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Sample records for histological species markers

  1. Protein species as diagnostic markers

    NARCIS (Netherlands)

    Steffen, Pascal; Kwiatkowski, Marcel; Robertson, Wesley D.; Zarrine-Afsar, Mash; Deterra, Diana; Richter, Verena; Schlueter, Hartmut

    2016-01-01

    Many diseases are associated with protein species perturbations. A prominent example of an established diagnostic marker is the glycated protein species of hemoglobin, termed HbA1c. HbA1c concentration is increased in the blood of diabetes mellitus patients due to their poor control of blood glucose

  2. Histological features of oral epithelium in seven animal species: As a reference for selecting animal models.

    Science.gov (United States)

    Sa, Guoliang; Xiong, Xuepeng; Wu, Tianfu; Yang, Jincheng; He, Sangang; Zhao, Yifang

    2016-01-01

    Several animals have been used as models for basic and clinical research on oral mucosa. Few studies have focused on the selection of an appropriate animal model. This study aimed to provide histological references for selecting a potential model. Histological features were assessed by exploring 6 morphological characteristics and 2 immunohistochemical markers. The morphological characteristics included keratinization, basal membrane appearance, epithelial thickness, rete ridge length, adjacent rete ridge distance, and regional variation; the immunohistochemical markers included Ki67 (a proliferative marker) and Cytokeratin 19 (CK19; a stemness marker). The histological similarity of each species compared to humans was calculated according to the designated scoring criteria. The results showed that the buccal mucosae from dog and pig were non-keratinized, with similar rete ridge length and distance, compared to that of humans. The dog, rat, and cavy mucosae had analogous gross appearances in the basal membrane. The dog oral mucosae shared similar epithelial thickness with human oral mucosae. Compared to the human mucosa, the dog, pig, rat, and rabbit mucosae exhibited corresponding regional variations. The Ki67-positive cells in human and canine mucosae were predominantly localized in the suprabasal layers, whereas most of the proliferative cells were in the basal layer in other species. CK19 immunoreactivities were detected only in human and canine mucosae. The canine mucosae gained the highest point value (14), whereas the scores for the pig, rat, rabbit, cavy, sheep, and buffalo mucosae were 8, 6, 5, 5, 5, and 2, respectively. The histological variations in the oral epithelium of diverse animal species are considerable; the mucosae from dogs are most similar to human mucosae, implicating its histological basis as an animal model. Copyright © 2015 Elsevier B.V. All rights reserved.

  3. HISTOLOGICAL MARKERS OF DEGENERATION AND REGENERATION OF THE HUMAN INTERVERTEBRAL DISK

    OpenAIRE

    PELETTI-FIGUEIRÓ, MANUELA; AGUIAR, ISRAEL SILVEIRA DE; PAESI, SUELEN; MACHADO, DENISE CANTARELLI; ECHEVERRIGARAY, SERGIO; ROESCH-ELY, MARIANA; FALAVIGNA, ASDRUBAL; HENRIQUES, JOÃO ANTONIO PÊGAS

    2017-01-01

    ABSTRACT Objective: To define histological scores for intervertebral disc degeneration that would enable the definition of morphological characteristics of disease, besides improving knowledge of the lumbar degenerative disc disease by means of immunohistochemical markers. Methods: Hematoxylin and Eosin, Alcian/PAS, Masson Trichrome and Safranin O/FCF staining was used on the intervertebral disc degeneration sections of patients with lumbar degenerative disc disease. The protein markers d...

  4. Appendicitis in paediatric age group: Correlation between preoperative inflammatory markers and postoperative histological diagnosis

    Directory of Open Access Journals (Sweden)

    Peter Mekhail

    2011-01-01

    Full Text Available Introduction: Clinical diagnosis of appendicitis can be challenging, particularly in the paediatric age group. There is an increased risk of perforation in paediatrics; therefore, a need for sensitive and specific diagnostic tool is mandatory. Aim: The aim of this study is to evaluate the role of preoperative inflammatory markers in supporting the clinical diagnosis of appendicitis in the paediatric age group. Materials and Methods: Retrospective study of 268 emergency paediatric appendicectomies performed in a District General Hospital in Wales, over a period of seven years (2002-2009. The data collected from hospital database include preoperative inflammatory markers, C-reactive protein (CRP and white blood cells count (WBCC and post-operative histology. Statistical analysis was performed using Fisher′s exact test. Results: The median age group in the study was 12 (2-16. 141 (53% patients were <12 years, while 127 (47% patients were 12-16 years old. Male : female ratio = 1 : 1 (134 each. Inflammatory markers were not done for 94 patients (35%. CRP was done for 149 cases (55.6%, while WBCC was done for 172 cases (64%. Both markers were done together for 147 cases (54.8%. Histology was positive (inflamed / gangrenous appendix in 202 cases (75.4%. Eight cases were associated with Enterobious vermicularis infestation and one patient had carcinoid tumour. The sensitivity and specificity of CRP were 82% and 60%, respectively, with positive predictive value (PPV of 87% (P<0.0001, while those of WBCC were 80% and 59%, respectively, with PPV of 88% (P<0.0001. The sensitivity and specificity of both markers together were 80% and 70%, respectively, with PPV= 81% (P = 3.11E-8. 94 patients (35% had an appendicectomy operation based on clinical diagnosis alone without preoperative inflammatory markers having been tested. In 28 cases (30% out of these, postoperative histology revealed normal appendix (P = 0.18. Conclusion: CRP and WBCC are simple tests

  5. Familial breast cancer. Part II: Relationships with histology, staging, steroid receptors and serum tumor markers.

    Science.gov (United States)

    Gavrilov, I; Nacheva, M; Tzingilev, D

    2002-01-01

    To identify differences in clinical characteristics, histological features, hormone receptor status, and tumor marker expression between patients with sporadic and familial breast cancer. As in the previous Part I of this study, two groups of women with breast cancer were compared. The first group (group I) included 504 patients with a family history of breast cancer. The second (control) group (group II) consisted of 300 patients not reporting such a history in their relatives. The examined parameters in this report were stage and axillary lymph node involvement at the time of the initial diagnosis, treatment methods, hormone receptor status, and serum levels of the tumor markers CEA and CA 15.3. The data were processed and analysed using the SPSS statistical package. The statistical significance of differences between groups and subgroups was evaluated by x(2) Pearson's test and Student's paired t-test. Compared to sporadic cases, patients with familial breast cancer were more often diagnosed at an advanced III or IV stage; metastatic involvement of the regional lymph nodes was more frequent in group I patients. In the same group more radical surgical procedures combined with chemotherapy and local irradiation were performed. In group I the percentage of negative hormone receptors was higher (35.3% versus 22.6%; p result of their particular characteristics, these patients require more radical surgical techniques combined with pre- or postoperative local radiotherapy and systemic chemotherapy.

  6. Histological features of rheumatoid arthritis patients having antibodies to enterobacterial common antigens: correlation of antibody levels with semiquantitative histologic scores and laboratory markers.

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    Aoki, S; Mitsui, T

    2005-01-01

    To ascertain whether clinically diagnosed rheumatoid arthritis (RA) patients having antibodies to enterobacterial common antigens (ECA) in synovial fluid (SF) have a histological appearance characteristic of RA synovitis. Twenty-five RA patients for which synovial biopsy specimens were preserved, were selected from 58 patients with RA tested for antibodies to ECA in SF The synovial tissue specimens were examined histologically using a semiquantitative scoring system with quantitative counts. The correlation of anti-ECA antibody levels with total scores for synovitis and laboratory markers in three RA patient groups (markedly positive, moderately to slightly positive, and negative according to anti-ECA antibody levels) was analyzed statistically. Histologic examination in the markedly positive RA group (total score for synovitis, range 18-20 points) revealed typical histological features of rheumatoid synovitis. Total scores for synovitis were significantly higher in both the markedly positive and moderately to slightly positive RA groups than in the negative RA group. A comparison of anti-ECA antibody levels with total scores for synovitis revealed a strong and significant correlation. Furthermore, levels of anti-ECA antibodies were also correlated with rheumatoid factor and C-reactive protein. Clinically diagnosed RA patients having anti-ECA antibodies in SF showed typical or characteristic histological features of RA synovitis. Our data suggest that a group of RA patients with an entrobacterial etiology exists in larger groups of patients with RA which is thought to be a heterogeneous disease.

  7. Antismooth muscle and antiactin antibodies are indirect markers of histological and biochemical activity of autoimmune hepatitis.

    Science.gov (United States)

    Couto, Claudia A; Bittencourt, Paulo L; Porta, Gilda; Abrantes-Lemos, Clarice P; Carrilho, Flair J; Guardia, Bianca D; Cançado, Eduardo L R

    2014-02-01

    Reactivity and titers of autoantibodies vary during the course of autoimmune hepatitis (AIH), and some autoantibodies have been associated with disease activity and adverse outcomes after treatment. The aim of this study was to assess the autoantibody behavior in AIH and its significance as predictors of biochemical and histological remission. A total of 117 patients with AIH (mean age 18.6 [4-69] years) were evaluated and tested for autoantibodies at disease onset and successively (mean 3.2 [2-6] times) after a mean follow-up evaluation of 70 [20-185] months. Antismooth muscle (ASMA), antiliver kidney microsome type 1 (anti-LKM1), antiliver cytosol type 1 (anti-LC1), antimitochondrial, antinuclear (ANA), and antiactin antibodies (AAA) were determined at disease onset and 379 other times during the follow-up evaluation through indirect immunofluorescence in rodent tissues, HEp-2 cells, and human fibroblasts. Anti-SLA/LP were assessed 45 times in the follow-up evaluation of 19 patients using enzyme-linked immunosorbent assay (ELISA). Upon admission, AIH types 1 and 2 were observed in 95 and 17 patients, respectively. Five subjects had AIH with anti-SLA/LP as the sole markers. Patients initially negative for AAA did not develop these antibodies thereafter. ANA were detected de novo in six and three subjects with AIH types 1 and 2, respectively. After treatment, only ASMA (>1:80) and AAA (>1:40) were significantly associated with biochemical (76.9% and 79.8%) and histological features (100% and 100%) of disease activity (P < 0.001). With the exception of ANA, the autoantibody profile does not markedly vary in the course of AIH. The persistence of high titers of ASMA and/or AAA in patients with AIH is associated with disease activity. © 2013 by the American Association for the Study of Liver Diseases.

  8. Fiducial markers for MR histological correlation in ex vivo or short-term in vivo animal experiments: a screening study.

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    Rouvière, Olivier; Reynolds, Carol; Le, Yuan; Lai, Jinping; Roberts, Lewis R; Felmlee, Joel P; Ehman, Richard L

    2006-01-01

    To test injectable fiducial markers for magnetic resonance (MR) histological correlation in ex vivo or in vivo animal experiments. A total of 35 potential markers were tested ex vivo in pork muscle. The end-points were: 1) visibility, size, and shape on MR images and at macroscopic examination; 2) 24-hour stability; and 3) microscopic appearance. Selected markers were injected in vivo (rabbit's muscle and breast tumor tissue) to test their three-hour in vivo stability and their potential toxicity. Finally, different dilutions of the two best markers were assessed again through the same screening tests to determine whether their size on MR images could be customized by dilution. Two fluid acrylic paints containing inorganic pigments were found to be potentially interesting markers. On MR images, they created well-defined susceptibility artifacts. The markers made with iridescent bronze paint (iron oxide coated mica particles) were readily visible on microscopy and their size on MR images could be customized by dilution. The iridescent stainless steel paint (iron, chromium, nickel) created ex vivo the smallest markers in tissue but needed colloidal iron staining to be visible on microscopy and could not be easily diluted. Fluid acrylic paints are potentially interesting markers for MR histological correlation. Further studies are needed to assess their long-term properties.

  9. Comparative histology of muscle in free ranging cetaceans: shallow versus deep diving species.

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    Sierra, E; Fernández, A; Espinosa de los Monteros, A; Díaz-Delgado, J; Bernaldo de Quirós, Y; García-Álvarez, N; Arbelo, M; Herráez, P

    2015-10-30

    Different marine mammal species exhibit a wide range of diving behaviour based on their breath-hold diving capabilities. They are classically categorized as long duration, deep-diving and short duration, shallow-diving species. These abilities are likely to be related to the muscle characteristics of each species. Despite the increasing number of publications on muscle profile in different cetacean species, very little information is currently available concerning the characteristics of other muscle components in these species. In this study, we examined skeletal muscle fiber type, fiber size (cross sectional area and lesser diameter), intramuscular substrates, and perimysium-related structures, by retrospective study in 146 stranded cetaceans involving 15 different species. Additionally, we investigated diving profile-specific histological features. Our results suggest that deep diving species have higher amount of intramyocyte lipid droplets, and evidence higher percentage of intramuscular adipose tissue, and larger fibre sizes in this group of animals.

  10. Microsatellite Markers for the Invasive Species Bidens alba (Asteraceae

    Directory of Open Access Journals (Sweden)

    Yong-Bin Lu

    2014-05-01

    Full Text Available Premise of the study: Microsatellite markers were developed in the invasive species Bidens alba (Asteraceae to assess its population structure and to facilitate tracking its expansion in China. Methods and Results: Using 454 pyrosequencing, 20 microsatellite primer sets were developed for B. alba. The markers were tested on one population of B. alba (30 individuals and one population of the closely related B. pilosa (30 individuals in China. For B. alba, all of the markers were polymorphic, and the number of alleles per locus ranged from three to 32. The expected heterozygosity values were from 0.3787 to 0.9284, and the Shannon–Wiener index was from 0.6796 to 2.8401. Conclusions: These markers will be useful for investigating the genetic structure, genetic diversity, and invasion dynamics of B. alba and will also be useful in studies of B. pilosa.

  11. Metagenomic species profiling using universal phylogenetic marker genes

    DEFF Research Database (Denmark)

    Sunagawa, Shinichi; Mende, Daniel R; Zeller, Georg

    2013-01-01

    To quantify known and unknown microorganisms at species-level resolution using shotgun sequencing data, we developed a method that establishes metagenomic operational taxonomic units (mOTUs) based on single-copy phylogenetic marker genes. Applied to 252 human fecal samples, the method revealed...

  12. Prognostic role of histological necrosis for nonmetastatic clear cell renal cell carcinoma: correlation with pathological features and molecular markers.

    Science.gov (United States)

    Minervini, Andrea; Di Cristofano, Claudio; Gacci, Mauro; Serni, Sergio; Menicagli, Michele; Lanciotti, Michele; Salinitri, Giuseppe; Rocca, Carlo Della; Lapini, Alberto; Nesi, Gabriella; Bevilacqua, Generoso; Minervini, Riccardo; Carini, Marco

    2008-10-01

    We defined the prognostic role of tumor necrosis and its extent in nonmetastatic clear cell renal cell carcinoma. Also, we further investigated its pathogenesis by correlating this tumor feature with other pathological characteristics and molecular markers related to the von Hippel Lindau-hypoxia inducible factor pathway and to tumor proliferation. A total of 213 patients with nonmetastatic clear cell renal cell carcinoma were evaluated. Mean followup was 66 months. The presence and extent of histological necrosis were correlated with clinicopathological factors, Ki-67 antigen expression calculated by the MIB-1 (Ki-67 antibody) index, pVHL, HIF-1alpha, the tumor infiltrating lymphocyte subset and cancer specific survival. Histological necrosis was present in 63.8% of clear cell renal cell carcinoma cases. Necrosis was significantly associated with grade and the degree of tumor infiltrating lymphocytes, while its extent correlated significantly with grade, the degree of tumor infiltrating lymphocytes and stage. Tumor necrosis was a significant prognostic factor, which was confirmed even when limiting analysis to patients with intracapsular renal cell carcinoma. On multivariate analysis histological necrosis was not an independent predictor of cancer specific survival. The extent of tumor necrosis was not a significant prognostic factor. The presence and extent of histological necrosis was not associated with high Ki-67 expression and it did not correlate with pVHL expression or with nuclear and cytoplasmic HIF-1alpha expression. Based on our results we cannot support histological necrosis and its extent as prognostic factors for clear cell renal cell carcinoma. Efforts should be made to develop nomograms that use routinely available and objective predictor variables. The precise mechanism that causes tumor necrosis remains unknown but the host immune response might significantly contribute to its development.

  13. [Application of ISSR molecular marker in invasive plant species study].

    Science.gov (United States)

    Gui, Fu-Rong; Guo, Jian-Ying; Wan, Fang-Hao

    2007-04-01

    Alien species invasion is one of the most important drivers of worldwide environmental change, which may result in environmental degradation, biodiversity loss, and food and water shortage. It may also increase the possibility and severity of natural disasters, and damage international trade and benefits. In last two decades, DNA-based molecular markers were widely used to detect the genetic diversity of invaded alien species. Inter-simple sequence repeat (ISSR) is a microsatellite-based technique, with the superiorities of simple, quick, reliable, and generating higher levels of DNA polymorphism, and being used as a new molecular marker for genetic study. This paper introduced the principles, characteristics and procedures of ISSR, and summarized its applications in studying the genetic structure, genetic diversity, origin, distribution mode, phylogenesis, and breeding features of invasive plants.

  14. Investigation of potential early Histologic markers of pediatric inflammatory bowel disease.

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    Bass, Julie A; Friesen, Craig A; Deacy, Amanda D; Neilan, Nancy A; Bracken, Julia M; Shakhnovich, Valentina; Singh, Vivekanand

    2015-10-13

    Early manifestations of pediatric inflammatory bowel disease (IBD) can be relatively nonspecific. Initial mucosal biopsies may not be conclusive, delaying the diagnosis until subsequent biopsies demonstrate typical histologic features of IBD. We hypothesized that certain inflammatory cell types may be utilized as early histologic indicators of IBD in children. A retrospective analysis compared histologic findings from initially inconclusive or negative endoscopic studies in 22 patients who were subsequently diagnosed with IBD (after diagnostic endoscopy) to those of 20 comparison patients with functional abdominal pain matched for age, gender, and study type. A pediatric pathologist, blinded to study group, reviewed biopsies for histologic abnormalities. Eosinophil densities were obtained from the stomach, duodenum, and rectosigmoid areas. Immunohistochemistry (IHC) staining for tumor necrosis factor-α (TNF-α) and matrix metalloproteinase-9 (MMP-9) was performed on the stomach and rectosigmoid areas. Gastritis and colonic crypt distortion were present in the IBD group at a greater rate (61 % vs. 22 %, p = 0.020; 34 % vs. 4 %, p = 0.008, respectively). Peak and mean eosinophil densities in the rectosigmoid area were greater in the IBD group (17.0/hpf vs. 5.0/hpf, p = 0.0063; 12.3/hpf vs. 4.2/hpf, p = 0.0106, respectively). TNF-α and MMP-9 staining did not reveal any significant differences. Our data suggests that significantly greater inflammation in the stomach, crypt distortion in the colon, and eosinophilia in the rectosigmoid distinguished the IBD group from the comparison group at the time of the initial endoscopic evaluation.

  15. Development of simple sequence repeat markers in cymbopogon species.

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    Kumar, Jitendra; Verma, Vijeshwar; Shahi, Ashok Kumar; Qazi, Gulam Nab; Balyan, Harindra Singh

    2007-03-01

    The genus Cymbopogon comprises about 140 species, which produce characteristic aromatic essential oils. However, the phenotypic identification of species of Cymbopogon has been difficult as a result of widespread occurrence of natural variants, which differ in ploidy levels and chemotaxonomic complexities. Therefore, we have developed a set of simple sequence repeat markers from a genomic library of Cymbopogon jwarancusa to help in the precise identification of the species (including accessions) of Cymbopogon. For this purpose, we isolated 16 simple sequence repeat containing genomic deoxyribonucleic acid clones of C. jwarancusa, which contained a total of 32 simple sequence repeats with a range of 1 to 3 simple sequence repeats per clone. The majority (68.8%) of the 32 simple sequence repeats comprised dinucleotide repeat motifs followed by simple sequence repeats with trinucleotide (21.8%) and other higher order repeat motifs. Eighteen (81.8%) of the 22 designed primers for the above simple sequence repeats amplified products of expected sizes, when tried with genomic DNA of C. jwarancusa, the source species. Thirteen (72.2%) of the 18 functional primers detected polymorphism among the three species of Cymbopogon (C. flexuosus, C. pendulus and C. jwarancusa) and amplified a total of 95 alleles (range 1-18 alleles) with a PIC value of 0.44 to 0.96 per simple sequence repeat. Thus, the higher allelic range and high level of polymorphism demonstrated by the newly developed simple sequence repeat markers are likely to have many applications such as in improvement of essential oil quality by authentication of Cymbopogon species and varieties and mapping or tagging the genes controlling agronomically important traits of essential oils, which can further be utilized in marker assisted breeding.

  16. Markers of fibrosis and epithelial to mesenchymal transition demonstrate field cancerization in histologically normal tissue adjacent to breast tumors

    Science.gov (United States)

    Trujillo, Kristina A.; Heaphy, Christopher M.; Mai, Minh; Vargas, Keith M.; Jones, Anna C.; Vo, Phung; Butler, Kimberly S.; Joste, Nancy E.; Bisoffi, Marco; Griffith, Jeffrey K

    2011-01-01

    Previous studies have shown that a field of genetically altered but histologically normal tissue extends 1 cm or more from the margins of human breast tumors. The extent, composition and biological significance of this field are only partially understood, but the molecular alterations in affected cells could provide mechanisms for limitless replicative capacity, genomic instability and a microenvironment that supports tumor initiation and progression. We demonstrate by microarray, qRT-PCR and immunohistochemistry a signature of differential gene expression that discriminates between patient-matched, tumor-adjacent histologically normal breast tissues located 1 cm and 5 cm from the margins of breast adenocarcinomas (TAHN-1 and TAHN-5, respectively). The signature includes genes involved in extracellular matrix remodeling, wound healing, fibrosis and epithelial to mesenchymal transition (EMT). Myofibroblasts, which are mediators of wound healing and fibrosis, and intra-lobular fibroblasts expressing MMP2, SPARC, TGF-β3, which are inducers of EMT, were both prevalent in TAHN-1 tissues, sparse in TAHN-5 tissues, and absent in normal tissues from reduction mammoplasty. Accordingly, EMT markers S100A4 and vimentin were elevated in both luminal and myoepithelial cells, and EMT markers α-smooth muscle actin and SNAIL were elevated in luminal epithelial cells of TAHN-1 tissues. These results identify cellular processes that are differentially activated between TAHN-1 and TAHN-5 breast tissues, implicate myofibroblasts as likely mediators of these processes, provide evidence that EMT is occurring in histologically normal tissues within the affected field and identify candidate biomarkers to investigate whether or how field cancerization contributes to the development of primary or recurrent breast tumors. PMID:21105047

  17. Anatomy and histology of the prostate and glands of Cowper in three species of neotropical bats.

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    Miotti, María Daniela; Mollerach, Marcos I; Barquez, Ruben M

    2018-03-01

    The reproductive accessory glands (RAG) are essential components in reproduction because their secretion products ensure survival, viability, and sperm motility. The objective of this study was to characterize and compare the morphological and histological structure of the RAG in three species of bats of the genus Sturnira (S. erythromos, S. lilium, and S. oporaphilum). The RAG complex comprise a compact gland (prostate), which surrounds the urethra, and a pair of Glands of Cowper at the base of penis. Anatomical and histologically, the prostate are differentiated in two regions, ventral and dorsal. The dorsal region has tubuloalveolar glands with secretions fine granular or accumulations of a gel-like substance with bubbles and the ventral region, has alveolar glands with secretory cells form a single-layer of small cells. The seminal vesicles are absent. The prostatic morphology of the three species is similar to that of other studied Stenodermatinae and Desmodontinae, but differs from other subfamilies of Phyllostomidae (Carollinae, Glossophaginae, and Phyllostominae) as that of Molossidae and Vespertilionidae. The RAG complex has no annual variation in relation to functionality or size, but it is variable depending on age (subadults and adults). This agrees with the annual reproductive pattern described for these species in these latitudes, where adult males are reproductively active throughout the year. © 2017 Wiley Periodicals, Inc.

  18. [Clinical and clinico-histological markers in chronic destructive adult periodontitis].

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    Hernández Vallejo, G; García Rodríguez, M D; Tejerina Lobo, J M; López Sánchez, A F; De la Roca, C

    1989-05-01

    This study was designed to evaluate the significance and interrelationship of clinical parameters and their association with histologic changes in advanced destructive periodontitis. 158 patients with PDI greater than 4 (Ramfjord) were selected, evaluating the size, contouring, bleeding, consistency, colour and gingival pain. Epithelial ulceration of soft periodontal pockets were also evaluated. The results showed a statistically significant association between purplish colour and gingival fibrosis and advanced stage of the disease. Gingival bleeding on probing was the most important clinical parameter in advanced phases of the disease, either alone or in association with other parameters such as the presence of epithelial ulcerations. The Periodontal Disease Index (Ramfjord) has proven effective in the evaluation of generalized patterns of disease.

  19. Novel Molecular Markers of Malignancy in Histologically Normal and Benign Breast

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    Aejaz Nasir

    2011-01-01

    Full Text Available To detect the molecular changes of malignancy in histologically normal breast (HNB tissues, we recently developed a novel 117-gene-malignancy-signature. Here we report validation of our leading malignancy-risk-genes, topoisomerase-2-alpha (TOP2A, minichromosome-maintenance-protein-2 (MCM2 and “budding-uninhibited-by-benzimidazoles-1-homolog-beta” (BUB1B at the protein level. Using our 117-gene malignancy-signature, we classified 18 fresh-frozen HNB tissues from 18 adult female breast cancer patients into HNB-tissues with low-grade (HNB-LGMA; =9 and high-grade molecular abnormality (HNB-HGMA; =9. Archival sections of additional HNB tissues from these patients, and invasive ductal carcinoma (IDC tissues from six other patients were immunostained for these biomarkers. TOP2A/MCM2 expression was assessed as staining index (% and BUB1B expression as H-scores (0–300. Increasing TOP2A, MCM2, and BUB1B protein expression from HNB-LGMA to HNB-HGMA tissues to IDCs validated our microarray-based molecular classification of HNB tissues by immunohistochemistry. We also demonstrated an increasing expression of TOP2A protein on an independent test set of HNB/benign/reductionmammoplasties, atypical-ductal-hyperplasia with and without synchronous breast cancer, DCIS and IDC tissues using a custom tissue microarray (TMA. In conclusion, TOP2A, MCM2, and BUB1B proteins are potential molecular biomarkers of malignancy in histologically normal and benign breast tissues. Larger-scale clinical validation studies are needed to further evaluate the clinical utility of these molecular biomarkers.

  20. Skin histology and its role in heat dissipation in three pinniped species

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    Khamas Wael A

    2012-08-01

    Full Text Available Abstract Background Pinnipeds have a thick blubber layer and may have difficulty maintaining their body temperature during hot weather when on land. The skin is the main thermoregulatory conduit which emits excessive body heat. Methods Thorough evaluation of the skin histology in three pinniped species; the California sea lion-Zalophus californianus, the Pacific harbor seal-Phoca vitulina richardsi, and the Northern elephant seal-Mirounga angustirostris, was conducted to identify the presence, location and distribution of skin structures which contribute to thermoregulation. These structures included hair, adipose tissue, sweat glands, vasculature, and arteriovenous anastomoses (AVA. Thermal imaging was performed on live animals of the same species to correlate histological findings with thermal emission of the skin. Results The presence and distribution of skin structures directly relates to emissivity of the skin in all three species. Emissivity of skin in phocids (Pacific harbor and Northern elephant seals follows a different pattern than skin in otariids (California sea lions. The flipper skin in phocids tends to be the most emissive region during hot weather and least emissive during cold weather. On the contrary in otariids, skin of the entire body has a tendency to be emissive during both hot and cold weather. Conclusion Heat dissipation of the skin directly relates to the presence and distribution of skin structures in all three species. Different skin thermal dissipation patterns were observed in phocid versus otariid seals. Observed thermal patterns can be used for proper understanding of optimum thermal needs of seals housed in research facilities, rescue centers and zoo exhibits.

  1. OXA-258 from Achromobacter ruhlandii: a species-specific marker.

    Science.gov (United States)

    Papalia, Mariana; Almuzara, Marisa; Cejas, Daniela; Traglia, German; Ramírez, Maria Soledad; Galanternik, Laura; Vay, Carlos; Gutkind, Gabriel; Radice, Marcela

    2013-05-01

    A new blaOXA-258 gene is described as a species-specific taxonomic marker for Achromobacter ruhlandii isolates (all recovered from cystic fibrosis patients). Even though OXA-258 differs from OXA-114 variants, isolates could be misidentified as A. xiloxosidans by the amplification of an inner fragment from the OXA-coding gene. A robust identification of A. ruhlandii can be achieved by sequencing this single OXA gene, as well as by a more laborious recently proposed multilocus sequence-typing (MLST) scheme.

  2. Proteinuria as a Noninvasive Marker for Renal Allograft Histology and Failure: An Observational Cohort Study.

    Science.gov (United States)

    Naesens, Maarten; Lerut, Evelyne; Emonds, Marie-Paule; Herelixka, Albert; Evenepoel, Pieter; Claes, Kathleen; Bammens, Bert; Sprangers, Ben; Meijers, Björn; Jochmans, Ina; Monbaliu, Diethard; Pirenne, Jacques; Kuypers, Dirk R J

    2016-01-01

    Proteinuria is routinely measured to assess renal allograft status, but the diagnostic and prognostic values of this measurement for renal transplant pathology and outcome remain unclear. We included 1518 renal allograft recipients in this prospective, observational cohort study. All renal allograft biopsy samples with concomitant data on 24-hour proteinuria were included in the analyses (n=2274). Patients were followed for ≥7 years post-transplantation. Compared with proteinuria proteinuria 0.3-1.0 g/24 h, 2.17 (95% CI, 1.49 to 3.18; Pproteinuria 1.0-3.0 g/24 h, and 3.01 (95% CI, 1.75 to 5.18; Pproteinuria >3.0 g/24 h, independent of GFR and allograft histology. The predictive performance of proteinuria for graft failure was lower at 3 months after transplant (area under the receiver-operating characteristic curve [AUC] 0.64, Pproteinuria were repeat transplantation, mean arterial pressure, transplant glomerulopathy, microcirculation inflammation, and de novo/recurrent glomerular disease. The discriminatory power of proteinuria for these intragraft injury processes was better in biopsy samples obtained >3 months after transplant (AUC 0.73, Pproteinuria >1.0 g/24 h. These data support current clinical guidelines to routinely measure proteinuria after transplant, but illustrate the need for more sensitive biomarkers of allograft injury and prognosis. Copyright © 2016 by the American Society of Nephrology.

  3. Proteinuria as a Noninvasive Marker for Renal Allograft Histology and Failure: An Observational Cohort Study

    Science.gov (United States)

    Lerut, Evelyne; Emonds, Marie-Paule; Herelixka, Albert; Evenepoel, Pieter; Claes, Kathleen; Bammens, Bert; Sprangers, Ben; Meijers, Björn; Jochmans, Ina; Monbaliu, Diethard; Pirenne, Jacques; Kuypers, Dirk R.J.

    2016-01-01

    Proteinuria is routinely measured to assess renal allograft status, but the diagnostic and prognostic values of this measurement for renal transplant pathology and outcome remain unclear. We included 1518 renal allograft recipients in this prospective, observational cohort study. All renal allograft biopsy samples with concomitant data on 24-hour proteinuria were included in the analyses (n=2274). Patients were followed for ≥7 years post-transplantation. Compared with proteinuria failure were 1.14 (95% confidence interval [95% CI], 0.81 to 1.60; P=0.50), for proteinuria 0.3–1.0 g/24 h, 2.17 (95% CI, 1.49 to 3.18; P3.0 g/24 h, independent of GFR and allograft histology. The predictive performance of proteinuria for graft failure was lower at 3 months after transplant (area under the receiver-operating characteristic curve [AUC] 0.64, P3 months after transplant (AUC 0.73, P1.0 g/24 h. These data support current clinical guidelines to routinely measure proteinuria after transplant, but illustrate the need for more sensitive biomarkers of allograft injury and prognosis. PMID:26152270

  4. PET/MR in invasive ductal breast cancer: correlation between imaging markers and histological phenotype.

    Science.gov (United States)

    Catalano, Onofrio Antonio; Horn, Gary Lloyd; Signore, Alberto; Iannace, Carlo; Lepore, Maria; Vangel, Mark; Luongo, Angelo; Catalano, Marco; Lehman, Constance; Salvatore, Marco; Soricelli, Andrea; Catana, Ciprian; Mahmood, Umar; Rosen, Bruce Robert

    2017-03-28

    Differences in genetics and receptor expression (phenotypes) of invasive ductal breast cancer (IDC) impact on prognosis and treatment response. Immunohistochemistry (IHC), the most used technique for IDC phenotyping, has some limitations including its invasiveness. We explored the possibility of contrast-enhanced positron emission tomography magnetic resonance (CE-FDG PET/MR) to discriminate IDC phenotypes. 21 IDC patients with IHC assessment of oestrogen receptor (ER), progesterone receptor (PR), human epidermal growth factor-2 (HER2), and antigen Ki-67 (Ki67) underwent CE-FDG PET/MR. Magnetic resonance-perfusion biomarkers, apparent diffusion coefficient (ADC), and standard uptake value (SUV) were compared with IHC markers and phenotypes, using a Student's t-test and one-way ANOVA. ER/PR- tumours demonstrated higher Kepmean and SUVmax than ER or PR+ tumours. HER2- tumours displayed higher ADCmean, Kepmean, and SUVmax than HER2+tumours. Only ADCmean discriminated Ki67⩽14% tumours (lower ADCmean) from Ki67>14% tumours. PET/MR biomarkers correlated with IHC phenotype in 13 out of 21 patients (62%; P=0.001). Positron emission tomography magnetic resonance might non-invasively help discriminate IDC phenotypes, helping to optimise individual therapy options.

  5. Greek PDO saffron authentication studies using species specific molecular markers.

    Science.gov (United States)

    Bosmali, I; Ordoudi, S A; Tsimidou, M Z; Madesis, P

    2017-10-01

    Saffron, the spice produced from the red stigmas of the flower of Crocus sativus L. is a frequent target of fraud and mislabeling practices that cannot be fully traced using the ISO 3632 trade standard specifications and test methods. A molecular approach is proposed herein as a promising branding strategy for the authentication of highly esteemed saffron brands such as the Greek Protected Designation of Origin (PDO) "Krokos Kozanis". Specific ISSR (inter-simple sequence repeat) markers were used to assess for the first time, the within species variability of several populations of C. sativus L. from the cultivation area of "Krokos Kozanis" as well as the potential differences with the band pattern produced by other Crocus species. Then, species-specific markers were developed taking advantage of an advanced molecular technique such as the HRM analysis coupled with universal DNA barcoding regions (trnL) (Bar-HRM) and applied to saffron admixtures with some of the most common plant adulterants (Calendula officinalis, Carthamus tinctorius, Gardenia jasminoides, Zea mays and Curcuma longa). The sensitivity of the procedure was tested for turmeric as a case study whereas HPLC-fluorescence determination of secondary metabolites was also employed for comparison. The overall results indicated that the Bar-HRM approach is quite effective in terms of specificity and sensitivity. Its effectiveness regarding the detection of turmeric was comparable to that of a conventional HPLC method (0.5% vs 1.0%, w/w). Yet, the proposed DNA-based method is much faster, cost-effective and can be used even by non-geneticists, in any laboratory having access to an HRM-capable real-time PCR instrumentation. It can be, thus, regarded as a strong analytical tool in saffron authentication studies. Copyright © 2017 Elsevier Ltd. All rights reserved.

  6. In vitro propagation of rare species Ruscus aculeatus L. and histological peculiarities of the regenerants

    Directory of Open Access Journals (Sweden)

    Anca AIFTIMIE-PĂUNESCU

    2012-05-01

    Full Text Available The present study belongs to the international efforts for plant conservation in the areas endangered by human activities. Ruscus aculeatus L. is one of the threatened plants (included in all national red list of vascular plants from Romania that grow in the Natural Park Comana, Southern Romania.Seedlings and fragments of rhizome, from plants grown in the natural habitat have been used for in vitro plant regeneration and multiplication. After successfully rooting and acclimatization of the regenerated plantlets, histological studies have been performed in order to compare the regenerants from in vitro cultures with plants from natural habitat. The results indicated that this plant species can be multiplicated, rooted and acclimatized on synthetic medium (MS supplemented with NAA, IBA, kinetin and BAP with a good efficiency and the regenerants develop a only a few structural modification under vitroculture conditions, with no major consequences for a normal physiology and plant acclimatization.

  7. Anatomy and histology of the Fibrocartilago humerocapsularis in some species of European wild birds.

    Science.gov (United States)

    Canova, Marco; Bombardi, Cristiano; De Sordi, Nadia; Clavenzani, Paolo; Grandis, Annamaria

    2014-07-01

    The occurrence and structure of the fibrocartilago humerocapsularis (FHC) in the shoulders of 72 subjects of various species of wild birds were evaluated by gross dissection and histological examination with the purpose of increasing the body of knowledge regarding this structure and verifying the functional hypotheses submitted in the past in other species. The results showed that the FHC has a conical shape with a narrow cavity on the inside. The structure is heterogeneous in the various species and consists of different tissues, such as hyaline cartilage, fibrous cartilage, and bone. From the data obtained in this study, there does not appear to be any correlation between ossification and the weight of the prey lifted, wing shape, and aging. This study also provided interesting preliminary data regarding the ossification of the FHC. In fact, in the Hooded Crow (Corvus cornix), the ossification seemed to be correlated with the mechanical stimulation of flying. Additional studies are necessary to confirm this hypothesis. © 2014 Wiley Periodicals, Inc.

  8. Authentication Markers for Five Major Panax Species Developed via Comparative Analysis of Complete Chloroplast Genome Sequences.

    Science.gov (United States)

    Nguyen, Van Binh; Park, Hyun-Seung; Lee, Sang-Choon; Lee, Junki; Park, Jee Young; Yang, Tae-Jin

    2017-08-02

    Ginseng represents a set of high-value medicinal plants of different species: Panax ginseng (Asian ginseng), Panax quinquefolius (American ginseng), Panax notoginseng (Chinese ginseng), Panax japonicus (Bamboo ginseng), and Panax vietnamensis (Vietnamese ginseng). Each species is pharmacologically and economically important, with differences in efficacy and price. Accordingly, an authentication system is needed to combat economically motivated adulteration of Panax products. We conducted comparative analysis of the chloroplast genome sequences of these five species, identifying 34-124 InDels and 141-560 SNPs. Fourteen InDel markers were developed to authenticate the Panax species. Among these, eight were species-unique markers that successfully differentiated one species from the others. We generated at least one species-unique marker for each of the five species, and any of the species can be authenticated by selection among these markers. The markers are reliable, easily detectable, and valuable for applications in the ginseng industry as well as in related research.

  9. Some Aspects of the Anatomy and Histology of Digestive Tracts in Two Sympatric Species of Freshwater Fishes

    Directory of Open Access Journals (Sweden)

    Taher Ba-Omar

    2003-06-01

    Full Text Available Comparative anatomy and histology of the digestive tracts of two sympatric species of freshwater fish, Aphanius dispar (Cyprinodontidae and Garra barreimiae (Cyprinidae are studied. Morphometric measurements of alimentary canal such as length and the number and height of rugae in sections have been made for both species. Relationships between these morphometric characters and the total length of fish have been evaluated. The ratio between the length of alimentary canal and total length of fish in both species reflects their feeding habits. Histology of the ‘stomach’ and ‘intestine’ of these two species as shown by light microscopy has been described and compared. Results of this study are used to discuss the query whether these species have true stomachs.

  10. Isolation and characterization of ten polymorphic microsatellite markers for three cryptic Gammarus fossarum (Amphipoda) species

    OpenAIRE

    Westram A. M.; Jokela J.; Keller I

    2010-01-01

    The ecologically important stream invertebrate Gammarus fossarum is a morphospecies that includes at least three genetically differentiated biological species. We developed ten microsatellite markers and tested them in a total of 208 individuals from all three known cryptic species (types A B and C). All markers were polymorphic and successfully amplified in type A nine in type B and five in type C. There were up to 11 alleles per marker and species.

  11. Some Aspects of the Anatomy and Histology of Digestive Tracts in Two Sympatric Species of Freshwater Fishes

    OpenAIRE

    Taher Ba-Omar; Reginald Victor; Daniel Tobias

    2003-01-01

    Comparative anatomy and histology of the digestive tracts of two sympatric species of freshwater fish, Aphanius dispar (Cyprinodontidae) and Garra barreimiae (Cyprinidae) are studied. Morphometric measurements of alimentary canal such as length and the number and height of rugae in sections have been made for both species. Relationships between these morphometric characters and the total length of fish have been evaluated. The ratio between the length of alimentary canal and total length of f...

  12. Use of microsatellite markers in management of conifer forest species

    Science.gov (United States)

    Craig S. Echt

    1999-01-01

    Within the past ten years a new class of genetic marker1 has risen to prominence as the tool of choice for many geneticists. Microsatellite DNAs, or simple sequence repeats (SSRs), were first characterized as highly informative genetic markers in humans (Weber and May, 1990; Litt and Luty, 1990), and have since been found in practically all...

  13. Cross-species amplification of human microsatellite markers in pig ...

    Indian Academy of Sciences (India)

    Online only: http://www.ias.ac.in/jgenet/OnlineResources/90/e6.pdf]. Introduction. Microsatellite markers characterized in one ... genetic studies including paternity testing, pedigree analy- sis, population genetic studies etc., in captive ... stocks for future conservation breeding. Genetic markers are the basic tools to assess ...

  14. Distinguishing the Chinese materia medica Tiepishihu from similar Dendrobium species of the same genus using histological and microscopic method.

    Science.gov (United States)

    Yu, Kun-Zi; Yan, Hua; Tai, Hai-Chuan; Zhang, Nan-Ping; Cheng, Xian-Long; Guo, Zeng-Xi; Ma, Shuang-Cheng; Wei, Feng

    2017-07-01

    The Chinese Materia Medica, Tiepishihu, used as a tonic for over one thousand years, is a well-known precious medicine in China. According to the Chinese Pharmacopoeia, its source is the species Dendrobium officinale Kimura et Migo, which is distinguished from other species in Dendrobium genus. However, these species from the same genus are similar with Tiepishihu and caused confusion in the market. To find a quick and simple method to distinguish Tiepishihu from other similar species, histologic and microscopic methods were combined together to investigate the transverse section of stem of Tiepishihu and other similar species. Phloroglucinol test solution with hydrochloric acid was used to reveal the lignified tissue by staining the transverse section of Tiepishihu and similar species. Results revealed the unique identification characteristics to distinguish Tiepishihu from similar species, which were difficult to distinguish by other methods. The identification characteristics of Tiepishihu include the cells of vascular bundle sheath were stained red, parenchyma cells were not stained red. What's more, other species can be distinguished from each other with microscopic and histological characteristics. These characteristics proved stable and can be easily observed by normal light microscopic examination. This method is rapid, accurate, stable, and inexpensive. © 2017 Wiley Periodicals, Inc.

  15. Genetic markers in the species of rice ( Oryza L.) indigenous to Nigeria

    African Journals Online (AJOL)

    ... lower outer leaf sheath; and ripen-hull coloration have good value as markers in the identification of rice species and are also useful in tracing gene flow in a population of hybrid swarm. The use of these markers by our group has enhanced the understanding of the population dynamics in rice hybrid swarms as species, ...

  16. The Effects of Short-Term Propofol and Dexmedetomidine on Lung Mechanics, Histology, and Biological Markers in Experimental Obesity.

    Science.gov (United States)

    Heil, Luciana Boavista Barros; Santos, Cíntia L; Santos, Raquel S; Samary, Cynthia S; Cavalcanti, Vinicius C M; Araújo, Mariana M P N; Poggio, Hananda; Maia, Lígia de A; Trevenzoli, Isis Hara; Pelosi, Paolo; Fernandes, Fatima C; Villela, Nivaldo R; Silva, Pedro L; Rocco, Patricia R M

    2016-04-01

    Administering anesthetics to the obese population requires caution because of a variety of reasons including possible interactions with the inflammatory process observed in obese patients. Propofol and dexmedetomidine have protective effects on pulmonary function and are widely used in short- and long-term sedation, particularly in intensive care unit settings in lean and obese subjects. However, the functional and biological effects of these drugs in obesity require further elucidation. In a model of diet-induced obesity, we compared the short-term effects of dexmedetomidine versus propofol on lung mechanics and histology, as well as biological markers of inflammation and oxidative stress modulation in obesity. Wistar rats (n = 56) were randomly fed a standard diet (lean) or experimental diet (obese) for 12 weeks. After this period, obese animals received sodium thiopental intraperitoneally and were randomly allocated into 4 subgroups: (1) nonventilated (n = 4) for molecular biology analysis only (control); (2) sodium thiopental (n = 8); (3) propofol (n = 8); and (4) dexmedetomidine (n = 8), which received continuous IV administration of the corresponding agents and were mechanically ventilated (tidal volume = 6 mL/kg body weight, fraction of inspired oxygen = 0.4, positive end-expiratory pressure = 3 cm H2O) for 1 hour. Compared with lean animals, obese rats did not present increased body weight but had higher total body and trunk fat percentages, airway resistance, and interleukin-6 levels in the lung tissue (P = 0.02, P = 0.0027, and P = 0.01, respectively). In obese rats, propofol, but not dexmedetomidine, yielded increased airway resistance, bronchoconstriction index (P = 0.016, P = 0.02, respectively), tumor necrosis factor-α, and interleukin-6 levels, as well as lower levels of nuclear factor-erythroid 2-related factor-2 and glutathione peroxidase (P = 0.001, Bonferroni-corrected t test). In this model of diet-induced obesity, a 1-hour propofol infusion

  17. Development of Multiplexed Marker Sets to Identify the Most Relevant Poplar Species for Breeding

    Directory of Open Access Journals (Sweden)

    Hilke Schroeder

    2017-12-01

    Full Text Available Within the genus Populus, about 30 species are classified into six sections, of which some are cross-compatible. Besides naturally occurring hybrids, huge breeding programs have led to a high number of artificially produced hybrids, for which the determination of genetically involved species by morphological characteristics is often difficult. This necessitates the use of molecular markers for the identification of both maternal as well as paternal species, and in the case of complex hybrids, the genealogy. For this reason, we developed new chloroplast and nuclear markers for the differentiation of up to 19 poplar species, with one to 32 individuals per species regularly used in breeding programs based on already known barcoding, other chloroplast regions, and nuclear genes of interest. We developed methods to identify species by either species-specific nucleotide variations or, when no initial information for the species was given, by using a set of markers either in a procedure of exclusion or in a multiplexed marker set. The developed markers can all be used with low-cost equipment, and some can additionally be applied using a genetic analyzer. We combined these markers in multiplexes for a very fast and easy-to-use application for the identification of poplar species and their hybrids.

  18. Relationship between Psidium species (Myrtaceae) by resistance gene analog markers: focus on nematode resistance.

    Science.gov (United States)

    Noia, L R; Tuler, A C; Ferreira, A; Ferreira, M F S

    2017-03-16

    Guava (Psidium guajava L.) crop is severely affected by the nematode Meloidogyne enterolobii. Native Psidium species have been reported as sources of resistance against this nematode. Knowledge on the molecular relationship between Psidium species based on plant resistance gene analogs (RGA) can be useful in the genetic breeding of guava for resistance to M. enterolobii. In this study, RGA markers from conserved domains, and structural features of plant R genes, were employed to characterize Psidium species and establish genetic proximity, with a focus on nematode resistance. SSR markers were also applied owing to their neutral nature, thus differing from RGA markers. For this, species reported as sources of resistance to M. enterolobii, such as P. cattleianum and P. friedrichsthalianum, as well as species occurring in the Atlantic Rainforest and susceptible genotypes, were investigated. In 10 evaluated Psidium species, high interspecific genetic variability was verified through RGA and SSR markers, with intraspecific variation in P. guajava higher with SSR, as was expected. Resistant species were clustered by RGA markers, and differential amplicons among genotypes resistant and susceptible to M. enterolobii were identified. Knowledge on the molecular relationships between Psidium species constitutes useful information for breeding of the guava tree, providing direction for hybridization and material for rootstocks. Additionally, the genetic relationship between native species, which have been little studied, and P. guajava were estimated by RGAs, which were confirmed as important markers for genetic diversity related to pathogen resistance.

  19. Inferring Species Trees Directly from Biallelic Genetic Markers: Bypassing Gene Trees in a Full Coalescent Analysis

    Science.gov (United States)

    Bryant, David; Bouckaert, Remco; Felsenstein, Joseph; Rosenberg, Noah A.; RoyChoudhury, Arindam

    2012-01-01

    The multispecies coalescent provides an elegant theoretical framework for estimating species trees and species demographics from genetic markers. However, practical applications of the multispecies coalescent model are limited by the need to integrate or sample over all gene trees possible for each genetic marker. Here we describe a polynomial-time algorithm that computes the likelihood of a species tree directly from the markers under a finite-sites model of mutation effectively integrating over all possible gene trees. The method applies to independent (unlinked) biallelic markers such as well-spaced single nucleotide polymorphisms, and we have implemented it in SNAPP, a Markov chain Monte Carlo sampler for inferring species trees, divergence dates, and population sizes. We report results from simulation experiments and from an analysis of 1997 amplified fragment length polymorphism loci in 69 individuals sampled from six species of Ourisia (New Zealand native foxglove). PMID:22422763

  20. Cross-species applicability of chicken microsatellite markers for ...

    African Journals Online (AJOL)

    We obtained blood samples of 57 Indian ducks (Anas platyrhynchos) belonging to three indigenous duck populations of geographically distinct locations of the country and genotyped them using chicken microsatellite markers. Twenty three of the 30 loci were amplified and 17 loci yielded high success rate (> 91%).

  1. Barcoding markers for Pneumocystis species in wildlife : Fungal Biology

    NARCIS (Netherlands)

    Danesi, P.; Da Rold, G.; Rizzoli, A.; Hauffe, H. C.; Marangon, S.; Samerpitak, K.; Demanche, C.; Guillot, J.; Capelli, G.; De Hoog, S. G.

    2016-01-01

    Lung specimens (n = 216) from six wildlife species were examined for occurrence of Pneumocystis species in pulmonary tissues. Among small mammals the shrew Sorex antinorii (80 %) were most frequently colonized. In contrast, foxes and badgers did not yield positive amplification. Host-specificity was

  2. New Microsatellite Markers for Tricyrtis macrantha (Convallariaceae and Cross-Amplification in Closely Related Species

    Directory of Open Access Journals (Sweden)

    Noriko Ohki

    2013-05-01

    Full Text Available Premise of the study: Microsatellite markers were characterized in Tricyrtis macrantha (sect. Brachycyrtis, Convallariaceae, a vulnerable species endemic to Japan, to investigate its genetic diversity and population structure. Methods and Results: Eleven microsatellite markers were developed. The number of alleles per locus ranged from one to seven, and genetic diversity per locus ranged from 0.142 to 0.812. Four markers were successfully amplified in other species of sect. Brachycyrtis (T. ishiiana, T. ishiiana var. surugensis, and T. macranthopsis. Conclusions: The microsatellite markers can be used to investigate the genetic diversity and population structure of the vulnerable and endangered species of Tricyrtis sect. Brachycyrtis, to aid in the development of conservation strategies for each species.

  3. Comparative histology of muscle in free ranging cetaceans: shallow versus deep diving species

    OpenAIRE

    Sierra, E.; Fernández, A; Espinosa de los Monteros, A.; Díaz-Delgado, J.; Y. Bernaldo de Quirós; N. García-Álvarez; Arbelo, M.; Herráez, P

    2015-01-01

    Different marine mammal species exhibit a wide range of diving behaviour based on their breath-hold diving capabilities. They are classically categorized as long duration, deep-diving and short duration, shallow-diving species. These abilities are likely to be related to the muscle characteristics of each species. Despite the increasing number of publications on muscle profile in different cetacean species, very little information is currently available concerning the characteristics of other...

  4. Genetic Diversity and Structure of Lolium Species Surveyed on Nuclear Simple Sequence Repeat and Cytoplasmic Markers

    Directory of Open Access Journals (Sweden)

    Hongwei Cai

    2017-04-01

    Full Text Available To assess the genetic diversity and population structure of Lolium species, we used 32 nuclear simple sequence repeat (SSR markers and 7 cytoplasmic gene markers to analyze a total of 357 individuals from 162 accessions of 9 Lolium species. This survey revealed a high level of polymorphism, with an average number of alleles per locus of 23.59 and 5.29 and an average PIC-value of 0.83 and 0.54 for nuclear SSR markers and cytoplasmic gene markers, respectively. Analysis of molecular variance (AMOVA revealed that 16.27 and 16.53% of the total variation was due to differences among species, with the remaining 56.35 and 83.47% due to differences within species and 27.39 and 0% due to differences within individuals in 32 nuclear SSR markers set and 6 chloroplast gene markers set, respectively. The 32 nuclear SSR markers detected three subpopulations among 357 individuals, whereas the 6 chloroplast gene markers revealed three subpopulations among 160 accessions in the STRUCTURE analysis. In the clustering analysis, the three inbred species clustered into a single group, whereas the outbreeding species were clearly divided, especially according to nuclear SSR markers. In addition, almost all Lolium multiflorum populations were clustered into group C4, which could be further divided into three subgroups, whereas Lolium perenne populations primarily clustered into two groups (C2 and C3, with a few lines that instead grouped with L. multiflorum (C4 or Lolium rigidum (C6. Together, these results will useful for the use of Lolium germplasm for improvement and increase the effectiveness of ryegrass breeding.

  5. Genome-Wide Microsatellite Characterization and Marker Development in the Sequenced Brassica Crop Species

    Science.gov (United States)

    Shi, Jiaqin; Huang, Shunmou; Zhan, Jiepeng; Yu, Jingyin; Wang, Xinfa; Hua, Wei; Liu, Shengyi; Liu, Guihua; Wang, Hanzhong

    2014-01-01

    Although much research has been conducted, the pattern of microsatellite distribution has remained ambiguous, and the development/utilization of microsatellite markers has still been limited/inefficient in Brassica, due to the lack of genome sequences. In view of this, we conducted genome-wide microsatellite characterization and marker development in three recently sequenced Brassica crops: Brassica rapa, Brassica oleracea and Brassica napus. The analysed microsatellite characteristics of these Brassica species were highly similar or almost identical, which suggests that the pattern of microsatellite distribution is likely conservative in Brassica. The genomic distribution of microsatellites was highly non-uniform and positively or negatively correlated with genes or transposable elements, respectively. Of the total of 115 869, 185 662 and 356 522 simple sequence repeat (SSR) markers developed with high frequencies (408.2, 343.8 and 356.2 per Mb or one every 2.45, 2.91 and 2.81 kb, respectively), most represented new SSR markers, the majority had determined physical positions, and a large number were genic or putative single-locus SSR markers. We also constructed a comprehensive database for the newly developed SSR markers, which was integrated with public Brassica SSR markers and annotated genome components. The genome-wide SSR markers developed in this study provide a useful tool to extend the annotated genome resources of sequenced Brassica species to genetic study/breeding in different Brassica species. PMID:24130371

  6. Development of New Candidate Gene and EST-Based Molecular Markers for Gossypium Species.

    Science.gov (United States)

    Buyyarapu, Ramesh; Kantety, Ramesh V; Yu, John Z; Saha, Sukumar; Sharma, Govind C

    2011-01-01

    New source of molecular markers accelerate the efforts in improving cotton fiber traits and aid in developing high-density integrated genetic maps. We developed new markers based on candidate genes and G. arboreum EST sequences that were used for polymorphism detection followed by genetic and physical mapping. Nineteen gene-based markers were surveyed for polymorphism detection in 26 Gossypium species. Cluster analysis generated a phylogenetic tree with four major sub-clusters for 23 species while three species branched out individually. CAP method enhanced the rate of polymorphism of candidate gene-based markers between G. hirsutum and G. barbadense. Two hundred A-genome based SSR markers were designed after datamining of G. arboreum EST sequences (Mississippi Gossypium arboreum  EST-SSR: MGAES). Over 70% of MGAES markers successfully produced amplicons while 65 of them demonstrated polymorphism between the parents of G. hirsutum and G. barbadense RIL population and formed 14 linkage groups. Chromosomal localization of both candidate gene-based and MGAES markers was assisted by euploid and hypoaneuploid CS-B analysis. Gene-based and MGAES markers were highly informative as they were designed from candidate genes and fiber transcriptome with a potential to be integrated into the existing cotton genetic and physical maps.

  7. Genome-wide microsatellite characterization and marker development in the sequenced Brassica crop species.

    Science.gov (United States)

    Shi, Jiaqin; Huang, Shunmou; Zhan, Jiepeng; Yu, Jingyin; Wang, Xinfa; Hua, Wei; Liu, Shengyi; Liu, Guihua; Wang, Hanzhong

    2014-02-01

    Although much research has been conducted, the pattern of microsatellite distribution has remained ambiguous, and the development/utilization of microsatellite markers has still been limited/inefficient in Brassica, due to the lack of genome sequences. In view of this, we conducted genome-wide microsatellite characterization and marker development in three recently sequenced Brassica crops: Brassica rapa, Brassica oleracea and Brassica napus. The analysed microsatellite characteristics of these Brassica species were highly similar or almost identical, which suggests that the pattern of microsatellite distribution is likely conservative in Brassica. The genomic distribution of microsatellites was highly non-uniform and positively or negatively correlated with genes or transposable elements, respectively. Of the total of 115 869, 185 662 and 356 522 simple sequence repeat (SSR) markers developed with high frequencies (408.2, 343.8 and 356.2 per Mb or one every 2.45, 2.91 and 2.81 kb, respectively), most represented new SSR markers, the majority had determined physical positions, and a large number were genic or putative single-locus SSR markers. We also constructed a comprehensive database for the newly developed SSR markers, which was integrated with public Brassica SSR markers and annotated genome components. The genome-wide SSR markers developed in this study provide a useful tool to extend the annotated genome resources of sequenced Brassica species to genetic study/breeding in different Brassica species.

  8. Novel chemotaxonomic markers of the Alternaria infectoria species-group

    DEFF Research Database (Denmark)

    Christensen, K.B.; Van Klink, J.W.; Weavers, R.T.

    2005-01-01

    Two new structurally related metabolites, novae-zelandin A (1) and novae-zelandin B (2), as well as the novel metabolite 4Z-infectopyrone (3) were purified from extracts of filamentous fungi belonging to the Alternaria infectoria species-group. The structures were elucidated by a combination of 1 D...

  9. Evaluation of four single-locus markers for leishmania species discrimination by sequencing

    NARCIS (Netherlands)

    van der Auwera, Gert; Ravel, Christophe; Verweij, Jaco J.; Bart, Aldert; Schönian, Gabriele; Felger, Ingrid

    2014-01-01

    Several genetic markers have been described for discriminating Leishmania species. In most reported cases, one or a few polymorphisms are the basis of species identification, and the methods were validated on a limited number of strains from a particular geographical region. Therefore, most

  10. Phylogenetic study of some Aporrectodea species based on molecular markers

    OpenAIRE

    Briard, Charlène; Qiu, Jiang-Ping; Qi, Zhao; Guernion, Muriel; Cluzeau, Daniel

    2012-01-01

    The Nicodrilus genus is not accepted in the nomenclature according to ICZN; Aporrectodea term is used. However, according to Bouché, Aporrectodea and Allolobophora genera are not homogeneous and are supposed as polyphyletic genera. The aim is to study the phylogenetic structure of Aporrectodea genus in order to verify its cladistic nature and its taxonomical validity. In this work, five species, belonging to the Aporrectodea genus, as the most common in France are studied. First, we use usual...

  11. The fur Gene as a New Phylogenetic Marker for Vibrionaceae Species Identification

    DEFF Research Database (Denmark)

    Machado, Henrique; Gram, Lone

    2015-01-01

    Microbial taxonomy is essential in all areas of microbial science. The 16S rRNA gene sequence is one of the main phylogenetic species markers; however, it does not provide discrimination in the family Vibrionaceae, where other molecular techniques allow better interspecies resolution. Although...... an in silico approach based on genomes from 103 Vibrionaceae strains, we demonstrate here the high resolution of the fur gene in the identification of Vibrionaceae species and its usefulness as a phylogenetic marker. The fur gene showed within-species similarity higher than 95%, and the relationships inferred...

  12. The effect of Hydro Alcoholic Extract of Quercus Species on Lipid Peroxidation and Brain Histology Following Cerebral Ischemia in Rats

    Directory of Open Access Journals (Sweden)

    R Zareh Ghafri

    2014-09-01

    Full Text Available Background & aim: The production of free radicals and lipid peroxidation are harmful to health. The aim of this study was to determine the effect of the ethanol extract of Quercus species on lipid peroxidation and the histology of the gyrus dentatus after rat cerebral ischemia. Methods: In the present experimental study, thirty male Wistar rats were divided randomly into three groups. Experimental groups 1 and 2 received 500 and 1000 mg kg hydro alcoholic extract of Quercus and control group were given distilled water at the same time, respectively. In all groups, both sides of common carotid artery was blocked and then opened for 15 minutes. After fifteen days, the mice were killed and the right and left hemisphere were used to determine the level of malondialdehyde by histological studies. Data were analyzed by one-way AOVA. Results: The average number of granular cells in the dentate gyrus of experimental groups were 32.5±1.5, 31.2±2.8, respectively, which was not significantly different in comparison to the control group (p>0.05. Conclusion: Hydro alcoholic extract of Quercus species inhibit lipid peroxidation by preventing the process of reducing ischemia-reperfusion after injury of nerve cells

  13. Development of genomic microsatellite markers in Coffea canephora and their transferability to other coffee species.

    Science.gov (United States)

    Poncet, Valérie; Dufour, Magali; Hamon, Perla; Hamon, Serge; de Kochko, Alexandre; Leroy, Thierry

    2007-12-01

    Of the 103 accepted Coffea species, 70% are threatened with extinction but only a few of them have been studied. A set of 40 polymorphic microsatellite markers was developed using a GA/GT-enriched Coffea canephora genomic library. Amplification of these markers was tested in accessions of C. heterocalyx (a Critically Endangered species) and C. pseudozanguebariae (a Vulnerable species) belonging to different African geographical clades. All microsatellites were polymorphic in C. canephora, with a mean allele number per polymorphic locus of more than 3 (at least 9 genotypes were tested). Observed and expected heterozygosities calculated for C. canephora and C. pseudozanguebariae varied from 0.10 to 0.91 and from 0.20 to 0.77, respectively. In total, 38 primer pairs (95%) were amplified in C. heterocalyx and C. pseudozanguebariae, indicating their high level of transferability across the genus Coffea. This large marker set will be useful for more extensive genetic studies of threatened Coffea species.

  14. Respective prognostic value of genomic grade and histological proliferation markers in early stage (pN0 breast carcinoma.

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    Fabien Reyal

    Full Text Available BACKGROUND: Genomic grade (GG is a 97-gene signature which improves the accuracy and prognostic value of histological grade (HG in invasive breast carcinoma. Since most of the genes included in the GG are involved in cell proliferation, we performed a retrospective study to compare the prognostic value of GG, Mitotic Index and Ki67 score. METHODS: A series of 163 consecutive breast cancers was retained (pT1-2, pN0, pM0, 10-yr follow-up. GG was computed using MapQuant Dx(R. RESULTS: GG was low (GG-1 in 48%, high (GG-3 in 31% and equivocal in 21% of cases. For HG-2 tumors, 50% were classified as GG-1, 18% as GG-3 whereas 31% remained equivocal. In a subgroup of 132 ER+/HER2- tumors GG was the most significant prognostic factor in multivariate Cox regression analysis adjusted for age and tumor size (HR = 5.23, p = 0.02. CONCLUSIONS: In a reference comprehensive cancer center setting, compared to histological grade, GG added significant information on cell proliferation in breast cancers. In patients with HG-2 carcinoma, applying the GG to guide the treatment scheme could lead to a reduction in adjuvant therapy prescription. However, based on the results observed and considering (i the relatively close prognostic values of GG and Ki67, (ii the reclassification of about 30% of HG-2 tumors as Equivocal GG and (iii the economical and technical requirements of the MapQuant micro-array GG test, the availability in the near future of a PCR-based Genomic Grade test with improved performances may lead to an introduction in clinical routine of this test for histological grade 2, ER positive, HER2 negative breast carcinoma.

  15. Respective prognostic value of genomic grade and histological proliferation markers in early stage (pN0) breast carcinoma.

    Science.gov (United States)

    Reyal, Fabien; Bollet, Marc A; Caly, Martial; Gentien, David; Carpentier, Sabrina; Peyro-Saint-Paul, Hélène; Pierga, Jean-Yves; Cottu, Paul; Dieras, Véronique; Sigal-Zafrani, Brigitte; Vincent-Salomon, Anne; Sastre-Garau, Xavier

    2012-01-01

    Genomic grade (GG) is a 97-gene signature which improves the accuracy and prognostic value of histological grade (HG) in invasive breast carcinoma. Since most of the genes included in the GG are involved in cell proliferation, we performed a retrospective study to compare the prognostic value of GG, Mitotic Index and Ki67 score. A series of 163 consecutive breast cancers was retained (pT1-2, pN0, pM0, 10-yr follow-up). GG was computed using MapQuant Dx(R). GG was low (GG-1) in 48%, high (GG-3) in 31% and equivocal in 21% of cases. For HG-2 tumors, 50% were classified as GG-1, 18% as GG-3 whereas 31% remained equivocal. In a subgroup of 132 ER+/HER2- tumors GG was the most significant prognostic factor in multivariate Cox regression analysis adjusted for age and tumor size (HR = 5.23, p = 0.02). In a reference comprehensive cancer center setting, compared to histological grade, GG added significant information on cell proliferation in breast cancers. In patients with HG-2 carcinoma, applying the GG to guide the treatment scheme could lead to a reduction in adjuvant therapy prescription. However, based on the results observed and considering (i) the relatively close prognostic values of GG and Ki67, (ii) the reclassification of about 30% of HG-2 tumors as Equivocal GG and (iii) the economical and technical requirements of the MapQuant micro-array GG test, the availability in the near future of a PCR-based Genomic Grade test with improved performances may lead to an introduction in clinical routine of this test for histological grade 2, ER positive, HER2 negative breast carcinoma.

  16. Development of microsatellite markers for six Tetranychus species by transfer from Tetranychus urticae genome.

    Science.gov (United States)

    Zhang, Jia; Sun, Jing-Tao; Jin, Peng-Yu; Hong, Xiao-Yue

    2016-09-01

    Microsatellite markers are frequently used to explore the population genetic structure of organisms. Spider mites (genus Tetranychus) are important agricultural pests. Several markers have been developed for T. urticae, but for other spider mites, few such markers are available, hampering studies of their population genetics. In this study, we developed and characterized microsatellite markers for six non-model spider mite species (T. truncatus, T. kanzawai, T. ludeni, T. piercei, T. phaselus and T. pueraricola) by cross-species amplification of markers in the T. urticae genome, in order to better understand the population structure of Tetranychus species. Among 228 screened loci, many were polymorphic, including 13 loci in T. urticae, 11 loci in T. truncatus, 15 loci in T. pueraricola, 23 loci in T. kanzawai, 19 loci in T. piercei, 11 loci in T. phaselus and 9 loci in T. ludeni. Sequence analysis determined that the fragment length variations of the transferred microsatellites were mainly due to the variations of the numbers of repeats. These new microsatellite markers should be useful for studying the population genetics of the seven Tetranychus species.

  17. Hepatic proliferation and angiogenesis markers are increased after portal deprivation in rats: a study of molecular, histological and radiological changes.

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    Florent Guérin

    Full Text Available To determine the pathogenesis of liver nodules, and lesions similar to obliterative portal venopathy, observed after portosystemic shunts or portal vein thrombosis in humans.We conducted an experimental study comparing portacaval shunt (PCS, total portal vein ligation (PVL, and sham (S operated rats. Each group were either sacrificed at 6 weeks (early or 6 months (late. Arterial liver perfusion was studied in vivo using CT, and histopathological changes were noted. Liver mRNA levels were quantified by RT-QPCR for markers of inflammation (Il10, Tnfa, proliferation (Il6st, Mki67, Hgf, Hnf4a, angiogenesis: (Vegfa, Vegfr 1, 2 and 3; Pgf, oxidative stress (Nos2, and 3, Hif1a, and fibrosis (Tgfb. PCS and PVL were compared to the S group.Periportal fibrosis and arterial proliferation was observed in late PCS and PVL groups. CT imaging demonstrated increased arterial liver perfusion in the PCS group. RT-QPCR showed increased inflammatory markers in PCS and PVL early groups. Tnfa and Il10 were increased in PCS and PVL late groups respectively. All proliferative markers increased in the PCS, and Hnf4a in the PVL early groups. Mki67 and Hnf4a were increased in the PCS late group. Nos3 was increased in the early and late PCS groups, and Hif1a was decreased in the PVL groups. Markers of angiogenesis were all increased in the early PCS group, and Vegfr3 and Pgf in the late PCS group. Only Vegfr3 was increased in the PVL groups. Tgf was increased in the PCS groups.Portal deprivation in rats induces a sustained increase in intrahepatic markers of inflammation, angiogenesis, proliferation, and fibrosis.

  18. Phylogenetic Relationships between Four Salix L. Species Based on DArT Markers

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    Jerzy A. Przyborowski

    2013-12-01

    Full Text Available The objectives of this study were to evaluate the usefulness of DArT markers in genotypic identification of willow species and describe genetic relationships between four willow species: Salix viminalis, S. purpurea, S. alba and S. triandra. The experimental plant material comprised 53 willow genotypes of these four species, which are popularly grown in Poland. DArT markers seem to identify Salix species with a high degree of accuracy. As a result, the examined species were divided into four distinct groups which corresponded to the four analyzed species. In our study, we observed that S. triandra was very different genetically from the other species, including S. alba which is generally classified into the same subgenus of Salix. The above corroborates the findings of other authors who relied on molecular methods to reveal that the classification of S. triandra to the subgenus Salix was erroneous. The Principal Coordinate Analysis (PCoA and the neighbor-joining dendrogram also confirmed the clear division of the studied willow genotypes into four clusters corresponding to individual species. This confirmed the usefulness of DArT markers in taxonomic analyses and identification of willow species.

  19. Genome- and transcriptome-assisted development of nuclear insertion/deletion markers for Calanus species (Copepoda: Calanoida) identification

    DEFF Research Database (Denmark)

    Smolina, I.; Kollias, S.; Poortvliet, M.

    2014-01-01

    Copepods of the genus Calanus are key zooplankton species in temperate to arctic marine ecosystems. Despite their ecological importance, species identification remains challenging. Furthermore, the recent report of hybrids among Calanus species highlights the need for diagnostic nuclear markers t...

  20. Analysis of genetic relationships of Central American and Mexican pines using RAPD markers that distinguish species

    OpenAIRE

    Furman, Burford J.; Grattapaglia, Dario; Dvorak, William S.; O'Malley, David M.

    1997-01-01

    Phylogenetic relationships were inferred for six Central American and Mexican pine species by analysing RAPD marker differences among pooled DNA samples. This population level pooling strategy discounts low-frequency allelic variation within taxa, thus obtaining a ‘cumulative genotype’ to compare among taxa. We used the morphologically based taxonomy of pines as the basis for inference concerning molecular marker divergence. Only RAPD polymorphisms that were repeatable and inte...

  1. Diffusion-weighted MRI in renal cell carcinoma: A surrogate marker for predicting nuclear grade and histological subtype

    Energy Technology Data Exchange (ETDEWEB)

    Goyal, Ankur; Sharma, Raju; Bhalla, Ashu S.; Gamanagatti, Shivanand (Dept. of Radiodiagnosis, All India Inst. of Medical Sciences (AIIMS), New Delhi (India)), Email: raju152@yahoo.com; Seth, Amlesh (Dept. of Urology, All India Inst. of Medical Sciences (AIIMS), New Delhi (India)); Iyer, Venkateswaran K.; Das, Prasenjit (Dept. of Pathology, All India Inst. of Medical Sciences (AIIMS), New Delhi (India))

    2012-04-15

    Background: Though previous investigators have attempted to evaluate its utility in characterization of focal renal lesions, diffusion-weighted MR imaging (DW MRI) in renal diseases is still an evolving field and its role in predicting the aggressiveness of renal cell carcinoma (RCC) is yet to be established. Purpose: To assess whether apparent diffusion coefficient (ADC) values can be used to determine the nuclear grade and histological subtype of RCCs and to identify the tumor attributes contributing to variation in ADC values. Material and Methods: The institutional ethics committee waived the requirement of informed consent for this retrospective study. The study cohort consisted of 33 patients who underwent MRI (with diffusion-weighted imaging at b values of 0 and 500 s/mm2) and were found to have 36 pathologically-proven RCCs. ADC values were determined for solid portions of RCC, cystic/hemorrhagic areas, and normal renal parenchyma. Histological subtype, nuclear grade, and cell count were determined for each lesion. ADC values were compared between different grades and subtypes and correlation with cell count was investigated. Receiver operating characteristic curves were drawn to establish cut-off ADC values. Results: There were 23 low grade (grades I and II) and 13 high grade tumors (grades III and IV). There were 32 clear-cell and four non-clear-cell RCCs. A decreasing trend of ADC values was seen with increasing grade and mean ADC of high grade RCC was significantly lower than low grade (1.3145 vs 1.6982 x 10-3 mm2/s) (P = 0.005). Mean ADC for clear-cell RCC was significantly higher than non-clear-cell RCC (1.6245 vs. 1.0412 x 10-3 mm2/s) (P = 0.005). ADC values higher than 1.7960 x 10-3 mm2/s were seen only with low grade and values greater than 1.4904 x 10-3 mm2/s were seen only with clear-cell RCC. Conclusion: ADC values provide a non-invasive means to predict the nuclear grade and histological subtype of RCC. Cellularity and morphology are other

  2. Development of microsatellite markers for Euryale ferox (Nymphaeaceae), an endangered aquatic plant species in Japan.

    Science.gov (United States)

    Imanishi, Ayumi; Kaneko, Shingo; Isagi, Yuji; Imanishi, Junichi; Natuhara, Yosihiro; Morimoto, Yukihiro

    2011-08-01

    Microsatellite markers were developed to investigate genetic diversity and genetic structure of Euryale ferox, a vulnerable aquatic plant. Ten microsatellite loci were isolated and characterized for this species. Eight loci showed polymorphisms with two or three alleles per locus. As for the polymorphic markers, the expected and observed heterozygosities ranged from 0.00 to 0.08 and 0.17 to 0.64, respectively. The 10 microsatellite markers described here will be useful for investigating genetic diversity, genetic structure, and gene flow between populations of E. ferox.

  3. Applications of molecular markers in the discrimination of Panax species and Korean ginseng cultivars (Panax ginseng

    Directory of Open Access Journals (Sweden)

    Ick Hyun Jo

    2017-10-01

    Full Text Available The development of molecular markers is one of the most useful methods for molecular breeding and marker-based molecular associated selections. Even though there is less information on the reference genome, molecular markers are indispensable tools for determination of genetic variation and identification of species with high levels of accuracy and reproducibility. The demand for molecular approaches for marker-based breeding and genetic discriminations in Panax species has greatly increased in recent times and has been successfully applied for various purposes. However, owing to the existence of diverse molecular techniques and differences in their principles and applications, there should be careful consideration while selecting appropriate marker types. In this review, we outline the recent status of different molecular marker applications in ginseng research and industrial fields. In addition, we discuss the basic principles, requirements, and advantages and disadvantages of the most widely used molecular markers, including restriction fragment length polymorphism, random amplified polymorphic DNA, sequence tag sites, simple sequence repeats, and single nucleotide polymorphisms.

  4. Applications of molecular markers in the discrimination of Panax species and Korean ginseng cultivars (Panax ginseng).

    Science.gov (United States)

    Jo, Ick Hyun; Kim, Young Chang; Kim, Dong Hwi; Kim, Kee Hong; Hyun, Tae Kyung; Ryu, Hojin; Bang, Kyong Hwan

    2017-10-01

    The development of molecular markers is one of the most useful methods for molecular breeding and marker-based molecular associated selections. Even though there is less information on the reference genome, molecular markers are indispensable tools for determination of genetic variation and identification of species with high levels of accuracy and reproducibility. The demand for molecular approaches for marker-based breeding and genetic discriminations in Panax species has greatly increased in recent times and has been successfully applied for various purposes. However, owing to the existence of diverse molecular techniques and differences in their principles and applications, there should be careful consideration while selecting appropriate marker types. In this review, we outline the recent status of different molecular marker applications in ginseng research and industrial fields. In addition, we discuss the basic principles, requirements, and advantages and disadvantages of the most widely used molecular markers, including restriction fragment length polymorphism, random amplified polymorphic DNA, sequence tag sites, simple sequence repeats, and single nucleotide polymorphisms.

  5. New Microsatellite Markers for Wild and Commercial Species of Passiflora (Passifloraceae and Cross-Amplification

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    Carlos B. M. Cerqueira-Silva

    2014-02-01

    Full Text Available Premise of the study: We developed the first microsatellites for Passiflora setacea and characterized new sets of markers for P. edulis and P. cincinnata, enabling further genetic diversity studies to support the conservation and breeding of passion fruit species. Methods and Results: We developed 69 microsatellite markers and, in conjunction with assessments of cross-amplification using primers available from the literature, present 43 new polymorphic microsatellite loci for three species of Passiflora. The mean number of alleles per locus was 3.1, and the mean values of the expected and observed levels of heterozygosity were 0.406 and 0.322, respectively. Conclusions: These microsatellite markers will be valuable tools for investigating the genetic diversity and population structure of wild and commercial species of passion fruit (Passiflora spp. and may be useful for developing conservation and improvement strategies by contributing to the understanding of the mating system and hybridization within the genus.

  6. Novel Microsatellite Markers Acquired from Rubus coreanus Miq. and Cross-Amplification in Other Rubus Species

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    Gi-An Lee

    2015-04-01

    Full Text Available The Rubus genus consists of more than 600 species that are distributed globally. Only a few Rubus species, including raspberries and blueberries, have been domesticated. Genetic diversity within and between Rubus species is an important resource for breeding programs. We developed genomic microsatellite markers using an SSR-enriched R. coreanus library to study the diversity of the Rubus species. Microsatellite motifs were discovered in 546 of 646 unique clones, and a dinucleotide repeat was the most frequent (75.3% type of repeat. From 97 microsatellite loci with reproducible amplicons, we acquired 29 polymorphic microsatellite markers in the Rubus coreanus collection. The transferability values ranged from 59.8% to 84% across six Rubus species, and Rubus parvifolius had the highest transferability value (84%. The average number of alleles and the polymorphism information content were 5.7 and 0.541, respectively, in the R. coreanus collection. The diversity index of R. coreanus was similar to the values reported for other Rubus species. A phylogenetic dendrogram based on SSR profiles revealed that seven Rubus species could be allocated to three groups, and that R. coreanus was genetically close to Rubus crataegifolius (mountain berry. These new microsatellite markers might prove useful in studies of the genetic diversity, population structure, and evolutionary relationships among Rubus species.

  7. Novel intron markers to study the phylogeny of closely related mammalian species

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    Castresana Jose

    2010-11-01

    Full Text Available Abstract Background Multilocus phylogenies can be used to infer the species tree of a group of closely related species. In species trees, the nodes represent the actual separation between species, thus providing essential information about their evolutionary history. In addition, multilocus phylogenies can help in analyses of species delimitation, gene flow and genetic differentiation within species. However, few adequate markers are available for such studies. Results In order to develop nuclear markers that can be useful in multilocus studies of mammals, we analyzed the mammalian genomes of human, chimpanzee, macaque, dog and cow. Rodents were excluded due to their unusual genomic features. Introns were extracted from the mammalian genomes because of their greater genetic variability and ease of amplification from the flanking exons. To an initial set of more than 10,000 one-to-one orthologous introns we applied several filters to select introns that belong to single-copy genes, show neutral evolutionary rates and have an adequate length for their amplification. This analysis led to a final list of 224 intron markers randomly distributed along the genome. To experimentally test their validity, we amplified twelve of these introns in a panel of six mammalian species. The result was that seven of these introns gave rise to a PCR band of the expected size in all species. In addition, we sequenced these bands and analyzed the accumulation of substitutions in these introns in five pairs of closely related species. The results showed that the estimated genetic distances in the five species pairs was quite variable among introns and that this divergence cannot be directly predicted from the overall intron divergence in mammals. Conclusions We have designed a new set of 224 nuclear introns with optimal features for the phylogeny of closely related mammalian species. A large proportion of the introns tested experimentally showed a perfect amplification

  8. Analysis of genetic diversity of certain species of Piper using RAPD-based molecular markers.

    Science.gov (United States)

    Chowdhury, Utpal; Tanti, Bhaben; Rethy, Parakkal; Gajurel, Padma Raj

    2014-09-01

    The utility of RAPD markers in assessing genetic diversity and phenetic relationships of six different species of Piper from Northeast India was investigated. Polymerase chain reaction (PCR) with four arbitrary 10-mer oligonucleotide primers applied to the six species produced a total of 195 marker bands, of which, 159 were polymorphic. On average, six RAPD fragments were amplified per reaction. In the UPGMA phenetic dendrogram based on Jaccard's coefficient, the different accessions of Piper showed a high level of genetic variation. This study may be useful in identifying diverse genetic stocks of Piper, which may then be conserved on a priority basis.

  9. Malignant melanoma in the penguin: characterization of the clinical, histologic, and immunohistochemical features of malignant melanoma in 10 individuals from three species of penguin.

    Science.gov (United States)

    Duncan, Ann E; Smedley, Rebecca; Anthony, Simon; Garner, Michael M

    2014-09-01

    Malignant melanomas are aggressive neoplasms that are relatively common in penguins compared to other avian species. In this study, the clinical and pathologic characteristics of melanocytic neoplasms in five macaroni (Eudyptes chrysolophus), three rock hopper (Eudyptes chrysocome), and two Humboldt (Spheniscus humboldti) penguins are described. Tumors most commonly occurred in the skin of the foot or hock, and were seen in the subcutaneous muscle, especially near the beak/oral cavity. Gross lesions were usually heavily pigmented, becoming raised and ulcerated over time. Humboldt penguins had a unique presentation, forming variably pigmented, cornified lesions in the inguinal area. Original case materials were obtained from all but two cases, and were assessed to define the characteristics of malignancy, evaluate four immunohistochemical markers for melanoma, and look for factors useful to informing prognosis and clinical decisions. Diagnosis was made histologically, based on morphologic features and pigmentation. Though not necessary for diagnosis, PNL-2 was found to be a useful immunohistochemical marker. HMB-45 showed unreliable positive labelling and S-100, Melan-A and Ki67 were not useful. Several factors were associated with prognosis, including gross surface dimension, mitotic index, depth of neoplastic cell invasion, and degree of surface ulceration. Metastatic spread occurred to the liver, lung, adrenal gland, brain, and bone; all lesions showed positive labelling to PNL-2. The average survival after diagnosis was 7 mo, though complete surgical excision of tumors less than 2.0 cm was curative in two cases and radiation therapy prolonged survival in one penguin. The underlying pathogenesis associated with the high prevalence of melanocytic neoplasms in captive penguins could not be identified. Three different molecular methods were performed to look for viral particles and results were negative. Advanced age is the most probable associated risk factor

  10. Validation of histology image registration

    Science.gov (United States)

    Shojaii, Rushin; Karavardanyan, Tigran; Yaffe, Martin; Martel, Anne L.

    2011-03-01

    The aim of this paper is to validate an image registration pipeline used for histology image alignment. In this work a set of histology images are registered to their correspondent optical blockface images to make a histology volume. Then multi-modality fiducial markers are used to validate the alignment of histology images. The fiducial markers are catheters perfused with a mixture of cuttlefish ink and flour. Based on our previous investigations this fiducial marker is visible in medical images, optical blockface images and it can also be localized in histology images. The properties of this fiducial marker make it suitable for validation of the registration techniques used for histology image alignment. This paper reports on the accuracy of a histology image registration approach by calculation of target registration error using these fiducial markers.

  11. Genetic diversity of wild and cultivated Rubus species in Colombia using AFLP and SSR markers

    Directory of Open Access Journals (Sweden)

    Sandra Bibiana Aguilar

    2007-01-01

    Full Text Available The Andean blackberry belongs to the genus Rubus, the largest of the Rosaceae family and one of the mostdiverse of the plant kingdom. In Colombia Rubus glaucus Benth, known as the Andean raspberry or blackberry, is one of thenine edible of the genus out of forty-four reported species. In this study wild and cultivated genotypes, collected in the CentralAndes of Colombia were analyzed by AFLP and SSR markers. Sexual reproduction seems to play an important role inmaintaining the genetic variability in R. glaucus, and the viability of using the SSR of Rubus alceifolius to characterizeColombian Rubus species was clearly demonstrated. All species evaluated produced very specific banding patterns,differentiating them from the others. Both AFLP and SSR produced bands exclusive to each of the following species: R.robustus, R. urticifolius, R. glaucus, and R. rosifolius. The SSR markers differentiated diploid and tetraploid genotypes of R.glaucus.

  12. DNA barcoding in Atlantic Forest plants: what is the best marker for Sapotaceae species identification?

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    Caio Vinicius Vivas

    2014-12-01

    Full Text Available The Atlantic Forest is a phytogeographic domain with a high rate of endemism and large species diversity. The Sapotaceae is a botanical family for which species identification in the Atlantic Forest is difficult. An approach that facilitates species identification in the Sapotaceae is urgently needed because this family includes threatened species and valuable timber species. In this context, DNA barcoding could provide an important tool for identifying species in the Atlantic Forest. In this work, we evaluated four plant barcode markers (matK, rbcL, trnH-psbA and the nuclear ribosomal internal transcribed spacer region -ITS in 80 samples from 26 species of Sapotaceae that occur in the Atlantic Forest. ITS yielded the highest average interspecific distance (0.122, followed by trnH-psbA (0.019, matK (0.008 and rbcL (0.002. For species discrimination, ITS provided the best results, followed by matK, trnH-psbA and rbcL. Furthermore, the combined analysis of two, three or four markers did not result in higher rates of discrimination than obtained with ITS alone. These results indicate that the ITS region is the best option for molecular identification of Sapotaceae species from the Atlantic Forest.

  13. Development of Microsatellite Markers for Lagerstroemia indica (Lythraceae and Related Species

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    Yang Liu

    2013-02-01

    Full Text Available Premise of the study: Microsatellite markers were developed and characterized to analyze genetic diversity within Lagerstroemia cultivars and related species. Methods and Results: Using simple sequence repeat (SSR-enriched libraries, 11 species-specific polymorphic genomic SSRs were developed from L. indica ‘Hong Die Fei Wu’. All primers were tested on 48 L. indica individuals from China, the United States, and France. The primers amplified four to 12 alleles per locus, including di-, tri-, and tetranucleotide repeats. Observed and expected heterozygosities ranged from 0.1875 to 0.7609 and 0.2836 to 0.8385, respectively. The primers were also highly cross-transferrable to L. subcostata, L. limii, L. fauriei, L. caudata, and L. speciosa. Conclusions: The new primers will enlarge the bank of SSRs available to genetic research of Lagerstroemia. These SSR markers will facilitate population genetics and molecular marker-assisted selection of L. indica.

  14. A validated source panel of SSR markers for effective discrimination of lentil species

    Science.gov (United States)

    Lentil (Lens culinaris Medic) is an important cool season food legume grown extensively in the world. This crop species has 14 chromosomes (2n=14), is a diploid and has a genome size of more than 4000 Mbp. Development of highly polymorphic molecular markers is a lentil research priority. In this stu...

  15. Genotype calling in tetraploid species from bi-allelic marker data using mixture models

    NARCIS (Netherlands)

    Voorrips, R.E.; Gort, G.; Vosman, B.

    2011-01-01

    Background: Automated genotype calling in tetraploid species was until recently not possible, which hampered genetic analysis. Modern genotyping assays often produce two signals, one for each allele of a bi-allelic marker. While ample software is available to obtain genotypes (homozygous for either

  16. Novel and cross-species microsatellite markers for parentage analysis in Sanderling

    NARCIS (Netherlands)

    Luttikhuizen, P.C.; Bol, A.; Witte, H.; van Bleijswijk, J.; Haddrath, O.; Baker, A.J.; Piersma, T.; Reneerkens, J.; Piersma, T.

    2011-01-01

    We isolated and tested six novel microsatellite loci in Sanderling (Calidris alba) from Greenland for paternity analyses. In addition, we tested 11 already published microsatellite markers which were originally developed for the congeneric species, the Pectoral Sandpiper (C. melanotos). All loci

  17. Potential vegetation markers – analytical pyrolysis of modern plant species representative of Neolithic SE Spain

    NARCIS (Netherlands)

    Schellekens, J.; Barbera, G.G.; Buurman, P.

    2013-01-01

    A selection of plant species that may have been relevant for the Neolithic in the SW Mediterranean have been characterised with pyrolysis gas chromatography mass spectrometry (pyrolysis–GC/MS) in search for molecular vegetation markers. Roots and aerial parts were analysed separately for the

  18. Characterization of North American Armillaria species: Genetic relationships determined by ribosomal DNA sequences and AFLP markers

    Science.gov (United States)

    M. -S. Kim; N. B. Klopfenstein; J. W. Hanna; G. I. McDonald

    2006-01-01

    Phylogenetic and genetic relationships among 10 North American Armillaria species were analysed using sequence data from ribosomal DNA (rDNA), including intergenic spacer (IGS-1), internal transcribed spacers with associated 5.8S (ITS + 5.8S), and nuclear large subunit rDNA (nLSU), and amplified fragment length polymorphism (AFLP) markers. Based on rDNA sequence data,...

  19. Isozyme and allozyme markers distinguishing two morphologically similar, medically important Mastomys species (Rodentia: Muridae

    Directory of Open Access Journals (Sweden)

    Van der Bank Herman FH

    2001-09-01

    Full Text Available Abstract Background Two common southern African mice species, Mastomys coucha and M. natalensis, are widely distributed throughout the subregion and overlap in many areas. They also share a high degree of morphological similarity, making them impossible to distinguish in the field at present. These multimammate mice are documented carriers of serious disease vectors causing Lassa fever, plague and encephalomyocarditis, which coupled to their cohabitation with humans in many areas, could pose a significant health risk. A preliminary study reported the presence of isozyme markers at three loci (GPI-2, PT-2, -3 in one population each of M. coucha and M. natalensis. Two additional populations (from the Vaal Dam and Richards Bay were sampled to determine the reliability of these markers, and to seek additional genetic markers. Results Fifteen proteins or enzymes provided interpretable results at a total of 39 loci. Additional fixed allele differences between the species were detected at AAT-1, ADH, EST-1, PGD-1, Hb-1 and -2. Average heterozygosities for M. coucha and M. natalensis were calculated as 0.018 and 0.032 respectively, with a mean genetic distance between the species of 0.26. Conclusions The confirmation of the isozyme and the detection of the additional allozyme markers are important contributions to the identification of these two medical and agricultural pest species.

  20. SNP-markers in Allium species to facilitate introgression breeding in onion

    NARCIS (Netherlands)

    Scholten, Olga E.; Kaauwen, van Martijn P.W.; Shahin, Arwa; Hendrickx, Patrick M.; Keizer, Paul; Burger-Meijer, Karin; Heusden, van Sjaak; Linden, van der Gerard; Vosman, Ben

    2016-01-01

    Background: Within onion, Allium cepa L., the availability of disease resistance is limited. The identification of sources of resistance in related species, such as Allium roylei and Allium fistulosum, was a first step towards the improvement of onion cultivars by breeding. SNP markers linked to

  1. Novel and cross-species microsatellite markers for parentage analysis in Sanderling Calidris alba

    NARCIS (Netherlands)

    Luttikhuizen, Pieternella C.; Bol, Anneke; Witte, Harry; van Bleijswijk, Judith; Haddrath, Oliver; Baker, Allan J.; Piersma, Theunis; Reneerkens, Jeroen

    We isolated and tested six novel microsatellite loci in Sanderling (Calidris alba) from Greenland for paternity analyses. In addition, we tested 11 already published microsatellite markers which were originally developed for the congeneric species, the Pectoral Sandpiper (C. melanotos). All loci

  2. Clinicopathologic studies in cognitively healthy aging and Alzheimer's disease: relation of histologic markers to dementia severity, age, sex, and apolipoprotein E genotype.

    Science.gov (United States)

    Berg, L; McKeel, D W; Miller, J P; Storandt, M; Rubin, E H; Morris, J C; Baty, J; Coats, M; Norton, J; Goate, A M; Price, J L; Gearing, M; Mirra, S S; Saunders, A M

    1998-03-01

    To study differences between subjects with Alzheimer disease (AD) and cognitively intact control subjects, with respect to brain histologic markers of AD, and the relationship of those markers in the AD group to severity of dementia, age at death, sex, and apolipoprotein E genotype. Washington University Alzheimer's Disease Research Center, St Louis, Mo. Consecutive neuropathologic series of 224 prospectively studied volunteer research subjects, 186 with dementia of the Alzheimer type (DAT) or "incipient" DAT and confirmed to have AD by postmortem examination and 13 cognitively intact subjects, confirmed to lack postmortem findings of AD. Brain densities (number per square millimeter) of senile plaques and neurofibrillary tangles, extent of cerebral amyloid angiopathy, cortical Lewy bodies, and apolipoprotein E genotype. Neocortical neurofibrillary tangle densities were substantially correlated with dementia severity, and to a greater degree than was true for senile plaque densities. When infarcts, hemorrhages, and Parkinson disease changes coexisted with AD, neurofibrillary tangle and senile plaque densities were lower. Plaque-predominant AD was found in a greater proportion of subjects with milder than more severe dementia. Entorhinal cortical Lewy bodies were no more frequent in plaque-predominant AD than in the remaining AD cases. Increasing age at death was negatively correlated with dementia severity and densities of senile plaques and neurofibrillary tangles. The apolipoprotein E epsilon4 allele frequency was greater in AD than in control subjects but decreased with increasing age. After controlling for dementia severity, senile plaque densities were only weakly related to epsilon4 allele frequency, and only in hippocampus. However, the degree of cerebral amyloid angiopathy was clearly related to epsilon4 allele frequency. Among subjects diagnosed during life as having DAT or incipient DAT, only 7% were found to have a neuropathologic disorder other than AD

  3. Use of genome sequence data in the design and testing of SSR markers for Phytophthora species

    Directory of Open Access Journals (Sweden)

    Cardle Linda

    2008-12-01

    Full Text Available Abstract Background Microsatellites or single sequence repeats (SSRs are a powerful choice of marker in the study of Phytophthora population biology, epidemiology, ecology, genetics and evolution. A strategy was tested in which the publicly available unigene datasets extracted from genome sequences of P. infestans, P. sojae and P. ramorum were mined for candidate SSR markers that could be applied to a wide range of Phytophthora species. Results A first approach, aimed at the identification of polymorphic SSR loci common to many Phytophthora species, yielded 171 reliable sequences containing 211 SSRs. Microsatellites were identified from 16 target species representing the breadth of diversity across the genus. Repeat number ranged from 3 to 16 with most having seven repeats or less and four being the most commonly found. Trinucleotide repeats such as (AAGn, (AGGn and (AGCn were the most common followed by pentanucleotide, tetranucleotide and dinucleotide repeats. A second approach was aimed at the identification of useful loci common to a restricted number of species more closely related to P. sojae (P. alni, P. cambivora, P. europaea and P. fragariae. This analysis yielded 10 trinucleotide and 2 tetranucleotide SSRs which were repeated 4, 5 or 6 times. Conclusion Key studies on inter- and intra-specific variation of selected microsatellites remain. Despite the screening of conserved gene coding regions, the sequence diversity between species was high and the identification of useful SSR loci applicable to anything other than the most closely related pairs of Phytophthora species was challenging. That said, many novel SSR loci for species other than the three 'source species' (P. infestans, P. sojae and P. ramorum are reported, offering great potential for the investigation of Phytophthora populations. In addition to the presence of microsatellites, many of the amplified regions may represent useful molecular marker regions for other studies as

  4. Characterization and cross-amplification of microsatellite markers in four species of anemonefish (Pomacentridae, Amphiprion spp.)

    KAUST Repository

    Bonin, Mary C.

    2015-04-09

    Anemonefish are iconic symbols of coral reefs and have become model systems for research on larval dispersal and population connectivity in coral reef fishes. Here we present 24 novel microsatellite markers across four species of anemonefish and also test 35 previously published markers for cross-amplification on two anemonefish species in order to facilitate further research on their population genetics and phylogenetics. Novel loci were isolated from sequences derived from microsatellite-enriched or 454 GS-FLX shotgun sequence libraries developed using congeneric DNA. Primer testing successfully identified 15 new microsatellite loci for A. percula, 4 for A. melanopus, 3 for A. akindynos, and 2 for A. omanensis. These novel microsatellite loci were polymorphic with a mean of 10 ± 1.6 SE (standard error) alleles per locus and an average observed heterozygosity of 0.647 ± 0.032 SE. Reliable cross-amplification of 12 and 26 of the 35 previously published Amphiprion markers was achieved for A. melanopus and A. akindynos, respectively, suggesting that the use of markers developed from the DNA of congeners can provide a quick and cost-effective alternative to the isolation of new loci. Together, the markers presented here provide an important resource for ecological, evolutionary, and conservation genetic research on anemonefishes that will inform broader conservation and management actions for coral reef fishes. © 2015 Senckenberg Gesellschaft für Naturforschung and Springer-Verlag Berlin Heidelberg

  5. Phylogeny and species delineation in European species of the genus Steganacarus (Acari, Oribatida) using mitochondrial and nuclear markers.

    Science.gov (United States)

    Kreipe, Victoria; Corral-Hernández, Elena; Scheu, Stefan; Schaefer, Ina; Maraun, Mark

    2015-06-01

    Species of the genus Steganacarus are soil-living oribatid mites (Acari, Phthiracaridae) with a ptychoid body. The phylogeny and species status of the species of Steganacarus are not resolved, some authors group all ten German species of Steganacarus within the genus Steganacarus whereas others split them into three subgenera, Steganacarus, Tropacarus and Atropacarus. Additionally, two species, S. magnus and T. carinatus, comprise morphotypes of questionable species status. We investigated the phylogeny and species status of ten European Steganacarus species, i.e. S. applicatus, S. herculeanus, S. magnus forma magna, S. magnus forma anomala, S. spinosus, Tropacarus brevipilus, T. carinatus forma carinata, T. carinatus forma pulcherrima, Atropacarus striculus and Rhacaplacarus ortizi. We used two molecular markers, a 251 bp fragment of the nuclear gene 28S rDNA (D3) and a 477 bp fragment of the mitochondrial COI region. The phylogeny based on a combined analysis of D3 and COI separated four subgenera (Steganacarus, Tropacarus and Atropacarus, Rhacaplacarus) indicating that they form monophyletic groups. The COI region separated all ten species of the genus Steganacarus and showed variation within some species often correlating with the geographic origin of the species. Resolution of the more conserved D3 region was limited, indicating that radiation events are rather recent. Overall, our results indicate that both genes alone cannot be used for phylogeny and barcoding since variation is too low in D3 and too high in COI. However, when used in combination these genes provide reliable insight into the phylogeny, radiation and species status of taxa of the genus Steganacarus.

  6. Isolation of microsatellite markers in a chaparral species endemic to southern California, Ceanothus megacarpus (Rhamnaceae).

    Science.gov (United States)

    Ishibashi, Caitlin D A; Shaver, Anthony R; Perrault, David P; Davis, Stephen D; Honeycutt, Rodney L

    2013-05-01

    Microsatellite (simple sequence repeat [SSR]) markers were developed for Ceanothus megacarpus, a chaparral species endemic to coastal southern California, to investigate potential processes (e.g., fragmentation, genetic drift, and interspecific hybridization) responsible for the genetic structure within and among populations distributed throughout mainland and island populations. • Four SSR-enriched libraries were used to develop and optimize 10 primer sets of microsatellite loci containing either di-, tri-, or tetranucleotide repeats. Levels of variation at these loci were assessed for two populations of C. megacarpus. Observed heterozygosity ranged from 0.250 to 0.885, and number of alleles ranged between four and 21 per locus. Eight to nine loci also successfully amplified in three other species of Ceanothus. • These markers should prove useful for evaluating the influence of recent and historical processes on genetic variation in C. megacarpus and related species.

  7. Isolation of microsatellite markers in a chaparral species endemic to southern California, Ceanothus megacarpus (Rhamnaceae)1

    Science.gov (United States)

    Ishibashi, Caitlin D. A.; Shaver, Anthony R.; Perrault, David P.; Davis, Stephen D.; Honeycutt, Rodney L.

    2013-01-01

    • Premise of the study: Microsatellite (simple sequence repeat [SSR]) markers were developed for Ceanothus megacarpus, a chaparral species endemic to coastal southern California, to investigate potential processes (e.g., fragmentation, genetic drift, and interspecific hybridization) responsible for the genetic structure within and among populations distributed throughout mainland and island populations. • Methods and Results: Four SSR-enriched libraries were used to develop and optimize 10 primer sets of microsatellite loci containing either di-, tri-, or tetranucleotide repeats. Levels of variation at these loci were assessed for two populations of C. megacarpus. Observed heterozygosity ranged from 0.250 to 0.885, and number of alleles ranged between four and 21 per locus. Eight to nine loci also successfully amplified in three other species of Ceanothus. • Conclusions: These markers should prove useful for evaluating the influence of recent and historical processes on genetic variation in C. megacarpus and related species. PMID:25202542

  8. Isolation of Microsatellite Markers in a Chaparral Species Endemic to Southern California, Ceanothus megacarpus (Rhamnaceae

    Directory of Open Access Journals (Sweden)

    Caitlin D. A. Ishibashi

    2013-05-01

    Full Text Available Premise of the study: Microsatellite (simple sequence repeat [SSR] markers were developed for Ceanothus megacarpus, a chaparral species endemic to coastal southern California, to investigate potential processes (e.g., fragmentation, genetic drift, and interspecific hybridization responsible for the genetic structure within and among populations distributed throughout mainland and island populations. Methods and Results: Four SSR-enriched libraries were used to develop and optimize 10 primer sets of microsatellite loci containing either di-, tri-, or tetranucleotide repeats. Levels of variation at these loci were assessed for two populations of C. megacarpus. Observed heterozygosity ranged from 0.250 to 0.885, and number of alleles ranged between four and 21 per locus. Eight to nine loci also successfully amplified in three other species of Ceanothus. Conclusions: These markers should prove useful for evaluating the influence of recent and historical processes on genetic variation in C. megacarpus and related species.

  9. Flavylium chromophores as species markers for dragon's blood resins from Dracaena and Daemonorops trees.

    Science.gov (United States)

    Sousa, Micaela M; Melo, Maria J; Parola, A Jorge; Seixas de Melo, J Sérgio; Catarino, Fernando; Pina, Fernando; Cook, Frances E M; Simmonds, Monique S J; Lopes, João A

    2008-10-31

    A simple and rapid liquid chromatographic method with diode-array UV-vis spectrophotometric detection has been developed for the authentication of dragon's blood resins from Dracaena and Daemonorops trees. Using this method it was discovered that the flavylium chromophores, which contribute to the red colour of these resins, differ among the species and could be used as markers to differentiate among species. A study of parameters, such as time of extraction, proportion of MeOH and pH, was undertaken to optimise the extraction of the flavyliums. This method was then used to make extracts from samples of dragon's blood resin obtained from material of known provenance. From the samples analysed 7,6-dihydroxy-5-methoxyflavylium (dracorhodin), 7,4'-dihydroxy-5-methoxyflavylium (dracoflavylium) and 7,4'-dihydroxyflavylium were selected as species markers for Daemonorops spp., Dracaena draco and Dracaena cinnabari, respectively. The chromatograms from these samples were used to build an HPLC-DAD database. The ability to discriminate among species of dragon's blood using the single marker compounds was compared with a principal components analysis of the chromatograms in the HPLC-DAD database. The results from the HPLC-DAD method based on the presence of these flavylium markers was unequivocal. The HPLC-DAD method was subsequently applied to 37 samples of dragon blood resins from the historical samples in the Economic Botany Collection, Royal Botanic Gardens, Kew. The method identified anomalies in how samples in this collection had been labelled. It is clear that the method can be used to evaluate the provenance of samples used in different areas of cultural heritage. It also could be used to monitor the trade of endangered species of dragon's blood and the species being used in complex formulations of traditional Chinese medicine.

  10. Detection of genetic variation in Ocimum species using RAPD and ISSR markers.

    Science.gov (United States)

    Patel, Hardik K; Fougat, Ranbir S; Kumar, Sushil; Mistry, Jigar G; Kumar, Mukesh

    2015-10-01

    There is a lack of information on the molecular characterization of Ocimum species and hence, efforts have been made under the present study to characterize 17 Ocimum genotypes belonging to 5 different species (O. basilicum, O. americanum, O. sanctum, O. gratissimum and O. Polystachyon) through random amplified polymorphic DNA (RAPD) and inter simple sequence repeats (ISSR) markers. PCR amplification using 20 RAPD primers generated a total of 506 loci, of which 490 (96.47 %) loci were found polymorphic. The PIC value for RAPD ranged from 0.907 (OPF 14) to 0.954 (OPC 11) with an average of 0.937. The ISSR primers generated a total of 238 loci, of them 234 (98.17 %) loci were polymorphic. The PIC value ranged from 0.892 (UBC 808) to 0.943 (ISSR A12) with an average of 0.923. The average Jaccard's similarity coefficient based on RAPD and ISSR analysis was 0.58 and 0.52, respectively. Clustering pattern of dendrogram generated using the pooled RAPD and ISSR data showed all Ocimum genotypes in their respective species groups at a cutoff value of 0.49 and 0.42, respectively. Many unique species-specific alleles were amplified by RAPD and ISSR markers. In both marker systems, a maximum number of unique alleles were observed in O. sanctum. The results of the present investigation provided valid guidelines for collection, conservation and characterization of Ocimum genetic resources.

  11. New microsatellite markers for Campanula pyramidalis (Campanulaceae) and cross-amplification in closely related species.

    Science.gov (United States)

    Radosavljević, Ivan; Jakse, Jernej; Satovic, Zlatko; Javornik, Branka; Janković, Ivana; Liber, Zlatko

    2015-03-01

    Microsatellite markers were identified and characterized to study the genetic diversity and structure, conservation status, taxonomy, and biogeography of subspecific taxa and populations of Campanula pyramidalis (Campanulaceae). Eleven microsatellite markers were developed from genomic libraries enriched for di- and trinucleotide repeats. A total of 80 alleles were observed in the tested natural population. The number of alleles per locus, observed heterozygosity, and expected heterozygosity ranged from four to 13, 0.217 to 0.913, and 0.521 to 0.895, respectively. The new microsatellite markers will be useful for studying genetic diversity and structure as well as for better assessing the conservation status of subspecific taxa and populations of C. pyramidalis. Furthermore, a set of seven loci was successfully cross-amplified in C. secundiflora and C. versicolor and will be of great value for addressing unsolved taxonomic and biogeographic issues within the C. pyramidalis species complex.

  12. New microsatellite markers for Campanula pyramidalis (Campanulaceae) and cross-amplification in closely related species1

    Science.gov (United States)

    Radosavljević, Ivan; Jakse, Jernej; Satovic, Zlatko; Javornik, Branka; Janković, Ivana; Liber, Zlatko

    2015-01-01

    Premise of the study: Microsatellite markers were identified and characterized to study the genetic diversity and structure, conservation status, taxonomy, and biogeography of subspecific taxa and populations of Campanula pyramidalis (Campanulaceae). Methods and Results: Eleven microsatellite markers were developed from genomic libraries enriched for di- and trinucleotide repeats. A total of 80 alleles were observed in the tested natural population. The number of alleles per locus, observed heterozygosity, and expected heterozygosity ranged from four to 13, 0.217 to 0.913, and 0.521 to 0.895, respectively. Conclusions: The new microsatellite markers will be useful for studying genetic diversity and structure as well as for better assessing the conservation status of subspecific taxa and populations of C. pyramidalis. Furthermore, a set of seven loci was successfully cross-amplified in C. secundiflora and C. versicolor and will be of great value for addressing unsolved taxonomic and biogeographic issues within the C. pyramidalis species complex. PMID:25798343

  13. Development of rapidly evolving intron markers to estimate multilocus species trees of rodents.

    Directory of Open Access Journals (Sweden)

    Ana Rodríguez-Prieto

    Full Text Available One of the major challenges in the analysis of closely related species, speciation and phylogeography is the identification of variable sequence markers that allow the determination of genealogical relationships in multiple genomic regions using coalescent and species tree approaches. Rodent species represent nearly half of the mammalian diversity, but so far no systematic study has been carried out to detect suitable informative markers for this group. Here, we used a bioinformatic pipeline to extract intron sequences from rodent genomes available in databases and applied a series of filters that allowed the identification of 208 introns that adequately fulfilled several criteria for these studies. The main required characteristics of the introns were that they had the maximum possible mutation rates, that they were part of single-copy genes, that they had an appropriate sequence length for amplification, and that they were flanked by exons with suitable regions for primer design. In addition, in order to determine the validity of this approach, we chose ten of these introns for primer design and tested them in a panel of eleven rodent species belonging to different representative families. We show that all these introns can be amplified in the majority of species and that, overall, 79% of the amplifications worked with minimum optimization of the annealing temperature. In addition, we confirmed for a pair of sister species the relatively high level of sequence divergence of these introns. Therefore, we provide here a set of adequate intron markers that can be applied to different species of Rodentia for their use in studies that require significant sequence variability.

  14. DEVELOPMENT OF EST-SSR MARKERS TO ASSESS GENETIC DIVERSITY OF BROCCOLI AND ITS RELATED SPECIES

    Directory of Open Access Journals (Sweden)

    Nur Kholilatul Izzah

    2017-01-01

    Full Text Available Development of Expressed Sequence Tag-Simple Sequence Repeat (EST-SSR markers derived from public database is known to be more efficient, faster and low cost. The objective of this study was to generate a new set of EST-SSR markers for broccoli and its related species and their usefulness for assessing their genetic diversity. A total of 202 Brassica oleracea ESTs were retrieved from NCBI and then assembled into 172 unigenes by means of CAP3 program. Identification of SSRs was carried out using web-based tool, RepeatMasker software. Afterwards, EST-SSR markers were developed using Primer3 program. Among the identified SSRs, trinucleotide repeats were the most common repeat types, which accounted for about 50%. A total of eight primer pairs were successfully designed and yielded amplification products. Among them, five markers were polymorphic and displayed a total of 30 alleles with an average number of six alleles per locus. The polymorphic markers were subsequently used for analyzing genetic diversity of 36 B. oleracea cultivars including 22 broccoli, five cauliflower and nine kohlrabi cultivars based on genetic similarity matrix as implemented in NTSYS program. At similarity coefficient of 61%, a UPGMA clustering dendrogram effectively separated 36 genotypes into three main groups, where 30 out of 36 genotypes were clearly discriminated. The result obtained in the present study would help breeders in selecting parental lines for crossing. Moreover, the novel EST-SSR markers developed in the study could be a valuable tool for differentiating cultivars of broccoli and related species.

  15. MWCNTs of different physicochemical properties cause similar inflammatory responses, but differences in transcriptional and histological markers of fibrosis in mouse lungs

    DEFF Research Database (Denmark)

    Poulsen, Sarah S.; Saber, Anne T.; Williams, Andrew

    2015-01-01

    Multi-walled carbon nanotubes (MWCNTs) are an inhomogeneous group of nanomaterials that vary in lengths, shapes and types of metal contamination, which makes hazard evaluation difficult. Here we present a toxicogenomic analysis of female C57BL/6 mouse lungs following a single intratracheal...... instillation of 0, 18, 54 or 162 mu g/mouse of a small, curled (CNTsmall, 0.8 +/- 0.1 mu m in length) or large, thick MWCNT (CNTLarge, 4 +/- 0.4 mu m in length). The two MWCNTs were extensively characterized by SEM and TEM imaging, thermogravimetric analysis, and Brunauer-Emmett-Teller surface area analysis....... Lung tissues were harvested 24 h, 3 days and 28 days post-exposure. DNA microarrays were used to analyze gene expression, in parallel with analysis of bron-choalveolar lavage fluid, lung histology, DNA damage (comet assay) and the presence of reactive oxygen species (dichlorodihydrofluorescein assay...

  16. Identification of male genotypes in Pistacia vera L. species using SSR markers

    Directory of Open Access Journals (Sweden)

    Najwa Motaeb Alhajjar

    2017-05-01

    Full Text Available Genetic identification among different 15 male genotypes of Pistacia vera L. species in comparison with five main commercial male cultivars accredited by Ministry of Agriculture (Adam, Jamil, Ebrahim, Elyas and Khalifa was achieved using SSR markers. Seventeen primer pairs out of Twenty SSR primers were able to amplify PCR products. SSR segregation produced 44 putative alleles, of which 34 were polymorphic (77.27%. Genetic similarity among all studied genotypes ranged from 0.45 between Jamil cultivar and MAS1 genotype to 1 between Ebrahim cultivar and MA1 genotype which means that they are identical. The UPGMA cluster analysis based on Jaccard’s coefficient grouped all genotypes into three main clusters. The number of alleles revealed by each SSR analysis ranged from 1 to 5, with a high level of expected heterozygosity (He 0.507. Co-dominant SSRs loci were observed in some studied genotypes giving a value 0.235 of observed heterozygosity (Ho. According to the polymorphic allele’s number and the expected heterozygosity; Marker Index (MI was 23.97. Our results concluded that SSR marker is an informative technique, which revealed high ability to differentiate individuals, and played an important role as a genetic marker for identification and evaluation studies within P. vera species.INTERNATIONAL JOURNAL OF ENVIRONMENTVolume-6, Issue-2, Mar-May 2017, Page: 30-42

  17. AFLP markers provide insights into the evolutionary relationships and diversification of New Caledonian Araucaria species (Araucariaceae).

    Science.gov (United States)

    Gaudeul, Myriam; Rouhan, Germinal; Gardner, Martin F; Hollingsworth, Peter M

    2012-01-01

    Despite its small size, New Caledonia is characterized by a very diverse flora and striking environmental gradients, which make it an ideal setting to study species diversification. Thirteen of the 19 Araucaria species are endemic to the territory and form a monophyletic group, but patterns and processes that lead to such a high species richness are largely unexplored. We used 142 polymorphic AFLP markers and performed analyses based on Bayesian clustering algorithms, genetic distances, and cladistics on 71 samples representing all New Caledonian Araucaria species. We examined correlations between the inferred evolutionary relationships and shared morphological, ecological, or geographic parameters among species, to investigate evolutionary processes that may have driven speciation. We showed that genetic divergence among the present New Caledonian Araucaria species is low, suggesting recent diversification rather than pre-existence on Gondwana. We identified three genetic groups that included small-leaved, large-leaved, and coastal species, but detected no association with soil preference, ecological habitat, or rainfall. The observed patterns suggested that speciation events resulted from both differential adaptation and vicariance. Last, we hypothesize that speciation is ongoing and/or there are cryptic species in some genetically (sometimes also morphologically) divergent populations. Further data are required to provide better resolution and understanding of the diversification of New Caledonian Araucaria species. Nevertheless, our study allowed insights into their evolutionary relationships and provides a framework for future investigations on the evolution of this emblematic group of plants in one of the world's biodiversity hotspots.

  18. Genetic analysis of species in the Genus Catasetum (ORCHIDACEAE) using RAPD Markers

    OpenAIRE

    Luciana do Valle Rego Oliveira; Ricardo Tadeu de Faria; Claudete de Fátima Ruas; Paulo Maurício Ruas; Melissa de Oliveira Santos; Carvalho,Valdemar P.

    2010-01-01

    In this work, RAPD molecular markers were used to access the genetic variability and to study the inter and intraespecifc relationship in a group of 37 species, including 56 individuals. A total of 15 RAPD primers were selected for DNA amplification. From a total of 221 bands analyzed, 209 (95%) were polymorphics. The level of interespecifc genetic similarity ranged from 37% between Catasetum complanatum and Catasetum laminatum to 83% between Catasetum triodon and Catasetum uncatum. The intra...

  19. [Sex determination in ten crane species by DNA marker EE0.6].

    Science.gov (United States)

    Mudrik, E A; Kashentseva, T A; Gamburg, E A; Politov, D V

    2013-12-01

    Using a unique DNA sequence of W-chromosome EE0.6, we carried out molecular sex determination in 383 individuals often species of cranes (Grusgrus L., G. leucogeranus Pallas, G. japonensis Muller, G. vipio Pallas, G. Canadensis L., G. antigone L., G. monacha Temminck, Anthropoides virgo L., Balearica regulorum Bennett, and B. pavonia L.) kept in zoos and other centers of captive propagation. In 211 birds, sex was determined or verified for the first time. The efficiency of using the sex marker EE0.6 for chicks and immature and adult cranes of different species, as well as for interspecific hybrids was shown.

  20. Novel Microsatellite Markers of Meretrix petechialis and Cross-species Amplification in Related Taxa (Bivalvia: Veneroida

    Directory of Open Access Journals (Sweden)

    Hyun-Sook Ko

    2012-11-01

    Full Text Available The Asian hard clam, Meretrix petechialis, is an economically important bivalve, but its catch and population sizes are decreasing rapidly, owing to many factors, including large-scale reclamation of its natural habitat on the western coast of the Korean peninsula. Attempts to restore the resources and production of this species require genetic structure and diversity information. In this study, we developed 15 microsatellite markers from a partial genomic library enriched in GT repeats. Nine of these markers were polymorphic, with an average allele number of six, and six were monomorphic in 95 tested individuals. No linkage disequilibrium was found between any pair of loci (p > 0.05, and deviations from the Hardy–Weinberg equilibrium (HWE test showing excess of heterozygotes was observed in only one of nine loci. In addition, no null alleles or genetic differentiation between two tested populations were detected. A cross-species amplification in 12 species of four families resulted in two M. petechialis-specific loci and three possible universal markers. This information will be useful in the future development of high-quality artificial seedlings and sustainable resource management.

  1. RAPD-SCAR marker and genetic relationship analysis of three Demodex species (Acari: Demodicidae).

    Science.gov (United States)

    Zhao, Ya-E; Wu, Li-Ping

    2012-06-01

    For a long time, classification of Demodex mites has been mainly based on their hosts and phenotype characteristics. The study was the first to conduct molecular identification and genetic relationship analysis for six isolates of three Demodex species by random amplified polymorphic DNA (RAPD) and sequence-characterized amplified region (SCAR) marker. Totally, 239 DNA fragments were amplified from six Demodex isolates with 10 random primers in RAPD, of which 165 were polymorphic. Using a single primer, at least five fragments and at most 40 in the six isolates were amplified, whereas within a single isolate, a range of 35-49 fragments were amplified. DNA fingerprints of primers CZ 1-9 revealed intra- and interspecies difference in six Demodex isolates, whereas primer CZ 10 only revealed interspecies difference. The genetic distance and dendrogram showed the intraspecific genetic distances were closer than the interspecific genetic distances. The interspecific genetic distances of Demodex folliculorum and Demodex canis (0.7931-0.8140) were shorter than that of Demodex brevis and D. canis (0.8182-0.8987). The RAPD-SCAR marker displayed primer CZ 10 could be applied to identify the three Demodex species. The 479-bp fragment was specific for D. brevis, and the 261-bp fragment was specific for D. canis. The conclusion was that the RAPD-SCAR multi-marker was effective in molecular identification of three Demodex species. The genetic relationship between D. folliculorum and D. canis was nearer than that between D. folliculorum and D. brevis.

  2. Lichenoid reaction as a potential immune response marker of intratreatment histological response during successful vismodegib treatment for a giant basal cell carcinoma.

    Science.gov (United States)

    Fosko, Scott W; Chu, Melinda B; Mattox, Adam R; Richart, John M; Burkemper, Nicole M; Slutsky, Jordan B

    2015-01-01

    We report an 83 year-old patient with a 13 × 7.5 cm(2) basal cell carcinoma (BCC) successfully treated with the combination of vismodegib and minimal surgery. On Day 109, a 0.9 cm papule suspicious for residual BCC was seen centrally within a large pink atrophic plaque. This lesion was excised; pathology confirmed BCC with negative surgical margins. Simultaneously, suspecting noncontiguous histologic response, we performed 21 biopsies at the periphery of the pretreatment tumor location. Seventeen (17/21, 81%) revealed lichenoid dermatitis. No tumor was seen on any. We believe the lichenoid dermatitis observed is a novel finding for two reasons. First, it may be considered a marker of a positive intratreatment response. This may help guide clinicians on the optimal treatment duration of vismodegib to maximize efficacy and mitigate side effects. Second, we think it suggests an additional mechanism of vismodegib action, possibly via local immune effects. Further investigations are warranted. © 2015 Wiley Periodicals, Inc.

  3. Multi-locus DNA barcoding identifies matK as a suitable marker for species identification in Hibiscus L.

    Science.gov (United States)

    Poovitha, Sundar; Stalin, Nithaniyal; Balaji, Raju; Parani, Madasamy

    2016-12-01

    The genus Hibiscus L. includes several taxa of medicinal value and species used for the extraction of natural dyes. These applications require the use of authentic plant materials. DNA barcoding is a molecular method for species identification, which helps in reliable authentication by using one or more DNA barcode marker. In this study, we have collected 44 accessions, representing 16 species of Hibiscus, distributed in the southern peninsular India, to evaluate the discriminatory power of the two core barcodes rbcLa and matK together with the suggested additional regions trnH-psbA and ITS2. No intraspecies divergence was observed among the accessions studied. Interspecies divergence was 0%-9.6% with individual markers, which increased to 0%-12.5% and 0.8%-20.3% when using two- and three-marker combinations, respectively. Differentiation of all the species of Hibiscus was possible with the matK DNA barcode marker. Also, in two-marker combinations, only those combinations with matK differentiated all the species. Though all the three-marker combinations showed 100% species differentiation, species resolution was consistently better when the matK marker formed part of the combination. These results clearly showed that matK is more suitable when compared to rbcLa, trnH-psbA, and ITS2 for species identification in Hibiscus.

  4. Genome-wide identification and transferability of microsatellite markers between Palmae species

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    Yong Xiao

    2016-10-01

    Full Text Available The Palmae family contains 202 genera and approximately 2800 species. Except for Elaeis guineensis and Phoenix dactylifera, almost no genetic and genomic information is available for Palmae species. Therefore, this is an obstacle to the conservation and genetic assessment of Palmae species, especially those that are currently endangered. The study was performed to develop a large number of microsatellite markers which can be used for genetic analysis in different Palmae species. Based on the assembled genome of Elaeis guineensis and Phoenix dactylifera, a total of 814 383 and 371 629 microsatellites were identified. Among these microsatellites identified in Elaeis guineensis, 734 509 primer pairs could be designed from the flanking sequences of these microsatellites. The majority (618 762 of these designed primer pairs had in silico products in the genome of Elaeis guineensis. These 618 762 primer pairs were subsequently used to in silico amplify the genome of Phoenix dactylifera. A total of 7 265 conserved microsatellites were identified between Elaeis guineensis and Phoenix dactylifera. One hundred and thirty-five primer pairs flanking the conserved SSRs were stochastically selected and validated to have high cross-genera transferability, varying from 16.7% to 93.3% with an average of 73.7%. These genome-wide conserved microsatellite markers will provide a useful tool for genetic assessment and conservation of different Palmae species in the future.

  5. Genome-Wide Identification and Transferability of Microsatellite Markers between Palmae Species

    Science.gov (United States)

    Xiao, Yong; Xia, Wei; Ma, Jianwei; Mason, Annaliese S.; Fan, Haikuo; Shi, Peng; Lei, Xintao; Ma, Zilong; Peng, Ming

    2016-01-01

    The Palmae family contains 202 genera and approximately 2800 species. Except for Elaeis guineensis and Phoenix dactylifera, almost no genetic and genomic information is available for Palmae species. Therefore, this is an obstacle to the conservation and genetic assessment of Palmae species, especially those that are currently endangered. The study was performed to develop a large number of microsatellite markers which can be used for genetic analysis in different Palmae species. Based on the assembled genome of E. guineensis and P. dactylifera, a total of 814 383 and 371 629 microsatellites were identified. Among these microsatellites identified in E. guineensis, 734 509 primer pairs could be designed from the flanking sequences of these microsatellites. The majority (618 762) of these designed primer pairs had in silico products in the genome of E. guineensis. These 618 762 primer pairs were subsequently used to in silico amplify the genome of P. dactylifera. A total of 7 265 conserved microsatellites were identified between E. guineensis and P. dactylifera. One hundred and thirty-five primer pairs flanking the conserved SSRs were stochastically selected and validated to have high cross-genera transferability, varying from 16.7 to 93.3% with an average of 73.7%. These genome-wide conserved microsatellite markers will provide a useful tool for genetic assessment and conservation of different Palmae species in the future. PMID:27826307

  6. SNP-markers in Allium species to facilitate introgression breeding in onion.

    Science.gov (United States)

    Scholten, Olga E; van Kaauwen, Martijn P W; Shahin, Arwa; Hendrickx, Patrick M; Keizer, L C Paul; Burger, Karin; van Heusden, Adriaan W; van der Linden, C Gerard; Vosman, Ben

    2016-08-31

    Within onion, Allium cepa L., the availability of disease resistance is limited. The identification of sources of resistance in related species, such as Allium roylei and Allium fistulosum, was a first step towards the improvement of onion cultivars by breeding. SNP markers linked to resistance and polymorphic between these related species and onion cultivars are a valuable tool to efficiently introgress disease resistance genes. In this paper we describe the identification and validation of SNP markers valuable for onion breeding. Transcriptome sequencing resulted in 192 million RNA seq reads from the interspecific F1 hybrid between A. roylei and A. fistulosum (RF) and nine onion cultivars. After assembly, reliable SNPs were discovered in about 36 % of the contigs. For genotyping of the interspecific three-way cross population, derived from a cross between an onion cultivar and the RF (CCxRF), 1100 SNPs that are polymorphic in RF and monomorphic in the onion cultivars (RF SNPs) were selected for the development of KASP assays. A molecular linkage map based on 667 RF-SNP markers was constructed for CCxRF. In addition, KASP assays were developed for 1600 onion-SNPs (SNPs polymorphic among onion cultivars). A second linkage map was constructed for an F2 of onion x A. roylei (F2(CxR)) that consisted of 182 onion-SNPs and 119 RF-SNPs, and 76 previously mapped markers. Markers co-segregating in both the F2(CxR) and the CCxRF population were used to assign the linkage groups of RF to onion chromosomes. To validate usefulness of these SNP markers, QTL mapping was applied in the CCxRF population that segregates for resistance to Botrytis squamosa and resulted in a QTL for resistance on chromosome 6 of A. roylei. Our research has more than doubled the publicly available marker sequences of expressed onion genes and two onion-related species. It resulted in a detailed genetic map for the interspecific CCxRF population. This is the first paper that reports the detection of

  7. Taxonomic confirmation of mud crab species (genus Scylla) in Bangladesh by nuclear and mitochondrial DNA markers.

    Science.gov (United States)

    Sarower, Mohammed Golam; Shahriar, Sheik Istiak Md; Nakamura, Hiromasa; Rouf, Muhammad Abdur; Okada, Shigeru

    2017-11-01

    Taxonomy of mud crabs genus Scylla has been misidentified for several years due to their high morphological plasticity. Several reports concerning mud crab have been published with misleading identification in Bangladesh. In this study, partial fragments of nuclear and mitochondrial DNA of Scylla species obtained from four locations along the Bangladesh coast were used to resolve taxonomical ambiguity of mud crab species. A single PCR product from the nuclear first internal transcribed spacer (ITS-1) marker and phylogenetic trees constructed based on 16S rDNA sequences indicated that all Scylla species obtained in this study were S. olivacea. Both molecular data and morphological characters revealed that S. olivacea is the only major species in Bangladesh coastal waters. Further, the 16S rDNA haplotypes significantly differed with known S. serrata by 33%. From this study it is clear that 'S. serrata' commonly reported from Bangladesh should be S. olivacea.

  8. SSR marker variations in Brassica species provide insight into the origin and evolution of Brassica amphidiploids.

    Science.gov (United States)

    Thakur, Ajay Kumar; Singh, Kunwar Harendra; Singh, Lal; Nanjundan, Joghee; Khan, Yasin Jeshima; Singh, Dhiraj

    2018-01-01

    Oilseed Brassica represents an important group of oilseed crops with a long history of evolution and cultivation. To understand the origin and evolution of Brassica amphidiploids, simple sequence repeat (SSR) markers were used to unravel genetic variations in three diploids and three amphidiploid Brassica species of U's triangle along with Eruca sativa as an outlier. Of 124 Brassica-derived SSR loci assayed, 100% cross-transferability was obtained for B. juncea and three subspecies of B. rapa, while lowest cross-transferability (91.93%) was obtained for Eruca sativa. The average % age of cross-transferability across all the seven species was 98.15%. The number of alleles detected at each locus ranged from one to six with an average of 3.41 alleles per primer pair. Neighbor-Joining-based dendrogram divided all the 40 accessions into two main groups composed of B. juncea/B. nigra/B. rapa and B. carinata/B. napus/B. oleracea. C-genome of oilseed Brassica species remained relatively more conserved than A- and B-genome. A- genome present in B. juncea and B. napus seems distinct from each other and hence provides great opportunity for generating diversity through synthesizing amphidiploids from different sources of A- genome. B. juncea had least intra-specific distance indicating narrow genetic base. B. rapa appears to be more primitive species from which other two diploid species might have evolved. The SSR marker set developed in this study will assist in DNA fingerprinting of various Brassica species cultivars, evaluating the genetic diversity in Brassica germplasm, genome mapping and construction of linkage maps, gene tagging and various other genomics-related studies in Brassica species. Further, the evolutionary relationship established among various Brassica species would assist in formulating suitable breeding strategies for widening the genetic base of Brassica amphidiploids by exploiting the genetic diversity present in diploid progenitor gene pools.

  9. Restricted variation in plant barcoding markers limits identification in closely related bryophyte species.

    Science.gov (United States)

    Hassel, Kristian; Segreto, Rossana; Ekrem, Torbjørn

    2013-11-01

    Species-level identification and delimitation of bryophytes using the proposed general barcode markers for land plants has been challenging. Bryophyta (mosses) is the second most species-rich group of land plants after angiosperms, and it is thus of great importance to find useful barcoding regions also for this group of plants. We investigated how the plastid regions atpF-atpH, rbcL and trnH-psbA and the nuclear ITS2 region performed as barcode markers on closely related bryophyte taxa of selected moss (Bartramia, Distichium, Fissidens, Meesia and Syntrichia) and liverwort (Blepharostoma) genera from boreal and arctic regions. We also evaluated how sequencing success of herbarium specimens is related to length of the sequenced fragment, specimen age and taxonomic group. Sequencing success was higher for shorter fragments and younger herbarium specimens, but was lower than expected in the genera Distichium and Fissidens, indicating imperfect universality of the primers used. None of the studied DNA barcode regions showed a consistent barcode gap across the studied genera. As a single locus, the region atpF-atpH performed slightly better than rbcL and ITS2 and much better than trnH-psbA in terms of grouping conspecific sequences in monophyletic groups. This marker also gave a higher percentage of correct hits when conducting blast searches on a local database of identified sequences. Concatenated data sets of two and three markers grouped more conspecific sequences in monophyletic groups, but the improvement was not great compared with atpF-atpH alone. A discussion of recent studies testing barcode regions for bryophytes is given. We conclude that atpF-atpH, rbcL and ITS2 are to be the most promising barcode markers for mosses. © 2013 John Wiley & Sons Ltd.

  10. Development of microsatellite markers in Cordia bifurcata (Boraginaceae) and cross-species amplification in Cordia inermis and Cordia pringlei.

    Science.gov (United States)

    Spoon, Tracey R; Kesseli, Rick V

    2008-09-01

    We developed 16 microsatellite markers in Cordia bifurcata, a Central and South American shrub. The markers show low polymorphism in C. bifurcata, a species suspected of self-fertilization or apomixis. Of four polymorphic loci, three had only two alleles. However, current research indicates that these markers hold value for interpopulational comparisons of C. bifurcata and for analyses of congeners. In Cordia inermis, a dioecious or subdioecious shrub, seven of the markers produced interpretable amplification products of which five showed polymorphism. In Cordia pringlei, a distylous shrub, nine of the markers produced interpretable amplification products of which six showed polymorphism. © 2008 The Authors. Journal compilation © 2008 Blackwell Publishing Ltd.

  11. Kaempferitrin from Uncaria guianensis (Rubiaceae) and its potential as a chemical marker for the species

    Energy Technology Data Exchange (ETDEWEB)

    Valente, Ligia M.M.; Liechocki, Sally; Barboza, Rodolfo S.; Paixao, Djavan da [Universidade Federal do Rio de Janeiro (UFRJ), RJ (Brazil). Inst. de Quimica], e-mail: valente@iq.ufrj.br; Bizarri, Carlos H.B.; Almeida, M. Beatriz S.; Benevides, Paulo J.C.; Siani, Antonio C. [Fundacao Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, RJ (Brazil). Inst. de Tecnologia em Farmacos; Magalhaes, Alvicler [Universidade Estadual de Campinas (UNICAMP), SP (Brazil). Inst. de Quimica

    2009-07-01

    Uncaria tomentosa (Willd.) DC. and U. guianensis (Aubl.) Gmel., known as cat's claw, are large woody vines native to the Amazonian and Central American rain forests. The species contain, in different proportions, indole and oxindole alkaloids, triterpenoid glycosides, sterols and proanthocyanidins. U. tomentosa can be chemically identified by its oxindole alkaloid profile and content, whereas U. guianensis has no satisfactorily established chemical markers. This work describes, for the first time, the isolation of kaempferol-3,7-O-(a)-dirhamnoside (kaempferitrin) in Uncaria species. Screening for this compound in leaves, stems or bark of both species through TLC and HPLC-DAD-MS showed the presence of kaempferitrin only in the leaves and stems of U. guianensis, at a ratio almost thirty six times greater in the leaves than in the stems. These results reveal the selectivity of U. guianensis to produce this bioactive flavonoid glycoside, and suggest this compound as a potential chemical marker for the species.(author)

  12. De novo transcriptome analysis and molecular marker development of two Hemarthria species

    Directory of Open Access Journals (Sweden)

    Xiu eHuang

    2016-04-01

    Full Text Available Hemarthria R. Br. is an important genus of perennial forage grasses that is widely used in subtropical and tropical regions. Hemarthria grasses have made remarkable contributions to the development of animal husbandry and agro-ecosystem maintenance; however, there is currently a lack of comprehensive genomic data available for these species. In this study, we used Illumina high-throughput deep sequencing to characterize of two agriculturally important Hemarthria materials, H. compressa ‘Yaan’ and H. altissima ‘1110.’ Sequencing runs that used each of four normalized RNA samples from the leaves or roots of the two materials yielded more than 24 million high-quality reads. After de novo assembly, 137,142 and 77,150 unigenes were obtained for ‘Yaan’ and ‘1110’, respectively. In addition, a total of 86,731 ‘Yaan’ and 48,645 ‘1110’ unigenes were successfully annotated. After consolidating the unigenes for both materials, 42,646 high-quality SNPs were identified in 10,880 unigenes and 10,888 SSRs were identified in 8,330 unigenes. To validate the identified markers, high quality PCR primers were designed for both SNPs and SSRs. We randomly tested 16 of the SNP primers and 54 of the SSR primers and found that the majority of these primers successfully amplified the desired PCR product. In addition, high cross-species transferability (61.11%-87.04% of SSR markers was achieved for four other Poaceae species. The amount of RNA sequencing data that was generated for these two Hemarthria species greatly increases the amount of genomic information available for Hemarthria and the SSR and SNP markers identified in this study will facilitate further advancements in genetic and molecular studies of the Hemarthria genus.

  13. Development of new microsatellite markers from Mango (Mangifera indica) and cross-species amplification.

    Science.gov (United States)

    Ravishankar, Kundapura Venkataramana; Mani, Bellam Hanumantha-Reddy; Anand, Lalitha; Dinesh, Makki Ramachandra

    2011-04-01

    Microsatellite markers were developed and characterized to assess the genetic diversity among mango (Mangifera indica) cultivars and to test their amplification in closely related species. Thirty-six microsatellite (simple sequence repeats; SSR) loci were isolated by a microsatellite-enriched partial genomic library method. Primers designed for these loci were characterized using 30 diverse mango cultivars. The number of alleles ranged from 3 to 19 with an average of 9.2 alleles per locus. Polymorphic information content values ranged from 0.185 to 0.920 with a mean of 0.687. The total value for the probability of identity was 2.42 × 10(-31). The newly identified SSRs would be useful in genetic diversity studies, finger-printing, and mapping. Loci from five related species, M. odorata, M. anadamanica, M. zeylanica, M. camptosperma, and M. griffithii, were successfully amplified using these SSR primers, showing their potential utility across species.

  14. New microsatellite markers for Salvia officinalis (Lamiaceae) and cross-amplification in closely related species.

    Science.gov (United States)

    Radosavljević, Ivan; Jakse, Jernej; Javornik, Branka; Satovic, Zlatko; Liber, Zlatko

    2011-11-01

    Microsatellite primers were identified to study the genetic diversity, population genetic structure, and relationships of common sage and closely related species. Nine novel polymorphic trinucleotide microsatellite loci were identified for Salvia officinalis. A total of 127 alleles were observed. The observed and expected heterozygosity values ranged from 0.375 to 0.880 and from 0.624 to 0.931, respectively. Nine new and 11 previously published microsatellite primers were tested for cross-amplification. The species with the most successful cross-amplification was S. fruticosa. The nine new microsatellite markers will be useful in genetic studies of wild and cultivated populations of common sage and are potentially useful in genetic studies of closely related species.

  15. Genetic diversity of functional food species Spinacia oleracea L. by protein markers.

    Science.gov (United States)

    Rashid, M; Yousaf, Z; Haider, M S; Khalid, S; Rehman, H A; Younas, A; Arif, A

    2014-01-01

    Exploration of genetic diversity contributes primarily towards crop improvement. Spinaciaoleracea L. is a functional food species but unfortunately the genetic diversity of this vegetable is still unexplored. Therefore, this research was planned to explore the genetic diversity of S. oleracea by using morphological and protein markers. Protein profile of 25 accessions was generated on sodium dodecyl sulphate polyacrylamide gel. Total allelic variation of 27 bands was found. Out of these, 20 were polymorphic and the rest of the bands were monomorphic. Molecular weights of the bands ranged from 12.6 to 91.2 kDa. Major genetic differences were observed in accession 20541 (Peshawar) followed by 20180 (Lahore) and 19902 (AVRDC). Significant differences exist in the protein banding pattern. This variation can further be studied by advanced molecular techniques, including two-dimensional electrophoresis and DNA markers.

  16. Evolutionary factors affecting the cross-species utility of newly developed microsatellite markers in seabirds.

    Science.gov (United States)

    Moodley, Yoshan; Masello, Juan F; Cole, Theresa L; Calderon, Luciano; Munimanda, Gopi K; Thali, Marco R; Alderman, Rachael; Cuthbert, Richard J; Marin, Manuel; Massaro, Melanie; Navarro, Joan; Phillips, Richard A; Ryan, Peter G; Suazo, Cristián G; Cherel, Yves; Weimerskirch, Henri; Quillfeldt, Petra

    2015-09-01

    Microsatellite loci are ideal for testing hypotheses relating to genetic segregation at fine spatio-temporal scales. They are also conserved among closely related species, making them potentially useful for clarifying interspecific relationships between recently diverged taxa. However, mutations at primer binding sites may lead to increased nonamplification, or disruptions that may result in decreased polymorphism in nontarget species. Furthermore, high mutation rates and constraints on allele size may also with evolutionary time, promote an increase in convergently evolved allele size classes, biasing measures of interspecific genetic differentiation. Here, we used next-generation sequencing to develop microsatellite markers from a shotgun genome sequence of the sub-Antarctic seabird, the thin-billed prion (Pachyptila belcheri), that we tested for cross-species amplification in other Pachyptila and related sub-Antarctic species. We found that heterozygosity decreased and the proportion of nonamplifying loci increased with phylogenetic distance from the target species. Surprisingly, we found that species trees estimated from interspecific FST provided better approximations of mtDNA relationships among the studied species than those estimated using DC , even though FST was more affected by null alleles. We observed a significantly nonlinear second order polynomial relationship between microsatellite and mtDNA distances. We propose that the loss of linearity with increasing mtDNA distance stems from an increasing proportion of homoplastic allele size classes that are identical in state, but not identical by descent. Therefore, despite high cross-species amplification success and high polymorphism among the closely related Pachyptila species, we caution against the use of microsatellites in phylogenetic inference among distantly related taxa. © 2015 John Wiley & Sons Ltd.

  17. Sequence characterized amplified region marker as a tool for selection of high-artemisinin containing species of Artemisia.

    Science.gov (United States)

    Asghari, Matin; Naghavi, Mohammad Reza; Hosseinzadeh, Abdol Hadi; Ranjbar, Mojtaba; Poorebrahim, Mansour

    2015-01-01

    Malaria is currently one of the most important causes of mortality in developing countries. High resistance to available antimalarial drugs has been reported frequently, thus it is crucial to focus on the discovery of new antimalarial drugs. Artemisinin, an effective antimalarial medication, is isolated from various Artemisia species. To identify the Artemisia species producing high quantity of artemisinin, eight species of Artemisia were screened with the genetic sequence characterized amplified region (SCAR) marker for higher quantity of artemisinin. The DNA band corresponding to SCAR marker was cloned into pGEM®-T Easy vector and sequenced. The content of artemisinin in tested species was also measured using high-performance liquid chromatography (HPLC) assay. The primers designed for high-artemisinin SCAR marker could amplify a specific band of approximately 1000 bp which was present in two Artemisia annua and Artemisia absinthium species. These SCAR marker sequences for two selected species were submitted into the GenBank databases under KC337116 and KC465952 accession numbers. HPLC analysis indicated that two selected Artemisia species, genetically recognized as high-artemisinin yielding plants, had higher artemisinin content in comparison to other examined species. Therefore, in this study, we propose developed SCAR marker as a complementary tool for confidently detection of high-artemisinin content in Artemisia species.

  18. Validation of EST-derived microsatellite markers for two Cerrado-endemic Campomanesia (Myrtaceae) species.

    Science.gov (United States)

    Miranda, E A G C; Boaventura-Novaes, C R D; Braga, R S; Reis, E F; Pinto, J F N; Telles, M P C

    2016-03-04

    We assessed the transferability of 120 EST-derived Eucalyptus microsatellite primers to Campomanesia adamantium and C. pubescens. Both species are berry trees native to the Brazilian Cerrado, and population genetic information is poor. Twelve markers were used to analyze the genetic variability of four sampled populations. Regarding DNA extraction, we sampled leaf tissues from two populations of each species (80 individuals). Of the 120 primers evaluated, 87 did not amplify any PCR products, and 21 rendered nonspecific amplification. Twelve primers were successfully transferred, providing a low combined probability of genetic identity for both species (5.718 x 10(-10) for C. adamantium; 1.182 x 10(-11) for C. pubescens) and a high probability of paternity exclusion (0.99939 for C. adamantium; 0.99982 for C. pubescens). The average number of alleles in the polymorphic loci was 6.8 for C. adamantium and 7.8 for C. pubescens, ranging from 2 to 16 alleles per locus. The observed heterozygosity values for C. adamantium and C. pubescens were 0.504 and 0.503, respectively, and the expected heterozygosity values for C. adamantium and C. pubescens were 0.517 and 0.579, respectively. The populations exhibited structured genetic variability with qP values of 0.105 for C. adamantium and 0.249 for C. pubescens. Thus, we concluded that these 12 microsatellite markers, transferred from Eucalyptus, were efficient for population genetic studies of C. adamantium and C. pubescens.

  19. Molecular Assortment of Lens Species with Different Adaptations to Drought Conditions Using SSR Markers.

    Science.gov (United States)

    Singh, Dharmendra; Singh, Chandan Kumar; Tomar, Ram Sewak Singh; Taunk, Jyoti; Singh, Ranjeet; Maurya, Sadhana; Chaturvedi, Ashish Kumar; Pal, Madan; Singh, Rajendra; Dubey, Sarawan Kumar

    2016-01-01

    The success of drought tolerance breeding programs can be enhanced through molecular assortment of germplasm. This study was designed to characterize molecular diversity within and between Lens species with different adaptations to drought stress conditions using SSR markers. Drought stress was applied at seedling stage to study the effects on morpho-physiological traits under controlled condition, where tolerant cultivars and wilds showed 12.8-27.6% and 9.5-23.2% reduction in seed yield per plant respectively. When juxtaposed to field conditions, the tolerant cultivars (PDL-1 and PDL-2) and wild (ILWL-314 and ILWL-436) accessions showed 10.5-26.5% and 7.5%-15.6% reduction in seed yield per plant, respectively under rain-fed conditions. The reductions in seed yield in the two tolerant cultivars and wilds under severe drought condition were 48-49% and 30.5-45.3% respectively. A set of 258 alleles were identified among 278 genotypes using 35 SSR markers. Genetic diversity and polymorphism information contents varied between 0.321-0.854 and 0.299-0.836, with mean value of 0.682 and 0.643, respectively. All the genotypes were clustered into 11 groups based on SSR markers. Tolerant genotypes were grouped in cluster 6 while sensitive ones were mainly grouped into cluster 7. Wild accessions were separated from cultivars on the basis of both population structure and cluster analysis. Cluster analysis has further grouped the wild accessions on the basis of species and sub-species into 5 clusters. Physiological and morphological characters under drought stress were significantly (P = 0.05) different among microsatellite clusters. These findings suggest that drought adaptation is variable among wild and cultivated genotypes. Also, genotypes from contrasting clusters can be selected for hybridization which could help in evolution of better segregants for improving drought tolerance in lentil.

  20. Species-specific markers provide molecular genetic evidence for natural introgression of bullhead catfishes in Hungary

    Science.gov (United States)

    Béres, Beatrix; Kánainé Sipos, Dóra; Müller, Tamás; Staszny, Ádám; Farkas, Milán; Bakos, Katalin; Urbányi, Béla

    2017-01-01

    Since three bullhead catfish species were introduced to Europe in the late 19th century, they have spread to most European countries. In Hungary, the brown bullhead (Ameiurus nebulosus) was more widespread in the 1970s–1980s, but the black bullhead (Ameiurus melas) has gradually supplanted since their second introduction in 1980. The introgressive hybridization of the two species has been presumed based on morphological examinations, but it has not previously been supported by genetic evidence. In this study, 11 different Hungarian habitats were screened with a new species-specific nuclear genetic, duplex PCR based, marker system to distinguish the introduced catfish species, Ameiurus nebulosus, Ameiurus melas, and Ameiurus natalis, as well as the hybrids of the first two. More than 460 specimens were analyzed using the above markers and additional mitochondrial sequence analyses were also conducted on >25% of the individuals from each habitat sampled. The results showed that only 7.9% of the specimens from two habitats belonged to Ameiurus nebulosus, and 92.1% were classified as Ameiurus melas of all habitats, whereas the presence of Ameiurus natalis was not detected. Two specimens (>0.4%) showed the presence of both nuclear genomes and they were identified as hybrids of Ameiurus melas and Ameiurus nebulosus. An additional two individuals showed contradicting results from the nuclear and mitochondrial assays as a sign of a possible footprint of introgressive hybridization that might have happened two or more generations before. Surprisingly, the level of hybridization was much smaller than expected based on the analyses of the North American continent’s indigenous stock from the hybrid zones. This phenomenon has been observed in several invasive fish species and it is regarded as an added level of complexity in the management of their rapid adaptation. PMID:28265489

  1. A survey of available molecular markers for Vertebrate species present in Comunidad de Madrid

    Directory of Open Access Journals (Sweden)

    Boto, L.

    2006-05-01

    Full Text Available In this paper I present a survey for molecular markers available for Vertebrate species inhabiting the Comunidad de Madrid, with the aim of being useful to researchers working on the characterization of animal biodiversity in this area.

    En este trabajo presento los resultados de una búsqueda en bases de datos de marcadores moleculares para especies de Vertebrados presentes en la Comunidad de Madrid, en la esperanza de que este trabajo pueda ser de utilidad para aquellos investigadores involucrados en la caracterización de biodiversidad animal en esta Comunidad

  2. Retrospective study of central nervous system lesions and association with Parelaphostrongylus species by histology and specific nested polymerase chain reaction in domestic camelids and wild ungulates.

    Science.gov (United States)

    Dobey, Carrie L; Grunenwald, Caroline; Newman, Shelley J; Muller, Lisa; Gerhold, Richard W

    2014-11-01

    Formalin-fixed, paraffin-embedded tissues from elk (Cervus elaphus), goats, and camelids with case histories and lesions suggestive of Parelaphostrongylus tenuis were examined by histology to characterize lesions that could aid in definitively diagnosing P. tenuis infection. Additionally, sections of paraffin-embedded tissue were used in a nested polymerase chain reaction (nPCR) using Parelaphostrongylus-specific primers to determine how PCR results corresponded with histological findings. Histological changes in brain and spinal cord consisted of linear tracks of hemorrhage; tracks or perivascular accumulations of hemosiderin-laden macrophages; acute foci of axonal degeneration and/or linear glial scars; and perivascular, parenchymal, or meningeal accumulations of eosinophils and/or lymphocytes and plasma cells. Of the 43 samples with histologic lesions consistent with neural larval migrans, 19 were PCR positive; however, only 8 were confirmed Parelaphostrongylus by DNA sequencing. Additionally, 1 goat was identified with a protostrongylid that had a 97% identity to both Parelaphostrongylus odocoilei and a protostrongylid nematode from pampas deer (Ozotoceros bezoarticus celer) from Argentina. None of the histologic lesions individually or in combination correlated statistically to positive molecular tests for the nematode. The results indicate that it is possible to extract Parelaphostrongylus DNA from formalin-fixed, paraffin-embedded tissue, but extended fixation presumably can cause DNA crosslinking. Nested PCR provides another diagnostic tool to identify the cause of neurologic disease in camelids and elk with histologic lesions consistent with neural larval migrans. Furthermore, potential novel protostrongylid DNA was detected from a goat with lesions consistent with P. tenuis infection, suggesting that other neurotropic Parelaphostrongylus species may occur locally. © 2014 The Author(s).

  3. Species-specific AFLP markers for identification of Zingiber officinale, Z. montanum and Z. zerumbet (Zingiberaceae).

    Science.gov (United States)

    Ghosh, S; Majumder, P B; Sen Mandi, S

    2011-02-08

    The Zingiber genus, which includes the herbs known as gingers, commonly used in cooking, is well known for its medicinal properties, as described in the Indian pharmacopoeia. Different members of this genus, although somewhat similar in morphology, differ widely in their pharmacological and therapeutic properties. The most important species of this genus, with maximal therapeutic properties, is Zingiber officinale (garden ginger), which is often adulterated with other less-potent Zingiber sp. There is an existing demand in the herbal drug industry for an authentication system for the Zingiber sp in order to facilitate their commercial use as genuine phytoceuticals. To this end, we used amplified fragment length polymorphism (AFLP) to produce DNA fingerprints for three Zingiber species. Sixteen collections (six of Z. officinale, five of Z. montanum, and five of Z. zerumbet) were used in the study. Seven selective primer pairs were found to be useful for all the accessions. A total of 837 fragments were produced by these primer pairs. Species-specific markers were identified for all three Zingiber species (91 for Z. officinale, 82 for Z. montanum, and 55 for Z. zerumbet). The dendogram analysis generated from AFLP patterns showed that Z. montanum and Z. zerumbet are phylogenetically closer to each other than to Z. officinale. The AFLP fingerprints of the Zingiber species could be used to authenticate Zingiber sp-derived drugs and to resolve adulteration-related problems faced by the commercial users of these herbs.

  4. Genetic relationships in Lens species and parentage determination of their interspecific hybrids using RAPD markers.

    Science.gov (United States)

    Ahmad, M; McNeil, D L; Fautrier, A G; Armstrong, K F; Paterson, A M

    1996-06-01

    Broadening of the genetic base and systematic exploitation of heterosis in cultivated lentils requires reliable information on genetic diversity in the germplasm. The ability of random amplified polymorphic DNA (RAPD) to distinguish among different taxa of Lens was evaluated for several geographically dispersed accessions/cultivars of four diploid Lens species. This study was carried out to assess whether RAPD data can provide additional evidence about the origin of the cultivated lentil and to measure genetic variability in lentil germplasm. Three cultivars of Lens culinaris ssp. culinaris, including one microsperma, and two macrosperma types, and four wild species (L. culinaris ssp. orientalis, L. odemensis and L. nigricans) were evaluated for genetic variability using a set of 1 11-mer and 14 random 10-mer primers. One hundred and fifty-eight reproducible and scorable DNA bands were observed from these primers. Genetic distances between each of the accessions were calculated from simple matching coefficients. Split decomposition analysis of the RAPD data allowed construction of an unrooted tree. This study revealed that (1) the level of intraspecific genetic variation in cultivated lentils is narrower than that in some wild species. (2) L. culinaris ssp. orientalis is the most likely candidate as a progenitor of the cultivated species, (3) L. nigricans accession W6 3222 (unknown) and L. c. ssp. orientalis W6 3244 (Turkey) can be reclassified as species of L. odemensis and (4) transmission of genetic material in Lens interspecific hybrids is genotypically specific, as identified by the RAPD markers in our study.

  5. Development of microsatellite markers of vandaceous orchids for species and variety identification.

    Science.gov (United States)

    Peyachoknagul, S; Nettuwakul, C; Phuekvilai, P; Wannapinpong, S; Srikulnath, K

    2014-07-24

    Vandaceous orchids are a group of orchid genera in the subfamily Vandoideae. Among this group, Mokara, Phalaenopsis, and Vanda are the most popular and commercially important orchids in Thailand. Novel microsatellite markers were developed from Mokara, the intergeneric hybrid from 3 genera Vanda, Ascocentrum, and Arachnis by using enriched method. Six primers from this study plus one primer previously developed from Vanda genome, a total of 7 markers, were selected to characterize 4 orchid genera (Mokara, Vanda, Rhynchostylis, and Ascocenda). The observed and expected heterozygosities varied in the 4 genera from 0.0000-1.0000 and 0.0000-0.8765, respectively. The transferability of these primers was also investigated in 76 vandaceous orchids from 12 genera. Three primer pairs, MOK26, MOK29, and MOK62, could successfully amplify the DNA of all samples, while MOK103 could be used with most of the samples. The total number of alleles from 76 samples ranged from 3 to 19 alleles per locus, with an average of 8.5714. Therefore, these markers could be used for variety/ species identification, certification and protection, genetic diversity, and evolutionary studies.

  6. MWCNTs of different physicochemical properties cause similar inflammatory responses, but differences in transcriptional and histological markers of fibrosis in mouse lungs

    Energy Technology Data Exchange (ETDEWEB)

    Poulsen, Sarah S., E-mail: spo@nrcwe.dk [National Research Centre for the Working Environment, Copenhagen DK-2100 (Denmark); Department of Science, Systems and Models, Roskilde University, DK-4000 Roskilde (Denmark); Saber, Anne T., E-mail: ats@nrcwe.dk [National Research Centre for the Working Environment, Copenhagen DK-2100 (Denmark); Williams, Andrew, E-mail: Andrew.williams@hc-sc.gc.ca [Environmental and Radiation Health Sciences Directorate, Health Canada, Ottawa, Ontario K1A 0K9 (Canada); Andersen, Ole, E-mail: oa@ruc.dk [Department of Science, Systems and Models, Roskilde University, DK-4000 Roskilde (Denmark); Købler, Carsten, E-mail: carko@nanotech.dtu.dk [Department of Micro- and Nanotechnology, Technical University of Denmark, DK-2800 Kgs. Lyngby (Denmark); Atluri, Rambabu, E-mail: rba@nrcwe.dk [Nanologica AB, SE-114 28 Stockholm (Sweden); Pozzebon, Maria E., E-mail: mariaelena.pozzebon@yahoo.it [Veneto Nanotech SCpA, ECSIN — European Centre for the Sustainable Impact of Nanotechnology, I-45100 Rovigo (Italy); Mucelli, Stefano P., E-mail: stefano.pozzimucelli@venetonanotech.it [Veneto Nanotech SCpA, ECSIN — European Centre for the Sustainable Impact of Nanotechnology, I-45100 Rovigo (Italy); Simion, Monica, E-mail: moni304ro@gmail.com [Laboratory of Nanobiotechnology, National Institute for Research and Development in Microtechnologies, 077190 Bucharest (Romania); Rickerby, David, E-mail: david.rickerby@jrc.ec.europa.eu [European Commission Joint Research Centre Institute for Environment and Sustainability, I-21027 Ispra, VA (Italy); Mortensen, Alicja, E-mail: almo@food.dtu.dk [National Food Institute, Technical University of Denmark, Søborg (Denmark); Jackson, Petra, E-mail: pja@nrcwe.dk [National Research Centre for the Working Environment, Copenhagen DK-2100 (Denmark); Kyjovska, Zdenka O., E-mail: zky@nrcwe.dk [National Research Centre for the Working Environment, Copenhagen DK-2100 (Denmark); and others

    2015-04-01

    Multi-walled carbon nanotubes (MWCNTs) are an inhomogeneous group of nanomaterials that vary in lengths, shapes and types of metal contamination, which makes hazard evaluation difficult. Here we present a toxicogenomic analysis of female C57BL/6 mouse lungs following a single intratracheal instillation of 0, 18, 54 or 162 μg/mouse of a small, curled (CNT{sub Small}, 0.8 ± 0.1 μm in length) or large, thick MWCNT (CNT{sub Large}, 4 ± 0.4 μm in length). The two MWCNTs were extensively characterized by SEM and TEM imaging, thermogravimetric analysis, and Brunauer–Emmett–Teller surface area analysis. Lung tissues were harvested 24 h, 3 days and 28 days post-exposure. DNA microarrays were used to analyze gene expression, in parallel with analysis of bronchoalveolar lavage fluid, lung histology, DNA damage (comet assay) and the presence of reactive oxygen species (dichlorodihydrofluorescein assay), to profile and characterize related pulmonary endpoints. Overall changes in global transcription following exposure to CNT{sub Small} or CNT{sub Large} were similar. Both MWCNTs elicited strong acute phase and inflammatory responses that peaked at day 3, persisted up to 28 days, and were characterized by increased cellular influx in bronchoalveolar lavage fluid, interstitial pneumonia and gene expression changes. However, CNT{sub Large} elicited an earlier onset of inflammation and DNA damage, and induced more fibrosis and a unique fibrotic gene expression signature at day 28, compared to CNT{sub Small}. The results indicate that the extent of change at the molecular level during early response phases following an acute exposure is greater in mice exposed to CNT{sub Large}, which may eventually lead to the different responses observed at day 28. - Highlights: • We evaluate the toxicogenomic response in mice following MWCNT instillation. • Two MWCNTs of different properties were examined and thoroughly characterized. • MWCNT exposure leads to increased pulmonary

  7. Transcriptome sequencing in an ecologically important tree species: assembly, annotation, and marker discovery

    Directory of Open Access Journals (Sweden)

    Benkman Craig W

    2010-03-01

    Full Text Available Abstract Background Massively parallel sequencing of cDNA is now an efficient route for generating enormous sequence collections that represent expressed genes. This approach provides a valuable starting point for characterizing functional genetic variation in non-model organisms, especially where whole genome sequencing efforts are currently cost and time prohibitive. The large and complex genomes of pines (Pinus spp. have hindered the development of genomic resources, despite the ecological and economical importance of the group. While most genomic studies have focused on a single species (P. taeda, genomic level resources for other pines are insufficiently developed to facilitate ecological genomic research. Lodgepole pine (P. contorta is an ecologically important foundation species of montane forest ecosystems and exhibits substantial adaptive variation across its range in western North America. Here we describe a sequencing study of expressed genes from P. contorta, including their assembly and annotation, and their potential for molecular marker development to support population and association genetic studies. Results We obtained 586,732 sequencing reads from a 454 GS XLR70 Titanium pyrosequencer (mean length: 306 base pairs. A combination of reference-based and de novo assemblies yielded 63,657 contigs, with 239,793 reads remaining as singletons. Based on sequence similarity with known proteins, these sequences represent approximately 17,000 unique genes, many of which are well covered by contig sequences. This sequence collection also included a surprisingly large number of retrotransposon sequences, suggesting that they are highly transcriptionally active in the tissues we sampled. We located and characterized thousands of simple sequence repeats and single nucleotide polymorphisms as potential molecular markers in our assembled and annotated sequences. High quality PCR primers were designed for a substantial number of the SSR loci

  8. Development of expressed sequence tag-simple sequence repeat markers for Chrysanthemum morifolium and closely related species.

    Science.gov (United States)

    Liu, H; Zhang, Q X; Sun, M; Pan, H T; Kong, Z X

    2015-07-13

    With the development of chrysanthemum breeding in recent years, an increasing number of wild species in genera related to Chrysanthemum were introduced to extend the genetic resources and facilitate the genetic improvement of chrysanthemums via hybridization. However, few simple sequence repeat (SSR) markers are available for marker-assisted breeding and population genetic studies of chrysanthemum and closely related species. Expressed sequence tags (ESTs) in public databases and cross-species transferable markers are considered to be a cost-effective means for developing sequence-based markers. In this study, 25 EST-SSRs were successfully developed from Chrysanthemum EST sequences for Chrysanthemum morifolium and closely related species. In total, 4164 unigene sequences were assembled from 7180 ESTs of chrysanthemum in GenBank, which were subsequently used to screen for the presence of microsatellites with the SSRIT software. The screening criteria were 8, 5, 4, and 3 repeating units for di-, tri-, tetra-, and penta- and higher-order nucleotides, respectively. Moreover, 310 SSR loci from 296 sequences were identified, and 198 primer pairs for SSR amplification were designed with the Primer Premier 5.0 software, of which 25 SSR loci showed polymorphic amplification in 52 species and varieties belonging to Chrysanthemum, Ajania, and Opisthopappus. The application of EST-SSR markers to the identification of intergeneric hybrids between Chrysanthemum and Ajania was demonstrated. Therefore, EST-SSRs can be developed for species that lack gene sequences or ESTs by utilizing ESTs of closely related species.

  9. Development of novel chloroplast microsatellite markers to identify species in the Agrostis complex (Poaceae) and related genera.

    Science.gov (United States)

    Maria L. Zapiola; Richard C. Cronn; Carol A. Mallory-Smith

    2010-01-01

    We needed a reliable way to identify species and confirm potential interspecific and intergeneric hybrids in a landscape-level study of gene flow from transgenic gylphosate-resistant Agrostis stolonifera (Poaceae) to compatible relatives. We developed 12 new polymorphic chloroplast microsatellite markers to aid in identifying species recipient of...

  10. The dual challenges of generality and specificity when developing environmental DNA markers for species and subspecies of Oncorhynchus

    Science.gov (United States)

    Taylor M. Wilcox; Kellie J. Carim; Kevin S. McKelvey; Michael Young; Michael K. Schwartz

    2015-01-01

    Environmental DNA (eDNA) sampling is a powerful tool for detecting invasive and native aquatic species. Often, species of conservation interest co-occur with other, closely related taxa. Here, we developed qPCR (quantitative PCR) markers which distinguish westslope cutthroat trout (Oncorhynchus clarkii lewsi), Yellowstone cutthroat trout (O. clarkii bouvieri...

  11. Widespread utility of highly informative AFLP molecular markers across divergent shark species.

    Science.gov (United States)

    Zenger, Kyall R; Stow, Adam J; Peddemors, Victor; Briscoe, David A; Harcourt, Robert G

    2006-01-01

    Population numbers of many shark species are declining rapidly around the world. Despite the commercial and conservation significance, little is known on even the most fundamental aspects of their population biology. Data collection that relies on direct observation can be logistically challenging with sharks. Consequently, molecular methods are becoming increasingly important to obtain knowledge that is critical for conservation and management. Here we describe an amplified fragment length polymorphism method that can be applied universally to sharks to identify highly informative genome-wide polymorphisms from 12 primer pairs. We demonstrate the value of our method on 15 divergent shark species within the superorder Galeomorphii, including endangered species which are notorious for low levels of genetic diversity. Both the endangered sand tiger shark (Carcharodon taurus, N = 18) and the great white shark (Carcharodon carcharias, N = 7) displayed relatively high levels of allelic diversity. A total of 59 polymorphic loci (H(e) = 0.373) and 78 polymorphic loci (H(e) = 0.316) were resolved in C. taurus and C. carcharias, respectively. Results from other sharks (e.g., Orectolobus ornatus, Orectolobus sp., and Galeocerdo cuvier) produced remarkably high numbers of polymorphic loci (106, 94, and 86, respectively) from a limited sample size of only 2. A major constraint to obtaining much needed genetic data from sharks is the time-consuming process of developing molecular markers. Here we demonstrate the general utility of a technique that provides large numbers of informative loci in sharks.

  12. Genetic diversity and population structure of six species of Capparis in Tunisia using AFLP markers.

    Science.gov (United States)

    Aichi-Yousfi, Haifa; Bahri, Bochra Amina; Medini, Maher; Rouz, Slim; Nejib Rejeb, Mohamed; Ghrabi-Gammar, Zeineb

    In order to study the genetic diversity, the phylogeographic pattern and hybridization between six Tunisian Capparis species, 213 accessions of Caper were genotyped with three primer combinations of amplified fragment length polymorphism (AFLP) markers. Out of 750 fragments generated, 636 were polymorphic and 407 of them were restricted to a single species. STRUCTURE and PCoA analyses clearly separated morphologically different populations into six distinct genetic ones. The UPGMA analysis grouped the species into three main clusters: G1 grouped C. spinosa subsp. spinosa var. spinosa and C. sicula subsp. sicula; G2 grouped C. ovata subsp. ovata and C. orientalis and G3 clustered C. zoharyi and C. aegyptia. Populations from G1, G2 and G3 were mainly distributed in arid, subhumid, and semi-arid bioclimates, respectively. Additional genetic studies on Capparis could help to identify genes underlying speciation events and local adaptation to geographic areas leading to the development of breeding programs. Copyright © 2016 Académie des sciences. Published by Elsevier SAS. All rights reserved.

  13. Nuclear markers reveal a complex introgression pattern among marine turtle species on the Brazilian coast.

    Science.gov (United States)

    Vilaça, Sibelle T; Vargas, Sarah M; Lara-Ruiz, Paula; Molfetti, Érica; Reis, Estéfane C; Lôbo-Hajdu, Gisele; Soares, Luciano S; Santos, Fabrício R

    2012-09-01

    Surprisingly, a high frequency of interspecific sea turtle hybrids has been previously recorded in a nesting site along a short stretch of the Brazilian coast. Mitochondrial DNA data indicated that as much as 43% of the females identified as Eretmochelys imbricata are hybrids in this area (Bahia State of Brazil). It is a remarkable find, because most of the nesting sites surveyed worldwide, including some in northern Brazil, presents no hybrids, and rare Caribbean sites present no more than 2% of hybrids. Thus, a detailed understanding of the hybridization process is needed to evaluate natural or anthropogenic causes of this regional phenomenon in Brazil, which could be an important factor affecting the conservation of this population. We analysed a set of 12 nuclear markers to investigate the pattern of hybridization involving three species of sea turtles: hawksbill (E. imbricata), loggerhead (Caretta caretta) and olive ridley (Lepidochelys olivacea). Our data indicate that most of the individuals in the crossings L. olivacea × E. imbricata and L. olivacea × C. caretta are F1 hybrids, whereas C. caretta × E. imbricata crossings present F1 and backcrosses with both parental species. In addition, the C. caretta × E. imbricata hybridization seems to be gender and species biased, and we also found one individual with evidence of multispecies hybridization among C. caretta × E. imbricata × Chelonia mydas. The overall results also indicate that hybridization in this area is a recent phenomenon, spanning at least two generations or ~40 years. © 2012 Blackwell Publishing Ltd.

  14. Microsatellite markers from the Ion Torrent: a multi-species contrast to 454 shotgun sequencing.

    Science.gov (United States)

    Elliott, Carole P; Enright, Neal J; Allcock, Richard J N; Gardner, Michael G; Meglécz, Emese; Anthony, Janet; Krauss, Siegfried L

    2014-05-01

    The development and screening of microsatellite markers have been accelerated by next-generation sequencing (NGS) technology and in particular GS-FLX pyro-sequencing (454). More recent platforms such as the PGM semiconductor sequencer (Ion Torrent) offer potential benefits such as dramatic reductions in cost, but to date have not been well utilized. Here, we critically compare the advantages and disadvantages of microsatellite development using PGM semiconductor sequencing and GS-FLX pyro-sequencing for two gymnosperm (a conifer and a cycad) and one angiosperm species. We show that these NGS platforms differ in the quantity of returned sequence data, unique microsatellite data and primer design opportunities, mostly consistent with the differences in read length. The strength of the PGM lies in the large amount of data generated at a comparatively lower cost and time. The strength of GS-FLX lies in the return of longer average length sequences and therefore greater flexibility in producing markers with variable product length, due to longer flanking regions, which is ideal for capillary multiplexing. These differences need to be considered when choosing a NGS method for microsatellite discovery. However, the ongoing improvement in read lengths of the NGS platforms will reduce the disadvantage of the current short read lengths, particularly for the PGM platform, allowing greater flexibility in primer design coupled with the power of a larger number of sequences. © 2013 John Wiley & Sons Ltd.

  15. CSGM Designer: a platform for designing cross-species intron-spanning genic markers linked with genome information of legumes.

    Science.gov (United States)

    Kim, Jin-Hyun; Lee, Chaeyoung; Hyung, Daejin; Jo, Ye-Jin; Park, Joo-Seok; Cook, Douglas R; Choi, Hong-Kyu

    2015-01-01

    Genetic markers are tools that can facilitate molecular breeding, even in species lacking genomic resources. An important class of genetic markers is those based on orthologous genes, because they can guide hypotheses about conserved gene function, a situation that is well documented for a number of agronomic traits. For under-studied species a key bottleneck in gene-based marker development is the need to develop molecular tools (e.g., oligonucleotide primers) that reliably access genes with orthology to the genomes of well-characterized reference species. Here we report an efficient platform for the design of cross-species gene-derived markers in legumes. The automated platform, named CSGM Designer (URL: http://tgil.donga.ac.kr/CSGMdesigner), facilitates rapid and systematic design of cross-species genic markers. The underlying database is composed of genome data from five legume species whose genomes are substantially characterized. Use of CSGM is enhanced by graphical displays of query results, which we describe as "circular viewer" and "search-within-results" functions. CSGM provides a virtual PCR representation (eHT-PCR) that predicts the specificity of each primer pair simultaneously in multiple genomes. CSGM Designer output was experimentally validated for the amplification of orthologous genes using 16 genotypes representing 12 crop and model legume species, distributed among the galegoid and phaseoloid clades. Successful cross-species amplification was obtained for 85.3% of PCR primer combinations. CSGM Designer spans the divide between well-characterized crop and model legume species and their less well-characterized relatives. The outcome is PCR primers that target highly conserved genes for polymorphism discovery, enabling functional inferences and ultimately facilitating trait-associated molecular breeding.

  16. Rapid Development of Microsatellite Markers for Plantago ovata Forsk.: Using Next Generation Sequencing and Their Cross-Species Transferability

    Directory of Open Access Journals (Sweden)

    Ranbir Singh Fougat

    2014-06-01

    Full Text Available Isabgol (Plantago ovata Forsk. is an important medicinal plant having high pharmacological activity in its seed husk, which is substantially used in the food, beverages and packaging industries. Nevertheless, isabgol lags behind in research, particularly for genomic resources, like molecular markers, genetic maps, etc. Presently, molecular markers can be easily developed through next generation sequencing technologies, more efficiently, cost effectively and in less time than ever before. This study was framed keeping in view the need to develop molecular markers for this economically important crop by employing a microsatellite enrichment protocol using a next generation sequencing platform (ion torrent PGM™ to obtain simple sequence repeats (SSRs for Plantago ovata for the very first time. A total of 3447 contigs were assembled, which contained 249 SSRs. Thirty seven loci were randomly selected for primer development; of which, 30 loci were successfully amplified. The developed microsatellite markers showed the amplification of the expected size and cross-amplification in another six species of Plantago. The SSR markers were unable to show polymorphism within P. ovata, suggesting that low variability exists within genotypes of P. ovata. This study suggests that PGM™ sequencing is a rapid and cost-effective tool for developing SSR markers for non-model species, and the markers so-observed could be useful in the molecular breeding of P. ovata.

  17. Genetic variation in the Solanaceae fruit bearing species lulo and tree tomato revealed by Conserved Ortholog (COSII markers

    Directory of Open Access Journals (Sweden)

    Felix Enciso-Rodríguez

    2010-01-01

    Full Text Available The Lulo or naranjilla (Solanum quitoense Lam. and the tree tomato or tamarillo (Solanum betaceum Cav. Sendt. are both Andean tropical fruit species with high nutritional value and the potential for becoming premium products in local and export markets. Herein, we present a report on the genetic characterization of 62 accessions of lulos (n = 32 and tree tomatoes (n = 30 through the use of PCR-based markers developed from single-copy conserved orthologous genes (COSII in other Solanaceae (Asterid species. We successfully PCR amplified a set of these markers for lulos (34 out of 46 initially tested and tree tomatoes (26 out of 41 for molecular studies. Six polymorphic COSII markers were found in lulo with a total of 47 alleles and five polymorphic markers in tree tomato with a total of 39 alleles in the two populations. Further genetic analyses indicated a high population structure (with F ST > 0.90, which may be a result of low migration between populations, adaptation to various niches and the number of markers evaluated. We propose COSII markers as sound tools for molecular studies, conservation and the breeding of these two fruit species.

  18. Genetic variation in the Solanaceae fruit bearing species lulo and tree tomato revealed by Conserved Ortholog (COSII) markers.

    Science.gov (United States)

    Enciso-Rodríguez, Felix; Martínez, Rodrigo; Lobo, Mario; Barrero, Luz Stella

    2010-04-01

    The Lulo or naranjilla (Solanum quitoense Lam.) and the tree tomato or tamarillo (Solanum betaceum Cav. Sendt.) are both Andean tropical fruit species with high nutritional value and the potential for becoming premium products in local and export markets. Herein, we present a report on the genetic characterization of 62 accessions of lulos (n = 32) and tree tomatoes (n = 30) through the use of PCR-based markers developed from single-copy conserved orthologous genes (COSII) in other Solanaceae (Asterid) species. We successfully PCR amplified a set of these markers for lulos (34 out of 46 initially tested) and tree tomatoes (26 out of 41) for molecular studies. Six polymorphic COSII markers were found in lulo with a total of 47 alleles and five polymorphic markers in tree tomato with a total of 39 alleles in the two populations. Further genetic analyses indicated a high population structure (with F(ST) > 0.90), which may be a result of low migration between populations, adaptation to various niches and the number of markers evaluated. We propose COSII markers as sound tools for molecular studies, conservation and the breeding of these two fruit species.

  19. Genetic variation in the Solanaceae fruit bearing species lulo and tree tomato revealed by Conserved Ortholog (COSII) markers

    Science.gov (United States)

    2010-01-01

    The Lulo or naranjilla (Solanum quitoense Lam.) and the tree tomato or tamarillo (Solanum betaceum Cav. Sendt.) are both Andean tropical fruit species with high nutritional value and the potential for becoming premium products in local and export markets. Herein, we present a report on the genetic characterization of 62 accessions of lulos (n = 32) and tree tomatoes (n = 30) through the use of PCR-based markers developed from single-copy conserved orthologous genes (COSII) in other Solanaceae (Asterid) species. We successfully PCR amplified a set of these markers for lulos (34 out of 46 initially tested) and tree tomatoes (26 out of 41) for molecular studies. Six polymorphic COSII markers were found in lulo with a total of 47 alleles and five polymorphic markers in tree tomato with a total of 39 alleles in the two populations. Further genetic analyses indicated a high population structure (with FST > 0.90), which may be a result of low migration between populations, adaptation to various niches and the number of markers evaluated. We propose COSII markers as sound tools for molecular studies, conservation and the breeding of these two fruit species. PMID:21637482

  20. DNA barcoding and development of species-specific markers for the identification of tea mosquito bugs (Miridae: Heteroptera) in India.

    Science.gov (United States)

    Rebijith, K B; Asokan, R; Kumar, N K Krishna; Srikumar, K K; Ramamurthy, V V; Bhat, P Shivarama

    2012-10-01

    Rapid, accurate, and timely identification of insects as a group is important and challenging worldwide, as they outnumber all other animals in number and diversity. DNA barcoding is a method for the identification of species in a wide range of animal taxa, which uses the 5' region of the mitochondrial cytochrome c oxidase-I (CO-I). Yet another easy, accurate, and economical method of species discrimination is by developing species-specific markers, which produce specific amplicon for the species in question. The method is handy because it is not limited by life stages, sex, polymorphism, and other factors. Herein, we measured the usefulness of CO-I for the species discrimination of mirids in India viz. Helopeltis antonii Signoret, H. thievora Waterhouse, H. bradyi Waterhouse, and Pachypeltis maesarum Kirkaldy in their various life stages. Furthermore, our study showed the utility of species-specific markers in differentiating H. antonii (295) and H. bradyi (514) regardless of their life stages. Analysis of CO-I gene revealed DNA barcode and species-specific markers will aid the identification of mirids in India and will stand as a decisive tool in formulating integrated pest management (IPM) strategy, quick identification of invasive and cryptic species, haplotypes, biotypes, and other factors, if any.

  1. Polymorphic DNA microsatellite markers for forensic individual identification and parentage analyses of seven threatened species of parrots (family Psittacidae

    Directory of Open Access Journals (Sweden)

    Catherine Jan

    2016-09-01

    Full Text Available The parrot family represents one of the bird group with the largest number of endangered species, as a result of habitat destruction and illegal trade. This illicit traffic involves the smuggling of eggs and animals, and the laundering through captive breeding facilities of wild-caught animals. Despite the huge potential of wildlife DNA forensics to determine with conclusive evidence illegal trade, current usage of DNA profiling approaches in parrots has been limited by the lack of suitable molecular markers specifically developed for the focal species and by low cross-species polymorphism. In this study, we isolated DNA microsatellite markers in seven parrot species threatened with extinction (Amazona brasiliensis, A. oratrix, A. pretrei, A. rhodocorytha, Anodorhynchus leari, Ara rubrogenys and Primolius couloni. From an enriched genomic library followed by 454 pyrosequencing, we characterized a total of 106 polymorphic microsatellite markers (mostly tetranucleotides in the seven species and tested them across an average number of 19 individuals per species. The mean number of alleles per species and across loci varied from 6.4 to 8.3, with the mean observed heterozygosities ranging from 0.65 to 0.84. Identity and parentage exclusion probabilities were highly discriminatory. The high variability displayed by these microsatellite loci demonstrates their potential utility to perform individual genotyping and parentage analyses, in order to develop a DNA testing framework to determine illegal traffic in these threatened species.

  2. Volume-Based F-18 FDG PET/CT Imaging Markers Provide Supplemental Prognostic Information to Histologic Grading in Patients With High-Grade Bone or Soft Tissue Sarcoma

    DEFF Research Database (Denmark)

    Andersen, Kim Francis; Fuglo, Hanna Maria; Rasmussen, Sine Hvid

    2015-01-01

    to 2012 including 92 patients with histologically verified high-grade BS (N = 37) or STS (N = 55). All patients underwent a pretreatment F-18 FDG PET/CT scan. Clinical data were registered. Measurements of the accuracy of metabolic tumor volume with a preset threshold of 40% of the maximum standardized...... analysis. Kaplan-Meier survival estimates and log-rank test were used to compare the degree of equality of survival distributions. Prognostic variables with related hazard ratios (HR) were assessed using Cox proportional hazards regression analysis.Forty-one of 92 patients died during follow-up (45%; 12 BS.......05, HR 3.37 [95% CI 1.02-11.11]). No significant results were demonstrated for MTV40%.Volume-based F-18 FDG PET/CT imaging markers in terms of pretreatment estimation of TLG provide supplemental prognostic information to histologic grading, with significant independent properties for prediction...

  3. Subtracted diversity array identifies novel molecular markers including retrotransposons for fingerprinting Echinacea species.

    Directory of Open Access Journals (Sweden)

    Alexandra Olarte

    Full Text Available Echinacea, native to the Canadian prairies and the prairie states of the United States, has a long tradition as a folk medicine for the Native Americans. Currently, Echinacea are among the top 10 selling herbal medicines in the U.S. and Europe, due to increasing popularity for the treatment of common cold and ability to stimulate the immune system. However, the genetic relationship within the species of this genus is unclear, making the authentication of the species used for the medicinal industry more difficult. We report the construction of a novel Subtracted Diversity Array (SDA for Echinacea species and demonstrate the potential of this array for isolating highly polymorphic sequences. In order to selectively isolate Echinacea-specific sequences, a Suppression Subtractive Hybridization (SSH was performed between a pool of twenty-four Echinacea genotypes and a pool of other angiosperms and non-angiosperms. A total of 283 subtracted genomic DNA (gDNA fragments were amplified and arrayed. Twenty-seven Echinacea genotypes including four that were not used in the array construction could be successfully discriminated. Interestingly, unknown samples of E. paradoxa and E. purpurea could be unambiguously identified from the cluster analysis. Furthermore, this Echinacea-specific SDA was also able to isolate highly polymorphic retrotransposon sequences. Five out of the eleven most discriminatory features matched to known retrotransposons. This is the first time retrotransposon sequences have been used to fingerprint Echinacea, highlighting the potential of retrotransposons as based molecular markers useful for fingerprinting and studying diversity patterns in Echinacea.

  4. Application of molecular markers to detect DNA damage caused by environmental pollutants in lichen species.

    Science.gov (United States)

    Cansaran-Duman, D; Altunkaynak, E; Aslan, A; Büyük, I; Aras, S

    2015-05-04

    Pseudevernia furfuracea L. (Zopf), Peltigera praetextata (Flörke ex Sommerf.) Zopf, Lobaria pulmonaria (L.) Hoffm., and Usnea longissima Ach. lichen species were used as bioindicators to assess the genotoxicity of air pollutants. In the present study, we examined significant environmetal pollutants and investigate how changes may lead to damage in DNA structure using RAPD markers. In the study area (Erzurum, Turkey), poor-quality lignite, which generates a large amount of sulfur dioxide, nitrogen oxides, and particle matter, is used for domestic heating, and vehicles also contribute to air pollution. Control lichen samples were collected far from large urban and industrial settlements and transplanted to four polluted sites for 4, 8, or 12 months. The total soluble protein content of the examined four lichen species did not significantly change with exposure time (P < 0.05). The four lichen samples exposed to the pollutants for 8 months had the highest ratio of DNA changes. The ratio of band differences in P. praetextata was higher than that in the other three lichen species, possibly because it has broad leaves that accumulated more pollutants. The average incidences of polymorphism were 64.14, 54.58, 65.76, and 43.06% for P. furfuracea, P. praetextata, L. pulmonaria, and U. longissima, respectively. The genomic template stability (GTS) significantly decreased following exposure to pollutants. GTS ratios revealed that the highest value (98.36%) belonged to U. longissima samples from Site 1 (10 m) after 4 months of exposure, and the lowest values belonged to P. praetextata (73.58%) from Site 3 (100 m) after 8 months of exposure. Based on our findings, we recommend the use of P. praetextata as an indicator of genotoxicity.

  5. The new histologic classification of lung primary adenocarcinoma subtypes is a reliable prognostic marker and identifies tumors with different mutation status: the experience of a French cohort.

    Science.gov (United States)

    Mansuet-Lupo, Audrey; Bobbio, Antonio; Blons, Hélène; Becht, Etienne; Ouakrim, Hanane; Didelot, Audrey; Charpentier, Marie-Christine; Bain, Serge; Marmey, Béatrice; Bonjour, Patricia; Biton, Jérôme; Cremer, Isabelle; Dieu-Nosjean, Marie-Caroline; Sautès-Fridman, Catherine; Régnard, Jean-François; Laurent-Puig, Pierre; Alifano, Marco; Damotte, Diane

    2014-09-01

    Histologic classification of lung adenocarcinoma subtype has a prognostic value in most studies. However, lung adenocarcinoma characteristics differ across countries. Here, we aimed at validating the prognostic value of this classification in a large French series of lung adenocarcinoma. We reviewed 407 consecutive lung adenocarcinomas operated on between 2001 and 2005 and reclassified them according to the International Association for the Study of Lung Cancer (IASLC)/American Thoracic Society (ATS)/European Respiratory Society (ERS) classification and subsequently graded them into low, intermediate, and high grade. We analyzed the relevance of this classification according to clinical, pathologic, and molecular analysis. Patients (median age, 61 years; 288 men) underwent lobectomy (n = 378) or pneumonectomy (n = 29). Patients' overall survival at 5 and 10 years was 53.2% and 32.6%, respectively. Union for International Cancer Control stage distribution was 189 stage I, 104 stage II, 107 stage III, and seven stage IV. Low-grade tumor was found in one patient, intermediate grade in 275 patients, and high grade in 131 patients. KRAS and EGFR mutations were detected in 34% and 9.6%, respectively. Histologic grade was significantly correlated with extent of resection (P = .01), thyroid transcriptional factor-1 expression (P = .00000001), vascular emboli (P = .03), and EGFR mutations (P = .01). Mucinous adenocarcinomas were associated with KRAS mutations (P = .003). At univariate analysis, age, extent of resection, histologic grade, pleural invasion, vascular emboli, pathologic T and N, and stage were predictive of survival. At multivariate analysis, age (P = .0001), histologic grade (P = .03), and stage (P = .000003) were independent prognostic factors. IASLC/ATS/ERS classification of lung adenocarcinomas predicts survival in French population. Histologic grade correlates with clinical, pathologic and molecular parameters suggesting different oncogenic pathways.

  6. Are both sympatric species Ilex perado and Ilex canariensis secretly hybridizing? Indication from nuclear markers collected in Tenerife

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    Manen Jean-François

    2004-11-01

    Full Text Available Abstract Background Intra-specific and intra-individual polymorphism is frequently observed in nuclear markers of Ilex (Aquifoliaceae and discrepancy between plastid and nuclear phylogenies is the rule in this genus. These observations suggest that inter-specific plastid or/and nuclear introgression played an important role in the process of evolution of Ilex. With the aim of a precise understanding of the evolution of this genus, two distantly related sympatric species collected in Tenerife (Canary Islands, I. perado and I. canariensis, were studied in detail. Introgression between these two species was previously never reported. One plastid marker (the atpB-rbcL spacer and two nuclear markers, the ribosomal internal transcribed spacer (ITS and the nuclear encoded plastid glutamine synthetase (nepGS were analyzed for 13 and 27 individuals of I. perado and I. canariensis, respectively. Results The plastid marker is intra-specifically constant and correlated with species identity. On the other hand, whereas the nuclear markers are conserved in I. perado, they are highly polymorphic in I. canariensis. The presence of pseudogenes and recombination in ITS sequences of I. canariensis explain this polymorphism. Ancestral sequence polymorphism with incomplete lineage sorting, or past or recent hybridization with an unknown species could explain this polymorphism, not resolved by concerted evolution. However, as already reported for many other plants, past or recent introgression of an alien genotype seem the most probable explanation for such a tremendous polymorphism. Conclusions Data do not allow the determination with certitude of the putative species introgressing I. canariensis, but I. perado is suspected. The introgression would be unilateral, with I. perado as the male donor, and the paternal sequences would be rapidly converted in highly divergent and consequently unidentifiable pseudogenes. At least, this study allows the establishment of

  7. Genetic variation of some hawthorn species based on phenotypic characteristics and RAPD marker

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    Javad Erfani-Moghadam

    2016-03-01

    Full Text Available Hawthorn (Crataegus spp. is an important forest fruit species in Iran. Genetic variability among some genotypes of hawthorn was investigated using morphological traits and random amplified polymorphic DNA (RAPD marker. The collected genotypes belonged to four species of Crataegus genus. High variability among genotypes was found for most of the traits. Results from the principal component analysis (PCA indicated that 85.05% of the observed variability was accounted by the first five components. The first two components explained about 55.24% of the total achieved variability. In PCA, fruit weight, fruit length, fruit diameter, fruit moisture, fruit dry matter, leaf length, leaf area, leaf width, number of leaves per node, seed weight and seed length were predominant in the first two components, indicating that they were useful for the assessment of hawthorn germplasm characterization. A total of 58 polymorphic bands were produced with 10 RAPD primers. The bands' sizes ranged from 180 to 2700 bp. The number of the observed polymorphic bands for each primer ranged from 4 to 8, with an average of 5.8 alleles per locus. The polymorphism information content was observed to be the highest (0.79 in the Oligo_32 locus, whereas the Oligo_339 locus had the lowest value of 0.64, with an average of 0.72, among the RAPD primers. The Jaccard's genetic similarity coefficient ranged from 0.12 to 0.95 among the genotypes. At a similarity coefficient of 0.46, the unweighted pair group method with arithmetic mean (UPGMA cluster analysis divided the genotypes into three major groups.

  8. Molecular characterization of twenty polymorphic microsatellite markers in the polyploid fruit tree species Syzygium samarangense (Myrtaceae).

    Science.gov (United States)

    Lai, J M; Tsai, C C; Yen, C R; Ko, Y Z; Chen, S R; Weng, I S; Lin, Y S; Chiang, Y C

    2015-10-21

    Syzygium samarangense (Blume) Merr. & Perry (wax apple) is an important commercial fruit tree in Southeast Asia. Here, microsatellite markers were developed to evaluate genetic diversity and distinguish cultivars in this species. In total, 161 microsatellite loci with sufficient flanking sequences to design primer sets were isolated from wax apple using a magnetic bead-enrichment method. Fifty-eight primer sets were designed based on the flanking sequences of each single sequence repeat (SSR) locus and were tested using 14 wax apple cultivars/lines. Twenty SSR loci were found to be polymorphic and transferable across the 14 wax apple cultivars/lines. The number of alleles and effective number of alleles detected per locus ranged from 4 to 12 and from 1.697 to 9.800, respectively. The expected heterozygosity ranged from 0.150 to 0.595 (mean = 0.414). Polymorphism information content values ranged from 0.502 to 0.866 (mean = 0.763). These new microsatellite loci will be of value for characterization of genetic diversity in wax apples and for the identification of cultivars.

  9. Using MiddRAD-seq data to develop polymorphic microsatellite markers for an endangered yew species

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    Hantao Qin

    2017-10-01

    Full Text Available Microsatellites are highly polymorphic markers which have been used in a wide range of genetic studies. In recent years, various sources of next-generation sequencing data have been used to develop new microsatellite loci, but compared with the more common shotgun genomic sequencing or transcriptome data, the potential utility of RAD-seq data for microsatellite ascertainment is comparatively under-used. In this study, we employed MiddRAD-seq data to develop polymorphic microsatellite loci for the endangered yew species Taxus florinii. Of 8,823,053 clean reads generated for ten individuals of a population, 94,851 (∼1% contained microsatellite motifs. These corresponded to 2993 unique loci, of which 526 (∼18% exhibited polymorphism. Of which, 237 were suitable for designing microsatellite primer pairs, and 128 loci were randomly selected for PCR validation and microsatellite screening. Out of the 128 primer pairs, 16 loci gave clear, reproducible patterns, and were then screened and characterized in 24 individuals from two populations. The total number of alleles per locus ranged from two to ten (mean = 4.875, and within-population expected heterozygosity from zero to 0.789 (mean = 0.530, indicating that these microsatellite loci will be useful for population genetics and speciation studies of T. florinii. This study represents one of few examples to mine polymorphic microsatellite loci from ddRAD data.

  10. Relationship between serum HBV-RNA levels and intrahepatic viral as well as histologic activity markers in entecavir-treated patients.

    Science.gov (United States)

    Wang, Jing; Yu, Yiqi; Li, Guojun; Shen, Chuan; Meng, Zhefeng; Zheng, Jianming; Jia, Yanhong; Chen, Shaolong; Zhang, Xiao; Zhu, Mengqi; Zheng, Jiangjiang; Song, Zhangzhang; Wu, Jing; Shao, Lingyun; Qian, Peiyu; Mao, Xiaona; Wang, Xuanyi; Huang, Yuxian; Zhao, Caiyan; Zhang, Jiming; Qiu, Chao; Zhang, Wenhong

    2017-09-21

    In diagnostics, serum hepatitis B virus (HBV)-RNA levels are valuable when the HBV-DNA load in circulation is effectively suppressed by nucleos(t)ide analogue (NUC) therapy. This study aimed to determine the intrahepatic viral replication activity reflected in serum HBV-RNA and whether HBV-RNA contributes to liver histological changes in patients treated with NUC. A cross-sectional set of serum and liver biopsy samples was obtained from patients treated with entecavir, who had undetectable levels of serum HBV-DNA. The correlations between serum HBV-RNA concentration and levels of peripheral and intrahepatic viral replicative forms, as well as histological scores, were analyzed. Quasispecies of serum HBV-RNA and intrahepatic viral replicative forms were examined by deep sequencing. HBV-RNA-positive hepatocytes were visualized by in situ hybridization. Serum HBV-RNA was detected in 35 of 47 patients (74.47%, 2.33-4.80log10copies/ml). These levels correlated not only with the intrahepatic HBV-RNA level and the ratio of intrahepatic HBV-RNA to covalently closed circular DNA (cccDNA), but also with the histological scores for grading and staging. Regarding quasispecies, serum HBV-RNA was dynamic and more genetically homogenous to simultaneously sampled intrahepatic HBV-RNA than to the cccDNA pool. In situ histology revealed that HBV-RNA-positive hepatocytes were clustered in foci, sporadically distributed across the lobules, and co-localized with hepatitis B surface antigen. Serum HBV-RNA levels reflect intrahepatic viral transcriptional activity and are associated with liver histopathology in patients receiving NUC therapy. Our study sheds light on the nature of HBV-RNA in the pathogenesis of chronic HBV infection and has implications for the management of chronic hepatitis B during NUC therapy. Serum HBV-RNA levels are indicative of the intrahepatic transcriptional activity of covalently closed circular DNA and are associated with liver histological changes in

  11. Nuclear species-diagnostic SNP markers mined from 454 amplicon sequencing reveal admixture genomic structure of modern citrus varieties.

    Science.gov (United States)

    Curk, Franck; Ancillo, Gema; Ollitrault, Frédérique; Perrier, Xavier; Jacquemoud-Collet, Jean-Pierre; Garcia-Lor, Andres; Navarro, Luis; Ollitrault, Patrick

    2015-01-01

    Most cultivated Citrus species originated from interspecific hybridisation between four ancestral taxa (C. reticulata, C. maxima, C. medica, and C. micrantha) with limited further interspecific recombination due to vegetative propagation. This evolution resulted in admixture genomes with frequent interspecific heterozygosity. Moreover, a major part of the phenotypic diversity of edible citrus results from the initial differentiation between these taxa. Deciphering the phylogenomic structure of citrus germplasm is therefore essential for an efficient utilization of citrus biodiversity in breeding schemes. The objective of this work was to develop a set of species-diagnostic single nucleotide polymorphism (SNP) markers for the four Citrus ancestral taxa covering the nine chromosomes, and to use these markers to infer the phylogenomic structure of secondary species and modern cultivars. Species-diagnostic SNPs were mined from 454 amplicon sequencing of 57 gene fragments from 26 genotypes of the four basic taxa. Of the 1,053 SNPs mined from 28,507 kb sequence, 273 were found to be highly diagnostic for a single basic taxon. Species-diagnostic SNP markers (105) were used to analyse the admixture structure of varieties and rootstocks. This revealed C. maxima introgressions in most of the old and in all recent selections of mandarins, and suggested that C. reticulata × C. maxima reticulation and introgression processes were important in edible mandarin domestication. The large range of phylogenomic constitutions between C. reticulata and C. maxima revealed in mandarins, tangelos, tangors, sweet oranges, sour oranges, grapefruits, and orangelos is favourable for genetic association studies based on phylogenomic structures of the germplasm. Inferred admixture structures were in agreement with previous hypotheses regarding the origin of several secondary species and also revealed the probable origin of several acid citrus varieties. The developed species-diagnostic SNP

  12. Nuclear Species-Diagnostic SNP Markers Mined from 454 Amplicon Sequencing Reveal Admixture Genomic Structure of Modern Citrus Varieties

    Science.gov (United States)

    Curk, Franck; Ancillo, Gema; Ollitrault, Frédérique; Perrier, Xavier; Jacquemoud-Collet, Jean-Pierre; Garcia-Lor, Andres; Navarro, Luis; Ollitrault, Patrick

    2015-01-01

    Most cultivated Citrus species originated from interspecific hybridisation between four ancestral taxa (C. reticulata, C. maxima, C. medica, and C. micrantha) with limited further interspecific recombination due to vegetative propagation. This evolution resulted in admixture genomes with frequent interspecific heterozygosity. Moreover, a major part of the phenotypic diversity of edible citrus results from the initial differentiation between these taxa. Deciphering the phylogenomic structure of citrus germplasm is therefore essential for an efficient utilization of citrus biodiversity in breeding schemes. The objective of this work was to develop a set of species-diagnostic single nucleotide polymorphism (SNP) markers for the four Citrus ancestral taxa covering the nine chromosomes, and to use these markers to infer the phylogenomic structure of secondary species and modern cultivars. Species-diagnostic SNPs were mined from 454 amplicon sequencing of 57 gene fragments from 26 genotypes of the four basic taxa. Of the 1,053 SNPs mined from 28,507 kb sequence, 273 were found to be highly diagnostic for a single basic taxon. Species-diagnostic SNP markers (105) were used to analyse the admixture structure of varieties and rootstocks. This revealed C. maxima introgressions in most of the old and in all recent selections of mandarins, and suggested that C. reticulata × C. maxima reticulation and introgression processes were important in edible mandarin domestication. The large range of phylogenomic constitutions between C. reticulata and C. maxima revealed in mandarins, tangelos, tangors, sweet oranges, sour oranges, grapefruits, and orangelos is favourable for genetic association studies based on phylogenomic structures of the germplasm. Inferred admixture structures were in agreement with previous hypotheses regarding the origin of several secondary species and also revealed the probable origin of several acid citrus varieties. The developed species-diagnostic SNP

  13. Origins of the amphiploid species Brassica napus L. investigated by chloroplast and nuclear molecular markers

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    Allender Charlotte J

    2010-03-01

    Full Text Available Abstract Background The amphiploid species Brassica napus (oilseed rape, Canola is a globally important oil crop yielding food, biofuels and industrial compounds such as lubricants and surfactants. Identification of the likely ancestors of each of the two genomes (designated A and C found in B. napus would facilitate incorporation of novel alleles from the wider Brassica genepool in oilseed rape crop genetic improvement programmes. Knowledge of the closest extant relatives of the genotypes involved in the initial formation of B. napus would also allow further investigation of the genetic factors required for the formation of a stable amphiploid and permit the more efficient creation of fully fertile re-synthesised B. napus. We have used a combination of chloroplast and nuclear genetic markers to investigate the closest extant relatives of the original maternal progenitors of B. napus. This was based on a comprehensive sampling of the relevant genepools, including 83 accessions of A genome B. rapa L. (both wild and cultivated types, 94 accessions of B. napus and 181 accessions of C genome wild and cultivated B. oleracea L. and related species. Results Three chloroplast haplotypes occurred in B. napus. The most prevalent haplotype (found in 79% of accessions was not present within the C genome accessions but was found at low frequencies in B. rapa. Chloroplast haplotypes characteristic of B. napus were found in a small number of wild and weedy B. rapa populations, and also in two accessions of cultivated B. rapa 'brocoletto'. Whilst introgression of the B. napus chloroplast type in the wild and weedy B. rapa populations has been proposed by other studies, the presence of this haplotype within the two brocoletto accessions is unexplained. Conclusions The distribution of chloroplast haplotypes eliminate any of the C genome species as being the maternal ancestor of the majority of the B. napus accessions. The presence of multiple chloroplast

  14. Distribution of Bio-accumulated Cd and Cr in two Vigna species and the Associated Histological Variations

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    Ratheesh Chandra, P.

    2010-04-01

    Full Text Available In nutrient culture experiments, bioaccumulation and anatomical effects of cadmium (CdCl2 - 20μM and chromium (K2Cr2O7 - 600 μM on the structure of root and stem was studied by histochemical and analytical methods in Vigna radiata and Vigna unguiculata. Each metal exerted specific influences on the anatomy of various tissues in root and stem. Histochemical localisation of cadmium and chromium was observed in the stained sections of root and stem. Atomic Absorption Spectrophotometric study revealed maximum accumulation of cadmium and chromium in the root tissue as compared to shoot with significant variation among the species. Abundant occurrences of densely stained deposits of chromium were seen in the root stelar region of V. unguiculata and to a lesser extend in V. radiata. Cadmium accumulation in V. radiata was comparatively more than that of V. unguiculata. The findings also revealed that the accumulation pattern of cadmium and chromium varies between species and hence is species specific.

  15. Identification of gene pools used in restoration and conservation by chloroplast microsatellite markers in Iberian pine species

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    Hernández-Tecles, Enrique; De las Heras, Jorge; Lorenzo, Zaida; Navascués, Miguel; Alia, Ricardo

    2017-11-01

    Aim of study: To contribute to the characterization of the origin of material used in afforestation, restoration or conservation activities by using Cp-SSR markers. Area of study: We used information from the natural range of Iberian pines, from Spain. Materials and methods: We used Iberian pines as an example to undertook gene pool characterization based on a wide Iberian sample of 97 populations from five Pinus species (Pinus halepensis, Pinus pinaster, Pinus nigra, Pinus sylvestris and Pinus uncinata). Haplotypes from each analyzed tree (derived from nine chloroplast microsatellites markers in P. halepensis and six in the rest of the species) were obtained. Based on this information we subdivided each species in regions (considering both genetic structure and its application in afforestation, restoration and conservation programs) and tested the assignation of populations to the different groups based on the genetic distance among samples. Main results: The rate of successful identification of populations among the different species was very high (> 94 %) for P. nigra, P. sylvestris and P. uncinata, high (81 %) for P. pinaster, and low (< 65 %) for P. halepensis. Research highlights: Chloroplast DNA markers from extensive population datasets can be used to assign the origin of the forest reproductive material in some pine species.

  16. Identification of gene pools used in restoration and conservation by chloroplast microsatellite markers in Iberian pine species

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    Enrique Hernández-Tecles

    2017-10-01

    Full Text Available Aim of study: To contribute to the characterization of the origin of material used in afforestation, restoration or conservation activities by using Cp-SSR markers. Area of study: We used information from the natural range of Iberian pines, from Spain. Materials and methods: We used Iberian pines as an example to undertook gene pool characterization based on a wide Iberian sample of 97 populations from five Pinus species (Pinus halepensis, Pinus pinaster, Pinus nigra, Pinus sylvestris and Pinus uncinata. Haplotypes from each analyzed tree (derived from nine chloroplast microsatellites markers in P. halepensis and six in the rest of the species were obtained. Based on this information we subdivided each species in regions (considering both genetic structure and its application in afforestation, restoration and conservation programs and tested the assignation of populations to the different groups based on the genetic distance among samples. Main results: The rate of successful identification of populations among the different species was very high (> 94 % for P. nigra, P. sylvestris and P. uncinata, high (81 % for P. pinaster, and low (< 65 % for P. halepensis. Research highlights: Chloroplast DNA markers from extensive population datasets can be used to assign the origin of the forest reproductive material in some pine species.

  17. Development of microsatellite markers for Hyacinth macaw (Anodorhynchus hyacinthinus) and their cross-amplification in other parrot species.

    Science.gov (United States)

    da Silva, Helder E; Presti, Flavia T; Wasko, Adriane P; Pinhal, Danillo

    2015-12-01

    Hyacinth macaw Anodorhynchus hyacinthinus is the largest parrot of the world and is considered vulnerable to extinction due to its habitat loss and illegal trade associated to the international pet market demand. Genetic studies on this species are still incipient to generate a consistent characterization of the population dynamics and to develop appropriate conservation strategies. In this sense, microsatellite markers may support the detection of a population genetic structure for this bird species. However, at this time, none Hyacinth macaw species-specific primers for microsatellite loci have been so far established. This study aimed to develop and characterize polymorphic microsatellite markers for A. hyacinthinus and to check for their cross-amplification in other parrot species. Sequences containing repeated dinucleotide motifs were prospected and optimized from a genomic library that was enriched for microsatellites using magnetic beads. The analyses of 43-57 samples from wild individuals of three distinct Brazilian subpopulations led to the characterization of five polymorphic microsatellite loci. Allele richness per locus ranged from two to 12. Three loci exhibited observed heterozygosity values higher than 50%, but the overall average value among all loci was close to 45%. In addition, successful primer cross-amplification was verified in seven other investigated species of Neotropical parrots. The newly developed markers have shown to be potentially useful for in situ and ex situ population studies to support future conservation actions of Hyacinth macaw and other parrots.

  18. The CYP51C gene, a reliable marker to resolve interspecific phylogenetic relationships within the Fusarium species complex and a novel target for species-specific PCR.

    Science.gov (United States)

    Fernández-Ortuño, Dolores; Loza-Reyes, Elisa; Atkins, Sarah L; Fraaije, Bart A

    2010-12-15

    Early diagnosis and control of different Fusarium species is essential for successful management of plant disease and subsequent prevention of toxins entering the food chain. This issue can be addressed using phylogenetic analyses and other molecular techniques, including the design of species-specific primers and corresponding PCR assays. In practice, only a few genes are sequenced for most species and insights into the evolutionary mechanisms at the species level usually stem from phylogenetic analyses of only one or a small number of genetic loci. This poses the question of whether the recovered tree accurately reflects the relationships among species or rather more local interrelationships particular to the genetic marker employed. This study examined if the Fusarium-specific CYP51C gene can be used to establish evolutionary relationships between Fusarium species and enable species-specific detection. The resolving power of the CYP51C gene was studied for 46 Fusarium isolates representing 18 different species. The resulting phylogeny analysis showed clear and well-structured separation of the isolates according to their species rank, synthesised toxin and Fusarium section. Moreover, a comparison between the individual CYP51C phylogeny and a reference tree (inferred from the concatenation of ITS, CYP51C, β-tubulin and TEF-1α sequences) indicated superior resolution of CYP51C relative to ITS and β-tubulin sequences. In addition to its suitability as a reliable marker for diagnosis of different toxigenic Fusarium species, we also show that the CYP51C gene is a promising target for development of species-specific PCR. This was demonstrated by the specific detection of Fusarium cerealis in grain samples of wheat. Copyright © 2010 Elsevier B.V. All rights reserved.

  19. Species identification of medicinal pteridophytes by a DNA barcode marker, the chloroplast psbA-trnH intergenic region.

    Science.gov (United States)

    Ma, Xin-Ye; Xie, Cai-Xiang; Liu, Chang; Song, Jing-Yuan; Yao, Hui; Luo, Kun; Zhu, Ying-Jie; Gao, Ting; Pang, Xiao-Hui; Qian, Jun; Chen, Shi-Lin

    2010-01-01

    Medicinal pteridophytes are an important group used in traditional Chinese medicine; however, there is no simple and universal way to differentiate various species of this group by morphological traits. A novel technology termed "DNA barcoding" could discriminate species by a standard DNA sequence with universal primers and sufficient variation. To determine whether DNA barcoding would be effective for differentiating pteridophyte species, we first analyzed five DNA sequence markers (psbA-trnH intergenic region, rbcL, rpoB, rpoC1, and matK) using six chloroplast genomic sequences from GeneBank and found psbA-trnH intergenic region the best candidate for availability of universal primers. Next, we amplified the psbA-trnH region from 79 samples of medicinal pteridophyte plants. These samples represented 51 species from 24 families, including all the authentic pteridophyte species listed in the Chinese pharmacopoeia (2005 version) and some commonly used adulterants. We found that the sequence of the psbA-trnH intergenic region can be determined with both high polymerase chain reaction (PCR) amplification efficiency (94.1%) and high direct sequencing success rate (81.3%). Combined with GeneBank data (54 species cross 12 pteridophyte families), species discriminative power analysis showed that 90.2% of species could be separated/identified successfully by the TaxonGap method in conjunction with the Basic Local Alignment Search Tool 1 (BLAST1) method. The TaxonGap method results further showed that, for 37 out of 39 separable species with at least two samples each, between-species variation was higher than the relevant within-species variation. Thus, the psbA-trnH intergenic region is a suitable DNA marker for species identification in medicinal pteridophytes.

  20. A comparison of PCR-based markers for the molecular identification of Sphagnum species of the section Acutifolia

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    Jakub Sawicki

    2011-07-01

    Full Text Available RAPDs, ISJs, ISSRs, ITS and katGs were applied to determine genetic relationships between common Sphagnum species of the section Acutifolia. Twenty populations were genotyped using ten ISJ primers, 12 pairs of katG primers, 10 ISSR and 10 RAPD primers, and a restriction analysis of ITS1 and ITS2. ISSR and katG markers revealed the greatest number of species-specific bands. An analysis of ITS1 and ITS2 regions with restriction enzymes also proved to be a highly effective tool for species identification.

  1. Molecular diversity and phylogeny of Triticum-Aegilops species possessing D genome revealed by SSR and ISSR markers

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    Moradkhani Hoda

    2015-12-01

    Full Text Available The aim of this study is investigation the applicability of SSR and ISSR markers in evaluating the genetic relationships in twenty accessions of Aegilops and Triticum species with D genome in different ploidy levels. Totally, 119 bands and 46 alleles were detected using ten primers for ISSR and SSR markers, respectively. Polymorphism Information Content values for all primers ranged from 0.345 to 0.375 with an average of 0.367 for SSR, and varied from 0.29 to 0.44 with the average 0.37 for ISSR marker. Analysis of molecular variance (AMOVA revealed that 81% (ISSR and 84% (SSR of variability was partitioned among individuals within populations. Comparing the genetic diversity of Aegilops and Triticum accessions, based on genetic parameters, shows that genetic variation of Ae. crassa and Ae. tauschii species are higher than other species, especially in terms of Nei’s gene diversity. Cluster analysis, based on both markers, separated total accessions in three groups. However, classification based on SSR marker data was not conformed to classification according to ISSR marker data. Principal co-ordinate analysis (PCoA for SSR and ISSR data showed that, the first two components clarified 53.48% and 49.91% of the total variation, respectively. This analysis (PCoA, also, indicated consistent patterns of genetic relationships for ISSR data sets, however, the grouping of accessions was not completely accorded to their own geographical origins. Consequently, a high level of genetic diversity was revealed from the accessions sampled from different eco-geographical regions of Iran.

  2. New molecular markers for fungal phylogenetics: two genes for species-level systematics in the Sordariomycetes (Ascomycota).

    Science.gov (United States)

    Walker, Donald M; Castlebury, Lisa A; Rossman, Amy Y; White, James F

    2012-09-01

    Although significant progress has been made resolving deep branches of the fungal tree of life, many fungal systematists are interested in species-level questions to both define species and assess fungal biodiversity. Fungal genome sequences are a useful resource to systematic biologists for developing new phylogenetic markers that better represent the whole genome. Here we report primers for two newly identified single-copy protein-coding genes, FG1093 and MS204, for use with ascomycetes. Although fungi were the focus of this study, this methodological approach could be easily applied to marker development for studies of other organisms. The tests used here to assess phylogenetic informativeness are computationally rapid, require only rudimentary datasets to evaluate existing or newly developed markers, and can be applied to other non-model organisms to assist in experimental design of phylogenetic studies. Phylogenetic utility of the markers was tested in two genera, Gnomoniopsis and Ophiognomonia (Gnomoniaceae, Diaporthales). The phylogenetic performance of β-tubulin, ITS, and tef-1α was compared with FG1093 and MS204. Phylogenies inferred from FG1093 and MS204 were largely in agreement with β-tubulin, ITS, and tef-1α although some topological conflict was observed. Resolution and support for branches differed based on the combination of markers used for each genus. Based on two independent tests of phylogenetic performance, FG1093 and MS204 were determined to be equal to or better than β-tubulin, ITS, and tef-1α in resolving species relationships. Differences were found in site-specific rate of evolution in all five markers. In addition, isolates from 15 orders and 22 families of Ascomycota were screened using primers for FG1093 and MS204 to demonstrate primer utility across a wide diversity of ascomycetes. The primer sets for the newly identified genes FG1093 and MS204 and methods used to develop them are useful additions to the ascomycete systematists

  3. Development of RAPD-SCAR markers for different Ganoderma species authentication by improved RAPD amplification and molecular cloning.

    Science.gov (United States)

    Fu, J J; Mei, Z Q; Tania, M; Yang, L Q; Cheng, J L; Khan, M A

    2015-05-25

    The sequence-characterized amplified region (SCAR) is a valuable molecular technique for the genetic identification of any species. This method is mainly derived from the molecular cloning of the amplified DNA fragments achieved from the random amplified polymorphic DNA (RAPD). In this study, we collected DNA from 10 species of Ganoderma mushroom and amplified the DNA using an improved RAPD technique. The amplified fragments were then cloned into a T-vector, and positive clones were screened, indentified, and sequenced for the development of SCAR markers. After designing PCR primers and optimizing PCR conditions, 4 SCAR markers, named LZ1-4, LZ2-2, LZ8-2, and LZ9-15, were developed, which were specific to Ganoderma gibbosum (LZ1-4 and LZ8-2), Ganoderma sinense (LZ2-2 and LZ8-2), Ganoderma tropicum (LZ8-2), and Ganoderma lucidum HG (LZ9-15). These 4 novel SCAR markers were deposited into GenBank with the accession Nos. KM391935, KM391936, KM391937, and KM391938, respectively. Thus, in this study we developed specific SCAR markers for the identification and authentication of different Ganoderma species.

  4. Species identification of Wickerhamomyces anomalus and related taxa using β-tubulin (β-tub) DNA barcode marker.

    Science.gov (United States)

    Huang, Chien-Hsun; Chang, Mu-Tzu; Huang, Lina

    2012-12-01

    Wickerhamomyces anomalus is used in food and feed processing, although the species has been reported as an opportunistic human pathogen, predominantly in neonates. Neither phenotypic nor the most frequently applied genotypic marker (D1/D2 LSU ribosomal DNA) provide sufficient resolution for accurate identification of this yeast. In this study, the β-tubulin gene was used for species identification by direct DNA sequencing and as marker in a species-specific PCR assay. The results showed that all examined W. anomalus strains were clearly distinguished from the closely related species by comparative sequence analysis of the β-tubulin gene. In addition, the species-specific primers were also developed based on the β-tubulin gene, which was employed for polymerase chain reaction with the template DNA of Wickerhamomyces strains. A single 218 bp species-specific band was found only in W. anomalus. Our data indicate that the phylogenetic relationships between these strains are easily resolved by sequencing of the β-tubulin gene and combined with species-specific PCR assay. Copyright © 2012 John Wiley & Sons, Ltd.

  5. A potential species-specific molecular marker suggests interspecific hybridization between sibling species Littorina arcana and L. saxatilis (Mollusca, Caenogastropoda) in natural populations.

    Science.gov (United States)

    Mikhailova, Natalia A; Gracheva, Yulia A; Backeljau, Thierry; Granovitch, Andrey I

    2009-12-01

    Three sister species of rough periwinkles, viz. Littorina saxatilis (Olivi 1792), L. arcana (Hannaford Ellis 1978) and L. compressa (Jeffreys 1865) from the Barents Sea (Russia), the White Sea (Russia) and the Norwegian Sea (Norway) were studied. The identification of two sibling species L. saxatilis and L. arcana is often difficult as both species have extremely similar shell morphology and reproductive systems. Only mature females can be unambiguously distinguished, with a jelly gland present in female L. arcana, but which is replaced by a brood pouch containing developing embryos in L. saxatilis. No clear-cut diagnostic features have been found to discriminate between males or juveniles of the two species. The very first diagnostic DNA marker (DNA fragment A2.8, 271 bp length) for L. arcana and L. saxatilis separation was developed. The marker was derived from apparently species-specific L. arcana DNA fragments obtained via Random Amplified Polymorphic DNA (RAPD) analysis. This fragment was cloned and sequenced, whereupon specific primers were designed and the amplification was surveyed in a large number of morphologically well-identified females of both species. Subsequently, the specific DNA marker was used for the identification of male L. arcana and partners in copulating pairs. In this way, we obtained evidence of possible interspecific hybridization between the sibling species L. arcana and L. saxatilis living in sympatry in natural populations: the presence of A2.8 fragment in 12% of morphologically well identified L. saxatilis females and its absence in 14% of morphologically well identified L. arcana females. The A2.8 fragment never amplified in L. saxatilis from sites without L. arcana. The A2.8 fragment did not amplify in L. compressa, not even in microsympatric populations, and we did not observe interspecific copulations between L. arcana and L. compressa.

  6. Development of new candidate gene and EST-based molecular markers for Gossypium species

    Science.gov (United States)

    New source of molecular markers accelerates the efforts in improving cotton fiber traits and aid in developing high-density integrated genetic maps. We developed new markers based on candidate genes and G. arboreum expressed sequence tag (EST) sequences, and validated them through amplification, ge...

  7. Genetic analysis of species in the Genus Catasetum (ORCHIDACEAE using RAPD Markers

    Directory of Open Access Journals (Sweden)

    Luciana do Valle Rego Oliveira

    2010-04-01

    Full Text Available In this work, RAPD molecular markers were used to access the genetic variability and to study the inter and intraespecifc relationship in a group of 37 species, including 56 individuals. A total of 15 RAPD primers were selected for DNA amplification. From a total of 221 bands analyzed, 209 (95% were polymorphics. The level of interespecifc genetic similarity ranged from 37% between Catasetum complanatum and Catasetum laminatum to 83% between Catasetum triodon and Catasetum uncatum. The intraspecifc genetic similarity varied 88% for the individuals of Catasetum triodon to 93% between the individuals of Catasetum atratum and Catasetum macrocarpum. These results would contribute to understand the genetic relationship in Catasetum, to define the strategies to establish a germplasm core collection for the genus and to provide support for breeding programs.Neste trabalho, marcadores moleculares de RAPD foram utilizados para acessar a variabilidade genética e estudar as relações interespecíficas e intraespecífica em um grupo de 37 espécies, compreendendo 56 plantas individuais. Um total de 15 primers foram selecionados para amplificação do DNA. De um total de 221 bandas analisadas, 209 (95% foram polimórficas. O nível de similaridade genética interespecífica variou de 37% entre Catasetum complanatum e Catasetum laminatums a 83% entre Catasetum triodon e Catasetum uncatum. A similaridade genética intraespecífica variou de 88% entre os indivíduos de Catasetum triodon a 93% entre os indivíduos de Catasetum atratum e Catasetum macrocarpum. Os resultados deste trabalho contribuem para o entendimento das relações interespecíficas no gênero Catasetum, para definir estratégias para o estabelecimento de um banco de germoplasma e para dar suporte a programas de melhoramento.

  8. Microsatellite markers reveal the below ground distribution of genets in two species of Rhizopogon forming tuberculate ectomycorrhizas on Douglas-fir.

    Science.gov (United States)

    Annette M. Kretzer; Susie Dunham; Randy Molina; Joseph W. Spatafora

    2003-01-01

    We have developed microsatellite markers for two sister species of Rhizopogon, R. vesiculosus and R. vinicolor (Boletales, Basidiomycota), and used selected markers to investigate genet size and distribution from ectomycorrhizal samples. Both species form ectomycorrhizas with tuberculate morphology on Douglas-fir (...

  9. Development, characterization and cross species amplification of polymorphic microsatellite markers from expressed sequence tags of turmeric (Curcuma longa L.).

    Science.gov (United States)

    Siju, S; Dhanya, K; Syamkumar, S; Sasikumar, B; Sheeja, T E; Bhat, A I; Parthasarathy, V A

    2010-02-01

    Expressed sequence tags (ESTs) from turmeric (Curcuma longa L.) were used for the screening of type and frequency of Class I (hypervariable) simple sequence repeats (SSRs). A total of 231 microsatellite repeats were detected from 12,593 EST sequences of turmeric after redundancy elimination. The average density of Class I SSRs accounts to one SSR per 17.96 kb of EST. Mononucleotides were the most abundant class of microsatellite repeat in turmeric ESTs followed by trinucleotides. A robust set of 17 polymorphic EST-SSRs were developed and used for evaluating 20 turmeric accessions. The number of alleles detected ranged from 3 to 8 per loci. The developed markers were also evaluated in 13 related species of C. longa confirming high rate (100%) of cross species transferability. The polymorphic microsatellite markers generated from this study could be used for genetic diversity analysis and resolving the taxonomic confusion prevailing in the genus.

  10. Species phylogeny and diversification process of Northeast Asian Pungitius revealed by AFLP and mtDNA markers

    DEFF Research Database (Denmark)

    Takahashi, Hiroshi; Møller, Peter Rask; Shedko, Sergei V.

    2016-01-01

    in Northeast Asia, although the taxonomy and evolutionary relationships among them remain unclear. We used amplified fragment length polymorphism (AFLP) and mitochondrial DNA (mtDNA) markers to infer phylogenies among individuals collected from sympatric and allopatric populations, including the type....... kaibarae, and P. bussei). The brackish-water, freshwater, and Omono types previously discovered in Japan were reidentified as P. pungitius, P. sinensis, and P. kaibarae, respectively. A marked incongruence was noted between the phylogenies of AFLP and mtDNA markers, suggesting the occasional occurrence...... of hybridization and mtDNA introgression among distinct species. Our results highlight that the marginal seas of Northeast Asia played a key role as barriers to or facilitators of gene flow in the evolution of species diversity of Pungitius concentrated in this region...

  11. Determining Intermediate Hosts for Opecoelidae and Microphallidae Species (Platyhelminthes: Trematoda) in the Southeastern Pacific Coast, Using Molecular Markers.

    Science.gov (United States)

    Leiva, Natalia Verónica; López, Zambra; González, María Teresa; Muñoz, Gabriela

    2017-02-01

    Metacercarial stages of digeneans were collected from decapod crustaceans inhabiting intertidal rocky zones in central Chile. The digeneans were identified through a molecular analysis based on the V4 region of the 18S ribosomal RNA gene. We analyzed 356 crustaceans belonging to 10 species, 115 intertidal fish belonging to 6 species, and 4 specimens of 1 coastal bird species. In total, 74.1% of crustaceans were parasitized with metacercariae. We found 1 species of Opecoelidae. This species showed low genetic divergence (0% and 0.1%) with adult digeneans found in intertidal fish and with the species Helicometrina labrisomi infesting a subtidal fish from northern Chile (Labrisomus philippii). Additionally, we found 2 species of Microphallidae, 1 closely related to Maritrema (1.3% genetic distance) and the other related to Microphallus (5% genetic distance). Therefore, our findings showed that the decapod crustaceans are relevant hosts in food webs from the southeastern Pacific coast. Furthermore, we found 5 species of crustaceans as second intermediate hosts for H. labrisomi and 2 species as secondary intermediate hosts for 2 Microphallidae, which contribute to elucidate parts of their life cycles through molecular markers and extended the host distribution of H. labrisomi in the southeastern Pacific coast.

  12. Comparative analysis of chromosomal localization of ribosomal and telomeric DNA markers in three species of Pyrgomorphidae grasshoppers

    Directory of Open Access Journals (Sweden)

    Olesya G. Buleu

    2017-09-01

    Full Text Available The karyotypes of three species of Pyrgomorphidae grasshoppers were studied: Zonocerus elegans (Thunberg, 1815, Pyrgomorpha guentheri (Burr, 1899 and Atractomorpha lata (Mochulsky, 1866. Data on karyotypes of P. guentheri and Z. elegans are reported here for the first time. All species have karyotypes consisting of 19 acrocentric chromosomes in males and 20 acrocentric chromosomes in females (2n♂=19, NF=19; 2n♀=20, NF=20 and X0/XX sex determination system. A comparative analysis of the localization of C-heterochromatin, clusters of ribosomal DNA, and telomere repeats revealed inter-species diversity in these cytogenetic markers. These differences indicate that the karyotype divergence in the species studied is not associated with structural chromosome rearrangements, but with the evolution of repeated DNA sequences.

  13. Comparative analysis of chromosomal localization of ribosomal and telomeric DNA markers in three species of Pyrgomorphidae grasshoppers.

    Science.gov (United States)

    Buleu, Olesya G; Jetybayev, Ilyas Y; Bugrov, Alexander G

    2017-01-01

    The karyotypes of three species of Pyrgomorphidae grasshoppers were studied: Zonocerus elegans (Thunberg, 1815), Pyrgomorpha guentheri (Burr, 1899) and Atractomorpha lata (Mochulsky, 1866). Data on karyotypes of P. guentheri and Z. elegans are reported here for the first time. All species have karyotypes consisting of 19 acrocentric chromosomes in males and 20 acrocentric chromosomes in females (2n♂=19, NF=19; 2n♀=20, NF=20) and X0/XX sex determination system. A comparative analysis of the localization of C-heterochromatin, clusters of ribosomal DNA, and telomere repeats revealed inter-species diversity in these cytogenetic markers. These differences indicate that the karyotype divergence in the species studied is not associated with structural chromosome rearrangements, but with the evolution of repeated DNA sequences.

  14. Otolith shape analysis and mitochondrial DNA markers distinguish three sand smelt species in the Atherina boyeri species complex in western Mediterranean

    Science.gov (United States)

    Boudinar, A. S.; Chaoui, L.; Quignard, J. P.; Aurelle, D.; Kara, M. H.

    2016-12-01

    Atherina boyeri is a common euryhaline teleost fish in the Mediterranean and adjacent areas, which inhabits coastal and estuarine waters, including coastal lagoons and more rarely inland waters. Several recent studies have pointed the possible existence of three distinct groups or species, one lagoon/freshwater group and two 'punctuated and unpunctuated on the flanks' marine groups, within an A. boyeri species complex. This study is a combined approach using otolith shape and molecular markers to better define the structure of the species in the western Mediterranean. Genetic differentiation and species delimitation among nine Atherina boyeri populations from several marine and lagoon/brakish habitat sites in Algeria, Tunisia and France were investigated using three mitochondrial (control region, Cyt b and 16S) and one nuclear markers (2nd intron of S7). For further phylogenetic and phylogeographic study, we added sequences from Genbank covering more areas (Ionian Sea, Adriatic Sea, Tyrrhenian Sea, Black Sea, Atlantic). Five groups were found. Two of them perfectly corresponded to two species already recognized Atherina presbyter and Atherina hepsetus, both living in marine waters; and three additional, including Atherina boyeri (brackish and freshwater environments) and two independent groups of marine punctated and unpunctated individuals. Those findings are corroborated by the study of the otolith contour shape of 362 individuals of seven populations from different habitats using Fourier analysis. Individuals could be discriminated into five groups based on the first two functions (Wilk's lambda = 0.07, p < 0.001). Samples from Ziama inlet, marine punctuated individuals and unpunctuated marine specimens from Annaba's Gulf formed three well separated groups. Specimens from Mellah and Mauguio lagoons formed another group. The last one includes individuals from Bizerte and Thau lagoons. The divergences between them strongly support the potential species within the

  15. Patterns of genetic structure and evidence of gene flow among Tunisian Citrus species based on informative nSSR markers.

    Science.gov (United States)

    Ben Romdhane, Meriam; Riahi, Leila; Selmi, Ayet; Zoghlami, Nejia

    2016-01-01

    This study investigates the extent of genetic diversity, phylogenetic relationships and the amount of gene flow among Tunisian Citrus species based on a set of 15 informative nuclear SSR molecular markers. Genotyping data highlighted an allelic richness among Tunisian Citrus species and has allowed the detection of 168 alleles among them 104.19 were effective. The partition of the total genetic diversity (HT=0.832) showed that the highest amount of variation within the Citrus species is HS=0.550, while the relative amount of the between-species genetic diversity GST does not exceed 0.338. This pattern of genetic structure was supported by low-to-moderate FST pairwise values and the presence of a gene flow (Nm) among the eight Citrus species. The lowest genetic differentiation was revealed between the species C. sinensis and C. insitorum (FST=0.111, Nm=1.99), while the highest genetic differentiation was recorded between the species C. aurantifolia and C. paradisi (FST=0.367, Nm=0.43). The established Neighbor Joining analysis showed that all genotypes were widely discriminated and clearly pooled according to their species of origin, with minor exceptions. Copyright © 2016 Académie des sciences. Published by Elsevier SAS. All rights reserved.

  16. Developing expressed sequence tag libraries and the discovery of simple sequence repeat markers for two species of raspberry (Rubus L.).

    Science.gov (United States)

    Bushakra, Jill M; Lewers, Kim S; Staton, Margaret E; Zhebentyayeva, Tetyana; Saski, Christopher A

    2015-10-26

    Due to a relatively high level of codominant inheritance and transferability within and among taxonomic groups, simple sequence repeat (SSR) markers are important elements in comparative mapping and delineation of genomic regions associated with traits of economic importance. Expressed sequence tags (ESTs) are a source of SSRs that can be used to develop markers to facilitate plant breeding and for more basic research across genera and higher plant orders. Leaf and meristem tissue from 'Heritage' red raspberry (Rubus idaeus) and 'Bristol' black raspberry (R. occidentalis) were utilized for RNA extraction. After conversion to cDNA and library construction, ESTs were sequenced, quality verified, assembled and scanned for SSRs.  Primers flanking the SSRs were designed and a subset tested for amplification, polymorphism and transferability across species. ESTs containing SSRs were functionally annotated using the GenBank non-redundant (nr) database and further classified using the gene ontology database. To accelerate development of EST-SSRs in the genus Rubus (Rosaceae), 1149 and 2358 cDNA sequences were generated from red raspberry and black raspberry, respectively. The cDNA sequences were screened using rigorous filtering criteria which resulted in the identification of 121 and 257 SSR loci for red and black raspberry, respectively. Primers were designed from the surrounding sequences resulting in 131 and 288 primer pairs, respectively, as some sequences contained more than one SSR locus. Sequence analysis revealed that the SSR-containing genes span a diversity of functions and share more sequence identity with strawberry genes than with other Rosaceous species. This resource of Rubus-specific, gene-derived markers will facilitate the construction of linkage maps composed of transferable markers for studying and manipulating important traits in this economically important genus.

  17. The use of ISSR markers for species determination and a genetic study of the invasive lionfish in Guanahacabibes, Cuba

    Directory of Open Access Journals (Sweden)

    Elizabeth Labastida

    2015-11-01

    Full Text Available The red lionfish (Pterois volitans and devil fire-fish (Pterois miles are invasive species that pose a threat to the biodiversity and stability of coral reefs in the Western Atlantic, Gulf of Mexico and Caribbean Sea. Species identification of lionfish is uncertain in some parts of Cuba, and research has mainly been focused on their biology and ecology. The principal aim of this study was to determine highly polymorphic markers (Inter Simple Sequence Repeat, ISSR that could be used in research on lionfish population genetics in addition to confirming the presence of Pterois species in the Guanahacabibes National Park. The genetic profile or "fingerprint" of individuals collected in Mexico, formally identified as P. volitans, was compared with the genetic profile of specimens from Cuba. There were very few "diagnostic bands" and a high number of "common bands", demonstrating that the same species exists in both countries. Furthermore, Nei's genetic distance and the unrooted tree do not show significant differences between both localities. In light of these results, we can confirm the presence of P. volitans in the Guanahacabibes National Park, Cuba. This study demonstrates the functionality of ISSR as a molecular tool for species identification and their application for genetic population studies of this invasive fish species.

  18. Comparison of Bacteroides-Prevotella 16S rRNA genetic markers for fecal samples from different animal species

    Science.gov (United States)

    Fogarty, L.R.; Voytek, M.A.

    2005-01-01

    To effectively manage surface and ground waters it is necessary to improve our ability to detect and identify sources of fecal contamination. We evaluated the use of the anaerobic bacterial group Bacteroides-Prevotella as a potential fecal indicator. Terminal restriction length polymorphism (T-RFLP) of the 16S rRNA genes from this group was used to determine differences in populations and to identify any unique populations in chickens, cows, deer, dogs, geese, horses, humans, pigs, and seagulls. The group appears to be a good potential fecal indicator in all groups tested except for avians. Cluster analysis of Bacteroides-Prevotella community T-RFLP profiles indicates that Bacteroides-Prevotella populations from samples of the same host species are much more similar to each other than to samples from different source species. We were unable to identify unique peaks that were exclusive to any source species; however, for most host species, at least one T-RFLP peak was identified to be more commonly found in that species, and a combination of peaks could be used to identify the source. T-RFLP profiles obtained from water spiked with known-source feces contained the expected diagnostic peaks from the source. These results indicate that the approach of identifying Bacteroides-Prevotella molecular markers associated with host species might be useful in identifying sources of fecal contamination in the environment.

  19. Microsatellite markers for the large blue butterflies Maculinea nausithous and Maculinea alcon (Lepidoptera : Lycaenidae) and their amplification in other Maculinea species

    DEFF Research Database (Denmark)

    Zeisset, I; Als, Thomas Damm; Settele, J

    2005-01-01

    We developed microsatellite markers for Maculinea nausithous and Maculinea alcon, two of five species of endangered large blue butterflies found in Europe. Two separate microsatellite libraries were constructed. Eleven markers were developed for M. nausithous and one for M. alcon. The primers were...

  20. Microsatellite markers for the large blue butterflies Maculinea nausithous and Maculinea alcon (Lepidoptera: Lycaenidae) and their amplification in other Maculinea species

    DEFF Research Database (Denmark)

    Zeisset, Inga; Damm Als, Thomas; Settele, Josef

    2005-01-01

    We developed microsatellite markers for Maculinea nausithous and Maculinea alcon, two of five species of endangered large blue butterflies found in Europe. Two separate microsatellite libraries were constructed. Eleven markers were developed for M. nausithous and one for M. alcon. The primers were...

  1. What Can Molecular Markers Tell Us About the Evolutionary History of Daphnia Species Complexes

    NARCIS (Netherlands)

    Schwenk, K.; Ender, A.; Streit, B.

    1995-01-01

    Despite the wealth of information on the ecology of Daphnia species, the systematics and phylogeny of the genus is still unresolved. The taxonomic uncertainties are based in part on the phenomenon of interspecific hybridization, which has been well documented for species of the D.

  2. Species relationships in the genus Agrostis based on flow cytometry and MITE-display molecular markers

    Science.gov (United States)

    It is estimated that there are between 150 and 200 species of Agrostis, and interspecific hybridization is a proven method for improving cultivated Agrostis species. The pool of publicly available Agrostis germplasm, available through the National Plant Germplasm System (NPGS), represents 17% of th...

  3. New molecular markers for fungal phylogenetics: Two genes for species level systematics in the Sordariomycetes (Ascomycota)

    Science.gov (United States)

    Although significant progress has been made resolving deep branches of the fungal tree of life in recent works, many fungal systematists are interested in species-level questions to both define species and to assess fungal biodiversity. Fungal genome sequences are a useful resource to systematic bio...

  4. Population genetics of invasive Bemisia tabaci cryptic species in the United States based on microsatellite markers

    Science.gov (United States)

    The Bemisia tabaci cryptic species complex of whiteflies contains two species, MEAM1 and MED, that are highly invasive in supportive climates the world over. In the United States MEAM1 occurs both in the field and in the greenhouse, but MED is only found in the greenhouse. In order to make inference...

  5. Molecular markers in keratins from Mysticeti whales for species identification of baleen in museum and archaeological collections.

    Science.gov (United States)

    Solazzo, Caroline; Fitzhugh, William; Kaplan, Susan; Potter, Charles; Dyer, Jolon M

    2017-01-01

    Baleen has been harvested by indigenous people for thousands of years, as well as collected by whalers as an additional product of commercial whaling in modern times. Baleen refers to the food-filtering system of Mysticeti whales; a full baleen rack consists of dozens of plates of a tough and flexible keratinous material that terminate in bristles. Due to its properties, baleen was a valuable raw material used in a wide range of artefacts, from implements to clothing. Baleen is not widely used today, however, analyses of this biomolecular tissue have the potential to contribute to conservation efforts, studies of genetic diversity and a better understanding of the exploitation and use of Mysticeti whales in past and recent times. Fortunately, baleen is present in abundance in museum natural history collections. However, it is often difficult or impossible to make a species identification of manufactured or old baleen. Here, we propose a new tool for biomolecular identification of baleen based on its main structural component alpha-keratin (the same protein that makes up hair and fingernails). With the exception of minke whales, alpha-keratin sequences are not yet known for baleen whales. We therefore used peptide mass fingerprinting to determine peptidic profiles in well documented baleen and evaluated the possibility of using this technique to differentiate species in baleen samples that are not adequately identified or are unidentified. We examined baleen from ten different species of whales and determined molecular markers for each species, including species-specific markers. In the case of the Bryde's whales, differences between specimens suggest distinct species or sub-species, consistent with the complex phylogeny of the species. Finally, the methodology was applied to 29 fragments of baleen excavated from archaeological sites in Labrador, Canada (representing 1500 years of whale use by prehistoric people), demonstrating a dominance of bowhead whale (Balaena

  6. Molecular markers for genetic diversity, gene flow and genetic population structure of freshwater mussel species.

    Science.gov (United States)

    Choupina, A B; Martins, I M

    2014-08-01

    Freshwater mussel species are in global decline. Anthropogenic changes of river channels and the decrease of autochthonous fish population, the natural hosts of mussels larval stages (glochidia), are the main causes. Therefore, the conservation of mussel species depends not only on habitat conservation, but also on the availability of the fish host. In Portugal, information concerning most of the mussel species is remarkably scarce. One of the most known species, Unio pictorum is also in decline however, in the basins of the rivers Tua and Sabor (Northeast of Portugal), there is some indication of relatively large populations. The aforementioned rivers can be extremely important for this species conservation not only in Portugal, but also in the remaining Iberian Peninsula. Thus, it is important to obtain data concerning Unio pictorum bioecology (distribution, habitat requirements, population structure, genetic variability, reproductive cycle and recruitment rates), as well as the genetic variability and structure of the population. Concomitantly, information concerning fish population structure, the importance of the different fish species as "glochidia" hosts and their appropriate density to allow effective mussel recruitment, will also be assessed. The achieved data is crucial to obtain information to develop effective management measures in order to promote the conservation of this bivalve species, the conservation of autochthonous fish populations, and consequently the integrity of the river habitats.

  7. Survey and analysis of microsatellites from transcript sequences in Phytophthora species: frequency, distribution, and potential as markers for the genus

    Directory of Open Access Journals (Sweden)

    Barreto Emiliano

    2006-09-01

    Full Text Available Abstract Background Members of the genus Phytophthora are notorious pathogens with world-wide distribution. The most devastating species include P. infestans, P. ramorum and P. sojae. In order to develop molecular methods for routinely characterizing their populations and to gain a better insight into the organization and evolution of their genomes, we used an in silico approach to survey and compare simple sequence repeats (SSRs in transcript sequences from these three species. We compared the occurrence, relative abundance, relative density and cross-species transferability of the SSRs in these oomycetes. Results The number of SSRs in oomycetes transcribed sequences is low and long SSRs are rare. The in silico transferability of SSRs among the Phytophthora species was analyzed for all sets generated, and primers were selected on the basis of similarity as possible candidates for transferability to other Phytophthora species. Sequences encoding putative pathogenicity factors from all three Phytophthora species were also surveyed for presence of SSRs. However, no correlation between gene function and SSR abundance was observed. The SSR survey results, and the primer pairs designed for all SSRs from the three species, were deposited in a public database. Conclusion In all cases the most common SSRs were trinucleotide repeat units with low repeat numbers. A proportion (7.5% of primers could be transferred with 90% similarity between at least two species of Phytophthora. This information represents a valuable source of molecular markers for use in population genetics, genetic mapping and strain fingerprinting studies of oomycetes, and illustrates how genomic databases can be exploited to generate data-mining filters for SSRs before experimental validation.

  8. Brain and sense organ anatomy and histology of two species of phyletically basal non-Antarctic thornfishes of the Antarctic suborder Notothenioidei (Perciformes: Bovichtidae).

    Science.gov (United States)

    Eastman, Joseph T; Lannoo, Michael J

    2007-06-01

    The predominantly non-Antarctic family Bovichtidae is phyletically basal within the perciform suborder Notothenioidei, the dominant component of the Antarctic fish fauna. In this article we focus on the South Atlantic bovichtids Bovichtus diacanthus, the klipfish from tide pools at Tristan da Cunha, and Cottoperca gobio, the frogmouth from the Patagonian shelf and Falkland Islands. We document the anatomy and histology of the brains, olfactory apparatus, retina, and cephalic lateral line system. We also use the microvascular casting agent Microfil to examine ocular vascular structures. We provide detailed drawings of the brains and cranial nerves of both species. Typical of perciforms, the brains of both species have a well-developed tectum and telencephalon and robust thalamic nuclei. The telencephalon of C. gobio is prominently lobed, with the dorsomedial nucleus more conspicuous than in any other notothenioid. The corpus cerebelli is relatively small and upright and, unlike other notothenioids, has prominent transverse sulci on the dorsal and caudal surfaces. Areas for lateral line mechanoreception (eminentia granularis and crista cerebellaris) are also conspicuous but olfactory, gustatory, and somatosensory areas are less prominent. The anterior lateral line nerve complex is larger than the posterior lateral line nerve in B. diacanthus, and in their cephalic lateral line systems both species possess branched membranous tubules (which do not contain neuromasts) with small pores. These are especially complex in B. diacanthus where they become increasingly branched and more highly pored in progressively larger specimens. Superficial neuromasts are sparse. Both species have duplex (cone and rod) retinae that are 1.25-fold thicker and have nearly 5-fold more photoreceptors and than those of most Antarctic notothenioids. Convergence ratios are also high for bovichtids. Bovichtus diacanthus has a yellow intraocular filter in the dorsal aspect of the cornea. Both

  9. 5S rDNA characterization in twelve Sciaenidae fish species (Teleostei, Perciformes: depicting gene diversity and molecular markers

    Directory of Open Access Journals (Sweden)

    Fernanda A. Alves-Costa

    2008-01-01

    Full Text Available In order to extend the genetic data on the Sciaenidae fish family, the present study had the purpose to characterize PCR-generated 5S rDNA repeats of twelve species of this group through PAGE (Polyacrylamide Gel Electrophoresis analysis. The results showed the occurrence of at least two different 5S rDNA size classes in all the species. Moreover, 5S rDNA repeats of one of the studied species - Isopisthus parvipinnis - were cloned and subjected to nucleotide sequencing and Southern blot membrane hybridization analyses, which permitted to confirm the existence of two major 5S rDNA classes. Phylogenetic analysis based on the nucleotide sequences of different 5S rDNA repeats of I. parvipinnis lead to their separation into two major clusters. These results may reflect the high dynamism that rules the evolution rate of 5S rDNA repeats. The obtained data suggest that 5S rDNA can be useful in genetic analyses to identify species-specific markers and determine relationships among species of the Sciaenidae group.

  10. The Dual Challenges of Generality and Specificity When Developing Environmental DNA Markers for Species and Subspecies of Oncorhynchus.

    Directory of Open Access Journals (Sweden)

    Taylor M Wilcox

    Full Text Available Environmental DNA (eDNA sampling is a powerful tool for detecting invasive and native aquatic species. Often, species of conservation interest co-occur with other, closely related taxa. Here, we developed qPCR (quantitative PCR markers which distinguish westslope cutthroat trout (Oncorhynchus clarkii lewsi, Yellowstone cutthroat trout (O. clarkii bouvieri, and rainbow trout (O. mykiss, which are of conservation interest both as native species and as invasive species across each other's native ranges. We found that local polymorphisms within westslope cutthroat trout and rainbow trout posed a challenge to designing assays that are generally applicable across the range of these widely-distributed species. Further, poorly-resolved taxonomies of Yellowstone cutthroat trout and Bonneville cutthroat trout (O. c. utah prevented design of an assay that distinguishes these recognized taxa. The issues of intraspecific polymorphism and unresolved taxonomy for eDNA assay design addressed in this study are likely to be general problems for closely-related taxa. Prior to field application, we recommend that future studies sample populations and test assays more broadly than has been typical of published eDNA assays to date.

  11. Development of environmental DNA markers for three aquatic invasive species for Savannah National Wildlife Refuge

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — The report concerns the development of species specific primers for Mayan cichlids, Asian Swamp Eels, and the lion fish which are considered aquatic invasive...

  12. Molecular markers discriminate closely related species Encarsia diaspidicola and Encarsia berlesei (Hymenoptera: Aphelinidae): biocontrol candidate agents for white peach scale in Hawaii.

    Science.gov (United States)

    De León, Jesse H; Neumann, Gabor; Follett, Peter A; Hollingsworth, Robert G

    2010-06-01

    We genetically characterized Encarsia diapsidicola Silvestri and Encarsia berlesei Howard (Hymenoptera: Aphelinidae) by two molecular methods: phylogenetic analysis of the cytochrome oxidase subunit I gene (COI) and intersimple sequence repeat-polymerase chain reaction (ISSR-PCR) DNA fingerprinting. These two closely related endoparasitoids are candidate biological control agents for the white peach scale, Pseudaulacaspis pentagona Targioni-Tozetti (Hemiptera: Diaspididae), in Hawaii. We developed species-specific COI molecular markers that discriminated the two species, and we tested the utility of the E. diaspidicola-specific COI marker to detect parasitism of white peach scale. The COI sequence data uncovered 46-bp differences between the two Encarsia spp. The level of COI genetic divergence between the two species was 9.7%, and the two clustered into their own clade on a parismonious phylogram. ISSR-PCR readily discriminated the two Encarsia spp. because each was observed with fixed species-specific banding patterns. The COI molecular markers were specific for each species because cross-reactivity was not observed with nontarget species. The E. diaspidicola-specific COI markers were successful at detecting parasitism of white peach scale by E. diaspidicola by 24 h. Both molecular marker types successfully discriminated the two Encarsia spp., whereas the COI markers will be useful as tools to assess levels of parasitism in the field and to study competitive interactions between parasitoids.

  13. CHARACTERIZATION OF 17 NEW MICROSATELLITE MARKERS FOR THE DINOFLAGELLATE ALEXANDRIUM FUNDYENSE (DINOPHYCEAE), A HARMFUL ALGAL BLOOM SPECIES.

    Science.gov (United States)

    Sehein, Taylor; Richlen, Mindy L; Nagai, Satoshi; Yasuike, Motoshige; Nakamura, Yoji; Anderson, Donald M

    2016-06-01

    Alexandrium fundyense is the toxic marine dinoflagellate responsible for "red tide" events in temperate and sub-arctic waters worldwide. In the Gulf of Maine (GOM) and Bay of Fundy in the Northwest Atlantic, blooms of A. fundyense recur annually, and are associated with major health and ecosystem impacts. In this region, microsatellite markers have been used to investigate genetic structure and gene flow; however, the loci currently available for this species were isolated from populations from Japan and the North Sea, and only a subset are suitable for the analysis of A. fundyense populations in the Northwest Atlantic. To facilitate future studies of A. fundyense blooms, both in this region and globally, we isolated and characterized 17 polymorphic microsatellite loci from 31 isolates collected from the GOM and from the Nauset Marsh System, an estuary on Cape Cod, MA, USA. These loci yielded between two and 15 alleles per locus, with an average of 7.1. Gene diversities ranged from 0.297 to 0.952. We then analyzed these same 31 isolates using previously published markers for comparison. We determined the new markers are sufficiently variable and better suited for the investigation of genetic structure, bloom dynamics, and diversity in the Northwest Atlantic.

  14. Polymorphic microsatellite markers for population analysis of a tephritid pest species, Bactrocera tryoni.

    Science.gov (United States)

    Kinnear, M W; Bariana, H S; Sved, J A; Frommer, M

    1998-11-01

    To obtain a set of microsatellite markers for the Queensland fruit fly Bactrocera tryoni, a genomic library was screened with a number of simple repeat oligonucleotide probes. Sequencing recovered 22 repeat loci. The microsatellite sequences were short, with repeat numbers ranging from five to 11. Of these, 16 polymerase chain reaction (PCR) primer sets yielded amplifiable products, which were tested on 53 flies from five widely separated sites. All loci showed polymorphism in the population sample, with the number of alleles ranging from two to 16. Several dinucleotide repeats showed alleles separated by single-base differences and multiple steps, suggesting a mutation process more complex than the stepwise mutation model.

  15. Evaluating Wheat Microsatellite Markers for the Use in Genetic Analysis of Thinopyrum, Dasypyrum, and Pseudoroegneria Species

    OpenAIRE

    Kroupin, Pavel Yu.; Divashuk, Mikhail G.; Fesenko, Igor A.; Karlov, Gennady I.

    2013-01-01

    A set of 42 SSRs of wheat were evaluated for their cross-amplification on the DNA of Thinopyrum ponticum, Thinopyrum intermedium, Thinopyrum elongatum, Thinopyrum bessarabicum, Pseudoroegneria stipifolia, and Dasypyrum villosum. The number of the wheat SSR markers that amplified DNA fragments with determined size for Th. ponticum was 33 (78.6%); for Th. intermedium, 28 (66.7%); for Th. elongatum, 24 (57.1%); for Th. bessarabicum, 24 (57.1%); for P. stipifolia, 26 (69.1%); and for D. villosum,...

  16. Markers of pathogenicity islands in strains of Aeromonas species of clinical and environmental origin

    Directory of Open Access Journals (Sweden)

    J M Ruiz-Ruiz

    2012-01-01

    Full Text Available The aim of this study was to investigate the presence of markers of pathogenicity islands that may be informative to detect the virulent PAI carriers of clinical and environmental strains of Aeromonas spp. isolated in Mexico. virB2, virB9 and virB11 genes were found in Aeromonas strains isolated from environmental and clinical sources while cagE and tfc16 genes were only in strains of environmental origin. Having performed the wide screening presented in this study, we now have a set of strains to map and confirm the presence of a pathogenicity island in Aeromonas strains isolated in Mexico.

  17. Whole plastome sequences from five ginger species facilitate marker development and define limits to barcode methodology.

    Directory of Open Access Journals (Sweden)

    Justin N Vaughn

    Full Text Available Plants from the Zingiberaceae family are a key source of spices and herbal medicines. Species identification within this group is critical in the search for known and possibly novel bioactive compounds. To facilitate precise characterization of this group, we have sequenced chloroplast genomes from species representing five major groups within Zingiberaceae. Generally, the structure of these genomes is similar to the basal angiosperm excepting an expansion of 3 kb associated with the inverted repeat A region. Portions of this expansion appear to be shared across the entire Zingiberales order, which includes gingers and bananas. We used whole plastome alignment information to develop DNA barcodes that would maximize the ability to differentiate species within the Zingiberaceae. Our computation pipeline identified regions of high variability that were flanked by highly conserved regions used for primer design. This approach yielded hitherto unexploited regions of variability. These theoretically optimal barcodes were tested on a range of species throughout the family and were found to amplify and differentiate genera and, in some cases, species. Still, though these barcodes were specifically optimized for the Zingiberaceae, our data support the emerging consensus that whole plastome sequences are needed for robust species identification and phylogenetics within this family.

  18. DNA barcoding in the cycadales: testing the potential of proposed barcoding markers for species identification of cycads.

    Science.gov (United States)

    Sass, Chodon; Little, Damon P; Stevenson, Dennis Wm; Specht, Chelsea D

    2007-11-07

    Barcodes are short segments of DNA that can be used to uniquely identify an unknown specimen to species, particularly when diagnostic morphological features are absent. These sequences could offer a new forensic tool in plant and animal conservation-especially for endangered species such as members of the Cycadales. Ideally, barcodes could be used to positively identify illegally obtained material even in cases where diagnostic features have been purposefully removed or to release confiscated organisms into the proper breeding population. In order to be useful, a DNA barcode sequence must not only easily PCR amplify with universal or near-universal reaction conditions and primers, but also contain enough variation to generate unique identifiers at either the species or population levels. Chloroplast regions suggested by the Plant Working Group of the Consortium for the Barcode of Life (CBoL), and two alternatives, the chloroplast psbA-trnH intergenic spacer and the nuclear ribosomal internal transcribed spacer (nrITS), were tested for their utility in generating unique identifiers for members of the Cycadales. Ease of amplification and sequence generation with universal primers and reaction conditions was determined for each of the seven proposed markers. While none of the proposed markers provided unique identifiers for all species tested, nrITS showed the most promise in terms of variability, although sequencing difficulties remain a drawback. We suggest a workflow for DNA barcoding, including database generation and management, which will ultimately be necessary if we are to succeed in establishing a universal DNA barcode for plants.

  19. DNA barcoding in the cycadales: testing the potential of proposed barcoding markers for species identification of cycads.

    Directory of Open Access Journals (Sweden)

    Chodon Sass

    Full Text Available Barcodes are short segments of DNA that can be used to uniquely identify an unknown specimen to species, particularly when diagnostic morphological features are absent. These sequences could offer a new forensic tool in plant and animal conservation-especially for endangered species such as members of the Cycadales. Ideally, barcodes could be used to positively identify illegally obtained material even in cases where diagnostic features have been purposefully removed or to release confiscated organisms into the proper breeding population. In order to be useful, a DNA barcode sequence must not only easily PCR amplify with universal or near-universal reaction conditions and primers, but also contain enough variation to generate unique identifiers at either the species or population levels. Chloroplast regions suggested by the Plant Working Group of the Consortium for the Barcode of Life (CBoL, and two alternatives, the chloroplast psbA-trnH intergenic spacer and the nuclear ribosomal internal transcribed spacer (nrITS, were tested for their utility in generating unique identifiers for members of the Cycadales. Ease of amplification and sequence generation with universal primers and reaction conditions was determined for each of the seven proposed markers. While none of the proposed markers provided unique identifiers for all species tested, nrITS showed the most promise in terms of variability, although sequencing difficulties remain a drawback. We suggest a workflow for DNA barcoding, including database generation and management, which will ultimately be necessary if we are to succeed in establishing a universal DNA barcode for plants.

  20. 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.

  1. 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.

  2. Delineation of the species Haemophilus influenzae by phenotype, multilocus sequence phylogeny, and detection of marker genes

    DEFF Research Database (Denmark)

    Nørskov-Lauritsen, Niels; Overballe, MD; Kilian, Mogens

    2009-01-01

    branching cluster, intermingled with strains of "H. intermedius" and cryptic genospecies biotype IV. Although H. influenzae is phenotypically more homogenous than some other Haemophilus species, the genetic diversity and multicluster structure of strains traditionally associated with H. influenzae make...... genospecies biotype IV, and the never formally validated species "Haemophilus intermedius". Multilocus sequence phylogeny based on six housekeeping genes separated a cluster encompassing the type and the reference strains of H. influenzae from 31 more distantly related strains. Comparison of 16S rRNA gene...

  3. Relaxin concentrations in serum and urine of endangered species: correlations with physiologic events and use as a marker of pregnancy.

    Science.gov (United States)

    Steinetz, Bernard G; Brown, Janine L; Roth, Terri L; Czekala, Nancy

    2005-05-01

    Many mammalian species are facing extinction due to problems created by human encroachment, agriculture, pollution, and willful slaughter. Among those at risk are the Asian and African elephant, Sumatran rhinoceros, and giant panda. Conservation groups try to save species in the wild by preserving habitat and limiting animal-human conflicts, often with limited success. Another alternative is to preserve the extant gene pool through captive breeding as a hedge against extinction. Measurement of circulating reproductive hormones is impractical for most wildlife species; determination of urinary or fecal hormone metabolites provides a more viable approach. To aid breeding management, one important tool is the ability to diagnose and monitor pregnancy, especially in species with long gestations (e.g., rhinos over 15 mo and elephants over 20 mo). Unfortunately, measuring progestins often is not useful diagnostically, because concentrations are similar during at least part of the pregnancy and the nonpregnant luteal phase in some species (e.g., elephants, rhinoceroses, and giant pandas). As serum relaxin reliably distinguishes between pregnancy and pseudopregnancy in bitches, relaxin measurement might also provide a method for detecting a successful pregnancy in endangered species. Appropriate immunoassay reagents have enabled the estimation of relaxin concentrations in the serum of elephants and rhinos and the determination of pregnancy establishment and the outcome. Relaxin was also detected in panda serum and urine. However, the extreme variability of the time between observed mating and parturition and the confounding factors of delayed implantation, pseudopregnancy, and frequent fetal resorptions made it impossible to use the panda relaxin data as a specific marker of pregnancy.

  4. Variability in secondary structure of 18S ribosomal RNA as topological marker for identification of Paramecium species.

    Science.gov (United States)

    Shakoori, Farah R; Tasneem, Fareeda; Al-Ghanim, K; Mahboob, S; Al-Misned, F; Jahan, Nusrat; Shakoori, Abdul Rauf

    2014-12-01

    Besides cytological and molecular applications, Paramecium is being used in water quality assessment and for determination of saprobic levels. An unambiguous identification of these unicellular eukaryotes is not only essential, but its ecological diversity must also be explored in the local environment. 18SrRNA genes of all the strains of Paramecium species isolated from waste water were amplified, cloned and sequenced. Phylogenetic comparison of the nucleotide sequences of these strains with 23 closely related Paramecium species from GenBank Database enabled identification of Paramecium multimicronucleatum and Paramecium jenningsi. Some isolates did not show significant close association with other Paramecium species, and because of their unique position in the phylogenetic tree, they were considered new to the field. In the present report, these isolates are being designated as Paramecium caudatum pakistanicus. In this article, secondary structure of 18SrRNA has also been analyzed as an additional and perhaps more reliable topological marker for species discrimination and for determining possible phylogenetic relationship between the ciliate species. On the basis of comparison of secondary structure of 18SrRNA of various isolated Paramacium strains, and among Paramecium caudatum pakistanicus, Tetrahymena thermophila, Drosophila melanogaster, and Homo sapiens, it can be deduced that variable regions are more helpful in differentiating the species at interspecific level rather than at intraspecific level. It was concluded that V3 was the least variable region in all the organisms, V2 and V7 were the longest expansion segments of D. melanogaster and there was continuous mutational bias towards G.C base pairing in H. sapiens. © 2014 Wiley Periodicals, Inc.

  5. DNA polymorphism analysis of Brucella lipopolysaccharide genes reveals marked differences in O-polysaccharide biosynthetic genes between smooth and rough Brucella species and novel species-specific markers

    Directory of Open Access Journals (Sweden)

    Cloeckaert Axel

    2009-05-01

    Full Text Available Abstract Background The lipopolysaccharide is a major antigen and virulence factor of Brucella, an important bacterial pathogen. In smooth brucellae, lipopolysaccharide is made of lipid A-core oligosaccharide and N-formylperosamine O-polysaccharide. B. ovis and B. canis (rough species lack the O-polysaccharide. Results The polymorphism of O-polysaccharide genes wbkE, manAO-Ag, manBO-Ag, manCO-Ag, wbkF and wbkD and wbo (wboA and wboB, and core genes manBcore and wa** was analyzed. Although most genes were highly conserved, species- and biovar-specific restriction patterns were found. There were no significant differences in putative N-formylperosamyl transferase genes, suggesting that Brucella A and M serotypes are not related to specific genes. In B. pinnipedialis and B. ceti (both smooth, manBO-Ag carried an IS711, confirming its dispensability for perosamine synthesis. Significant differences between smooth and rough species were found in wbkF and wbkD, two adjacent genes putatively related to bactoprenol priming for O-polysaccharide polymerization. B. ovis wbkF carried a frame-shift and B. canis had a long deletion partially encompassing both genes. In smooth brucellae, this region contains two direct repeats suggesting the deletion mechanism. Conclusion The results define species and biovar markers, confirm the dispensability of manBO-Ag for O-polysaccharide synthesis and contribute to explain the lipopolysaccharide structure of rough and smooth Brucella species.

  6. Microsatellite marker development based on next-generation sequencing for the smooth marron (Cherax cainii, Austin) and cross-species amplification in other Cherax species.

    Science.gov (United States)

    Loughnan, Shannon R; Beheregaray, Luciano B; Robinson, Nicholas A

    2015-08-25

    The smooth marron, Cherax cainii is an important freshwater crustacean species for aquaculture and for a local wild fishery. C. tenuimanus, commonly known as the hairy marron is under threat from environmental impacts and genetic introgression from C. cainii that is hampering the survival of wild C. tenuimanus stocks. Marron are endemic to the south-west of Western Australia and C. tenuimanus is restricted to only the Margaret River. To isolate microsatellite sequences, shotgun 454 pyrosequencing was performed resulting in 184,981 DNA sequence reads. Following screening for microsatellites, 8799 putative microsatellite loci were detected and PCR primers were designed for 968 of these. Ten microsatellite loci were screened in 30 captive C. cainii individuals with eight loci producing unambiguous results. The average number of alleles per locus was 4.7 and average H e was 0.474. Following an analysis of relatedness, 79% of captive dyads were assigned as unrelated. Utilising C. quadricarinatus and C. destructor, cross-species amplification tests were conducted and amplification was achieved at four of the eight loci. Using next-generation sequencing methods, eight polymorphic microsatellite loci were developed from C. cainii, with potential for cross amplification in other Cherax species. The markers can be utilised for studies of natural genetic stock structure and for monitoring relatedness levels and genetic variation in both wild and captive populations.

  7. Alkaloids as taxonomic markers in some species of Magnolia L. and Liriodendron L.

    Directory of Open Access Journals (Sweden)

    Mirosław Furmanowa

    2014-01-01

    Full Text Available Some Magnoliaceae cultivated in Poland were investigated: Liriodendron tulipifera L. and 6 species of magnolia: Magnolia acuminata L., M. denudata Desr., M. kobus DC., M. obovata Thunb., M. salicifolia Maxim. and M. tripetala L. For alkaloid detection in the leaves thin-,layer chromatography was used. In Liriodendron tulipifera L. and in all the Magnolia species liriodenine which exhibits cytostatic activity was detected. The extract of Liriodendron tulipifera L. leaves showed, beside liriodenine other spots on the chromatogram than did the magnolias. Alkaloids can be utilized in the chemotaxonomy of Magnoliaceae as a diagnostic trait. The results of the investigations indicate a certain distinctiveness of M. acuminata L., in agreement with those obtained by way of numerical taxonomy. Most similar as regards alkaloid content in leaves are M. obovata Thunb. and M. tripetala L.

  8. Prospects of molecular markers in Fusarium species diversity

    DEFF Research Database (Denmark)

    Nayaka, S. Chandra; Wulff, Ednar Gadelha; Udayashankar, A.C.

    2011-01-01

    Recent developments in genomics have opened up for newer opportunities to study the diversity and classification of fungi. The genus Fusarium contains many plant pathogens that attack diverse agricultural crops. Fusarium spp. are not only pathogenic to plants but are also known as toxin producers...... that negatively affect animal and human health. The identification of Fusarium species still remains one of the most critical issues in fungal taxonomy, given that the number of species recognized in the genus has been constantly changing in the last century due to the different taxonomic systems. This review......-known molecular techniques such as random amplified polymorphic DNA, amplification fragment length polymorphism, etc. to more modern ones such as DNA microarrays, DNA barcoding, and pyrosequencing and their application form the core of the review. Target regions in the genome which can be potential candidates...

  9. A Set of Novel Microsatellite Markers Developed for a Distylous Species Luculia gratissima (Rubiaceae

    Directory of Open Access Journals (Sweden)

    Hong Wang

    2011-10-01

    Full Text Available Luculia gratissima (Wall. Sweet (Rubiaceae is a perennial shrub distributed in the southeast margin of the Tibetan Plateau in southwest China and adjacent region of Nepal and Myanmar. The plant is a distylous species with reciprocally placed stigmas and anthers in each floral morph. By using the Fast Isolation by Amplified Fragment Length Polymorphism (AFLP of Sequences Containing (FIASCO repeats protocol, 19 primer sets were identified in two wild populations. Of these primers, 10 displayed polymorphisms and nine were monomorphic. The number of alleles per locus ranged from two to five, values for observed and expected heterozygosities ranged from 0.000 to 1.000 and from 0.289 to 0.760, with averages of 0.303 and 0.555, respectively. These microsatellite loci will facilitate further studies on breeding system, gene flow patterns, and population structure of L. gratissima and its allied species.

  10. Analysis of genetic structure and interrelationships in lentil species using morphological and SSR markers.

    Science.gov (United States)

    Koul, Priyanka Mohan; Sharma, Vikas; Rana, Maneet; Chahota, Rakesh K; Kumar, Shiv; Sharma, Tilak R

    2017-05-01

    Genetic structure and relationships of 130 lentil accessions belonging to six taxa were analysed. For this purpose, seven morphological traits and 31 polymorphic simple sequence repeat (SSR) primers were used for this purpose. Morphological traits grouped lentil accessions into five main clusters. SSR primers collectively amplified 139 polymorphic alleles in a range of 2-10 with an average of 4.48 alleles. The size of amplified alleles varied from 50 to 650 bp. Polymorphism information content (PIC) ranged from 0.02 to 0.85 with an average of 0.46. Neighbour-joining tree grouped accessions broadly according to their taxonomic ranks, except L. culinaris ssp. odemensis. Analysis of molecular variance (AMOVA) revealed that a major portion (82.0%) of genetic variance resided within species, while only 18% resided among species. Bayesian model-based STRUCTURE analysis assigned all accessions into five clusters and showed some admixture within individuals. Cluster analysis showed that cultivated Lens accessions of Ethiopian origin clustered separately, from other cultivated accessions indicating its distinct lineage. Among the analysed lentil species, L. culinaris ssp. odemensis seemed to have conserved genetic background and needs revision of its taxonomic status. Results of present study provide important information on genetic diversity and relationships among different wild and cultivated taxa of lentil. Thus, these results can be useful in designing breeding strategies for future improvement and taxonomic implications in lentil.

  11. AFLP markers reveal high clonal diversity and extreme longevity in four key arctic-alpine species.

    Science.gov (United States)

    de Witte, Lucienne C; Armbruster, Georg F J; Gielly, Ludovic; Taberlet, Pierre; Stöcklin, Jürg

    2012-03-01

    We investigated clonal diversity, genet size structure and genet longevity in populations of four arctic-alpine plants (Carex curvula, Dryas octopetala, Salix herbacea and Vaccinium uliginosum) to evaluate their persistence under past climatic oscillations and their potential resistance to future climate change. The size and number of genets were determined by an analysis of amplified fragment length polymorphisms and a standardized sampling design in several European arctic-alpine populations, where these species are dominant in the vegetation. Genet age was estimated by dividing the size by the annual horizontal size increment from in situ growth measurements. Clonal diversity was generally high but differed among species, and the frequency distribution of genet size was strongly left-skewed. The largest C. curvula genet had an estimated minimum age of c. 4100 years and a maximum age of c. 5000 years, although 84.8% of the genets in this species were postindustrial warming. The presence of genets in all size classes and the dominance of presumably young individuals suggest repeated recruitment over time, a precondition for adaptation to changing environmental conditions. Together, persistence and continuous genet turnover may ensure maximum ecosystem resilience. Thus, our results indicate that long-lived clonal plants in arctic-alpine ecosystems can persist, despite considerable climatic change. © 2011 Blackwell Publishing Ltd.

  12. Development of DArT marker platforms and genetic diversity assessment of the U.S. collection of the new oilseed crop lesquerella and related species.

    Science.gov (United States)

    Cruz, Von Mark V; Kilian, Andrzej; Dierig, David A

    2013-01-01

    The advantages of using molecular markers in modern genebanks are well documented. They are commonly used to understand the distribution of genetic diversity in populations and among species which is crucial for efficient management and effective utilization of germplasm collections. We describe the development of two types of DArT molecular marker platforms for the new oilseed crop lesquerella (Physaria spp.), a member of the Brassicaceae family, to characterize a collection in the National Plant Germplasm System (NPGS) with relatively little known in regards to the genetic diversity and traits. The two types of platforms were developed using a subset of the germplasm conserved ex situ consisting of 87 Physaria and 2 Paysonia accessions. The microarray DArT revealed a total of 2,833 polymorphic markers with an average genotype call rate of 98.4% and a scoring reproducibility of 99.7%. On the other hand, the DArTseq platform developed for SNP and DArT markers from short sequence reads showed a total of 27,748 high quality markers. Cluster analysis and principal coordinate analysis indicated that the different accessions were successfully classified by both systems based on species, by geographical source, and breeding status. In the germplasm set analyzed, which represented more than 80% of the P. fendleri collection, we observed that a substantial amount of variation exists in the species collection. These markers will be valuable in germplasm management studies and lesquerella breeding, and augment the microsatellite markers previously developed on the taxa.

  13. Genetic differentiation and phylogeography of partially sympatric species complex Rhizophora mucronata Lam. and R. stylosa Griff. using SSR markers.

    Science.gov (United States)

    Wee, Alison K S; Takayama, Koji; Chua, Jasher L; Asakawa, Takeshi; Meenakshisundaram, Sankararamasubramanian H; Onrizal; Adjie, Bayu; Ardli, Erwin Riyanto; Sungkaew, Sarawood; Malekal, Norhaslinda Binti; Tung, Nguyen Xuan; Salmo, Severino G; Yllano, Orlex Baylen; Saleh, M Nazre; Soe, Khin Khin; Tateishi, Yoichi; Watano, Yasuyuki; Baba, Shigeyuki; Webb, Edward L; Kajita, Tadashi

    2015-03-29

    Mangrove forests are ecologically important but globally threatened intertidal plant communities. Effective mangrove conservation requires the determination of species identity, management units, and genetic structure. Here, we investigate the genetic distinctiveness and genetic structure of an iconic but yet taxonomically confusing species complex Rhizophora mucronata and R. stylosa across their distributional range, by employing a suite of 20 informative nuclear SSR markers. Our results demonstrated the general genetic distinctiveness of R. mucronata and R. stylosa, and potential hybridization or introgression between them. We investigated the population genetics of each species without the putative hybrids, and found strong genetic structure between oceanic regions in both R. mucronata and R. stylosa. In R. mucronata, a strong divergence was detected between populations from the Indian Ocean region (Indian Ocean and Andaman Sea) and the Pacific Ocean region (Malacca Strait, South China Sea and Northwest Pacific Ocean). In R. stylosa, the genetic break was located more eastward, between populations from South and East China Sea and populations from the Southwest Pacific Ocean. The location of these genetic breaks coincided with the boundaries of oceanic currents, thus suggesting that oceanic circulation patterns might have acted as a cryptic barrier to gene flow. Our findings have important implications on the conservation of mangroves, especially relating to replanting efforts and the definition of evolutionary significant units in Rhizophora species. We outlined the genetic structure and identified geographical areas that require further investigations for both R. mucronata and R. stylosa. These results serve as the foundation for the conservation genetics of R. mucronata and R. stylosa and highlighted the need to recognize the genetic distinctiveness of closely-related species, determine their respective genetic structure, and avoid artificially promoting

  14. Phylogeographic structure of the commercially important tropical tree species Dryobalanops aromatica Gaertn. F. (Dipterocarpaceae revealed by microsatellite markers

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    Fifi Gus Dwiyanti

    2014-12-01

    Full Text Available Dryobalanops aromatica Gaertn. F. (Kapur is an economically important timber     species in Southeast Asia that can serve as a good model for studying the impact of the Pleistocene glaciations on the genetic diversity and distribution of species in tropical regions. Seven polymorphic microsatellite markers were        analyzed in five natural populations of D. aromatica (N = 120 individuals: Gunung Panti in Malay Peninsula, Lingga Island in Lingga Archipelago, Lambir Hills National Park, Limbang and Similajau National Park in Borneo. The level of gene diversity (HE for the five populations was relatively high with a range from 0.571 (Similajau to 0.729 (Gunung Panti. The high genetic diversity in the present study could be attributed to the larger refugia population sizes of D. aromatica than that of other species. The population genetic structure revealed two distinct groups: the Malay Peninsula-Lingga Archipelago and Borneo. This pattern suggests that populations in each geographical area might be the consequence of post-glacial expansion from one or two refugia, but that gene flow between different glacial refugia was fairly restricted. 

  15. Mining and characterization of EST-SSR markers for Zingiber officinale Roscoe with transferability to other species of Zingiberaceae.

    Science.gov (United States)

    Awasthi, Praveen; Singh, Ashish; Sheikh, Gulfam; Mahajan, Vidushi; Gupta, Ajai Prakash; Gupta, Suphla; Bedi, Yashbir S; Gandhi, Sumit G

    2017-10-01

    Zingiber officinale is a model spice herb, well known for its medicinal value. It is primarily a vegetatively propagated commercial crop. However, considerable diversity in its morphology, fiber content and chemoprofiles has been reported. The present study explores the utility of EST-derived markers in studying genetic diversity in different accessions of Z. officinale and their cross transferability within the Zingiberaceae family. A total of 38,115 ESTs sequences were assembled to generate 7850 contigs and 10,762 singletons. SSRs were searched in the unigenes and 515 SSR-containing ESTs were identified with a frequency of 1 SSR per 25.21 kb of the genome. These ESTs were also annotated using BLAST2GO. Primers were designed for 349 EST-SSRs and 25 primer pairs were randomly picked for EST SSR study. Out of these, 16 primer pairs could be optimized for amplification in different accessions of Z. officinale as well as other species belonging to Zingiberaceae. GES454, GES466, GES480 and GES486 markers were found to exhibit 100% cross-transferability among different members of Zingiberaceae.

  16. aes, the gene encoding the esterase B in Escherichia coli, is a powerful phylogenetic marker of the species

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    Tuffery Pierre

    2009-12-01

    Full Text Available Abstract Background Previous studies have established a correlation between electrophoretic polymorphism of esterase B, and virulence and phylogeny of Escherichia coli. Strains belonging to the phylogenetic group B2 are more frequently implicated in extraintestinal infections and include esterase B2 variants, whereas phylogenetic groups A, B1 and D contain less virulent strains and include esterase B1 variants. We investigated esterase B as a marker of phylogeny and/or virulence, in a thorough analysis of the esterase B-encoding gene. Results We identified the gene encoding esterase B as the acetyl-esterase gene (aes using gene disruption. The analysis of aes nucleotide sequences in a panel of 78 reference strains, including the E. coli reference (ECOR strains, demonstrated that the gene is under purifying selection. The phylogenetic tree reconstructed from aes sequences showed a strong correlation with the species phylogenetic history, based on multi-locus sequence typing using six housekeeping genes. The unambiguous distinction between variants B1 and B2 by electrophoresis was consistent with Aes amino-acid sequence analysis and protein modelling, which showed that substituted amino acids in the two esterase B variants occurred mostly at different sites on the protein surface. Studies in an experimental mouse model of septicaemia using mutant strains did not reveal a direct link between aes and extraintestinal virulence. Moreover, we did not find any genes in the chromosomal region of aes to be associated with virulence. Conclusion Our findings suggest that aes does not play a direct role in the virulence of E. coli extraintestinal infection. However, this gene acts as a powerful marker of phylogeny, illustrating the extensive divergence of B2 phylogenetic group strains from the rest of the species.

  17. aes, the gene encoding the esterase B in Escherichia coli, is a powerful phylogenetic marker of the species.

    Science.gov (United States)

    Lescat, Mathilde; Hoede, Claire; Clermont, Olivier; Garry, Louis; Darlu, Pierre; Tuffery, Pierre; Denamur, Erick; Picard, Bertrand

    2009-12-29

    Previous studies have established a correlation between electrophoretic polymorphism of esterase B, and virulence and phylogeny of Escherichia coli. Strains belonging to the phylogenetic group B2 are more frequently implicated in extraintestinal infections and include esterase B2 variants, whereas phylogenetic groups A, B1 and D contain less virulent strains and include esterase B1 variants. We investigated esterase B as a marker of phylogeny and/or virulence, in a thorough analysis of the esterase B-encoding gene. We identified the gene encoding esterase B as the acetyl-esterase gene (aes) using gene disruption. The analysis of aes nucleotide sequences in a panel of 78 reference strains, including the E. coli reference (ECOR) strains, demonstrated that the gene is under purifying selection. The phylogenetic tree reconstructed from aes sequences showed a strong correlation with the species phylogenetic history, based on multi-locus sequence typing using six housekeeping genes. The unambiguous distinction between variants B1 and B2 by electrophoresis was consistent with Aes amino-acid sequence analysis and protein modelling, which showed that substituted amino acids in the two esterase B variants occurred mostly at different sites on the protein surface. Studies in an experimental mouse model of septicaemia using mutant strains did not reveal a direct link between aes and extraintestinal virulence. Moreover, we did not find any genes in the chromosomal region of aes to be associated with virulence. Our findings suggest that aes does not play a direct role in the virulence of E. coli extraintestinal infection. However, this gene acts as a powerful marker of phylogeny, illustrating the extensive divergence of B2 phylogenetic group strains from the rest of the species.

  18. High-density marker profiling confirms ancestral genomes of Avena species and identifies D-genome chromosomes of hexaploid oat.

    Science.gov (United States)

    Yan, Honghai; Bekele, Wubishet A; Wight, Charlene P; Peng, Yuanying; Langdon, Tim; Latta, Robert G; Fu, Yong-Bi; Diederichsen, Axel; Howarth, Catherine J; Jellen, Eric N; Boyle, Brian; Wei, Yuming; Tinker, Nicholas A

    2016-11-01

    Genome analysis of 27 oat species identifies ancestral groups, delineates the D genome, and identifies ancestral origin of 21 mapped chromosomes in hexaploid oat. We investigated genomic relationships among 27 species of the genus Avena using high-density genetic markers revealed by genotyping-by-sequencing (GBS). Two methods of GBS analysis were used: one based on tag-level haplotypes that were previously mapped in cultivated hexaploid oat (A. sativa), and one intended to sample and enumerate tag-level haplotypes originating from all species under investigation. Qualitatively, both methods gave similar predictions regarding the clustering of species and shared ancestral genomes. Furthermore, results were consistent with previous phylogenies of the genus obtained with conventional approaches, supporting the robustness of whole genome GBS analysis. Evidence is presented to justify the final and definitive classification of the tetraploids A. insularis, A. maroccana (=A. magna), and A. murphyi as containing D-plus-C genomes, and not A-plus-C genomes, as is most often specified in past literature. Through electronic painting of the 21 chromosome representations in the hexaploid oat consensus map, we show how the relative frequency of matches between mapped hexaploid-derived haplotypes and AC (DC)-genome tetraploids vs. A- and C-genome diploids can accurately reveal the genome origin of all hexaploid chromosomes, including the approximate positions of inter-genome translocations. Evidence is provided that supports the continued classification of a diverged B genome in AB tetraploids, and it is confirmed that no extant A-genome diploids, including A. canariensis, are similar enough to the D genome of tetraploid and hexaploid oat to warrant consideration as a D-genome diploid.

  19. Molecular phylogenetic relationships among four species of the mangrove tree genus Bruguiera (Rhizophoraceae, as revealed by chromosome and RAPD markers

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    Pragnya Sahoo

    2007-06-01

    Full Text Available Analysis of karyotype, nuclear DNA content and RAPD markers were performed in four species of Bruguiera (Rhizophoraceae of Bhitarkanika mangrove forests, Orissa, India. Detailed karyotype analysis revealing 2n=34 in B. cylindrica and 2n=36 in B. gymnorrhiza was reported for the first time and 2n=34 in B. parviflora and B. sexangula was confirmed. On the basis of the common types of chromosomes present among Bruguiera, two distinct groups were found; one consists of B. cylindrica and B. parviflora and the other of B. gymnorrhiza and B. sexangula. The symmetrical karyotype with same chromosome types grouped B. cylindrica and B. parviflora together and presence of Type E chromosomes placed B. gymnorrhiza and B. sexangula in a separate group, suggesting their closer affinity in their respective group. Analysis of chromosome length, volume, INV and 4C DNA content confirmed this division. Nuclear DNA content was two-fold higher (~17.0 pg in the second group than in the first (~8.0 pg. The amplification products generated through RAPD revealed 1-9 amplicons with size variations from 600 bp to 2 500 bp with 49.31% genetic similarity between B. gymnorrhiza and B. sexangula and 47.10% in between B. cylindrica and B. parviflora. The high copy number marker band (~ 1 100 bp yielded in OPN-15 primer in B. parviflora the characteristic DNA marker, which was cloned and used as probes for assessment of genetic diversity, and demonstrated its close genetic affinity to B. cylindrica. B. gymnorrhiza and B. sexangula also produced similar marker bands of ~600 bp and ~2 200 bp in the same primer. All of the cytological, 4C DNA content and RAPD data confirmed the existence of two taxonomically distinct groups of Bruguiera: one consisting of B. cylindrica and B. parviflora and the other of B. gymnorrhiza and B. sexangula as placed earlier (1862 in the tribe Rhizophoreae by Bentham and Hooker, on the basis of the flowering habits of Bruguiera. Genetically, the B

  20. Development of new genomic microsatellite markers from robusta coffee (Coffea canephora Pierre ex A. Froehner) showing broad cross-species transferability and utility in genetic studies.

    Science.gov (United States)

    Hendre, Prasad Suresh; Phanindranath, Regur; Annapurna, V; Lalremruata, Albert; Aggarwal, Ramesh K

    2008-04-30

    Species-specific microsatellite markers are desirable for genetic studies and to harness the potential of MAS-based breeding for genetic improvement. Limited availability of such markers for coffee, one of the most important beverage tree crops, warrants newer efforts to develop additional microsatellite markers that can be effectively deployed in genetic analysis and coffee improvement programs. The present study aimed to develop new coffee-specific SSR markers and validate their utility in analysis of genetic diversity, individualization, linkage mapping, and transferability for use in other related taxa. A small-insert partial genomic library of Coffea canephora, was probed for various SSR motifs following conventional approach of Southern hybridisation. Characterization of repeat positive clones revealed a very high abundance of DNRs (1/15 Kb) over TNRs (1/406 kb). The relative frequencies of different DNRs were found as AT > AG > AC, whereas among TNRs, AGC was the most abundant repeat. The SSR positive sequences were used to design 58 primer pairs of which 44 pairs could be validated as single locus markers using a panel of arabica and robusta genotypes. The analysis revealed an average of 3.3 and 3.78 alleles and 0.49 and 0.62 PIC per marker for the tested arabicas and robustas, respectively. It also revealed a high cumulative PI over all the markers using both sib-based (10-6 and 10-12 for arabicas and robustas respectively) and unbiased corrected estimates (10-20 and 10-43 for arabicas and robustas respectively). The markers were tested for Hardy-Weinberg equilibrium, linkage dis-equilibrium, and were successfully used to ascertain generic diversity/affinities in the tested germplasm (cultivated as well as species). Nine markers could be mapped on robusta linkage map. Importantly, the markers showed ~92% transferability across related species/genera of coffee. The conventional approach of genomic library was successfully employed although with low

  1. Histological Changes in Gills of Two Fish Species as Indicators of Water Quality in Jansen Lagoon (São Luís, Maranhão State, Brazil

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    Débora M. S. Santos

    2014-12-01

    Full Text Available Water quality of the Jansen Lagoon (São Luís, Maranhão State, Brazil was assessed through histological biomarkers and microbiological parameters. To this end, 29 fish specimens (11 Centropomus undecimalis and 18 Sardinella sp and eight water samples were collected during the rainy and dry periods of 2013. The lagoon water showed thermotolerant coliform indices above the limit set forth in CONAMA Resolution 357/2005. Histological changes observed in the gills were: lifting of the respiratory epithelium, hyperplasia of the lamellar epithelium, incomplete and complete fusion of several lamellae, disorganization of the lamellae, congestion of blood vessels, aneurysms, hypertrophy of the respiratory epithelium, hemorrhage and rupture of the lamellar epithelium and parasite. The histological alteration index (HAI average value to Sardinella sp was 31.8 and to C. undecimalis was 22.2. The average HAI value in both species corresponds to category 21–50, with tissue injuries being classified from moderate to severe. The presence of histological injuries and the HAI values indicate that the fish sampled from the Jansen Lagoon are reacting to non-specific xenobiotics present at the site.

  2. Histological Changes in Gills of Two Fish Species as Indicators of Water Quality in Jansen Lagoon (São Luís, Maranhão State, Brazil)

    Science.gov (United States)

    Santos, Débora M. S.; Melo, Mércia Regina S.; Mendes, Denise Carla S.; Rocha, Iolanda Karoline B. S.; Silva, Jakeline Priscila L.; Cantanhêde, Sildiane M.; Meletti, Paulo C.

    2014-01-01

    Water quality of the Jansen Lagoon (São Luís, Maranhão State, Brazil) was assessed through histological biomarkers and microbiological parameters. To this end, 29 fish specimens (11 Centropomus undecimalis and 18 Sardinella sp) and eight water samples were collected during the rainy and dry periods of 2013. The lagoon water showed thermotolerant coliform indices above the limit set forth in CONAMA Resolution 357/2005. Histological changes observed in the gills were: lifting of the respiratory epithelium, hyperplasia of the lamellar epithelium, incomplete and complete fusion of several lamellae, disorganization of the lamellae, congestion of blood vessels, aneurysms, hypertrophy of the respiratory epithelium, hemorrhage and rupture of the lamellar epithelium and parasite. The histological alteration index (HAI) average value to Sardinella sp was 31.8 and to C. undecimalis was 22.2. The average HAI value in both species corresponds to category 21–50, with tissue injuries being classified from moderate to severe. The presence of histological injuries and the HAI values indicate that the fish sampled from the Jansen Lagoon are reacting to non-specific xenobiotics present at the site. PMID:25514148

  3. Molecular markers reveal spatially segregated cryptic species in a critically endangered fish, the common skate (Dipturus batis).

    Science.gov (United States)

    Griffiths, Andrew M; Sims, David W; Cotterell, Stephen P; El Nagar, Aliya; Ellis, Jim R; Lynghammar, Arve; McHugh, Matthew; Neat, Francis C; Pade, Nicolas G; Queiroz, Nuno; Serra-Pereira, Bárbara; Rapp, Toby; Wearmouth, Victoria J; Genner, Martin J

    2010-05-22

    Many sharks and skates are particularly vulnerable to overfishing because of their large size, slow growth, late maturity and low fecundity. In Europe dramatic population declines have taken place in common skate (Dipturus batis L.), one of the largest demersal fish in regional shelf seas, leading to extirpations from substantial parts of its former range. Here we report the discovery of cryptic species in common skate collected from the northeast Atlantic continental shelf. Data from nuclear microsatellite markers indicated two clearly distinct clades and phylogenetic analysis of mitochondrial DNA sequences demonstrated monophyly of each one of them. Capture locations showed evidence of strong spatial segregation, with one taxon occurring mainly in waters off the southern British Isles and around Rockall, while the other was restricted to more northerly shelf waters. These apparently cryptic species showed overlapping substrate and depth preferences, but distributional limits were closely related to temperature gradients, potentially indicating thermal limits to their distributions. This discovery of hidden diversity within a large, critically endangered marine vertebrate demonstrates how marine biodiversity can be underestimated, even in such a relatively well-studied and heavily exploited region.

  4. Population genetic structure of wild and hatchery black rockfish Sebastes inermis in Korea, assessed using cross-species microsatellite markers.

    Science.gov (United States)

    An, H S; Kim, E-M; Lee, J-H; Noh, J K; An, C M; Yoon, S J; Park, K D; Myeong, J-I

    2011-10-13

    The population structure of the black rockfish, Sebastes inermis (Sebastidae), was estimated using 10 microsatellite loci developed for S. schlegeli on samples of 174 individuals collected from three wild and three hatchery populations in Korea. Reduced genetic variation was detected in hatchery strains [overall number of alleles (N(A)) = 8.07; allelic richness (A(R)) = 7.37; observed heterozygosity (H(O)) = 0.641] compared with the wild samples (overall N(A) = 8.43; A(R) = 7.83; H(O) = 0.670), but the difference was not significant. Genetic differentiation among the populations was significant (overall F(ST) = 0.0237, P hatchery strains and between wild and hatchery strains, but not among the wild populations, indicating high levels of gene flow along the southern coast of Korea, even though the black rockfish is a benthic, non-migratory marine species. Genetic differentiation among the hatchery strains could reflect genetic drift due to intensive breeding practices. Thus, in the interests of optimal resource management, genetic variation should be monitored and inbreeding controlled within stocks in commercial breeding programs. Information on genetic population structure based on cross-species microsatellite markers can aid in the proper management of S. inermis populations.

  5. Molecular markers reveal spatially segregated cryptic species in a critically endangered fish, the common skate (Dipturus batis)

    Science.gov (United States)

    Griffiths, Andrew M.; Sims, David W.; Cotterell, Stephen P.; El Nagar, Aliya; Ellis, Jim R.; Lynghammar, Arve; McHugh, Matthew; Neat, Francis C.; Pade, Nicolas G.; Queiroz, Nuno; Serra-Pereira, Bárbara; Rapp, Toby; Wearmouth, Victoria J.; Genner, Martin J.

    2010-01-01

    Many sharks and skates are particularly vulnerable to overfishing because of their large size, slow growth, late maturity and low fecundity. In Europe dramatic population declines have taken place in common skate (Dipturus batis L.), one of the largest demersal fish in regional shelf seas, leading to extirpations from substantial parts of its former range. Here we report the discovery of cryptic species in common skate collected from the northeast Atlantic continental shelf. Data from nuclear microsatellite markers indicated two clearly distinct clades and phylogenetic analysis of mitochondrial DNA sequences demonstrated monophyly of each one of them. Capture locations showed evidence of strong spatial segregation, with one taxon occurring mainly in waters off the southern British Isles and around Rockall, while the other was restricted to more northerly shelf waters. These apparently cryptic species showed overlapping substrate and depth preferences, but distributional limits were closely related to temperature gradients, potentially indicating thermal limits to their distributions. This discovery of hidden diversity within a large, critically endangered marine vertebrate demonstrates how marine biodiversity can be underestimated, even in such a relatively well-studied and heavily exploited region. PMID:20106849

  6. Uncovering Differences in Virulence Markers Associated with Achromobacter Species of CF and Non-CF Origin.

    Science.gov (United States)

    Filipic, Brankica; Malesevic, Milka; Vasiljevic, Zorica; Lukic, Jovanka; Novovic, Katarina; Kojic, Milan; Jovcic, Branko

    2017-01-01

    Achromobacter spp. are recognized as emerging pathogens in hospitalized as well as in cystic fibrosis (CF) patients. From 2012 to 2015, we collected 69 clinical isolates (41 patient) of Achromobacter spp. from 13 patients with CF (CF isolates, n = 32) and 28 patients receiving care for other health conditions (non-CF isolates, n = 37). Molecular epidemiology and virulence potential of isolates were examined. Antimicrobial susceptibility, motility, ability to form biofilms and binding affinity to mucin, collagen, and fibronectin were tested to assess their virulence traits. The nrdA gene sequencing showed that A. xylosoxidans was the most prevalent species in both CF and non-CF patients. CF patients were also colonized with A. dolens/A. ruhlandii, A. insuavis, and A. spiritinus strains while non-CF group was somewhat less heterogenous, although A. insuavis, A. insolitus, and A. piechaudii strains were detected beside A. xylosoxidans. Three strains displayed clonal distribution, one among patients from the CF group and two among non-CF patients. No significant differences in susceptibility to antimicrobials were observed between CF and non-CF patients. About one third of the isolates were classified as strong biofilm producers, and the proportion of CF and non-CF isolates with the ability to form biofilm was almost identical. CF isolates were less motile compared to the non-CF group and no correlation was found between swimming phenotype and biofilm formation. On the other hand, CF isolates exhibited higher affinity to bind mucin, collagen, and fibronectin. In generall, CF isolates from our study exhibited in vitro properties that could be of importance for the colonization of CF patients.

  7. Uncovering Differences in Virulence Markers Associated with Achromobacter Species of CF and Non-CF Origin

    Directory of Open Access Journals (Sweden)

    Brankica Filipic

    2017-05-01

    Full Text Available Achromobacter spp. are recognized as emerging pathogens in hospitalized as well as in cystic fibrosis (CF patients. From 2012 to 2015, we collected 69 clinical isolates (41 patient of Achromobacter spp. from 13 patients with CF (CF isolates, n = 32 and 28 patients receiving care for other health conditions (non-CF isolates, n = 37. Molecular epidemiology and virulence potential of isolates were examined. Antimicrobial susceptibility, motility, ability to form biofilms and binding affinity to mucin, collagen, and fibronectin were tested to assess their virulence traits. The nrdA gene sequencing showed that A. xylosoxidans was the most prevalent species in both CF and non-CF patients. CF patients were also colonized with A. dolens/A. ruhlandii, A. insuavis, and A. spiritinus strains while non-CF group was somewhat less heterogenous, although A. insuavis, A. insolitus, and A. piechaudii strains were detected beside A. xylosoxidans. Three strains displayed clonal distribution, one among patients from the CF group and two among non-CF patients. No significant differences in susceptibility to antimicrobials were observed between CF and non-CF patients. About one third of the isolates were classified as strong biofilm producers, and the proportion of CF and non-CF isolates with the ability to form biofilm was almost identical. CF isolates were less motile compared to the non-CF group and no correlation was found between swimming phenotype and biofilm formation. On the other hand, CF isolates exhibited higher affinity to bind mucin, collagen, and fibronectin. In generall, CF isolates from our study exhibited in vitro properties that could be of importance for the colonization of CF patients.

  8. Genetic Variability in Nicotianatabacum and Nicotiana Species as Revealed by RAPD Markers: 1. Development of the RAPD Procedure

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    del Piano L

    2014-12-01

    Full Text Available At present there is no information about the level of genetic variability in N. tabacum and in the Nicotiana genus as revealed by random amplified polymorphic DNA (RAPD. Such knowledge could be useful for taxonomic and breeding purposes. The aim of this paper is to assess the potential application of the DNA polymorphisms generated by RAPD markers within this genus and in tobacco. As rigorously standardized reaction conditions are required to obtain a reproducible RAPD marker, four rapid DNA extraction methods were compared and several parameters of the reaction conditions for the random polymorphic DNA amplification were analysed and optimized. The DNA of six-week-old leaves of N. tabacum var. Samsun was obtained with the following methods differing in the strategy of purification: the cetyltrimethylammonium bromide (CTAB method, that of Edwards, nucleon phytopure system and the method of Goring. Reproducible amplification profiles were obtained with all the methods except for Edwards'. As regards amplification conditions, the effects of primer-template annealing temperature, of a final extension step, of the number of cycles and of the length of extension time in each cycle were analysed. Moreover, the effects on amplification reaction of the DNA amount, of MgCl2, primer and deoxynucleotide triphosphate (dNTP concentration were evaluated. Then DNA of 12 Nicotiana species and Nicotianatabacum was amplified with primers OPA-01 and OPA-13 which revealed a considerable polymorphism. The same primers used to analyse 36 var. of N. tabacum belonging to different types, showed identical amplification profiles. Further amplification experiments were carried out with only 12 of the tobacco lines; three primers among the 12 assayed revealed one polymorphic fragment each.

  9. Application of long-chain alcohols as faecal markers to estimate diet composition of horses and cattle fed with herbaceous and woody species.

    Science.gov (United States)

    López López, C; Celaya, R; Santos, A S; Rodrigues, M A M; Osoro, K; Ferreira, L M M

    2015-11-01

    Utilization of long-chain alcohols (LCOH) as diet composition markers in horses and cattle was assessed in a study conducted with 12 mature crossbreed mares (385±47 kg BW) and six adult non-lactating cows (499±36 kg BW) of Asturiana de los Valles breed. The LCOH data were combined with alkane and long-chain fatty acid (LCFA) data to test the applicability of combining these markers to estimate diet composition. Animals were randomly divided into groups of three animals and received a daily total amount of 1.0 kg dry matter/100 kg BW of diets composed of different proportions of ryegrass (Lolium perenne) and woody species (Ulex gallii and heather). Diet composition was estimated from even-chain LCOH (C(20)-OH to C(30)-OH) combined or not with alkane (C(25)-C(31) and C(33)) and/or LCFA (C(22)-FA to C(28)-FA, C(30)-FA, C(32)-FA and C(34)-FA) concentrations in diet components and faeces by least-squares procedures, using marker faecal concentrations uncorrected for incomplete faecal recovery (FR0) or corrected using mean recoveries across diets within animal species (FR1). Results showed large differences between plant species in their LCOH profiles, and that these markers offered additional discriminatory information to that provided by alkanes and LCFA. The LCOH markers were incompletely recovered in the faeces of both animal species. In cattle, LCOH FR tended to increase with carbon-chain length in a linear manner in both diets (P diet estimates. Correction of faecal LCOH concentrations to incomplete FR led to more accurate diet composition estimates in both animal species. Results obtained in this study suggest the usefulness of LCOH markers combined with alkanes and LCFA to estimate diet composition of horses and cattle grazing mixed grassy-woody plant communities.

  10. Are adjunctive markers useful in routine cervical cancer screening? Application of p16(INK4a) and HPV-PCR on ThinPrep samples with histological follow-up

    DEFF Research Database (Denmark)

    Schledermann, D; Andersen, B T; Bisgaard, K

    2008-01-01

    4a) interpretation.A total of 232 ThinPrep samples were stained for p16(INK4a), and HPV-DNA PCR was performed on 107 specimens with inclusion of both benign and abnormal cytology. Histological follow-up information was collected.The diagnostic sensitivity of ASC+ with CIN2+ in histology as endpoint...

  11. Development of new polymorphic microsatellite markers for three closely related plant-pathogenic Phytophthora species using 454-pyrosequencing and their potential applications.

    Science.gov (United States)

    Schoebel, Corine N; Jung, Esther; Prospero, Simone

    2013-10-01

    Phytophthora spp. (oomycetes) are causal agents of devastating diseases on a high number of crops, ornamentals, and native plants worldwide. Neutral molecular markers are increasingly being used to investigate the genetic population structure and possible pathways of spread of different plant pathogens, including Phytophthora spp. In this study, polymorphic microsatellite markers were developed for three species of the former Phytophthora citricola species complex-namely, P. multivora, P. plurivora, and P. pini (P. citricola I)-using the 454-pyrosequencing technique. In total, 35 polymorphic microsatellite loci were found and further characterized: 11 for P. plurivora, 16 for P. multivora, and 8 for P. pini. Microsatellites with dinucleotide motifs repeated 6 to 10 times were the most common for all three species. On average, 65 alleles per species and 5.3 alleles per locus were detected. Most loci were characterized by a low observed heterozygosity, which might be due to the homothallic mating system of the three Phytophthora spp. targeted. Cross amplification of the newly developed markers was tested on 17 Phytophthora spp. belonging to five different internal transcribed spacer clades. Transferability success was generally low and decreased with increasing genetic distance from the species to the three target species. A set of four loci was selected to easily discriminate P. plurivora, P. multivora, and P. pini on the basis of presence or absence of a polymerase chain reaction amplicon on an agarose gel.

  12. Species-diagnostic single-nucleotide polymorphism and sequence-tagged site markers for the parasitic wasp genus nasonia (Hymenoptera: Pteromalidae)

    NARCIS (Netherlands)

    Niehuis, O.; Judson, A. K.; Werren, J. H.; Hunter, W. B.; Dang, P. M.; Dowd, S. E.; Grillenberger, B.; Beukeboom, L. W.; Gadau, J.

    Wasps of the genus Nasonia are important biological control agents of house flies and related filth flies, which are major vectors of human pathogens. Species of Nasonia (Hymenoptera: Pteromalidae) are not easily differentiated from one another by morphological characters, and molecular markers for

  13. SNPs in Multi-Species Conserved Sequences (MCS as useful markers in association studies: a practical approach

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    Pericak-Vance Margaret A

    2007-08-01

    Full Text Available Abstract Background Although genes play a key role in many complex diseases, the specific genes involved in most complex diseases remain largely unidentified. Their discovery will hinge on the identification of key sequence variants that are conclusively associated with disease. While much attention has been focused on variants in protein-coding DNA, variants in noncoding regions may also play many important roles in complex disease by altering gene regulation. Since the vast majority of noncoding genomic sequence is of unknown function, this increases the challenge of identifying "functional" variants that cause disease. However, evolutionary conservation can be used as a guide to indicate regions of noncoding or coding DNA that are likely to have biological function, and thus may be more likely to harbor SNP variants with functional consequences. To help bias marker selection in favor of such variants, we devised a process that prioritizes annotated SNPs for genotyping studies based on their location within Multi-species Conserved Sequences (MCSs and used this process to select SNPs in a region of linkage to a complex disease. This allowed us to evaluate the utility of the chosen SNPs for further association studies. Previously, a region of chromosome 1q43 was linked to Multiple Sclerosis (MS in a genome-wide screen. We chose annotated SNPs in the region based on location within MCSs (termed MCS-SNPs. We then obtained genotypes for 478 MCS-SNPs in 989 individuals from MS families. Results Analysis of our MCS-SNP genotypes from the 1q43 region and comparison to HapMap data confirmed that annotated SNPs in MCS regions are frequently polymorphic and show subtle signatures of selective pressure, consistent with previous reports of genome-wide variation in conserved regions. We also present an online tool that allows MCS data to be directly exported to the UCSC genome browser so that MCS-SNPs can be easily identified within genomic regions of

  14. Dense genetic linkage maps of three Populus species (Populus deltoides, P. nigra and P. trichocarpa) based on AFLP and microsatellite markers.

    Science.gov (United States)

    Cervera, M T; Storme, V; Ivens, B; Gusmão, J; Liu, B H; Hostyn, V; Van Slycken, J; Van Montagu, M; Boerjan, W

    2001-06-01

    Populus deltoides, P. nigra, and P. trichocarpa are the most important species for poplar breeding programs worldwide. In addition, Populus has become a model for fundamental research on trees. Linkage maps were constructed for these three species by analyzing progeny of two controlled crosses sharing the same female parent, Populus deltoides cv. S9-2 x P. nigra cv. Ghoy and P. deltoides cv. S9-2 x P. trichocarpa cv. V24. The two-way pseudotestcross mapping strategy was used to construct the maps. Amplified fragment length polymorphism (AFLP) markers that segregated 1:1 were used to form the four parental maps. Microsatellites and sequence-tagged sites were used to align homoeologous groups between the maps and to merge linkage groups within the individual maps. Linkage analysis and alignment of the homoeologous groups resulted in 566 markers distributed over 19 groups for P. deltoides covering 86% of the genome, 339 markers distributed over 19 groups for P. trichocarpa covering 73%, and 369 markers distributed over 28 groups for P. nigra covering 61%. Several tests for randomness showed that the AFLP markers were randomly distributed over the genome.

  15. Development of intron length polymorphism markers in genes encoding diketide-CoA synthase and curcumin synthase for discriminating Curcuma species.

    Science.gov (United States)

    Kita, Tomoko; Komatsu, Katsuko; Zhu, Shu; Iida, Osamu; Sugimura, Koji; Kawahara, Nobuo; Taguchi, Hiromu; Masamura, Noriya; Cai, Shao-Qing

    2016-03-01

    Various Curcuma rhizomes have been used as medicines or spices in Asia since ancient times. It is very difficult to distinguish them morphologically, especially when they are boiled and dried, which causes misidentification leading to a loss of efficacy. We developed a method for discriminating Curcuma species by intron length polymorphism markers in genes encoding diketide-CoA synthase and curcumin synthase. This method could apply to identification of not only fresh plants but also samples of crude drugs or edible spices. By applying this method to Curcuma specimens and samples, and constructing a dendrogram based on these markers, seven Curcuma species were clearly distinguishable. Moreover, Curcuma longa specimens were geographically distinguishable. On the other hand, Curcuma kwangsiensis (gl type) specimens also showed intraspecies polymorphism, which may have occurred as a result of hybridization with other Curcuma species. The molecular method we developed is a potential tool for global classification of the genus Curcuma. Copyright © 2015 Elsevier Ltd. All rights reserved.

  16. Isolation and characterization of microsatellite markers from the olive fly, Bactrocera oleae, and their cross-species amplification in the Tephritidae family

    Directory of Open Access Journals (Sweden)

    Kakani Evdoxia G

    2008-12-01

    Full Text Available Abstract Background The Tephritidae family of insects includes the most important agricultural pests of fruits and vegetables, belonging mainly to four genera (Bactrocera, Ceratitis, Anastrepha and Rhagoletis. The olive fruit fly, Bactrocera oleae, is the major pest of the olive fruit. Currently, its control is based on chemical insecticides. Environmentally friendlier methods have been attempted in the past (Sterile Insect Technique, albeit with limited success. This was mainly attributed to the lack of knowledge on the insect's behaviour, ecology and genetic structure of natural populations. The development of molecular markers could facilitate the access in the genome and contribute to the solution of the aforementioned problems. We chose to focus on microsatellite markers due to their abundance in the genome, high degree of polymorphism and easiness of isolation. Results Fifty-eight microsatellite-containing clones were isolated from the olive fly, Bactrocera oleae, bearing a total of sixty-two discrete microsatellite motifs. Forty-two primer pairs were designed on the unique sequences flanking the microsatellite motif and thirty-one of them amplified a PCR product of the expected size. The level of polymorphism was evaluated against wild and laboratory flies and the majority of the markers (93.5% proved highly polymorphic. Thirteen of them presented a unique position on the olive fly polytene chromosomes by in situ hybridization, which can serve as anchors to correlate future genetic and cytological maps of the species, as well as entry points to the genome. Cross-species amplification of these markers to eleven Tephritidae species and sequencing of thirty-one of the amplified products revealed a varying degree of conservation that declines outside the Bactrocera genus. Conclusion Microsatellite markers are very powerful tools for genetic and population analyses, particularly in species deprived of any other means of genetic analysis. The

  17. Isolation and characterization of microsatellite markers from the olive fly, Bactrocera oleae, and their cross-species amplification in the Tephritidae family

    Science.gov (United States)

    Augustinos, Antonios A; Stratikopoulos, Elias E; Drosopoulou, Eleni; Kakani, Evdoxia G; Mavragani-Tsipidou, Penelope; Zacharopoulou, Antigone; Mathiopoulos, Kostas D

    2008-01-01

    Background The Tephritidae family of insects includes the most important agricultural pests of fruits and vegetables, belonging mainly to four genera (Bactrocera, Ceratitis, Anastrepha and Rhagoletis). The olive fruit fly, Bactrocera oleae, is the major pest of the olive fruit. Currently, its control is based on chemical insecticides. Environmentally friendlier methods have been attempted in the past (Sterile Insect Technique), albeit with limited success. This was mainly attributed to the lack of knowledge on the insect's behaviour, ecology and genetic structure of natural populations. The development of molecular markers could facilitate the access in the genome and contribute to the solution of the aforementioned problems. We chose to focus on microsatellite markers due to their abundance in the genome, high degree of polymorphism and easiness of isolation. Results Fifty-eight microsatellite-containing clones were isolated from the olive fly, Bactrocera oleae, bearing a total of sixty-two discrete microsatellite motifs. Forty-two primer pairs were designed on the unique sequences flanking the microsatellite motif and thirty-one of them amplified a PCR product of the expected size. The level of polymorphism was evaluated against wild and laboratory flies and the majority of the markers (93.5%) proved highly polymorphic. Thirteen of them presented a unique position on the olive fly polytene chromosomes by in situ hybridization, which can serve as anchors to correlate future genetic and cytological maps of the species, as well as entry points to the genome. Cross-species amplification of these markers to eleven Tephritidae species and sequencing of thirty-one of the amplified products revealed a varying degree of conservation that declines outside the Bactrocera genus. Conclusion Microsatellite markers are very powerful tools for genetic and population analyses, particularly in species deprived of any other means of genetic analysis. The presented set of

  18. Extensive Chromosome Homoeology among Brassiceae Species Were Revealed by Comparative Genetic Mapping with High-Density EST-Based SNP Markers in Radish (Raphanus sativus L.)‡

    Science.gov (United States)

    Li, Feng; Hasegawa, Yoichi; Saito, Masako; Shirasawa, Sachiko; Fukushima, Aki; Ito, Toyoaki; Fujii, Hiroshi; Kishitani, Sachie; Kitashiba, Hiroyasu; Nishio, Takeshi

    2011-01-01

    A linkage map of expressed sequence tag (EST)-based markers in radish (Raphanus sativus L.) was constructed using a low-cost and high-efficiency single-nucleotide polymorphism (SNP) genotyping method named multiplex polymerase chain reaction–mixed probe dot-blot analysis developed in this study. Seven hundred and forty-six SNP markers derived from EST sequences of R. sativus were assigned to nine linkage groups with a total length of 806.7 cM. By BLASTN, 726 markers were found to have homologous genes in Arabidopsis thaliana, and 72 syntenic regions, which have great potential for utilizing genomic information of the model species A. thaliana in basic and applied genetics of R. sativus, were identified. By construction and analysis of the genome structures of R. sativus based on the 24 genomic blocks within the Brassicaceae ancestral karyotype, 23 of the 24 genomic blocks were detected in the genome of R. sativus, and half of them were found to be triplicated. Comparison of the genome structure of R. sativus with those of the A, B, and C genomes of Brassica species and that of Sinapis alba L. revealed extensive chromosome homoeology among Brassiceae species, which would facilitate transfer of the genomic information from one Brassiceae species to another. PMID:21816873

  19. Extensive chromosome homoeology among Brassiceae species were revealed by comparative genetic mapping with high-density EST-based SNP markers in radish (Raphanus sativus L.).

    Science.gov (United States)

    Li, Feng; Hasegawa, Yoichi; Saito, Masako; Shirasawa, Sachiko; Fukushima, Aki; Ito, Toyoaki; Fujii, Hiroshi; Kishitani, Sachie; Kitashiba, Hiroyasu; Nishio, Takeshi

    2011-10-01

    A linkage map of expressed sequence tag (EST)-based markers in radish (Raphanus sativus L.) was constructed using a low-cost and high-efficiency single-nucleotide polymorphism (SNP) genotyping method named multiplex polymerase chain reaction-mixed probe dot-blot analysis developed in this study. Seven hundred and forty-six SNP markers derived from EST sequences of R. sativus were assigned to nine linkage groups with a total length of 806.7 cM. By BLASTN, 726 markers were found to have homologous genes in Arabidopsis thaliana, and 72 syntenic regions, which have great potential for utilizing genomic information of the model species A. thaliana in basic and applied genetics of R. sativus, were identified. By construction and analysis of the genome structures of R. sativus based on the 24 genomic blocks within the Brassicaceae ancestral karyotype, 23 of the 24 genomic blocks were detected in the genome of R. sativus, and half of them were found to be triplicated. Comparison of the genome structure of R. sativus with those of the A, B, and C genomes of Brassica species and that of Sinapis alba L. revealed extensive chromosome homoeology among Brassiceae species, which would facilitate transfer of the genomic information from one Brassiceae species to another.

  20. Detection of genome donor species of neglected tetraploid crop Vigna reflexo-pilosa (creole bean, and genetic structure of diploid species based on newly developed EST-SSR markers from azuki bean (Vigna angularis.

    Directory of Open Access Journals (Sweden)

    Sompong Chankaew

    Full Text Available Vigna reflexo-pilosa, which includes a neglected crop, is the only one tetraploid species in genus Vigna. The ancestral species that make up this allotetraploid species have not conclusively been identified, although previous studies suggested that a donor genome of V. reflexo-pilosa is V. trinervia. In this study, 1,429 azuki bean EST-SSR markers were developed of which 38 EST-SSR primer pairs that amplified one product in diploid species and two discrete products in tetraploid species were selected to analyze 268 accessions from eight taxa of seven Asian Vigna species including V. reflexo-pilosa var. glabra, V. reflexo-pilosa var. reflexo-pilosa, V. exilis, V. hirtella, V. minima, V. radiata var. sublobata, V. tenuicaulis and V. trinervia to identify genome donor of V. reflexo-pilosa. Since both diploid and tetraploid species were analyzed and each SSR primer pair detected two loci in the tetraploid species, we separated genomes of the tetraploid species into two different diploid types, viz. A and B. In total, 445 alleles were detected by 38 EST-SSR markers. The highest gene diversity was observed in V. hirtella. By assigning the discrete PCR products of V. reflexo-pilosa into two distinguished genomes, we were able to identify the two genome donor parents of créole bean. Phylogenetic and principal coordinate analyses suggested that V. hirtella is a species complex and may be composed of at least three distinct taxa. Both analyses also clearly demonstrated that V. trinervia and one taxon of V. hirtella are the genome donors of V. reflexo-pilosa. Gene diversity indicates that the evolution rate of EST-SSRs on genome B of créole bean might be faster than that on genome A. Species relationship among the Vigna species in relation to genetic data, morphology and geographical distribution are presented.

  1. Evaluation of a novel 16S rRNA/tRNAVal mitochondrial marker for the identification and phylogenetic analysis of shrimp species belonging to the superfamily Penaeoidea.

    Science.gov (United States)

    Calo-Mata, Pilar; Pascoal, Ananias; Fernández-No, Inmaculada; Böhme, Karola; Gallardo, José M; Barros-Velázquez, Jorge

    2009-08-15

    In this study, we infer the phylogenetic relationships within commercial shrimp using sequence data from a novel mitochondrial marker consisting of an approximately 530-bp region of the 16S ribosomal RNA (rRNA)/transfer RNA (tRNA)(Val) genes compared with two other mitochondrial genes: 16S rRNA and cytochrome c oxidase I (COI). All three mitochondrial markers were considerably AT rich, exhibiting values up to 78.2% for the species Penaeus monodon in the 16S rRNA/tRNA(Val) genes, notably higher than the average among other Malacostracan mitochondrial genomes. Unlike the 16S rRNA and COI genes, the 16S rRNA/tRNA(Val) marker evidenced that Parapenaeus is more closely related to Metapenaeus than to Solenocera, a result that seems to be more in agreement with the taxonomic status of these genera. To our knowledge, our study using the 16S rRNA/tRNA(Val) gene as a marker for phylogenetic analysis offers the first genetic evidence to confirm that Pleoticus muelleri and Solenocera agassizi constitute a separate group and that they are more related to each other than to genera belonging to the family Penaeidae. The 16S rRNA/tRNA(Val) region was also found to contain more variable sites (56%) than the other two regions studied (33.4% for the 16S rRNA region and 42.7% for the COI region). The presence of more variable sites in the 16S rRNA/tRNA(Val) marker allowed the interspecific differentiation of all 19 species examined. This is especially useful at the commercial level for the identification of a large number of shrimp species, particularly when the lack of morphological characteristics prevents their differentiation.

  2. Parasitological and histological analysis of a new species of the genus Thalohanellus and description of a myxozoan parasite (Myxosporea: Bivalvulida from cultured ornamental goldfish, Carassius auratus L.

    Directory of Open Access Journals (Sweden)

    Mandira Saha

    2017-11-01

    Full Text Available An ornamental fish parasitological survey of West Bengal, India during the year 2014–16 revealed that goldfish, Carassius auratus, was the most susceptible species for myxozoan infestation. This communication revealed the presence of two myxosporean species belonging to the genera Myxobolus and Thelohanellus. Although myxozoan infestation has been determined by isolating small to large, spherical to ellipsoidal plasmodia up to 0.5–2.5 mm were filled with disporic pansporoblasts and mature spores. M. ichkeulensis and one new species T. dipaki n. sp. have been isolated infecting the ornamental goldfish (Carassius auratus for the first time in India. In the present study, new host, and new locality for M. ichkeulensis have been reported. The description of M. ichkeulensis is being considered as a first report from India. Spore of T. dipaki n. sp. measures uniquely 13.99 ± 0.60 × 9.82 ± 0.60 μm in size, having a one globular pyriform polar capsule measuring 7.45 ± 0.62 × 5.91 ± 0.39 μm. The severity of newly isolated myxozoan infestation has also been assessed by the histopathological changes of fins of the hostfish. A combination of light and scanning electron microscopic observation along with its severity of infestation, comparison of same and closely related species has been incorporated to identify the new species. The paper deals with the diversity, distribution and taxonomic descriptions of new and known myxozoan species along with new host, locality records and incidence of infestation.

  3. Assessment of Functional EST-SSR Markers (Sugarcane in Cross-Species Transferability, Genetic Diversity among Poaceae Plants, and Bulk Segregation Analysis

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    Shamshad Ul Haq

    2016-01-01

    Full Text Available Expressed sequence tags (ESTs are important resource for gene discovery, gene expression and its regulation, molecular marker development, and comparative genomics. We procured 10000 ESTs and analyzed 267 EST-SSRs markers through computational approach. The average density was one SSR/10.45 kb or 6.4% frequency, wherein trinucleotide repeats (66.74% were the most abundant followed by di- (26.10%, tetra- (4.67%, penta- (1.5%, and hexanucleotide (1.2% repeats. Functional annotations were done and after-effect newly developed 63 EST-SSRs were used for cross transferability, genetic diversity, and bulk segregation analysis (BSA. Out of 63 EST-SSRs, 42 markers were identified owing to their expansion genetics across 20 different plants which amplified 519 alleles at 180 loci with an average of 2.88 alleles/locus and the polymorphic information content (PIC ranged from 0.51 to 0.93 with an average of 0.83. The cross transferability ranged from 25% for wheat to 97.22% for Schlerostachya, with an average of 55.86%, and genetic relationships were established based on diversification among them. Moreover, 10 EST-SSRs were recognized as important markers between bulks of pooled DNA of sugarcane cultivars through BSA. This study highlights the employability of the markers in transferability, genetic diversity in grass species, and distinguished sugarcane bulks.

  4. Introgression evidence and phylogenetic relationships among three (ParaMisgurnus species as revealed by mitochondrial and nuclear DNA markers

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    Jakovlić I.

    2013-01-01

    Full Text Available The taxonomy of (ParaMisgurnus genera is still debated. We therefore used mitochondrial and nuclear DNA markers to analyze the phylogenetic relationships among Misgurnus anguillicaudatus, Paramisgurnus dabryanus and Misgurnus fossilis. Differing phylogenetic signals from mitochondrial and nuclear marker data suggest an introgression event in the history of M. anguillicaudatus and M. mohoity. No substantial genetic evidence was found that Paramisgurnus dabryanus should be classified as a separate genus.

  5. Molecular characterization of cultivated species of the genus Pachyrhizus Rich. ex DC. by AFLP markers

    DEFF Research Database (Denmark)

    Santayana, Monica; Rossel, Genoveva; Núñez, Jorge

    2014-01-01

    ) molecular markers in order to estimate genetic diversity and interspecific relationships. To complement molecular marker information, individuals from each accession were analyzed in order to confirmploidy levels. Eight AFLP primer combinations detected 136 (68.7 %) polymorphic bands. Shannon’s diversity...... diploid (2n=2x=22), which is characteristic of the tribe Phaseoleae. Finally, a misclassified accession of P. tuberosus was identified. Molecular characterization of accessions is necessary for efficient management of germplasm collections....

  6. HistologiQuiz

    DEFF Research Database (Denmark)

    Brent, Mikkel Bo

    2015-01-01

    HistologiQuiz er en quiz-app udviklet til almen og speciel histologi. Den består af mere end 1400 spørgsmål og over 320 histologiske billeder. Alle spørgsmål tager udgangspunkt i lærebogen Genesers Histologi af Annemarie Brüel m.fl.......HistologiQuiz er en quiz-app udviklet til almen og speciel histologi. Den består af mere end 1400 spørgsmål og over 320 histologiske billeder. Alle spørgsmål tager udgangspunkt i lærebogen Genesers Histologi af Annemarie Brüel m.fl....

  7. Genome size, cytogenetic data and transferability of EST-SSRs markers in wild and cultivated species of the genus Theobroma L. (Byttnerioideae, Malvaceae.

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    Rangeline Azevedo da Silva

    Full Text Available The genus Theobroma comprises several trees species native to the Amazon. Theobroma cacao L. plays a key economic role mainly in the chocolate industry. Both cultivated and wild forms are described within the genus. Variations in genome size and chromosome number have been used for prediction purposes including the frequency of interspecific hybridization or inference about evolutionary relationships. In this study, the nuclear DNA content, karyotype and genetic diversity using functional microsatellites (EST-SSR of seven Theobroma species were characterized. The nuclear content of DNA for all analyzed Theobroma species was 1C = ~ 0.46 pg. These species presented 2n = 20 with small chromosomes and only one pair of terminal heterochromatic bands positively stained (CMA+/DAPI- bands. The small size of Theobroma ssp. genomes was equivalent to other Byttnerioideae species, suggesting that the basal lineage of Malvaceae have smaller genomes and that there was an expansion of 2C values in the more specialized family clades. A set of 20 EST-SSR primers were characterized for related species of Theobroma, in which 12 loci were polymorphic. The polymorphism information content (PIC ranged from 0.23 to 0.65, indicating a high level of information per locus. Combined results of flow cytometry, cytogenetic data and EST-SSRs markers will contribute to better describe the species and infer about the evolutionary relationships among Theobroma species. In addition, the importance of a core collection for conservation purposes is highlighted.

  8. Genome size, cytogenetic data and transferability of EST-SSRs markers in wild and cultivated species of the genus Theobroma L. (Byttnerioideae, Malvaceae).

    Science.gov (United States)

    da Silva, Rangeline Azevedo; Souza, Gustavo; Lemos, Lívia Santos Lima; Lopes, Uilson Vanderlei; Patrocínio, Nara Geórgia Ribeiro Braz; Alves, Rafael Moysés; Marcellino, Lucília Helena; Clement, Didier; Micheli, Fabienne; Gramacho, Karina Peres

    2017-01-01

    The genus Theobroma comprises several trees species native to the Amazon. Theobroma cacao L. plays a key economic role mainly in the chocolate industry. Both cultivated and wild forms are described within the genus. Variations in genome size and chromosome number have been used for prediction purposes including the frequency of interspecific hybridization or inference about evolutionary relationships. In this study, the nuclear DNA content, karyotype and genetic diversity using functional microsatellites (EST-SSR) of seven Theobroma species were characterized. The nuclear content of DNA for all analyzed Theobroma species was 1C = ~ 0.46 pg. These species presented 2n = 20 with small chromosomes and only one pair of terminal heterochromatic bands positively stained (CMA+/DAPI- bands). The small size of Theobroma ssp. genomes was equivalent to other Byttnerioideae species, suggesting that the basal lineage of Malvaceae have smaller genomes and that there was an expansion of 2C values in the more specialized family clades. A set of 20 EST-SSR primers were characterized for related species of Theobroma, in which 12 loci were polymorphic. The polymorphism information content (PIC) ranged from 0.23 to 0.65, indicating a high level of information per locus. Combined results of flow cytometry, cytogenetic data and EST-SSRs markers will contribute to better describe the species and infer about the evolutionary relationships among Theobroma species. In addition, the importance of a core collection for conservation purposes is highlighted.

  9. Sequence analysis of the 3’-untranslated region of HSP70 (type I genes in the genus Leishmania: its usefulness as a molecular marker for species identification

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    Requena Jose M

    2012-04-01

    Full Text Available Abstract Background The Leishmaniases are a group of clinically diverse diseases caused by parasites of the genus Leishmania. To distinguish between species is crucial for correct diagnosis and prognosis as well as for treatment decisions. Recently, sequencing of the HSP70 coding region has been applied in phylogenetic studies and for identifying of Leishmania species with excellent results. Methods In the present study, we analyzed the 3’-untranslated region (UTR of Leishmania HSP70-type I gene from 24 strains representing eleven Leishmania species in the belief that this non-coding region would have a better discriminatory capacity for species typing than coding regions. Results It was observed that there was a remarkable degree of sequence conservation in this region, even between species of the subgenus Leishmania and Viannia. In addition, the presence of many microsatellites was a common feature of the 3´-UTR of HSP70-I genes in the Leishmania genus. Finally, we constructed dendrograms based on global sequence alignments of the analyzed Leishmania species and strains, the results indicated that this particular region of HSP70 genes might be useful for species (or species complex typing, improving for particular species the discrimination capacity of phylogenetic trees based on HSP70 coding sequences. Given the large size variation of the analyzed region between the Leishmania and Viannia subgenera, direct visualization of the PCR amplification product would allow discrimination between subgenera, and a HaeIII-PCR-RFLP analysis might be used for differentiating some species within each subgenera. Conclusions Sequence and phylogenetic analyses indicated that this region, which is readily amplified using a single pair of primers from both Old and New World Leishmania species, might be useful as a molecular marker for species discrimination.

  10. A Comparison of Microsatellites in Phytopathogenic Aspergillus Species in Order to Develop Markers for the Assessment of Genetic Diversity among Its Isolates.

    Science.gov (United States)

    Mahfooz, Sahil; Singh, Satyendra P; Mishra, Nishtha; Mishra, Aradhana

    2017-01-01

    The occurrence of Microsatellites (SSRs) has been witnessed in most of the fungal genomes however its abundance varies across species. In the present study, we analyzed the frequency of SSRs in the whole genome and transcripts of two phyto-pathogenic (Aspergillus niger and Aspergillus terreus) and compared them with two non-pathogenic (Aspergillus nidulans and Aspergillus oryzae) Aspergillus. Higher relative abundance and relative density of SSRs were observed in the whole genome and transcript sequences of the pathogenic Aspergillus when compared to the non-pathogenic. The relative abundance and density of SSRs were positively correlated with the G+C content of transcripts. Among the different classes of SSR, the percentage of tetra-nucleotide SSRs were maximum in A. niger (36.7%) and A. oryzae (35.9%) whereas A. nidulans and A. terreus preferred tri-nucleotide SSRs (38.2 and 42.1%) in whole genome sequences. In transcripts, tri-nucleotide SSRs were the most abundant whereas di-nucleotide SSRs were the least favored. Motif conservation study among the transcripts revealed conservation of only 27% motif within Aspergillus species. Furthermore, a similar relationship among the Ascomycetes was obtained on the basis of motif conservation and conserved genes (rDNA). To analyze the diversity present within the Indian isolates of Aspergillus, primers were successfully designed for 692 motifs in A. niger and A. terreus of which 20 were selected for diversity analysis. Among all the markers amplified, 10 markers (83.3%) were polymorphic, whereas remaining two markers (16.6%) were monomorphic. Ten polymorphic markers acquired in this investigation showed the utility of recently created SSR markers in the assessment of genetic diversity among various isolates of Aspergillus.

  11. Genome-Wide Discovery of Microsatellite Markers from Diploid Progenitor Species, Arachis duranensis and A. ipaensis, and Their Application in Cultivated Peanut (A. hypogaea

    Directory of Open Access Journals (Sweden)

    Chuanzhi Zhao

    2017-07-01

    Full Text Available Despite several efforts in the last decade toward development of simple sequence repeat (SSR markers in peanut, there is still a need for more markers for conducting different genetic and breeding studies. With the effort of the International Peanut Genome Initiative, the availability of reference genome for both the diploid progenitors of cultivated peanut allowed us to identify 135,529 and 199,957 SSRs from the A (Arachis duranensis and B genomes (Arachis ipaensis, respectively. Genome sequence analysis showed uneven distribution of the SSR motifs across genomes with variation in parameters such as SSR type, repeat number, and SSR length. Using the flanking sequences of identified SSRs, primers were designed for 51,354 and 60,893 SSRs with densities of 49 and 45 SSRs per Mb in A. duranensis and A. ipaensis, respectively. In silico PCR analysis of these SSR markers showed high transferability between wild and cultivated Arachis species. Two physical maps were developed for the A genome and the B genome using these SSR markers, and two reported disease resistance quantitative trait loci (QTLs, qF2TSWV5 for tomato spotted wilt virus (TSWV and qF2LS6 for leaf spot (LS, were mapped in the 8.135 Mb region of chromosome A04 of A. duranensis. From this genomic region, 719 novel SSR markers were developed, which provide the possibility for fine mapping of these QTLs. In addition, this region also harbors 652 genes and 49 of these are defense related genes, including two NB-ARC genes, three LRR receptor-like genes and three WRKY transcription factors. These disease resistance related genes could contribute to resistance to viral (such as TSWV and fungal (such as LS diseases in peanut. In summary, this study not only provides a large number of molecular markers for potential use in peanut genetic map development and QTL mapping but also for map-based gene cloning and molecular breeding.

  12. Clinico-Histologic Conferences: Histology and Disease

    Science.gov (United States)

    Shaw, Phyllis A.; Friedman, Erica S.

    2012-01-01

    Providing a context for learning information and requiring learners to teach specific content has been demonstrated to enhance knowledge retention. To enhance students' appreciation of the role of science and specifically histology in clinical reasoning, disease diagnosis, and treatment, a new teaching format was created to provide clinical…

  13. Comparison of genomes of eight species of sections Linum and Adenolinum from the genus Linum based on chromosome banding, molecular markers and RAPD analysis.

    Science.gov (United States)

    Muravenko, Olga V; Yurkevich, Olga Yu; Bolsheva, Nadezhda L; Samatadze, Tatiana E; Nosova, Inna V; Zelenina, Daria A; Volkov, Alexander A; Popov, Konstantin V; Zelenin, Alexander V

    2009-03-01

    Karyotypes of species sects. Linum and Adenolinum have been studied using C/DAPI-banding, Ag-NOR staining, FISH with 5S and 26S rDNA and RAPD analysis. C/DAPI-banding patterns enabled identification of all homologous chromosome pairs in the studied karyotypes. The revealed high similarity between species L. grandiflorum (2n = 16) and L. decumbens by chromosome and molecular markers proved their close genome relationship and identified the chromosome number in L. decumbens as 2n = 16. The similarity found for C/DAPI-banding patterns between species with the same chromosome numbers corresponds with the results obtained by RAPD-analysis, showing clusterization of 16-, 18- and 30-chromosome species into three separate groups. 5S rDNA and 26S rDNA were co-localized in NOR-chromosome 1 in the genomes of all species investigated. In 30-chromosome species, there were three separate 5S rDNA sites in chromosomes 3, 8 and 13. In 16-chromosome species, a separate 5S rDNA site was also located in chromosome 3, whereas in 18-chromosome species it was found in the long arm of NOR-chromosome 1. Thus, the difference in localization of rDNA sites in species with 2n = 16, 2n = 30 and 2n = 18 confirms taxonomists opinion, who attributed these species to different sects. Linum and Adenolinum, respectively. The obtained results suggest that species with 2n = 16, 2n = 18 and 2n = 30 originated from a 16-chromosome ancestor.

  14. Development of novel microsatellite markers for Holothurian scabra (Holothuriidae), Apostichopus japonicas (Stichopodidae) and cross-species testing in other sea cucumbers

    Science.gov (United States)

    Shangguan, Jingbo; Li, Zhongbao

    2017-06-01

    Thirty-five new microsatellite loci from the sea cucumbers Holothurian scabra (Jaeger, 1833) and Apostichopus japonicas (Selenka, 1867) were screened and characterized using the method of magnetic bead enrichment. Of the twenty-four polymorphic loci tested, eighteen were consistent with Hardy-Weinberg equilibrium after a modified false discovery rate (B-Y FDR) correction, whereas six showed statistically significant deviations (CHS2 and CHS11: P <0.014790; FCS1, FCS6, FCS8 and FCS14: P <0.015377). Furthermore, four species of plesiomorphous and related sea cucumbers (Holothurian scabra, Holothuria leucospilota, Stichopus horrens and Apostichopus japonicas) were tested for mutual cross-amplification using a total of ninety microsatellite loci. Although transferability and universality of all loci were generally low, the results of the cross-species study showed that the markers can be applied to identify individuals to species according to the presence or absence of specific microsatellite alleles. The microsatellite markers reported here will contribute to the study of genetic diversity, assisted breeding, and population conservation in sea cucumbers, as well as allow for the identification of individuals to closely related species.

  15. Genetic variation and relationships among Ulex (Fabaceae) species in southern Spain and northern Morocco assessed by chloroplast microsatellite (cpSSR) markers.

    Science.gov (United States)

    Cubas, Paloma; Pardo, Cristina; Tahiri, Hikmat

    2005-12-01

    Genetic variation in 27 populations of Ulex species from southern Spain and northern Morocco (Betic-Rif arc) was assessed using 11 chloroplast microsatellite (cpSSR) markers, which revealed 47 different haplotypes. These nonrecombinant, haploid markers allow measurement of genetic variation in closely related species of Ulex where molecular phylogenetic analyses have not provided a clear view of interspecific relationships. Discriminant analysis indicates that the haplotypes are useful to differentiate among species, and analysis of molecular variance (AMOVA) shows high levels of differentiation among populations. The minimum spanning tree (MST), that represents the connections between the haplotypes, suggests that the eastern Rifean U. africanus haplotypes are more genetically related than those from southern Spain. The latter may have lost genetic diversity while colonizing new habitats, eventually differentiating into U. baeticus and U. scaber. Hybridization between these populations, followed by polyploidization, may have originated the tetraploids (U. congestus and U. borgiae) that colonized new habitats associated with acidic rocks. Separate groupings of U. scaber populations may indicate multiple origins from different stocks. Diversification in this group of Ulex species could be related to the opening of the Alboran Sea by Middle Miocene, when the populations from Morocco and Spain became isolated from each other.

  16. Developing expressed sequence tag libraries and the discovery of simple sequence repeat markers for two species of raspberry (Rubus L.)

    Science.gov (United States)

    Background: Due to a relatively high level of codominant inheritance and transferability within and among taxonomic groups, simple sequence repeat (SSR) markers are important elements in comparative mapping and delineation of genomic regions associated with traits of economic importance. Expressed S...

  17. A microsatellite-based consensus linkage map for species of Eucalyptus and a novel set of 230 microsatellite markers for the genus

    Directory of Open Access Journals (Sweden)

    Williams Emlyn R

    2006-09-01

    Full Text Available Abstract Background Eucalypts are the most widely planted hardwood trees in the world occupying globally more than 18 million hectares as an important source of carbon neutral renewable energy and raw material for pulp, paper and solid wood. Quantitative Trait Loci (QTLs in Eucalyptus have been localized on pedigree-specific RAPD or AFLP maps seriously limiting the value of such QTL mapping efforts for molecular breeding. The availability of a genus-wide genetic map with transferable microsatellite markers has become a must for the effective advancement of genomic undertakings. This report describes the development of a novel set of 230 EMBRA microsatellites, the construction of the first comprehensive microsatellite-based consensus linkage map for Eucalyptus and the consolidation of existing linkage information for other microsatellites and candidate genes mapped in other species of the genus. Results The consensus map covers ~90% of the recombining genome of Eucalyptus, involves 234 mapped EMBRA loci on 11 linkage groups, an observed length of 1,568 cM and a mean distance between markers of 8.4 cM. A compilation of all microsatellite linkage information published in Eucalyptus allowed us to establish the homology among linkage groups between this consensus map and other maps published for E. globulus. Comparative mapping analyses also resulted in the linkage group assignment of other 41 microsatellites derived from other Eucalyptus species as well as candidate genes and QTLs for wood and flowering traits published in the literature. This report significantly increases the availability of microsatellite markers and mapping information for species of Eucalyptus and corroborates the high conservation of microsatellite flanking sequences and locus ordering between species of the genus. Conclusion This work represents an important step forward for Eucalyptus comparative genomics, opening stimulating perspectives for evolutionary studies and

  18. Species boundaries and host range of tortoise mites (Uropodoidea phoretic on bark beetles (Scolytinae, using morphometric and molecular markers.

    Directory of Open Access Journals (Sweden)

    Wayne Knee

    Full Text Available Understanding the ecology and evolutionary history of symbionts and their hosts requires accurate taxonomic knowledge, including clear species boundaries and phylogenies. Tortoise mites (Mesostigmata: Uropodoidea are among the most diverse arthropod associates of bark beetles (Curculionidae: Scolytinae, but their taxonomy and host associations are largely unstudied. We tested the hypotheses that (1 morphologically defined species are supported by molecular data, and that (2 bark beetle uropodoids with a broad host range comprise cryptic species. To do so, we assessed the species boundaries of uropodoid mites collected from 51 host species, across 11 countries and 103 sites, using morphometric data as well as partial cytochrome oxidase I (COI and nuclear large subunit ribosomal DNA (28S. Overall, morphologically defined species were confirmed by molecular datasets, with a few exceptions. Twenty-nine of the 36 uropodoid species (Trichouropoda, Nenteria and Uroobovella collected in this study had narrow host ranges, while seven species had putative broad host ranges. In all but one species, U. orri, our data supported the existence of these host generalists, which contrasts with the typical finding that widespread generalists are actually complexes of cryptic specialists.

  19. Species boundaries and host range of tortoise mites (Uropodoidea) phoretic on bark beetles (Scolytinae), using morphometric and molecular markers.

    Science.gov (United States)

    Knee, Wayne; Beaulieu, Frédéric; Skevington, Jeffrey H; Kelso, Scott; Cognato, Anthony I; Forbes, Mark R

    2012-01-01

    Understanding the ecology and evolutionary history of symbionts and their hosts requires accurate taxonomic knowledge, including clear species boundaries and phylogenies. Tortoise mites (Mesostigmata: Uropodoidea) are among the most diverse arthropod associates of bark beetles (Curculionidae: Scolytinae), but their taxonomy and host associations are largely unstudied. We tested the hypotheses that (1) morphologically defined species are supported by molecular data, and that (2) bark beetle uropodoids with a broad host range comprise cryptic species. To do so, we assessed the species boundaries of uropodoid mites collected from 51 host species, across 11 countries and 103 sites, using morphometric data as well as partial cytochrome oxidase I (COI) and nuclear large subunit ribosomal DNA (28S). Overall, morphologically defined species were confirmed by molecular datasets, with a few exceptions. Twenty-nine of the 36 uropodoid species (Trichouropoda, Nenteria and Uroobovella) collected in this study had narrow host ranges, while seven species had putative broad host ranges. In all but one species, U. orri, our data supported the existence of these host generalists, which contrasts with the typical finding that widespread generalists are actually complexes of cryptic specialists.

  20. Molecular genetic diversity assessment of Citrus species grown in Iran revealed by SSR, ISSR and CAPS molecular markers

    Directory of Open Access Journals (Sweden)

    Ata Allah Sharafi

    2017-12-01

    Full Text Available In this study, genetic diversity in 19 citrus cultivars was analyzed using Simple Sequence Repeat (SSR, Inter-simple Sequence Repeat (ISSR and cleaved amplified polymorphic sequence (CAPS markers. Nine primers for SSR, nine ISSR primers and two primers for CAPS were used for allele scoring. One chloroplast DNA region (rbcL-ORF106 and one mitochondrial DNA region (18S-5S were analyzed using cleaved amplified polymorphic sequence (CAPS marker in 19 citrus accessions grown in Iran. In total, 45 SSR and 131 ISSR polymorphic alleles and tree organelle genome types were detected. Cluster analysis of SSR and ISSR data was performed using UPGMA method and based on Jaccard's coefficient. The result of this investigation showed that the SSR and ISSR primers were highly informative and efficient in detecting genetic variability and relationships of the citrus accessions. And CAPS marker analysis Results showed that Bakraee and one of off type Mexican lime had banding pattern similar to Clementine Mandarin, while Pummelo regarded as maternal parent of other studied genotypes Citron regarded as father parent showed definite banding pattern among 19 studied genotypes which it confirmed Cytoplasmic inheritance from mother cellular organelles.

  1. Cryptic species, phenotypic plasticity, and complex life histories: Assessing deep-sea faunal diversity with molecular markers

    Science.gov (United States)

    Vrijenhoek, Robert C.

    2009-09-01

    Many new species of animals have been discovered during the past 40 years of deep-ocean exploration, particularly in chemosynthetic habitats such as hydrothermal vents and cold-water hydrocarbon seeps. Estimating species diversity in these environments is difficult, however, because insufficient sampling often fails to capture the range of organismic variability in time and space. Molecular systematic studies have revealed a number of taxonomic problems that derive from insufficient sampling and a shallow knowledge base regarding many deep-sea taxa. For example, numerous morphologically cryptic species exist among the vesicomyid clams and lepetodrilid limpets that dominate vents and seeps worldwide, suggesting that species richness may be significantly underestimated in these taxa. In contrast, discrete morphotypes of siboglinid tubeworms that are products of developmental plasticity were assigned synonymous species names. Also, distinct juvenile and adult forms of vent shrimp were assigned synonymous genus and species names. Though molecular studies have resolved many of these problems, they are not a panacea because they also suffer from insufficient sampling of taxa and genes, and from contamination of DNA sequences. Working carefully together, molecular and traditional systematists should eventually generate more accurate species lists that allow unbiased estimates of species richness in deep-sea environments.

  2. Systematic development of Phytophthora species-specific mitochondrial diagnostic markers for economically important members of the genus

    Science.gov (United States)

    The genus Phytophthora contains many invasive species to the USA that have the potential to cause significant damage to agriculture and native ecosystems. A genus and species-specific diagnostic assay was previously reported based on mitochondrial gene order differences that allowed for the systemat...

  3. Importance of ice algae and pelagic phytoplankton as food sources revealed by fatty acid trophic markers in a keystone species (Mytilus trossulus) from the High Arctic

    DEFF Research Database (Denmark)

    Thyrring, Jakob; Tremblay, Réjean; Sejr, Mikael Kristian

    2017-01-01

    composition in the hepatopancreas and in the gill tissue of an intertidal temperate keystone species (Mytilus trossulus) at its northernmost limit in Greenland (77°N). Fatty acid trophic markers (FATM) suggested that the diet mainly consisted of diatoms while the intertidal was covered by sea ice. During...... the following open-water period, food preferences shifted to pelagic dinoflagellates, and by the end of summer, food consisted of a diatom/dinoflagellates mixture. The contributions of macroalgae detritus, zooplankton and bacteria to the diet of M. trossulus were relatively low. We furthermore found that M...

  4. The substructure of three repetitive DNA regions of Schistosoma haematobium group species as a potential marker for species recognition and interbreeding detection.

    Science.gov (United States)

    Abbasi, Ibrahim; Webster, Bonnie L; King, Charles H; Rollinson, David; Hamburger, Joseph

    2017-08-01

    Schistosoma haematobium is the causative agent of human urogenital schistosomiasis affecting ~112 million people in Africa and the Middle East. The parasite is transmitted by snails of the genus Bulinus, which also transmit other closely related human and animal schistosomes. The accurate discrimination of S. haematobium from species infecting animals will aid effective control and elimination programs. Previously we have shown the utility of different repetitive nuclear DNA sequences (DraI, sh73bp, and sh77bp) for the identification of S. haematobium-group species and inter-repeat sequences for discriminating S. haematobium from S. bovis. In this current study we clarify the structural arrangement and association between the three repetitive sequences (DraI, sh73bp, and sh77bp) in both S. haematobium and S. bovis, with a unique repeat linker being found in S. haematobium (Sh64bp repeat linker) and in S. bovis (Sb30bp repeat linker). Sequence data showed that the 3'-end of the repeat linker was connected to the DraI repetitive sequence array, and at the 5'-end of the repeat linker sh73bp and sh77bp were arranged in an alternating manner. Species-specific oligonucleotides were designed targeting the species-specific repeat linkers and used in a reverse line blot (RLB) hybridization assay enabling differentiation between S. haematobium and S. bovis. The assay was used to discriminate natural infections in wild caught Bulinus globosus. This research enabled the characterisation of species-specific DNA regions that enabled the design of species-specific oligonucleotides that can be used to rapidly differentiate between S. haematobium and S. bovis and also have the potential to aid the detection of natural hybridization between these two species.

  5. Fast and sensitive determination of camel’s and goat's meat and milk using species-specific genetic markers

    OpenAIRE

    Abdel-Rahman S.M.; Elmaghraby A.M.; Haggag A.S.

    2015-01-01

    For the fast and sensitive determination of camel's and goat's meat and milk, species-specific regions (SSR) of follicle stimulating hormone receptor (FSHR) gene in both camel and goat were amplified using PCR technique. DNA was extracted from small amount of muscles (0.05 gm) and very little of fresh milk (100 μl) to amplify specific DNA sequences of FSHR gene in both camel and goat using designed species-specific primer pairs. PCR amplified fragment size ...

  6. The complete chloroplast genome of 17 individuals of pest species Jacobaea vulgaris: SNPs, microsatellites and barcoding markers for population and phylogenetic studies.

    Science.gov (United States)

    Doorduin, Leonie; Gravendeel, Barbara; Lammers, Youri; Ariyurek, Yavuz; Chin-A-Woeng, Thomas; Vrieling, Klaas

    2011-04-01

    Invasive individuals from the pest species Jacobaea vulgaris show different allocation patterns in defence and growth compared with native individuals. To examine if these changes are caused by fast evolution, it is necessary to identify native source populations and compare these with invasive populations. For this purpose, we are in need of intraspecific polymorphic markers. We therefore sequenced the complete chloroplast genomes of 12 native and 5 invasive individuals of J. vulgaris with next generation sequencing and discovered single-nucleotide polymorphisms (SNPs) and microsatellites. This is the first study in which the chloroplast genome of that many individuals within a single species was sequenced. Thirty-two SNPs and 34 microsatellite regions were found. For none of the individuals, differences were found between the inverted repeats. Furthermore, being the first chloroplast genome sequenced in the Senecioneae clade, we compared it with four other members of the Asteraceae family to identify new regions for phylogentic inference within this clade and also within the Asteraceae family. Five markers (ndhC-trnV, ndhC-atpE, rps18-rpl20, clpP and psbM-trnD) contained parsimony-informative characters higher than 2%. Finally, we compared two procedures of preparing chloroplast DNA for next generation sequencing.

  7. The Complete Chloroplast Genome Sequences of Aconitum pseudolaeve and Aconitum longecassidatum, and Development of Molecular Markers for Distinguishing Species in the Aconitum Subgenus Lycoctonum

    Directory of Open Access Journals (Sweden)

    Inkyu Park

    2017-11-01

    Full Text Available Aconitum pseudolaeve Nakai and Aconitum longecassidatum Nakai, which belong to the Aconitum subgenus Lycoctonum, are distributed in East Asia and Korea. Aconitum species are used in herbal medicine and contain highly toxic components, including aconitine. A. pseudolaeve, an endemic species of Korea, is a commercially valuable material that has been used in the manufacture of cosmetics and perfumes. Although Aconitum species are important plant resources, they have not been extensively studied, and genomic information is limited. Within the subgenus Lycoctonum, which includes A. pseudolaeve and A. longecassidatum, a complete chloroplast (CP genome is available for only one species, Aconitum barbatum Patrin ex Pers. Therefore, we sequenced the complete CP genomes of two Aconitum species, A. pseudolaeve and A. longecassidatum, which are 155,628 and 155,524 bp in length, respectively. Both genomes have a quadripartite structure consisting of a pair of inverted repeated regions (51,854 and 52,108 bp, respectively separated by large single-copy (86,683 and 86,466 bp and small single-copy (17,091 and 16,950 bp regions similar to those in other Aconitum CP genomes. Both CP genomes consist of 112 unique genes, 78 protein-coding genes, 4 ribosomal RNA (rRNA genes, and 30 transfer RNA (tRNA genes. We identified 268 and 277 simple sequence repeats (SSRs in A. pseudolaeve and A. longecassidatum, respectively. We also identified potential 36 species-specific SSRs, 53 indels, and 62 single-nucleotide polymorphisms (SNPs between the two CP genomes. Furthermore, a comparison of the three Aconitum CP genomes from the subgenus Lycoctonum revealed highly divergent regions, including trnK-trnQ, ycf1-ndhF, and ycf4-cemA. Based on this finding, we developed indel markers using indel sequences in trnK-trnQ and ycf1-ndhF. A. pseudolaeve, A. longecassidatum, and A. barbatum could be clearly distinguished using the novel indel markers AcoTT (Aconitum trnK-trnQ and Aco

  8. The Complete Chloroplast Genome Sequences of Aconitum pseudolaeve and Aconitum longecassidatum, and Development of Molecular Markers for Distinguishing Species in the Aconitum Subgenus Lycoctonum.

    Science.gov (United States)

    Park, Inkyu; Yang, Sungyu; Choi, Goya; Kim, Wook Jin; Moon, Byeong Cheol

    2017-11-21

    Aconitum pseudolaeve Nakai and Aconitum longecassidatum Nakai, which belong to the Aconitum subgenus Lycoctonum, are distributed in East Asia and Korea. Aconitum species are used in herbal medicine and contain highly toxic components, including aconitine. A. pseudolaeve, an endemic species of Korea, is a commercially valuable material that has been used in the manufacture of cosmetics and perfumes. Although Aconitum species are important plant resources, they have not been extensively studied, and genomic information is limited. Within the subgenus Lycoctonum, which includes A. pseudolaeve and A. longecassidatum, a complete chloroplast (CP) genome is available for only one species, Aconitum barbatum Patrin ex Pers. Therefore, we sequenced the complete CP genomes of two Aconitum species, A. pseudolaeve and A. longecassidatum, which are 155,628 and 155,524 bp in length, respectively. Both genomes have a quadripartite structure consisting of a pair of inverted repeated regions (51,854 and 52,108 bp, respectively) separated by large single-copy (86,683 and 86,466 bp) and small single-copy (17,091 and 16,950 bp) regions similar to those in other Aconitum CP genomes. Both CP genomes consist of 112 unique genes, 78 protein-coding genes, 4 ribosomal RNA (rRNA) genes, and 30 transfer RNA (tRNA) genes. We identified 268 and 277 simple sequence repeats (SSRs) in A. pseudolaeve and A. longecassidatum, respectively. We also identified potential 36 species-specific SSRs, 53 indels, and 62 single-nucleotide polymorphisms (SNPs) between the two CP genomes. Furthermore, a comparison of the three Aconitum CP genomes from the subgenus Lycoctonum revealed highly divergent regions, including trnK-trnQ, ycf1-ndhF, and ycf4-cemA. Based on this finding, we developed indel markers using indel sequences in trnK-trnQ and ycf1-ndhF. A. pseudolaeve, A. longecassidatum, and A. barbatum could be clearly distinguished using the novel indel markers AcoTT (Aconitum trnK-trnQ) and AcoYN (Aconitum

  9. Hyper-variable regions in 18S rDNA of Strongyloides spp. as markers for species-specific diagnosis.

    Science.gov (United States)

    Hasegawa, Hideo; Hayashida, Shotaro; Ikeda, Yatsukaho; Sato, Hiroshi

    2009-03-01

    Four hyper-variable regions (HVR-I to -IV) found in 18S ribosomal DNA sequences were compared among 34 isolates of 15 species of the genus Strongyloides to evaluate their diagnostic value. HVR-I to -III were short, and plural species exhibit the same nucleotide arrangement. Meanwhile, HVR-IV had 23 to 39 nucleotides, showing species-specific arrangements, except Strongyloides ransomi and Strongyloides venezuelensis, which had the same nucleotide sequence in HVR-IV but were readily distinguished by the difference in HVR-I and -III. Isolates of Strongyloides stercoralis from humans of USA, Japan, and Philippines, chimpanzees, and dogs had an identical sequence in this region. Meanwhile, intraspecific polymorphism in HVR-IV nucleotide arrangement was observed among isolates of Strongyloides fuelleborni and Strongyloides callosciureus, presumably reflecting process of geographical dispersal and adaptation to the hosts.

  10. Isolation and characterization of 29 microsatellite markers for the bumphead parrotfish, Bolbometopon muricatum, and cross amplification in 12 related species

    KAUST Repository

    Priest, Mark

    2014-10-14

    We isolated and characterized 29 microsatellite loci for the bumphead parrotfish, Bolbometopon muricatum, a wide-ranging parrotfish listed as vulnerable by the International Union for Conservation of Nature (IUCN). The 29 loci were tested on 95 individuals sampled from the Solomon Islands. The number of alleles ranged from two to ten. Evidence of linkage disequilibrium was found for only one pair of loci (Bm54 and Bm112). Two loci (Bm20 and Bm119) showed significant departure from Hardy-Weinberg equilibrium. We also tested each locus for amplification and polymorphism on 11 other scarine labrid species and one labrid species. Amplification success ranged from zero to ten loci per species. These microsatellite loci are the first specific set for B. muricatum and will be a useful tool for assessing genetic population structure, genetic diversity, and parentage in future studies.

  11. Identification of species-specific nuclear insertions of mitochondrial DNA (numts) in gorillas and their potential as population genetic markers

    Science.gov (United States)

    Clark Nicholas, Jonathan; Wildschutte Julia, Vera Halo; DiMattio, Kelly; Jensen-Seaman, Michael Ignatius; Anthony, Nicola Mary

    2014-01-01

    The first hyper-variable region (HV1) of the mitochondrial control region (MCR) has been widely used as a molecular tool in population genetics, but inadvertent amplification of nuclear translocated copies of mitochondrial DNA (numts) in gorillas has compromised the use of mitochondrial DNA in population genetic studies. At least three putative classes (I, II, III) of gorilla-specific HV1 MCR numts have been uncovered over the past decade. However, the number, size and location of numt loci in gorillas and other apes are completely unknown. Furthermore, little work to date has assessed the utility of numts as candidate population genetic markers. In the present study, we screened Bacterial Artificial Chromosome (BAC) genomic libraries in the chimpanzee and gorilla to compare patterns of mitochondrial-wide insertion in both taxa. We conducted an intensive BLAST search for numts in the gorilla genome and compared the prevalence of numt loci originating from the MCR with other great ape taxa. Additional gorilla-specific MCR numts were retrieved either through BAC library screens or using an anchored-PCR (A-PCR) amplification using genomic DNA from five unrelated gorillas. Locus-specific primers were designed to identify numt insertional polymorphisms and evaluate their potential as population genetic markers. Mitochondrial-wide surveys of chimpanzee and gorilla BACs showed that the number of numts does not differ between these two taxa. However, MCR numts are more abundant in chimpanzees than in other great apes. We identified and mapped 67 putative gorilla-specific numts, including two that contain the entire HV1 domain, cluster with sequences from two numt classes (I, IIb) and will likely co-amplify with mitochondrial sequences using most published HV1 primers. However, phylogenetic analysis coupled with post-hoc analysis of mitochondrial variation can successfully differentiate nuclear sequences. Insertional polymorphisms were evident in three out of five numts

  12. Chorismate mutase: an alternatively spliced parasitism gene and a diagnostic marker for three important Globodera nematode species

    Science.gov (United States)

    The chorismate mutase gene is widely distributed in both cyst and root-knot nematode species and believed to play a critical role in nematode parasitism. In this study, we cloned a new chorismate mutase gene (Gt-cm-1) from Globodera tabacum and further characterized the gene structure in both G. tab...

  13. Genome-assisted development of nuclear intergenic sequence markers for entomopathogenic fungi of the Metarhizium anisopliae species complex

    Science.gov (United States)

    Entomopathogenic fungi in the genus Metarhizium have proven useful for the biological control of economically important pests across the globe. Understanding the true diversity of this group is hampered by convergent morphologies between species. The application of molecular techniques has enabled...

  14. Detection of recent hybridization between sympatric Chilean Puya species (Bromeliaceae) using AFLP markers and reconstruction of complex relationships.

    Science.gov (United States)

    Schulte, Katharina; Silvestro, Daniele; Kiehlmann, Elke; Vesely, Sanja; Novoa, Patricio; Zizka, Georg

    2010-12-01

    The Chilean Puya species constitute a monophyletic group, co-occurring in different species combinations within the country and displaying a remarkable morphological variability. Here, we studied the importance of recent hybridization and introgression in the group and reconstructed the complex inter- and intraspecific relationships. Amplified fragment length polymorphism (AFLP) analysis, including 109 accessions of all Chilean Puya species and four putative hybrids, yielded 984 characters. Three main genetic groups were revealed, with the chilensis group (P. chilensis, P. gilmartiniae, P. boliviensis) diverging first, and the alpestris (P. alpestris, P. berteroniana) and coerulea group (P. venusta, P. coerulea) forming sister groups. STRUCTURE analyses confirmed a hybrid origin of morphologically intermediate individuals, and detected several additional hybrids. Hybrids were found between the chilensis and alpestris group, and between the alpestris and coerulea group. Exclusion of hybrids improved phylogenetic reconstructions. The study demonstrates that the detection of hybrids within Bromeliaceae can be difficult based on morphological characters alone and that efficient reproductive barriers may only slowly establish, leading to hybridization between closely related sympatric species. The importance of hybridization for the rapid diversification of Puya is discussed. Copyright © 2010 Elsevier Inc. All rights reserved.

  15. Development, cross-species/genera transferability of novel EST-SSR markers and their utility in revealing population structure and genetic diversity in sugarcane

    KAUST Repository

    Singh, Ram K.

    2013-07-01

    Sugarcane (Saccharum spp. hybrid) with complex polyploid genome requires a large number of informative DNA markers for various applications in genetics and breeding. Despite the great advances in genomic technology, it is observed in several crop species, especially in sugarcane, the availability of molecular tools such as microsatellite markers are limited. Now-a-days EST-SSR markers are preferred to genomic SSR (gSSR) as they represent only the functional part of the genome, which can be easily associated with desired trait. The present study was taken up with a new set of 351 EST-SSRs developed from the 4085 non redundant EST sequences of two Indian sugarcane cultivars. Among these EST-SSRs, TNR containing motifs were predominant with a frequency of 51.6%. Thirty percent EST-SSRs showed homology with annotated protein. A high frequency of SSRs was found in the 5\\'UTR and in the ORF (about 27%) and a low frequency was observed in the 3\\'UTR (about 8%). Two hundred twenty-seven EST-SSRs were evaluated, in sugarcane, allied genera of sugarcane and cereals, and 134 of these have revealed polymorphism with a range of PIC value 0.12 to 0.99. The cross transferability rate ranged from 87.0% to 93.4% in Saccharum complex, 80.0% to 87.0% in allied genera, and 76.0% to 80.0% in cereals. Cloning and sequencing of EST-SSR size variant amplicons revealed that the variation in the number of repeat-units was the main source of EST-SSR fragment polymorphism. When 124 sugarcane accessions were analyzed for population structure using model-based approach, seven genetically distinct groups or admixtures thereof were observed in sugarcane. Results of principal coordinate analysis or UPGMA to evaluate genetic relationships delineated also the 124 accessions into seven groups. Thus, a high level of polymorphism adequate genetic diversity and population structure assayed with the EST-SSR markers not only suggested their utility in various applications in genetics and genomics in

  16. De novo assembly and characterization of leaf transcriptome for the development of functional molecular markers of the extremophile multipurpose tree species Prosopis alba.

    Science.gov (United States)

    Torales, Susana L; Rivarola, Máximo; Pomponio, María F; Gonzalez, Sergio; Acuña, Cintia V; Fernández, Paula; Lauenstein, Diego L; Verga, Aníbal R; Hopp, H Esteban; Paniego, Norma B; Poltri, Susana N Marcucci

    2013-10-14

    Prosopis alba (Fabaceae) is an important native tree adapted to arid and semiarid regions of north-western Argentina which is of great value as multipurpose species. Despite its importance, the genomic resources currently available for the entire Prosopis genus are still limited. Here we describe the development of a leaf transcriptome and the identification of new molecular markers that could support functional genetic studies in natural and domesticated populations of this genus. Next generation DNA pyrosequencing technology applied to P. alba transcripts produced a total of 1,103,231 raw reads with an average length of 421 bp. De novo assembling generated a set of 15,814 isotigs and 71,101 non-assembled sequences (singletons) with an average of 991 bp and 288 bp respectively. A total of 39,000 unique singletons were identified after clustering natural and artificial duplicates from pyrosequencing reads.Regarding the non-redundant sequences or unigenes, 22,095 out of 54,814 were successfully annotated with Gene Ontology terms. Moreover, simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs) were searched, resulting in 5,992 and 6,236 markers, respectively, throughout the genome. For the validation of the the predicted SSR markers, a subset of 87 SSRs selected through functional annotation evidence was successfully amplified from six DNA samples of seedlings. From this analysis, 11 of these 87 SSRs were identified as polymorphic. Additionally, another set of 123 nuclear polymorphic SSRs were determined in silico, of which 50% have the probability of being effectively polymorphic. This study generated a successful global analysis of the P. alba leaf transcriptome after bioinformatic and wet laboratory validations of RNA-Seq data.The limited set of molecular markers currently available will be significantly increased with the thousands of new markers that were identified in this study. This information will strongly contribute to genomics

  17. Molecular differentiation of three loach species (Pisces, Cobitidae) based on the nuclear 5S rDNA marker.

    Science.gov (United States)

    Kirtiklis, Lech; Boroń, Alicja; Ptasznik, Piotr; Lusková, Vera; Lusk, Stanislav

    2011-01-01

    The diversity of the 5S rDNA fragment among three loach species: Cobitis taenia, C. elongatoides and Sabanejewia aurata was investigated using universal PCR primers for this gene. Three amplification products were obtained: 220 bp length for C. taenia and C. elongatoides, and 330 bp for S. aurata. Two amplicons with the same length (in Cobitis) were digested with TaqI restriction endonuclease. This enzyme found one restriction site T/CGA in the C. elongatoides fragment, while in the case of C. taenia no cleavage effect was observed. On this basis we constructed an easy and cheap method for loach species discrimination. It seems adequate for effective support of conservation initiatives for endangered loaches.

  18. Microsatellite markers for the relict tree Aextoxicon punctatum: the only species in the Chilean endemic family Aextoxicaceae.

    Science.gov (United States)

    Núñez-Ávila, Mariela C; Uriarte, María; Marquet, Pablo A; Armesto, Juan J

    2011-02-01

    We screened 10 microsatellite loci for the dioecious, rainforest tree Aextoxicon punctatum, a species belonging to a monotypic family and genus, endemic to southwestern South America (30-43°S). Polymorphisms were evaluated in 108 adult trees from four populations, including the northern and southern extremes of the geographic range of Aextoxicon in Chile. All 10 microsatellites revealed polymorphic variation. A total of 69, 57, 59, and 69 alleles were found in 40 (Fray Jorge), 19 (Santa Ines), 21 (Quebrada del Tigre), and 28 (Guabun) individual trees, respectively. The mean expected heterozygosity per population ranged from 0.70 to 0.72. These polymorphic microsatellites will be useful in assessing the genetic structure and conservation status of Aextoxicon throughout its historically fragmented geographic range. Parentage analysis will provide additional insights into the key historical and contemporary processes that have mediated population differentiation in this species.

  19. Transcriptomic Analysis of the Endangered Neritid Species Clithon retropictus: De Novo Assembly, Functional Annotation, and Marker Discovery

    Directory of Open Access Journals (Sweden)

    So Young Park

    2016-07-01

    Full Text Available An aquatic gastropod belonging to the family Neritidae, Clithon retropictus is listed as an endangered class II species in South Korea. The lack of information on its genomic background limits the ability to obtain functional data resources and inhibits informed conservation planning for this species. In the present study, the transcriptomic sequencing and de novo assembly of C. retropictus generated a total of 241,696,750 high-quality reads. These assembled to 282,838 unigenes with mean and N50 lengths of 736.9 and 1201 base pairs, respectively. Of these, 125,616 unigenes were subjected to annotation analysis with known proteins in Protostome DB, COG, GO, and KEGG protein databases (BLASTX; E ≤ 0.00001 and with known nucleotides in the Unigene database (BLASTN; E ≤ 0.00001. The GO analysis indicated that cellular process, cell, and catalytic activity are the predominant GO terms in the biological process, cellular component, and molecular function categories, respectively. In addition, 2093 unigenes were distributed in 107 different KEGG pathways. Furthermore, 49,280 simple sequence repeats were identified in the unigenes (>1 kilobase sequences. This is the first report on the identification of transcriptomic and microsatellite resources for C. retropictus, which opens up the possibility of exploring traits related to the adaptation and acclimatization of this species.

  20. Transcriptomic Analysis of the Endangered Neritid Species Clithon retropictus: De Novo Assembly, Functional Annotation, and Marker Discovery.

    Science.gov (United States)

    Park, So Young; Patnaik, Bharat Bhusan; Kang, Se Won; Hwang, Hee-Ju; Chung, Jong Min; Song, Dae Kwon; Sang, Min Kyu; Patnaik, Hongray Howrelia; Lee, Jae Bong; Noh, Mi Young; Kim, Changmu; Kim, Soonok; Park, Hong Seog; Lee, Jun Sang; Han, Yeon Soo; Lee, Yong Seok

    2016-07-22

    An aquatic gastropod belonging to the family Neritidae, Clithon retropictus is listed as an endangered class II species in South Korea. The lack of information on its genomic background limits the ability to obtain functional data resources and inhibits informed conservation planning for this species. In the present study, the transcriptomic sequencing and de novo assembly of C. retropictus generated a total of 241,696,750 high-quality reads. These assembled to 282,838 unigenes with mean and N50 lengths of 736.9 and 1201 base pairs, respectively. Of these, 125,616 unigenes were subjected to annotation analysis with known proteins in Protostome DB, COG, GO, and KEGG protein databases (BLASTX; E ≤ 0.00001) and with known nucleotides in the Unigene database (BLASTN; E ≤ 0.00001). The GO analysis indicated that cellular process, cell, and catalytic activity are the predominant GO terms in the biological process, cellular component, and molecular function categories, respectively. In addition, 2093 unigenes were distributed in 107 different KEGG pathways. Furthermore, 49,280 simple sequence repeats were identified in the unigenes (>1 kilobase sequences). This is the first report on the identification of transcriptomic and microsatellite resources for C. retropictus, which opens up the possibility of exploring traits related to the adaptation and acclimatization of this species.

  1. Transferability of simple sequence repeat (SSR) markers developed in guava (Psidium guajava L.) to four Myrtaceae species.

    Science.gov (United States)

    Rai, Manoj K; Phulwaria, Mahendra; Shekhawat, N S

    2013-08-01

    Present study demonstrated the cross-genera transferability of 23 simple sequence repeat (SSR) primer pairs developed for guava (Psidium guajava L.) to four new targets, two species of eucalypts (Eucalyptus citriodora, Eucalyptus camaldulensis), bottlebrush (Callistemon lanceolatus) and clove (Syzygium aromaticum), belonging to the family Myrtaceae and subfamily Myrtoideae. Off the 23 SSR loci assayed, 18 (78.2%) gave cross-amplification in E. citriodora, 14 (60.8%) in E. camaldulensis and 17-17 (73.9%) in C. lanceolatus and S. aromaticum. Eight primer pairs were found to be transferable to all four species. The number of alleles detected at each locus ranged from one to nine, with an average of 4.8, 2.6, 4.5 and 4.6 alleles in E. citriodora, E. camaldulensis, C. lanceolatus and S. aromaticum, respectively. The high levels of cross-genera transferability of guava SSRs may be applicable for the analysis of intra- and inter specific genetic diversity of target species, especially in E. citriodora, C. lanceolatus and S. aromaticum, for which till date no information about EST-derived as well as genomic SSR is available.

  2. Clinical and Histologic Mimickers of Celiac Disease.

    Science.gov (United States)

    Kamboj, Amrit K; Oxentenko, Amy S

    2017-08-17

    Celiac disease is an autoimmune disorder of the small bowel, classically associated with diarrhea, abdominal pain, and malabsorption. The diagnosis of celiac disease is made when there are compatible clinical features, supportive serologic markers, representative histology from the small bowel, and response to a gluten-free diet. Histologic findings associated with celiac disease include intraepithelial lymphocytosis, crypt hyperplasia, villous atrophy, and a chronic inflammatory cell infiltrate in the lamina propria. It is important to recognize and diagnose celiac disease, as strict adherence to a gluten-free diet can lead to resolution of clinical and histologic manifestations of the disease. However, many other entities can present with clinical and/or histologic features of celiac disease. In this review article, we highlight key clinical and histologic mimickers of celiac disease. The evaluation of a patient with serologically negative enteropathy necessitates a carefully elicited history and detailed review by a pathologist. Medications can mimic celiac disease and should be considered in all patients with a serologically negative enteropathy. Many mimickers of celiac disease have clues to the underlying diagnosis, and many have a targeted therapy. It is necessary to provide patients with a correct diagnosis rather than subject them to a lifetime of an unnecessary gluten-free diet.

  3. The Characteristics of Cytochrome C Oxidase Gene Subunit I in Wild Silkmoth Cricula trifenestrata Helfer and Its Evaluation for Species Marker

    Directory of Open Access Journals (Sweden)

    Suriana

    2012-08-01

    Full Text Available The study was conducted to assess the characteristics of partial gene of cytochrome C oxidase subunit I (COI of wild silkmoth Cricula trifenestrata, and to detect the diagnostic sites from these gene for evaluation as species marker. A total of fifteen larvae of C. tifenestrata were collected from Bogor, Purwakarta, and Bantul Regencies. Genomic DNA was extracted from silk gland of individual larvae, then amplified by PCR method and sequenced. DNA sequencing was done to characterize their nucleotide and amino acid contents. The results showed that 595 nucleotides at the 5 ‘end of COI gene of C. tifenestrata was conserved at the species level, but varies at the family level. Nucleotide dominated by thymine and adenine bases (± 70%. There were 25 diagnostic sites for C. tifenestrata, and four diagnostic sites for genus level. One hundred eigthty nine (189 amino acids were alignment, and only one percent of the genes was varied among species. The 107th amino acid (valine and 138th (threonine were diagnostics amino acid for C. tifenestrata. Based on nucleotides and amino acids sequences, the phylogeny showed that C. tifenestrata lied on the same nodes with Antheraea, so the Saturniidae family is monophyletic.

  4. Validation of quantitative polymerase chain reaction methodology for monitoring DNA as a surrogate marker for species material contamination in porcine heparin.

    Science.gov (United States)

    Auguste, C; Dereux, S; Rousset, M; Anger, P

    2012-07-01

    Heparin is a widely used intravenous anticoagulant comprising of a very complex mixture of glycosaminoglycan chains, mainly derived from porcine intestinal mucosa. The species of origin and the absence of contaminants from other species are important determinants of the different physicochemical characteristics of heparin. They also determine the potential for introducing infectious and adventitious agents into heparin batches destined for medicinal use. We perform routine quantitative polymerase chain reaction (Q-PCR) release tests to confirm the quality of all crude heparin batches, including those used for the manufacture of enoxaparin sodium. Here we further demonstrate that the assessment of the DNA content in crude heparin is a good surrogate marker of contamination at the mucosa level. After spiking porcine mucosa with ovine mucosa and processing this material to form crude heparin, we were able to observe similar ratios of species-specific DNA in both the starting and end products. Experiments performed with 3,000 and 1,500 ppm contamination found these concentrations to be well above the detection limit for our assay of heparin batches. Additionally this Q-PCR method can be used to detect contamination in mucosa, thus providing a tool capable of monitoring for contaminants throughout the crude heparin manufacturing process. Q-PCR analysis of industrial crude heparin samples has confirmed over time the value of this method to assess the pure porcine origin of heparin.

  5. Comparison of histological features, and description of histopathological lesions in thyroid glands from three species of free-ranging sharks from the northwestern Atlantic, the blue shark, Prionace glauca (L.), the shortfin mako, Isurus oxyrhinchus Rafinesque, and the thresher, Alopias vulpinus (Bonnaterre).

    Science.gov (United States)

    Borucinska, J D; Tafur, M

    2009-09-01

    Abstract Histomorphological features of piscine thyroids are widely accepted and frequently used as bioindicators of environmental pollution. This despite the fact that there is marked variation in thyroid morphology resulting from numerous pathological and physiological conditions. Our hypothesis was that there will be variations in histological features in thyroids collected from different shark species during the summer season in the northwestern Atlantic. To test our hypothesis, we examined histological features encountered in grossly normal thyroids from three species of sharks, the shortfin mako, Isurus oxyrhinchus, thresher, Alopias vulpinus and blue sharks, Prionace glauca. In addition, microscopic lesions from these thyroids were described. Ninety-four sharks were collected in summer 2001, 2002 and 2004. Routine, haematoxylin and eosin-stained paraffin-embedded sections were studied by light microscopy. We found inter-species but not intra-species variation in histological patterns of thyroids, which were distinct enough to allow 'blind' assignment of a thyroid to the specific species. The most common lesions encountered were lymphofollicular hyperplasia and chronic thyroiditis. In addition, one case each of intravascular larval nematodes and a myxosporean infection was found. Our results provide the first data on species-specific morphology of thyroids collected during summer months from sharks. The results indicate that familiarity with normal thyroid morphology is crucial before using shark thyroids in biomonitoring of environmental contamination or interpreting data from this gland in shark-health studies.

  6. Textbook of comparative histology

    National Research Council Canada - National Science Library

    Andrew, W

    1959-01-01

    ... made to their environment over the course of the eons during which life has existed on this earth. In this sense, it is hoped that the study of Comparative Histology will be accepted as a desirable part of a liberal education...

  7. Gastritis: the histology report.

    Science.gov (United States)

    Rugge, Massimo; Pennelli, Gianmaria; Pilozzi, Emanuela; Fassan, Matteo; Ingravallo, Giuseppe; Russo, Valentina M; Di Mario, Francesco

    2011-03-01

    Gastritis is defined as inflammation of the gastric mucosa. In histological terms, it is distinguishable into two main categories, i.e. non-atrophic and atrophic. In the gastric mucosa, atrophy is defined as the loss of appropriate glands. There are several etiological types of gastritis, their different etiology being related to different clinical manifestations and pathological features. Atrophic gastritis (resulting mainly from long-standing Helicobacter pylori infection) is a major risk factor for the onset of (intestinal type) gastric cancer. The extent and site of the atrophic changes correlate significantly with the cancer risk. The current format for histology reporting in cases of gastritis fails to establish an immediate link between gastritis phenotype and risk of malignancy. Building on current knowledge of the biology of gastritis, an international group of pathologists [Operative Link for Gastritis Assessment (OLGA)] has proposed a system for reporting gastritis in terms of its stage (the OLGA Staging System): this system places the histological phenotypes of gastritis on a scale of progressively increasing gastric cancer risk, from the lowest (Stage 0) to the highest (Stage IV). The aim of this tutorial is to provide unequivocal information on how to standardize histology reports on gastritis in diagnostic practice. Copyright © 2011 Editrice Gastroenterologica Italiana S.r.l. Published by Elsevier Ltd.. All rights reserved.

  8. Histologic classification of gliomas

    NARCIS (Netherlands)

    Perry, Arie; Wesseling, Pieter|info:eu-repo/dai/nl/157872866

    2016-01-01

    Gliomas form a heterogeneous group of tumors of the central nervous system (CNS) and are traditionally classified based on histologic type and malignancy grade. Most gliomas, the diffuse gliomas, show extensive infiltration in the CNS parenchyma. Diffuse gliomas can be further typed as astrocytic,

  9. Channel catfish BAC-end sequences for marker development and assessment of syntenic conservation with other fish species.

    Science.gov (United States)

    Xu, P; Wang, S; Liu, L; Peatman, E; Somridhivej, B; Thimmapuram, J; Gong, G; Liu, Z

    2006-08-01

    In the present study, 25 195 BAC ends for channel catfish (Ictalurus punctatus) were sequenced, generating 20 366 clean BAC-end sequences (BES), with an average read length of 557 bp after trimming. A total of 11 414 601 bp were generated, representing approximately 1.2% of the catfish genome. Based on this survey, the catfish genome was found to be highly AT-rich, with 60.7% A+T and 39.3% G+C. Approximately 12% of the catfish genome consisted of dispersed repetitive elements, with the Tc1/mariner transposons making up the largest percentage by base pair (4.57%). Microsatellites were detected in 17.5% of BES. Catfish BACs were anchored to the zebrafish and Tetraodon genome sequences by BLASTN, generating 16% and 8.2% significant hits (E < e(-5)) respectively. A total of 1074 and 773 significant hits were unique to the zebrafish and Tetraodon genomes, respectively, of which 417 and 406, respectively, were identified as known genes in other species, providing a major genome resource for comparative genomic mapping.

  10. Characterization of Global Transcriptome Using Illumina Paired-End Sequencing and Development of EST-SSR Markers in Two Species of Gynostemma (Cucurbitaceae).

    Science.gov (United States)

    Zhao, Yue-Mei; Zhou, Tao; Li, Zhong-Hu; Zhao, Gui-Fang

    2015-11-30

    Gynostemma pentaphyllum is an important medicinal herb of the Cucurbitaceae family, but limited genomic data have hindered genetic studies. In this study, transcriptomes of two closely-related Gynostemma species, Gynostemma cardiospermum and G. pentaphyllum, were sequenced using Illumina paired-end sequencing technology. A total of 71,607 nonredundant unigenes were assembled. Of these unigenes, 60.45% (43,288) were annotated based on sequence similarity search with known proteins. A total of 11,059 unigenes were identified in the Kyoto Encyclopedia of Genes and Genomes Pathway (KEGG) database. A total of 3891 simple sequence repeats (SSRs) were detected in 3526 nonredundant unigenes, 2596 primer pairs were designed and 360 of them were randomly selected for validation. Of these, 268 primer pairs yielded clear products among six G. pentaphyllum samples. Thirty polymorphic SSR markers were used to test polymorphism and transferability in Gynostemma. Finally, 15 SSR makers that amplified in all 12 Gynostemma species were used to assess genetic diversity. Our results generated a comprehensive sequence resource for Gynostemma research.

  11. Low support for separate species within the redpoll complex (Carduelis flammea-hornemanni-cabaret) from analyses of mtDNA and microsatellite markers.

    Science.gov (United States)

    Marthinsen, Gunnhild; Wennerberg, Liv; Lifjeld, Jan T

    2008-06-01

    The redpoll complex, consisting of three currently recognized species (Carduelis flammea, C. hornemanni and C. cabaret), is polytypic in biometry, morphology, physiology and behaviour. However, previous genetic work has not revealed any indications of genetic differentiation. We analysed sequence variation in the mtDNA control region, and allele frequencies of supposedly faster evolving microsatellites (n=10), in an attempt to detect molecular genetic support for the three species, as well as two subspecies of C. flammea (ssp. flammea and rostrata), within this complex. We used samples from two subspecies of the twite (Carduelis flavirostris, ssp. flavirostris and rufostrigata) as outgroup. We found no structure among redpoll individuals in mtDNA haplotypes or microsatellite allele frequencies, and only marginal differences between redpoll taxa in analyses of molecular variance (AMOVAs) of predefined groups. In contrast, the two twite subspecies constituted two well-supported monophyletic groups. Our study thus strengthens previous indications of low genetic support for current redpoll taxa. Two major alternative interpretations exist. Either redpolls form a single gene pool with geographical polymorphisms possibly explained by Bergmann's and Gloger's rules, or there are separate gene pools of recent origin but with too little time elapsed for genetic differentiation to have evolved in the investigated markers. Future studies should therefore examine whether reproductive isolation mechanisms and barriers to gene flow exist in areas with sympatric breeding.

  12. Analysis of genetic diversity and population structure of oil palm (Elaeis guineensis) from China and Malaysia based on species-specific simple sequence repeat markers.

    Science.gov (United States)

    Zhou, L X; Xiao, Y; Xia, W; Yang, Y D

    2015-12-08

    Genetic diversity and patterns of population structure of the 94 oil palm lines were investigated using species-specific simple sequence repeat (SSR) markers. We designed primers for 63 SSR loci based on their flanking sequences and conducted amplification in 94 oil palm DNA samples. The amplification result showed that a relatively high level of genetic diversity was observed between oil palm individuals according a set of 21 polymorphic microsatellite loci. The observed heterozygosity (Ho) was 0.3683 and 0.4035, with an average of 0.3859. The Ho value was a reliable determinant of the discriminatory power of the SSR primer combinations. The principal component analysis and unweighted pair-group method with arithmetic averaging cluster analysis showed the 94 oil palm lines were grouped into one cluster. These results demonstrated that the oil palm in Hainan Province of China and the germplasm introduced from Malaysia may be from the same source. The SSR protocol was effective and reliable for assessing the genetic diversity of oil palm. Knowledge of the genetic diversity and population structure will be crucial for establishing appropriate management stocks for this species.

  13. Nuclear markers support the mitochondrial phylogeny of Vipera ursinii-renardi complex (Squamata: Viperidae) and species status for the Greek meadow viper.

    Science.gov (United States)

    Mizsei, Edvárd; Jablonski, Daniel; Roussos, Stephanos A; Dimaki, Maria; Ioannidis, Yannis; Nilson, Göran; Nagy, Zoltán T

    2017-01-31

    Meadow vipers (Vipera ursinii-renardi complex) are small-bodied snakes that live in either lowland grasslands or montane subalpine-alpine meadows spanning a distribution from France to western China. This complex has previously been the focus of several taxonomic studies which were based mainly on morphological, allozyme or immunological characters and did not clearly resolve the relationships between the various taxa. Recent mitochondrial DNA analyses found unexpected relationships within the complex which had taxonomical consequences for the detected lineages. The most surprising was the basal phylogenetic position of Vipera ursinii graeca, a taxon described almost 30 years ago from the mountains of Greece. We present here new analyses of three nuclear markers (BDNF, NT3, PRLR; a first for studies of meadow and steppe vipers) as well as analyses of newly obtained mitochondrial DNA sequences (CYT B, ND4).Our Bayesian analyses of nuclear sequences are concordant with previous studies of mitochondrial DNA, in that the phylogenetic position of the graeca clade is a clearly distinguished and distinct lineage separated from all other taxa in the complex. These phylogenetic results are also supported by a distinct morphology, ecology and isolated distribution of this unique taxon. Based on several data sets and an integrative species concept we recommend to elevate this taxon to species level: Vipera graeca Nilson & Andrén, 1988 stat. nov.

  14. Differential gene flow of mitochondrial and nuclear DNA markers among chromosomal races of Australian morabine grasshoppers (Vandiemenella, viatica species group).

    Science.gov (United States)

    Kawakami, T; Butlin, R K; Adams, M; Saint, K M; Paull, D J; Cooper, S J B

    2007-12-01

    Recent theoretical developments have led to a renewed interest in the potential role of chromosomal rearrangements in speciation. Australian morabine grasshoppers (genus Vandiemenella, viatica species group) provide an excellent study system to test this potential role of chromosomal rearrangements because they show extensive chromosomal variation and formed the basis of a classic chromosomal speciation model. There are three chromosomal races, viatica19, viatica17, and P24(XY), on Kangaroo Island, South Australia, forming five parapatric populations with four putative contact zones among them. We investigate the extent to which chromosomal variation among these populations may be associated with barriers to gene flow. Population genetic and phylogeographical analyses using 15 variable allozyme loci and the elongation factor-1alpha (EF-1alpha) gene indicate that the three races represent genetically distinct taxa. In contrast, analyses of the mitochondrial cytochrome c oxidase subunit I (COI) gene show the presence of three distinctive and geographically localized groups that do not correspond with the distribution of the chromosomal races. These discordant population genetic patterns are likely to result from introgressive hybridization between the chromosomal races and range expansions/contractions. Overall, these results suggest that reduction of nuclear gene flow may be associated with chromosomal variation, or underlying genetic variation linked with chromosomal variation, whereas mitochondrial gene flow appears to be independent of this variation in these morabine grasshoppers. The identification of an intact contact zone between P24(XY) and viatica17 offers considerable potential for further investigation of molecular mechanisms that maintain distinct nuclear genomes among the chromosomal races.

  15. Developing Universal Genetic Tools for Rapid and Efficient Deletion Mutation in Vibrio Species Based on Suicide T-Vectors Carrying a Novel Counterselectable Marker, vmi480.

    Directory of Open Access Journals (Sweden)

    Peng Luo

    Full Text Available Despite that Vibrio spp. have a significant impact on the health of humans and aquatic animals, the molecular basis of their pathogenesis is little known, mainly due to the limited genetic tools for the functional research of genes in Vibrio. In some cases, deletion of target DNAs in Vibrio can be achieved through the use of suicide vectors. However, these strategies are time-consuming and lack universality, and the widely used counterselectable gene sacB does not work well in Vibrio cells. In this study, we developed universal genetic tools for rapid and efficient deletion mutations in Vibrio species based on suicide T-Vectors carrying a novel counterselectable marker, vmi480. We explored two uncharacterized genes, vmi480 and vmi470, in a genomic island from Vibrio mimicus VM573 and confirmed that vmi480 and vmi470 constitute a two-component toxin-antitoxin system through deletion and expression of vmi480 and vmi470. The product of vmi480 exhibited strong toxicity to Escherichia coli cells. Based on vmi480 and the PBAD or PTAC promoter system, we constructed two suicide T-vectors, pLP11 and pLP12, and each of these vectors contained a multiple cloning region with two AhdI sites. Both vectors linearized by AhdI digestion could be stored and directly ligated with purified PCR products without a digestion step. By using pLP11 and pLP12 coupled with a highly efficient conjugation system provided by E. coli β2163, six genes from four representative Vibrio species were easily deleted. By using the counterselective marker vmi480, we obtained 3-12 positive colonies (deletion mutants among no more than 20 colonies randomly selected on counterselection plates. The strategy does not require the digestion of PCR products and suicide vectors every time, and it avoids large-scale screening colonies on counterselective plates. These results demonstrate that we successfully developed universal genetic tools for rapid and efficient gene deletion in Vibrio

  16. Genome survey of pistachio (Pistacia vera L.) by next generation sequencing: Development of novel SSR markers and genetic diversity in Pistacia species.

    Science.gov (United States)

    Ziya Motalebipour, Elmira; Kafkas, Salih; Khodaeiaminjan, Mortaza; Çoban, Nergiz; Gözel, Hatice

    2016-12-07

    Pistachio (Pistacia vera L.) is one of the most important nut crops in the world. There are about 11 wild species in the genus Pistacia, and they have importance as rootstock seed sources for cultivated P. vera and forest trees. Published information on the pistachio genome is limited. Therefore, a genome survey is necessary to obtain knowledge on the genome structure of pistachio by next generation sequencing. Simple sequence repeat (SSR) markers are useful tools for germplasm characterization, genetic diversity analysis, and genetic linkage mapping, and may help to elucidate genetic relationships among pistachio cultivars and species. To explore the genome structure of pistachio, a genome survey was performed using the Illumina platform at approximately 40× coverage depth in the P. vera cv. Siirt. The K-mer analysis indicated that pistachio has a genome that is about 600 Mb in size and is highly heterozygous. The assembly of 26.77 Gb Illumina data produced 27,069 scaffolds at N50 = 3.4 kb with a total of 513.5 Mb. A total of 59,280 SSR motifs were detected with a frequency of 8.67 kb. A total of 206 SSRs were used to characterize 24 P. vera cultivars and 20 wild Pistacia genotypes (four genotypes from each five wild Pistacia species) belonging to P. atlantica, P. integerrima, P. chinenesis, P. terebinthus, and P. lentiscus genotypes. Overall 135 SSR loci amplified in all 44 cultivars and genotypes, 41 were polymorphic in six Pistacia species. The novel SSR loci developed from cultivated pistachio were highly transferable to wild Pistacia species. The results from a genome survey of pistachio suggest that the genome size of pistachio is about 600 Mb with a high heterozygosity rate. This information will help to design whole genome sequencing strategies for pistachio. The newly developed novel polymorphic SSRs in this study may help germplasm characterization, genetic diversity, and genetic linkage mapping studies in the genus Pistacia.

  17. The species origin of the cellular microenvironment influences markers of beta cell fate and function in EndoC-βH1 cells.

    Science.gov (United States)

    Jeffery, N; Richardson, S; Beall, C; Harries, L W

    2017-12-15

    Interaction between islet cell subtypes and the extracellular matrix influences beta-cell function in mammals. The tissue architecture of rodent islets is very different to that of human islets; cell-to-cell communication and interaction with the extracellular matrix may vary between species. In this work, we have compared the responses of the human EndoC-βH1 cell line to non-human and human-derived growth matrices in terms of growth morphology, gene expression and glucose-stimulated insulin secretion (GSIS). EndoC-βH1 cells demonstrated a greater tendency to form cell clusters when cultured in a human microenvironment and exhibited reduced alpha cell markers at the mRNA level; mean expression difference - 0.23 and - 0.51; p = 0.009 and 0.002 for the Aristaless-related homeobox (ARX) and Glucagon (GCG) genes respectively. No differences were noted in the protein expression of mature beta cell markers such as Pdx1 and NeuroD1 were noted in EndoC-βH1 cells grown in a human microenvironment but cells were however more sensitive to glucose (4.3-fold increase in insulin secretion following glucose challenge compared with a 1.9-fold increase in cells grown in a non-human microenvironment; p = 0.0003). Our data suggests that the tissue origin of the cellular microenvironment has effects on the function of EndoC-βH1 cells in vitro, and the use of a more human-like culture microenvironment may bring benefits in terms of increased physiological relevance. Copyright © 2017 Elsevier Inc. All rights reserved.

  18. Conversion of chromosome-specific RAPDs into SCAR-based anchor markers for onion linkage maps and its application to genetic analyses inother Allium species

    NARCIS (Netherlands)

    Masuzaki, S.; Miyazaki, T.; McCallum, J.; Heusden, van A.W.; Kik, C.; Yamashita, K.; Tashiro, Y.

    2008-01-01

    Integration of previously developed Allium cepa linkage maps requires the availability of anchor markers for each of the eight chromosomes of shallot (A. cepa L. common group Aggregatum). To this end, eight RAPD markers originating from our previous research were converted into SCAR markers via

  19. Biomarcadores histológicos em duas espécies de bagres estuarinos da Costa Maranhense, Brasil Histology biomarkers in two estuarine catfish species from the Maranhense Coast, Brazil

    Directory of Open Access Journals (Sweden)

    D.B.P.Sousa

    2013-04-01

    Full Text Available Neste estudo objetivou-se validar lesões branquiais como biomarcadores em peixes de importância econômica (Sciades herzbergii e Bagre bagre capturados pela pesca artesanal em dois locais diferenciados da Baía de São Marcos, MA, a fim de selecionar um táxon como bioindicador capaz de ser utilizado em programas de biomonitoramento. O primeiro ponto (S1 foi utilizado como uma área de referência - Ilha dos Caranguejos -, e o segundo ponto (S2 foi considerado potencialmente impactado - Complexo Portuário de São Luís, MA. Encontraram-se várias alterações histológicas para as duas espécies em S2, destacando-se: estreitamento lamelar, teleangectasia, fusão e descolamento do epitélio da lamela secundária. Lesões branquiais em B. bagre coletados em S1 também foram observadas, não sendo possível diferenciar os indivíduos das duas áreas analisadas. Os dados indicam que S. herzbergii é um bioindicador mais apropriado para análise de biomarcadores de contaminação aquática.This study aimed to validate branchial lesions as a biomarker in fish (Sciades herzbergii and Bagre bagre caught by traditional fishing in two different places at São Marcos Bay, MA, in order to select a bioindicator taxon which can be used in biomonitoring programs. The first point (S1 was used as a reference area - Caranguejos (Crab Island and the second point (S2 was considered potentially impacted - Port Complex of São Luis, MA. Several histological changes were found for both species in S2, including: narrowing lamellar, teleangectasy, fusion and separation of secondary lamellar epithelium. Gill lesions in B. bagre collected were also observed in S1, it is not possible to differentiate between individuals of the two areas analyzed. The data indicate that S. herzbergii is more appropriate as a bioindicator for analysis of biomarkers of aquatic contamination.

  20. New gSSR and EST-SSR markers reveal high genetic diversity in the invasive plant Ambrosia artemisiifolia L. and can be transferred to other invasive Ambrosia species.

    Science.gov (United States)

    Meyer, Lucie; Causse, Romain; Pernin, Fanny; Scalone, Romain; Bailly, Géraldine; Chauvel, Bruno; Délye, Christophe; Le Corre, Valérie

    2017-01-01

    Ambrosia artemisiifolia L., (common ragweed), is an annual invasive and highly troublesome plant species originating from North America that has become widespread across Europe. New sets of genomic and expressed sequence tag (EST) based simple sequence repeats (SSRs) markers were developed in this species using three approaches. After validation, 13 genomic SSRs and 13 EST-SSRs were retained and used to characterize the genetic diversity and population genetic structure of Ambrosia artemisiifolia populations from the native (North America) and invasive (Europe) ranges of the species. Analysing the mating system based on maternal families did not reveal any departure from complete allogamy and excess homozygosity was mostly due the presence of null alleles. High genetic diversity and patterns of genetic structure in Europe suggest two main introduction events followed by secondary colonization events. Cross-species transferability of the newly developed markers to other invasive species of the Ambrosia genus was assessed. Sixty-five percent and 75% of markers, respectively, were transferable from A. artemisiifolia to Ambrosia psilostachya and Ambrosia tenuifolia. 40% were transferable to Ambrosia trifida, this latter species being seemingly more phylogenetically distantly related to A. artemisiifolia than the former two.

  1. Isolation and characterization of polymorphic microsatellite markers in Tetranychus urticae and cross amplification in other Tetranychidae and Phytoseiidae species of economic importance.

    Science.gov (United States)

    Sabater-Muñoz, B; Pascual-Ruiz, S; Gómez-Martínez, M A; Jacas, J A; Hurtado, M A

    2012-05-01

    Tetranychus urticae Koch is a cosmopolitan phytophagous mite considered as the most polyphagous species among spider mites. Population genetic studies using molecular markers such as microsatellites have proven to be extremely informative to address questions about population structure, phylogeography and host preferences. The aim of this study was to increase the available molecular tools to gain insight into the genetic structure of T. urticae populations of citrus orchards, which might help in their management. Five microsatellite DNA libraries were developed using probes with the motifs CT, CTT, GT and CAC following the FIASCO protocol. Positive clones, those that included the insert with the microsatellite, were detected using the PIMA-PCR technique. Combinations of primers were designed on 22 out of 32 new microsatellites loci and their polymorphism was tested in four populations sampled along the eastern coast of Spain. Eleven successful amplifications were obtained. Cross amplification was tested in the tetranychids Aphlonobia histricina, Eutetranychus banksi, E. orientalis, Oligonychus perseae, Panonychus citri, Tetranychus evansi, T. okinawanus and T. turkestani, and the phytoseiids Amblyseius swirskii, A. cucumeris, A. andersoni, Euseius stipulatus, Neoseiulus barkeri, N. californicus, Phytoseiulus persimilis and Typhlodromus phialatus. Eight successful cross amplifications were obtained.

  2. Radiocarbon as a bio marker of urban pollution in leaves of evergreen species sampled in Rome and in rural areas (Lazio-Central Italy)

    Energy Technology Data Exchange (ETDEWEB)

    Alessio, M.; Improta, S. [La Sapienza University, Rome (Italy). Department of Physics; Anselmi, S. [University of Molise, Isernia (Italy). Department of Sciences and Technologies for the Environment; Conforto, L.; Manfra, L. [La Sapienza University, Rome (Italy). Department of Earth Sciences; Manes, F. [La Sapienza University, Rome (Italy). Department of Plant Biology

    2002-11-01

    The aim of the present study is the use of {sup 14}C, sampled in leaves of evergreen species, as a natural geochemical marker to estimate the contribution of artificial sources (heating plants, vehicles, etc.) to the complex of atmospheric gases in an urban environment. Leaves were chosen due to sampling easiness and their reliability: in particular the evergreen species, being exposed all the year round to pollutants are especially indicated for bioindication and biomonitoring studies. The response to atmospheric pollutants has been studied of two plant species (Quercus ilex L., Pinus pinea L.) measuring isotopic ({sup 14}r, {delta}{sup 13}C), chemical (Pb concentration) and ecophysiological (gaseous exchange and leaf fluorescence of chlorophyll a) parameters. Leaves of holm-oaks and stone pine needles collected over a 3-year time span in an urban park in Rome (Villa Ada) and in reference localities outside the city on the Tyrrhenian coast and in the pre-Appennine area have been analysed. In Villa Ada measurements were carried out along a transect from the road bordering the park towards the interior; all the parameters, together in agreement, showed a decreasing pollution gradient towards the inner park. It was possible to estimate a 5.5{+-}0.3% contribution of CO{sub 2} from fossil fuels close to the road, decreasing to 1.7{+-}0.3% at <300 m from it towards the inner park. The isotopic analyses conducted on stone pines and holm-oaks show that {sup 14}C provides indications on the degree of pollution from fossil fuels, while {delta}{sup 13}C appears to be conditioned mainly by the interspecific difference, and also by many other environmental factors that affect the plant functionality. Results confirmed that radiocarbon is a useful tool in environmental studies, allowing to quantify the contributions of CO{sub 2} of anthropic origin: this parameter, together with appropriate isotopic, chemical and ecophysiological analyses, could provide a good indication of the

  3. Age-specific gene expression signatures for breast tumors and cross-species conserved potential cancer progression markers in young women.

    Science.gov (United States)

    Colak, Dilek; Nofal, Asmaa; Albakheet, Albandary; Nirmal, Maimoona; Jeprel, Hatim; Eldali, Abdelmoneim; Al-Tweigeri, Taher; Tulbah, Asma; Ajarim, Dahish; Malik, Osama Al; Inan, Mehmet S; Kaya, Namik; Park, Ben H; Bin Amer, Suad M

    2013-01-01

    Breast cancer in young women is more aggressive with a poorer prognosis and overall survival compared to older women diagnosed with the disease. Despite recent research, the underlying biology and molecular alterations that drive the aggressive nature of breast tumors associated with breast cancer in young women have yet to be elucidated. In this study, we performed transcriptomic profile and network analyses of breast tumors arising in Middle Eastern women to identify age-specific gene signatures. Moreover, we studied molecular alterations associated with cancer progression in young women using cross-species comparative genomics approach coupled with copy number alterations (CNA) associated with breast cancers from independent studies. We identified 63 genes specific to tumors in young women that showed alterations distinct from two age cohorts of older women. The network analyses revealed potential critical regulatory roles for Myc, PI3K/Akt, NF-κB, and IL-1 in disease characteristics of breast tumors arising in young women. Cross-species comparative genomics analysis of progression from pre-invasive ductal carcinoma in situ (DCIS) to invasive ductal carcinoma (IDC) revealed 16 genes with concomitant genomic alterations, CCNB2, UBE2C, TOP2A, CEP55, TPX2, BIRC5, KIAA0101, SHCBP1, UBE2T, PTTG1, NUSAP1, DEPDC1, HELLS, CCNB1, KIF4A, and RRM2, that may be involved in tumorigenesis and in the processes of invasion and progression of disease. Array findings were validated using qRT-PCR, immunohistochemistry, and extensive in silico analyses of independently performed microarray datasets. To our knowledge, this study provides the first comprehensive genomic analysis of breast cancer in Middle Eastern women in age-specific cohorts and potential markers for cancer progression in young women. Our data demonstrate that cancer appearing in young women contain distinct biological characteristics and deregulated signaling pathways. Moreover, our integrative genomic and cross-species

  4. The Susan G. Komen for the Cure Tissue Bank at the IU Simon Cancer Center: a unique resource for defining the "molecular histology" of the breast

    National Research Council Canada - National Science Library

    Sherman, Mark E; Figueroa, Jonine D; Henry, Jill E; Clare, Susan E; Rufenbarger, Connie; Storniolo, Anna Maria

    2012-01-01

    "Molecular histology" of the breast may be conceptualized as encompassing the normative ranges of histologic structure and marker expression in normal breast tissues in relation to a woman's age and life experiences...

  5. Conflicting patterns of genetic structure produced by nuclear and mitochondrial markers in the Oregon Slender Salamander (Batrachoseps wrighti): implications for conservation efforts and species management

    Science.gov (United States)

    Miller, Mark; Haig, Susan M.; Wagner, R.S.

    2005-01-01

    Endemic to Oregon in the northwestern US, the Oregon slender salamander (Batrachoseps wrighti) is a terrestrial plethodontid found associated with late successional mesic forests. Consequently, forest management practices such as timber harvesting may impact their persistence. Therefore, to infer possible future effects of these practices on population structure and differentiation, we used mitochondrial DNA sequences (cytochrome b) and RAPD markers to analyze 22 populations across their range. Phylogenetic analyses of sequence data (774 bp) revealed two historical lineages corresponding to northern and southern-distributed populations. Relationships among haplotypes and haplotype diversity within lineages suggested that the northern region may have more recently been colonized compared to the southern region. In contrast to the mitochondrial data, analyses of 46 RAPD loci suggested an overall pattern of isolation-by-distance in the set of populations examined and no particularly strong clustering of populations based on genetic distances. We propose two non-exclusive hypotheses to account for discrepancies between mitochondrial and nuclear data sets. First, our data may reflect an overall ancestral pattern of isolation-by-distance that has subsequently been influenced by vicariance. Alternately, our analyses may suggest that male-mediated gene flow and female philopatry are important contributors to the pattern of genetic diversity. We discuss the importance of distinguishing between these two hypotheses for the purposes of identifying conservation units and note that, regardless of the relative contribution of each mechanism towards the observed pattern of diversity, protection of habitat will likely prove critical for the long-term persistence of this species.

  6. Source apportionment of carbonaceous chemical species to fossil fuel combustion, biomass burning and biogenic emissions by a coupled radiocarbon-levoglucosan marker method

    Science.gov (United States)

    Salma, Imre; Németh, Zoltán; Weidinger, Tamás; Maenhaut, Willy; Claeys, Magda; Molnár, Mihály; Major, István; Ajtai, Tibor; Utry, Noémi; Bozóki, Zoltán

    2017-11-01

    An intensive aerosol measurement and sample collection campaign was conducted in central Budapest in a mild winter for 2 weeks. The online instruments included an FDMS-TEOM, RT-OC/EC analyser, DMPS, gas pollutant analysers and meteorological sensors. The aerosol samples were collected on quartz fibre filters by a low-volume sampler using the tandem filter method. Elemental carbon (EC), organic carbon (OC), levoglucosan, mannosan, galactosan, arabitol and mannitol were determined, and radiocarbon analysis was performed on the aerosol samples. Median atmospheric concentrations of EC, OC and PM2.5 mass were 0.97, 4.9 and 25 µg m-3, respectively. The EC and organic matter (1.6 × OC) accounted for 4.8 and 37 %, respectively, of the PM2.5 mass. Fossil fuel (FF) combustion represented 36 % of the total carbon (TC = EC + OC) in the PM2.5 size fraction. Biomass burning (BB) was a major source (40 %) for the OC in the PM2.5 size fraction, and a substantial source (11 %) for the PM10 mass. We propose and apply here a novel, straightforward, coupled radiocarbon-levoglucosan marker method for source apportionment of the major carbonaceous chemical species. The contributions of EC and OC from FF combustion (ECFF and OCFF) to the TC were 11.0 and 25 %, respectively, EC and OC from BB (ECBB and OCBB) were responsible for 5.8 and 34 %, respectively, of the TC, while the OC from biogenic sources (OCBIO) made up 24 % of the TC. The overall relative uncertainty of the OCBIO and OCBB contributions was assessed to be up to 30 %, while the relative uncertainty for the other apportioned species is expected to be below 20 %. Evaluation of the apportioned atmospheric concentrations revealed some of their important properties and relationships among them. ECFF and OCFF were associated with different FF combustion sources. Most ECFF was emitted by vehicular road traffic, while the contribution of non-vehicular sources such as domestic and industrial heating or cooking using gas, oil or coal

  7. Marker chromosomes.

    Science.gov (United States)

    Rao, Kiran Prabhaker; Belogolovkin, Victoria

    2013-04-01

    Marker chromosomes are a morphologically heterogeneous group of structurally abnormal chromosomes that pose a significant challenge in prenatal diagnosis. Phenotypes associated with marker chromosomes are highly variable and range from normal to severely abnormal. Clinical outcomes are very difficult to predict when marker chromosomes are detected prenatally. In this review, we outline the classification, etiology, cytogenetic characterization, and clinical consequences of marker chromosomes, as well as practical approaches to prenatal diagnosis and genetic counseling.

  8. Serum markers of liver fibrosis

    DEFF Research Database (Denmark)

    Veidal, Sanne Skovgård; Bay-Jensen, Anne-Christine; Tougas, Gervais

    2010-01-01

    BACKGROUND: Fibrosis is a central histological feature of chronic liver diseases and is characterized by the accumulation and reorganization of the extracellular matrix. The gold standard for assessment of fibrosis is histological evaluation of a percutaneous liver biopsy. Albeit a considerable......-epitopes, may be targeted for novel biochemical marker development in fibrosis. We used the recently proposed BIPED system (Burden of disease, Investigative, Prognostic, Efficacy and Diagnostic) to characterise present serological markers. METHODS: Pubmed was search for keywords; Liver fibrosis, neo......, a systematic use of the neo-epitope approach, i.e. the quantification of peptide epitopes generated from enzymatic cleavage of proteins during extracellular remodeling, may prove productive in the quest to find new markers of liver fibrosis....

  9. Comparative histological studies on the intestinal wall between the prenatal, the postnatal and the adult of the two species of Egyptian bats. Frugivorous Rousettus aegyptiacus and insectivorous Taphozous nudiventris

    Directory of Open Access Journals (Sweden)

    Atteyat Selim

    2015-05-01

    Full Text Available The present study was planned to find the effect of different feeding habits on the structure of the duodenum and small intestine of adult, prenatal and postnatal of both fructivorous Rousettus aegyptiacus and the insectivorous Taphozous nudiventris using the histological and the histochemical techniques. Histologically, the duodenal wall of R. aegyptiacus and T. nudiventris is composed of the typical layers: mucosa, submucosa, muscularis and serosa, we observed that the mucosa with finger like villi and very sharp apices in prenatal and adult of R. aegyptiacus but compact finger like villi in T. nudiventris. Scattered among the columnar epithelium goblet cells which less numerous in R. aegyptiacus than in T. nudiventris. Brunner’s glands are less numerous also in R. aegyptiacus than in T. nudiventris. In postnatal the mucosa with pyramidal like villi in R. aegyptiacus and finger like villi in T. nudiventris. In ileum the intestinal glands are less numerous in R. aegyptiacus than in T. nudiventris. In prenatal the goblet cells are less developed in R. aegyptiacus and T. nudiventris. The intestinal glands are less developed also in R. aegyptiacus and T. nudiventris but in the postnatal the goblet cells and the intestinal gland are few in number in both R. aegyptiacus and T. nudiventris.

  10. Source apportionment of carbonaceous chemical species to fossil fuel combustion, biomass burning and biogenic emissions by a coupled radiocarbon–levoglucosan marker method

    Directory of Open Access Journals (Sweden)

    I. Salma

    2017-11-01

    Full Text Available An intensive aerosol measurement and sample collection campaign was conducted in central Budapest in a mild winter for 2 weeks. The online instruments included an FDMS-TEOM, RT-OC/EC analyser, DMPS, gas pollutant analysers and meteorological sensors. The aerosol samples were collected on quartz fibre filters by a low-volume sampler using the tandem filter method. Elemental carbon (EC, organic carbon (OC, levoglucosan, mannosan, galactosan, arabitol and mannitol were determined, and radiocarbon analysis was performed on the aerosol samples. Median atmospheric concentrations of EC, OC and PM2.5 mass were 0.97, 4.9 and 25 µg m−3, respectively. The EC and organic matter (1.6  ×  OC accounted for 4.8 and 37 %, respectively, of the PM2.5 mass. Fossil fuel (FF combustion represented 36 % of the total carbon (TC  =  EC + OC in the PM2.5 size fraction. Biomass burning (BB was a major source (40 % for the OC in the PM2.5 size fraction, and a substantial source (11 % for the PM10 mass. We propose and apply here a novel, straightforward, coupled radiocarbon–levoglucosan marker method for source apportionment of the major carbonaceous chemical species. The contributions of EC and OC from FF combustion (ECFF and OCFF to the TC were 11.0 and 25 %, respectively, EC and OC from BB (ECBB and OCBB were responsible for 5.8 and 34 %, respectively, of the TC, while the OC from biogenic sources (OCBIO made up 24 % of the TC. The overall relative uncertainty of the OCBIO and OCBB contributions was assessed to be up to 30 %, while the relative uncertainty for the other apportioned species is expected to be below 20 %. Evaluation of the apportioned atmospheric concentrations revealed some of their important properties and relationships among them. ECFF and OCFF were associated with different FF combustion sources. Most ECFF was emitted by vehicular road traffic, while the contribution of non-vehicular sources such as

  11. Histologic Mimics of Basal Cell Carcinoma.

    Science.gov (United States)

    Stanoszek, Lauren M; Wang, Grace Y; Harms, Paul W

    2017-11-01

    - Basal cell carcinoma (BCC) is the most common human malignant neoplasm and is a frequently encountered diagnosis in dermatopathology. Although BCC may be locally destructive, it rarely metastasizes. Many diagnostic entities display morphologic and immunophenotypic overlap with BCC, including nonneoplastic processes, such as follicular induction over dermatofibroma; benign follicular tumors, such as trichoblastoma, trichoepithelioma, or basaloid follicular hamartoma; and malignant tumors, such as sebaceous carcinoma or Merkel cell carcinoma. Thus, misdiagnosis has significant potential to result in overtreatment or undertreatment. - To review key features distinguishing BCC from histologic mimics, including current evidence regarding immunohistochemical markers useful for that distinction. - Review of pertinent literature on BCC immunohistochemistry and differential diagnosis. - In most cases, BCC can be reliably diagnosed by histopathologic features. Immunohistochemistry may provide useful ancillary data in certain cases. Awareness of potential mimics is critical to avoid misdiagnosis and resulting inappropriate management.

  12. Development of microsatellite markers in Myotis sodalis and cross-species amplification in M. gricescens, M. leibii, M. lucifugus, and M. septentrionalis

    Science.gov (United States)

    Robert G. Trujillo; Sybill K. Amelon

    2009-01-01

    The Indiana bat (Myotis sodalis) is a highly endangered vespertilionid bat whose distribution is associated with limestone caves in the eastern United States. We present nine new polymorphic nuclear microsatellite markers for Myotis sodalis developed using an enriched library method. A total of 62 M. sodalis...

  13. Molecular marker applications in plants.

    Science.gov (United States)

    Hayward, Alice C; Tollenaere, Reece; Dalton-Morgan, Jessica; Batley, Jacqueline

    2015-01-01

    Individuals within a population of a sexually reproducing species will have some degree of heritable genomic variation caused by mutations, insertion/deletions (INDELS), inversions, duplications, and translocations. Such variation can be detected and screened using molecular, or genetic, markers. By definition, molecular markers are genetic loci that can be easily tracked and quantified in a population and may be associated with a particular gene or trait of interest. This chapter will review the current major applications of molecular markers in plants.

  14. Asbestos exposure increases the incidence of histologically confirmed usual interstitial pneumonia.

    Science.gov (United States)

    Kawabata, Yoshinori; Shimizu, Yoshihiko; Hoshi, Eishin; Murai, Kazumi; Kanauchi, Tetsu; Kurashima, Kazuyoshi; Sugita, Yutaka

    2016-02-01

    We hypothesized that asbestos exposure increases the incidence of macroscopically visible and histologically confirmed usual interstitial pneumonia (histological UIP). We retrospectively examined 1718 cases (1202 males; mean age 66.7 years) who underwent lobectomy for resection of pleuropulmonary tumours. Objective markers for asbestos exposure included: the presence of malignant pleural mesothelioma, the presence of pleural plaques (PPs) and asbestos bodies in the histological specimen. Risk factors for histological UIP were examined. Two separate groups were studied: 183 with asbestos exposure, and 239 with histological UIP. The 183 cases with asbestos exposure had higher rates of positive occupational history and histological UIP (31%) than the remaining 1535. Among the asbestos-exposed group, small numbers of asbestos bodies were found in histological specimens of 21 cases of histological UIP. PPs and asbestos bodies were more frequent in the 239 patients with histological UIP than in the remaining 1479 UIP-negative patients. Multivariate analysis showed that asbestos exposure, especially positivity for asbestos bodies, that does not meet the current criteria for asbestosis increases the risk of histological UIP (P Asbestos exposure causes asbestosis and increases the incidence of histological UIP. © 2015 John Wiley & Sons Ltd.

  15. [Histologic findings in kidney tumors].

    Science.gov (United States)

    Hora, M; Ouda, Z; Schejbalová, E; Chudácek, Z; Mukensnabl, P

    1997-01-01

    The authors present a group of 304 adult patients (with the exception of one child with a Wilms tumour) from 1988-95 with the diagnosis of a primary renal tumour treated by surgery and subsequently subjected to histological examination. The tumours were in 83.9% clear renal cell tumours (Grawitz carcinoma), 4.3% were papillary carcinomas, 3.3% renal cortical adenomas, 3.9% oncocytomas and 2.0% non-differentiated carcinomas, 0.7% angiomyolipomas, 0.7% chromophobe cell renal carcinomas, 0.7% secondaries (carcinoma of the breast and testis), 0.7% multilocular cysts, one case each (0.3%) Wilms tumour, malignant lymphoma, necrotic histologically not classifiable tumour. The authors give a more detailed account of multilocular cystic RCC (which accounts for 5.9% Grawitz tumours), papillary tumours, chromophobe cell renal carcinoma, oncoytoma and angiomyolipoma. The authors correlate briefly the histological findings with preoperative graphic examinations. They are very sceptical as regards assessment of the histological type of tumour from preoperative graphic examination (with the exception of angiomyolipoma). Finally the authors suggest classification of renal expansions from the urologists aspect-in the first place from preoperative graphic examinations for non-neoplastic lesions (in particular cysts and hypertrophy of the columna Bertini), parenchymatous tumours and tumours of the renal pelvis and secondly (mainly in parenchymatous tumours) histological classification is taken into account.

  16. A high-density SNP genotyping array for Brassica napus and its ancestral diploid species based on optimised selection of single-locus markers in the allotetraploid genome.

    Science.gov (United States)

    Clarke, Wayne E; Higgins, Erin E; Plieske, Joerg; Wieseke, Ralf; Sidebottom, Christine; Khedikar, Yogendra; Batley, Jacqueline; Edwards, Dave; Meng, Jinling; Li, Ruiyuan; Lawley, Cynthia Taylor; Pauquet, Jérôme; Laga, Benjamin; Cheung, Wing; Iniguez-Luy, Federico; Dyrszka, Emmanuelle; Rae, Stephen; Stich, Benjamin; Snowdon, Rod J; Sharpe, Andrew G; Ganal, Martin W; Parkin, Isobel A P

    2016-10-01

    The Brassica napus Illumina array provides genome-wide markers linked to the available genome sequence, a significant tool for genetic analyses of the allotetraploid B. napus and its progenitor diploid genomes. A high-density single nucleotide polymorphism (SNP) Illumina Infinium array, containing 52,157 markers, was developed for the allotetraploid Brassica napus. A stringent selection process employing the short probe sequence for each SNP assay was used to limit the majority of the selected markers to those represented a minimum number of times across the highly replicated genome. As a result approximately 60 % of the SNP assays display genome-specificity, resolving as three clearly separated clusters (AA, AB, and BB) when tested with a diverse range of B. napus material. This genome specificity was supported by the analysis of the diploid ancestors of B. napus, whereby 26,504 and 29,720 markers were scorable in B. oleracea and B. rapa, respectively. Forty-four percent of the assayed loci on the array were genetically mapped in a single doubled-haploid B. napus population allowing alignment of their physical and genetic coordinates. Although strong conservation of the two positions was shown, at least 3 % of the loci were genetically mapped to a homoeologous position compared to their presumed physical position in the respective genome, underlying the importance of genetic corroboration of locus identity. In addition, the alignments identified multiple rearrangements between the diploid and tetraploid Brassica genomes. Although mostly attributed to genome assembly errors, some are likely evidence of rearrangements that occurred since the hybridisation of the progenitor genomes in the B. napus nucleus. Based on estimates for linkage disequilibrium decay, the array is a valuable tool for genetic fine mapping and genome-wide association studies in B. napus and its progenitor genomes.

  17. (SSR) markers

    African Journals Online (AJOL)

    uwerhiavwe

    Variability was observed for six ... rapid increase in climate change, so there is need to develop high yielding ... the past decade including assessment of genetic diversity in maize ... The SSR gel images and marker data were processed using.

  18. Assessment of Tools for Marker-Assisted Selection in a Marine Commercial Species: Significant Association between MSTN-1 Gene Polymorphism and Growth Traits

    Directory of Open Access Journals (Sweden)

    Irma Sánchez-Ramos

    2012-01-01

    Full Text Available Growth is a priority trait from the point of view of genetic improvement. Molecular markers linked to quantitative trait loci (QTL have been regarded as useful for marker-assisted selection in complex traits as growth. Polymorphisms have been studied in five candidate genes influencing growth in gilthead seabream (Sparus aurata: the growth hormone (GH, insulin-like growth factor-1 (IGF-1, myostatin (MSTN-1, prolactin (PRL, and somatolactin (SL genes. Specimens evaluated were from a commercial broodstock comprising 131 breeders (from which 36 males and 44 females contributed to the progeny. In all samples eleven gene fragments, covering more than 13,000 bp, generated by PCR-RFLP, were analyzed; tests were made for significant associations between these markers and growth traits. ANOVA results showed a significant association between MSTN-1 gene polymorphism and growth traits. Pairwise tests revealed several RFLPs in the MSTN-1 gene with significant heterogeneity of genotypes among size groups. PRL and MSTN-1 genes presented linkage disequilibrium. The MSTN-1 gene was mapped in the centromeric region of a medium-size acrocentric chromosome pair.

  19. Assessment of tools for marker-assisted selection in a marine commercial species: significant association between MSTN-1 gene polymorphism and growth traits.

    Science.gov (United States)

    Sánchez-Ramos, Irma; Cross, Ismael; Mácha, Jaroslav; Martínez-Rodríguez, Gonzalo; Krylov, Vladimir; Rebordinos, Laureana

    2012-01-01

    Growth is a priority trait from the point of view of genetic improvement. Molecular markers linked to quantitative trait loci (QTL) have been regarded as useful for marker-assisted selection in complex traits as growth. Polymorphisms have been studied in five candidate genes influencing growth in gilthead seabream (Sparus aurata): the growth hormone (GH), insulin-like growth factor-1 (IGF-1), myostatin (MSTN-1), prolactin (PRL), and somatolactin (SL) genes. Specimens evaluated were from a commercial broodstock comprising 131 breeders (from which 36 males and 44 females contributed to the progeny). In all samples eleven gene fragments, covering more than 13,000 bp, generated by PCR-RFLP, were analyzed; tests were made for significant associations between these markers and growth traits. ANOVA results showed a significant association between MSTN-1 gene polymorphism and growth traits. Pairwise tests revealed several RFLPs in the MSTN-1 gene with significant heterogeneity of genotypes among size groups. PRL and MSTN-1 genes presented linkage disequilibrium. The MSTN-1 gene was mapped in the centromeric region of a medium-size acrocentric chromosome pair.

  20. The potential use of n-alkanes, long-chain alcohols and long-chain fatty acids as diet composition markers: indoor validation with sheep and herbage species from the rangeland of Inner Mongolia of China.

    Science.gov (United States)

    Lin, L J; Zhu, X Y; Jiang, C; Luo, H L; Wang, H; Zhang, Y J; Hong, F Z

    2012-03-01

    To investigate the potential use of n-alkanes (alkanes), long-chain alcohols (alcohols) and long-chain fatty acids (acids) for estimating the diet composition of sheep, in a feeding trial. A total of 18 sheep were assigned randomly to three different diets (diet A, diet B and diet C) containing up to eight herbage species (Leymus chinensis, Leymus dasystachys, Elymus sibiricum, Chenopodium album, Puccinellia chinampoensis, Medicago sativa, Saussurea sinuata and Bromus inermis). Faecal recoveries of alkanes, alcohols and acids were determined, and diet compositions were estimated using different combinations of alkanes, alcohols and acids. The faecal concentrations of individual alkanes, alcohols and acids were corrected using the mean recovery of the dietary treatment that the respective animal belonged to (diet recovery), or the mean recovery across all dietary treatments (general recovery). In general, diets did not affect the faecal recovery values for alkanes, alcohols and acids, and no difference in accuracy was found between diet composition estimates based on dietary recovery and general recovery. The accuracy of diet composition estimates declined as the number of dietary components increased from four to eight herbage species (P diet composition were obtained with the combinations of two or three marker types instead of alkanes alone. Moreover, results showed that excluding minor diet components from the calculations decreased (P diet composition estimates, whereas including extra non-grazed herbage species did not reduce (P > 0.05) the quality of diet composition estimates. These results confirmed the usefulness of alkanes, alcohols and acids as markers for determining complex diet composition of sheep. However, a negative impact on the accuracy of diet composition estimates, caused by missing minor diet components from the calculation of diet composition, could happen when plant wax markers are used to estimate the diet composition of free

  1. Odontogenic Tumor Markers - An Overview

    Science.gov (United States)

    Premalatha, B R; Patil, Shankargouda; Rao, Roopa S; Reddy, Narendranatha P; Indu, M

    2013-01-01

    The practice of pathology is currently undergoing significant change, due to advances in the field of molecular pathology. Tumor markers are molecules that help the pathologists for confirmatory diagnosis of histopathologically confounding lesions. Odontogenic tumors are relatively rare with estimated incidence of less than 0.5 cases/ 100,000 population per year. Odontogenic tumors can pose diagnostic challenges because of overlapping histology. But, appropriate diagnosis is crucial as their treatment modality and prognosis differ; in these situations tumor markers can be helpful. But lack of comprehensive literature on specific markers for odontogenic tumors imposes pathologists to think aimlessly about various markers to arrive at an appropriate diagnosis. With this background, it is our attempt at compiling diagnostically important odontogenic tumor markers. Also, a note is added on tumor behaviour studies in common clinically important odontogenic tumors: Ameloblastoma and Keratocystic odontogenic tumor. How to cite this article: Premalatha B R, Patil S, Rao R S, Reddy N P, Indu M. Odontogenic Tumor Markers - An Overview. J Int Oral Health 2013; 5(2):65-75. How to cite this article: Premalatha B R, Patil S, Rao R S, Reddy N P, Indu M. Odontogenic Tumor Markers - An Overview. J Int Oral Health 2013; 5(2):65-75 PMID:24155593

  2. Reordering Histology to Enhance Engagement

    Science.gov (United States)

    Amerongen, Helen

    2011-01-01

    In redesigning the preclinical curriculum and shifting from a discipline-based approach to an organ system-based approach, faculty at the University of Arizona College of Medicine in Tucson took the opportunity to restructure the sequence of introductory histology content to make it more engaging and relevant. In this article, the author describes…

  3. Effectiveness of microsatellite and SNP markers for parentage and identity analysis in species with low genetic diversity: the case of European bison

    DEFF Research Database (Denmark)

    Torskarska, M; Marshall, T; Kowalczyk, R

    2009-01-01

    The European bison (Bison bonasus) has recovered successfully after a severe bottleneck about 90 years ago. Pedigree analysis indicates that over 80% of the genes in the contemporary population descend from just 2 founder individuals and the pedigree-based inbreeding coefficient averages almost 0.......5, while microsatellite heterozygosity is around 0.3. This paper presents a comparison of the effectiveness of 17 microsatellite and 960 SNP markers in paternity and identity analysis in the Lowland line of European bison ('pure' European bison). Identity analysis revealed that 16% of the microsatellite...

  4. Histological Studies of the Calvarial Development of One-Humped ...

    African Journals Online (AJOL)

    Similarly, there were regularly arranged osteocytes within the trabecular matrix; and the intertrabecular spaces were more obvious. The findings of this research would help in understanding the microscopic anatomy of the developing calvaria in this animal species. Keywords: Histology, calvaria, one-humped, camel, fetuses

  5. Molecular differences in the mitochondrial cytochrome oxidase I (mtCOI) gene and development of a species-specific marker for onion thrips, Thrips tabaci Lindeman, and melon thrips, T. palmi Karny (Thysanoptera: Thripidae), vectors of tospoviruses (Bunyaviridae).

    Science.gov (United States)

    Asokan, R; Krishna Kumar, N K; Kumar, Vikas; Ranganath, H R

    2007-10-01

    A quick and developmental-stage non-limiting method of the identification of vectors of tospoviruses, such as Thrips tabaci and T. palmi, is important in the study of vector transmission, insecticide resistance, biological control, etc. Morphological identification of these thrips vectors is often a stumbling block in the absence of a specialist and limited by polymorphism, sex, stage of development, etc. Molecular identification, on the other hand, is not hampered by the above factors and can easily be followed by a non-specialist with a little training. The mitochondrial cytochrome oxidase I (mtCOI) exhibits reliable inter-species variations as compared to the other markers. In this communication, we present the differences in the mtCOI partial sequence of morphologically identified specimens of T. tabaci and T. palmi collected from onion and watermelon, respectively. Species-specific markers, identified in this study, could successfully determine T. tabaci and T. palmi, which corroborated the morphological identification. Phylogenetic analyses showed that both T. tabaci and T. palmi formed different clades as compared to the other NCBI accessions. The implication of these variations in vector efficiency has to be investigated further. The result of this investigation is useful in the quick identification of T. tabaci and T. palmi, a critical factor in understanding the epidemiology of the tospoviruses, their management and also in quarantine.

  6. [Study of two species of mussels, Mytilus trossulus and Mytilus galloprovincialis (Bivalvia, Mytilidae) and their hybrids, using PCR markers, in Peter the Great Bay of the Sea of Japan].

    Science.gov (United States)

    Skurikhina, L A; kartavtsev, Iu F; Chichvarkhin, A Iu; Pan'kova, M V

    2001-12-01

    Bivalve mollusks of the genus Mytilus (M. trossulus and M. galloprovincialis) occurring in Peter the Great Bay of the Sea of Japan were first studied in Russia. A region of nonrepetitive sequences of the gene encoding the polyphenolic adhesive protein bissus was used as a species-specific genetic marker. After amplification using specific primers, a 126-bp fragment was found to amplify in all representatives of M. galloprovincialis collected from driftwood in the gulf Posset (the southwestern part of Peter the Great Bay). M. trossulus specimens from the same region were shown to have a 168-bp fragment. In Vostok Gulf (the eastern part of Peter the Great Bay), both artificially grown mussels and those from natural habitats contained a 168-bp fragment or two fragments (126- and 168-bp) that corresponded to a hybrid form between the above species. The possibility of using this genetic marker to identify closely related Mytilus strains and their hybrids in similar habitats, near the Primorye coast in particular, was demonstrated. The presence of approximately 9% of hybrid specimens confirms that a zone of hybridization between M. trossulus and M. galloprovincialis may exist in this region.

  7. The Impact of Experimental Hypoxia and Subsequent Normoxia on the Content of Some Ions and Markers of Physiological Stress-adaptation in Gastropod Species Lymnaea stagnalis

    Directory of Open Access Journals (Sweden)

    Lubyaga J.А.

    2014-12-01

    Full Text Available The purpose of this study was to evaluate the influence of hypoxia and subsequent normoxiaon the maintenance of respiratory pigment hemocyanin, total protein, lactate and some ions (Na +, K +, Ca2+, NH4+, Mg2+ in the mantle liquid in palaearctic gastropod species Lymnaea stagnalis. It was shown that short-term experimental hypoxia leads to the activation of the physiological mechanisms of stress adaptation in widespread Palaearctic eurybiotic gastropod species and does not lead to the activation of the stress-resistance mechanisms on the biochemical and molecular levels.

  8. Dense genetic linkage maps of three Populus species (Populus deltoides, P. nigra and P. trichocarpa) based on AFLP and microsatellite markers.

    OpenAIRE

    Cervera, M.t.; Storme, V; Ivens, B; Gusmão, J; Liu, B. H.; Hostyn, V; Van Slycken, J; Van Montagu, M; Boerjan, W.

    2001-01-01

    Populus deltoides, P. nigra, and P. trichocarpa are the most important species for poplar breeding programs worldwide. In addition, Populus has become a model for fundamental research on trees. Linkage maps were constructed for these three species by analyzing progeny of two controlled crosses sharing the same female parent, Populus deltoides cv. S9-2 x P. nigra cv. Ghoy and P. deltoides cv. S9-2 x P. trichocarpa cv. V24. The two-way pseudotestcross mapping strategy was used to construct the ...

  9. (SSR) markers

    African Journals Online (AJOL)

    HP-PROBOOK

    2016-10-05

    Oct 5, 2016 ... Cluster analysis was constructed using DARwin program version 6.0. Forty eight (48) coconut individuals were clustered into three groups. Key words: Coconut palm (Cocos nucifera ... markers, cluster analysis, diversity. INTRODUCTION ... industry in Kenya (Muhammed et al., 2013). Furthermore, the slow ...

  10. (SRAP) markers

    African Journals Online (AJOL)

    STORAGESEVER

    2009-06-03

    Jun 3, 2009 ... are a very powerful tool for characterization and genetic diversity estimation. Many molecular marker techniques have been successfully used in identification and genetic diversity analysis in mulberry, such as RAPD (Xiang et al., 1995; Feng et al., 1996; Zhao and Pan, 2004),. AFLP (Sharma and Sharma, ...

  11. (SSR) markers

    African Journals Online (AJOL)

    SAM

    2014-07-30

    Jul 30, 2014 ... and attempt crosses for genetic improvement of the crop. Key words: Capsicum, genetic diversity, molecular characterization, simple sequence repeats (SSR) markers. INTRODUCTION. Chilli pepper (Capsicum annuum L.) (Solanaceae) has a chromosome number 2n=2x=24. It is indigenous to South.

  12. (SSR) markers

    African Journals Online (AJOL)

    Yomi

    2012-04-03

    Apr 3, 2012 ... Oilseed rape (Brassica napus L.) is an important oilseed crop worldwide. The objective of this research was to study the genetic diversity and relationships of B. napus accessions using simple sequence repeat (SSR). A set of 217 genotypes was characterized using 37 SSR markers of mapping on the B.

  13. (RAPD) markers

    African Journals Online (AJOL)

    Administrator

    2011-09-21

    Sep 21, 2011 ... Biotechnol. Biotechnol. Equip.14: 16-18. Belaj A, Satovic Z, Cipriani G, Baldoni L, Testolin R, Rallo L, Trujillo I. (2003). Comparative study of the discriminating capacity of RAPD,. AFLP and SSR markers and of their effectiveness in establishing genetic relationships in olive. Theor. Appl. Genet. 107: 736-744 ...

  14. [Comparative analysis of diploid species of Avena l. using cytogenetic and biochemical markers: Avena canariensis baum et fedak and A. longiglumis dur].

    Science.gov (United States)

    Shelukhina, O Iu; Badaeva, E D; Brezhneva, T A; Loskutov, I G; Pukhal'skiĭ, V A

    2008-06-01

    The diploid oat species containing the A genome of two types (Al and Ac) were studied by electrophoresis of grain storage proteins (avenins), chromosome C-banding, and in situ hybridization with probes pTa71 and pTa794. The karyotypes of the studied species displayed similar C-banding patterns but differed in size and morphology of several chromosomes, presumably, resulting from structural rearrangements that took place during the divergence of A genomes from a common ancestor. In situ hybridization demonstrated an identical location of the 45S and 5S rRNA gene loci in Avena canariensis and A. longiglumis similar to that in the A. strigosa genome. However, the 5S rDNA locus in A. longiglumis (5S rDNA1) was considerably decreased in the chromosome 3A1 long arm. The analysis demonstrated that these oat species were similar in the avenin component composition, although individual accessions differed in the electrophoretic mobilities of certain components. A considerable similarity of A. canariensis and A. longiglumis to the Avena diploid species carrying the As genome variant was demonstrated.

  15. Rapid Screening for Flavone C-Glycosides in the Leaves of Different Species of Bamboo and Simultaneous Quantitation of Four Marker Compounds by HPLC-UV/DAD

    Directory of Open Access Journals (Sweden)

    Jin Wang

    2012-01-01

    Full Text Available A strategy for analyzing flavone C-glucosides in the leaves of different species of bamboo was developed. Firstly, the flavone C-glycosides were extracted from the bamboo leaves (51 species in 17 genera with methanol and chromatographed on silica gel 60 plates in automatic developing chamber (ADC2, and a qualitative survey using simple derivatization steps with the NP reagent was carried out. The flavone C-glycosides were found in 40 of 51 species of bamboo examined. Secondly, an HPLC method with photodiode array and multiple wavelength detector was optimized and validated for the simultaneous determination of flavone C-glycosides, including isoorientin, isovitexin, orientin, and vitexin in the leaves of three species of bamboo and the flavone C-glycosides were confirmed by LC/MS. The optimized HPLC method proved to be linear in the concentration range tested (0.2–100 μg/mL, r2≥0.9997, precise (RSD≤1.56%, and accurate (88–106%. The concentration ranges of isoorientin, isovitexin, orientin, and vitexin in three bamboo leaves samples were 1.00–2.78, 0–0.31, 0–0.07, and 0.20–0.68 mg/g, respectively. The proposed method was validated to be simple and reliable and can be a tool for quality control of bamboo leaf extract or its commercial products.

  16. STUDI HISTOLOGI LIMPA SAPI BALI

    Directory of Open Access Journals (Sweden)

    Ni Luh Eka Setiasih

    2012-11-01

    Full Text Available The objective of this study to find out the histological of spleen of bali cattle. Thespleenwere collected from 20 bali cattle in Pesanggaran abattoir, Denpasar and thenevaluated microscopically. Histological findings were assessed by H-E stainpreparations.Microscopically, showed that the spleen of bali cattle consists of capsule,white and red pulp. The capsule composed of connective tissue and smooth muscle withthick of these layer is 24,3 ± 3,7 ?m. The white pulp subdivided into the marginal zone andthe follicle. It is composed of reticulocyte (lymphocytes and macrophages andreticular fibers. The red pulp composed of arterioles, capillary, and vascular sinusoidswhich are large numbers of erythrocytes, macrophages, dendritic cells, plasma cells andsparse lymphocytes.

  17. Rapid diagnosis of the economically important fruit fly, Bactrocera correcta (Diptera: Tephritidae) based on a species-specific barcoding cytochrome oxidase I marker.

    Science.gov (United States)

    Jiang, F; Li, Z H; Deng, Y L; Wu, J J; Liu, R S; Buahom, N

    2013-06-01

    The guava fruit fly, Bactrocera correcta (Bezzi) (Diptera: Tephritidae), is an invasive pest of fruit and vegetable crops that primarily inhabits Southeast Asia and which has the potential to become a major threat within both the Oriental and Australian oceanic regions as well as California and Florida. In light of the threat posed, it is important to develop a rapid, accurate and reliable method to identify B. correcta in quarantine work in order to provide an early warning to prevent its widespread invasion. In the present study, we describe a species-specific polymerase chain reaction assay for the diagnosis of B. correcta using mitochondrial DNA cytochrome oxidase I (mtDNA COI) barcoding genes. A B. correcta-specific primer pair was designed according to variations in the mtDNA COI barcode sequences among 14 fruit fly species. The specificity and sensitivity of the B. correcta-specific primer pair was tested based on the presence or absence of a band in the gel profile. A pair of species-specific B. correcta primers was successfully designed and named BCOR-F/BCOR-R. An ∼280 bp fragment was amplified from specimens belonging to 17 geographical populations and four life stages of B. correcta, while no such diagnostic bands were present in any of the 14 other related fruit fly species examined. Sensitivity test results demonstrated that successful amplification can be obtained with as little as 1 ng μl⁻¹ of template DNA. The species-specific PCR analysis was able to successfully diagnose B. correcta, even in immature life stages, and from adult body parts. This method proved to be a robust single-step molecular technique for the diagnosis of B. correcta with respect to potential plant quarantine.

  18. Histological Value of Duodenal Biopsies

    Directory of Open Access Journals (Sweden)

    Limci Gupta

    2005-01-01

    Full Text Available This study was performed to see the value of histopathological diagnosis in management of patients with duodenal biopsies; to look for correlation of histology and serology in suspected cases of coeliac disease; the reasons for taking duodenal biopsies and whether proper adequate histories are provided on the forms sent with request for histopathological view on duodenal biopsies. Here are the observations of the study followed by the discussion.

  19. Comparative analysis of genetic diversity among species of Chrysanthemum and its related genera using inter-simple sequence repeat and sequence-related amplified polymorphism markers.

    Science.gov (United States)

    Zhang, X; Zhang, F; Zhao, H; Guan, Z; Chen, S; Jiang, J; Fang, W; Chen, F

    2014-10-20

    In this study, inter-simple sequence repeats (ISSRs) and sequence-related amplified polymorphism (SRAP) were applied to assess the genetic diversity in 38 species of Chrysanthemum and related genera. A total of 204 and 567 bands were amplified by 24 ISSR and 25 SRAP primers, of which 196 (97%) and 557 (99%) were polymorphic, respectively. The ISSR-based genetic similarity ranged from 0.016 to 0.886 and averaged 0.201, while the SRAP-based genetic similarity varied from 0.010 to 0.811 and averaged 0.122. Both the ISSR and SRAP techniques revealed similar clustering patterns and grouped species of Chrysanthemum and Ajania together. The results of principal coordinate analysis corroborated the unweighted pair group method with arithmetic average clustering. Additionally, results from ISSR and SRAP data were significantly correlated (r = 0.89, P chrysanthemum in future distant interspecific breeding.

  20. A histology-based fish health assessment of four commercially and ...

    African Journals Online (AJOL)

    The health status of four commercially and ecologically important fish species from the Okavango Delta was assessed, using a histology-based health assessment protocol, to establish baseline data for future toxicity studies. Following the calculation of a necropsy-based health assessment index (HAI), the histological ...

  1. Hippocampal-related memory deficits and histological damage induced by neonatal ionizing radiation exposure. Role of oxidative status.

    Science.gov (United States)

    Caceres, Lucila Guadalupe; Aon Bertolino, Laura; Saraceno, Gustavo Ezequiel; Zorrilla Zubilete, María Aurelia; Uran, Soledad Lucía; Capani, Francisco; Guelman, Laura Ruth

    2010-02-02

    Ionizing radiations induce oxidative stress on target tissues, mainly through the generation of reactive oxygen species (ROS). However, there are few data available on the behavioral effects of moderate doses of ionizing radiation. The aim of the present work was to evaluate the performance of adult rats irradiated at birth in different hippocampal-dependent behavioral tasks and to establish a relationship with the oxidative status and histological changes in rat hippocampus (Hip). Male Wistar rats were irradiated with 5 Gy of X rays between 24 and 48 h after birth. Thirty days later, rats were subjected to open field, object recognition and inhibitory avoidance tasks. In addition, oxidative status markers as well as protein kinase C (PKC) activity and histological changes were assessed in control and irradiated Hip. Results show an impairment in recognition and habituation memories in 30-day-old animals exposed to neonatal ionizing radiation, both at short- (ST) and at long-term (LT), whereas an improvement in associative memory was observed at ST. In addition, histological alterations were observed in irradiated Hip. Although an increase in ROS levels and PKC activity were found in irradiated Hip, no changes in the antioxidant enzymes superoxide dismutase (SOD) and catalase (CAT) were observed. Taken together, our results support the hypothesis that an increased PKC activity, induced by neonatal ionizing radiation on rat Hip, could play a role in the generation of an imbalance between ROS levels and antioxidant systems and might underlie radiation-induced hippocampal histological damage as well as the Hip-dependent behavioral changes found in irradiated rats. (c) 2009 Elsevier B.V. All rights reserved.

  2. No Genetic Diversity at Molecular Markers and Strong Phenotypic Plasticity in Populations of Ranunculus nodiflorus, an Endangered Plant Species in France

    Science.gov (United States)

    Noel, Florence; Machon, Nathalie; Porcher, Emmanuelle

    2007-01-01

    Background and Aims Although conservation biology has long focused on population dynamics and genetics, phenotypic plasticity is likely to play a significant role in population viability. Here, an investigation is made into the relative contribution of genetic diversity and phenotypic plasticity to the phenotypic variation in natural populations of Ranunculus nodiflorus, a rare annual plant inhabiting temporary puddles in the Fontainebleau forest (Paris region, France) and exhibiting metapopulation dynamics. Methods The genetic diversity and phenotypic plasticity of quantitative traits (morphological and fitness components) were measured in five populations, using a combination of field measurements, common garden experiments and genotyping at microsatellite loci. Key Results It is shown that populations exhibit almost undetectable genetic diversity at molecular markers, and that the variation in quantitative traits observed among populations is due to a high level of phenotypic plasticity. Despite the lack of genetic diversity, the natural population of R. nodiflorus exhibits large population sizes and does not appear threatened by extinction; this may be attributable to large phenotypic plasticity, enabling the production of numerous seeds under a wide range of environmental conditions. Conclusions Efficient conservation of the populations can only be based on habitat management, to favour the maintenance of microenvironmental variation and the resulting strong phenotypic plasticity. In contrast, classical actions aiming to improve genetic diversity are useless in the present case. PMID:17468109

  3. Tumour marker expression in blood and lymphatic vessels of human ...

    African Journals Online (AJOL)

    The behaviour of tumours cannot be effectively assessed on histological tissue sections only, hence, specific bi-ological markers were used to predict tumour behaviour. The biological markers at the same time must provide prognostic information, necessary for the treatment of patients. The immunostaining of antibodies ...

  4. Evaluation and histological maturation characteristics of fibrous ...

    African Journals Online (AJOL)

    osseous lesions (FOLS) that are generally considered to be separate entities distinguishable by histologic and radiographic features. The histological maturation of these lesions involves an initial fibrous state, an intermediate mixed and a final ...

  5. Identifikasi Keragaman Genetik Gen 12S Ribomsom RNA Sebagai Penanda Genetik untuk Penentuan Spesies Kuskus (IDENTIFICATION OF GENETIC DIVERSITY 12SRRNA GENES AS GENETIC MARKER FOR DETERMINING SPECIES CUSCUS

    Directory of Open Access Journals (Sweden)

    Rini Widayanti

    2015-08-01

    Full Text Available Cuscus is marsupial’s animal (Phalageridae which has limited spread in eastern Indonesia (Sulawesi,Maluku, Papua, Australia and Papua New Guinea. The ex-situ and in-situ conservation of cuscus undercaptivating condition is an alternative solution to protect cuscus from extinction. This study aimed todetermine nucleotide sequence and genetic markers on 12Sr RNA gene with sequencing method of eachspecies on three islands. Whole genome DNA was extracted from 17 samples of cuscus obtained fromdifferent habitats, Sulawesi (2 individual, Maluku (7 individual, and Papua (8 individual according tothe protocol of Qiamp DNA Blood Mini Kit (Qiagen, and then it was used as template for amplificationof 12Sr RNA gene by using PCR. PCR product were then purified using column chromatography and wereused as template for sequencing reaction. Result sequencing of 12Sr RNA gene were analyzed usingMEGA program version 6. PCR product gives a result nucleotida of 958 bp according to databasegenebank, sequencing product gives result nucleotida of 896 bp and found of 105 different nucleotide sites.Filogram based on nucleotide sequences 12SrRNA gene from Sulawesi cuscus is Ailurops ursinus whereasthe cuscus from Papua and Maluku is Phalanger sp. and Spilocuscus maculatus species. Thirteen nucleotidasites were found, sites no 67 (A/G, 89 (G/C, 137 (T/C, 285 (G/A, 468 (T/C, 595 (T/C, 598 (T/C, 647 (T/C,654 (G/A, 665 (T/C, 769 (C/T, 874 (C/T, and 876 (A/G which can be used as genetic marker betweenPhalanger genera from Papua and Maluku, and three nucleotida sites (sites no 127 (G/A, 481 (C/T, and885 (T/C can be used as genetic marker between Spilocuscus genera from Papua and Maluku.

  6. Double origin of the racer goby (Babka gymnotrachelus in Poland revealed with mitochondrial marker. Possible implications for the species alien/native status

    Directory of Open Access Journals (Sweden)

    Michal Grabowski

    2015-09-01

    Full Text Available In mid-1990s racer goby, Babka gymnotrachelus, penetrated to the Vistula and Western Bug rivers in Poland through the canal connecting the Baltic and the Black Sea basins, namely the Vistula and Dnieper drainages. In early 2000s, the species was reported from Polish section of the Strwiąż River that is an affluent of the Dniester River that drains to the Black Sea basin. According to the Polish legislation, the racer goby has been enlisted in as an alien invasive species that may pose threat to local biota. Our analysis of the mtDNA cytochrome b diversity revealed that the Vistula/Western Bug and Strwiąż populations are different genetic units. First one originated from the Dnieper River, while the second derives from the Dniester River. According to the results of mismatch analysis, both are in the stage of demographic and spatial expansion. The haplotype frequencies in population from the Vistula/Western Bug differ significantly from those in the source population in Dnieper, suggesting founder effect, possibly due to human-mediated introduction of low number of individuals. On the other side, the population in Strwiąż does not differ in structure from the one in Dniester, providing a hint towards spontaneous range expansion. Interpretation of our results in light of historical data lead to the conclusion that presence of racer goby in Strwiąż was probably overlooked in previous, spatially limited, studies. Thus, in Strwiąż the species should not be treated as alien, contrary to its status in the Vistula drainage. This double origin of racer goby populations in Poland creates a peculiar situation for national legislation procedures as one population is alien and invasive, while the other one is not. In light of our findings, the population from Strwiąż should be recognised as a special case. Steps should be undertaken to raise public awareness to prevent translocation of the gobies between the rivers to prevent deterioration of the

  7. [Analysis of mtDNA and Nuclear Markers Points to Homoploid Hybrid Origin of the New Species of Far Eastern Redfins of the Genus Tribolodon (Pisces, Cyprinidae)].

    Science.gov (United States)

    Polyakova, N E; Semina, A V; Brykov, V A

    2015-11-01

    The nucleotide sequences of two mitochondrial genes (cytochrome c oxidase subunit I, COI, and cytochrome b, cyt b) and four nuclear genes (growth hormone gene GH1, ribosomal protein S7 gene RP1, recombination activating gene RAG1, and rhodopsin gene RH) from the Far Eastern redfins of the genus Tribolodon were examined to clarify the status of the southern form of T. hakonensis. Nucleotide sequence analysis of the mitochondrial genes showed differences of 2.6% between individuals of T. hakonensis inhabiting the north and south of the range. Analysis of the nuclear genes showed that Tribolodon sp. (southern form of T. hakonensis) has a mosaic of nuclear genes received from the Pacific redfin T. brandtii and big-scaled redfin T. hakonensis. It is suggested that the new species could have formed as a result of homoploid hybridization between the true T. hakonensis (by original description) and T. brandtii, which probably made it possible for this species to occupy a new ecological niche.

  8. Comparative histology of mouse, rat, and human pelvic ligaments.

    Science.gov (United States)

    Iwanaga, Ritsuko; Orlicky, David J; Arnett, Jameson; Guess, Marsha K; Hurt, K Joseph; Connell, Kathleen A

    2016-11-01

    The uterosacral (USL) and cardinal ligaments (CL) provide support to the uterus and pelvic organs, and the round ligaments (RL) maintain their position in the pelvis. In women with pelvic organ prolapse (POP), the connective tissue, smooth muscle, vasculature, and innervation of the pelvic support structures are altered. Rodents are commonly used animal models for POP research. However, the pelvic ligaments have not been defined in these animals. In this study, we hypothesized that the gross anatomy and histological composition of pelvic ligaments in rodents and humans are similar. We performed an extensive literature search for anatomical and histological descriptions of the pelvic support ligaments in rodents. We also performed anatomical dissections of the pelvis to define anatomical landmarks in relation to the ligaments. In addition, we identified the histological components of the pelvic ligaments and performed quantitative analysis of the smooth muscle bundles and connective tissue of the USL and RL. The anatomy of the USL, CL, and RL and their anatomical landmarks are similar in mice, rats, and humans. All species contain the same cellular components and have similar histological architecture. However, the cervical portion of the mouse USL and RL contain more smooth muscle and less connective tissue compared with rat and human ligaments. The pelvic support structures of rats and mice are anatomically and histologically similar to those of humans. We propose that both mice and rats are appropriate, cost-effective models for directed studies in POP research.

  9. Investigations in generalized osteoarthritis. Part 2: special histological features in generalized osteoarthritis (histological investigations in Heberden's nodes using a histological score).

    Science.gov (United States)

    Irlenbusch, U; Dominick, G

    2006-05-01

    In accordance with the literature, our previous epidemiological, clinical and genetical investigations have confirmed a correlation between generalized osteoarthritis (GOA) and Heberden's nodes. Heberden's nodes can be considered as genetic markers for the existence of a generalized osteoarthritic predisposition. The present study's concern was to establish whether there are special histological features in this disease. Layered sections of 218 distal finger joints from 56 deceased persons were investigated using a histological-histochemical score modified by Mankin. In Heberden's nodes, we found all the typical degradative sequences of the osteoarthritic process but also some specific modifications. The osteoarthritis (OA) starts with a subchondral ossification and manifests a reactive tidemark flaking. At this time, the surface of the cartilage is not yet destroyed. Later on, there is progression of general degradation. Significant differentiation from the control group is possible using a histological score. In patients with Heberden's nodes, the OA starts with the subchondral ossification. Heberden's nodes are the specific manifestation of GOA in the distal finger joints. Further studies are therefore required to assess whether the same pathogenetic mechanism can be seen in OA of the large joints in GOA.

  10. Histology of the first fish

    Science.gov (United States)

    Smith, M.P.; Sansom, I.J.; Repetski, J.E.

    1996-01-01

    THE first description of Anatolepis Bockelie & Fortey was from early Ordovician sediments of Ny Friesland, Spitsbergen1,2, but the genus is now known from many localities in North America and Greenland, ranging in age from the Late Cambrian period to the Early Ordovician3-6. Although initially interpreted as an agnathan fish2,3 that predated other representatives7, this has been widely disputed because the available histological data were unconvincing6,8-10 and the scales fell outside the known morphological range of other accepted early vertebrates9-11. Further doubt was cast upon the vertebrate affinity of Anatolepis when specimens from East Greenland were interpreted as the cuticular fragments of aglaspid arthropods6, although this interpretation has also been refuted12. Here we report on the morphology and histology of large collections of Anatolepis, and demonstrate the presence of dentine, a tissue unique to vertebrates, confirming that the taxon is both a vertebrate and the oldest known fish.

  11. Relationship between two androgenetic clam species, Corbicula leana and Corbicula fluminea, inferred from mitochondrial cytochrome b and nuclear 28S rRNA markers.

    Science.gov (United States)

    Komaru, Akira; Yamada, Mitsuya; Houki, Shouji

    2013-05-01

    Two shell color types, yellow (type I) and brown (type II), of hermaphrodite Corbicula fluminea clams from Ritto, Shiga Prefecture, Japan, are sympatric with both male and hermaphrodite Corbicula leana. In the present study, the mitochondrial DNA (mtDNA) cytochrome b and nuclear 28S rRNA genes of C. fluminea were sequenced to construct a haplotype network in order to investigate the genetic relationship with C. leana. Ninety C. fluminea samples revealed only two cytb haplotypes; the majority (97.8%) were CB7, while the remainder were CB1. In C. leana, only CB1 was detected in hermaphrodites, but both CB1 and CB7 were detected in males. Nuclear 28S rRNA haplotypes of C. fluminea type I individuals were divergent from those of hermaphrodite C. leana. However, C. fluminea type I clams shared haplotypes with male C. leana individuals, whereas C. fluminea type II individuals shared haplotypes with both hermaphrodite and male C. leana samples. These results suggest that it may be difficult to define a clear genetic border between these species.

  12. Evidence of Natural Hybridization and Introgression between Vasconcellea Species (Caricaceae) from Southern Ecuador Revealed by Chloroplast, Mitochondrial and Nuclear DNA Markers

    Science.gov (United States)

    VAN DROOGENBROECK, B.; KYNDT, T.; ROMEIJN-PEETERS, E.; VAN THUYNE, W.; GOETGHEBEUR, P.; ROMERO-MOTOCHI, J. P.; GHEYSEN, G.

    2006-01-01

    • Background and Aims Vasconcellea × heilbornii is believed to be of natural hybrid origin between V. cundinamarcensis and V. stipulata, and is often difficult to discriminate from V. stipulata on morphological grounds. The aim of this paper is to examine individuals of these three taxa and of individuals from the closely related species V. parviflora and V. weberbaueri, which all inhabit a hybrid zone in southern Ecuador. • Methods Molecular data from mitochondrial, chloroplast and nuclear DNA from 61 individuals were analysed. • Key Results Molecular analysis confirmed occasional contemporary hybridization between V. stipulata, V. cundinamarcensis and V. × heilbornii and suggested the possible involvement of V. weberbaueri in the origin of V. × heilbornii. In addition, the molecular data indicated unidirectional introgression of the V. cundinamarcensis nuclear genome into that of V. stipulata. Several of the individuals examined with morphology similar to that of V. stipulata had genetic traces of hybridization with V. cundinamarcensis, which only seems to act as pollen donor in interspecific hybridization events. Molecular analyses also strongly suggested that most of the V. × heilbornii individuals are not F1 hybrids but instead are progeny of repeated backcrosses with V. stipulata. • Conclusions The results of the present study point to the need for re-evaluation of natural populations of V. stipulata and V. × heilbornii. In general, this analysis demonstrates the complex patterns of genetic and morphological diversity found in natural plant hybrid zones. PMID:16500954

  13. Comparative digital cartilage histology for human and common osteoarthritis models

    Directory of Open Access Journals (Sweden)

    Pedersen DR

    2013-02-01

    Full Text Available Douglas R Pedersen, Jessica E Goetz, Gail L Kurriger, James A MartinDepartment of Orthopaedics and Rehabilitation, University of Iowa, Iowa City, IA, USAPurpose: This study addresses the species-specific and site-specific details of weight-bearing articular cartilage zone depths and chondrocyte distributions among humans and common osteoarthritis (OA animal models using contemporary digital imaging tools. Histological analysis is the gold-standard research tool for evaluating cartilage health, OA severity, and treatment efficacy. Historically, evaluations were made by expert analysts. However, state-of-the-art tools have been developed that allow for digitization of entire histological sections for computer-aided analysis. Large volumes of common digital cartilage metrics directly complement elucidation of trends in OA inducement and concomitant potential treatments.Materials and methods: Sixteen fresh human knees, 26 adult New Zealand rabbit stifles, and 104 bovine lateral plateaus were measured for four cartilage zones and the cell densities within each zone. Each knee was divided into four weight-bearing sites: the medial and lateral plateaus and femoral condyles.Results: One-way analysis of variance followed by pairwise multiple comparisons (Holm–Sidak method at a significance of 0.05 clearly confirmed the variability between cartilage depths at each site, between sites in the same species, and between weight-bearing articular cartilage definitions in different species.Conclusion: The present study clearly demonstrates multisite, multispecies differences in normal weight-bearing articular cartilage, which can be objectively quantified by a common digital histology imaging technique. The clear site-specific differences in normal cartilage must be taken into consideration when characterizing the pathoetiology of OA models. Together, these provide a path to consistently analyze the volume and variety of histologic slides necessarily generated

  14. Comparative molecular and histological grading of epithelial dysplasia of the oral cavity and the oropharynx

    NARCIS (Netherlands)

    Tabor, M.P.; Braakhuis, B.J.M.; van der Wal, J.E.; van Diest, P.J.; Leemans, C.R.; Brakenhoff, R.H.; Kummer, J.A.

    2003-01-01

    Histological grading of epithelial dysplasia in the oral cavity and oropharynx is used to predict the risk for cancer and to determine the treatment strategy. This grading, however, is subjective and not well reproducible. Recent publications have shown that molecular markers are promising in cancer

  15. Caracterização genética de espécies de Passiflora por marcadores moleculares análogos a genes de resistência Genetic characterization of Passiflora species via resistance genes analog markers

    Directory of Open Access Journals (Sweden)

    Mariana da Silva Paula

    2010-03-01

    pathogens have been identified in accessions of Passiflora germplasm. In the present research we evaluate by using RGAs ("resistance gene analogs" markers the genetic diversity of accessions belonging to eight wild species (P. setacea, P. nitida, P. serratodigitata, P. caerulea, P. gibertii, P. odontophyla, P. eduli, and P. coccinea as well as one interspecific hybrid (P. setacea. x P. coccinea. A remarkable diversity was observed among the RGA eletrophoretic profiles of the accessions, allowing the annotation of 96 polymorphic amplicons able to discriminate at least one pair of accessions. The levels of genetic dissimilarity in this group of Passiflora accessions (using exclusively this collection of RGA markers ranged from 0.40 to 0.89. The sequence analysis of a subgroup of RGA amplicons indicated that they correspond to genomic regions that encompass typical disease resistance gene motifs described in other plant species. Our results indicate a quite variable structural repertoire of RGA segments in Passiflora species with many of them being potentially useful as molecular markers for germplasm fingerprinting systems and also for assisted selection strategies in disease resistance breeding programs in this crop.

  16. Genetic variations among passion fruit species using rapd markers Variação genética entre espécies de maracujá utilizando marcadores rapd

    Directory of Open Access Journals (Sweden)

    Ana Paula de Andrade Aukar

    2002-12-01

    Full Text Available It has been evaluated the genetic variability through the use of RAPD molecular markers on the following passionflower species: Passiflora amethystina, P. caerulea, P. cincinnata, P. coccinea, P. serrato digitata, P. foetida, P. maliformis, P. alata, P. giberti, P. laurifolia, P. macrocarpa, P. nitida, P. setacea, P. suberosa, P. ligularis, P. capsularis, P. edulis Sims and its botanical variety P. edulis Sims f. flavicarpa Deg. In this research work, the analyses of the random amplified polymorphic DNA products (RAPD were employed to estimate the genetic diversity and the taxonomic linkage within the species above. The total of 21 primers were used in this study which generated 270 different polymorphic products. It was possible to detect that the Passiflora species had shown a similarity of 17,3%, and between Passiflora edulis Sims and Passiflora edulis Sims f. flavicarpa a similarity of 34,35% has been found. The rate of similarity within edulis specie is low, making it clear that a large variability between the yellow and the purple forms exists.Foram avaliadas as variações genéticas através de marcadores moleculares RAPD, as seguintes espécies de maracujá: Passiflora amethystina, P. caerulea, P. cincinnata, P. coccinea, P. serrato digitata, P. foetida, P. maliformis, P. alata, P. giberti, P. laurifolia, P. macrocarpa, P. nitida, P. setacea, P. suberosa, P. ligularis, P. capsularis, P. edulis Sims e sua variedade botânica P. edulis Sims f. flavicarpa Deg. Neste estudo, a análise dos produtos da amplificação ao acaso do DNA polimórfico (RAPD foi usada para estimar a diversidade genética e as relações taxonômicas entre as espécies. Foram utilizados 21 "primers", que produziram um total de 270 bandas polimórficas. Verificou-se que as espécies de Passiflora apresentaram uma média de similaridade de 17,3%, e entre Passiflora edulis Sims e Passiflora edulis Sims f. flavicarpa, de 34,35%. Pode-se perceber que o valor de

  17. Productivity standards for histology laboratories.

    Science.gov (United States)

    Buesa, René J

    2010-04-01

    The information from 221 US histology laboratories (histolabs) and 104 from 24 other countries with workloads from 600 to 116 000 cases per year was used to calculate productivity standards for 23 technical and 27 nontechnical tasks and for 4 types of work flow indicators. The sample includes 254 human, 40 forensic, and 31 veterinary pathology services. Statistical analyses demonstrate that most productivity standards are not different between services or worldwide. The total workload for the US human pathology histolabs averaged 26 061 cases per year, with 54% between 10 000 and less than 30 000. The total workload for 70% of the histolabs from other countries was less than 20 000, with an average of 15 226 cases per year. The fundamental manual technical tasks in the histolab and their productivity standards are as follows: grossing (14 cases per hour), cassetting (54 cassettes per hour), embedding (50 blocks per hour), and cutting (24 blocks per hour). All the other tasks, each with their own productivity standards, can be completed by auxiliary staff or using automatic instruments. Depending on the level of automation of the histolab, all the tasks derived from a workload of 25 cases will require 15.8 to 17.7 hours of work completed by 2.4 to 2.7 employees with 18% of their working time not directly dedicated to the production of diagnostic slides. This article explains how to extrapolate this productivity calculation for any workload and different levels of automation. The overall performance standard for all the tasks, including 8 hours for automated tissue processing, is 3.2 to 3.5 blocks per hour; and its best indicator is the value of the gross work flow productivity that is essentially dependent on how the work is organized. This article also includes productivity standards for forensic and veterinary histolabs, but the staffing benchmarks for histolabs will be the subject of a separate article. Copyright 2010 Elsevier Inc. All rights reserved.

  18. Esquemas de histología

    OpenAIRE

    Iglesias Rozas, José Rafael, 1942-

    1982-01-01

    Cuarenta y siete diagramas de estructuras histológicas extraídas de un atlas de histología, obra de Radivoj Vase Krstić. Forty-seven diagrams of histological structures from an atlas of histiology by Radivoj Vase Krstić.

  19. Comparative Histology of Plasma Treated Tissue

    Science.gov (United States)

    Rick, Kyle

    2009-10-01

    Atmospheric plasmas applied in surgical settings have unique characteristics found in histological results from animal tissue studies. This is evident in both ex vivo bench tissue tests and in vivo fresh tissue. Examples of these histological features are presented as results of a comparative study between plasma treated, common medical argon coagulation, and electrosurgery.

  20. Exogenous fibrolytic enzymes to unlock nutrients: Histological ...

    African Journals Online (AJOL)

    Exogenous fibrolytic enzymes to unlock nutrients: Histological investigation of its effects on fibre degradation in ruminants. ... There is a need for a better understanding of the mode-of-action of exogenous fibrolytic enzymes (EFE) used as additives in ruminant feeds. ... Keywords: Fibre digestion, histology, in vitro digestion ...

  1. REVIEW ARTICLE Complications, disease profile and histological ...

    African Journals Online (AJOL)

    14 SA JOURNAL OF RADIOLOGY • March 2011. REVIEW ARTICLE. Complications, disease profile and histological yield from percutaneous renal biopsy .... ranged from 13 months to 72 years (average 41.5 years) and race was included in the analysis. Information was collected from clinical notes, and histology results.

  2. Histological description of Cerdocyon thous (Linnaeus, 1766 respiratory system

    Directory of Open Access Journals (Sweden)

    Marla P. Rocha

    Full Text Available ABSTRACT: The massive agricultural expansion converted the Cerdocyon thous, a South American native predator, in vulnerable specie. Basic data, such as histological description, are important to raise awareness on animal species, helping on preservation strategies. Considering the difficult in obtain samples, as the euthanasia of wild animals for this purpose is not allowed, data on histology are very scarce or inexistent. The objective of this paper was to provide a detailed histological description of the trachea and bronchial tree of the crab-eating fox Cerdocyon thous (Linnaeus, 1766. The specimens (one adult male and one adult female used were provided by the Federal University of Pelotas (Pelotas, RS, Brazil Rehabilitation Center of Wild Fauna (NURFS. Tissue samples were fixed in 10% formalin and included in paraffin. After slicing, samples were stained with HE (hematoxylin and eosin, PAS (periodic acid-Schiff and resorcin fuchsin. Trachea had an average diameter of 7.87mm, and approximately 57% of the mucosa ciliated pseudo-stratified columnar epithelium was composed of goblet cells, mostly in the dorsal region. Bronchia and bronchioles had a mucosal fold with higher number of goblet cells. Using all these techniques there is no great remarkable differences from C. thous trachea and lung, when compared with the previous described structures for carnivores and most mammals, except for the goblet cells “regionalization”. Described results are important to understand the animal physiological and behavioral habits, allowing the development of preservation and protection strategies.

  3. Histological stain evaluation for machine learning applications

    Directory of Open Access Journals (Sweden)

    Jimmy C Azar

    2013-01-01

    Full Text Available Aims: A methodology for quantitative comparison of histological stains based on their classification and clustering performance, which may facilitate the choice of histological stains for automatic pattern and image analysis. Background: Machine learning and image analysis are becoming increasingly important in pathology applications for automatic analysis of histological tissue samples. Pathologists rely on multiple, contrasting stains to analyze tissue samples, but histological stains are developed for visual analysis and are not always ideal for automatic analysis. Materials and Methods: Thirteen different histological stains were used to stain adjacent prostate tissue sections from radical prostatectomies. We evaluate the stains for both supervised and unsupervised classification of stain/tissue combinations. For supervised classification we measure the error rate of nonlinear support vector machines, and for unsupervised classification we use the Rand index and the F-measure to assess the clustering results of a Gaussian mixture model based on expectation-maximization. Finally, we investigate class separability measures based on scatter criteria. Results: A methodology for quantitative evaluation of histological stains in terms of their classification and clustering efficacy that aims at improving segmentation and color decomposition. We demonstrate that for a specific tissue type, certain stains perform consistently better than others according to objective error criteria. Conclusions: The choice of histological stain for automatic analysis must be based on its classification and clustering performance, which are indicators of the performance of automatic segmentation of tissue into morphological components, which in turn may be the basis for diagnosis.

  4. IDENTIFIKASI DAGING SAPI BALI DENGAN METODE HISTOLOGIS

    Directory of Open Access Journals (Sweden)

    Ni Ketut Suwiti

    2012-09-01

    Full Text Available ABSTRAK Telah dilakukan penelitian identifikasi daging sapi bali dengan metode histologis yakni melakukan pengamatan terhadap struktur mikroskopis. Sampel daging sapi bali. berupa muskulus pectoralis profundus, diperoleh dari pasar swalayan di Denpasar. Sampel difiksasi, didehidrasi dan diembedding dalam parafin selanjutnya dilakukan pemotongan dengan mikrotom ketebalan 4 - 5 µ. Dibuat sediaan histologis dengan metode pewarnaan Harris-Haematoxilin-Eosin. Pengamatan terhadap struktur histologi dilakukan dengan mikroskop cahaya binokuler pembesaran 450x. Hasil penelitian menunjukkan struktur histologi daging sapi bali terdiri atas serabut otot skelet longitudinal dan tranversal dengan multinuklleus. Nukleus terletak dipinggir sel. Ditemukan jaringan ikat padat dan jaringan lemak dengan pembuluh darah. Diameter serabut otot berukuran 8,40 ± 1,41 µm. Pada pengamatan histologis juga ditemukan : endomisium, perimisium dan epimisium IDENTIFICATION OF BALI CATTLE MEAT WITH HISTOLOGICAL METHODS ABSTRACT A study to identification the microscopic structure of bali cattle meat by histological methods, has been carried out. The meat bali cattle samples were collected from musculus pectoralis profundus has been taken from Denpasar supermarket. The tissue samples were fixed, dehydrated and embedded in paraffin and 4 - 5 µ. sections. Harris-Haematoxilin-Eosin staining method, using to identified of histological structure. Microscopic analysis was performed using a binocular light microscope (450X. The study showed that, histological structure of bali cattle beef was composed by longitudinally and transverselly skeletal muscle with a multinucleated. The nuclei in the periphery of the cell, there are dense connective tissue, fat, with small blood vessels. The skeletal myofibers diameter of muscle is 8.40 ± 1,41 µm. We observed for the presence of : endomysium , perimysium and epimysium.

  5. The histological slides and drawings of cajal

    National Research Council Canada - National Science Library

    Garcia-Lopez, Pablo; Garcia-Marin, Virginia; Freire, Miguel

    2010-01-01

    ... (Cajal Institute, CSIC, Madrid, Spain). In this article, we catalogue and analyse more than 4,500 of Cajal's histological preparations, the same preparations he used during his scientific career...

  6. SE Marine Mammal Histology/Tissue data

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Tissue samples are collected from stranded marine mammals in the Southeastern United States. These tissue samples are examined histologically and evaluated to...

  7. Achilles tendon assessed with sonoelastography: histologic agreement

    National Research Council Canada - National Science Library

    Klauser, Andrea S; Miyamoto, Hideaki; Tamegger, Mario; Faschingbauer, Ralph; Moriggl, Bernhard; Klima, Guenther; Feuchtner, Gudrun M; Kastlunger, Martin; Jaschke, Werner R

    2013-01-01

    ...) and sonoelastography of the Achilles tendon with findings at histologic assessment. This study was conducted with the approval of the institutional review boards, and all cadavers were in legal custody of the study institution...

  8. DNA markers in plant improvement: an overview.

    Science.gov (United States)

    Kumar, L S

    1999-09-01

    The progress made in DNA marker technology has been tremendous and exciting. DNA markers have provided valuable tools in various analyses ranging from phylogenetic analysis to the positional cloning of genes. The development of high-density molecular maps which has been facilitated by PCR-based markers, have made the mapping and tagging of almost any trait possible. Marker-assisted selection has the potential to deploy favorable gene combinations for disease control. Comparative studies between incompatible species using these markers has resulted in synteny maps which are useful not only in predicting genome organization and evolution but also have practical application in plant breeding. DNA marker technology has found application in fingerprinting genotypes, in determining seed purity, in systematic sampling of germplasm, and in phylogenetic analysis. This review discusses the use of this technology for the genetic improvement of plants.

  9. An osteological and histological investigation of cranial joints in geckos.

    Science.gov (United States)

    Payne, Samantha L; Holliday, Casey M; Vickaryous, Matthew K

    2011-03-01

    Cranial kinesis is a widespread feature of gekkotan lizards. Previous studies of kinesis in lizards often described the relevant, mobile joints as synovial, thus characterized by the presence of a synovial cavity lined with articular cartilage. To date however, detailed investigations of cranial joint histology are lacking. We examined eight cranial joints (quadrate-articular, quadrate-pterygoid, quadrate-otooccipital, quadrate-squamosal, epipterygoid-prootic, epipterygoid-pterygoid, basisphenoid-pterygoid, and frontal-parietal) in five gekkotan species (Oedura lesueuerii, Eublepharis macularius, Hemitheconyx caudicinctus, Tarentola annularis, and Chondrodactylous bibronii) using microcomputed tomography and serial histology. Particular focus was given to the relationship between the bony and soft-tissue components of the joint. Our results demonstrate that only three of these joints are synovial: the quadrate-articular, epipterygoid-pterygoid, and basisphenoid-pterygoid joints. The frontal-parietal and quadrate-pterygoid joints are syndesmosis (fibrous), the epipterygoid-prootic and quadrate-otooccipital joints are synchondroses (cartilaginous without a synovial cavity) and the quadrate-squamosal joint was not present. Based on previous descriptions, we determine that the structure of some cranial joints is variable among lizard taxa. We caution that osteology does not necessarily predict cranial joint histology. Although the functional implications of these findings remain to be explored we note that the development of synovial joints appears to be associated with a neural crest origin for the elements involved. Copyright © 2011 Wiley-Liss, Inc.

  10. Registration methodology for histological sections and in vivo imaging of human prostate.

    Science.gov (United States)

    Park, Hyunjin; Piert, Morand R; Khan, Asra; Shah, Rajal; Hussain, Hero; Siddiqui, Javed; Chenevert, Thomas L; Meyer, Charles R

    2008-08-01

    Registration enables quantitative spatial correlation of features from different imaging modalities. Our objective is to register in vivo imaging with histologic sections of the human prostate so that histologic truth can be correlated with in vivo imaging features. In vivo imaging of the prostate included T2-weighted anatomic and diffusion weighted 3-T magnetic resonance imaging (MRI) as well as 11C-choline positron emission tomography (PET). In addition, ex vivo 3-T MRI of the prostate specimen, histology, and associated block face photos of the prostate specimen were obtained. A standard registration method based on mutual information (MI) and thin-plate spline (TPS) was applied. Registration among in vivo imaging modalities is well established; however, accurate registration involving histology is difficult. Our approach breaks up the difficult direct registration of histology and in vivo imaging into achievable subregistration tasks involving intermediate ex vivo modalities like block face photography and specimen MRI. Results of subregistration tasks are combined to compute the intended, final registration between in vivo imaging and histology. The methodology was applied to two patients and found to be clinically feasible. Overall registered anatomic MRI, diffusion MRI, and 11C-choline PET aligned well with histology qualitatively for both patients. There is no ground truth of registration accuracy as the scans are real patient scans. An indirect validation of the registration accuracy has been proposed comparing tumor boundary markings found in diffusion MRI and histologic sections. Registration errors for two patients between diffusion MRI and histology were 3.74 and 2.26 mm. This proof of concept paper demonstrates a method based on intrinsic image information content for successfully registering in vivo imaging of the human prostate with its post-resection histology, which does not require the use of extrinsic fiducial markers. The methodology

  11. Esophageal Carcinoma Histology Affects Perioperative Morbidity Following Open Esophagogastrectomy

    Directory of Open Access Journals (Sweden)

    Charles E. Woodall

    2008-01-01

    Full Text Available Background. Esophagectomy for esophageal cancer is being practiced routinely with favorable results at many centers. We sought to determine if tumor histology is a powerful surrogate marker for perioperative morbidity. Methods. Seventy three consecutive patients managed operatively were reviewed from our prospectively maintained database. Results. Adenocarcinoma (AC was present in 52 (71% and squamous cell (SCC in 21 (29%. The use of neoadjuvant therapy was similar for the AC (34.62% and SCC (42.86% groups. The SCC group had a higher incidence of prior pulmonary disease than the AC group (23.8% versus 5.8%, resp.; =.03. SCC patients were more likely to have a prolonged ICU stay than AC patients (=.004 despite similar complication rates, EBL, and prognostic nutritional index. The SCC group did, however, experience higher grades of complications (=.0053. Conclusions. Presence of SCC was the single best predictor of prolonged ICU stay and more severe complications as defined by this study. Only a past history of pulmonary disease was different between the two histologic subgroups.

  12. Molecular markers in the surgical margin of oral carcinomas

    DEFF Research Database (Denmark)

    Bilde, Anders; von Buchwald, Christian; Dabelsteen, Erik

    2009-01-01

    epithelium in the surgical resection margin may explain the local recurrence rate. The purpose of this study is to investigate the presence of senescence markers, which may represent early malignant changes in the margin that in routine pathological evaluations are classified as histologically normal...

  13. Morphological and histological identification of Paramphistomum cervi (Trematoda: Paramiphistoma in the rumen of infected sheep

    Directory of Open Access Journals (Sweden)

    Vijayata Chaoudhary

    2015-01-01

    Full Text Available Aim: This study was undertaken to identify Paramphistomum cervi on the basis of its morphology and histology to be the common cause of paramphistomosis in infected sheep and its differentiation from other similar Paramphistomes in Gujarat. Materials and Methods: Adult rumen flukes were recovered from the rumen of naturally infected sheep slaughtered in various abattoirs in Gujarat. Some adult flukes were flattened and stained in Borax carmine, and some were sectioned in the median sagittal plane and histological slides of the flukes were prepared for detailed morphological and histological studies. Result: Microscopic pictures of the parasite used in identification define the similarity in the morphology and histology of the anterior sucker, pharynx, esophagus, genital atrium, posterior sucker (acetabulum and testes to the P. cervi. Conclusion: It can be concluded that the most common species found in sheep infected with Paramphistomosis is P. cervi on the basis of its histo-morphological appearance in Gujarat.

  14. Comprehensive histological evaluation of bone implants

    Science.gov (United States)

    Rentsch, Claudia; Schneiders, Wolfgang; Manthey, Suzanne; Rentsch, Barbe; Rammelt, Stephan

    2014-01-01

    To investigate and assess bone regeneration in sheep in combination with new implant materials classical histological staining methods as well as immunohistochemistry may provide additional information to standard radiographs or computer tomography. Available published data of bone defect regenerations in sheep often present none or sparely labeled histological images. Repeatedly, the exact location of the sample remains unclear, detail enlargements are missing and the labeling of different tissues or cells is absent. The aim of this article is to present an overview of sample preparation, staining methods and their benefits as well as a detailed histological description of bone regeneration in the sheep tibia. General histological staining methods like hematoxylin and eosin, Masson-Goldner trichrome, Movat’s pentachrome and alcian blue were used to define new bone formation within a sheep tibia critical size defect containing a polycaprolactone-co-lactide (PCL) scaffold implanted for 3 months (n = 4). Special attention was drawn to describe the bone healing patterns down to cell level. Additionally one histological quantification method and immunohistochemical staining methods are described. PMID:24504113

  15. Polymorphic microsatellite markers for genetic studies of African ...

    African Journals Online (AJOL)

    Many wild animal species lack informative genetic markers for analysing genetic variation and structure, which is essential for effective long term conservation and management. We present heterologous microsatellite markers in six Tanzanian antelope species including: grant's gazelle, hartebeest, eland, roan, impala and ...

  16. Tanycytic Ependymoma: A Challenging Histological Diagnosis

    Directory of Open Access Journals (Sweden)

    Khaled M. Krisht

    2013-01-01

    Full Text Available Tanycytic ependymoma is a rare form of ependymoma that usually arises in the intramedullary spine. It has a unique histology emphasized by the inconspicuous ependymal pattern of cells and close resemblance to schwannoma and astrocytoma. The authors report a 50-year-old man with a cervical tanycytic ependymoma that was initially thought to be a schwannoma. The frozen histology section showed spindle cells with oval and elongated nuclei with occasional hemosiderin deposits present suggesting a preliminary diagnosis of schwannoma. Immunohistochemical staining of the permanent section revealed strong immunoreactivity for glial fibrillary acidic protein with intermittent S-100 positivity, confirming that the tumor was a tanycytic ependymoma. This underlines the challenges involved in making an accurate diagnosis and demonstrates that careful and detailed histological inspection with immunohistochemical stains and ultrastructural microscopy may be necessary to distinguish tanycytic ependymoma from other neoplasms.

  17. Correlation between clinical and histologic pulp diagnoses.

    Science.gov (United States)

    Ricucci, Domenico; Loghin, Simona; Siqueira, José F

    2014-12-01

    Clinicians routinely face conditions in which they have to decide whether the dental pulp can be saved or not. This study evaluated how reliable the clinical diagnosis of normal pulp/reversible pulpitis (savable pulp) or irreversible pulpitis (nonsavable pulp) is when compared with the histologic diagnosis. The study material consisted of 95 teeth collected consecutively in a general practice over a 5-year period and extracted for reasons not related to this study. Based on clinical criteria, teeth were categorized as having normal pulps, reversible pulpitis, or irreversible pulpitis. The former 2 were grouped together because they represent similar conditions in terms of prognosis. Teeth were processed for histologic and histobacteriologic analyses, and pulps were categorized as healthy, reversibly inflamed, or irreversibly inflamed according to defined criteria. The number of matching clinical/histologic diagnosis was recorded. The clinical diagnosis of normal pulp/reversible pulpitis matched the histologic diagnosis in 57 of 59 (96.6%) teeth. Correspondence of the clinical and histologic diagnosis of irreversible pulpitis occurred in 27 of 32 (84.4%) cases. Infection advancing to the pulp tissue was a common finding in teeth with irreversible pulpitis but was never observed in normal/reversibly inflamed pulps. Findings using defined criteria for clinical and histologic classification of pulp conditions revealed a good agreement, especially for cases with no disease or reversible disease. This means that the classification of pulp conditions as normal pulps, reversible pulpitis, and irreversible pulpitis has high chances of guiding the correct therapy in the large majority of cases. However, there is still a need for refined and improved means for reliable pulp diagnosis. Copyright © 2014 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

  18. DNA marker technology for wildlife conservation

    OpenAIRE

    Arif, Ibrahim A.; Haseeb A. Khan; Bahkali, Ali H.; Al Homaidan, Ali A.; Ahmad H. Al Farhan; Al Sadoon, Mohammad; Shobrak, Mohammad

    2011-01-01

    Use of molecular markers for identification of protected species offers a greater promise in the field of conservation biology. The information on genetic diversity of wildlife is necessary to ascertain the genetically deteriorated populations so that better management plans can be established for their conservation. Accurate classification of these threatened species allows understanding of the species biology and identification of distinct populations that should be managed with utmost care...

  19. Forehead wrinkles: a histological and immunohistochemical evaluation.

    Science.gov (United States)

    El-Domyati, Moetaz; Medhat, Walid; Abdel-Wahab, Hossam M; Moftah, Noha H; Nasif, Ghada A; Hosam, Wael

    2014-09-01

    Wrinkles are associated with cutaneous aging especially on sun-exposed skin. Despite they are considered a major topic in cosmetic dermatology, very few reports have studied the specific histological and immunohistochemical changes characteristic for wrinkles. The study aims to evaluate the histological and immunohistochemical changes of static forehead wrinkles in relation to surrounding photoaged skin. Biopsy specimens were obtained from the forehead wrinkles of 20 volunteers of Glogau's class III-IV wrinkles. Using histological and immunostaining methods coupled with computerized morphometric analysis, measurement of epidermal thickness and quantitative evaluation of total elastin and tropoelastin as well as collagen types I, III, and VII were performed for skin biopsies. In the wrinkle site, there was statistically significant lower epidermal thickness (P = 0.001), elastin (P wrinkle site and adjacent photoaged skin regarding collagen type I (P = 0.07) or III (P = 0.07). This study detected some histological and immunohistochemical differences in the wrinkle site when compared to adjacent photoaged skin. This may help in understanding the pathophysiology of facial wrinkling as well as its ideal way of management. © 2014 Wiley Periodicals, Inc.

  20. Sclerosing PEComa: A Histologic Surprise | Valiathan | African ...

    African Journals Online (AJOL)

    Sclerosing PEComa: A Histologic Surprise. M Valiathan, BP Sunil, L Rao, V Geetha, P Hedge. Abstract. PEComa represents a group of mesenchymal tumors consisting of perivascular epithelioid cells. We present a 50-year old female patient with a rare distinctive variant, sclerosing PEComa, characterized by extensive ...

  1. Histological and immunohistochemical evaluation of sentinel lymph ...

    African Journals Online (AJOL)

    of sentinel lymph nodes in breast cancer at a tertiary hospital in the ... To determine effective histological examination of sentinel lymph node (SLN) sections for the detection of metastatic breast carcinoma. ... protocols for the histopathological assessment of SLN in breast carcinoma especially in resourcelimited settings.

  2. Evaluation and histological maturation characteristics of fibrous ...

    African Journals Online (AJOL)

    Evaluation and histological maturation characteristics of fibrous dysplasia and ossifying fibroma: a case series. ... diagnosed as OF and FD were retrieved from the archival records of the Departments of Oral Surgery/Oral Pathology and Histopathology/Morbid Anatomy, Muhimbili University of Health and Allied Sciences.

  3. Exogenous fibrolytic enzymes to unlock nutrients: Histological ...

    African Journals Online (AJOL)

    Useni , Alain

    2013-07-08

    Jul 8, 2013 ... Abstract. There is a need for a better understanding of the mode-of-action of exogenous fibrolytic enzymes. (EFE) used as additives in ruminant feeds. Four forages, treated with EFE, were evaluated in vitro and histologically, in an attempt to determine the effect of EFE on tissue degradation. Weeping love ...

  4. Reptilian spermatogenesis: A histological and ultrastructural perspective.

    Science.gov (United States)

    Gribbins, Kevin M

    2011-07-01

    Until recently, the histology and ultrastructural events of spermatogenesis in reptiles were relatively unknown. Most of the available morphological information focuses on specific stages of spermatogenesis, spermiogenesis, and/or of the mature spermatozoa. No study to date has provided complete ultrastructural information on the early events of spermatogenesis, proliferation and meiosis in class Reptilia. Furthermore, no comprehensive data set exists that describes the ultrastructure of the entire ontogenic progression of germ cells through the phases of reptilian spermatogenesis (mitosis, meiosis and spermiogenesis). The purpose of this review is to provide an ultrastructural and histological atlas of spermatogenesis in reptiles. The morphological details provided here are the first of their kind and can hopefully provide histological information on spermatogenesis that can be compared to that already known for anamniotes (fish and amphibians), birds and mammals. The data supplied in this review will provide a basic model that can be utilized for the study of sperm development in other reptiles. The use of such an atlas will hopefully stimulate more interest in collecting histological and ultrastructural data sets on spermatogenesis that may play important roles in future nontraditional phylogenetic analyses and histopathological studies in reptiles.

  5. Gingival pigmentation (cause, treatment and histological preview

    Directory of Open Access Journals (Sweden)

    Rehab A. Abdel Moneim

    2017-06-01

    Full Text Available Facial appearance depends on several oral and extraoral factors. The gingiva is an important intraoral tissue which when affected particularly by pigmentation is mainly responsible for the unpleasant appearance. Several causes of gingival pigmentation were previously mentioned in text together with the possible techniques of treatment. In this review, we will focus on this topic with a histological point of view.

  6. Histological Characteristics of Bruises with Different Age

    Directory of Open Access Journals (Sweden)

    Irena Kostadinova-Petrova

    2017-10-01

    CONCLUSION: A detailed analysis of tissue changes in bruises every day from the initiation until their recovery, a detailed description of the histological finding can be given, which will be supported in the precise determination of the age of the injuries themselves.

  7. vaginal histological changes of the baboon

    African Journals Online (AJOL)

    2009-04-04

    Apr 4, 2009 ... VAGINAL HISTOLOGICAL CHANGES OF THE BABOON DURING THE NORMAL MENSTRUAL CYCLE AND. PREGNANCY. A. Nyachieo ... During the luteal phase, menstrual phase and pregnancy the squamous epithelium was ... point, an endoscopic cup (Karl Storz, GmbH & Co. KG, Germany) was used ...

  8. Histology. Notes for Students of Animal Husbandry.

    Science.gov (United States)

    Price, Charles J.; Reed, Josephine E.

    This document approaches the subject of Histology by way of simple independent unicellular organisms through the lower levels of cell organization and specialization to a detailed study of the highly complex tissues of vertebrate animals. Emphasis is placed on structure, but function is explained in some detail. The relationships between tissues…

  9. REVIEW ARTICLE Complications, disease profile and histological ...

    African Journals Online (AJOL)

    the diagnosis, treatment and long-term outcome of glomerular disease. Biopsies are specifically necessary in cases of: ... and (iv) the histological yield of the biopsies (amount of nephrons per biopsy taken) using this technique. .... infiltration of 10 ml of 2% lignocaine as local anaesthetic. All patients were prone with a pillow ...

  10. Cross-species amplification of 105 Lolium perenne SSR loci in 23 species within the Poaceae

    DEFF Research Database (Denmark)

    Jensen, Louise Bach; Holm, Preben Bach; Lübberstedt, Thomas

    2007-01-01

    Amplification of 105 Lolium perenne SSR markers was studied in 23 grass species representing seven tribes from three subfamilies of Poaceae. Twelve of the SSR markers are published for the first time. Between 2% and 96% of the SSR markers could be amplified within a given species. A subset of eight...

  11. New Colors for Histology: Optimized Bivariate Color Maps Increase Perceptual Contrast in Histological Images

    Science.gov (United States)

    Kather, Jakob Nikolas; Weis, Cleo-Aron; Marx, Alexander; Schuster, Alexander K.; Schad, Lothar R.; Zöllner, Frank Gerrit

    2015-01-01

    Background Accurate evaluation of immunostained histological images is required for reproducible research in many different areas and forms the basis of many clinical decisions. The quality and efficiency of histopathological evaluation is limited by the information content of a histological image, which is primarily encoded as perceivable contrast differences between objects in the image. However, the colors of chromogen and counterstain used for histological samples are not always optimally distinguishable, even under optimal conditions. Methods and Results In this study, we present a method to extract the bivariate color map inherent in a given histological image and to retrospectively optimize this color map. We use a novel, unsupervised approach based on color deconvolution and principal component analysis to show that the commonly used blue and brown color hues in Hematoxylin—3,3’-Diaminobenzidine (DAB) images are poorly suited for human observers. We then demonstrate that it is possible to construct improved color maps according to objective criteria and that these color maps can be used to digitally re-stain histological images. Validation To validate whether this procedure improves distinguishability of objects and background in histological images, we re-stain phantom images and N = 596 large histological images of immunostained samples of human solid tumors. We show that perceptual contrast is improved by a factor of 2.56 in phantom images and up to a factor of 2.17 in sets of histological tumor images. Context Thus, we provide an objective and reliable approach to measure object distinguishability in a given histological image and to maximize visual information available to a human observer. This method could easily be incorporated in digital pathology image viewing systems to improve accuracy and efficiency in research and diagnostics. PMID:26717571

  12. New Colors for Histology: Optimized Bivariate Color Maps Increase Perceptual Contrast in Histological Images.

    Directory of Open Access Journals (Sweden)

    Jakob Nikolas Kather

    Full Text Available Accurate evaluation of immunostained histological images is required for reproducible research in many different areas and forms the basis of many clinical decisions. The quality and efficiency of histopathological evaluation is limited by the information content of a histological image, which is primarily encoded as perceivable contrast differences between objects in the image. However, the colors of chromogen and counterstain used for histological samples are not always optimally distinguishable, even under optimal conditions.In this study, we present a method to extract the bivariate color map inherent in a given histological image and to retrospectively optimize this color map. We use a novel, unsupervised approach based on color deconvolution and principal component analysis to show that the commonly used blue and brown color hues in Hematoxylin-3,3'-Diaminobenzidine (DAB images are poorly suited for human observers. We then demonstrate that it is possible to construct improved color maps according to objective criteria and that these color maps can be used to digitally re-stain histological images.To validate whether this procedure improves distinguishability of objects and background in histological images, we re-stain phantom images and N = 596 large histological images of immunostained samples of human solid tumors. We show that perceptual contrast is improved by a factor of 2.56 in phantom images and up to a factor of 2.17 in sets of histological tumor images.Thus, we provide an objective and reliable approach to measure object distinguishability in a given histological image and to maximize visual information available to a human observer. This method could easily be incorporated in digital pathology image viewing systems to improve accuracy and efficiency in research and diagnostics.

  13. A protocol for combining fluorescent proteins with histological stains for diverse cell wall components.

    Science.gov (United States)

    Ursache, Robertas; Andersen, Tonni Grube; Marhavý, Peter; Geldner, Niko

    2018-01-01

    Higher plant function is contingent upon the complex three-dimensional (3D) architecture of plant tissues, yet severe light scattering renders deep, 3D tissue imaging very problematic. Although efforts to 'clear' tissues have been ongoing for over a century, many innovations have been made in recent years. Among them, a protocol called ClearSee efficiently clears tissues and diminishes chlorophyll autofluorescence while maintaining fluorescent proteins - thereby allowing analysis of gene expression and protein localisation in cleared samples. To further increase the usefulness of this protocol, we have developed a ClearSee-based toolbox in which a number of classical histological stains for lignin, suberin and other cell wall components can be used in conjunction with fluorescent reporter lines. We found that a number of classical dyes are highly soluble in ClearSee solution, allowing the old staining protocols to be enormously simplified; these additionally have been unsuitable for co-visualisation with fluorescent markers due to harsh fixation and clearing. Consecutive staining with several dyes allows 3D co-visualisation of distinct cell wall modifications with fluorescent proteins - used as transcriptional reporters or protein localisation tools - deep within tissues. Moreover, the protocol is easily applied on hand sections of different organs. In combination with confocal microscopy, this improves image quality while decreasing the time and cost of embedding/sectioning. It thus provides a low-cost, efficient method for studying thick plant tissues which are usually cumbersome to visualise. Our ClearSee-adapted protocols significantly improve and speed up anatomical and developmental investigations in numerous plant species, and we hope they will contribute to new discoveries in many areas of plant research. © 2017 The Authors The Plant Journal © 2017 John Wiley & Sons Ltd.

  14. Assessing Date Palm Genetic Diversity Using Different Molecular Markers.

    Science.gov (United States)

    Atia, Mohamed A M; Sakr, Mahmoud M; Adawy, Sami S

    2017-01-01

    Molecular marker technologies which rely on DNA analysis provide powerful tools to assess biodiversity at different levels, i.e., among and within species. A range of different molecular marker techniques have been developed and extensively applied for detecting variability in date palm at the DNA level. Recently, the employment of gene-targeting molecular marker approaches to study biodiversity and genetic variations in many plant species has increased the attention of researchers interested in date palm to carry out phylogenetic studies using these novel marker systems. Molecular markers are good indicators of genetic distances among accessions, because DNA-based markers are neutral in the face of selection. Here we describe the employment of multidisciplinary molecular marker approaches: amplified fragment length polymorphism (AFLP), start codon targeted (SCoT) polymorphism, conserved DNA-derived polymorphism (CDDP), intron-targeted amplified polymorphism (ITAP), simple sequence repeats (SSR), and random amplified polymorphic DNA (RAPD) to assess genetic diversity in date palm.

  15. Histological quantification of maize stem sections from FASGA-stained images.

    Science.gov (United States)

    Legland, David; El-Hage, Fadi; Méchin, Valérie; Reymond, Matthieu

    2017-01-01

    Crop species are of increasing interest both for cattle feeding and for bioethanol production. The degradability of the plant material largely depends on the lignification of the tissues, but it also depends on histological features such as the cellular morphology or the relative amount of each tissue fraction. There is therefore a need for high-throughput phenotyping systems that quantify the histology of plant sections. We developed custom image processing and an analysis procedure for quantifying the histology of maize stem sections coloured with FASGA staining and digitalised with whole microscopy slide scanners. The procedure results in an automated segmentation of the input images into distinct tissue regions. The size and the fraction area of each tissue region can be quantified, as well as the average coloration within each region. The measured features can discriminate contrasted genotypes and identify changes in histology induced by environmental factors such as water deficit. The simplicity and the availability of the software will facilitate the elucidation of the relationships between the chemical composition of the tissues and changes in plant histology. The tool is expected to be useful for the study of large genetic populations, and to better understand the impact of environmental factors on plant histology.

  16. Correlation of the presence and extent of loss of heterozygosity mutations with histological classifications of Barrett’s esophagus

    Directory of Open Access Journals (Sweden)

    Ellsworth Eric

    2012-12-01

    Full Text Available Abstract Background Recent advances in the management of Barrett’s Esophagus (BE have placed greater emphasis on accurate diagnosis of BE as well as better prediction of risk for progression to esophageal adenocarcinoma (EAC. Histological evaluation of BE is particularly challenging with significant inter-observer variability. We explored the presence and extent of genomic instability in BE biopsy specimens as a means to add supplementary information to the histological classification and clinical decision-making related to early disease. Methods We reviewed histology slides from 271 patients known to have BE. Using histological features as a guide, we microdissected target cell populations with various histological classifications of BE (intestinal metaplasia, “indefinite for dysplasia”, low grade dysplasia, or high grade dysplasia. DNA was extracted from microdissected targets and analyzed for loss of heterozygosity (LOH using a panel of 16 LOH mutational markers associated with tumor suppressor genes at chromosomal loci 1p, 3p, 5q, 9p, 10q, 17p, 17q, 18q, 21q, 22q. The presence or absence of mutations and the clonality of each mutation were determined for each marker. Results The presence and clonal expansion of LOH mutations was formulated into mutational load (ML for each microdissected target analyzed. ML correlated with the histological classification of microdissected targets, with increasingly severe histology having higher ML. Three levels of mutation load (no ML, low ML, and high ML were defined based on the population of microdissected targets histologically classified as intestinal metaplasia. All microdissected targets with dysplasia had mutations, with a high ML consistently present in high grade dysplasia targets. Microdissected targets histologically classified as intestinal metaplasia or “indefinite for dysplasia” spanned a range of no, low, and high ML. Conclusions The results of this study reinforce the association

  17. Histological and Transcriptomic Analysis during Bulbil Formation in Lilium lancifolium

    Directory of Open Access Journals (Sweden)

    Panpan Yang

    2017-08-01

    Full Text Available Aerial bulbils are an important propagative organ, playing an important role in population expansion. However, the detailed gene regulatory patterns and molecular mechanism underlying bulbil formation remain unclear. Triploid Lilium lancifolium, which develops many aerial bulbils on the leaf axils of middle-upper stem, is a useful species for investigating bulbil formation. To investigate the mechanism of bulbil formation in triploid L. lancifolium, we performed histological and transcriptomic analyses using samples of leaf axils located in the upper and lower stem of triploid L. lancifolium during bulbil formation. Histological results indicated that the bulbils of triploid L. lancifolium are derived from axillary meristems that initiate de novo from cells on the adaxial side of the petiole base. Transcriptomic analysis generated ~650 million high-quality reads and 11,871 differentially expressed genes (DEGs. Functional analysis showed that the DEGs were significantly enriched in starch and sucrose metabolism and plant hormone signal transduction. Starch synthesis and accumulation likely promoted the initiation of upper bulbils in triploid L. lancifolium. Hormone-associated pathways exhibited distinct patterns of change in each sample. Auxin likely promoted the initiation of bulbils and then inhibited further bulbil formation. High biosynthesis and low degradation of cytokinin might have led to bulbil formation in the upper leaf axil. The present study achieved a global transcriptomic analysis focused on gene expression changes and pathways' enrichment during upper bulbil formation in triploid L. lancifolium, laying a solid foundation for future molecular studies on bulbil formation.

  18. Optical Histology: High-Resolution Visualization of Tissue Microvasculature

    Science.gov (United States)

    Moy, Austin Jing-Ming

    resolution, depth sectioned images of the microvasculature in mouse brain and the coronary microvasculature in mouse heart. Future directions of optical histology include the potential to facilitate visualization of the entire microvascular structure of an organ as well as visualization of other tissue molecular markers of interest.

  19. Histology and proteinuria after renal transplantation.

    Science.gov (United States)

    Serón, Daniel; Burgos, Dolores; Alonso, Angel

    2012-01-01

    Proteinuria is a nonspecific sign of the troubled renal allograft. Small increases of proteinuria more than 150 mg/d are associated with poor renal allograft survival. During the 90s, it was assumed that chronic allograft nephropathy, defined as the presence of interstitial fibrosis and tubular atrophy, was the histologic lesion responsible for proteinuria and renal function deterioration in most kidneys. Thus, the interest to pursue a histologic diagnosis in patients with proteinuria or renal function deterioration faded during this period. In 2005, the criteria to diagnose chronic humoral rejection, a condition that in the previous year was not distinguished from chronic allograft nephropathy (CAN), were defined. The description of chronic humoral rejection as a major cause of proteinuria and graft loss represented a change of paradigm because it became clear that chronic humoral rejection and other conditions such as recurrence of original disease, de novo glomerulonephritis, polyomavirus infection, and others are responsible for proteinuria. These conditions can be diagnosed on histologic and clinical grounds, provided that special techniques such as C4d, immunofluorescence, immunohistochemistry, electron microscopy, and determination of donor specific antibodies are used. Thus, it became rather clear that proteinuria should be studied by means of a renal biopsy, especially if we take into consideration that there is very poor correlation between the amount of proteinuria and the disease responsible for it. Studies based on surveillance biopsies showed that histologic diagnosis precedes clinical manifestations. Despite the lack of clinical trials, series of patients have shown that different entities respond to different treatments, further reinforcing the idea that early diagnosis and early treatment may contribute to improve graft outcome. Copyright © 2012 Elsevier Inc. All rights reserved.

  20. Metanephric Adenoma: clinical, imaging, and histological findings

    Energy Technology Data Exchange (ETDEWEB)

    Torricelli, Fabio Cesar Miranda; Marchini, Giovanni Scala, E-mail: fabio_torri@yahoo.com.b [Universidade de Sao Paulo (USP), SP (Brazil). Faculdade de Medicina. Dept. de Urologica; Campos, Rodrigo Sousa Madeira [Hospital do Servidor Publico Estadual, Sao Paulo, SP (Brazil). Dept. de Urologia; Gil, Antonio Otero [Instituto Dante Pazanezzi, Sao Paulo, SP (Brazil)

    2011-07-01

    Metanephric adenoma (MA), also designated nephrogenic nephroma or renal epithelial tumor resembling immature nephron, has just been recently recognized as a special type of benign renal epithelial tumor. Only few reports are found in the literature regarding this rare renal tumor. The purpose of this paper is to describe our clinical, imaging and histological / immunohistochemical observations of MA diagnosed in two patients and compare these data to previous information reported in medical databases (author)

  1. [Hodgkin's disease--a histologic problem

    DEFF Research Database (Denmark)

    Lauritzen, A.F.; Specht, L.; Nissen, N.I.

    1989-01-01

    Since the Rye classification of Hodgkin's disease, many lesions which resemble Hodgkin's disease microscopically have been described. The histological features of Hodgkin's disease, including the BNLI subclassification of nodular sclerosis, and the lesions which resemble Hodgkin's disease...... microscopically such as reactive lymph node hyperplasias, some non-Hodgkin's B- and T-cell lymphomas are reviewed. Recent reclassifications of lymphomas originally diagnosed as Hodgkin's disease have indicated that the disease was overdiagnosed, before the description of these lesions and before the development...

  2. Next-Generation Molecular Histology Using Highly Multiplexed Ion Beam Imaging (MIBI) of Breast Cancer Tissue Specimens for Enhanced Clinical Guidance

    Science.gov (United States)

    2015-07-01

    channels specific for each region of interest. Histone H3 and dsDNA are being used as nuclear markers; lamin A/C and nuclear pore complex are...AWARD NUMBER: W81XWH-14-1-0180 TITLE: Next-Generation Molecular Histology Using Highly Multiplexed Ion Beam Imaging (MIBI) of Breast Cancer Tissue...4. TITLE AND SUBTITLE Next-Generation Molecular Histology Using Highly Multiplexed Ion Beam Imaging (MIBI) of Breast Cancer Tissue Specimens for

  3. The histological nature of epulides in dogs.

    Science.gov (United States)

    Verstraete, F J; Ligthelm, A J; Weber, A

    1992-02-01

    The histological characteristics of a series of 154 oral tumours with the clinical appearance of epulides in 129 dogs were reviewed. Diagnoses were based on current criteria in human oral pathology and compared with the original diagnoses. The histological findings suggested that the majority of epulides in the dog can be classified as focal fibrous hyperplasia (43.5 per cent), peripheral ameloblastoma (17.5 per cent), peripheral odontogenic fibroma (WHO type) (16.9 per cent) and pyogenic granuloma (1.95 per cent). In addition, a number of other odontogenic tumours (1.95 per cent) and non-odontogenic tumours (18.2 per cent) such as fibrosarcoma and squamous cell carcinoma, which are not traditionally associated with the clinical appearance of an epulis, were diagnosed. Of 74 lesions that were previously diagnosed as fibromatous and ossifying epulides, 50 (68 per cent) were reclassified as focal fibrous hyperplasia and 21 (28 per cent) as peripheral odontogenic fibroma (WHO type). The majority of lesions (76 per cent), which were originally classified as acanthomatous epulis, were found to be peripheral ameloblastoma. In addition, three squamous cell carcinomas, two rare odontogenic tumours and two cases of focal fibrous hyperplasia were diagnosed in this classification. It was concluded that, as in man, the term epulis is a clinically descriptive term and that the renal nature of these lesions should be determined histologically.

  4. Normal Vulvar Histology: Variation by Site.

    Science.gov (United States)

    Day, Tania; Holland, Seán M; Scurry, James

    2016-01-01

    The aim of the study was to assess the histology of normal vulvar skin with attention to anatomic location and epithelium type. We performed a retrospective histologic review of 118 vulvar biopsies and excisions obtained between 2010 and 2014 with adjacent normal skin or mucosa. Exclusions included age younger than 18 years, vestibulectomy, labiaplasty, inflammatory dermatoses, and insufficient normal tissue for assessment. Stratum corneum morphology was assessed as basket weave, compact, or intermediate. Stratum granulosum cell layer number and epithelial thickness were recorded. Dermal lymphocytic infiltrate was described as nil, sparse, moderate, or dense. Fischer exact test, Pearson χ, and Student t test were used for statistical analysis. There were 7 cases from mons pubis, 11 from perineum, 83 from labia, and 17 from vestibule. In the skin, the stratum corneum morphology was basket weave in 31%, compact in 35%, and intermediate in 34%. Stratum corneum at the mons pubis was uniformly basket weave, whereas at perineum, it was either compact or intermediate (7/7 vs 0/11; p histological findings. Pathologists need to be aware of site-related differences of the vulvar epithelium to avoid overdiagnosis of pathological conditions.

  5. Identifikasi Keragaman Genetik Gen 12S Ribomsom RNA Sebagai Penanda Genetik untuk Penentuan Spesies Kuskus (IDENTIFICATION OF GENETIC DIVERSITY 12SRRNA GENES AS GENETIC MARKER FOR DETERMINING SPECIES CUSCUS)

    OpenAIRE

    Rini Widayanti; Hery Wijayanto; Woro Danur Wendo; Rony Marsyal Kunda

    2015-01-01

    Cuscus is marsupial’s animal (Phalageridae) which has limited spread in eastern Indonesia (Sulawesi,Maluku, Papua), Australia and Papua New Guinea. The ex-situ and in-situ conservation of cuscus undercaptivating condition is an alternative solution to protect cuscus from extinction. This study aimed todetermine nucleotide sequence and genetic markers on 12Sr RNA gene with sequencing method of eachspecies on three islands. Whole genome DNA was extracted from 17 samples of cuscus obtained fromd...

  6. TROPONIN T AND HISTOLOGICAL CHARACTERISTICS OF RAT MYOCARDIAL INFARCTION INDUCED BY ISOPROTERENOL

    Science.gov (United States)

    Hasić, Sabaheta; Jadrić, Radivoj; Kiseljaković, Emina; Mornjaković, Zakira; Winterhalter-Jadrić, Mira

    2007-01-01

    Tin our investigation, we used short-time model of myocardial infarction of rats induced by high dose of isoproterenol (ISP). We investigated cardiac troponin T blood level (cTnT) and histologi-cal characteristics of rat myocardium. ISP, single, intraperitoneal dose 250 mg/kg was given to male, adult, Wistar rats (n=12). Rats were distributed depending on their body weight in subgroups: ISP I (BW 260-280g) and ISP II (BW 250-400g). Control group (n=9) was treated with intraperitoneal dose of 0,95% NaCl. Cardiac TnT was measured by electrochemiluminiscence (ECLA) sandwich immunoassay in rat serum 4 hours after ISP application. Rats’ hearts were dissected and examined by qualitative histological method (HE). Statistical significance was set at 0,05. There was significant difference in cTnT of ISP II (p=0,0001) vs. control and ISP I (p<0,05) vs. control. Significant difference was beetween ISP I and ISP II subgroups (p<0.001). The accent of histological changes of myocardium was on nuclei of cell. Cells showed acydophilic changes and nuclei disappearance as signs of coagulative necrosis development. Extensivity of histological changes were different beetween ISP I and ISP II subgroup. Used dose of ISP induced development of myocardial necrosis in rats. Suben-docardial portion of myocardium was more vulnerability than subepicardial portion. Rats of ISP II had more extensive histological changes than these in ISP I. Administered doses of ISP enabled cTnT utilization as a marker of myocardial necrosis. PMID:17848144

  7. Beyond Histological Remission: Intramucosal Calprotectin as a Potential Predictor of Outcomes in Ulcerative Colitis.

    Science.gov (United States)

    Guirgis, Marianne; Wendt, Emily; Wang, Lai Mun; Walsh, Alissa; Burger, Daniel; Bryant, Robert V; Kent, Alex; Adamson, Rebecca; Brain, Oliver; Travis, Simon P L; Keshav, Satish

    2017-04-01

    Histological remission and low faecal calprotectin are positive prognostic factors in ulcerative colitis [UC]. Intramucosal calprotectin [iMC], which can be readily determined by immunohistochemistry, has not so far been evaluated as a predictor of outcome in UC. We aimed to investigate the relationship between iMC and clinical, endoscopic, and histological measures of remission in UC, and the independent prognostic value of iMC. Ambulant patients with UC were recruited for a study comparing clinical activity indices. Sigmoidoscopy and biopsy were performed at the index visit. Clinical, endoscopic, and histological activity were scored and iMC semi-quantitatively measured using immunohistochemistry for the S100A8/9 heterodimer on colonic biopsies, scored as the mean number of positive cells in five high-power fields [HPF]. At the end of follow-up [6 years], data on steroid use, hospitalisation, and colectomy ['adverse outcomes'] were collected. iMC was determined in 83 patients and 20 controls, and correlated with clinical, endoscopic, and histological activity [r = 0.51, 0.65, 0.53, p > 0.001, respectively]. iMC was lowest (median 2.4, interquartile range [IQR]: 5.2-5, p iMC > 5/HPF was associated with adverse outcome (hazard ratio [HR] 3.36, confidence interval [CI] 1.58, 7.15, p iMC > 5 cells/HPF avoided an adverse outcome after 1, 3, and 6 years, respectively. iMC was lowest in patients with concordant clinical, endoscopic, and histological remission. Median iMC > 5/HPF was associated with adverse outcomes despite histological remission. Therefore iMC is a potentially useful independent marker of activity.

  8. Single-species versus dual-species probiotic supplementation as an emerging therapeutic strategy for obesity.

    Science.gov (United States)

    Karimi, G; Jamaluddin, R; Mohtarrudin, N; Ahmad, Z; Khazaai, H; Parvaneh, M

    2017-10-01

    Recent studies have reported beneficial effects of specific probiotics on obesity. However, the difference in the anti-obesity effects of probiotics as single species and dual species is still uncertain. Therefore, we aimed to compare the efficacy of single and dual species of bacteria on markers of obesity in high-fat diet-induced obese rats. A total of 40 male Sprague-Dawley rats were assigned to one of five groups of varying diets as follows: standard diet, high fat diet (HFD), HFD supplemented with Lactobacillus casei strain Shirota, HFD supplemented with Bifidobacterium longum and HFD supplemented with a mixture of these two bacterial species. After 15 weeks of supplementation, the animals were examined for changes in body weight, body fat, total count of bacteria in fecal, blood serum lipid profile, leptin, adiponectin and inflammatory biomarkers. Histological analysis of the liver and adipose tissue was performed and the hepatic mRNA expression levels of genes related to lipid metabolism were measured. It was found that probiotic supplementation of either B. longum or a mixture of B. longum and LcS bacteria significantly reduced weight and triglycerides in the HFD groups. Supplementation of B. longum bacteria showed better results in terms of modulating leptin level, fat mass, adipocyte size and lipoprotein lipase expression, as well as increasing adiponectin and peroxisome proliferator-activated receptors-γ expression compared to dual species of bacteria. No significant differences were observed in the total count of fecal bacteria, glucose and inflammatory biomarker levels between supplemented groups. B. longum supplementation in obesity was more beneficial in metabolic profile changes than the mixture species. Copyright © 2017 The Italian Society of Diabetology, the Italian Society for the Study of Atherosclerosis, the Italian Society of Human Nutrition, and the Department of Clinical Medicine and Surgery, Federico II University. Published by Elsevier B

  9. 53 original article histological and biochemical markers of the liver of ...

    African Journals Online (AJOL)

    boaz

    University of Technology, P.M.B. 4000, Ogbomoso, Oyo State, Nigeria. E mail: koladipo2k3@yahoo.co.uk. ABSTRACT ... polymerization of DNA from viral RNA has been an important therapeutic target for the treatment of ... reverse transcriptase at amino acid residues 181 and. 188. This site is close to but not directly at the.

  10. Histological and biochemical markers of the liver of male Wistar rats ...

    African Journals Online (AJOL)

    Background: Mechanism of action of nevirapine in the prophylaxis treatment and treatment of HIV-1 may involve elevations in levels of alanine aminotransferase, aspartate aminotransferase, alkaline phosphatase and other biomarkers of liver function. This study presents the hepatotoxic effect of nevirapine suspension ...

  11. Autoimmune hepatitis, one disease with many faces: Etiopathogenetic, clinico-laboratory and histological characteristics

    Science.gov (United States)

    Gatselis, Nikolaos K; Zachou, Kalliopi; Koukoulis, George K; Dalekos, George N

    2015-01-01

    Autoimmune hepatitis (AIH) is an unresolving progressive liver disease of unknown etiology characterized by hypergammaglobulinemia, autoantibodies detection and interface hepatitis. Due to the absence of specific diagnostic markers and the large heterogeneity of its clinical, laboratory and histological features, AIH diagnosis may be potentially difficult. Therefore, in this in-depth review we summarize the substantial progress on etiopathogenesis, clinical, serological and histological phenotypes of AIH. AIH has a global distribution affecting any age, both sexes and all ethnic groups. Clinical manifestations vary from asymptomatic to severe or rarely fulminant hepatitis. Hypergammaglobulinemia with selective elevation of IgG is found in most cases. Autoimmune attack is perpetuated, possibly via molecular mimicry, and favored by the impaired control of T-regulatory cells. Histology (interface hepatitis, emperipolesis and hepatic rosette formation) and autoantibodies detection although not pathognomonic, are still the hallmark for a timely diagnosis. AIH remains a major diagnostic challenge. AIH should be considered in every case in the absence of viral, metabolic, genetic and toxic etiology of chronic or acute hepatitis. Laboratory personnel, hepato-pathologists and clinicians need to become more familiar with disease expressions and the interpretation of liver histology and autoimmune serology to derive maximum benefit for the patient. PMID:25574080

  12. Serotonin, neural markers and memory

    Directory of Open Access Journals (Sweden)

    Alfredo eMeneses

    2015-07-01

    Full Text Available Diverse neuropsychiatric disorders present dysfunctional memory and no effective treatment exits for them; likely as result of the absence of neural markers associated to memory. Neurotransmitter systems and signaling pathways have been implicated in memory and dysfunctional memory; however, their role is poorly understood. Hence, neural markers and cerebral functions and dysfunctions are revised. To our knowledge no previous systematic works have been published addressing these issues. The interactions among behavioral tasks, control groups and molecular changes and/or pharmacological effects are mentioned. Neurotransmitter receptors and signaling pathways, during normal and abnormally functioning memory with an emphasis on the behavioral aspects of memory are revised. With focus on serotonin, since as it is a well characterized neurotransmitter, with multiple pharmacological tools, and well characterized downstream signaling in mammals’ species. 5-HT1A, 5-HT4, 5-HT5, 5-HT6 and 5-HT7 receptors as well as SERT (serotonin transporter seem to be useful neural markers and/or therapeutic targets. Certainly, if the mentioned evidence is replicated, then the translatability from preclinical and clinical studies to neural changes might be confirmed. Hypothesis and theories might provide appropriate limits and perspectives of evidence

  13. Usefulness of systematic histological examination in routine forensic autopsy.

    Science.gov (United States)

    de la Grandmaison, Geoffroy Lorin; Charlier, Philippe; Durigon, Michel

    2010-01-01

    The forensic community does not agree on the need to perform histological examination at forensic autopsy. The aim of our study was to determine the usefulness of systematic standard histology in forensic autopsies. A prospective study was carried out on 428 autopsy cases for which standard histological examination was systematic. Mechanism of death not shown by gross anatomic findings was discovered by histology in about 40% of the cases. Cause of death was established by only histology in 8.4% of the cases. Microscopic findings affected the manner of death in 13% of the cases. Histology provided complementary information about prior medical condition of the deceased in about 49% of the cases. Traumatic lesions were better documented by histology in about 22% of the cases. According to the results of our study, systematic standard histology for the main organs should be used in routine forensic autopsies.

  14. Anatomy, histology, and ultrasonography of the normal adrenal gland in brown lemur: Eulemur fulvus.

    Science.gov (United States)

    Raharison, Fidiniaina; Bourges Abella, Nathalie; Sautet, Jean; Deviers, Alexandra; Mogicato, Giovanni

    2017-04-01

    The medical care currently to brown lemurs (Eulemur fulvus) is limited by a lack of knowledge of their anatomy. The aim of this study was to describe the anatomy and histology and obtain ultrasonographic measurements of normal adrenal glands in these animals. The adrenal glands of four lemurs cadavers were used for the anatomical and histological studies, and those of 15 anesthetized lemurs were examined by ultrasonography. Anatomically, the adrenal glands of brown lemurs are comparable to those of other species. The histological findings showed that the cortex is organized into three distinct layers, whereas most domestic mammals have an additional zone. The surface area of the adrenal glands increased with body weight, and the area of the right adrenal was slightly larger than the left. We suggest using ultrasonography to aid the etiological diagnosis of behavioral abnormalities that might be due to dysfunctions of the adrenal gland. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  15. Clinical and histological features of nonalcoholic steatohepatitis in Iranian patients

    Directory of Open Access Journals (Sweden)

    Haghpanah Babak

    2003-10-01

    Full Text Available Abstract Background Although several studies have been performed on risk factors and natural course of NASH, it seems that NASH tends to be more than a disease confined to strict boundaries. The objective of this study was to assess the clinical and paraclinical features and risk factors for non-alcoholic steatohepatitis (NASH patients in an Iranian population Methods Patients with histologically confirmed NASH who had elevated liver aminotransaminases, negative serologic markers of viral or autoimmune hepatitis and no findings in favor of metabolic liver disease were enrolled. A careful history was taken regarding alcohol intake. Results 53 patients consisting of 32 male and 21 female entered the study. The mean age was 37.8 ± 11.3 years. Twenty-six patients (55.3% were overweight, 15 (31.9% obese, 40 (75.5% dyslipidemic, and three patients (5.7% were diabetic. Liver biopsy showed mild steatosis in 35.7%, moderate steatosis in 53.6%, and severe forms in 10.7%. In 80.2% of patients, portal inflammation was present, and 9.4% had cirrhosis. The amount of increase in liver enzymes bore no relationship with fibrosis, portal inflammation, and degree of steatosis. Conclusions The patients in our study showed a male predominancy and were somewhat younger than other studies.

  16. Current Issues in Histology, Biology and Prognosis of Hodgkin Lymphoma

    Directory of Open Access Journals (Sweden)

    Marjanović Goran

    2017-06-01

    Full Text Available High risk Hodgkin lymphoma patients may occasionally have borderline characteristics similar to gray zone lymphomas and T-cell/histiocyte rich B cell lymphomas. These entities require different and more aggressive treatment modalities. Aggressive behavior is often associated with disturbances caused by Epstein Barr virus, or immune evasion caused by overexpression of check point inhibitors PDL-1 and PDL-2 coupled with the lack of expression of Class I and II MHC molecules. Galectin-1, TARC, sCD163 and other surrogate markers of immunosuppression in Hodgkin lymphoma may be useful for the assessment of treatment response. The improvements in lymphoma management diminished the importance of prognostic factors unified in the International Prognostic Scoring system, reducing them from 7 to 3 factors that remained relevant. Interim PET analysis is the only method able to identify resistant patients while chemotherapy is ongoing, thus enabling adjustment of treatment according to the treatment response. Efforts for stratification of patients according to disease histology, biology, microenvironment, clinical scoring systems and PET scan are ongoing. Current breakthroughs have set strong background for novel therapies with monoclonal antibodies and check point inhibitors that will result in improvement of management of high risk patients.

  17. Correlation between ICDAS and histology: Differences between stereomicroscopy and microradiography with contrast solution as histological techniques.

    Directory of Open Access Journals (Sweden)

    Samara de Azevedo Gomes Campos

    Full Text Available Detection of occlusal caries with visual examination using ICDAS correlates strongly with histology under stereomicroscopy (SM, but dentin aspects under SM are ambiguous regarding mineral content. Thus, our aim was to test two null hypotheses: SM and microradiography result in similar correlations between ICDAS and histology; SM and microradiography result in similar positive (PPV and negative predictive values (NPV of ICDAS cut-off 1-2 (scores 0-2 as sound with histological threshold D3 (demineralization in the inner third of dentin. Occlusal surfaces of extracted permanent teeth (n = 115 were scored using ICDAS. Undemineralized ground sections were histologically scored using both SM without contrast solution and microradiography after immersion in Thoulet's solution 1.47 for 24 h (MRC. Correlation between ICDAS and histology differed from SM (0.782 to MRC (0.511 (p = 0.0002, with a large effect size "q" of 0.49 (95% CI: 0.638/0.338. For ICDAS cut-off 1-2 and D3, PPV from MRC (0.56 was higher than that from SM (0.28 (p< 0.00001; effect size h = 0.81, and NPV from MRC (0.72 was lower than that from SM (1,00 (p < 0.00001; effect size h = 1.58. In conclusion, SM overestimated the correlation between ICDAS and lesion depth, and underestimated the number of occlusal surfaces with ICDAS cut-off 1-2 and deep dentin demineralization.

  18. Isolation of compound microsatellite markers in Begonia fenicis (Begoniaceae) endemic to East and Southeast Asian islands.

    Science.gov (United States)

    Nakamura, Koh; Huang, Chiun-Jr; Rubite, Rosario Rivera; Leong, Wai-Chao; Kono, Yoshiko; Yang, Hsun-An; Peng, Ching-I

    2012-01-01

    We developed compound microsatellite markers for Begonia fenicis, a species endemic to eastern and southeastern Asian islands, to investigate geographical genetic structure. Using the compound microsatellite marker technique, 21 markers were developed and six polymorphic markers were characterized for samples from four islands in Taiwan and southern Japan. The number of alleles per locus ranged from two to six (mean = 4.33). Observed and expected heterozygosities were 0.125-0.725 (0.383) and 0.498-0.719 (0.641), and polymorphic information content was 0.371-0.664 (0.567). The interspecific transferability of the 21 markers was evaluated for eight species of the section Diploclinium from the Philippines; 15 markers were successfully amplified in one to eight species. These results indicate the utility of the six microsatellite markers in B. fenicis to investigate geographical genetic structure. The transferable markers are potentially useful for other species of the section.

  19. Development and characterization of 21 polymorphic microsatellite markers for the barren-ground shrew, Sorex ugyunak (Mammalia: Sorcidae), through next-generation sequencing, and cross-species amplification in the masked shrew, S. cinereus

    Science.gov (United States)

    Sonsthagen, S.A.; Sage, G.K.; Fowler, M.; Hope, A.G.; Cook, J.A.; Talbot, S.L.

    2013-01-01

    We used next generation shotgun sequencing to develop 21 novel microsatellite markers for the barren-ground shrew (Sorex ugyunak), which were polymorphic among individuals from northern Alaska. The loci displayed moderate allelic diversity (averaging 6.81 alleles per locus) and heterozygosity (averaging 70 %). Two loci deviated from Hardy–Weinberg equilibrium (HWE) due to heterozygote deficiency. While the population did not deviate from HWE overall, it showed significant linkage disequilibrium suggesting this population is not in mutation-drift equilibrium. Nineteen of 21 loci were polymorphic in masked shrews (S. cinereus) from interior Alaska and exhibited linkage equilibrium and HWE overall. All loci yielded sufficient variability for use in population studies.

  20. Anatomy and histology of the frontalis muscle.

    Science.gov (United States)

    Costin, Bryan R; Plesec, Thomas P; Sakolsatayadorn, Natta; Rubinstein, Tal J; McBride, Jennifer M; Perry, Julian D

    2015-01-01

    To determine the gross and histologic configurations of the medial and lateral frontalis muscle. After making a midcoronal incision and bluntly dissecting to the orbital rim, the frontalis muscle was marked and measured. A protractor was used to measure the frontalis-orbicularis angle (FOA) and, when present, the angle of central bifurcation (AOB). Three strips of full-thickness forehead soft tissue measuring 0.5 cm × 8 cm were excised 3, 4.5, and 6 cm above the supraorbital notch and analyzed histologically for the presence of skeletal muscle fibers. Data were analyzed using 2-sample t tests, paired t tests, Pearson correlations, and mixed effect models. A p value of ≤ 0.05 was considered statistically significant. Sixty-four hemifaces of 32 cadavers (16 males) were dissected. All specimens were Caucasian. The average age was 78.2 years (range, 56-102 years). The average FOA was 88.7° (13.0°), and the average AOB was 90.0° (26.4°). A visible midline bifurcation occurred in 28 of 32 subjects (88%) at an average height of 4.7 cm (range, 2.4-7.2 cm) superior to the supraorbital notch. Continuous skeletal muscle fibers were present within the midline bifurcation histologically in 89%, 75%, and 11% of specimens 3.5, 5.0, and 6.5 cm above the supraorbital notch, respectively. In 46% of individuals, skeletal muscle fibers were continuously present microscopically within the gross bifurcation. While a medial frontalis muscle bifurcation occurs grossly in most senescent Caucasians, muscle fibers exist microscopically within this zone in nearly half of individuals.

  1. Histological changes in the gills of Clarias gariepinus (Teleostei ...

    African Journals Online (AJOL)

    Histological changes in the gills of Clarias gariepinus (Teleostei: Clariidae) from a polluted South African urban aquatic system. ... A semi-quantitative histological assessment was used to investigate histological changes in the gills of Clarias gariepinus from Marais Dam and Rietvlei Dam near Pretoria, which receive ...

  2. Endoscopic and Histologic Evaluations of Patients Referred for ...

    African Journals Online (AJOL)

    The most common histologic finding was chronic gastritis, which was found in 27 (49.5) patients. Conclusion: Upper gastrointestinal endoscopy with biopsy for histology is important in the evaluation of patients referred because of one indication or the other. Biopsy should always be obtained for histology even when the ...

  3. Ethnic variation of the histological subtypes of renal cell carcinoma ...

    African Journals Online (AJOL)

    The commonest histological variant in each of the ethnic groups, irrespective of sex, was clear cell carcinoma which accounted for 79.7% of all the histological subtypes found in Chinese, for 70.5% in Malaysian and 77.4% in Indian patients. The sarcomatoid histological subtype was found in 4.3% of the studied population ...

  4. Integration of Histology Lectures and Practical Teaching in China

    Science.gov (United States)

    Lu, Xiaoye; Cheng, Xin; Li, Ke; Lee, Kenneth Ka Ho; Yang, Xuesong

    2016-01-01

    Objectives: Human histology is a discipline concerning the study of microscopic structures of human tissues and organs--with the aid of light or electron microscopes. Traditional teaching of histology is composed of two separated components, theory and practice. The main disadvantage with traditional histology teaching is the detachment of theory…

  5. The histological slides and drawings of Cajal

    Directory of Open Access Journals (Sweden)

    Pablo Garcia-Lopez

    2010-03-01

    Full Text Available Ramon y Cajal´s studies in the world of neuroscience provoked a radical change in the course of its history. For this reason he is considered as the father of modern neuroscience. Some of his items are housed at the Cajal Museum (Cajal Institute, CSIC, Madrid, Spain. In this article, we will present an analysis of Cajal’s effects used in his research that could help to understand his enormous scientific production, and that offers some curious insights into his work and his legacy. Furthermore, we present some images relating Cajal’s scientific drawings with his histological slides.

  6. Oral fibrolipoma: A rare histological variant

    Directory of Open Access Journals (Sweden)

    Treville Pereira

    2014-01-01

    Full Text Available Lipomas are benign soft tissue mesenchymal neoplasms. Fibrolipoma is a histological variant of lipoma that mostly affects the buccal mucosa and causes functional and cosmetic disabilities. The diagnosis and differentiation of fibrolipoma with clinically similar lesions such as fibroma and pleomorphic adenoma is very essential for a correct treatment plan and complete follow-up. This article presents a case of a 35-year-old female with a fibrolipoma on the lingual marginal gingiva of the mandibular left third molar.

  7. Plant breeding with marker-assisted selection in Brazil

    OpenAIRE

    Sakiyama,Ney Sussumu; Ramos, Helaine Christine Cancela; Caixeta, Eveline Teixeira; Pereira,Messias Gonzaga

    2014-01-01

    Over the past three decades, molecular marker studies reached extraordinary advances, especially for sequencing and bioinformatics techniques. Marker-assisted selection became part of the breeding program routines of important seed companies, in order to accelerate and optimize the cultivar developing processes. Private seed companies increasingly use marker-assisted selection, especially for the species of great importance to the seed market, e.g. corn, soybean, cotton, and sunflower. In the...

  8. Embryonic Stem Cell Markers

    Directory of Open Access Journals (Sweden)

    Lan Ma

    2012-05-01

    Full Text Available Embryonic stem cell (ESC markers are molecules specifically expressed in ES cells. Understanding of the functions of these markers is critical for characterization and elucidation for the mechanism of ESC pluripotent maintenance and self-renewal, therefore helping to accelerate the clinical application of ES cells. Unfortunately, different cell types can share single or sometimes multiple markers; thus the main obstacle in the clinical application of ESC is to purify ES cells from other types of cells, especially tumor cells. Currently, the marker-based flow cytometry (FCM technique and magnetic cell sorting (MACS are the most effective cell isolating methods, and a detailed maker list will help to initially identify, as well as isolate ESCs using these methods. In the current review, we discuss a wide range of cell surface and generic molecular markers that are indicative of the undifferentiated ESCs. Other types of molecules, such as lectins and peptides, which bind to ESC via affinity and specificity, are also summarized. In addition, we review several markers that overlap with tumor stem cells (TSCs, which suggest that uncertainty still exists regarding the benefits of using these markers alone or in various combinations when identifying and isolating cells.

  9. Microsatellite loci in an endangered fern species, Athyrium viridescentipes (Woodsiaceae), and cross‐species amplification

    National Research Council Canada - National Science Library

    Izuno, Ayako; Takamiya, Masayuki; Kaneko, Shingo; Isagi, Yuji

    2011-01-01

    • Premise of the study: Microsatellite markers were characterized in Athyrium viridescentipes , a critically endangered fern species in Japan, to investigate its genetic diversity and population structure...

  10. Clinicopathological parameters associated with histological background and recurrence after surgical intervention of vocal cord leukoplakia.

    Science.gov (United States)

    Cui, Weixin; Xu, Wen; Yang, Qingwen; Hu, Rong

    2017-06-01

    Histological examination of biopsy shows usefulness in the diagnosis of vocal cord leukoplakia; however, in considerable amount of cases, the examination cannot provide definitive diagnosis of malignancy from benign conditions such as hyperplasia and dysplasia. The present work therefore was aimed to identify clinicopathological factors and molecular markers predictive of recurrence and malignant transformation of vocal cord leukoplakia.Clinical data of 555 cases of vocal cord leukoplakia enrolled from July 1999 to June 2014 were analyzed. The cohort consisted of keratosis (n = 137), hyperplasia (n = 139), dysplasia (n = 177), and primary (n = 10) and invasive (n = 46) carcinoma. Correlations between patients' backgrounds, clinicopathological factors, molecular markers (p53, p16, Ki67, cytokeratin, and proliferating cell nuclear antigen), and histology backgrounds were examined using by Pearson Chi-squared or Fisher exact test. Reflux symptom index (RSI) and reflux finding score (RFS) before and after treatment were compared using Wilcoxon signed-rank test. Risk factors for disease recurrence were identified using Cox proportional hazards models of multivariate analysis. Time to recurrence was analyzed using log-rank test of Kaplan-Meier method.In the present cohort, alcohol drinking was found associated with GRBAS grade (P = .0258) and the site (P = .0298) of leukoplakia. For the different disease types, chief complaint (P = .0179), GRBAS grade (P = .0101), mucosal wave (P leukoplakia was predictive of a lower risk of recurrence (odds ratio, 0.378; 95% confidence interval, 0.197-0.723; P = .0033). Absence of mucosal wave was associated with a shorter time-to-recurrence (P = .0357).The present work identified clinicopathological factors and molecular markers associated with the different histology of vocal cord leukoplakia, and also the prognostic factor for the low risk of recurrence after surgery.

  11. Regional Variations in Orbicularis Oculi Histology.

    Science.gov (United States)

    Costin, Bryan R; Plesec, Thomas P; Kopplin, Laura J; Chundury, Rao V; McBride, Jennifer M; Levine, Mark R; Perry, Julian D

    2015-01-01

    To investigate and compare the histologic compositions of the pretarsal, preseptal, and orbital orbicularis oculi muscle (OOM) using nonpreserved, fresh-frozen, human cadavers. The OOM was exposed using sharp and blunt dissection. A metric ruler was used to measure and mark 0.5 cm × 1 cm samples from each portion of the right, superior OOM. Samples were excised, fixed in formalin, and completely embedded in paraffin. Five-micrometer-thick, hematoxylin- and eosin-stained sections were generated for each sample and analyzed by an anatomical pathologist. The relative percentages of the 4 main tissue types (skeletal muscle, fibrous tissue, adipose tissue, and neurovascular tissue) were quantified. Forty-two samples were obtained from 14 Caucasian cadavers. On average, the pretarsal samples were composed of 83.5% skeletal muscle, 0.0% adipose, 5.0% neurovascular, and 11.5% fibrous tissue. Average preseptal OOM was 46.5% skeletal muscle, 12.7% adipose, 9.2% neurovascular, and 31.5% fibrous tissue. The orbital OOM was, on average, 42.7% skeletal muscle, 32.7% adipose tissue, 6.9% neurovascular, and 17.7% fibrous tissue. The OOM represents a histologically heterogeneous structure.

  12. [Abdominal wall prostheses. Biomechanic and histological study].

    Science.gov (United States)

    Rath, A M; Zhang, J; Amouroux, J; Chevrel, J P

    1996-01-01

    The best prosthetic material is one which provides the best mechanical resistance with the best biological tolerance. In order to assess the mechanical and histological properties of abdominal wall prostheses, we performed experimental tests in animal models comparing four materials: polypropylene, dacron, polyglactine 910 and a dacron-polyglactine 910 composite. One hundred thirty rabbits were used including 10 controls and 120 test animals. A medial laparotomy was closed with an antemuscular aponevrotic prosthesis in the test animals. Animals were sacrificed at one, two and three months after the operation. Abdominal wall and prosthesis samples were tested to determine resistance to pressure and extension, deformability and elasticity. Histology tests were also done to determine resistance quality and biological tolerance. Dacron was tolerated best and was less resistant than polypropylene, though resistance was satisfactory. There was no advantage with polyglactine compared with non-resorbable prostheses; its only indication would be a septic site. The composite material tested had a resistance comparable with that of dacron but was less well tolerated.

  13. Normal and pathological breast, the histological basis

    Energy Technology Data Exchange (ETDEWEB)

    Guinebretiere, J.M. [Department of Pathology, Centre Rene-Huguenin, 35 rue Dailly, 92210 Saint Cloud (France)]. E-mail: jm.guinebretiere@stcloud-huguenin.org; Menet, E. [Department of Pathology, Centre Rene-Huguenin, 35 rue Dailly, 92210 Saint Cloud (France); Tardivon, A. [Department of Radiology, Institut Curie, 26 rue d' Ulm, 75248 Paris Cedex 5 (France); Cherel, P. [Department of Radiology, Centre Rene-Huguenin, 35 rue Dailly, 92210 Saint Cloud (France); Vanel, D. [Department of Diagnostic Radiology, Institut Gustave-Roussy, 39 rue Camille Desmoulins, 94805 Villejuif (France)

    2005-04-01

    Breast tissue is heterogeneous, associating connective and glandular structures, which grow and change cyclically under hormonal regulation. Hormones are also thought to be the main determinant of the major benign and malignant pathologies encountered in the breast. Benign lesions are more frequent and fibrocystic changes are by far the most common among them. They usually associate different entities (adenosis, fibrosis, cysts and hyperplasia) but vary in intensity and extension. Thus, their clinical and radiographic presentation is extremely different from one patient to another. Adenofibroma is the most frequent tumour. It also undergoes modifications according to hormonal conditions. About 90% of malignant tumours are primary carcinoma. The incidence of intra-ductal carcinoma has risen dramatically since the development of screening because of its ability to induce calcification. Two mechanisms could be involved in the formation of calcification: one active (tumour cell secretion of vesicles), the other passive (necrotic cell fragments are released). Invasive carcinoma comprises numerous histological types. Stromal reactions essentially determines their shape: a fibrous reaction commonly found in ductal carcinoma creates a stellate lesion while other stroma, inflammatory (medullary carcinoma), vascular (papillary carcinoma) or mucinous determine nodular lesions whose borders push the surrounding tissue. The histological features which give rise to the radiographic pattern will be emphasised.

  14. Development of thirty-four novel polymorphic microsatellite markers ...

    Indian Academy of Sciences (India)

    China and northward to the Ariake Sound of southwestern ... Keywords. microsatellite markers; cross-species amplification; genetic structure; Coilia ectenes. Journal of ..... The nature of the microsatellite markers has made them particularly amenable for genetic analysis of natural populations (Jarne and Lagoda. 1996).

  15. Molecular markers: a potential resource for ginger genetic diversity studies.

    Science.gov (United States)

    Ismail, Nor Asiah; Rafii, M Y; Mahmud, T M M; Hanafi, M M; Miah, Gous

    2016-12-01

    Ginger is an economically important and valuable plant around the world. Ginger is used as a food, spice, condiment, medicine and ornament. There is available information on biochemical aspects of ginger, but few studies have been reported on its molecular aspects. The main objective of this review is to accumulate the available molecular marker information and its application in diverse ginger studies. This review article was prepared by combing material from published articles and our own research. Molecular markers allow the identification and characterization of plant genotypes through direct access to hereditary material. In crop species, molecular markers are applied in different aspects and are useful in breeding programs. In ginger, molecular markers are commonly used to identify genetic variation and classify the relatedness among varieties, accessions, and species. Consequently, it provides important input in determining resourceful management strategies for ginger improvement programs. Alternatively, a molecular marker could function as a harmonizing tool for documenting species. This review highlights the application of molecular markers (isozyme, RAPD, AFLP, SSR, ISSR and others such as RFLP, SCAR, NBS and SNP) in genetic diversity studies of ginger species. Some insights on the advantages of the markers are discussed. The detection of genetic variation among promising cultivars of ginger has significance for ginger improvement programs. This update of recent literature will help researchers and students select the appropriate molecular markers for ginger-related research.

  16. Molecular markers associated with salt tolerance in Egyptian wheats

    African Journals Online (AJOL)

    use

    techniques have been developed, a wealth of new DNA marker technologies has arisen enabling the generation of high-density molecular maps for all the major crop species. Molecular markers have also been extensively used to analyze the genetic diversity in crop plants. Based on the data obtained by RAPD analysis, ...

  17. (SSR) markers that are polymorphic between cultivars in Brassica ...

    African Journals Online (AJOL)

    ajl user 1

    2012-02-07

    Feb 7, 2012 ... there are still a limited number of DNA markers that may provide sufficient anchors for mapping inheritable traits ... As a byproduct of massive EST sequencing, it became possible to develop microsatellite-associated markers ..... several grass species. Theor. Appl. Genet. 109: 783-791. Scott KD, Eggler P, ...

  18. Markers of Field Cancerization: Proposed Clinical Applications in Prostate Biopsies

    Directory of Open Access Journals (Sweden)

    Kristina A. Trujillo

    2012-01-01

    Full Text Available Field cancerization denotes the occurrence of genetic, epigenetic, and biochemical aberrations in structurally intact cells in histologically normal tissues adjacent to cancerous lesions. This paper tabulates markers of prostate field cancerization known to date and discusses their potential clinical value in the analysis of prostate biopsies, including diagnosis, monitoring progression during active surveillance, and assessing efficacy of presurgical neoadjuvant and focal therapeutic interventions.

  19. Markers of Field Cancerization: Proposed Clinical Applications in Prostate Biopsies

    Science.gov (United States)

    Trujillo, Kristina A.; Jones, Anna C.; Griffith, Jeffrey K.; Bisoffi, Marco

    2012-01-01

    Field cancerization denotes the occurrence of genetic, epigenetic, and biochemical aberrations in structurally intact cells in histologically normal tissues adjacent to cancerous lesions. This paper tabulates markers of prostate field cancerization known to date and discusses their potential clinical value in the analysis of prostate biopsies, including diagnosis, monitoring progression during active surveillance, and assessing efficacy of presurgical neoadjuvant and focal therapeutic interventions. PMID:22666601

  20. Polymorphic microsatellite markers for genetic studies of African ...

    African Journals Online (AJOL)

    Administrator

    2011-09-26

    Sep 26, 2011 ... Many wild animal species lack informative genetic markers for analysing genetic variation and ... Game Reserves (MGR) and surrounding game controlled areas ..... the threatened Apennine chamois (Rupicapra pyrenaica.

  1. Inheritance and identification of SCAR marker linked to bacterial wilt ...

    African Journals Online (AJOL)

    STORAGESEVER

    2009-10-19

    Oct 19, 2009 ... Key word: Eggplant, bacterial wilt-resistance, molecular marker, inheritance. ... hundreds of plant species, including many crops such as tomato, potato ... rotation, adjusting the date of planting, cultural methods and soil ...

  2. Increased mean platelet volume is related to histologic severity of primary biliary cirrhosis

    OpenAIRE

    Tahtaci, Mustafa; Yurekli, Oyku T.; Bolat, Aylin D.; Balci, Serdar; Akin, Fatma E.; Buyukasik, Naciye S.; Ersoy, Osman

    2015-01-01

    Aim To evaluate the main platelet volume (MPV) as a severity marker in patients with primary biliary cirrhosis (PBC). Materials and methods Thirty-nine patients with biopsy-proven and as yet untreated PBC followed between January 2008 and January 2015 were included in this study. Liver biopsies were categorized as early stage (stage 1 and 2 according to Scheuer?s histological stage) and late stage (Scheuer?s stage 3 and 4). As part of the routine evaluation, all PBC patients had their full bl...

  3. Anatomy and histology of the lower urinary tract.

    Science.gov (United States)

    Pradidarcheep, Wisuit; Wallner, Christian; Dabhoiwala, Noshir F; Lamers, Wouter H

    2011-01-01

    The function of the lower urinary tract is basically storage of urine in the bladder and the at-will periodic evacuation of the stored urine. Urinary incontinence is one of the most common lower urinary tract disorders in adults, but especially in the elderly female. The urethra, its sphincters, and the pelvic floor are key structures in the achievement of continence, but their basic anatomy is little known and, to some extent, still incompletely understood. Because questions with respect to continence arise from human morbidity, but are often investigated in rodent animal models, we present findings in human and rodent anatomy and histology. Differences between males and females in the role that the pelvic floor plays in the maintenance of continence are described. Furthermore, we briefly describe the embryologic origin of ureters, bladder, and urethra, because the developmental origin of structures such as the vesicoureteral junction, the bladder trigone, and the penile urethra are often invoked to explain (clinical) observations. As the human pelvic floor has acquired features in evolution that are typical for a species with bipedal movement, we also compare the pelvic floor of humans with that of rodents to better understand the rodent (or any other quadruped, for that matter) as an experimental model species. The general conclusion is that the "Bauplan" is well conserved, even though its common features are sometimes difficult to discern.

  4. The urine marker test

    DEFF Research Database (Denmark)

    Elbe, Anne-Marie; Jensen, Stine Nylandsted; Elsborg, Peter

    2016-01-01

    of this new method via two questionnaires (n = 253). Furthermore, a third study (n = 91) investigated whether ingestion of the marker can identify the urine as coming from a specific person and whether the marker interferes with the detection of prohibited substances. RESULTS AND CONCLUSIONS: The results...... indicate that this new method finds wide acceptance both from athletes who have only heard about the procedure and those who have actually tested the new method. Furthermore, the marker, which can identify urine as coming from a specific person, does not interfere with the detection of prohibited...... that athletes are actually delivering their own urine. A method that can be used to alleviate the negative impact of a supervised urination procedure and which can also identify urine as coming from a specific athlete is the urine marker test. Monodisperse low molecular weight polyethylene glycols (PEGs...

  5. VT Roadside Historic Markers

    Data.gov (United States)

    Vermont Center for Geographic Information — Roadside Historic Site Marker program has proven an effective way to commemorate Vermont’s many people, events, and places of regional, statewide, or national...

  6. Are We Throwing Histology out with the Microscope? A Look at Histology from the Physician's Perspective

    Science.gov (United States)

    Pratt, Rebecca L.

    2009-01-01

    A trend in medical schools across the United States is the refurbishing of histology laboratories with digital microscopy systems. Although such systems may reduce curricular time, they do not teach basic microscope skills, and students who learn solely with these systems may be less prepared for their practices or specialties, particularly in…

  7. Rapid Authentication of the Herbal Medicine Plant Species Aralia continentalis Kitag. and Angelica biserrata C.Q. Yuan and R.H. Shan Using ITS2 Sequences and Multiplex-SCAR Markers

    Directory of Open Access Journals (Sweden)

    Wook Jin Kim

    2016-02-01

    Full Text Available Accurate identification of the plant species that are present in herbal medicines is important for quality control. Although the dried roots of Aralia continentalis (Araliae Continentalis Radix and Angelica biserrata (Angelicae Pubescentis Radix are used in the same traditional medicine, namely Dok-Hwal in Korean and Du-Huo in Chinese, the medicines are described differently in the national pharmacopeia. Further confusion arises from the distribution of dried Levisticum officinale and Heracleum moellendorffii roots as the same medicine. Medicinal ingredients from all four plants are morphologically similar, and discrimination is difficult using conventional methods. Molecular identification methods offer rapidity and accuracy. The internal transcribed spacer 2 (ITS2 region of the nuclear ribosomal RNA gene (rDNA was sequenced in all four plant species, and the sequences were used to design species-specific primers. Primers for each species were then combined to allow sample analysis in a single PCR reaction. Commercial herbal medicine samples were obtained from Korea and China and analyzed using the multiplex assay. The assay successfully identified authentic medicines and also identified inauthentic or adulterated samples. The multiplex assay will be a useful tool for identification of authentic Araliae Continentalis Radix and/or Angelicae Pubescentis Radix preparations in Korea and China.

  8. Rapid Authentication of the Herbal Medicine Plant Species Aralia continentalis Kitag. and Angelica biserrata C.Q. Yuan and R.H. Shan Using ITS2 Sequences and Multiplex-SCAR Markers.

    Science.gov (United States)

    Kim, Wook Jin; Moon, Byeong Cheol; Yang, Sungyu; Han, Kyeong Suk; Choi, Goya; Lee, A Yeong

    2016-02-29

    Accurate identification of the plant species that are present in herbal medicines is important for quality control. Although the dried roots of Aralia continentalis (Araliae Continentalis Radix) and Angelica biserrata (Angelicae Pubescentis Radix) are used in the same traditional medicine, namely Dok-Hwal in Korean and Du-Huo in Chinese, the medicines are described differently in the national pharmacopeia. Further confusion arises from the distribution of dried Levisticum officinale and Heracleum moellendorffii roots as the same medicine. Medicinal ingredients from all four plants are morphologically similar, and discrimination is difficult using conventional methods. Molecular identification methods offer rapidity and accuracy. The internal transcribed spacer 2 (ITS2) region of the nuclear ribosomal RNA gene (rDNA) was sequenced in all four plant species, and the sequences were used to design species-specific primers. Primers for each species were then combined to allow sample analysis in a single PCR reaction. Commercial herbal medicine samples were obtained from Korea and China and analyzed using the multiplex assay. The assay successfully identified authentic medicines and also identified inauthentic or adulterated samples. The multiplex assay will be a useful tool for identification of authentic Araliae Continentalis Radix and/or Angelicae Pubescentis Radix preparations in Korea and China.

  9. Retrospective analysis of a Computer-Aided Detection (CAD) system in full-field digital mammography in correlation to tumor histology; Retrospektive Analyse eines computerassistierten Detektions-Systems (CAD) in der digitalen Vollfeldmammographie in Abhaengigkeit von der Histologie

    Energy Technology Data Exchange (ETDEWEB)

    Obenauer, S.; Sohns, C.; Grabbe, E. [Abt. Diagnostische Radiologie, Georg-August-Univ. Goettingen (Germany); Werner, C. [Abt. fuer Medizinische Statistik, Georg-August-Univ. Goettingen (Germany)

    2005-08-01

    Purpose: to evaluate the usefulness of a computer-aided detection (CAD) system in full-field digital mammography in correlation to tumor histology. Material and methods: a total of 476 patients (226 patients with histologically proven malignant tumors, 250 healthy women) took part in this study. The mammograms were studied retrospectively, using the CAD system Image Checker. For 226 patients digital mammograms in MLO-projection were available. For 186 of these patients the CC-projection was also available. CAD markers that correlated with histologically proven carcinomas were considered to be true-positive markers. All other CAD markers were considered to be false-positive. Histologically proven carcinomas without markers were false-negative results. The dependence of the CAD markers placement upon the different carcinoma histologies was studied using the Chi-square test. Results: no significant difference could be proven for the detectability of malignant breast lesions of different histologic types. For the detectability of ductal carcinoma in situ (DCIS), invasive ductal carcinoma (IDC), invasive lobular carcinoma (ILC), lobular carcinoma in situ (LCIS), tubular carcinoma and ductulo-lobular carcinoma, the true positives were 71.1%, 75%, 70.7%, 70%, 60% and 80%, respectively, in the MLO projection and 83.9%, 75.9%, 81.8%, 77.8%, 87.5% and 33.3%, respectively, in the CC projection. There was an average of 0.5 false-positive markers per mammographic image. Conclusion: The histologic type of carcinoma seems to have no influence on detectability when using the CAD system. The high rate of false-positive markers shows, however, the limited specificity of the CAD system and that improvements are necessary. (orig.)

  10. Evaluation of DNA markers for fish identification

    Directory of Open Access Journals (Sweden)

    Maurizio Gilli

    2013-02-01

    Full Text Available Species substitution is a common commercial fraud, mainly applied to fish species. It is thus important to have analytical methods for species identification. DNA analysis can be a suitable technique: some mitochondrial genes are actually recognized as valuable markers for species discrimination. Aim of this work was thus to evaluate the capability of cytb and COI genes to discriminate the species of fish (n=89 which are commonly substituted. In the last four years of activity on field, the laboratory analysed, using the FINS method (Forensically Informative Nucleotide Sequencing, 146 samples, belonging to several fish species, sent by veterinary officers in the frame of their activities of control: in this work, results about number and kind of fraud are reported. Additionally, samples directly purchased by the lab were examined. The obtained results showed that the genetic markers have a high discriminatory power and that the method is highly suitable. The frequent detection of species substitution in the samples collected on field showed the importance of controlling this kind of frauds in the fish market.

  11. Myocardial Tissue Characterization: Histological and Pathophysiological Correlation.

    Science.gov (United States)

    Treibel, T A; White, S K; Moon, J C

    2014-01-01

    Cardiovascular magnetic resonance imaging (CMR) has become the gold standard not only for cardiac volume and function quantification, but for a key unique strength: non-invasive myocardial tissue characterization. Several different techniques, separately or in combination, can detect and quantify early and established myocardial pathological processes permitting better diagnosis, prognostication and tracking of therapy. The authors will focus on the histological and pathophysiological evidence of these imaging parameters in the characterization of edema, infarction, scar and fibrosis. In addition to laying out the strengths and weaknesses of each modality, the reader will be introduced to rapid developments in T1 and T2 mapping as well as the use of contrast-derived extracellular volume for quantification of diffuse fibrosis.

  12. Histological findings after brown recluse spider envenomation.

    Science.gov (United States)

    Elston, D M; Eggers, J S; Schmidt, W E; Storrow, A B; Doe, R H; McGlasson, D; Fischer, J R

    2000-06-01

    Histologic specimens from 41 rabbits were studied for changes resulting from the manual injection of brown recluse spider venom. Major findings included a mixed inflammatory cell infiltrate, coagulative tissue necrosis, and vasculitis. All specimens demonstrated a well-delineated zone of eosinophilic staining recognizable as "mummified" coagulative necrosis of the epidermis and dermis. A dense band of neutrophils bordered the zone of necrosis. Immediately adjacent to the neutrophilic band, small vessel vasculitis was a universal finding. Degranulated eosinophils and neutrophils and macrophages filled with eosinophilic granules were common. Inflammatory foci were often centered on groups of lipocytes within the dermis. Large vessel vasculitis resembling that seen in polyarteritis nodosa was present deep to 7 of the 40 eschars. Large vessel vasculitis may contribute to the large zones of necrosis seen after some brown recluse spider bites. Eosinophils may play a role in tissue damage after envenomation.

  13. Histological observation for needle-tissue interactions.

    Science.gov (United States)

    Nakagawa, Yoshiyuki; Koseki, Yoshihiko

    2013-01-01

    We histologically investigated tissue fractures and deformations caused by ex vivo needle insertions. The tissue was formalin-fixed while the needle remained in the tissue. Following removal of the needle, the tissue was microtomed, stained, and observed microscopically. This method enabled observations of cellular and tissular conditions where deformations caused by needle insertions were approximately preserved. For this study, our novel method presents preliminary findings related with tissue fractures and the orientation of needle blade relative to muscle fibers. When the needle blade was perpendicular to the muscle fiber, transfiber fractures and relatively large longitudinal deformations occurred. When the needle blade was parallel to the muscle fiber, interfiber fractures and relatively small longitudinal deformations occurred. This made a significant difference in the resistance force of the needle insertions.

  14. Microsatellite markers of water buffalo, Bubalus bubalis - development, characterisation and linkage disequilibrium studies

    Directory of Open Access Journals (Sweden)

    Vaidhegi R

    2009-10-01

    Full Text Available Abstract Background Microsatellite markers are highly polymorphic and widely used in genome mapping and population genetic studies in livestock species. River buffalo, Bubalus bubalis is an economically important livestock species, though only a limited number of microsatellite markers have been reported thus far in this species. Results In the present study, using two different approaches 571 microsatellite markers have been characterized for water buffalo. Of the 571 microsatellite markers, 498 were polymorphic with average heterozygosity of 0.51 on a panel of 24 unrelated buffalo. Fisher exact test was used to detect LD between the marker pairs. Among the 137550 pairs of marker combination, 14.58% pairs showed significant LD (P Conclusion The high conservation of cattle microsatellite loci in water buffalo promises the usefulness of the cattle microsatellites markers on buffalo. The polymorphic markers characterised in this study will contribute to genetic linkage and radiation hybrid mapping of water buffalo and population genetic studies.

  15. Histología de agallas en dos especies de Verbenaceae

    Directory of Open Access Journals (Sweden)

    Eucariz Esther Villazón de Pinzón

    1990-01-01

    Full Text Available The purpose of this paper is to show, by the histological study of the stem of two different species of Verbenaceae, the morphological changes undergone by the plant tissues caused by the Arthropods'larvae. Such larvae induce and organize the morphogenesis of the gall for their own benefit. As the larva is nourished, the plant's responses is to increase the number of cells in the affected organ.

  16. Gross, histologic, and micro-computed tomographic anatomy of the lacrimal system of snakes

    OpenAIRE

    Souza, NM; Maggs, DJ; Park, SA; Puchalski, SM; Reilly, CM; Paul-Murphy, J; Murphy, CJ

    2015-01-01

    © 2014 American College of Veterinary Ophthalmologists. Objective: To describe the lacrimal system of snakes using contrast micro-computed tomography (micro-CT) with 3-dimensional reconstruction, fluorescein passage ('Jones') testing, histology, and gross dissection. Animals studied: One royal python and 19 snake cadavers representing 10 species. Procedures: Direct observation following injection of fluorescein into the subspectacular space, micro-CT following injection of three contrast agen...

  17. Species status and population structure of the newly described Tursiops australis (the Burrunan dolphin)and Tursiops truncatus (the common bottlenose dolphin)in southern Australian waters, assessed using genetic markers and morphology.

    OpenAIRE

    Charlton, Kate

    2017-01-01

    Taxonomic relationships and affinities within the cetacean genus Tursiops have been plagued with controversy, with historically upwards of 20 species being described and later all synonymised with the common bottlenose dolphin T. truncatus. Numerous studies have demonstrated that Tursiops is polyphyletic. Tursiops truncatus is morphologically and genetically diverse and exhibits distinct 'ecotypes' with coastal/inshore popUlations often distinct from offshore populations. Recently, a 'worldwi...

  18. Rapid Authentication of the Herbal Medicine Plant Species Aralia continentalis Kitag. and Angelica biserrata C.Q. Yuan and R.H. Shan Using ITS2 Sequences and Multiplex-SCAR Markers

    OpenAIRE

    Wook Jin Kim; Byeong Cheol Moon; Sungyu Yang; Kyeong Suk Han; Goya Choi; A Yeong Lee

    2016-01-01

    Accurate identification of the plant species that are present in herbal medicines is important for quality control. Although the dried roots of Aralia continentalis (Araliae Continentalis Radix) and Angelica biserrata (Angelicae Pubescentis Radix) are used in the same traditional medicine, namely Dok-Hwal in Korean and Du-Huo in Chinese, the medicines are described differently in the national pharmacopeia. Further confusion arises from the distribution of dried Levisticum officinale and Herac...

  19. Histological evidence for muscle insertion in extant amniote femora: implications for muscle reconstruction in fossils.

    Science.gov (United States)

    Petermann, Holger; Sander, Martin

    2013-04-01

    Since the 19th century, identification of muscle attachment sites on bones has been important for muscle reconstructions, especially in fossil tetrapods, and therefore has been the subject of numerous biological and paleontological studies. At the microscopic level, in histological thin sections, the only features that can be used reliably for identifying tendon-bone or muscle-tendon-bone interactions are Sharpey's fibers. Muscles, however, do not only attach to the bone indirectly with tendons, but also directly. Previous studies failed to provide new indicators for muscle attachment, or to address the question of whether muscles with direct attachment can be identified histologically. However, histological identification of direct muscle attachments is important because these attachments do not leave visible marks (e.g. scars and rugosities) on the bone surface. We dissected the right hind limb and mapped the muscle attachment sites on the femur of one rabbit (Oryctolagus cuniculus), one Alligator mississippiensis, and one turkey (Meleagris cuniculus). We then extracted the femur and prepared four histological thin sections for the rabbit and the turkey and five histological thin sections for the alligator. Sharpey's fibers, vascular canal orientation, and a frayed periosteal margin can be indicators for indirect but also direct muscle attachment. Sharpey's fibers can be oriented to the cutting plane of the thin section at high angles, and two Sharpey's fibers orientations can occur in one area, possibly indicating a secondary force axis. However, only about 60% of mapped muscle attachment sites could be detected in thin sections, and frequently histological features suggestive of muscle attachment occurred outside mapped sites. While these insights should improve our ability to successfully identify and reconstruct muscles in extinct species, they also show the limitations of this approach. © 2013 The Authors Journal of Anatomy © 2013 Anatomical Society.

  20. Development of a Large Set of Microsatellite Markers in Zapote Mamey (Pouteria sapota (Jacq. H.E. Moore & Stearn and Their Potential Use in the Study of the Species

    Directory of Open Access Journals (Sweden)

    Renée S. Arias

    2015-06-01

    Full Text Available Pouteria sapota is known for its edible fruits that contain unique carotenoids, as well as for its fungitoxic, anti-inflammatory and anti-oxidant activity. However, its genetics is mostly unknown, including aspects about its genetic diversity and domestication process. We did high-throughput sequencing of microsatellite-enriched libraries of P. sapota, generated 5223 contig DNA sequences, 1.8 Mbp, developed 368 microsatellites markers and tested them on 29 individuals from 10 populations (seven wild, three cultivated from Mexico, its putative domestication center. Gene ontology BLAST analysis of the DNA sequences containing microsatellites showed potential association to physiological functions. Genetic diversity was slightly higher in cultivated than in the wild gene pool (HE = 0.41 and HE = 0.35, respectively, although modified Garza–Williamson Index and Bottleneck software showed evidence for a reduction in genetic diversity for the cultivated one. Neighbor Joining, 3D Principal Coordinates Analysis and assignment tests grouped most individuals according to their geographic origin but no clear separation was observed between wild or cultivated gene pools due to, perhaps, the existence of several admixed populations. The developed microsatellites have a great potential in genetic population and domestication studies of P. sapota but additional sampling will be necessary to better understand how the domestication process has impacted the genetic diversity of this fruit crop.

  1. Myeloid sarcomas: a histologic, immunohistochemical, and cytogenetic study

    Directory of Open Access Journals (Sweden)

    Rodgers William H

    2007-10-01

    Full Text Available Abstract Context. - Myeloid sarcoma (MS is a neoplasm of immature granulocytes, monocytes, or both involving any extramedullary site. The correct diagnosis of MS is important for adequate therapy, which is often delayed because of a high misdiagnosis rate. Objective. - To evaluate the lineage differentiation of neoplastic cells in MS by immunohistochemistry, and to correlate the results with clinicopathologic findings and cytogenetic studies. Design. - Histologic and immunohistochemical examinations were performed on formalin-fixed paraffin-embedded tissue samples from 13 cases of MS. They were classified according to the World Health Organization criteria. Chromosomal analysis data were available in 11 cases. Clinical, pathological, and cytogenetic findings were analyzed. Results. - The study included six male and seven female patients with an age range of 25 to 72 years (mean, 49.3 years and a male to female ratio of 1:1.2. MS de novo occurred in 4/13 (31% of cases examined. The most sensitive immunohistochemical markers were CD43 and lysozyme present in all cases with MS (13/13, 100%. All de novo MS showed a normal karyotype, monoblastic differentiation, and lack of CD34. The most common chromosomal abnormalities in MS associated with a hematopoietic disorder were trisomy 8 and inv(16 (2/11, 18%. Conclusion. - An immunohistochemical panel including CD43, lysozyme, myeloperoxidase (MPO, CD68 (or CD163, CD117, CD3 and CD20 can successfully identify the vast majority of MS variants in formalin-fixed paraffin-embedded tissue sections. The present report expands the spectrum of our knowledge showing that de novo MS has frequent monoblastic differentiation and frequently carries a normal karyotype.

  2. Different Achilles Tendon Pathologies Show Distinct Histological and Molecular Characteristics

    Directory of Open Access Journals (Sweden)

    Franka Klatte-Schulz

    2018-01-01

    Full Text Available Reasons for the development of chronic tendon pathologies are still under debate and more basic knowledge is needed about the different diseases. The aim of the present study was therefore to characterize different acute and chronic Achilles tendon disorders. Achilles tendon samples from patients with chronic tendinopathy (n = 7, chronic ruptures (n = 6, acute ruptures (n = 13, and intact tendons (n = 4 were analyzed. The histological score investigating pathological changes was significantly increased in tendinopathy and chronic ruptures compared to acute ruptures. Inflammatory infiltration was detected by immunohistochemistry in all tendon pathology groups, but was significantly lower in tendinopathy compared to chronic ruptures. Quantitative real-time PCR (qRT-PCR analysis revealed significantly altered expression of genes related to collagens and matrix modeling/remodeling (matrix metalloproteinases, tissue inhibitors of metalloproteinases in tendinopathy and chronic ruptures compared to intact tendons and/or acute ruptures. In all three tendon pathology groups markers of inflammation (interleukin (IL 1β, tumor necrosis factor α, IL6, IL10, IL33, soluble ST2, transforming growth factor β1, cyclooxygenase 2, inflammatory cells (cluster of differentaition (CD 3, CD68, CD80, CD206, fat metabolism (fatty acid binding protein 4, peroxisome proliferator-activated receptor γ, CCAAT/enhancer-binding protein α, adiponectin, and innervation (protein gene product 9.5, growth associated protein 43, macrophage migration inhibitory factor were detectable, but only in acute ruptures significantly regulated compared to intact tendons. The study gives an insight into structural and molecular changes of pathological processes in tendons and might be used to identify targets for future therapy of tendon pathologies.

  3. Aneuploidy involving chromosome 1 may be an early predictive marker of intestinal type gastric cancer

    Energy Technology Data Exchange (ETDEWEB)

    Williams, L. [Royal Glamorgan Hospital, Ynysmaerdy, Llantrisant CF72 8XR (United Kingdom); Somasekar, A. [Institute of Life Science, Swansea School of Medicine, Swansea University, Swansea SA28PP (United Kingdom); Neath Port Talbot Hospital, Abertawe Bro Morgannwg University NHS Trust, Baglan Way, Port Talbot SA12 7BX (United Kingdom); Davies, D.J.; Cronin, J.; Doak, S.H. [Institute of Life Science, Swansea School of Medicine, Swansea University, Swansea SA28PP (United Kingdom); Alcolado, R. [Royal Glamorgan Hospital, Ynysmaerdy, Llantrisant CF72 8XR (United Kingdom); Williams, J.G. [Neath Port Talbot Hospital, Abertawe Bro Morgannwg University NHS Trust, Baglan Way, Port Talbot SA12 7BX (United Kingdom); Griffiths, A.P. [Department of Histopathology, Morriston Hospital, Abertawe Bro Morgannwg University NHS Trust, Morriston, SA66NL (United Kingdom); Baxter, J.N. [Department of Surgery, Morriston Hospital, Abertawe Bro Morgannwg University NHS Trust, Morriston, SA66NL (United Kingdom); Jenkins, G.J.S., E-mail: g.j.jenkins@swansea.ac.uk [Institute of Life Science, Swansea School of Medicine, Swansea University, Swansea SA28PP (United Kingdom)

    2009-10-02

    Intestinal type gastric cancer is a significant cause of mortality, therefore a better understanding of its molecular basis is required. We assessed if either aneuploidy or activity of the oncogenic transcription factor nuclear factor kappa B (NF-{kappa}B), increased incrementally during pre-malignant gastric histological progression and also if they correlated with each other in patient samples, as they are both induced by oxygen free radicals. In a prospective study of 54 (aneuploidy) and 59 (NF-{kappa}B) consecutive patients, aneuploidy was assessed by interphase fluorescent in situ hybridisation (FISH) for chromosome 1. NF-{kappa}B was assessed by expression of interleukin-8 (IL-8), and in a subset, by immunohistochemistry (IHC) for active p65. Aneuploidy levels increased incrementally across the histological series. 2.76% of cells with normal histology (95% CI, 2.14-3.38%) showed background levels of aneuploidy, this increased to averages of 3.78% (95% CI, 3.21-4.35%), 5.89% (95% CI, 3.72-8.06%) and 7.29% (95% CI, 4.73-9.85%) of cells from patients with gastritis, Helicobacter pylori positive gastritis and atrophy/intestinal metaplasia (IM) respectively. IL-8 expression was only increased in patients with current H. pylori infection. NF-{kappa}B analysis showed some increased p65 activity in inflamed tissues. IL-8 expression and aneuploidy level were not linked in individual patients. Aneuploidy levels increased incrementally during histological progression; were significantly elevated at very early stages of neoplastic progression and could well be linked to cancer development and used to assess cancer risk. Reactive oxygen species (ROS) induced in early gastric cancer are presumably responsible for the stepwise accumulation of this particular mutation, i.e. aneuploidy. Hence, aneuploidy measured by fluorescent in situ hybridisation (FISH) coupled to brush cytology, would be worthy of consideration as a predictive marker in gastric cancer and could be

  4. Non-alcoholic fatty liver disease - histological scoring systems: a large cohort single-center, evaluation study.

    Science.gov (United States)

    Rastogi, Archana; Shasthry, Saggere Muralikrishna; Agarwal, Ayushi; Bihari, Chhagan; Jain, Priyanka; Jindal, Ankur; Sarin, Shiv

    2017-11-01

    Non-alcoholic fatty liver disease (NAFLD) is an increasingly common cause of chronic liver disease. Till date, liver biopsy remains the gold standard for identification and quantification of the wide histological spectra of NAFLD. Histological scorings are very useful and widely applied for the diagnosis and management in clinical trials and follow-up studies of non-alcoholic steatohepatitis (NASH). However, in view of scarce published literature, there is a need to evaluate them in large cohort of NAFLD. This study was aimed to evaluate the two histological scoring systems (NAS-CRN, SAF) in the diagnosis of NAFLD and to assess the role of histological characteristics as injury markers in NAFLD. Retrospective histological study of liver biopsies of 1000 patients diagnosed as NAFLD, between 2010 and 2016, was conducted. Histopathologic evaluation and semiquantiative scoring based on NAS-CRN and SAF algorithm and their correlation with serum aminotransferase and fibrosis were performed. Liver biopsies were classified according to the NAS-CRN scoring, as NAS fibrosis; however, higher stages of fibrosis were significantly more prevalent in definite NASH, excluding burnt-out cirrhosis. Serum ALT was significantly associated with increasing stages of fibrosis (p fibrosis (p fibrosis stages (p fibrosis. Exclusion of fibrosis is a limitation with both scores. © 2017 APMIS. Published by John Wiley & Sons Ltd.

  5. [Markers of brain tumors].

    Science.gov (United States)

    Fumagalli, R; Pezzotta, S; Bernini, F; Racagni, G

    1984-05-19

    Biological markers of tumors are compounds or enzymatic activities measurable in body fluids. Their presence or concentration must be linked to tumoral growth. The markers of the central nervous system tumors are detected in CSF. Alpha-feto-protein, carcinoembryonic antigen, human chorionic gonadotropin, adenohypophyseal peptide hormones, enzymes, etc., have found some application in the early diagnosis of leptomeningeal metastasis. Other applications involve the early detection and recurrency of primary brain tumors, as well as the evaluation of efficacy of their therapy. The tests based on the CSF content of desmosterol and polyamines have been studied extensively. Their rationale is discussed and specificity, sensitivity, efficiency and predictive value are considered. Experimental results concerning a new possible biochemical marker, based on CSF concentration of cyclic adenosine monophosphate, are reported.

  6. Histologic distribution of borderline ovarian tumors worldwide: a systematic review

    OpenAIRE

    Song, Taejong; Lee, Yoo-Young; Choi, Chel Hun; Kim, Tae-Joong; Lee, Jeong-Won; Bae, Duk-Soo; Kim, Byoung-Gie

    2013-01-01

    Objective The histologic types of borderline ovarian tumors (BOTs) exhibit striking differences in clinical behavior and prognosis. Yet, there is no information available on the histologic distribution of BOTs according to geographic region. The purpose of this study was to systematically review this issue worldwide. Methods A comprehensive search of the literature was conducted using electronic databases. Studies were eligible if BOTs were investigated and the histologic distribution of the ...

  7. Comparison of histological grading and large-scale genomic status (DNA ploidy) as prognostic tools in oral dysplasia.

    Science.gov (United States)

    Sudbø, J; Bryne, M; Johannessen, A C; Kildal, W; Danielsen, H E; Reith, A

    2001-07-01

    Approximately one in ten oral white patches (leukoplakia) are histologically classified as dysplasia, with a well-documented potential for developing into oral squamous cell carcinoma (OSCC). Histological grading in oral dysplasia has limited prognostic value, whereas large-scale genomic status (DNA ploidy, nuclear DNA content) is an early marker of malignant transformation in several tissues. Biopsies from 196 patients with oral leukoplakia histologically typed as dysplasia were investigated. Inter-observer agreement among four experienced pathologists performing a simplified grading was assessed by Cohen's kappa values. For 150 of the 196 cases, it was also possible to assess large-scale genomic status and compare its prognostic impact with that of histological grading. Disease-free survival was estimated by life-table methods, with a mean follow-up time of 103 months (range 4-165 months). The primary considered end-point was the subsequent occurrence of OSCC. For grading of the total of 196 cases, kappa values ranged from 0.17 to 0.33 when three grading groups (mild, moderate, and severe dysplasia) were considered, and from 0.21 to 0.32 when two groups (low grade and high grade) were considered (p=0.41). For the 150 cases in which large-scale genomic status was also assessed, kappa values for the histological grading ranged from 0.21 to 0.33 for three grading groups and from 0.27 to 0.34 for two grading groups (p=0.47). In survival analysis, histological grading was without significant prognostic value for any of the four observers (p 0.14-0.44), in contrast to DNA ploidy (p=0.001). It is concluded that DNA ploidy in oral dysplasia has a practical prognostic value, unlike histological grading of the same lesions. Copyright 2001 John Wiley & Sons, Ltd.

  8. The hippocampus and exercise: histological correlates of MR-detected volume changes.

    Science.gov (United States)

    Biedermann, Sarah V; Fuss, Johannes; Steinle, Jörg; Auer, Matthias K; Dormann, Christof; Falfán-Melgoza, Claudia; Ende, Gabriele; Gass, Peter; Weber-Fahr, Wolfgang

    2016-04-01

    Growing evidence indicates that physical exercise increases hippocampal volume. This has consistently been shown in mice and men using magnetic resonance imaging. On the other hand, histological studies have reported profound alterations on a cellular level including increased adult hippocampal neurogenesis after exercise. A combined investigation of both phenomena has not been documented so far although a causal role of adult neurogenesis for increased hippocampal volume has been suggested before. We investigated 20 voluntary wheel running and 20 sedentary mice after a period of 2 month voluntary wheel running. Half of each group received focalized hippocampal irradiation to inhibit neurogenesis prior to wheel running. Structural MRI and histological investigations concerning newborn neurons (DCX), glial cells (GFAP), microglia, proliferating and pyknotic cells, neuronal activation, as well as blood vessel density and arborisation were performed. In a regression model, neurogenesis was the marker best explaining hippocampal gray matter volume. Individual analyses showed a positive correlation of gray matter volume with DCX-positive newborn neurons in the subgroups, too. GFAP-positive cells significantly interacted with gray matter volume with a positive correlation in sham-irradiated mice and no correlation in irradiated mice. Although neurogenesis appears to be an important marker of higher hippocampal gray matter volume, a monocausal relationship was not indicated, requesting further investigations.

  9. Histologic and molecular analysis of patient derived xenografts of high-grade serous ovarian carcinoma

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    Ruifen Dong

    2016-09-01

    Full Text Available Abstract Background Patient derived xenografts (PDX are generated by transplanting the original patient’s tumor tissue into immune-deficient mice. Unlike xenograft models derived from cell lines, PDX models can better preserve the histopathology from the original patient and molecular pathways. High-grade serous carcinoma (HGSC is a deadly form of ovarian/fallopian tube cancer whose response to current chemotherapies varies widely due to patient variability. Therefore, a PDX model can provide a valuable tool to study and test treatment options for each individual patient. Methods In this study, over 200 PDX tumors from nine HGSC were analyzed to investigate the nature and behavior of PDX tumors originating from HGSC. PDX tumors were serially passaged (from P0 to P4 and tumors were grafted orthotopically under the ovarian bursa or subcutaneously. Results Comparative analysis of the histology and molecular markers of tumors from over 200 PDX tumor-bearing mice, revealed that the tumors maintained similar histologies, stem cell populations, and expression for the majority of the tested oncogenic markers, compared to the primary tumors. However, a significant loss of steroid hormone receptors and altered expression of immunoresponsive genes in PDX tumors were also noted. Conclusion Our findings provide substantial new information about PDX tumor characteristics from HGSC which will be valuable towards the development of personalized therapy and new drug development for HGSC.

  10. Automated recognition of cell phenotypes in histology images based on membrane- and nuclei-targeting biomarkers

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    Tözeren Aydın

    2007-09-01

    Full Text Available Abstract Background Three-dimensional in vitro culture of cancer cells are used to predict the effects of prospective anti-cancer drugs in vivo. In this study, we present an automated image analysis protocol for detailed morphological protein marker profiling of tumoroid cross section images. Methods Histologic cross sections of breast tumoroids developed in co-culture suspensions of breast cancer cell lines, stained for E-cadherin and progesterone receptor, were digitized and pixels in these images were classified into five categories using k-means clustering. Automated segmentation was used to identify image regions composed of cells expressing a given biomarker. Synthesized images were created to check the accuracy of the image processing system. Results Accuracy of automated segmentation was over 95% in identifying regions of interest in synthesized images. Image analysis of adjacent histology slides stained, respectively, for Ecad and PR, accurately predicted regions of different cell phenotypes. Image analysis of tumoroid cross sections from different tumoroids obtained under the same co-culture conditions indicated the variation of cellular composition from one tumoroid to another. Variations in the compositions of cross sections obtained from the same tumoroid were established by parallel analysis of Ecad and PR-stained cross section images. Conclusion Proposed image analysis methods offer standardized high throughput profiling of molecular anatomy of tumoroids based on both membrane and nuclei markers that is suitable to rapid large scale investigations of anti-cancer compounds for drug development.

  11. Cytochrome P450, acetylcholinesterase and gonadal histology for evaluating contaminant exposure levels in fishes from a highly eutrophic brackish ecosystem: the Orbetello Lagoon, Italy.

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    Corsi, I; Mariottini, M; Sensini, C; Lancini, L; Focardi, S

    2003-02-01

    Biochemical markers and ovarian histology were investigated in prespawning females of grass goby (Zosterisessor ophiocephalus) and grey mullet (Mugil cephalus) collected, respectively, in late spring and summer 2000 in four sites of a highly eutrophic brackish ecosystem of central Italy, the Orbetello Lagoon. Exposure to chlorinated and aromatic hydrocarbons was evaluated in fish livers by the somatic liver index (SLI) and by measuring 7-ethoxyresorufin-O-deethylase (EROD) and benzo(a)pyrene monooxygenase (BaPMO) activities. Acetylcholinesterase (AChE) activity was measured in brain and gills to evaluate exposure to organophosphates (OPs) and carbamates (CBs). The gonad somatic index (GSI) was used to confirm ovarian maturation and ovarian histology was investigated as a potential biomarker for environmental effects. Samples from the Western Basin, near a sewage treatment plant (STP) off the town of Orbetello, showed higher SLI values and higher EROD and BaPMO activities than those collected from the Ansedonia Canal (AC) in the Eastern Basin (pNassa Canal (NC), connected with the sea, for grey mullet both located in the Western Basin as well. Low brain AChE activity was observed in both species from the reference sites (AR and NC) in association with the presence of anomalies in developing oocytes: unexpectedly small in grass goby and irregular disintegrated cytoplasm in grey mullet. The results indicate that the Western Basin is more polluted than the Eastern Basin particularly in the Orbetello where the sewage treatment plant may be a source of aromatic and chlorinated compounds while the Albegna River and the Nassa Canal may be sources of OPs and CBs.

  12. Histological analysis of muscles of Landes geese

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    Peter Haščík

    2010-01-01

    Full Text Available The aim of this study was histological and histochemical analyze of musculus pectoralis major (MPM and musculus biceps femoris (MBF of 12-weeks old Landes geese husbandry by sex from Hruboňovo (Czech Republic. The geese had live weight of 3979.0 g and the ganders had live weight of 4779.0 g. Higher α White fiber percentage representation of musculus pectoralis major and musculus biceps femoris of 12-weeks old Landes geese histological analyses we followed. Representation of sex identical MBF was 60.0% (gander and 64.1% (geese and MPM was 47.6% (ganders and 51.1% (geese. The lowest α Red fibre percentage content in MPM was 6.7% (ganders and 4.7% (geese and β Red fiber in MBF was 10.7% (ganders and 9.5% (geese. No statistically significant differences (P ≥ 0,05 among sex in the fat cells thickness of geese were found, but significant differences (P ≤ 0,01 was found in MBF fat cells between ganders (26.3 μm and geese (21.9 μm. Highest thickness of α White fibre in muscles breast and femoral were found in both sex and lowest was found in β Red fibre. Muscles fibres thickness was higher femoral muscles in average (59.9 μm – ganders; 58.3 μm – geese opposite breast muscles (47.7 μm – ganders, 44.9 μm – geese, what is the mean higher consistence of femoral muscles for consumer. In term of lowest musculus fiber thickness of Landes geese in average were 44.9 μm – MPM, 58.3 μm – MBF opposite of ganders 47.7 μm – MPM, 59.9 μm – MBF. Higher α White fibre representation was both muscles (51.1% – MPM, 64.1% – MBF. We recommended for experience used in­di­vi­dual rearing of male.

  13. Histological study of the annular ligament in the rabbitfish eye (Siganus sp.

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    Marziye Asli

    2012-12-01

    Full Text Available Rabbitfish is economically valuable teleost species which lives in shallow coastalwaters. Two species of rabbit fish have been recognized in southern sea of Iran (Persiangulf as namely Siganus sutor and Siganus javus. In the current study, in order toinvestigate the histology of the annular ligament of the S. javus’ eye, the prepared sectionsof the eyes of twelve healthy specimens were studied under light microscope. The resultsrevealed that annular ligament is a crescent shape structure which is situated between thescleral stroma anteriorly and the iris posteriorly. It contains a vascularized, amorphousand granular matrix with fibers of dense connective tissue; high glycogen content andmelanin pigments.

  14. Tumor Markers: An Overview

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    Ajay G Nayak

    2010-01-01

    Full Text Available Oral cancer is a potentially fatal disease that has been the bane of clinicians throughout the world. Though various modalities of management exist, early detection still provides the best hope for any cancer patient Advances in molecular diagnosis have led to a plethora of choices being available in the fight against cancer. Abnormal cellular products elucidated from malignant cells can be detected and measured in various body tissues and fluids and constitute tumor markers. The various clinical applications and their limitations are covered in the brief overview to help the oral medicine specialist understand the relevant advances made in the field of tumor markers.

  15. A histological ontology of the human cardiovascular system.

    Science.gov (United States)

    Mazo, Claudia; Salazar, Liliana; Corcho, Oscar; Trujillo, Maria; Alegre, Enrique

    2017-10-02

    In this paper, we describe a histological ontology of the human cardiovascular system developed in collaboration among histology experts and computer scientists. The histological ontology is developed following an existing methodology using Conceptual Models (CMs) and validated using OOPS!, expert evaluation with CMs, and how accurately the ontology can answer the Competency Questions (CQ). It is publicly available at http://bioportal.bioontology.org/ontologies/HO and https://w3id.org/def/System . The histological ontology is developed to support complex tasks, such as supporting teaching activities, medical practices, and bio-medical research or having natural language interactions.

  16. A combined post-mortem magnetic resonance imaging and quantitative histological study of multiple sclerosis pathology

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    Kolasinski, James; Chance, Steven A.; DeLuca, Gabriele C.; Esiri, Margaret M.; Chang, Eun-Hyuk; Palace, Jacqueline A.; McNab, Jennifer A.; Jenkinson, Mark; Miller, Karla L.; Johansen-Berg, Heidi

    2012-01-01

    Multiple sclerosis is a chronic inflammatory neurological condition characterized by focal and diffuse neurodegeneration and demyelination throughout the central nervous system. Factors influencing the progression of pathology are poorly understood. One hypothesis is that anatomical connectivity influences the spread of neurodegeneration. This predicts that measures of neurodegeneration will correlate most strongly between interconnected structures. However, such patterns have been difficult to quantify through post-mortem neuropathology or in vivo scanning alone. In this study, we used the complementary approaches of whole brain post-mortem magnetic resonance imaging and quantitative histology to assess patterns of multiple sclerosis pathology. Two thalamo-cortical projection systems were considered based on their distinct neuroanatomy and their documented involvement in multiple sclerosis: lateral geniculate nucleus to primary visual cortex and mediodorsal nucleus of the thalamus to prefrontal cortex. Within the anatomically distinct thalamo-cortical projection systems, magnetic resonance imaging derived cortical thickness was correlated significantly with both a measure of myelination in the connected tract and a measure of connected thalamic nucleus cell density. Such correlations did not exist between these markers of neurodegeneration across different thalamo-cortical systems. Magnetic resonance imaging lesion analysis depicted clearly demarcated subcortical lesions impinging on the white matter tracts of interest; however, quantitation of the extent of lesion-tract overlap failed to demonstrate any appreciable association with the severity of markers of diffuse pathology within each thalamo-cortical projection system. Diffusion-weighted magnetic resonance imaging metrics in both white matter tracts were correlated significantly with a histologically derived measure of tract myelination. These data demonstrate for the first time the relevance of functional

  17. Angiogenic and lymphangiogenic profiles in histological variants of papillary thyroid carcinoma.

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    Skuletic, Vesna; Radosavljevic, Gordana D; Pantic, Jelena; Markovic, Bojana Simovic; Jovanovic, Ivan; Jankovic, Nikola; Petrovic, Dusica; Jevtovic, Andra; Dzodic, Radan; Arsenijevic, Nebojsa

    2017-06-30

    INTRODUCTION    Papillary thyroid carcinoma (PTC) is a well‑differentiated tumor that occurs in several histological variants whose biological behaviors remain unclear. Angiogenesis and lymphangiogenesis are critical processes that enable tumor progression. OBJECTIVES    The aim of this study was to evaluate the angiogenic and lymphangiogenic phenotypes of PTC, considering the differences between histological variants. PATIENTS AND METHODS    Angiogenic and lymphangiogenic profiles were analyzed by determining microvascular density (MVD) and lymphatic vessel density (LVD) in 73 cases of PTC, using immunohistochemistry. To assess the biological markers involved in blood and lymph vessel formation, the expression of vascular endothelial growth factor (VEGF), cyclooxygenase 2 (COX‑2), and p27kip1 (p27) was determined. RESULTS    MVD was significantly higher in patients with high‑risk PTC and in those with local extrathyroidal and vascular invasion. Positive VEGF expression was strongly associated with high MVD and age‑related tumor enlargement. The presence of lymph vessel invasion was associated with the expression of either VEGF or COX‑2. The analysis of angiogenesis and lymphangiogenesis in different histological variants of PTC revealed elevated LVD rather than MVD in the follicular variant of PTC (FV‑PTC).Lower MVD was observed in FV‑PTC relative to the classic variant of PTC (CV‑PTC). The frequency of VEGF‑positive tumors was higher in CV‑PTC than in FV‑PTC. A significant association between COX‑2 and p27 expression was observed in FV‑PTC but not in CV‑PTC.  CONCLUSIONS    These results suggest that VEGF, COX‑2, and p27 may be important biological markers that determine the angiogenic and lymphangiogenic potentials of PTC, particularly between the follicular and classic variants.

  18. Histological study of white rhinoceros integument.

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    Jeffrey H Plochocki

    Full Text Available In this study, we report findings from a microscopic analysis of the white rhinoceros (Ceratotherium simum integumentary ultrastructure. Skin samples from the cheek, shoulder, flank and rump were taken from a 46-year-old female southern white rhinoceros and examined using H&E and elastic histological stains. The epidermis was thickest in the flank (1.003 mm followed by the rump, cheek and shoulder. The stratum corneum comprised more than half the epidermal thickness. Numerous melanin granules were found in the basal and spinosum layers. The epidermal-dermal junction was characterized by abundant papillary folds increasing surface contact between integument layers. Most of the dermal thickness consisted of organized collagen bundles with scattered elastic fibers. Collagen fiber bundles were thickest in the flank (210.9 μm followed by shoulder, rump and cheek. Simple coiled sweat glands were present in the dermis, but hair and sebaceous glands were absent. Together, these data suggest the white rhinoceros has a unique integumentary system among large terrestrial herbivores.

  19. Comparative anatomy and histology of xenarthran osteoderms.

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    Hill, Robert V

    2006-12-01

    Reconstruction of soft tissues in fossil vertebrates is an enduring challenge for paleontologists. Because inferences must be based on evidence from hard tissues (typically bones or teeth), even the most complete fossils provide only limited information about certain organ systems. Osteoderms ("dermal armor") are integumentary bones with high fossilization potential that hold information about the anatomy of the skin in many extant and fossil amniotes. Their importance for functional morphology and phylogenetic research has recently been recognized, but studies have focused largely upon reptiles, in which osteoderms are most common. Among mammals, osteoderms occur only in members of the clade Xenarthra, which includes armadillos and their extinct relatives: glyptodonts, pampatheres, and, more distantly, ground sloths. Here, I present new information on the comparative morphology and histology of osteoderms and their associated soft tissues in 11 extant and fossil xenarthrans. Extinct mylodontid sloths possessed simple, isolated ossicles, the presence of which is likely plesiomorphic for Xenarthra. More highly derived osteoderms of glyptodonts, pampatheres, and armadillos feature complex articulations and surface ornamentation. Osteoderms of modern armadillos are physically associated with a variety of soft tissues, including nerve, muscle, gland, and connective tissue. In some cases, similar osteological features may be caused by two or more different tissue types, rendering soft-tissue inferences for fossil osteoderms equivocal. Certain osteological structures, however, are consistently associated with specific soft-tissue complexes and therefore represent a relatively robust foundation upon which to base soft-tissue reconstructions of extinct xenarthrans. Copyright 2006 Wiley-Liss, Inc.

  20. Are Histologic Studies of Adenotonsillectomy Really Necessary?

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    Rebechi, Giseli

    2013-09-01

    Full Text Available Introduction: In most ear, nose, and throat services, it is routine to send the material extracted from tonsillectomy for histologic study to research malignancy, to analyze suspect material, or to provide medical-legal documentation. Recent studies have shown that this routine analysis is dispensable. Objective: To evaluate the actual need and perform a cost–benefit analysis of routine histopathologic examination in tonsillectomy with no signs or symptoms of malignancy. Methods: A retrospective observational study evaluated the charts of patients undergoing adenotonsillectomy, tonsillectomy, or adenoidectomy from January 2008 to September 2009 at the Institute of Otorhinolaryngology CEMA-SP. Costs of this test for the public health system were analyzed and the literature reviewed. Results: We studied 281 patients between 2 and 22 years of age; 142 (50.5% were male and 139 (49.5% were female. Of the surgeries, 201 were adenotonsillectomies (71.5%, 41 were tonsillectomies (14.5%, and 39 were adenoidectomies (14%. The most common indication for surgery was recurrent infection (63.3%. None of study patients had clinical suspicion of malignancy. The tests showed a cost of R$20.03 per tonsil analyzed. Conclusion: Routine histopathologic examination in patients undergoing adenotonsillectomy with no signs or symptoms of malignancy is dispensable and increases the cost of the surgeries.

  1. Histological demonstration of healing in experimental aneurysms.

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    Killer, M; Plenk, H; Minnich, B; Al-Schameri, R; Lametschwantner, A; Richling, B

    2009-08-01

    Recanalisation of aneurysms after interventional therapy is still an unsolved problem. The aim of this study is to demonstrate the angiographic and histological evidence of healing after endovascular embolisation of experimental aneurysms. We evaluated the healing reaction in experimental aneurysms treated with HydroCoils and platinum coils. After microsurgical construction of aneurysms in 24 rabbits, embolisation was performed. Four animals were sacrificed immediately after embolisation and 5 after 1 month, 3 months and 6 months, respectively, the remaining served as control group. Serial plastic-embedded ground sections of the parent arteries-aneurysm complexes were evaluated by light microscopy. Thrombus organisation in the aneurysms resulted in fibrovascular tissue formation between bare platinum and HydroCoils from the walls of the aneurysms towards the centre of the sac over time. In the clefts between HydroCoils only thin strands of granulation tissue were observed. From one month on, there was a neointimal layer covering the coil mass at the aneurysm orifice. Progressive occlusion by the expanding hydrogel polymers on the coils seemed to result in a durable healing reaction in the aneurismal sac in a short-term follow-up period. Georg Thieme Verlag KG Stuttgart * New York.

  2. Tracheotomy in growing rats: histological aspects

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    Manna Mônica Cecília Bochetti

    2003-01-01

    Full Text Available PURPOSE: To compare morphologically three different types of tracheotomy in growing rats, applying microsurgical technique. METHODS: EPM-1 Wistar growing rats (n=57 weighing 88gm and aged 35 days were randomized in four groups, according tracheotomy incision type (longitudinal, transverse and tracheal segment excision, and sham group. Following intramuscular anesthesia with ketamine and xylazine, the trachea was exposed and incised, according to the group, and a hand-made endotracheal cannula was inserted into the organ, under sterile conditions. This cannula was removed after 7 days, and animals have been sacrificed 30 days later. Tracheas samples were submitted to histological study, stained by hematoxylin-eosin and Masson trichrome, evaluating fibrosis, inflammatory infiltrate and epidermoid metaplasia. RESULTS: There was more frequency of inflammatory infiltrate at the tracheal epithelium in the tracheal segment excision group (87% compared to the longitudinal (40% and transverse (36% incision groups (p=0.009. Evaluating epidermoid metaplasia, tracheal segment excision and the longitudinal groups presented 33% and 40%, respectively, compared to 0% of the transverse group (p=0.03. Concerning to fibrosis, in a global comparison (p=0.1 among the three groups there was no difference, however, compared to the longitudinal group the transverse group showed lower level of fibrosis (p=0.04. Sham group did not present any relevant morphologic alterations and it was used as reference pattern. CONCLUSION: Taken together, our data show that tracheal segment excision promotes more epithelium aggression and transverse tracheal incision shows less morphologic alterations.

  3. Anatomy and Histology of an Epicanthal Fold.

    Science.gov (United States)

    Park, Jae Woo; Hwang, Kun

    2016-06-01

    The aim of this study is to elucidate the precise anatomical and histological detail of the epicanthal fold.Thirty-two hemifaces of 16 Korean adult cadavers were used in this study (30 hemifaces with an epicanthal fold, 2 without an epicanthal fold). In 2 patients who had an epicanthoplasty, the epicanthal folds were sampled.In a dissection, the periorbital skin and subcutaneous tissues were removed and the epicanthal fold was observed in relation to each part of the orbicularis oculi muscle. Specimens including the epicanthal fold were embeddedin in paraffin, sectioned at 10 um, and stained with Hematoxylin-Eosin. The horizontal section in the level of the paplebral fissure was made and the prepared slides were observed under a light microscope.In the specimens without an epicanthal fold, no connection between the upper preseptal muscle and the lower preseptal muscle was found. In the specimens with an epicanthal fold, a connection of the upper preseptal muscle to the lower preseptal muscle was observed. It was present in all 15 hemifaces (100%). There was no connection between the pretarsal muscles. In a horizontal section, the epicanthal fold was composed of 3 compartments: an outer skin lining, a core structure, and an innerskin lining. The core structure was mainly composed of muscular fibers and fibrotic tissue and they were intermingled.Surgeons should be aware of the anatomical details of an epicanthal fold. In removing or reconstructing an epicanthal fold, the fibromuscular core band should also be removed or reconstructed.

  4. Image analysis of vocal fold histology

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    Reinisch, Lou; Garrett, C. Gaelyn

    2001-05-01

    To visualize the concentration gradients of collagen, elastin and ground substance in histologic sections of vocal folds, an image enhancement scheme was devised. Slides stained with Movat's solution were viewed on a light microscope. The image was digitally photographed. Using commercially available software, all pixels within a color range are selected from the mucosa presented on the image. Using the Movat's pentachrome stain, yellow to yellow-brown pixels represented mature collagen, blue to blue-green pixels represented young collagen (collagen that is not fully cross-linked) and black to dark violet pixels represented elastin. From each of the color range selections, a black and white image was created. The pixels not within the color range were black. The selected pixels within the color range were white. The image was averaged and smoothed to produce 256 levels of gray with less spatial resolution. This new grey-scale image showed the concentration gradient. These images were further enhanced with contour lines surrounding equivalent levels of gray. This technique is helpful to compare the micro-anatomy of the vocal folds. For instance, we find large concentration of the collagen deep in the mucosa and adjacent to the vocalis muscle.

  5. Histological investigations on the Tyrolean Ice Man.

    Science.gov (United States)

    Hess, M W; Klima, G; Pfaller, K; Künzel, K H; Gaber, O

    1998-08-01

    The 5,200-year-old Tyrolean Ice Man discovered in 1991 in the Otztal Alps is the world's most ancient known human glacier mummy. Histological investigation was aimed at 1) optimizing specimen preparation and 2) documenting the preservation state of (sub)cellular components. Minute pieces of frozen tissue were removed endoscopically from rib bone and cartilage, major blood vessels, oral cavity and alimentary tract, liver, spleen, diaphragm, respiratory system, femoral muscle and nerve, sympathetic trunk, brain, and skin. Double fixation with glutaraldehyde followed by osmium tetroxide and embedding in Epon/Araldite epoxy resins proved to be the method of choice for both light and transmission electron microscopy combined with classical histochemistry. In particular, mild evacuation of the desiccated tissue was determined to be essential to ensure homogeneous infiltration with fixatives and resins; as a result, sections of excellent quality could be obtained with any kind of sample. With regard to the preservation degree of (sub)cellular components, distinct tissue-specific patterns were observed. There were highly intact skeletal and connective tissues proper, however, most interestingly, there were remarkably intact nervous tissue components as well. By contrast, epithelial, muscle, and reticular connective tissues as well as blood had generally disintegrated due to autolysis, freeze/thaw damage, and adipocere formation. For a tentative interpretation of these patterns, we considered general aspects of cryopreservation, such as physicochemical properties of subcellular constituents and tissue physiology.

  6. Reproducibility for histologic parameters in peritoneal mesothelioma.

    Science.gov (United States)

    Hartman, Douglas J; Borczuk, Alain; Dacic, Sanja; Krasinskas, Alyssa

    2017-09-01

    Histologic subtype is recognized as a prognostic factor in malignant pleural mesothelioma. Specifically, epithelial morphology is associated with a better prognosis than other subtypes, and the same association is observed in peritoneal malignant mesothelioma. Recently, prognostic differences based on morphologic subtypes of epithelial peritoneal malignant mesothelioma were reported. Herein, we report the interobserver variability across four pathologists at three institutions. The authors independently reviewed 67 cases of malignant peritoneal epithelioid mesotheliomas and subclassified them according to their epithelial subtype: papillary, tubulopapillary, trabecular, micropapillary, solid and/or pleomorphic. The cases were also evaluated by each author for several other histopathologic parameters including depth of invasion, nuclear grade, lymphocytic host response, mitotic count/index, presence of lymphovascular invasion, and stromal desmoplasia. The interobserver agreement for histopathologic parameters was highest for mitotic rate (κ=0.36) and primary epithelial subtype (κ=0.32). The interobserver variability for solid subtype pattern was moderate (κ=0.49). We found that the interobserver variability for most histopathologic parameters is poor. Copyright © 2017 Elsevier Inc. All rights reserved.

  7. Urinary sediment suggests lupus nephritis histology.

    Science.gov (United States)

    Martínez-Martínez, M U; Llamazares-Azuara, L M de G; Martínez-Galla, D; Mandeville, P B; Valadez-Castillo, F; Román-Acosta, S; Borjas-García, J A; Abud-Mendoza, C

    2017-05-01

    Objectives The objective of this paper was to evaluate correlations between kidney biopsy indexes (activity and chronicity) and urinary sediment findings; the secondary objective was to find which components of urinary sediment can discriminate proliferative from other classes of lupus nephritis. Methods Lupus nephritis patients scheduled for a kidney biopsy were included in our study. The morning before the kidney biopsy, we took urine samples from each patient. Receiver operating characteristic (ROC) curves were plotted to determine the area under the curve (AUC) of each test for detecting proliferative lupus nephritis; a classification tree was calculated to select a set of values that best-predicted lupus nephritis classes. Results We included 51 patients, 36 of whom were women (70.6%). Correlations of lupus nephritis activity index with the counts in the urinary sediment of erythrocytes (isomorphic and dysmorphic), acanthocytes, and leukocytes were 0.65 ( p < 0.0001) 0.62 ( p < 0.0001) and 0.22 ( p = 0.1228), respectively. Correlations of lupus nephritis chronicity index with the counts of erythrocytes, acanthocytes, and leukocytes were 0.60 ( p ≤ 0.0001), 0.52 ( p = 0.0001) and 0.17 ( p = 0.2300), respectively. Our classification tree had an accuracy of 84.3%. Conclusions Evaluation of urine sediment reflects lupus nephritis histology.

  8. Are Histologic Studies of Adenotonsillectomy Really Necessary?

    Science.gov (United States)

    Rebechi, Giseli; Pontes, Thiago Euênio; Braga, Elias Lobo; Matos, Willian Maduel; Rebechi, Fernando; Matsuyama, Cícero

    2013-01-01

    Introduction In most ear, nose, and throat services, it is routine to send the material extracted from tonsillectomy for histologic study to research malignancy, to analyze suspect material, or to provide medical-legal documentation. Recent studies have shown that this routine analysis is dispensable. Objective To evaluate the actual need and perform a cost–benefit analysis of routine histopathologic examination in tonsillectomy with no signs or symptoms of malignancy. Methods A retrospective observational study evaluated the charts of patients undergoing adenotonsillectomy, tonsillectomy, or adenoidectomy from January 2008 to September 2009 at the Institute of Otorhinolaryngology CEMA-SP. Costs of this test for the public health system were analyzed and the literature reviewed. Results We studied 281 patients between 2 and 22 years of age; 142 (50.5%) were male and 139 (49.5%) were female. Of the surgeries, 201 were adenotonsillectomies (71.5%), 41 were tonsillectomies (14.5%), and 39 were adenoidectomies (14%). The most common indication for surgery was recurrent infection (63.3%). None of study patients had clinical suspicion of malignancy. The tests showed a cost of R$20.03 per tonsil analyzed. Conclusion Routine histopathologic examination in patients undergoing adenotonsillectomy with no signs or symptoms of malignancy is dispensable and increases the cost of the surgeries. PMID:25992042

  9. Histologic scoring indices for evaluation of disease activity in Crohn's disease.

    Science.gov (United States)

    Novak, Gregor; Parker, Claire E; Pai, Rish K; MacDonald, John K; Feagan, Brian G; Sandborn, William J; D'Haens, Geert; Jairath, Vipul; Khanna, Reena

    2017-07-21

    histological indices fulfilled the inclusion criteria.Inter-rater reliability was assessed in one study. For the Naini and Cortina Score, estimates of correlation were 'almost perfect', ranging from r = 0.94 to 0.96. The methodological quality of this study with respect to reliability was 'good'.With respect to validity, correlation estimates between various histological scoring systems and Crohn's disease activity as measured by objective markers of inflammation (including C-reactive protein, erythrocyte sedimentation rate, fecal calprotectin and fecal lactoferrin); endoscopic disease activity scores; clinical disease activity scores; and quality of life questionnaires were reported. Comparisons between histologic scoring indices and endoscopic scoring indices ranged from no correlation to 'substantial' (r = 0.779). The methodological quality of the studies that explored validity ranged form 'poor' to 'good'.Responsiveness data were available in seven studies. After subjects were administered a treatment of known efficacy, statistically significant change in the index score was demonstrated in five studies with respect to six indices. Two studies failed to indicate whether there was statistically significant change in the index score post-treatment. With regard to methodological quality, six of the studies were rated as 'poor' and one of the studies was rated as 'fair'.Feasibility was assessed by one study. The Naini and Cortina Score was shown to be simple to use and feasible for every given case. Currently there is no fully validated histological scoring index for evaluation of Crohn's disease activity. Development of a validated histological scoring index for Crohn's disease is a clinical and research priority.

  10. Development and validation of new SSR markers from expressed regions in the garlic genome

    Science.gov (United States)

    Limited number of simple sequence repeat (SSR) markers is available for the genome of garlic (Allium sativum L.) although SSR markers have become one of the most preferred marker systems because they are typically co-dominant, reproducible, cross species transferable and highly polymorphic. In this ...

  11. Molecular markers. Amplified fragment length polymorphism