in Japanese patients.Materials and Methods: One hundred forty-two Japanese patients with NTG and 101 Japanese healthy controls were recruited. Patients exhibiting a comparatively early onset were selected as this suggests that genetic factors may show stronger involvement. Genotyping and assessment of allelic diversity was performed on 13 highly polymorphic microsatellite markers in and around the GLC3A locus.Results: There were decreased frequencies of the 444 allele of D2S0416i and the 258 allele of D2S0425i in cases compared to controls (P = 0.022 and P = 0.034, respectively. However, this statistical significance disappeared when corrected (Pc > 0.05. We did not find any significant association between the remaining 11 microsatellite markers, including D2S177, which may be associated with CYP1B1, and NTG (P > 0.05.Conclusions: Our study showed no association between the GLCA3 locus and NTG, suggesting that the CYP1B1 gene, which is reportedly involved in a range of glaucoma phenotypes, may not be an associated factor in the pathogenesis of NTG.Keywords: GLCA3, microsatellite, normal tension glaucoma, polymorphism

  15. Evidence for widespread convergent evolution around human microsatellites.

    Directory of Open Access Journals (Sweden)

    Edward J Vowles

    2004-08-01

    Full Text Available Microsatellites are a major component of the human genome, and their evolution has been much studied. However, the evolution of microsatellite flanking sequences has received less attention, with reports of both high and low mutation rates and of a tendency for microsatellites to cluster. From the human genome we generated a database of many thousands of (AC(n flanking sequences within which we searched for common characteristics. Sequences flanking microsatellites of similar length show remarkable levels of convergent evolution, indicating shared mutational biases. These biases extend 25-50 bases either side of the microsatellite and may therefore affect more than 30% of the entire genome. To explore the extent and absolute strength of these effects, we quantified the observed convergence. We also compared homologous human and chimpanzee loci to look for evidence of changes in mutation rate around microsatellites. Most models of DNA sequence evolution assume that mutations are independent and occur randomly. Allowances may be made for sites mutating at different rates and for general mutation biases such as the faster rate of transitions over transversions. Our analysis suggests that these models may be inadequate, in that proximity to even very short microsatellites may alter the rate and distribution of mutations that occur. The elevated local mutation rate combined with sequence convergence, both of which we find evidence for, also provide a possible resolution for the apparently contradictory inferences of mutation rates in microsatellite flanking sequences.

  16. Quantitative Proteomic Analysis of Mitochondrial Proteins Reveals Pro-Survival Mechanisms in the Perpetuation of Radiation-Induced Genomic Instability

    Energy Technology Data Exchange (ETDEWEB)

    Thomas, Stefani N.; Waters, Katrina M.; Morgan, William F.; Yang, Austin; Baulch, Janet E.

    2012-07-26

    Radiation induced genomic instability is a well-studied phenomenon that is measured as mitotically heritable genetic alterations observed in the progeny of an irradiated cell. The mechanisms that perpetuate this instability are unclear, however, a role for chronic oxidative stress has consistently been demonstrated. In the chromosomally unstable LS12 cell line, oxidative stress and genomic instability were correlated with mitochondrial dysfunction. To clarify this mitochondrial dysfunction and gain insight into the mechanisms underlying radiation induced genomic instability we have evaluated the mitochondrial sub-proteome and performed quantitative mass spectrometry (MS) analysis of LS12 cells. Of 98 quantified mitochondrial proteins, 17 met criteria for fold changes and reproducibility; and 11 were statistically significant in comparison with the stable parental GM10115 cell line. Previous observations implicated defects in the electron transport chain (ETC) in the LS12 cell mitochondrial dysfunction. Proteomic analysis supports these observations, demonstrating significantly reduced levels of mitochondrial cytochrome c, the intermediary between complexes III and IV of the ETC. Results also suggest that LS12 cells compensate for ETC dysfunction and oxidative stress through increased levels of tricarboxylic acid cycle enzymes and up-regulation of proteins that protect against oxidative stress and apoptosis. More than one cellular defect is likely to contribute to the genomic instability phenotype. These data suggest that LS12 cells have adapted mechanisms that allow survival under sub-optimal conditions of oxidative stress and compromised mitochondrial function to perpetuate genomic instability.

  17. Assessment of Slope Instability and Risk Analysis of Road Cut Slopes in Lashotor Pass, Iran

    Directory of Open Access Journals (Sweden)

    Mohammad Hossein Taherynia

    2014-01-01

    Full Text Available Assessment of the stability of natural and artificial rock slopes is an important topic in the rock mechanics sciences. One of the most widely used methods for this purpose is the classification of the slope rock mass. In the recent decades, several rock slope classification systems are presented by many researchers. Each one of these rock mass classification systems uses different parameters and rating systems. These differences are due to the diversity of affecting parameters and the degree of influence on the rock slope stability. Another important point in rock slope stability is appraisal hazard and risk analysis. In the risk analysis, the degree of danger of rock slope instability is determined. The Lashotor pass is located in the Shiraz-Isfahan highway in Iran. Field surveys indicate that there are high potentialities of instability in the road cut slopes of the Lashotor pass. In the current paper, the stability of the rock slopes in the Lashotor pass is studied comprehensively with different classification methods. For risk analyses, we estimated dangerous area by use of the RocFall software. Furthermore, the dangers of falling rocks for the vehicles passing the Lashotor pass are estimated according to rockfall hazard rating system.

  18. A new instability index for unstable mode selection in squeal prediction by complex eigenvalue analysis

    Science.gov (United States)

    Brunetti, J.; Massi, F.; D`Ambrogio, W.; Berthier, Y.

    2016-09-01

    During these last decades the modal instability of systems, generated by frictional contact forces, has been the subject of a huge amount of works in friction induced vibration literature. Linear and nonlinear numerical analyses have been largely investigated to predict and reproduce squeal vibrations. While nonlinear transient analysis needs large computational efforts, results of Complex Eigenvalue Analysis (CEA) suffer from an over-prediction issue and it is not able to predict correctly the mode that will become effectively unstable in case of several unstable eigenvalues. Because the CEA has been adopted as an efficient tool for brake design, a more reliable index is here proposed, from the CEA outputs and energetic considerations, to identify the mode that will become effectively unstable. A modular lumped model is developed to reproduce friction induced vibrations. The use of the eigenvalue real part, as discriminant of the system instability, is here combined with information coming from the eigenvectors, projected on the equilibrium position, to account for the energy flows involved in the squeal phenomena. This approach allows to define a Modal Absorption Index (MAI). The MAI allows for comparing unstable modes of the same system and is applied in this paper to predict, by CEA outputs, the unstable mode that will effectively result in squeal vibrations.

  19. Time domain analysis of superradiant instability for the charged stringy black hole–mirror system

    Directory of Open Access Journals (Sweden)

    Ran Li

    2015-11-01

    Full Text Available It has been proved that the charged stringy black holes are stable under the perturbations of massive charged scalar fields. However, superradiant instability can be generated by adding the mirror-like boundary condition to the composed system of charged stringy black hole and scalar field. The unstable boxed quasinormal modes have been calculated by using both analytical and numerical methods. In this paper, we further provide a time domain analysis by performing a long time evolution of charged scalar field configuration in the background of the charged stringy black hole with the mirror-like boundary condition imposed. We have used the ingoing Eddington–Finkelstein coordinates to derive the evolution equation, and adopted Pseudo-spectral method and the forth-order Runge–Kutta method to evolve the scalar field with the initial Gaussian wave packet. It is shown by our numerical scheme that Fourier transforming the evolution data coincides well with the unstable modes computed from frequency domain analysis. The existence of the rapid growth mode makes the charged stringy black hole a good test ground to study the nonlinear development of superradiant instability.

  20. Time domain analysis of superradiant instability for the charged stringy black hole-mirror system

    Science.gov (United States)

    Li, Ran; Tian, Yu; Zhang, Hongbao; Zhao, Junkun

    2015-11-01

    It has been proved that the charged stringy black holes are stable under the perturbations of massive charged scalar fields. However, superradiant instability can be generated by adding the mirror-like boundary condition to the composed system of charged stringy black hole and scalar field. The unstable boxed quasinormal modes have been calculated by using both analytical and numerical methods. In this paper, we further provide a time domain analysis by performing a long time evolution of charged scalar field configuration in the background of the charged stringy black hole with the mirror-like boundary condition imposed. We have used the ingoing Eddington-Finkelstein coordinates to derive the evolution equation, and adopted Pseudo-spectral method and the forth-order Runge-Kutta method to evolve the scalar field with the initial Gaussian wave packet. It is shown by our numerical scheme that Fourier transforming the evolution data coincides well with the unstable modes computed from frequency domain analysis. The existence of the rapid growth mode makes the charged stringy black hole a good test ground to study the nonlinear development of superradiant instability.

  1. Time domain analysis of superradiant instability for the charged stringy black hole–mirror system

    Energy Technology Data Exchange (ETDEWEB)

    Li, Ran, E-mail: 021149@htu.cn [Department of Physics, Henan Normal University, Xinxiang 453007 (China); Tian, Yu, E-mail: ytian@ucas.ac.cn [School of Physics, University of Chinese Academy of Sciences, Beijing 100049 (China); State Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing 100190 (China); Zhang, Hongbao, E-mail: hzhang@vub.ac.be [Department of Physics, Beijing Normal University, Beijing 100875 (China); Theoretische Natuurkunde, Vrije Universiteit Brussel, and The International Solvay Institutes, Pleinlaan 2, B-1050 Brussels (Belgium); Zhao, Junkun, E-mail: zhaojkun1991@163.com [Department of Physics, Henan Normal University, Xinxiang 453007 (China)

    2015-11-12

    It has been proved that the charged stringy black holes are stable under the perturbations of massive charged scalar fields. However, superradiant instability can be generated by adding the mirror-like boundary condition to the composed system of charged stringy black hole and scalar field. The unstable boxed quasinormal modes have been calculated by using both analytical and numerical methods. In this paper, we further provide a time domain analysis by performing a long time evolution of charged scalar field configuration in the background of the charged stringy black hole with the mirror-like boundary condition imposed. We have used the ingoing Eddington–Finkelstein coordinates to derive the evolution equation, and adopted Pseudo-spectral method and the forth-order Runge–Kutta method to evolve the scalar field with the initial Gaussian wave packet. It is shown by our numerical scheme that Fourier transforming the evolution data coincides well with the unstable modes computed from frequency domain analysis. The existence of the rapid growth mode makes the charged stringy black hole a good test ground to study the nonlinear development of superradiant instability.

  2. Analysis of rainfall-induced slope instability using a field of local factor of safety

    Science.gov (United States)

    Lu, Ning; Şener-Kaya, Başak; Wayllace, Alexandra; Godt, Jonathan W.

    2012-01-01

    Slope-stability analyses are mostly conducted by identifying or assuming a potential failure surface and assessing the factor of safety (FS) of that surface. This approach of assigning a single FS to a potentially unstable slope provides little insight on where the failure initiates or the ultimate geometry and location of a landslide rupture surface. We describe a method to quantify a scalar field of FS based on the concept of the Coulomb stress and the shift in the state of stress toward failure that results from rainfall infiltration. The FS at each point within a hillslope is called the local factor of safety (LFS) and is defined as the ratio of the Coulomb stress at the current state of stress to the Coulomb stress of the potential failure state under the Mohr-Coulomb criterion. Comparative assessment with limit-equilibrium and hybrid finite element limit-equilibrium methods show that the proposed LFS is consistent with these approaches and yields additional insight into the geometry and location of the potential failure surface and how instability may initiate and evolve with changes in pore water conditions. Quantitative assessments applying the new LFS field method to slopes under infiltration conditions demonstrate that the LFS has the potential to overcome several major limitations in the classical FS methodologies such as the shape of the failure surface and the inherent underestimation of slope instability. Comparison with infinite-slope methods, including a recent extension to variably saturated conditions, shows further enhancement in assessing shallow landslide occurrence using the LFS methodology. Although we use only a linear elastic solution for the state of stress with no post-failure analysis that require more sophisticated elastoplastic or other theories, the LFS provides a new means to quantify the potential instability zones in hillslopes under variably saturated conditions using stress-field based methods.

  3. Analysis of the genetic diversity between Gentile di Puglia, Sopravissana and Sarda sheep breeds using microsatellite markers

    Directory of Open Access Journals (Sweden)

    Gennaro Catillo

    2010-01-01

    Full Text Available Two Italian sheep breeds – Gentile di Puglia and Sopravissana – have undergone a consistent decline in numbers and have been widely substituted by the Sarda breed, which gives higher milk yield. With the aim to provide a basis for con- servation decisions, the genetic variability of the three breeds was investigated in this study. DNA of 60 animals was PCR amplified at the following microsatellite loci: CSSM43, CSSM47, CSSM60, TGLA110, TGLA122, TGLA126, TGLA377, ETH3, ETH10, ETH225, NRAMP1, OARCP20 and SPS115. Allele frequencies, gene diversity and genetic distances were calculat- ed. The highest differences in allele frequencies were found at the following loci: TGLA377, TGLA122, NRAMP1, OARCP20 and ETH3, while at the other loci the most frequent alleles were the same. The average inbreeding rate was 0.156 in the Gentile di Puglia, 0.158 in the Sopravissana and 0.137 in the Sarda. Average gene diversity of the analysed microsatel- lites was 0.59. Genetic distance between Gentile di Puglia and Sopravissana (0.081 indicates moderate differentiation; distances between the Sarda and the endangered breeds – 0.111 from the Gentile di Puglia and 0.107 from the Sopravissana - indicate a medium-high differentiation rate. The disappearance of the two less productive breeds would entail a consistent loss of genetic diversity. The inbreeding values are low enough to allow the implementation of sound conservation programmes.

  4. Genetic diversity within and among four South European native horse breeds based on microsatellite DNA analysis: implications for conservation.

    Science.gov (United States)

    Solis, A; Jugo, B M; Mériaux, J C; Iriondo, M; Mazón, L I; Aguirre, A I; Vicario, A; Estomba, A

    2005-01-01

    In the present study, genetic analyses of diversity and differentiation were performed on four Basque-Navarrese semiferal native horse breeds. In total, 417 animals were genotyped for 12 microsatellite markers. Mean heterozygosity was higher than in other horse breeds, surely as a consequence of management. Although the population size of some of these breeds has declined appreciably in the past century, no genetic bottleneck was detected in any of the breeds, possibly because it was not narrow enough to be detectable. In the phylogenetic tree, the Jaca Navarra breed was very similar to the Pottoka, but appeared to stand in an intermediate position between this and the meat breeds. Assuming that Pottoka is the breed less affected by admixture, the others gradually distanced themselves from it through varying influences from outside breeds, among other factors. In a comparative study with other breeds, the French breeds Ardanais, Comtois, and Breton were the closest to the four native breeds. Three different approaches for evaluating the distribution of genetic diversity were applied. The high intrabreed variability of Euskal Herriko Mendiko Zaldia (EHMZ) was pointed out in these analyses. In our opinion, cultural, economic, and scientific factors should also be considered in the management of these horse breeds.

  5. Genetic diversity and differentiation of masu salmon (Oncorhynchus masou masou) between and within cultured populations inferred from microsatellite DNA analysis

    Institute of Scientific and Technical Information of China (English)

    Zhiying JIA; Yuyong ZHANG; Shuqiang CHEN; Lianyu SHI

    2012-01-01

    Masu salmon,Oncorhynchus masou masou,is one of the most valuable fishery species that has been introduced to China,though to date no studies on the genetic diversity and genetic relationship among hatchery populations has been performed with molecular markers.We undertook such a study and sampled 120 individuals from three hatchery stocks and analyzed 20 microsatellite loci.All loci were polymorphic and a total of 91 alleles were detected.A relatively low level of genetic diversity was revealed with effective number of allele of 3.1094,3.3299 and 3.1894 and expected heterozygosity of 0.6600,0.6648 and 0.6638 in the three stocks,respectively.Deviations from Hardy-Weinberg equilibrium were found due to heterozygote deficit.Accordingly,evidence of genetic bottlenecks were found in the three stocks.An individual assignment test demonstrated that 85% of individuals were correctly assigned into their original stocks.Pairwise Fst revealed that significant differentiation occurred between these three stocks.The results of the study indicated that disequilibrium of genetic structure and differentiation has occurred in all three stocks.This information collectively provides a basis for measures to avoid of loss of genetic diversity and introgression in Chinese aquaculture.

  6. Analysis of Rayleigh-Taylor Instability Part I: Bubble and Spike Count

    Energy Technology Data Exchange (ETDEWEB)

    Kamath, C; Gezahegne, A; Miller, P

    2006-08-08

    The use of high-performance computers to simulate hydrodynamic instabilities has resulted in the generation of massive amounts of data. One aspect of the analysis of this data involves the identification and characterization of coherent structures known as ''bubbles'' and ''spikes''. This can be a challenge as there is no precise definition of these structures, and the large size of the data, as well as its distributed nature, precludes any extensive experimentation with different definitions and analysis algorithms. In this report, we describe the use of image processing techniques to identify and count bubbles and spikes in the Rayleigh-Taylor instability, which occurs when an initially perturbed interface between a heavier fluid and a lighter fluid is allowed to grow under the influence of gravity. We analyze data from two simulations, one a large-eddy simulation with 30 terabytes of analysis data, and the other a direct numerical simulation with 80 terabytes of analysis data. We consider different techniques to first convert the three-dimensional data to two dimensions and then count the structures of interest in the two-dimensional data. Our analysis of the bubble and spike counts over time indicates that there are four distinct regimes in the process of the mixing of the two fluids, starting from the initial linear stage, followed by the non-linear stage with weak turbulence, the mixing transition stage, and the final stage of strong turbulence. We also show that our results are relatively insensitive to the parameters used in our algorithms.

  7. Theoretical analysis of mode instability in high-power fiber amplifiers

    DEFF Research Database (Denmark)

    Hansen, Kristian Rymann; Alkeskjold, Thomas Tanggaard; Broeng, Jes;

    2013-01-01

    We present a simple theoretical model of transverse mode instability in high-power rare-earth doped fiber amplifiers. The model shows that efficient power transfer between the fundamental and higher-order modes of the fiber can be induced by a nonlinear interaction mediated through the thermo......-optic effect, leading to transverse mode instability. The temporal and spectral characteristics of the instability dynamics are investigated, and it is shown that the instability can be seeded by both quantum noise and signal intensity noise, while pure phase noise of the signal does not induce instability...

  8. Functionally relevant microsatellites in sugarcane unigenes

    Directory of Open Access Journals (Sweden)

    Singh Nagendra K

    2010-11-01

    Full Text Available Abstract Background Unigene sequences constitute a rich source of functionally relevant microsatellites. The present study was undertaken to mine the microsatellites in the available unigene sequences of sugarcane for understanding their constitution in the expressed genic component of its complex polyploid/aneuploid genome, assessing their functional significance in silico, determining the extent of allelic diversity at the microsatellite loci and for evaluating their utility in large-scale genotyping applications in sugarcane. Results The average frequency of perfect microsatellite was 1/10.9 kb, while it was 1/44.3 kb for the long and hypervariable class I repeats. GC-rich trinucleotides coding for alanine and the GA-rich dinucleotides were the most abundant microsatellite classes. Out of 15,594 unigenes mined in the study, 767 contained microsatellite repeats and for 672 of these putative functions were determined in silico. The microsatellite repeats were found in the functional domains of proteins encoded by 364 unigenes. Its significance was assessed by establishing the structure-function relationship for the beta-amylase and protein kinase encoding unigenes having repeats in the catalytic domains. A total of 726 allelic variants (7.42 alleles per locus with different repeat lengths were captured precisely for a set of 47 fluorescent dye labeled primers in 36 sugarcane genotypes and five cereal species using the automated fragment analysis system, which suggested the utility of designed primers for rapid, large-scale and high-throughput genotyping applications in sugarcane. Pair-wise similarity ranging from 0.33 to 0.84 with an average of 0.40 revealed a broad genetic base of the Indian varieties in respect of functionally relevant regions of the large and complex sugarcane genome. Conclusion Microsatellite repeats were present in 4.92% of sugarcane unigenes, for most (87.6% of which functions were determined in silico. High level of

  9. Prognostic values of chromosome 18q microsatellite alterations in stage Ⅱ colonic carcinoma

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    AIM: To investigate the prognostic value of chromosome 18q microsatellite alterations (MA) in stage Ⅱ colon cancer. METHODS: One hundred and six patients with sporadic stage Ⅱ colon cancer were enrolled in this study. DNA was extracted from formalin-fixed, paraffin-embedded tumor and adjacent normal mucosal tissue samples. MA, including loss of heterozygosity (LOH) and microsatellite instability (MSI), was analyzed by polymerase chain reaction, polyacrylamide gel-electrophoresis and DNA sequencing at 5 micr...

  10. Dynamical Analysis of Stock Market Instability by Cross-correlation Matrix

    Science.gov (United States)

    Takaishi, Tetsuya

    2016-08-01

    We study stock market instability by using cross-correlations constructed from the return time series of 366 stocks traded on the Tokyo Stock Exchange from January 5, 1998 to December 30, 2013. To investigate the dynamical evolution of the cross-correlations, crosscorrelation matrices are calculated with a rolling window of 400 days. To quantify the volatile market stages where the potential risk is high, we apply the principal components analysis and measure the cumulative risk fraction (CRF), which is the system variance associated with the first few principal components. From the CRF, we detected three volatile market stages corresponding to the bankruptcy of Lehman Brothers, the 2011 Tohoku Region Pacific Coast Earthquake, and the FRB QE3 reduction observation in the study period. We further apply the random matrix theory for the risk analysis and find that the first eigenvector is more equally de-localized when the market is volatile.

  11. Cold gas in cluster cores: Global stability analysis and non-linear simulations of thermal instability

    CERN Document Server

    Choudhury, Prakriti Pal

    2015-01-01

    We perform global linear stability analysis and idealized numerical simulations in global thermal balance to understand the condensation of cold gas from hot/virial atmospheres (coronae), in particular the intracluster medium (ICM). We pay particular attention to geometry (e.g., spherical versus plane-parallel) and the nature of the gravitational potential. Global linear analysis gives a similar value for the fastest growing thermal instability modes in spherical and Cartesian geometries. Simulations and observations suggest that cooling in halos critically depends on the ratio of the cooling time to the free-fall time ($t_{cool}/t_{ff}$). Extended cold gas condenses out of the ICM only if this ratio is smaller than a threshold value close to 10. Previous works highlighted the difference between the nature of cold gas condensation in spherical and plane-parallel atmospheres; namely, cold gas condensation appeared easier in spherical atmospheres. This apparent difference due to geometry arises because the prev...

  12. Microsatellite analysis of Rosa damascena Mill. accessions reveals genetic similarity between genotypes used for rose oil production and old Damask rose varieties.

    Science.gov (United States)

    Rusanov, K; Kovacheva, N; Vosman, B; Zhang, L; Rajapakse, S; Atanassov, A; Atanassov, I

    2005-08-01

    Damask roses are grown in several European and Asiatic countries for rose oil production. Twenty-six oil-bearing Rosa damascena Mill. accessions and 13 garden Damask roses were assayed by molecular markers. Microsatellite genotyping demonstrated that R. damascena Mill. accessions from Bulgaria, Iran, and India and old European Damask rose varieties possess identical microsatellite profiles, suggesting a common origin. At the same time, the data indicated that modern industrial oil rose cultivation is based on a very narrow genepool and that oil rose collections contain many genetically identical accessions. The study of long-term vegetative propagation of the Damask roses also reveals high somatic stability for the microsatellite loci analyzed.

  13. Modal analysis of gravitational instabilities in nearly Keplerian, counter-rotating collisionless discs

    Science.gov (United States)

    Gulati, Mamta; Saini, Tarun Deep

    2017-02-01

    We present a modal analysis of instabilities of counter-rotating, self-gravitating collisionless stellar discs, using the recently introduced modified WKB formulation of spiral density waves for collisionless systems by Gulati & Saini. The discs are assumed to be axisymmetric and in coplanar orbits around a massive object at the common centre of the discs. The mass in both discs is assumed to be much smaller than the mass of the central object. For each disc, the disc particles are assumed to be in near circular orbits. The two discs are coupled to each other gravitationally. The perturbed dynamics of the discs evolves on the order of the precession time-scale of the discs, which is much longer than the Keplerian time-scale. We present results for the azimuthal wavenumber m = 1 and 2, for the full range of disc mass ratio between the prograde and retrograde discs. The eigenspectra are in general complex, therefore all eigenmodes are unstable. Eigenfunctions are radially more compact for m = 1 as compared to m = 2. Pattern speed of eigenmodes is always prograde with respect to the more massive disc. The growth rate of unstable modes increases with increasing mass fraction in the retrograde disc, and decreases with m; therefore, m = 1 instability is likely to play the dominant role in the dynamics of such systems.

  14. FINANCIAL INSTABILITY AND POLITICAL INSTABILITY

    Directory of Open Access Journals (Sweden)

    Ionescu Cristian

    2012-12-01

    Full Text Available There is an important link between the following two variables: financial instability and political instability. Often, the link is bidirectional, so both may influence each other. This is way the lately crisis are becoming larger and increasingly complex. Therefore, the academic environment is simultaneously talking about economic crises, financial crises, political crises, social crises, highlighting the correlation and causality between variables belonging to the economic, financial, political and social areas, with repercussions and spillover effects that extend from one area to another. Given the importance, relevance and the actuality of the ones described above, I consider that at least a theoretical analysis between economic, financial and political factors is needed in order to understand the reality. Thus, this paper aims to find links and connections to complete the picture of the economic reality.

  15. Harmonic Instability Assessment Using State-Space Modeling and Participation Analysis in Inverter-Fed Power Systems

    DEFF Research Database (Denmark)

    Wang, Yanbo; Wang, Xiongfei; Blaabjerg, Frede

    2017-01-01

    This paper presents a harmonic instability analysis method using state-space modeling and participation analysis in the inverter-fed ac power systems. A full-order state-space model for the droop-controlled Distributed Generation (DG) inverter is built first, including the time delay of the digit...

  16. 柑橘全爪螨微卫星位点鉴定与信息分析%Analysis of Microsatellite Loci fromPanonychus citri Based on Enriched Microsatellite Library and Transcriptome Dataset

    Institute of Scientific and Technical Information of China (English)

    魏丹丹; 刘燕; 杜洋; 李刚; 李婷; 袁明龙; 王进军

    2016-01-01

    重复类型,占总数的53.86%;其次为两碱基核心重复类型,占总数的43.36%;而四、五、六碱基重复类型以及复合型的SSR数量均较少,且数量差异不大,共占EST-SSR总数的2.78%。柑橘全爪螨EST-SSR核心重复次数主要集中在5—10次。【结论】采用磁珠富集法,并将酶切、接头连接一步化,可提高个体微小的螨类及微小昆虫SSR的富集效率。柑橘全爪螨gSSR核心重复次数要远多于从转录组数据库获得的EST-SSR。总体而言,gSSR和EST-SSR中的三碱基重复SSR具有更好的优化率。此外,柑橘全爪螨gSSR具有微卫星家族现象。%Objective] The objective of this study is to construct the microsatellite-enriched libraries, and identify genomic- microsatellite (gSSR) from the genome of the citrus red mite,Panonychus citri. Meanwhile, a large number of gene-microsatellite (EST-SSR) markers were also indentified from the transcriptome database ofP. citri. Based on these SSR sequences, the selected SSR primer pairs were validated.[Method]On the basis of isolating high quality genomic DNA ofP. citri, enriched microsatellite libraries were constructed by streptavidin-coated magnetic beads utilizing methodologies that exploit the strong affinity between biotin and the protein streptavidin. A fast and easy protocol was proposed through a combination of two different published methods. Briefly, genomic DNA was digested by the restriction enzyme and then ligated to designed adaptors. Microsatellite-containing DNA fragments were captured by streptavidin-coated magnetic beads. The beads affinity capture of microsatellite repeats using biotinylated oligonucleotide probes. Subsequently, PCR was used to amplify the captured molecules for transferring single strand DNA to double strand DNA. The PCR products were then ligated to pGEM-T Easy vector and transformed into Trans5α competent cells. Then, clones from these libraries were screened for microsatellite content. Meanwhile

  17. Balanced scorecard of effectiveness analysis of the “Balanced scorecard method of analysis” and risk analysis of financial instability (of a bankrupt) of an enterprise (firm)

    OpenAIRE

    2015-01-01

    The significance and essence of balanced scorecard of effectiveness analysis of the “Balanced scorecard method of analysis” and its application for analyzing the risk of financial instability of an enterprise have been considered.

  18. Survey and analysis of simple sequence repeats in the Laccaria bicolor genome, with development of microsatellite markers

    Energy Technology Data Exchange (ETDEWEB)

    Labbe, Jessy L [ORNL; Murat, Claude [INRA, Nancy, France; Morin, Emmanuelle [INRA, Nancy, France; Le Tacon, F [UMR, France; Martin, Francis [INRA, Nancy, France

    2011-01-01

    It is becoming clear that simple sequence repeats (SSRs) play a significant role in fungal genome organization, and they are a large source of genetic markers for population genetics and meiotic maps. We identified SSRs in the Laccaria bicolor genome by in silico survey and analyzed their distribution in the different genomic regions. We also compared the abundance and distribution of SSRs in L. bicolor with those of the following fungal genomes: Phanerochaete chrysosporium, Coprinopsis cinerea, Ustilago maydis, Cryptococcus neoformans, Aspergillus nidulans, Magnaporthe grisea, Neurospora crassa and Saccharomyces cerevisiae. Using the MISA computer program, we detected 277,062 SSRs in the L. bicolor genome representing 8% of the assembled genomic sequence. Among the analyzed basidiomycetes, L. bicolor exhibited the highest SSR density although no correlation between relative abundance and the genome sizes was observed. In most genomes the short motifs (mono- to trinucleotides) were more abundant than the longer repeated SSRs. Generally, in each organism, the occurrence, relative abundance, and relative density of SSRs decreased as the repeat unit increased. Furthermore, each organism had its own common and longest SSRs. In the L. bicolor genome, most of the SSRs were located in intergenic regions (73.3%) and the highest SSR density was observed in transposable elements (TEs; 6,706 SSRs/Mb). However, 81% of the protein-coding genes contained SSRs in their exons, suggesting that SSR polymorphism may alter gene phenotypes. Within a L. bicolor offspring, sequence polymorphism of 78 SSRs was mainly detected in non-TE intergenic regions. Unlike previously developed microsatellite markers, these new ones are spread throughout the genome; these markers could have immediate applications in population genetics.

  19. Molecular phylogenetics and microsatellite analysis reveal cryptic species of speckled dace (Cyprinidae: Rhinichthys osculus) in Oregon's Great Basin.

    Science.gov (United States)

    Hoekzema, Kendra; Sidlauskas, Brian L

    2014-08-01

    Speckled dace (Rhinichthys osculus) is a small cyprinid that occurs throughout western North America and is the most commonly occurring fish in Oregon. Because of the high genetic and morphological variation in this species across its range, it has been referred to as a species complex; however, no revision to its taxonomy has occurred since 1984. Here, the phylogenetics and population genetics of speckled dace are examined throughout Oregon's Great Basin to describe genetic variation and infer the geographic boundaries between distinct taxonomic entities and populations. We tested the validity of a putative subspecies, Foskett Spring speckled dace, that occurs in a single spring within Warner Valley in Southeast Oregon and is listed Federally as threatened. Dace were collected from Foskett Spring and all surrounding basins containing speckled dace (Warner, Goose Lake, Lake Abert, Silver Lake, and Malheur), as well as Stinking Lake Spring (located within Malheur), created phylogenetic trees from mitochondrial ND2 and nuclear S7 sequence data, and genotyped eight microsatellite loci for population-level analyses. Three highly divergent clades warrant species-level status: Malheur stream dace, Stinking Lake Spring dace, and dace from the other four basins combined. Although Foskett Spring dace were not monophyletic, substantial population structure occurs at the basin-level and separates Foskett Spring dace from other dace in the surrounding Warner Valley. Thus, we recommend ESU status for the isolated population of speckled dace in Foskett Spring. The high, previously unrecognized, taxonomic diversity within this region indicates a need for a range-wide phylogeographic study of speckled dace and an investigation of the morphological distinctiveness of the putative new species.

  20. Numerical analysis of flow instability in the water wall of a supercritical CFB boiler with annular furnace

    Science.gov (United States)

    Xie, Beibei; Yang, Dong; Xie, Haiyan; Nie, Xin; Liu, Wanyu

    2016-08-01

    In order to expand the study on flow instability of supercritical circulating fluidized bed (CFB) boiler, a new numerical computational model considering the heat storage of the tube wall metal was presented in this paper. The lumped parameter method was proposed for wall temperature calculation and the single channel model was adopted for the analysis of flow instability. Based on the time-domain method, a new numerical computational program suitable for the analysis of flow instability in the water wall of supercritical CFB boiler with annular furnace was established. To verify the code, calculation results were respectively compared with data of commercial software. According to the comparisons, the new code was proved to be reasonable and accurate for practical engineering application in analysis of flow instability. Based on the new program, the flow instability of supercritical CFB boiler with annular furnace was simulated by time-domain method. When 1.2 times heat load disturbance was applied on the loop, results showed that the inlet flow rate, outlet flow rate and wall temperature fluctuated with time eventually remained at constant values, suggesting that the hydrodynamic flow was stable. The results also showed that in the case of considering the heat storage, the flow in the water wall is easier to return to stable state than without considering heat storage.

  1. Basmati aromatic rice genotypes of India using microsatellite markers

    African Journals Online (AJOL)

    Administrator

    Aromatic rice is preferred by consumers all over the world due to its flavor and palatability. ... A dendrogram based on cluster analysis by microsatellite polymorphism grouped all the ..... and Basmati 370) showed a higher degree of similarity.

  2. Microsatellite analysis of Rosa damascena Mill. accessions reveals genetic similarity between genotypes used for rose oil production and old Damask rose varieties

    OpenAIRE

    Rusanov, K.; Kovacheva, N.; Vosman, B.J.; Zhang, L.; Rajapakse, S; Atanassov, A.; Atanassov, I.

    2005-01-01

    Damask roses are grown in several European and Asiatic countries for rose oil production. Twenty-six oil-bearing Rosa damascena Mill. accessions and 13 garden Damask roses were assayed by molecular markers. Microsatellite genotyping demonstrated that R. damascena Mill. accessions from Bulgaria, Iran, and India and old European Damask rose varieties possess identical microsatellite profiles, suggesting a common origin. At the same time, the data indicated that modern industrial oil rose cultiv...

  3. Transport and micro-instability analysis of JET H-mode plasma during pellet fueling

    Science.gov (United States)

    Klaywittaphat, P.; Onjun, T.

    2017-02-01

    Transport and micro-instability analysis in a JET H-mode plasma discharge 53212 during the pellet fueling operation is carried out using the BALDUR integrated predictive modeling code with a combination of the NCLASS neoclassical transport model and an anomalous core transport model (either Mixed B/gB or MMM95 model). In this work, the evolution of plasma current, plasma density and temperature profiles is carried out and, consequently, the plasma’s behaviors during the pellet operation can be observed. The NGS pellet model with the Grad-B drift effect included is used to describe pellet ablation and its behaviors when a pellet is launched into hot plasma. The simulation shows that after each pellet enters the plasma, there is a strong perturbation on the plasma causing a sudden change of both thermal and particle profiles, as well as the thermal and particle transports. For the simulation using MMM95 transport model, the change of both thermal and particle transports during pellet injection are found to be dominated by the transport due to the resistive ballooning modes due to the increase of collisionality and resistivity near the plasma edge. For the simulation based on mixed B/gB transport model, it is found that the change of transport during the pellet injection is dominated by the Bohm term. Micro-instability analysis of the plasma during the time of pellet operation is also carried out for the simulations based on MMM95 transport model. It is found that the ion temperature gradient mode is destabilized due to an increase of temperature gradient in the pellet effective region, while the trapped electron mode is stabilized due to an increase of collisionality in that region.

  4. Isocitrate dehydrogenase 1 R132C mutation occurs exclusively in microsatellite stable colorectal cancers with the CpG island methylator phenotype.

    Science.gov (United States)

    Whitehall, V L J; Dumenil, T D; McKeone, D M; Bond, C E; Bettington, M L; Buttenshaw, R L; Bowdler, L; Montgomery, G W; Wockner, L F; Leggett, B A

    2014-11-01

    The CpG Island Methylator Phenotype (CIMP) is fundamental to an important subset of colorectal cancer; however, its cause is unknown. CIMP is associated with microsatellite instability but is also found in BRAF mutant microsatellite stable cancers that are associated with poor prognosis. The isocitrate dehydrogenase 1 (IDH1) gene causes CIMP in glioma due to an activating mutation that produces the 2-hydroxyglutarate oncometabolite. We therefore examined IDH1 alteration as a potential cause of CIMP in colorectal cancer. The IDH1 mutational hotspot was screened in 86 CIMP-positive and 80 CIMP-negative cancers. The entire coding sequence was examined in 81 CIMP-positive colorectal cancers. Forty-seven cancers varying by CIMP-status and IDH1 mutation status were examined using Illumina 450K DNA methylation microarrays. The R132C IDH1 mutation was detected in 4/166 cancers. All IDH1 mutations were in CIMP cancers that were BRAF mutant and microsatellite stable (4/45, 8.9%). Unsupervised hierarchical cluster analysis identified an IDH1 mutation-like methylation signature in approximately half of the CIMP-positive cancers. IDH1 mutation appears to cause CIMP in a small proportion of BRAF mutant, microsatellite stable colorectal cancers. This study provides a precedent that a single gene mutation may cause CIMP in colorectal cancer, and that this will be associated with a specific epigenetic signature and clinicopathological features.

  5. Determination of microsatellite repeats in the human thyroid peroxidase (TPOX) gene using an automated gene analysis system with nanoscale engineered biomagnetite.

    Science.gov (United States)

    Nakagawa, Takahito; Maruyama, Kohei; Takeyama, Haruko; Matsunaga, Tadashi

    2007-04-15

    The number of repeat in the microsatellite region (AATG)(5-14) of the human thyroid peroxidase gene (TOPX) was determined using an automated DNA analysis system with nano-scale engineered biomagnetite. Thermal melting curve analysis of DNA duplexes on biomagnetite indicated that shorter repeat sequences (less than 9 repeats) were easily discriminated. However, it was difficult to determine the number of repeats at more than nine. In order to improve the selectivity of this method for the longer repeats, a "double probe hybridization assay" was performed in which an intermediate probe was used to replace a target repeat sequence having more than 9 repeats with a shorter sequence possessing less than 9 repeats. Thermal probe melting curve analyses and Tm determination confirmed that the target with 10 repeats was converted to 5 repeats, 11 repeats converted to 4 and 12 to 3, respectively. Furthermore, rapid determination of repeat numbers was possible by measuring fluorescence intensities obtained by probe dissociation at 56 and 66 degrees C, and 40, 60 and 80 degrees C for signal normalization.

  6. GENETIC INSTABILITY IN CERVICAL CARCINOMA

    Institute of Scientific and Technical Information of China (English)

    赵旻; 伍欣星; 邱小萍; 李晖; 戴天力; 谭云

    2002-01-01

    Objective: The role of human papillomavirus (HPV) in the development of cervical carcinoma has been clearly established but other factors could be involved in cervical tumorigenesis such as loss of heterozygosity (LOH) and microsatellite instability (MI). The aim of the present study was to investigate the genetic instability in cervical carcinoma tissues and provide evidence for discoveringnew tumor suppressor genes and screening diagnostic molecular marker of cervical carcinoma. Methods: Fifty primary cervical carcinoma samples from high-incidence area were analyzed by PCR for HPV16 infection, LOH and microsatellite instability. Results: HPV16 was detected in 88% of the cases. Sixty-six percent of total cases showed LOH with no more than 3 different loci per case. The highest frequency of the allelic loss was found in D18S474 (18q21, 40.5%). MI was detected in 4 cases (8%) only. Conclusion: Different percentages of LOH on specific chromosomal regions were found and MI was very infrequent in cervical carcinoma. The putative suppressor gene(s) could be located on specific chromosome regions such as 18q, and genetic instability could be involved in cervical tumorigenesis.

  7. Microsatellites in the Genome of the Edible Mushroom, Volvariella volvacea

    Directory of Open Access Journals (Sweden)

    Ying Wang

    2014-01-01

    Full Text Available Using bioinformatics software and database, we have characterized the microsatellite pattern in the V. volvacea genome and compared it with microsatellite patterns found in the genomes of four other edible fungi: Coprinopsis cinerea, Schizophyllum commune, Agaricus bisporus, and Pleurotus ostreatus. A total of 1346 microsatellites have been identified, with mono-nucleotides being the most frequent motif. The relative abundance of microsatellites was lower in coding regions with 21 No./Mb. However, the microsatellites in the V. volvacea gene models showed a greater tendency to be located in the CDS regions. There was also a higher preponderance of trinucleotide repeats, especially in the kinase genes, which implied a possible role in phenotypic variation. Among the five fungal genomes, microsatellite abundance appeared to be unrelated to genome size. Furthermore, the short motifs (mono- to tri-nucleotides outnumbered other categories although these differed in proportion. Data analysis indicated a possible relationship between the most frequent microsatellite types and the genetic distance between the five fungal genomes.

  8. Molecular Analysis of Microsatellite Mutagenesis in Soybean (Glycine max)%大豆微卫星诱发突变的分子分析

    Institute of Scientific and Technical Information of China (English)

    朱保葛; 孙勇如

    2004-01-01

    Microsatellite or SSR marker is an efficient tool for plant genotype identification, molecular mapping and marker-assisted selection. Objective of this study is to analyze the mutagenized microsatellite variations in soybean genome and reveal nature of these mutations. In the present study, mutations at fifteen microsatellite loci were detected in genomic DNAs of soybean mutant E182 induced by EMS (ethyne metyl sulfate) using PCR amplification of 485 pairs of SSR primers. These fifteen mutagenized microsatellite loci with repeat number variation were Satt005, Satt117, Satt185, Satt282, Satt290, Satt420, Satt452, Satt483, Satt569, Satt579, Satt600, Satt602, Sat_086, Sat_107 and Sat_135, respectively. Sequencing results of these fifteen loci indicated that microsatellite sequences at Satt282, Satt483, Satt579, Satt600 and Satt602 loci were respectively deleted 1-, 3-, 8-, 20- and 1-trinucleotide (all [ATT]1-20 except for [CAA]8[TAA]12 at Satt600 locus) repeats, which made allele sizes at these five loci decrease 3, 9, 24, 60 and 3 bp, respectively. And while microsatellite sequences at the other ten mutated loci, Satt005, Satt117, Satt185, Satt290, Satt420, Satt452, Satt569 and Sat_086, Sat_107, Sat_135, were respectively inserted 1-, 6-, 6-, 3-, 4-, 3-, 8-trinucleotide repeats (ATT)1-8 and 12-, 6-, 16-dinucleotide repeats (AT)6-16, making allele sizes at these ten loci increase 3, 18, 18, 9, 12, 9, 24, 24, 12, 32 bp, respectively. On the other hand, eleven events of base mutations were detected in flanking regions at seven (Sat-107, Satt185, Satt282, Satt420, Satt569, Satt579 and Satt600) of fifteen mutated microsatellite loci. These base mutations consisted of 6 transitions (4T→C and 2 A→G), 2 transvertions (A→T and T→A), 1 insertion (T) and 2 deletions (A and T). The experimental results proved that EMS mutagenesis could cause different types of mutations at microsatellite multilocus in soybean genome, including repeat number variations in microsatellite

  9. Is early-onset microsatellite and chromosomally stable colorectal cancer a hallmark of a genetic susceptibility syndrome?

    NARCIS (Netherlands)

    Kets, C.M.; Krieken, J.H.J.M. van; Erp, P.E.J. van; Feuth, T.; Jacobs, Y.H.A.; Brunner, H.G.; Ligtenberg, M.J.L.; Hoogerbrugge, N.

    2008-01-01

    Most colorectal cancers show either microsatellite or chromosomal instability. A subset of colorectal cancers, especially those diagnosed at young age, is known to show neither of these forms of genetic instability and thus might have a distinct pathogenesis. Colorectal cancers diagnosed at young

  10. Microsatellite genotyping of carnation varieties

    NARCIS (Netherlands)

    Smulders, M.J.M.; Noordijk, Y.; Rus-Kortekaas, W.; Bredemeijer, G.M.M.; Vosman, B.

    2003-01-01

    A set of 11 sequence-tagged microsatellite markers for carnation (Dianthus caryophyllus) was developed using a DNA library enriched for microsatellites. Supplemented with three markers derived from sequence database entries, these were used to genotype carnation varieties using a semi-automated fluo

  11. A consensus microsatellite-based linkage map for the hermaphroditic bay scallop (Argopecten irradians and its application in size-related QTL analysis.

    Directory of Open Access Journals (Sweden)

    Hongjun Li

    Full Text Available Bay scallop (Argopecten irradians is one of the most economically important aquaculture species in China. In this study, we constructed a consensus microsatellite-based genetic linkage map with a mapping panel containing two hybrid backcross-like families involving two subspecies of bay scallop, A. i. irradians and A. i. concentricus. One hundred sixty-one microsatellite and one phenotypic (shell color markers were mapped to 16 linkage groups (LGs, which corresponds to the haploid chromosome number of bay scallop. The sex-specific map was 779.2 cM and 781.6 cM long in female and male, respectively, whereas the sex-averaged map spanned 849.3 cM. The average resolution of integrated map was 5.9 cM/locus and the estimated coverage was 81.3%. The proportion of distorted markers occurred more in the hybrid parents, suggesting that the segregation distortion was possibly resulted from heterospecific interaction between genomes of two subspecies of bay scallop. The overall female-to-male recombination rate was 1.13:1 across all linked markers in common to both parents, and considerable differences in recombination also existed among different parents in both families. Four size-related traits, including shell length (SL, shell height (SH, shell width (SW and total weight (TW were measured for quantitative trait loci (QTL analysis. Three significant and six suggestive QTL were detected on five LGs. Among the three significant QTL, two (qSW-10 and qTW-10, controlling SW and TW, respectively were mapped on the same region near marker AiAD121 on LG10 and explained 20.5% and 27.7% of the phenotypic variance, while the third (qSH-7, controlling SH was located on LG7 and accounted for 15.8% of the phenotypic variance. Six suggestive QTL were detected on four different LGs. The linkage map and size-related QTL obtained in this study may facilitate marker-assisted selection (MAS in bay scallop.

  12. Genomic instability in squamous cell carcinoma of the head and neck.

    Science.gov (United States)

    Field, J K

    1996-01-01

    The role of genomic instability in the development of squamous cell carcinoma (SCCHN) has become apparent with the publication of three major allelotype analysis of this disease, as well as many publications which have concentrated on specific target regions. The measurement of accumulated genetic alterations or fractional allele loss, as determined by allelotype analysis, provides a useful molecular indicator of tumour behaviour. In one major study, a positive correlation was found between FAL > median value and lymph node metastasis and also with a poor clinical outcome. In addition the recognition of microsatellite instability as a marker of DNA repair defects has provided a further molecular marker of the disease process and that loss of heterozygosity analysis and microsatellite instability appear to be independent genetic events in the development of SCCHN. Furthermore, the recognition of a number of novel target regions in SCCHN on chromosome arms, 1 p, 3p, 8p, 9p, 13q, 17p and 18q and our understanding of the role of certain oncogenes and tumour suppressor genes and their interaction with human papillomavirus has provided further elucidation of the neoplastic process. Even though this review describes a number of molecular events in SCCHN, the sequence of events still eludes the scientific community at present.

  13. Effect of LiCl in Polymer Solution on the Instable Part of Electrospinning Nanofibers: Theoretical Analysis and Experimental Verification

    Institute of Scientific and Technical Information of China (English)

    QIN Xiao-hong; JIA Lin; LI Ni

    2010-01-01

    In this paper, the theoretical analysis proves that the relationship between radius r of jet and the axial distance z from the onset of whipping instability follows an allometric law in the form r ∝ z-1/4 whatever surface charge parameter a is. Polyvinylalcohol (PVA) was used to study the effect of surface charge on the variation of jet diameter with axial coordinate after the onset of whipping instability during electrospinning by adding LiCI. The experiment shows that the relationship between radius r of jet and the axial distance z from the onset of whipping instability also follows the law in the form r∝ z-1/4 whenthe content of LiCl is from 0.2 wt% to 4 wt%. That is, the law does not depend upon the content of salt, and the theoretical prediction agrees quite well with the experimental data.

  14. SnoN expression is differently regulated in microsatellite unstable compared with microsatellite stable colorectal cancers

    Directory of Open Access Journals (Sweden)

    Leggett Barbara A

    2006-10-01

    Full Text Available Abstract Background SnoN is an important regulator of the transforming growth factor beta (TGFβ signalling pathway and has been shown to exhibit both tumour promotion and suppression activity. Methods To further explore the role of this complex molecule in colorectal tumorigenesis, we examined 52 paired normal and tumour colorectal specimens stratified by level of microsatellite instability; 18 with high-level microsatellite instability (MSI-H and 34 microsatellite stable (MSS. SnoN transcript expression was quantitated by real-time PCR and analysed with respect to clinical indicators of prognosis. Results Within the MSI-H subgroup, SnoN was commonly either up-regulated (6/18, 33% or down-regulated (7/18, 39%. A significantly different distribution of SnoN expression was observed in MSS cancers compared with MSI-H (P ≤ 0.001. Whilst 17/34 (50% of MSS tumours demonstrated up-regulation, none showed down-regulated expression. Within the MSI-H subgroup, up-regulation was significantly correlated with lack of repeat tract mutation in the TGFβRII gene (P ≤ 0.025, suggesting that SnoN is more frequently up-regulated in the presence of functional TGFβ signalling. Conclusion Together these data support the notion that SnoN has both oncogenic and tumour suppressive properties depending on other genetic changes within the tumour, and that the MSI-H pathway of colorectal tumorigenesis presents an excellent model for the study of these opposing functions.

  15. Comparison of microsatellite distribution in genomes of Centruroides exilicauda and Mesobuthus martensii.

    Science.gov (United States)

    Wang, Chen; Kubiak, Lukasz Jakub; Du, Lian-Ming; Li, Wu-Jiao; Jian, Zuo-Yi; Tang, Ce; Fan, Zhen-Xin; Zhang, Xiu-Yue; Yue, Bi-Song

    2016-12-05

    In this study, we characterized the distribution of microsatellites in the genomes and genes of Centruroides exilicauda and Mesobuthus martensii, carried out Gene Ontology (GO) analysis and GO enrichment analysis of coding sequences (CDSs) with microsatellite (SSR). In addition, over-represented GO functions related to environmental interactions, development process and methylation were identified to develop functional markers and facilitate further analysis of microsatellite function in the genes of scorpions. Location analysis indicated that microsatellites were predominantly concentrated at both ends of genes. Most genes containing microsatellite had the SSR present at only one locus, from which we infer that the number of SSRs per gene is limited even though intragenic tandem repeats can generate functional variability. Lastly, we identified 75 SSRs in 64 genes of 54 expanded gene families and 1 SSR in the toxin gene of Mesobuthus martensii, allowing future studies on the effect of microsatellites on gene function.

  16. Evidence of Chromosomal Instability in Prostate Cancer Determined by Spectral Karyotyping (SKY and Interphase FISH Analysis

    Directory of Open Access Journals (Sweden)

    Ben Beheshti

    2001-01-01

    Full Text Available The way in which cytogenetic aberrations develop in prostate cancer (Cap is poorly understood. Spectral karyotype (SKY analysis of Cap cell lines has shown that they have unstable karyotypes and also have features associated with chromosomal instability (CIN. To accurately determine the incidence of de novo structural and numerical aberrations in vitro in Cap, we performed SKY analysis of three independent clones derived from one representative cell line, DU145. The frequent generation of new chromosomal rearrangements and a wide variation in the number of structural aberrations within two to five passages suggested that this cell line exhibited some of the features associated with a CIN phenotype. To study numerical cell-to-cell variation, chromosome 8 aneusomy was assessed in the LNCaP, DU145, and PC-3 cell lines and a patient cohort of 15 Cap primary tumors by interphase fluorescence in situ hybridization (FISH. This analysis showed that a high frequency of numerical alteration affecting chromosome 8 was present in both in vitro and in Cap tissues. In comparison to normal controls, the patient cohort had a statistically significant (P<.05, greater frequency of cells with one and three centromere 8 copies. These data suggest that a CIN-like process may be contributing towards the generation of de novo numerical and structural chromosome abnormalities in Cap.

  17. The effectiveness of physiotherapy treatment on balance dysfunction and postural instability in persons with Parkinson’s disease: a systematic review and meta-analysis

    OpenAIRE

    Yitayeh, Asmare; Teshome, Amare

    2016-01-01

    Background Balance dysfunction and postural instability in Parkinson’s disease are among the most relevant determinants of an impaired quality of life. Physiotherapy interventions are essential to reduce the level of disability by treating balance dysfunction and postural instability. The aim of this systematic review with meta-analysis was to test the effectiveness of conventional physiotherapy interventions in the management of balance dysfunction and postural instability in Persons with id...

  18. Exome-wide somatic microsatellite variation is altered in cells with DNA repair deficiencies.

    Directory of Open Access Journals (Sweden)

    Zalman Vaksman

    Full Text Available Microsatellites (MST, tandem repeats of 1-6 nucleotide motifs, are mutational hot-spots with a bias for insertions and deletions (INDELs rather than single nucleotide polymorphisms (SNPs. The majority of MST instability studies are limited to a small number of loci, the Bethesda markers, which are only informative for a subset of colorectal cancers. In this paper we evaluate non-haplotype alleles present within next-gen sequencing data to evaluate somatic MST variation (SMV within DNA repair proficient and DNA repair defective cell lines. We confirm that alleles present within next-gen data that do not contribute to the haplotype can be reliably quantified and utilized to evaluate the SMV without requiring comparisons of matched samples. We observed that SMV patterns found in DNA repair proficient cell lines without DNA repair defects, MCF10A, HEK293 and PD20 RV:D2, had consistent patterns among samples. Further, we were able to confirm that changes in SMV patterns in cell lines lacking functional BRCA2, FANCD2 and mismatch repair were consistent with the different pathways perturbed. Using this new exome sequencing analysis approach we show that DNA instability can be identified in a sample and that patterns of instability vary depending on the impaired DNA repair mechanism, and that genes harboring minor alleles are strongly associated with cancer pathways. The MST Minor Allele Caller used for this study is available at https://github.com/zalmanv/MST_minor_allele_caller.

  19. Pre-test analysis for identification of natural circulation instabilities in TALL-3D facility

    Energy Technology Data Exchange (ETDEWEB)

    Kööp, Kaspar, E-mail: kaspar@safety.sci.kth.se; Jeltsov, Marti, E-mail: marti@safety.sci.kth.se; Grishchenko, Dmitry, E-mail: dmitry@safety.sci.kth.se; Kudinov, Pavel, E-mail: pavel@safety.sci.kth.se

    2017-04-01

    Highlights: • Global optimum search method was used to identify a region of instability. • Parametric study was used for detailed investigation of system behavior modes. • The results include identification of sustained mass flow rate oscillations. • Recommendations are made for selection of optimal experimental conditions. - Abstract: TALL-3D facility is a lead-bismuth eutectic (LBE) thermal-hydraulic loop designed to provide experimental data on thermal-hydraulics phenomena for validation of stand-alone and coupled System Thermal Hydraulics (STH) and Computational Fluid Dynamics (CFD) codes. Pre-test analysis is crucial for proper choice of experimental conditions at which the experimental data would be most useful for code validation and benchmarking. The goal of this work is to identify these conditions at which the experiment is challenging for the STH codes yet minimizes the 3D-effects from the test section on the loop dynamics. The analysis is focused on the identification of limit cycle flow oscillations in the TALL-3D facility main heater leg using a global optimum search tool GA-NPO to find a general region in the parameter space where oscillatory behavior is expected. As a second step a grid study is conducted outlining the boundaries between different stability modes. Phenomena, simulation results and methodology for selection of the test parameters are discussed in detail and recommendations for experiments are provided.

  20. Time domain analysis of superradiant instability for the charged stringy black hole-mirror system

    CERN Document Server

    Li, Ran; Zhang, Hongbao; Zhao, Junkun

    2015-01-01

    It has been proved that the charged stringy black holes are stable under the perturbations of massive charged scalar fields. However, superradiant instability can be generated by adding the mirror-like boundary condition to the composed system of charged stringy black hole and scalar field. The unstable boxed quasinormal modes have been calculated by using both analytical and numerical method. In this paper, we further provide a time domain analysis by performing a long time evolution of charged scalar field configuration in the background of the charged stringy black hole with the mirror-like boundary condition imposed. We have used the ingoing Eddington-Finkelstein coordinates to derive the evolution equation, and adopted Pseudo-spectral method and the forth-order Runge-Kutta method to evolve the scalar field with the initial Gaussian wave packet. It is shown by our numerical scheme that Fourier transforming the evolution data coincides well with the unstable modes computed from frequency domain analysis. T...

  1. Dynamic instability analysis of single walled Carbone Nano Tubes conveying fluid under generalized boundary conditions

    Directory of Open Access Journals (Sweden)

    Azrar A.

    2012-07-01

    Full Text Available The dynamic instabilities of Carbon NanoTubes (CNTs conveying fluid are modeled and numerically simulated based on the nonlocal elasticity theory. The small scale parameter and the fluid-tube interaction effects on the dynamic behaviors of the CNT-fluid system as well as the instabilities induced by the fluid-velocity are investigated. The critical fluid-velocity and frequency-amplitude relationships as well as the flutter and divergence instability types and the associated time responses can be obtained based on the presented methodological approach.

  2. Analyses of carnivore microsatellites and their intimate association with tRNA-derived SINEs

    Directory of Open Access Journals (Sweden)

    Bosch Montserrat

    2006-10-01

    Full Text Available Abstract Background The popularity of microsatellites has greatly increased in the last decade on account of their many applications. However, little is currently understood about the factors that influence their genesis and distribution among and within species genomes. In this work, we analyzed carnivore microsatellite clones from GenBank to study their association with interspersed repeats and elucidate the role of the latter in microsatellite genesis and distribution. Results We constructed a comprehensive carnivore microsatellite database comprising 1236 clones from GenBank. Thirty-three species of 11 out of 12 carnivore families were represented, although two distantly related species, the domestic dog and cat, were clearly overrepresented. Of these clones, 330 contained tRNALys-derived SINEs and 357 contained other interspersed repeats. Our rough estimates of tRNA SINE copies per haploid genome were much higher than published ones. Our results also revealed a distinct juxtaposition of AG and A-rich repeats and tRNALys-derived SINEs suggesting their coevolution. Both microsatellites arose repeatedly in two regions of the insterspersed repeat. Moreover, microsatellites associated with tRNALys-derived SINEs showed the highest complexity and less potential instability. Conclusion Our results suggest that tRNALys-derived SINEs are a significant source for microsatellite generation in carnivores, especially for AG and A-rich repeat motifs. These observations indicate two modes of microsatellite generation: the expansion and variation of pre-existing tandem repeats and the conversion of sequences with high cryptic simplicity into a repeat array; mechanisms which are not specific to tRNALys-derived SINEs. Microsatellite and interspersed repeat coevolution could also explain different distribution of repeat types among and within species genomes. Finally, due to their higher complexity and lower potential informative content of microsatellites

  3. Analyses of carnivore microsatellites and their intimate association with tRNA-derived SINEs.

    Science.gov (United States)

    López-Giráldez, Francesc; Andrés, Olga; Domingo-Roura, Xavier; Bosch, Montserrat

    2006-10-23

    The popularity of microsatellites has greatly increased in the last decade on account of their many applications. However, little is currently understood about the factors that influence their genesis and distribution among and within species genomes. In this work, we analyzed carnivore microsatellite clones from GenBank to study their association with interspersed repeats and elucidate the role of the latter in microsatellite genesis and distribution. We constructed a comprehensive carnivore microsatellite database comprising 1236 clones from GenBank. Thirty-three species of 11 out of 12 carnivore families were represented, although two distantly related species, the domestic dog and cat, were clearly overrepresented. Of these clones, 330 contained tRNALys-derived SINEs and 357 contained other interspersed repeats. Our rough estimates of tRNA SINE copies per haploid genome were much higher than published ones. Our results also revealed a distinct juxtaposition of AG and A-rich repeats and tRNALys-derived SINEs suggesting their coevolution. Both microsatellites arose repeatedly in two regions of the interspersed repeat. Moreover, microsatellites associated with tRNALys-derived SINEs showed the highest complexity and less potential instability. Our results suggest that tRNALys-derived SINEs are a significant source for microsatellite generation in carnivores, especially for AG and A-rich repeat motifs. These observations indicate two modes of microsatellite generation: the expansion and variation of pre-existing tandem repeats and the conversion of sequences with high cryptic simplicity into a repeat array; mechanisms which are not specific to tRNALys-derived SINEs. Microsatellite and interspersed repeat coevolution could also explain different distribution of repeat types among and within species genomes.Finally, due to their higher complexity and lower potential informative content of microsatellites associated with tRNALys-derived SINEs, we recommend avoiding

  4. A matter of life or death: how microsatellites emerge in and vanish from the human genome.

    Science.gov (United States)

    Kelkar, Yogeshwar D; Eckert, Kristin A; Chiaromonte, Francesca; Makova, Kateryna D

    2011-12-01

    Microsatellites--tandem repeats of short DNA motifs--are abundant in the human genome and have high mutation rates. While microsatellite instability is implicated in numerous genetic diseases, the molecular processes involved in their emergence and disappearance are still not well understood. Microsatellites are hypothesized to follow a life cycle, wherein they are born and expand into adulthood, until their degradation and death. Here we identified microsatellite births/deaths in human, chimpanzee, and orangutan genomes, using macaque and marmoset as outgroups. We inferred mutations causing births/deaths based on parsimony, and investigated local genomic environments affecting them. We also studied birth/death patterns within transposable elements (Alus and L1s), coding regions, and disease-associated loci. We observed that substitutions were the predominant cause for births of short microsatellites, while insertions and deletions were important for births of longer microsatellites. Substitutions were the cause for deaths of microsatellites of virtually all lengths. AT-rich L1 sequences exhibited elevated frequency of births/deaths over their entire length, while GC-rich Alus only in their 3' poly(A) tails and middle A-stretches, with differences depending on transposable element integration timing. Births/deaths were strongly selected against in coding regions. Births/deaths occurred in genomic regions with high substitution rates, protomicrosatellite content, and L1 density, but low GC content and Alu density. The majority of the 17 disease-associated microsatellites examined are evolutionarily ancient (were acquired by the common ancestor of simians). Our genome-wide investigation of microsatellite life cycle has fundamental applications for predicting the susceptibility of birth/death of microsatellites, including many disease-causing loci.

  5. Modal analysis of gravitational instabilities in nearly Keplerian, counter-rotating collisionless discs

    CERN Document Server

    Gulati, Mamta

    2016-01-01

    We present a modal analysis of instabilities of counter-rotating, self-gravitating collisionless stellar discs, using the recently introduced modified WKB formulation of spiral density waves for collisionless systems (Gulati \\& Saini). The discs are assumed to be axisymmetric and in coplanar orbits around a massive object at the common center of the discs. The mass in both discs is assumed to be much smaller than the mass of the central object. For each disc, the disc particles are assumed to be in near circular orbits. The two discs are coupled to each other gravitationally. The perturbed dynamics of the discs evolves on the order of the precession time scale of the discs, which is much longer than the Keplerian time scale. We present results for the azimuthal wave number $m=1$ and $m=2$, for the full range of disc mass ratio between the prograde and retrograde discs. The eigenspectra are in general complex, therefore all eigenmodes are unstable. Eigenfunctions are radially more compact for $m = 1$ as co...

  6. Experimental design and instability analysis of coaxial electrospray process for microencapsulation of drugs and imaging agents.

    Science.gov (United States)

    Si, Ting; Zhang, Leilei; Li, Guangbin; Roberts, Cynthia J; Yin, Xiezhen; Xu, Ronald

    2013-07-01

    Recent developments in multimodal imaging and image-guided therapy requires multilayered microparticles that encapsulate several imaging and therapeutic agents in the same carrier. However, commonly used microencapsulation processes have multiple limitations such as low encapsulation efficiency and loss of bioactivity for the encapsulated biological cargos. To overcome these limitations, we have carried out both experimental and theoretical studies on coaxial electrospray of multilayered microparticles. On the experimental side, an improved coaxial electrospray setup has been developed. A customized coaxial needle assembly combined with two ring electrodes has been used to enhance the stability of the cone and widen the process parameter range of the stable cone-jet mode. With this assembly, we have obtained poly(lactide-co-glycolide) microparticles with fine morphology and uniform size distribution. On the theoretical side, an instability analysis of the coaxial electrified jet has been performed based on the experimental parameters. The effects of process parameters on the formation of different unstable modes have been studied. The reported experimental and theoretical research represents a significant step toward quantitative control and optimization of the coaxial electrospray process for microencapsulation of multiple drugs and imaging agents in multimodal imaging and image-guided therapy.

  7. Rayleigh-Taylor instability under curved substrates: An optimal transient growth analysis

    Science.gov (United States)

    Balestra, Gioele; Brun, P.-T.; Gallaire, François

    2016-12-01

    We investigate the stability of thin viscous films coated on the inside of a horizontal cylindrical substrate. In such a case, gravity acts both as a stabilizing force through the progressive drainage of the film and as a destabilizing force prone to form droplets via the Rayleigh-Taylor instability. The drainage solution, derived from lubrication equations, is found asymptotically stable with respect to infinitesimally small perturbations, although in reality, droplets often form. To resolve this paradox, we perform an optimal transient growth analysis for the first-order perturbations of the liquid's interface, generalizing the results of Trinh et al. [Phys. Fluids 26, 051704 (2014), 10.1063/1.4876476]. We find that the system displays a linear transient growth potential that gives rise to two different scenarios depending on the value of the Bond number (prescribing the relative importance of gravity and surface tension forces). At low Bond numbers, the optimal perturbation of the interface does not generate droplets. In contrast, for higher Bond numbers, perturbations on the upper hemicircle yield gains large enough to potentially form droplets. The gain increases exponentially with the Bond number. In particular, depending on the amplitude of the initial perturbation, we find a critical Bond number above which the short-time linear growth is sufficient to trigger the nonlinear effects required to form dripping droplets. We conclude that the transition to droplets detaching from the substrate is noise and perturbation dependent.

  8. Identification and quantification analysis of nonlinear dynamics properties of combustion instability in a diesel engine

    Science.gov (United States)

    Yang, Li-Ping; Ding, Shun-Liang; Litak, Grzegorz; Song, En-Zhe; Ma, Xiu-Zhen

    2015-01-01

    The cycling combustion instabilities in a diesel engine have been analyzed based on chaos theory. The objective was to investigate the dynamical characteristics of combustion in diesel engine. In this study, experiments were performed under the entire operating range of a diesel engine (the engine speed was changed from 600 to 1400 rpm and the engine load rate was from 0% to 100%), and acquired real-time series of in-cylinder combustion pressure using a piezoelectric transducer installed on the cylinder head. Several methods were applied to identify and quantitatively analyze the combustion process complexity in the diesel engine including delay-coordinate embedding, recurrence plot (RP), Recurrence Quantification Analysis, correlation dimension (CD), and the largest Lyapunov exponent (LLE) estimation. The results show that the combustion process exhibits some determinism. If LLE is positive, then the combustion system has a fractal dimension and CD is no more than 1.6 and within the diesel engine operating range. We have concluded that the combustion system of diesel engine is a low-dimensional chaotic system and the maximum values of CD and LLE occur at the lowest engine speed and load. This means that combustion system is more complex and sensitive to initial conditions and that poor combustion quality leads to the decrease of fuel economy and the increase of exhaust emissions.

  9. Identification and quantification analysis of nonlinear dynamics properties of combustion instability in a diesel engine

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Li-Ping, E-mail: yangliping302@hrbeu.edu.cn; Ding, Shun-Liang; Song, En-Zhe; Ma, Xiu-Zhen [Institute of Power and Energy Engineering, Harbin Engineering University, No. 145-1, Nantong Street, Nangang District, Harbin 150001 (China); Litak, Grzegorz [Faculty of Mechanical Engineering, Lublin University of Technology, Nadbystrzycka 36, 20-618 Lublin (Poland)

    2015-01-15

    The cycling combustion instabilities in a diesel engine have been analyzed based on chaos theory. The objective was to investigate the dynamical characteristics of combustion in diesel engine. In this study, experiments were performed under the entire operating range of a diesel engine (the engine speed was changed from 600 to 1400 rpm and the engine load rate was from 0% to 100%), and acquired real-time series of in-cylinder combustion pressure using a piezoelectric transducer installed on the cylinder head. Several methods were applied to identify and quantitatively analyze the combustion process complexity in the diesel engine including delay-coordinate embedding, recurrence plot (RP), Recurrence Quantification Analysis, correlation dimension (CD), and the largest Lyapunov exponent (LLE) estimation. The results show that the combustion process exhibits some determinism. If LLE is positive, then the combustion system has a fractal dimension and CD is no more than 1.6 and within the diesel engine operating range. We have concluded that the combustion system of diesel engine is a low-dimensional chaotic system and the maximum values of CD and LLE occur at the lowest engine speed and load. This means that combustion system is more complex and sensitive to initial conditions and that poor combustion quality leads to the decrease of fuel economy and the increase of exhaust emissions.

  10. Examining experiences of transition, instability and coping for young offenders in the community: A qualitative analysis.

    Science.gov (United States)

    Heath, Rebecca A; Priest, Helena M

    2016-04-01

    This article explores experiences of transition, instability and coping using a qualitative approach with young offenders within a specialist forensic child and adolescent mental health service (CAMHS). Participants were four young people (aged 14-17 years) on community orders under the supervision of local youth offending teams (YOTs). Semi-structured interviews were conducted and data analysed using an inductive thematic analysis approach. Three main themes were identified: (i) people and places; (ii) growth; and (iii) managing difficult experiences. Findings suggest that young offenders are exposed to a wide range of challenging contextual factors including unpredictable or inadequate home environments, numerous transitions (between family members/foster placements and schools), limited engagement with educational settings and a lack of social support, supporting the findings of Paton et al. Findings also portrayed a sense of participants' 'psychological growth' with development along a trajectory from a young child 'acting out' in response to the environments in which they were living; through a more reflective stage, in which they were able to begin to consider the situations they found themselves in; before reaching a position in which they were able to look beyond their day-to-day circumstances with some hope that their lives could be different in the future. Furthermore, accounts revealed that these young people had a limited range of functional coping strategies and had largely negative experiences of services. Clinical implications and the need for further research developing professionals' understanding of the influence of early experiences on young offenders' behaviour are discussed.

  11. Identification and quantification analysis of nonlinear dynamics properties of combustion instability in a diesel engine.

    Science.gov (United States)

    Yang, Li-Ping; Ding, Shun-Liang; Litak, Grzegorz; Song, En-Zhe; Ma, Xiu-Zhen

    2015-01-01

    The cycling combustion instabilities in a diesel engine have been analyzed based on chaos theory. The objective was to investigate the dynamical characteristics of combustion in diesel engine. In this study, experiments were performed under the entire operating range of a diesel engine (the engine speed was changed from 600 to 1400 rpm and the engine load rate was from 0% to 100%), and acquired real-time series of in-cylinder combustion pressure using a piezoelectric transducer installed on the cylinder head. Several methods were applied to identify and quantitatively analyze the combustion process complexity in the diesel engine including delay-coordinate embedding, recurrence plot (RP), Recurrence Quantification Analysis, correlation dimension (CD), and the largest Lyapunov exponent (LLE) estimation. The results show that the combustion process exhibits some determinism. If LLE is positive, then the combustion system has a fractal dimension and CD is no more than 1.6 and within the diesel engine operating range. We have concluded that the combustion system of diesel engine is a low-dimensional chaotic system and the maximum values of CD and LLE occur at the lowest engine speed and load. This means that combustion system is more complex and sensitive to initial conditions and that poor combustion quality leads to the decrease of fuel economy and the increase of exhaust emissions.

  12. Quasi-linear analysis of ion Weibel instability in the earth's neutral sheet

    Science.gov (United States)

    Lui, Anthony T. Y.; Yoon, Peter H.; Chang, Chia-Lie

    1993-01-01

    A quasi-linear analysis of the ion Weibel instability (IWI) for waves with parallel propagation is carried out for parameters appropriate to the earth's neutral sheet during the substorm interval. For ion drift speed reaching sizable fraction of the ion thermal speed, unstable waves grow to a nonlinear regime in a time interval greater than an ion gyroperiod. The saturation level is attained with current density reduced to about 15-28 percent of its preactivity level. The unstable wave amplitude normalized to the initial ambient field is found to be in the range of 0.2-0.8. This is accompanied by ion heating along the magnetic field with the parallel temperature being enhanced by 25-90 percent. Thus, the IWI can provide nonadiabatic heating of ions in current disruptions during substorms. The associated anomalous resistivity is estimated to be about 1 x 10 exp -7 to 1 x 10 exp -6 s, which is about 11 to 12 orders of magnitude above the classical resistivity.

  13. Instability analysis of cosmic viscoelastic gyro-gravitating clouds in the presence of dark matter

    Science.gov (United States)

    Karmakar, Pralay Kumar; Das, Papari

    2017-08-01

    A classical formalism for the weakly nonlinear instability analysis of a gravitating rotating viscoelastic gaseous cloud in the presence of gyratory dark matter is presented on the cosmic Jeans flat scales of space and time. The constituent neutral gaseous fluid (NGF) and dark matter fluid (DMF) are inter-coupled frictionally via mutual gravity alone. Application of standard nonlinear perturbation techniques over the complex gyro-gravitating clouds results in a unique conjugated pair of viscoelastic forced Burgers (VFB) equations. The VFB pair is conjointly twinned by correlational viscoelastic effects. There is no regular damping term here, unlike, in the conventional Burgers equation for the luminous (bright) matter solely. Instead, an interesting linear self-consistent derivative force-term naturalistically appears. A numerical illustrative platform is provided to reveal the micro-physical insights behind the weakly non-linear natural diffusive eigen-modes. It is fantastically seen that the perturbed NGF evolves as extended compressive solitons and compressive shock-like structures. In contrast, the perturbed DMF grows as rarefactive extended solitons and hybrid shocks. The latter is micro-physically composed of rarefactive solitons and compressive shocks. The consistency and reliability of the results are validated in the panoptic light of the existing reports based on the preeminent nonlinear advection-diffusion-based Burgers fabric. At the last, we highlight the main implications and non-trivial futuristic applications of the explored findings.

  14. Pancreatic mucinous noncystic (colloid) carcinomas and intraductal papillary mucinous carcinomas are usually microsatellite stable.

    Science.gov (United States)

    Lüttges, Jutta; Beyser, Kurt; Pust, Susanne; Paulus, Anja; Rüschoff, Josef; Klöppel, Günter

    2003-06-01

    Pancreatic mucinous noncystic (colloid) carcinomas (MNCC) differ from the usual ductal adenocarcinomas in their mucin expression profile and share with many extrapancreatic mucinous carcinomas the expression of MUC2. Because mucinous carcinomas are frequently associated with mutations of the DNA mismatch repair genes, causing them to exhibit the so-called mutator phenotype, we decided to investigate whether MNCCs of the pancreas are characterized by microsatellite instability (MSI). Twelve carcinomas with a mucinous phenotype (8 mucinous noncystic carcinomas, 3 intraductal papillary-mucinous carcinomas with an invasive muconodular component, and 1 ductal adenocarcinoma with an extensive mucinous noncystic component) and 11 ductal adenocarcinomas were immunostained with monoclonal antibodies to the mismatch repair gene products hMLH1, hMSH2, and hMSH6. For MSI analysis, DNA was isolated from microdissected tissue, and five primary microsatellites (BAT 25, BAT 26, D5S346, D17S250, and D2S123) were analyzed. MSI was diagnosed in case a novel allele was found, compared with the normal tissue. The criterion for LOH was a 75% signal reduction. All carcinomas tested exhibited nuclear expression of mismatch repair gene products, except for one MNCC that also showed MSI at the molecular level. The data suggest that pancreatic carcinomas with a mucinous phenotype (MUC2+/MUC1-) do not appear to normally exhibit mutations in the mismatch repair genes and therefore differ in their carcinogenesis from those in other organs.

  15. Neonatal neosporosis in a 2-week-old Bernese mountain dog infected with multiple Neospora caninum strains based on MS10 microsatellite analysis.

    Science.gov (United States)

    Prandini da Costa Reis, Rodrigo; Crisman, Robin; Roser, Margie; Malik, Richard; Šlapeta, Jan

    2016-05-15

    Neonatal neosporosis is a challenging disease to diagnose in neonatal and young puppies because the first signs of this condition may not be strongly suggestive of an infectious aetiology. Within two weeks of birth, three of four pups died with a subacute clinical course, some with dyspnea, some with diarrhoea and some with neurologic signs. Neosporosis was diagnosed post-mortem, but only after microscopic examination of tissues collected at necropsy. Histological findings consisted of (i) necrotizing, diffuse interstitial pneumonia associated with intralesional protozoa and (ii) necrotizing multifocal myocarditis with mineralization and intralesional protozoa. No significant alterations were found in the cerebrum or cerebellum (spinal cord was not examined). Immunohistochemistry confirmed protozoal stages and cysts were Neospora caninum. Immunohistochemistry for Toxoplasma gondii was negative. Lung and heart were the most severely affected tissues with large numbers of free zoites, BAG5 positive bradyzoites and tissue cysts of N. caninum further confirmed by N. caninum-specific quantitative real-time PCR. One affected pup which displayed knuckling, ataxia and diarrhoea were treated with trimethoprim sulfadiazine and clindamycin, and made a complete recovery. This surviving pup (at 8 weeks-of-age) and dam were both positive for N. caninum antibody (reciprocal titres 4096 and 256, respectively). Three other intact bitches on the same property were seropositive for N. caninum, suggesting horizontal transmission and a common source of infection, possibly due to consumption of infected meat. Analysis using microsatellite-10 (MS10) demonstrated that multiple strains of N. caninum were present. It was likely that all MS10 N. caninum strains were transplacentally transmitted from dam to pups. This is the first time that multiple N. caninum strains have been demonstrated to be vertically transmitted in dogs. N. caninum should be considered in the differential diagnosis for

  16. Deciphering diversity in populations of various linguistic and ethnic affiliations of different geographical regions of India: analysis based on 15 microsatellite markers

    Indian Academy of Sciences (India)

    V. K. Kashyap; Richa Ashma; Sonali Gaikwad; B. N. Sarkar; R. Trivedi

    2004-04-01

    The extent of genetic polymorphism at fifteen autosomal microsatellite markers in 54 ethnically, linguistically and geographically diverse human populations of India was studied to decipher intrapopulation diversity. The parameters used to quantify intrapopulation diversity were average allele diversity, average heterozygosity, allele range (base pairs), and number of alleles. Multilocus genotype frequencies calculated for selected populations were utilized for testing conformity with the assumption of Hardy–Weinberg equilibrium. The exact test values, after Bonferroni correction, showed significant deviation amongst Gowda (vWA, Penta E); Dhangar, Satnami and Gounder (D8S1179); Hmar (FGA); Kuki and Balti (vWA) groups. Relatively low number of alleles and allelic diversity (base-pairs size) had been observed in populations of central India as compared with southern and northern regions of the country. The communities of Indo-Caucasoid ethnic origin and Indo-European linguistic family (Kshatriya of Uttar Pradesh) showed highest allelic diversity, as well as rare alleles, not reported in any other Indian populations. Analysis based on average heterozygosity was also found to be lowest among the populations of central India (0.729) and highest among the populations from north (0.777) and west (0.784) regions of the country, having Indo-Caucasoid ethnic origin and Austro-Asiatic linguistic affiliation. The maximum power of discrimination (85%–89%) had been observed at loci FGA, Penta E, D18S51 and D21S11, suggested high intrapopulation diversity in India. Genetic diversity revealed by STR markers was consistent with the known demographic histories of populations. Thus, the present study clearly demonstrated that the intrapopulation diversity is not only present at the national level, but also within smaller geographical regions of the country. This is the first attempt to understand the extent of diversity within populations of India at such a large scale at genomic

  17. Analysis of genetic diversity and population structure within Florida coconut (Cocos nucifera L.) germplasm using microsatellite DNA, with special emphasis on the Fiji Dwarf cultivar.

    Science.gov (United States)

    Meerow, Alan W; Wisser, Randall J; Brown, J Steven; Kuhn, David N; Schnell, Raymond J; Broschat, Timothy K

    2003-02-01

    Using 15 simple sequence repeat (SSR) microsatellite DNA loci, we analyzed genetic variation within Cocos nucifera germplasm collections at two locations in south Florida, representing eight cultivars. The loci were also used in a parentage analysis of progeny of the 'Fiji Dwarf' variety at both locations. A total of 67 alleles were detected, with eight the highest number at any one locus. These loci identified 83 of the 110 individual palms. Gene diversity of the 15 loci ranged from 0.778 to 0.223, with a mean of 0.574. 'Fiji Dwarf', 'Malayan Dwarf', 'Green Niño' and 'Red Spicata' cultivars resolve as distinct clusters in a neighbor joining tree using modified Rogers distance, while the tall varieties form two aggregates. The highest gene diversity was found in the tall cultivars (H = 0.583 cumulatively), and the lowest in the 'Malayan Dwarf' (H = 0.202). After the tall coconuts, the 'Fiji Dwarf' was most genetically diverse (H = 0.436), and had the largest number of unique alleles. Genetic identity is highest among the 'Malayan Dwarf' phenotypes, and between the tall varieties. The 'Red Malayan Dwarf' is genetically distinct from the 'Green' and 'Yellow Malayan Dwarf' phenotypes, which cannot be distinguished with the SSR loci used. Off-type 'Malayan Dwarf' phenotypes (putative hybrids with talls) can be identified genotypically. Parentage analyses of 30 'Fiji Dwarf' progeny propagated from five adults surrounded by other cultivars estimate that only 20% of the progeny were out-crossed to the other varieties, while 40-46% were possible selfs. This suggests that a seed-production orchard of the variety maintained at reasonable distance from other varieties, will likely yield only 'Fiji Dwarf' genotypes. Our data are discussed in the context of hypotheses of coconut dissemination around the world.

  18. Characterization of nine polymorphic microsatellite markers in sprat ( Sprattus sprattus L.)

    DEFF Research Database (Denmark)

    Dailianis, T.; Limborg, Morten; Hanel, R.;

    2008-01-01

    Nine polymorphic microsatellites were isolated from sprat (Sprattus sprattus) using a microsatellite enrichment protocol and selective hybridization with a biotinylated (AC)(12) probe. The loci showed different variation patterns in a Baltic Sea population (44 individuals) with mean number...... of alleles at 12.7 and mean observed heterozygosity at 0.78. These microsatellite loci are expected to be used for taxonomic considerations in sprat, stock differentiation and population genetic analysis....

  19. Dendritic cell and macrophage infiltration in microsatellite-unstable and microsatellite-stable colorectal cancer.

    Science.gov (United States)

    Bauer, Kathrin; Michel, Sara; Reuschenbach, Miriam; Nelius, Nina; von Knebel Doeberitz, Magnus; Kloor, Matthias

    2011-09-01

    High level microsatellite instability (MSI-H) is a hallmark of Lynch syndrome-associated colorectal cancer (CRC). MSI-H CRC express immunogenic tumour antigens as a consequence of DNA mismatch repair deficiency-induced frameshift mutations. Consequently, frameshift antigen-specific immune responses are commonly observed in patients with Lynch syndrome-associated MSI-H CRC. Dendritic cells (DC) and macrophages play a crucial role in the induction and modulation of immune responses. We here analysed DC and macrophage infiltration in MSI-H and microsatellite-stable CRC. Sixty-nine CRC (MSI-H, n = 33; microsatellite-stable, n = 36) were examined for the density of tumour-infiltrating DC, Foxp3-positive regulatory T cells, and CD163-positive macrophages. In MSI-H lesions, S100-positive and CD163-positive cell counts were significantly higher compared to microsatellite-stable lesions (S100: epithelium P = 0.018, stroma P = 0.042; CD163: epithelium P < 0.001, stroma P = 0.046). Additionally, numbers of CD208-positive mature DC were significantly elevated in the epithelial compartment of MSI-H CRC (P = 0.027). High numbers of tumour-infiltrating Foxp3-positive T cells were detected in tumours showing a low proportion of CD208-positive, mature DC among the total number of S100-positive cells. Our study demonstrates that infiltration with DC, mature DC, and macrophages is elevated in MSI-H compared to microsatellite-stable CRC. The positive correlation of Foxp3-positive Treg cell density with a low proportion of mature DC suggests that impaired DC maturation may contribute to local immune evasion in CRC. Our results demonstrate that DC and macrophages in the tumour environment likely play an important role in the induction of antigen-specific immune responses in Lynch syndrome. Moreover, impaired DC maturation might contribute to local immune evasion in CRC.

  20. Analysis of beta-catenin, Ki-ras, and microsatellite stability in azoxymethane-induced colon tumors of BDIX/Orl Ico rats

    DEFF Research Database (Denmark)

    Sørensen, Nanna Møller; Kobaek-Larsen, Morten; Bonne, Anita

    2003-01-01

    The aim of the study reported here was to investigate whether the azoxymethane (AOM)-induced colon cancer rat model mimics the human situation with regard to microsatellite stability, changes in expression of beta-catenin, and/or changes in the sequence of the proto-oncogene Ki-ras. Colon cancer ...

  1. Microsatellite analysis of Rosa damascena Mill. accessions reveals genetic similarity between genotypes used for rose oil production and old Damask rose varieties

    NARCIS (Netherlands)

    Rusanov, K.; Kovacheva, N.; Vosman, B.J.; Zhang, L.; Rajapakse, S.; Atanassov, A.; Atanassov, I.

    2005-01-01

    Damask roses are grown in several European and Asiatic countries for rose oil production. Twenty-six oil-bearing Rosa damascena Mill. accessions and 13 garden Damask roses were assayed by molecular markers. Microsatellite genotyping demonstrated that R. damascena Mill. accessions from Bulgaria, Iran

  2. Development of a high-throughput microsatellite typing approach for forensic and population genetic analysis of wild and domestic African Bovini

    NARCIS (Netherlands)

    Greyling, B.J.; Kryger, P.; Plessis, du S.; Hooft, van W.F.; Helden, van P.; Getz, W.M.; Bastos, A.D.S.

    2008-01-01

    Conservation management and forensic traceability of African buffalo and cattle rely on the timely provision of unbiased and accurate genetic information. An approach in which 17 cattle microsatellite markers are co-electrophoresed, following amplification in three core multiplex reactions was estab

  3. GENETIC ALTERRATIONS OF MICROSATELLITE MARKERS AT CHROMOSOME 17 IN NON-SMALL CELL LUNG CANCER

    Institute of Scientific and Technical Information of China (English)

    GUO; Xue-jun

    2001-01-01

    [1]Froudarakis ME, Bouros D, Spandidos DA, et al. Microsatellite instability and loss of heterozygosity at chromosomes 17 in non-small cell lung cancer [J]. Chest 1998; 113:1091.[2]Fong KM, Zimmerman PV, Smith PJ. Microsatellite instability and other molecular abnormalities in non-small cell lung cancer [J]. Cancer Res 1994; 54:2098.[3]Mountain CF. A new international staging system for lung cancer [J]. Chest 1986; 89(suppl):225.[4]Shridhar V, Siegfried J, Hunt J, et al. Genetic instability of microsatellite sequences in many non-small cell lung carcinomas [J]. Cancer Res 1994; 54:2084.[5]Loeb LA. Microsatellite instability: Marker of a mutator phenotype in cancer [J]. Cancer Res 1994; 54:5059.[6]Sanchez CM, Monzo M, Rosell R, et al. Detection of chromosome 3p alterations in serum DNA of non-small cell lung cancer patients [J]. Ann Oncol 1989; 113.

  4. Analysis on mechanism and key factors of surrounding rock instability in deeply inclined roadway affected by argillation and water seepage

    Institute of Scientific and Technical Information of China (English)

    Ma Rui; Li Guichen; Zhang Nong; Liu Cong; Wei Yinghao; Zhang Ming

    2015-01-01

    Based on the characteristics of surrounding rocks for deeply inclined roadway affected by argillation and water seepage, a structure model of layer crack plate was established to analyze the shear sliding insta-bility mechanism. Through solid mechanics analysis of anchored surrounding rock with defect from water seepage, combined with numerical analysis for instability mechanism under water seepage in deeply inclined roadway, key factors were proposed. Results show that with increasing height of layer crack plate, lateral buckling critical load value for high wall of the roadway decreases;there is a multi-stage distribution for tensile stress along the anchor bolt with defect under pulling state condition;groundwater seepage seriously affects the strength of surrounding rock of the roadway, to some extent the plastic zone of the high side rises up to 8 m. Finally some support strategies were proposed for the inclined roadway and successfully applied to Haoyuan coal mine in Tiela mining area, western China.

  5. First Identification of Polymorphic Microsatellite Markers in the Burgundy Truffle, Tuber aestivum (Tuberaceae

    Directory of Open Access Journals (Sweden)

    Virginie Molinier

    2013-02-01

    Full Text Available Premise of the study: Tuber aestivum, the most common truffle in Europe, plays an important role in the commercial truffle market. For the first time, microsatellite primers were developed to investigate polymorphism within this species. Methods and Results: Using direct shotgun pyrosequencing, 15 polymorphic microsatellites were identified out of the 7784 perfect microsatellites present in the 534620 reads obtained. Tested on 75 samples, these microsatellites were highly polymorphic. The number of alleles varied from four to 15, and the expected heterozygosity ranged from 0.266 to 0.620. A multilocus analysis allowed the identification of 63 genotypes over the 75 samples analyzed. Conclusions: Direct shotgun pyrosequencing is a fast and relatively low-cost technique allowing identification of microsatellites in nonmodel species. The microsatellites developed in this study will be useful in population genetic studies to infer the evolutionary history of this species.

  6. XSS-10 microsatellite flight demonstration program results

    Science.gov (United States)

    Davis, Thomas M.; Melanson, David

    2004-08-01

    Air Force Research Laboratory"s space experiment XSS-10 was flown on the Air Force Global Positioning Satellite (GPS) mission IIR-8 launched on January 29, 2003. The mission objectives of XSS-10 were to demonstrate autonomous navigation, proximity operations, and inspection of a Resident Space Object (RSO). XSS-10 was a 28-kilogram micro-satellite was launched as a secondary mission on a Delta II expendable launch vehicle carrying a GPS satellite. XSS-10 was equipped with a visible camera, a star sensor, and mini SGLS system, all specially built for this program. In addition, a visible camera was attached to the second stage to observe the release of the micro-satellite and observe its maneuvers. Following the release of the GPS satellite, the Delta II initiated three depletion burns to reorient into an 800 KM circular orbit. The XSS-II was ejected from the Delta II second stage approximately 18 hours after launch. Operating autonomously on a preplanned course, XSS-10 performed its mission of navigating around the Delta II second stage at preplanned positions; the micro-satellite took images of the second stage and send them back to earth in real time. During these demonstrations the XSS-10 mission operations team accomplished responsive checkout of the micro-satellite and all of its subsystems, autonomous navigation on a preplanned course and a variety of algorithms and mission operations that pave the way for more ambitious missions in the future. This paper will discuss the results of the mission and post mission analysis of the XSS-10 space flight.

  7. Experimental demonstration of bow-shock instability and its numerical analysis

    Science.gov (United States)

    Kikuchi, Y.; Ohnishi, N.; Ohtani, K.

    2016-07-01

    An experimental demonstration was carried out in a ballistic range at high Mach numbers with the low specific heat ratio gas hydrofluorocarbon HFC-134a to observe the unstable bow-shock wave generated in front of supersonic blunt objects. The shadowgraph images obtained from the experiments showed instability characteristics, in which the disturbances grow and flow downstream and the wake flow appears wavy because of the shock oscillation. Moreover, the influence of the body shape and specific heat ratio on the instability was investigated for various experimental conditions. Furthermore, the observed features, such as wave structure and disturbance amplitude, were captured by numerical simulations, and it was demonstrated that computational fluid dynamics could effectively simulate the physical instability. In addition, it was deduced that the shock instability is induced by sound emissions from the edge of the object. This inference supports the dependence of the instability on the specific heat ratio and Mach number because the shock stand-off distance is affected by these parameters and limits the sound wave propagation.

  8. Frequent alteration of MLL3 frameshift mutations in microsatellite deficient colorectal cancer.

    Directory of Open Access Journals (Sweden)

    Yoshiyuki Watanabe

    Full Text Available BACKGROUND: MLL3 is a histone 3-lysine 4 methyltransferase with tumor-suppressor properties that belongs to a family of chromatin regulator genes potentially altered in neoplasia. Mutations in MLL3 were found in a whole genome analysis of colorectal cancer but have not been confirmed by a separate study. METHODS AND RESULTS: We analyzed mutations of coding region and promoter methylation in MLL3 using 126 cases of colorectal cancer. We found two isoforms of MLL3 and DNA sequencing revealed frameshift and other mutations affecting both isoforms of MLL3 in colorectal cancer cells and 19 of 134 (14% primary colorectal samples analyzed. Moreover, frameshift mutations were more common in cases with microsatellite instability (31% both in CRC cell lines and primary tumors. The largest isoform of MLL3 is transcribed from a CpG island-associated promoter that has highly homology with a pseudo-gene on chromosome 22 (psiTPTE22. Using an assay which measured both loci simultaneously we found prominent age related methylation in normal colon (from 21% in individuals less than 25 years old to 56% in individuals older than 70, R = 0.88, p<0.001 and frequent hypermethylation (83% in both CRC cell lines and primary tumors. We next studied the two loci separately and found that age and cancer related methylation was solely a property of the pseudogene CpG island and that the MLL3 loci was unmethylated. CONCLUSIONS: We found that frameshift mutations of MLL3 in both CRC cells and primary tumor that were more common in cases with microsatellite instability. Moreover, we have shown CpG island-associated promoter of MLL3 gene has no DNA methylation in CRC cells but also primary tumor and normal colon, and this region has a highly homologous of pseudo gene (psiTPTE22 that was age relate DNA methylation.

  9. First Microsatellite Markers Developed from Cupuassu ESTs: Application in Diversity Analysis and Cross-Species Transferability to Cacao.

    Science.gov (United States)

    Ferraz Dos Santos, Lucas; Moreira Fregapani, Roberta; Falcão, Loeni Ludke; Togawa, Roberto Coiti; Costa, Marcos Mota do Carmo; Lopes, Uilson Vanderlei; Peres Gramacho, Karina; Alves, Rafael Moyses; Micheli, Fabienne; Marcellino, Lucilia Helena

    2016-01-01

    The cupuassu tree (Theobroma grandiflorum) (Willd. ex Spreng.) Schum. is a fruitful species from the Amazon with great economical potential, due to the multiple uses of its fruit´s pulp and seeds in the food and cosmetic industries, including the production of cupulate, an alternative to chocolate. In order to support the cupuassu breeding program and to select plants presenting both pulp/seed quality and fungal disease resistance, SSRs from Next Generation Sequencing ESTs were obtained and used in diversity analysis. From 8,330 ESTs, 1,517 contained one or more SSRs (1,899 SSRs identified). The most abundant motifs identified in the EST-SSRs were hepta- and trinucleotides, and they were found with a minimum and maximum of 2 and 19 repeats, respectively. From the 1,517 ESTs containing SSRs, 70 ESTs were selected based on their functional annotation, focusing on pulp and seed quality, as well as resistance to pathogens. The 70 ESTs selected contained 77 SSRs, and among which, 11 were polymorphic in cupuassu genotypes. These EST-SSRs were able to discriminate the cupuassu genotype in relation to resistance/susceptibility to witches' broom disease, as well as to pulp quality (SST/ATT values). Finally, we showed that these markers were transferable to cacao genotypes, and that genome availability might be used as a predictive tool for polymorphism detection and primer design useful for both Theobroma species. To our knowledge, this is the first report involving EST-SSRs from cupuassu and is also a pioneer in the analysis of marker transferability from cupuassu to cacao. Moreover, these markers might contribute to develop or saturate the cupuassu and cacao genetic maps, respectively.

  10. First Microsatellite Markers Developed from Cupuassu ESTs: Application in Diversity Analysis and Cross-Species Transferability to Cacao.

    Directory of Open Access Journals (Sweden)

    Lucas Ferraz Dos Santos

    Full Text Available The cupuassu tree (Theobroma grandiflorum (Willd. ex Spreng. Schum. is a fruitful species from the Amazon with great economical potential, due to the multiple uses of its fruit´s pulp and seeds in the food and cosmetic industries, including the production of cupulate, an alternative to chocolate. In order to support the cupuassu breeding program and to select plants presenting both pulp/seed quality and fungal disease resistance, SSRs from Next Generation Sequencing ESTs were obtained and used in diversity analysis. From 8,330 ESTs, 1,517 contained one or more SSRs (1,899 SSRs identified. The most abundant motifs identified in the EST-SSRs were hepta- and trinucleotides, and they were found with a minimum and maximum of 2 and 19 repeats, respectively. From the 1,517 ESTs containing SSRs, 70 ESTs were selected based on their functional annotation, focusing on pulp and seed quality, as well as resistance to pathogens. The 70 ESTs selected contained 77 SSRs, and among which, 11 were polymorphic in cupuassu genotypes. These EST-SSRs were able to discriminate the cupuassu genotype in relation to resistance/susceptibility to witches' broom disease, as well as to pulp quality (SST/ATT values. Finally, we showed that these markers were transferable to cacao genotypes, and that genome availability might be used as a predictive tool for polymorphism detection and primer design useful for both Theobroma species. To our knowledge, this is the first report involving EST-SSRs from cupuassu and is also a pioneer in the analysis of marker transferability from cupuassu to cacao. Moreover, these markers might contribute to develop or saturate the cupuassu and cacao genetic maps, respectively.

  11. Analysis of the flow instability among channels of the OTSG in the naval craft NPP

    Energy Technology Data Exchange (ETDEWEB)

    Hou, Su-xia; Luo, Ji-jun; Xu, Jun; Liu, Jie-yu [Xi' an Hi-Tech Institute, Shaanxi (China)

    2014-11-15

    The instability occurring of the OTSG (Once-Through Steam Generator) in naval craft nuclear power plants is presented by the multivariable frequency domain theory. As concerning coupling interactions of the OTSG tubing, it is more accurate for analyzing the instability of OTSG compared to the common single variable method. A mathematical model for the system is derived from the fundamental equations by using the perturbation, Laplace-transform and the nodalization techniques. The stable boundary and parameters which influence the stability of the system are evaluated through computer simulation.

  12. Mitochondrial microsatellite instability in gastric cancer and its precancerous lesions

    Institute of Scientific and Technical Information of China (English)

    Xian-Long Ling; Dian-Chun Fang; Rong-Quan Wang; Shi-Ming Yang; Li Fang

    2004-01-01

    AIM: To evaluate the role of mitochondrial microsatelliteinstability (mtMSI) in gastric carcinogenesis. METHODS: MtMSI was measured with PCR-single strand conformation polymophism (PCR-SSCP) in 68 cases of advanced gastric cancer, 40 cases of chronic gastritis, 30 cases of intestinal metaplasia and 20 cases of dysplasia.RESULTS: MtMSI was observed in 12.5% (5 of 40) of chronic gastritis, 20.0% (6 of 30) of intestinal metaplasia, 25.0% (5 of 20) of dysplasia and 38.2% (26 of 68) of gastric cancer. These findings showed a sequential accumulation of mtMSI in the histological progression from chonic gastritis to gastric cancer. An association of mtMSI with intestinal histological type and distal location was found (P=0.001 and P=0.002), whereas no significant correlation was found between mtMSI and age at diagnosis, sex, tumor size, depthof invasion, lymph node spread and clinical stages (P>0.05).CONCLUSION: MtMSI may play an early and importantrole in the gastric carcinogenesis pathway, especially in the intestinal type and distal gastric cancer.

  13. Transferability of cucumber microsatellite markers used for phylogenetic analysis and population structure study in bottle gourd (Lagenaria siceraria (Mol.) Standl.).

    Science.gov (United States)

    Bhawna; Abdin, M Z; Arya, L; Verma, M

    2015-02-01

    Improved breeding for developing fruit quality in bottle gourd (Lagenaria siceraria (Mol.) Standl.) necessitates knowledge regarding its genetic diversity. To achieve this, a set of 108 locus-specific SSR markers has been developed in bottle gourd by cross-species transferability from 995 mapped Cucumis sativus SSR markers. During screening, 280 primer pairs amplified in the bottle gourd germplasm, which were further evaluated in a diverse set of 42 lines, resulting in 19 polymorphic, 89 monomorphic, 15 with multiple bands, and the rest 157 showed no or very non-specific amplification. The 19 polymorphic primer pairs produced a total of 54 alleles. Gene diversity, Shannon's information index, and Nei's coefficient of differentiation were calculated suggesting a moderate genetic variation at the species level. A model-based population structure analysis divided these germplasm into two subpopulations. This marker set will be applicable for evaluating the genetic structure for association mapping, DNA fingerprinting, and mounting linkage maps and will be a practical tool set for further genetics. This study provides one of the first quantitative views of population genetic variation in bottle gourd.

  14. Isolation and characterization of microsatellite markers and analysis of genetic diversity in Chinese jujube (Ziziphus jujuba Mill..

    Directory of Open Access Journals (Sweden)

    Siqi Wang

    Full Text Available Chinese jujube (Ziziphus jujuba Mill, 2n = 2× = 24, Rhamnaceae is an economically important Chinese native species. It has high nutritional value, and its medicinal properties have led to extensive use in traditional oriental medicine. The characterization of genotypes using molecular markers is important for genetic studies and plant breeding. However, few simple sequence repeat (SSR markers are available for this species. In this study, 1,488 unique SSR clones were isolated from Z. jujuba 'Dongzao' using enriched genomic libraries coupled with a three-primer colony PCR screening strategy, yielding a high enrichment rate of 73.3%. Finally, 1,188 (80.87% primer pairs were amplified successfully in the size expected for 'Dongzao'. A total of 350 primer pairs were further selected and evaluated for their ability to detect polymorphisms across a panel of six diverse cultivars; among these, 301 primer pairs detected polymorphisms, and the polymorphism information content (PIC value across all loci ranged from 0.15 to 0.82, with an average of 0.52. An analysis of 76 major cultivars employed in Chinese jujube production using 31 primer pairs revealed comparatively high genetic diversity among these cultivars. Within-population differences among individuals accounted for 98.2% of the observed genetic variation. Neighbor-joining clustering divided the cultivars into three main groups, none of which correspond to major geographic regions, suggesting that the genetics and geographical origin of modern Chinese jujube cultivars might not be linked. The current work firstly reports the large-scale development of Chinese jujube SSR markers. The development of these markers and their polymorphic information represent a significant improvement in the available Chinese jujube genomic resources and will facilitate both genetic and breeding applications, further accelerating the development of new cultivars.

  15. Analysis of the instability growth rate during the jetbackground interaction in a magnetic field

    Institute of Scientific and Technical Information of China (English)

    Miroslav Hork(y); Petr Kulhánek

    2013-01-01

    The two-stream instability is common,responsible for many observed phenomena in nature,especially the interaction of jets of various origins with the background plasma (e.g.extragalactic jet interacting with the cosmic background).The dispersion relation that does not consider magnetic fields is described by the wellknown Buneman relation.In 2011,Bohata,Bren and Kulánek derived the relation for the two-stream instability without the cold limit,with the general orientation of a magnetic field,and arbitrary stream directions.The maximum value of the imaginary part of the individual dispersion branches ωn(k) is of interest from a physical point of view.It represents the instability growth rate which is responsible for the onset of turbulence mode and subsequent reconnection on the scale of the ion radius accompanied by a strong plasma thermalization.The paper presented here is focused on the non-relativistic instability growth rate and its dependence on various input parameters,such as magnitude and direction of magnetic field,sound velocity,plasma frequency of the jet and direction of the wave vector during the jet-intergalactic medium interaction.The results are presented in plots and can be used for determination of the plasma parameter values close to which the strong energy transfer and thermalization between the jet and the background plasma occur.

  16. Analysis of oscillational instabilities in acoustic levitation using the finite-difference time-domain method

    DEFF Research Database (Denmark)

    Santillan, Arturo Orozco

    2011-01-01

    The aim of the work described in this paper has been to investigate the use of the finite-difference time-domain method to describe the interactions between a moving object and a sound field. The main objective was to simulate oscillational instabilities that appear in single-axis acoustic...

  17. Analysis of beta-catenin, Ki-ras, and microsatellite stability in azoxymethane-induced colon tumors of BDIX/Orl Ico rats.

    Science.gov (United States)

    Sørensen, Nanna Møller; Kobaek-Larsen, Morten; Bonne, Anita; van Zutphen, Bert; Fenger, Claus; Kristiansen, Karsten; Ritskes-Hoitinga, Merel

    2003-12-01

    The aim of the study reported here was to investigate whether the azoxymethane (AOM)-induced colon cancer rat model mimics the human situation with regard to microsatellite stability, changes in expression of beta-catenin, and/or changes in the sequence of the proto-oncogene Ki-ras. Colon cancer was induced by administration of four weekly doses of AOM (15 mg/kg of body weight per week) separated by a one-week break between the second and third injections. As the histopathologic characteristics of this model resemble those of the human counterpart, further characterization of the genetic changes was undertaken. The animals were euthanized 28 to 29 weeks after the first AOM injection, and tumor specimens were taken for histologic and DNA analyses. Since microsatellite variation was found in only a few (< 2%) specimens, the model can be considered as having stable microsatellites. This result is in accordance with those of similar studies in other rat models and with most human colorectal cancers. Immunohistochemical analyses of beta-catenin did not reveal loss of gene activity, nor did the sequencing of Ki-ras reveal mutations. These results are in contrast to most findings in comparable rat studies. The deviations may be due to differences in exposure to the carcinogen or difference in strain and/or age. The lack of beta-catenin and Ki-ras alterations in this colon cancer model is unlike human sporadic colorectal cancers where these genetic changes are common findings.

  18. Mechanical instability

    CERN Document Server

    Krysinski, Tomasz

    2013-01-01

    This book presents a study of the stability of mechanical systems, i.e. their free response when they are removed from their position of equilibrium after a temporary disturbance. After reviewing the main analytical methods of the dynamical stability of systems, it highlights the fundamental difference in nature between the phenomena of forced resonance vibration of mechanical systems subjected to an imposed excitation and instabilities that characterize their free response. It specifically develops instabilities arising from the rotor-structure coupling, instability of control systems, the se

  19. Collective instabilities

    Energy Technology Data Exchange (ETDEWEB)

    K.Y. Ng

    2003-08-25

    The lecture covers mainly Sections 2.VIII and 3.VII of the book ''Accelerator Physics'' by S.Y. Lee, plus mode-coupling instabilities and chromaticity-driven head-tail instability. Besides giving more detailed derivation of many equations, simple interpretations of many collective instabilities are included with the intention that the phenomena can be understood more easily without going into too much mathematics. The notations of Lee's book as well as the e{sup jwt} convention are followed.

  20. Microsatellite profiles as a basis for intellectual property protection in grape

    NARCIS (Netherlands)

    Ibanez, J.; Eeuwijk, van F.A.

    2003-01-01

    The use of microsatellite analysis in a forensic procedure for establishing infringement on plant breeders¿ rights in vegetatively propagated crops was evaluated. A reference collection of 45 seedless grape varieties was chosen as reference collection. Matching probabilities of grape microsatellite

  1. Detailed deletion mapping of loss of heterozygosity on 9p13-23 in laryngeal squamous cell carcinoma by microsatellite analysis

    Institute of Scientific and Technical Information of China (English)

    徐先发; 高燕宁; 程书鈞

    2004-01-01

    Background This study was designed to investigate the hot spots of microsatellite loss of heterozygosity (LOH) on 9p13-23 in laryngeal squamous cell carcinoma and to find out the correlation between the incidence of microsatellite LOH and the clinicopathological parameters.Methods Tumor tissues were obtained from paraffin embedded sections with microdissection. Genomic DNA was extracted from tumor tissues and peripheral blood lymphocytes with the phenol-chloroform. Polymerase chain reaction (PCR) amplification and denaturing gel electrophoresis were carried out in a set of 42 squamous cell carcinoma (SCC) of larynx and corresponding peripheral blood lymphocytes using 13 highly polymorphic microsatellite markers on 9p13-23. The correlation was analyzed between microsatellite LOH at the high frequency on 9p13-23 and clinicopathological parameters in the patients with squamous cell carcinoma of larynx.Results Of the 42 laryngeal cancers, 41 (97.6%) showed LOH in at least one of the microsatellite markers tested on 9p13-23. The most frequently deleted marker was D9S162 in 17 of the 19 (89.5%) informative samples. The marker D9S171, which is located on 9p21, had LOH detected in 12 of the 15 informative cases (80.0%). LOH at the D9S1748 marker (closest to the p16 gene locus) was detected in 18 of the 36 informative cases (50.0%). Allelic deletion mapping revealed two minimal regions of LOH encompassing markers D9S161-D9S171 on 9p21 and IFNA-D9S162 on 9p22-23. Multiple LOH (≥4) on 9p21-23 was found more frequently in the patients under 60 years, with supraglottic SCC or cervical lymph node metastasis than those over 60 years, with glottic SCC or without cervical lymph node metastasis (P<0.01 or 0.01, 0.05, respectively). On the contrary, there was no correlation between T stages or pathologic classification and the frequency of LOH on 9p21-23 in 42 SCC of Larynx.Conclusions These findings imply the presence of at least two putative tumor suppressor genes on 9p13-23 in

  2. Coupled hydrogeological and geomechanical modelling for the analysis of large slope instabilities.

    Science.gov (United States)

    Laloui, Lyesse; Ferrari, Alessio; Bonnard, Christophe

    2010-05-01

    Slowly-moving landslides (average velocity between 2 and 10 cm/year) are quite frequent in mountainous or hilly areas and they may display occasional crises, generally due to exceptional climatic conditions. The hazard related to these events cannot be analysed in terms of probability analysis, as the number of recorded past events is generally very small and climate changes could significantly modify the environmental setting. Quantitative relationships relating climatic condition fluctuations and sliding area velocity must then be pursued by taking into account the most relevant physical processes involved in the landslide behaviours. Conventional stability analyses are unable to deal with such questions because they do not allow the velocity fields to be determined. With regard to the behaviour of large slope instabilities, a methodology is presented which aims to describe the behaviour of slow-moving landslides by means of a coupled hydrogeological and geomechanical modelling framework. As it is well known, the evolution of the pore water pressure within the landslide body is often recognized as the main cause for the occurrence of displacement accelerations. In this sense the interaction among the hydrological and the mechanical responses must be considered to analyse the landslide behaviour, with the aim of quantitatively relating pore water pressure variations and movements. For a given case study, pore water pressure evolutions in space and time are obtained from a duly calibrated finite element hydrogeological model, which can take into account the role of several key factors such as infiltration, preferential flows and vegetation. Computed groundwater pressures resulting from the hydrogeological simulations are introduced as nodal forces in a finite element geomechanical model in order to calculate stress evolutions and displacements. The use of advanced constitutive models based on the generalised effective stress concept allows taking into account

  3. Abiotic stress leads to somatic and heritable changes in homologous recombination frequency, point mutation frequency and microsatellite stability in Arabidopsis plants

    Energy Technology Data Exchange (ETDEWEB)

    Yao Youli, E-mail: youli.yao@uleth.ca [Department of Biological Sciences, University of Lethbridge, Lethbridge, T1K 3M4 Alberta (Canada); Kovalchuk, Igor, E-mail: igor.kovalchuk@uleth.ca [Department of Biological Sciences, University of Lethbridge, Lethbridge, T1K 3M4 Alberta (Canada)

    2011-02-10

    In earlier studies, we showed that abiotic stresses, such as ionizing radiation, heavy metals, temperature and water, trigger an increase in homologous recombination frequency (HRF). We also demonstrated that many of these stresses led to inheritance of high-frequency homologous recombination, HRF. Although an increase in recombination frequency is an important indicator of genome rearrangements, it only represents a minor portion of possible stress-induced mutations. Here, we analyzed the influence of heat, cold, drought, flood and UVC abiotic stresses on two major types of mutations in the genome, point mutations and small deletions/insertions. We used two transgenic lines of Arabidopsis thaliana, one allowing an analysis of reversions in a stop codon-containing inactivated {beta}-glucuronidase transgene and another one allowing an analysis of repeat stability in a microsatellite-interrupted {beta}-glucuronidase transgene. The transgenic Arabidopsis line carrying the {beta}-glucuronidase-based homologous recombination substrate was used as a positive control. We showed that the majority of stresses increased the frequency of point mutations, homologous recombination and microsatellite instability in somatic cells, with the frequency of homologous recombination being affected the most. The analysis of transgenerational changes showed an increase in HRF to be the most prominent effect observed in progeny. Significant changes in recombination frequency were observed upon exposure to all types of stress except drought, whereas changes in microsatellite instability were observed upon exposure to UVC, heat and cold. The frequency of point mutations in the progeny of stress-exposed plants was the least affected; an increase in mutation frequency was observed only in the progeny of plants exposed to UVC. We thus conclude that transgenerational changes in genome stability in response to stress primarily involve an increase in recombination frequency.

  4. Abiotic stress leads to somatic and heritable changes in homologous recombination frequency, point mutation frequency and microsatellite stability in Arabidopsis plants.

    Science.gov (United States)

    Yao, Youli; Kovalchuk, Igor

    2011-02-10

    In earlier studies, we showed that abiotic stresses, such as ionizing radiation, heavy metals, temperature and water, trigger an increase in homologous recombination frequency (HRF). We also demonstrated that many of these stresses led to inheritance of high-frequency homologous recombination, HRF. Although an increase in recombination frequency is an important indicator of genome rearrangements, it only represents a minor portion of possible stress-induced mutations. Here, we analyzed the influence of heat, cold, drought, flood and UVC abiotic stresses on two major types of mutations in the genome, point mutations and small deletions/insertions. We used two transgenic lines of Arabidopsis thaliana, one allowing an analysis of reversions in a stop codon-containing inactivated β-glucuronidase transgene and another one allowing an analysis of repeat stability in a microsatellite-interrupted β-glucuronidase transgene. The transgenic Arabidopsis line carrying the β-glucuronidase-based homologous recombination substrate was used as a positive control. We showed that the majority of stresses increased the frequency of point mutations, homologous recombination and microsatellite instability in somatic cells, with the frequency of homologous recombination being affected the most. The analysis of transgenerational changes showed an increase in HRF to be the most prominent effect observed in progeny. Significant changes in recombination frequency were observed upon exposure to all types of stress except drought, whereas changes in microsatellite instability were observed upon exposure to UVC, heat and cold. The frequency of point mutations in the progeny of stress-exposed plants was the least affected; an increase in mutation frequency was observed only in the progeny of plants exposed to UVC. We thus conclude that transgenerational changes in genome stability in response to stress primarily involve an increase in recombination frequency.

  5. Comprehensive experimental and numerical analysis of instability phenomena in pump turbines

    Science.gov (United States)

    Gentner, Ch; Sallaberger, M.; Widmer, Ch; Bobach, B.-J.; Jaberg, H.; Schiffer, J.; Senn, F.; Guggenberger, M.

    2014-03-01

    The changes in the electricity market have led to changed requirements for the operation of pump turbines. Utilities need to change fast and frequently between pumping and generating modes and increasingly want to operate at off-design conditions for extended periods. Operation of the units in instable areas of the machine characteristic is not acceptable and may lead to self-excited vibration of the hydraulic system. In turbine operation of pump turbines unstable behaviour can occur at low load off-design operation close to runaway conditions (S-shape of the turbine characteristic). This type of instability may impede the synchronization of the machine in turbine mode and thus increase start-up and switch over times. A pronounced S-shaped instability can also lead to significant drop of discharge in the event of load rejection. Low pressure on the suction side and in the tail-race tunnel could cause dangerous separation of the water column. Understanding the flow features that lead to the instable behaviour of pump turbines is a prerequisite to the design of machines that can fulfil the growing requirements relating to operational flexibility. Flow simulation in these instability zones is demanding due to the complex and highly unsteady flow patterns. Only unsteady simulation methods are able to reproduce the governing physical effects in these operating regions. ANDRITZ HYDRO has been investigating the stability behaviour of pump turbines in turbine operation in cooperation with several universities using simulation and measurements. In order to validate the results of flow simulation of unstable operating points, the Graz University of Technology (Austria) performed detailed experimental investigations. Within the scope of a long term research project, the operating characteristics of several pump turbine runners have been measured and flow patterns in the pump turbine at speed no load and runaway have been examined by 2D Laser particle image velocimetry (PIV

  6. Streak instability and generation of hairpin-vortices by a slotted jet in channel crossflow: Experiments and linear stability analysis

    Science.gov (United States)

    Philip, Jimmy; Karp, Michael; Cohen, Jacob

    2016-01-01

    Streaks and hairpin-vortices are experimentally generated in a laminar plane Poiseuille crossflow by injecting a continuous jet through a streamwise slot normal to the crossflow, with air as the working media. Small disturbances form stable streaks, however, higher disturbances cause the formation of streaks which undergo instability leading to the generation of hairpin vortices. Particular emphasis is placed on the flow conditions close to the generation of hairpin-vortices. Measurements are carried out in the cases of natural and phase-locked disturbance employing smoke visualisation, particle image velocimetry, and hot-wire anemometry, which include, the dominant frequency, wavelength, and the disturbance shape (or eigenfunctions) associated with the coherent part of the velocity field. A linear stability analysis for both one- and two-dimensional base-flows is carried out to understand the mechanism of instability and good agreement of wavelength and eigenfunctions are obtained when compared to the experimental data, and a slight under-prediction of the growth-rates by the linear stability analysis consistent with the final nonlinear stages in transitional flows. Furthermore, an energy analysis for both the temporal and spatial stability analysis revels the dominance of the symmetric varicose mode, again, in agreement with the experiments, which is found to be governed by the balance of the wallnormal shear and dissipative effects rather than the spanwise shear. In all cases the anti-symmetric sinuous modes governed by the spanwise shear are found to be damped both in analysis and in our experiments.

  7. MHD Instability Analysis of Liquid Metal Free Surface Jet Flow in Non-Uniform Magnetic Fields (Part Ⅱ)

    Institute of Scientific and Technical Information of China (English)

    XUZenyu; KANGWeishan; PANChuanjie; DENHongyin; ZHANGYanxu

    2003-01-01

    In lost paper of magneto-hydrodynamic instability analysis of liquid metal free surface jet flow (Part Ⅰ), the magneto-hydrodynamic instability was analyzed for the jet flow in a transverse non-uniform magnetic field, BT. But, as all known, for the real conditions of liquid metal limiter-divertor plasma-facing components are in toroidal and poloidal fields. So, we try to analyze the magneto-hydrodynamic instability of the jet flow (hereby only for circular shape cross section jet flow) in the zone of non-uniform magnetic fields,

  8. A breast cancer meta-analysis of two expression measures of chromosomal instability reveals a relationship with younger age at diagnosis and high risk histopathological variables

    DEFF Research Database (Denmark)

    Endesfelder, David; McGranahan, Nicholas; Birkbak, Nicolai Juul;

    2011-01-01

    . In a breast cancer meta-analysis of 2423 patients we examine the relationship between clinicopathological parameters and two distinct chromosomal instability gene expression signatures in order to address whether younger age at diagnosis is associated with increased tumour genome instability. We find that CIN......, assessed by the two independently derived CIN expression signatures, is significantly associated with increased tumour size, ER negative or HER2 positive disease, higher tumour grade and younger age at diagnosis in ER negative breast cancer. These data support the hypothesis that chromosomal instability...

  9. Does political instability lead to higher and more volatile inflation?: A panel data analysis

    Directory of Open Access Journals (Sweden)

    Aisen Ari

    2007-01-01

    Full Text Available Economists generally accept the proposition that high and volatile inflation rates generate inefficiencies that reduce society’s welfare. Furthermore studies have shown that inflation is harmful to economic growth. However determining the causes of the worldwide diversity of inflationary experiences is an important challenge not yet satisfactorily confronted by the profession. Based on a broad dataset covering over 100 countries for the period 1975-1997 and using dynamic and static panel data econometric techniques, this paper shows that a higher degree of political instability is associated with both higher inflation levels and volatility. Not only does this paper advance the political economy literature establishing a relationship between inflation moments and political instability, but it also has important policy implications regarding the optimal design of inflation stabilization programs and of the institutions favorable to price stability.

  10. Failed anterior cruciate ligament reconstruction: analysis of factors leading to instability after primary surgery

    Institute of Scientific and Technical Information of China (English)

    MA Yong; AO Ying-fang; YU Jia-kuo; DAI Ling-hui; SHAO Zhen-xing

    2013-01-01

    Background Revision anterior cruciate ligament (ACL) surgery can be expected to become more common as the number of primary reconstruction keeps increasing.This study aims to investigate the factors causing instability after primary ACL reconstruction,which may provide an essential scientific base to prevent surgical failure.Methods One hundred and ten revision ACL surgeries were performed at our institute between November 2001 and July 2012.There were 74 men and 36 women,and the mean age at the time of revision was 27.6 years (range 16-56 years).The factors leading to instability after primary ACL reconstruction were retrospectively reviewed.Results Fifty-one knees failed because of bone tunnel malposition,with too anterior femoral tunnels (20 knees),posterior wall blowout (1 knee),vertical femoral tunnels (7 knees),too posterior tibial tunnels (12 knees),and too anterior tibial tunnels (10 knees).There was another knee performed with open surgery,where the femoral tunnel was drilled through the medial condyle and the tibial tunnel was too anterior.Five knees were found with malposition of the fixation.One knee with allograft was suspected of rejection and a second surgery had been made to take out the graft.Three knees met recurrent instability after postoperative infection.The other factors included traumatic (48 knees) and unidentified (12 knees).Conclusion Technical errors were the main factors leading to instability after primary ACL reconstructions,while attention should also be paid to the risk factors of re-injury and failure of graft incorporation.

  11. Vaccine instability in the cold chain: mechanisms, analysis and formulation strategies.

    Science.gov (United States)

    Kumru, Ozan S; Joshi, Sangeeta B; Smith, Dawn E; Middaugh, C Russell; Prusik, Ted; Volkin, David B

    2014-09-01

    Instability of vaccines often emerges as a key challenge during clinical development (lab to clinic) as well as commercial distribution (factory to patient). To yield stable, efficacious vaccine dosage forms for human use, successful formulation strategies must address a combination of interrelated topics including stabilization of antigens, selection of appropriate adjuvants, and development of stability-indicating analytical methods. This review covers key concepts in understanding the causes and mechanisms of vaccine instability including (1) the complex and delicate nature of antigen structures (e.g., viruses, proteins, carbohydrates, protein-carbohydrate conjugates, etc.), (2) use of adjuvants to further enhance immune responses, (3) development of physicochemical and biological assays to assess vaccine integrity and potency, and (4) stabilization strategies to protect vaccine antigens and adjuvants (and their interactions) during storage. Despite these challenges, vaccines can usually be sufficiently stabilized for use as medicines through a combination of formulation approaches combined with maintenance of an efficient cold chain (manufacturing, distribution, storage and administration). Several illustrative case studies are described regarding mechanisms of vaccine instability along with formulation approaches for stabilization within the vaccine cold chain. These include live, attenuated (measles, polio) and inactivated (influenza, polio) viral vaccines as well as recombinant protein (hepatitis B) vaccines. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

  12. 中国大、中型驴种遗传多样性的微卫星分析%Microsatellite Analysis of Genetic Diversity of Large and Middle-sized Donkey Breeds in China

    Institute of Scientific and Technical Information of China (English)

    朱文进; 苏咏梅

    2011-01-01

    [Objective] The paper aimed to reveal the genetic diversity of large and medium-sized donkey breeds of China. [Method] The genetic polymorphisms of 24 microsatellites in the eight large and medium-sized donkey breeds were studied by means of PCR, polyacrylamide gel electrophoresis and silver staining. [Result] The microsatellite of NVHEQ18 was medium polymorphic and the other 23 microsatellite loci were highly polymorphic. The average PIC (0.694 0), H (0.711 9 ) and E (2.9) of the eight donkey breed populations were all high, indicating that the gene polymorphisms and genetic diversity were relatively high. [Conclusion] The 24 microsatellite loci were effective markers for analysis of genetic relationships among the donkey breeds. The phylogenetic relationships among large and medium-sized donkey breeds were in accordance with their breeding history and distribution.%[目的]为分析我国大、中型驴品种遗传多样性.[方法]利用24个微卫星标记,对我国8个大、中型驴品种遗传多样性进行了检测.[结果]24个微卫星位点在8个驴品种中的多态信息含量除NVHEQ18为中度多态外,其余23个微卫星均为高度多态,8个驴种的平均PIC(0.694 0)、H(0.711 9)和E(3.94),表明基因多态性和遗传多样性相对较高.[结论]这24个微卫星可作为有效的遗传标记用于各驴品种的遗传多样性和系统发生关系的分析.我国大、中型驴品种的分子系统发生关系与其育成史和地理分布基本一致.

  13. Numerical Analysis of Slow-Wave Instabilities in Oversized Sinusoidaly Corrugated Waveguide Driven by Finitely Thick Annular Electron Beam

    OpenAIRE

    Otubo, Kosuke; Ogura, Kazuo; Yamakawa, Mitsuhisa; Takashima, Yusuke

    2010-01-01

    Three kinds of models are used for beam instability analyses: those based on a solid beam, an infinitesimally thin annular beam, and a finitely thick annular beam. In high-power experiments, the electron beam is an annulus of finite thickness. In this paper, a numerical code for a sinusoidally corrugated waveguide with a finitely thick annular beam is presented and compared with other models. Our analysis is based on a new version of the self-consistent linear theory that takes into account t...

  14. Stocking impact and temporal stability of genetic composition in a brackish northern pike population ( Esox lucius L.), assessed using microsatellite DNA analysis of historical and contemporary samples

    DEFF Research Database (Denmark)

    Larsen, Peter Foged; Hansen, Michael Møller; Eg Nielsen, Einar;

    2005-01-01

    During the last decade, brackish northern pike populations in Denmark have been subject to stocking programmes, using nonindigenous pike from freshwater lakes, in order to compensate for drastic population declines. The present study was designed to investigate the genetic impact of stocking...... freshwater pike into a brackish pike population in Stege Nor, Denmark. We analysed polymorphism at eight microsatellite loci in samples representing the indigenous Stege Nor population prior to stocking (ie from 1956 to 1957), along with a sample of the contemporary Stege Nor population and samples from...

  15. PERTURBATION ANALYSIS FOR MAGNETO-PLASTIC INSTABILITY OF FERROMAGNETIC BEAM-PLATES WITH GEOMETRIC IMPERFECTION

    Institute of Scientific and Technical Information of China (English)

    ZhouYouhe; GaoYuanwen; ZhengXiaojing

    2004-01-01

    The magneto-plastic instability of a ferromagnetic beam-type plate with simple supports and small initial imperfection is analytically investigated in this paper for that the plastic deformation of the plate with a linear-strain hardening relation is considered when the plate is located in a strong uniformly distributed magnetic field. After the distribution of magnetic fields related to the deflected configuration of plate is imaginably divided into two parts, i.e.,one is related to the flat plate and the other dependent on the perturbation of magnetic fields for which the plate configuration changes from the flat into the deformed state, the perturbation technique is employed to analyze the distribution of the perturbation magnetic fields in and out-of the magnetic medium of the ferromagnetic structure in a transverse magnetic field, which leads to some analytical formulae/solutions for the magnetic fields and the resulting magnetic force exerted on the plate. Based on them, the magneto-plastic buckling and snapping of the plate in a transverse magnetic field is discussed, and the critical magnetic field is analytically formulated in terms of the parameters of geometry and material of the plate employed by solving the governing equation of the magneto-plastic plate in the applied magnetic field. Further, the sensitivity of the initial imperfection on the magneto-plastic instability, expressed by an amplification function, is obtained by solving the dynamic equation of deflection of the plate after the inertial force in the transverse direction is taken into account. The results obtained show that the critical magnetic field is sensitive to the plastic characteristic, e.g., hardening coefficient, and the instability mode and deflection of the plate are dependent on the geometrical imperfection as well.

  16. Analysis of postoperative monitoring of patients undergoing shoulder arthroscopy for anterior instability.

    Science.gov (United States)

    Almeida, Alexandre; Menegotto, Samuel Millán; Almeida, Nayvaldo Couto de; Agostini, Ana Paula; Almeida, Letícia Agostini de

    2017-01-01

    Analyze the postoperative follow-up of patients undergoing shoulder arthroscopy for treatment of anterior instability and correlate with the prevalence of recurrence. A six-question survey was applied by phone and mail to 65 patients, seeking information on the current result of the surgical procedure. All patients were treated arthroscopically for anterior shoulder instability, with at least 12 months of postoperative time. Patients with associated posterior labial lesions and revision surgeries were not included. At the time of the survey the patients had a median of 56 (IQR: 34.5-110.5) postoperative months. The mean sample age was 24.6 years (maximum = 47, minimum = 12; SD = 7.3). Complaint of pain in the shoulder was observed in 20 patients (30.7%). Dislocation recurrence was observed in 10 patients (15.3%). Forty-four patients (67.6%) considered their shoulder normal, which was more frequent in non-recurrence patients (p < 0.001). Forty-three patients (66.1%) returned to their previous level of sport and there was no difference between recurrence and non-recurrence patients (p = 0.456). It was found that the prevalence of recurrence was 5.6 (95% CI: 1.30-24.46) times higher in individuals who abandoned monitoring before six months postoperatively (p = 0.012). The abandonment of postoperative monitoring in the early stages, when the patients receive orientation for muscle strengthening, proprioceptive education, and dangerous movements to avoid, can increase the rates of recurrent shoulder dislocation in patients treated for anterior instability by arthroscopy.

  17. Analysis of oscillational instabilities in acoustic levitation using the finite-difference time-domain method

    DEFF Research Database (Denmark)

    Santillan, Arturo Orozco

    2011-01-01

    The aim of the work described in this paper has been to investigate the use of the finite-difference time-domain method to describe the interactions between a moving object and a sound field. The main objective was to simulate oscillational instabilities that appear in single-axis acoustic...... levitation devices and to describe their evolution in time to further understand the physical mechanism involved. The study shows that the method gives accurate results for steady state conditions, and that it is a promising tool for simulations with a moving object....

  18. Corporate Debt Dynamics, Capital Accumulation, and Macroeconomic Instability: A Post-Keynesian Analysis

    OpenAIRE

    Min-Chang Ko; Sangheon Lee

    2015-01-01

    This study presents a simple model of corporate debt dynamics within the framework of the post-Keynesian theory of growth and distribution. Our model introduces corporate debt dynamics into a modified version of Lavoie's Minsky?Steindl model, yielding long-run results different from those of Lavoie (1995) and Hein (2007) by showing that a stable long-run equilibrium exists in both puzzling and normal cases. On the basis of these results, this study shows that Minsky¡¯s financial instability a...

  19. De novo transcriptome analysis and microsatellite marker development for population genetic study of a serious insect pest, Rhopalosiphum padi (L.) (Hemiptera: Aphididae)

    Science.gov (United States)

    Duan, Xinle; Wang, Kang; Su, Sha; Tian, Ruizheng; Li, Yuting

    2017-01-01

    The bird cherry-oat aphid, Rhopalosiphum padi (L.), is one of the most abundant aphid pests of cereals and has a global distribution. Next-generation sequencing (NGS) is a rapid and efficient method for developing molecular markers. However, transcriptomic and genomic resources of R. padi have not been investigated. In this study, we used transcriptome information obtained by RNA-Seq to develop polymorphic microsatellites for investigating population genetics in this species. The transcriptome of R. padi was sequenced on an Illumina HiSeq 2000 platform. A total of 114.4 million raw reads with a GC content of 40.03% was generated. The raw reads were cleaned and assembled into 29,467 unigenes with an N50 length of 1,580 bp. Using several public databases, 82.47% of these unigenes were annotated. Of the annotated unigenes, 8,022 were assigned to COG pathways, 9,895 were assigned to GO pathways, and 14,586 were mapped to 257 KEGG pathways. A total of 7,936 potential microsatellites were identified in 5,564 unigenes, 60 of which were selected randomly and amplified using specific primer pairs. Fourteen loci were found to be polymorphic in the four R. padi populations. The transcriptomic data presented herein will facilitate gene discovery, gene analyses, and development of molecular markers for future studies of R. padi and other closely related aphid species. PMID:28212394

  20. Genomewide high-density SNP linkage analysis of non-BRCA1/2 breast cancer families identifies various candidate regions and has greater power than microsatellite studies

    Directory of Open Access Journals (Sweden)

    Gonzalez-Neira Anna

    2007-08-01

    Full Text Available Abstract Background The recent development of new high-throughput technologies for SNP genotyping has opened the possibility of taking a genome-wide linkage approach to the search for new candidate genes involved in heredity diseases. The two major breast cancer susceptibility genes BRCA1 and BRCA2 are involved in 30% of hereditary breast cancer cases, but the discovery of additional breast cancer predisposition genes for the non-BRCA1/2 breast cancer families has so far been unsuccessful. Results In order to evaluate the power improvement provided by using SNP markers in a real situation, we have performed a whole genome screen of 19 non-BRCA1/2 breast cancer families using 4720 genomewide SNPs with Illumina technology (Illumina's Linkage III Panel, with an average distance of 615 Kb/SNP. We identified six regions on chromosomes 2, 3, 4, 7, 11 and 14 as candidates to contain genes involved in breast cancer susceptibility, and additional fine mapping genotyping using microsatellite markers around linkage peaks confirmed five of them, excluding the region on chromosome 3. These results were consistent in analyses that excluded SNPs in high linkage disequilibrium. The results were compared with those obtained previously using a 10 cM microsatellite scan (STR-GWS and we found lower or not significant linkage signals with STR-GWS data compared to SNP data in all cases. Conclusion Our results show the power increase that SNPs can supply in linkage studies.

  1. Chromosomal distribution patterns of the (AC)10 microsatellite and other repetitive sequences, and their use in chromosome rearrangement analysis of species of the genus Avena.

    Science.gov (United States)

    Fominaya, Araceli; Loarce, Yolanda; Montes, Alexander; Ferrer, Esther

    2017-03-01

    Fluorescence in situ hybridization (FISH) was used to determine the physical location of the (AC)10 microsatellite in metaphase chromosomes of six diploid species (AA or CC genomes), two tetraploid species (AACC genome), and five cultivars of two hexaploid species (AACCDD genome) of the genus Avena, a genus in which genomic relationships remain obscure. A preferential distribution of the (AC)10 microsatellite in the pericentromeric and interstitial regions was seen in both the A- and D-genome chromosomes, while in C-genome chromosomes the majority of signals were located in the pericentromeric heterochromatic regions. New large chromosome rearrangements were detected in two polyploid species: an intergenomic translocation involving chromosomes 17AL and 21DS in Avena sativa 'Araceli' and another involving chromosomes 4CL and 21DS in the analyzed cultivars of Avena byzantina. The latter 4CL-21DS intergenomic translocation differentiates clearly between A. sativa and A. byzantina. Searches for common hybridization patterns on the chromosomes of different species revealed chromosome 10A of Avena magna and 21D of hexaploid oats to be very similar in terms of the distribution of 45S and Am1 sequences. This suggests a common origin for these chromosomes and supports a CCDD rather than an AACC genomic designation for this species.

  2. Microsatellite analysis of maternity and the mating system in the Gulf pipefish Syngnathus scovelli, a species with male pregnancy and sex-role reversal.

    Science.gov (United States)

    Jones, A G; Avise, J C

    1997-03-01

    Highly variable microsatellite loci were employed to study the mating system of the sexually dimorphic Gulf pipefish Syngnathus scovelli. In this species, like others in the family Syngnathidae, 'pregnant' males provide all parental care. Gulf pipefish were collected from one locale in the northern Gulf of Mexico, and internally carried broods of 40 pregnant males were analysed genetically. By comparing multilocus microsatellite fingerprints for the inferred mothers against expected genotypic distributions from the population sample, it was determined that: (i) only one male had received eggs from more than a single female; and (ii) on two separate occasions, two different males had received eggs from the same female. Given the high power to detect multiple matings by males, the first finding indicates that only rarely are individual males impregnated by multiple females during the course of a pregnancy. Conversely, given the lower power to detect multiple matings by females due to sampling constraints, the second finding suggests a high frequency of multiple successful matings by females. Thus, this population of Gulf pipefish displays a polyandrous genetic mating system. The relevance of these genetic findings is discussed with regard to the evolution of secondary sex traits in this species, and in other syngnathids.

  3. Genetic diversity in population of largemouth bronze gudgeon (Coreius guichenoti Sauvage et Dabry) from Yangtze River determined by microsatellite DNA analysis.

    Science.gov (United States)

    Zhang, Futie; Tan, Deqing

    2010-01-01

    Largemouth bronze gudgeon (Coreius guichenoti Sauvage et Dabry 1874), one of the endemic fish species in the upper reaches of the Yangtze River in China, is a benthic and potamodromous fish that is typically found in rivers with torrential flow. Three dams in the Yangtze River, Ertan Dam, Three Gorges Dam and Gezhouba Dam, may have had vital impacts on the habitat and spawning behaviors of largemouth bronze gudgeon, and could ultimately threaten the survival of this fish. We studied the population genetic diversity of C. guichenoti samples collected at seven sites (JH, GLP, BX, HJ, MD, SDP and XB) within the Yangtze River and one of its tributaries, the Yalong River. Genetic diversity patterns were determined by analyzing genetic data from 11 polymorphic microsatellite loci. A high genetic diversity among these largemouth bronze gudgeon populations was indicated by the number of microsatellite alleles (A) and the expected heterozygosity (HE). No significant population variation occurred among GLP, BX, HJ and MD populations, but dramatic population differentiation was observed among JH and XB, two dam-blocked populations, versus other populations. Tests for bottlenecks did not indicate recent dramatic population declines and concurrent losses of genetic diversity in any largemouth bronze gudgeon populations. To the contrary, we found that dams accelerated the population differentiation of this fish.

  4. Tomographic analysis of the nonthermal x-ray bursts during disruption instability in the T-10 tokamak.

    Science.gov (United States)

    Savrukhin, P V; Ermolaeva, A I; Shestakov, E A; Khramenkov, A V

    2014-10-01

    Non-thermal x-ray radiation (Eγ up to 150 keV) is measured in the T-10 tokamaks during disruption instability using two sets of CdTe detectors (10 vertical and 7 horizontal view detectors). Special narrow cupper tubes collimators with lead screening and CdTe detectors integrated with amplifiers inside metallic containers provides enhanced spatial resolution of the system (r ∼ 3 cm) and assures protection from the parasitic hard x-ray (Eγ up to 1.5 MeV) and electromagnetic loads during disruption. Spatial localization of the nonthermal x-ray emissivity is reconstructed using tomographic Cormack technique with SVD matrix inversion. Analysis indicated appearance of an intensive non-thermal x-ray bursts during initial stage of the disruptions at high density. The bursts are characterized by repetitive spikes (2-3 kHz) of the x-ray emissivity from the plasma core area. Analysis indicated that the spikes can be connected with acceleration of the non-thermal electrons in enhanced longitudinal electric fields induced during energy quench at the disruption instability.

  5. Polymorphic microsatellite DNA markers in the penduline tit, Remiz pendulinus

    NARCIS (Netherlands)

    Meszaros, L. A.; Frauenfelder, N.; Van Der Velde, M.; Komdeur, J.; Szabad, J.

    2008-01-01

    To describe the exceptional mating system of the penduline tit, Remiz pendulinus, we aim to combine field observation records with DNA analysis based on polymorphic microsatellite DNA markers. Here we describe features of nine loci and their corresponding polymerase chain reaction primers. The obser

  6. A test of mink microsatellite markers in the ferret

    DEFF Research Database (Denmark)

    Anistoroaei, Razvan Marian; Christensen, Knud

    2006-01-01

    Short tandem repeats are a source of highly polymorphic markers in mammalian genomes. Genetic variations at these hypervariable loci is extensively used for linkage analysis and to identify individuals, and is very useful for interpopulation and interspecies studies. Fifty-nine microsatellite...

  7. Analysis of progressive failure of pillar and instability criterion based on gradient-dependent plasticity

    Institute of Scientific and Technical Information of China (English)

    王学滨

    2004-01-01

    A mechanical model for strain softening pillar is proposed considering the characteristics of progressive shear failure and strain localization. The pillar undergoes elastic, strain softening and slabbing stages. In the elastic stage, vertical compressive stress and deformation at upper end of pillar are uniform, while in the strain softening stage there appears nonuniform due to occurrence of shear bands, leading to the decrease of load-carrying capacity.In addition, the size of failure zone increases in the strain softening stage and reaches its maximum value when slabbing begins. In the latter two stages, the size of elastic core always decreases. In the slabbing stage, the size of failure zone remains a constant and the pillar becomes thinner. Total deformation of the pillar is derived by linearly elastic Hooke's law and gradient-dependent plasticity where thickness of localization band is determined according to the characteristic length. Post-peak stiffness is proposed according to analytical solution of averaged compressive stressaverage deformation curve. Instability criterion of the pillar and roof strata system is proposed analytically using instability condition given by Salamon. It is found that the constitutive parameters of material of pillar, the geometrical size of pillar and the number of shear bands influence the stability of the system; stress gradient controls the starting time of slabbing, however it has no influence on the post-peak stiffness of the pillar.

  8. Z-pinch equilibrium and instability analysis with digital holographic interferometry

    Science.gov (United States)

    Ross, M. P.; Shumlak, U.; Nelson, B. A.; Golingo, R. P.; Hughes, M. C.; Claveau, E. L.; Weed, J. R.; Forbes, E. G.; Doty, S. A.; Kim, B.

    2015-11-01

    The ZaP-HD Flow Z-Pinch project generates flow shear stabilized Z-pinches, providing a platform to explore how such plasmas could scale to HEDP and fusion reactor conditions. To scale up the plasma's density and temperature, it must be compressed to a smaller size making measurements more difficult. Digital holographic interferometry (DHI) employing a pulsed Nd:YAG laser and consumer DSLR camera can spatially resolve the plasma's electron density. The Fresnel reconstruction method allows expedient numerical data reconstruction. Obtaining electron density radial profiles relies on applying an Abel inversion to convert measured line-integrated density, and the inversion process provides an independent measure of plasma symmetry. Entire Z-pinch equilibria (n, P, T, and B profiles) can be computed by applying physical models to the density data. Tracking the time evolution of pressure and density can reveal the presence of non-adiabatic heating mechanisms. Imaging the size scales of instabilities enables relative measures of viscosity at different positions and times. Error estimation of measured density profiles is presented along with observed asymmetric instabilities. This work is supported by grants from the U.S. Department of Energy and the U.S. National Nuclear Security Administration.

  9. Parabolized Stability Equations analysis of nonlinear interactions with forced eigenmodes to control subsonic jet instabilities

    Energy Technology Data Exchange (ETDEWEB)

    Itasse, Maxime, E-mail: Maxime.Itasse@onera.fr; Brazier, Jean-Philippe, E-mail: Jean-Philippe.Brazier@onera.fr; Léon, Olivier, E-mail: Olivier.Leon@onera.fr; Casalis, Grégoire, E-mail: Gregoire.Casalis@onera.fr [Onera - The French Aerospace Lab, F-31055 Toulouse (France)

    2015-08-15

    Nonlinear evolution of disturbances in an axisymmetric, high subsonic, high Reynolds number hot jet with forced eigenmodes is studied using the Parabolized Stability Equations (PSE) approach to understand how modes interact with one another. Both frequency and azimuthal harmonic interactions are analyzed by setting up one or two modes at higher initial amplitudes and various phases. While single mode excitation leads to harmonic growth and jet noise amplification, controlling the evolution of a specific mode has been made possible by forcing two modes (m{sub 1}, n{sub 1}), (m{sub 2}, n{sub 2}), such that the difference in azimuth and in frequency matches the desired “target” mode (m{sub 1} − m{sub 2}, n{sub 1} − n{sub 2}). A careful setup of the initial amplitudes and phases of the forced modes, defined as the “killer” modes, has allowed the minimizing of the initially dominant instability in the near pressure field, as well as its estimated radiated noise with a 15 dB loss. Although an increase of the overall sound pressure has been found in the range of azimuth and frequency analyzed, the present paper reveals the possibility to make the initially dominant instability ineffective acoustically using nonlinear interactions with forced eigenmodes.

  10. Analysis of the crystal lattice instability for cage–cluster systems using the superatom model

    Energy Technology Data Exchange (ETDEWEB)

    Serebrennikov, D. A., E-mail: dserebrennikov@innopark.kantiana.ru, E-mail: dimafania@mail.ru; Clementyev, E. S. [I. Kant Baltic Federal University, “Functional Nanomaterials” Scientific–Educational Center (Russian Federation); Alekseev, P. A. [“Kurchatov Institute” National Research Center (Russian Federation)

    2016-09-15

    We have investigated the lattice dynamics for a number of rare-earth hexaborides based on the superatom model within which the boron octahedron is substituted by one superatom with a mass equal to the mass of six boron atoms. Phenomenological models have been constructed for the acoustic and lowenergy optical phonon modes in RB{sub 6} (R = La, Gd, Tb, Dy) compounds. Using DyB{sub 6} as an example, we have studied the anomalous softening of longitudinal acoustic phonons in several crystallographic directions, an effect that is also typical of GdB{sub 6} and TbB{sub 6}. The softening of the acoustic branches is shown to be achieved through the introduction of negative interatomic force constants between rare-earth ions. We discuss the structural instability of hexaborides based on 4f elements, the role of valence instability in the lattice dynamics, and the influence of the number of f electrons on the degree of softening of phonon modes.

  11. Analysis of the LSC microbunching instability in MaRIE linac reference design

    Energy Technology Data Exchange (ETDEWEB)

    Yampolsky, Nikolai [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2016-09-22

    In this report we estimate the effect of the microbunching instability in the MaRIE XFEL linac. The reference design for the linac is described in a separate report. The parameters of the L1, L2, and L3 linacs as well as BC1 and BC2 bunch compressors were the same as in the referenced report. The beam dynamics was assumed to be linear along the accelerator (which is a reasonable assumption for estimating the effect of the microbunching instability). The parameters of the bunch also match the parameters described in the referenced report. Additionally, it was assumed that the beam radius is equal to R = 100 m and does not change along linac. This assumption needs to be revisited at later studies. The beam dynamics during acceleration was accounted in the matrix formalism using a Matlab code. The input parameters for the linacs are: RF peak gradient, RF frequency, RF phase, linac length, and initial beam energy. The energy gain and the imposed chirp are calculated based on the RF parameters self-consistently. The bunch compressors are accounted in the matrix formalism as well. Each chicane is characterized by the beam energy and the R56 matrix element. It was confirmed that the linac and beam parameters described previously provide two-stage bunch compression with compression ratios of 10 and 20 resulting in the bunch of 3kA peak current.

  12. Analysis of the LSC microbunching instability in MaRIE linac reference design

    Energy Technology Data Exchange (ETDEWEB)

    Yampolsky, Nikolai [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2016-09-22

    In this report we estimate the effect of the microbunching instability in the MaRIE XFEL linac. The reference design for the linac is described in a separate report [1]. The parameters of the L1, L2, and L3 linacs as well as BC1 and BC2 bunch compressors were the same as in the referenced report. The beam dynamics was assumed to be linear along the accelerator (which is a reasonable assumption for estimating the effect of the microbunching instability). The parameters of the bunch also match the parameters described in [1]. Additionally it was assumed that the beam radius is eq