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1

Emerging concepts in biomarker discovery; The US-Japan workshop on immunological molecular markers in oncology  

PubMed Central

Supported by the Office of International Affairs, National Cancer Institute (NCI), the "US-Japan Workshop on Immunological Biomarkers in Oncology" was held in March 2009. The workshop was related to a task force launched by the International Society for the Biological Therapy of Cancer (iSBTc) and the United States Food and Drug Administration (FDA) to identify strategies for biomarker discovery and validation in the field of biotherapy. The effort will culminate on October 28th 2009 in the "iSBTc-FDA-NCI Workshop on Prognostic and Predictive Immunologic Biomarkers in Cancer", which will be held in Washington DC in association with the Annual Meeting. The purposes of the US-Japan workshop were a) to discuss novel approaches to enhance the discovery of predictive and/or prognostic markers in cancer immunotherapy; b) to define the state of the science in biomarker discovery and validation. The participation of Japanese and US scientists provided the opportunity to identify shared or discordant themes across the distinct immune genetic background and the diverse prevalence of disease between the two Nations. Converging concepts were identified: enhanced knowledge of interferon-related pathways was found to be central to the understanding of immune-mediated tissue-specific destruction (TSD) of which tumor rejection is a representative facet. Although the expression of interferon-stimulated genes (ISGs) likely mediates the inflammatory process leading to tumor rejection, it is insufficient by itself and the associated mechanisms need to be identified. It is likely that adaptive immune responses play a broader role in tumor rejection than those strictly related to their antigen-specificity; likely, their primary role is to trigger an acute and tissue-specific inflammatory response at the tumor site that leads to rejection upon recruitment of additional innate and adaptive immune mechanisms. Other candidate systemic and/or tissue-specific biomarkers were recognized that might be added to the list of known entities applicable in immunotherapy trials. The need for a systematic approach to biomarker discovery that takes advantage of powerful high-throughput technologies was recognized; it was clear from the current state of the science that immunotherapy is still in a discovery phase and only a few of the current biomarkers warrant extensive validation. It was, finally, clear that, while current technologies have almost limitless potential, inadequate study design, limited standardization and cross-validation among laboratories and suboptimal comparability of data remain major road blocks. The institution of an interactive consortium for high throughput molecular monitoring of clinical trials with voluntary participation might provide cost-effective solutions. PMID:19534815

Tahara, Hideaki; Sato, Marimo; Thurin, Magdalena; Wang, Ena; Butterfield, Lisa H; Disis, Mary L; Fox, Bernard A; Lee, Peter P; Khleif, Samir N; Wigginton, Jon M; Ambs, Stefan; Akutsu, Yasunori; Chaussabel, Damien; Doki, Yuichiro; Eremin, Oleg; Fridman, Wolf Herve; Hirohashi, Yoshihiko; Imai, Kohzoh; Jacobson, James; Jinushi, Masahisa; Kanamoto, Akira; Kashani-Sabet, Mohammed; Kato, Kazunori; Kawakami, Yutaka; Kirkwood, John M; Kleen, Thomas O; Lehmann, Paul V; Liotta, Lance; Lotze, Michael T; Maio, Michele; Malyguine, Anatoli; Masucci, Giuseppe; Matsubara, Hisahiro; Mayrand-Chung, Shawmarie; Nakamura, Kiminori; Nishikawa, Hiroyoshi; Palucka, A Karolina; Petricoin, Emanuel F; Pos, Zoltan; Ribas, Antoni; Rivoltini, Licia; Sato, Noriyuki; Shiku, Hiroshi; Slingluff, Craig L; Streicher, Howard; Stroncek, David F; Takeuchi, Hiroya; Toyota, Minoru; Wada, Hisashi; Wu, Xifeng; Wulfkuhle, Julia; Yaguchi, Tomonori; Zeskind, Benjamin; Zhao, Yingdong; Zocca, Mai-Britt; Marincola, Francesco M

2009-01-01

2

Emerging concepts in biomarker discovery; the US-Japan Workshop on Immunological Molecular Markers in Oncology.  

PubMed

Supported by the Office of International Affairs, National Cancer Institute (NCI), the "US-Japan Workshop on Immunological Biomarkers in Oncology" was held in March 2009. The workshop was related to a task force launched by the International Society for the Biological Therapy of Cancer (iSBTc) and the United States Food and Drug Administration (FDA) to identify strategies for biomarker discovery and validation in the field of biotherapy. The effort will culminate on October 28th 2009 in the "iSBTc-FDA-NCI Workshop on Prognostic and Predictive Immunologic Biomarkers in Cancer", which will be held in Washington DC in association with the Annual Meeting. The purposes of the US-Japan workshop were a) to discuss novel approaches to enhance the discovery of predictive and/or prognostic markers in cancer immunotherapy; b) to define the state of the science in biomarker discovery and validation. The participation of Japanese and US scientists provided the opportunity to identify shared or discordant themes across the distinct immune genetic background and the diverse prevalence of disease between the two Nations. Converging concepts were identified: enhanced knowledge of interferon-related pathways was found to be central to the understanding of immune-mediated tissue-specific destruction (TSD) of which tumor rejection is a representative facet. Although the expression of interferon-stimulated genes (ISGs) likely mediates the inflammatory process leading to tumor rejection, it is insufficient by itself and the associated mechanisms need to be identified. It is likely that adaptive immune responses play a broader role in tumor rejection than those strictly related to their antigen-specificity; likely, their primary role is to trigger an acute and tissue-specific inflammatory response at the tumor site that leads to rejection upon recruitment of additional innate and adaptive immune mechanisms. Other candidate systemic and/or tissue-specific biomarkers were recognized that might be added to the list of known entities applicable in immunotherapy trials. The need for a systematic approach to biomarker discovery that takes advantage of powerful high-throughput technologies was recognized; it was clear from the current state of the science that immunotherapy is still in a discovery phase and only a few of the current biomarkers warrant extensive validation. It was, finally, clear that, while current technologies have almost limitless potential, inadequate study design, limited standardization and cross-validation among laboratories and suboptimal comparability of data remain major road blocks. The institution of an interactive consortium for high throughput molecular monitoring of clinical trials with voluntary participation might provide cost-effective solutions. PMID:19534815

Tahara, Hideaki; Sato, Marimo; Thurin, Magdalena; Wang, Ena; Butterfield, Lisa H; Disis, Mary L; Fox, Bernard A; Lee, Peter P; Khleif, Samir N; Wigginton, Jon M; Ambs, Stefan; Akutsu, Yasunori; Chaussabel, Damien; Doki, Yuichiro; Eremin, Oleg; Fridman, Wolf Hervé; Hirohashi, Yoshihiko; Imai, Kohzoh; Jacobson, James; Jinushi, Masahisa; Kanamoto, Akira; Kashani-Sabet, Mohammed; Kato, Kazunori; Kawakami, Yutaka; Kirkwood, John M; Kleen, Thomas O; Lehmann, Paul V; Liotta, Lance; Lotze, Michael T; Maio, Michele; Malyguine, Anatoli; Masucci, Giuseppe; Matsubara, Hisahiro; Mayrand-Chung, Shawmarie; Nakamura, Kiminori; Nishikawa, Hiroyoshi; Palucka, A Karolina; Petricoin, Emanuel F; Pos, Zoltan; Ribas, Antoni; Rivoltini, Licia; Sato, Noriyuki; Shiku, Hiroshi; Slingluff, Craig L; Streicher, Howard; Stroncek, David F; Takeuchi, Hiroya; Toyota, Minoru; Wada, Hisashi; Wu, Xifeng; Wulfkuhle, Julia; Yaguchi, Tomonori; Zeskind, Benjamin; Zhao, Yingdong; Zocca, Mai-Britt; Marincola, Francesco M

2009-01-01

3

HIV Molecular Immunology Database  

NSDL National Science Digital Library

The HIV Molecular Immunology Database, associated with the Los Alamos National Laboratory, the University of California, and the US Department of Energy, "is an annotated, searchable collection of HIV-1 cytotoxic and helper T-cell epitopes and antibody binding sites." Links are provided to a number of other tools, as well as the associated HIV Immunology Database Compendia, which is downloadable in Adobe Acrobat (.pdf) format. The search functions are fairly easy to use with several drop down boxes to select the fields of interest.

2008-10-01

4

Immunological markers in neurological disorders.  

PubMed

Neurological dysfunction results from vascular, inflammatory, degenerative, neoplastic, metabolic or genetic causes. Of particular interest is a group of neurological symptoms thought to be linked to an underlying tumour, the so-called paraneoplastic syndromes. It is considered to be due to an attempt by the immune system to subjugate the growth of the tumour by triggering an antibody response against the neuronal antigens expressed by the neoplasm. The unfortunate consequence of this is an assault by the immune components on the nervous tissue, thereby rapidly precipitating a variety of neurological deficits. Every level of the nervous system is potentially vulnerable, with the disability being considered as irreversible due to the lack of regenerative capacity of the neurons. This phenomenon is rare, occurring at an approximate frequency of less than 1% of all tumours and often accompanied by the presence of specific high-titre autoantibodies in both the cerebrospinal fluid and blood. This group of antibodies are non-pathogenic markers for paraneoplastic neurological syndromes, which have expanded to almost 20 since the discovery, in 1986, of the first clinically relevant syndrome. More recently, a new generation of antineuronal antibodies against cell surface antigens, having a direct pathogenic role in causing the disease, has emerged to complement the existing repertoire. Neuronal antibodies are useful diagnostic markers of the brain disease and also, in some cases, may reveal an underlying malignancy, thus facilitating faster diagnosis and earlier treatment with consequently better prognosis. PMID:22113957

Karim, A R; Jacob, S

2012-01-01

5

Department and function: Group Leader, Laboratory of Molecular Immunology; Clinical  

E-print Network

Department and function: Group Leader, Laboratory of Molecular Immunology; Clinical Immunology in Immunology, Hannover Medical School Positions: 1994-1996: Research Associate, Dept. of Clinical Immunology, Hannover Medical School 1994: Visiting Scientist, Dept. of Immunology, University of Utrecht

Manstein, Dietmar J.

6

MOLECULAR MARKERS IN WILD TURKEY  

E-print Network

and conservation of wildlife species. In the wild turkey (Meleagris gallopavo), these markers have been used, hybridization, Meleagris gallopavo, micro- satellite, mitochondrial, molecular marker, population, subspecies

Latch, Emily K.

7

Mathematical Immunology at the molecular, cellular and population scales  

E-print Network

Mathematical Immunology at the molecular, cellular and population scales Carmen Molina of Manchester 18th of December 2012 carmen@maths.leeds.ac.uk #12;Physics Biology MathBio Immunology UK Math: populations 4 Theoretical Immunology 5 Mathematical Biology in the UK 6 Acknowledgements 2 / 50 #12;Physics

Wirosoetisno, Djoko

8

Postdoctoral Research Positions in Mucosal Immunology and Molecular Microbiology  

E-print Network

Postdoctoral Research Positions in Mucosal Immunology and Molecular Microbiology Two post-doctoral research positions are available at the Department of Microbiology and Immunology, Columbia University, New and microbiologists that have broad interests in mucosal immunology and host-commensal interactions and enjoy

Symington, Lorraine S.

9

Value of Immunological Markers in Predicting Responsiveness to Influenza Vaccination in Elderly Individuals  

Microsoft Academic Search

Elderly individuals are at high risk for morbidity and mortality when infected with influenza virus. Vacci- nations with inactivated virus are less effective in the elderly due to the declining competency of the aging immune system. We have explored whether immunological parameters predict poor anti-influenza virus vaccine responses and can be used as biological markers of immunosenescence. One hundred fifty-three

JORG J. GORONZY; JAMES W. FULBRIGHT; CYNTHIA S. CROWSON; GREGORY A. POLAND; WILLIAM M. O'FALLON; CORNELIA M. WEYAND

2001-01-01

10

AIDS. Author manuscript Comparison of viro-immunological marker changes between HIV-1 and  

E-print Network

AIDS. Author manuscript Page /1 11 Comparison of viro-immunological marker changes between HIV-1-2 infected patients . At AIDS stage, HIV-2 infected patients[11­13] [13­20] tend to have higher CD4 and HIV-2-infected patients in France Drylewicz Julia 1 2 , Matheron Sophie 3 , Lazaro Estibaliz 4

Boyer, Edmond

11

Molecular detection and immunological localization of gill Na /H exchanger in the dogfish (Squalus acanthias)  

E-print Network

Molecular detection and immunological localization of gill Na /H exchanger in the dogfish (Squalus-Shetlar AI, Weakley JC, Havird J, Freiji A, Evans DH, Edwards SL. Molecular detection and immunologicalDa protein in Western blots and immunologically recognized branchial cells having two patterns of protein

Evans, David H.

12

Molecular Immunology 46 (2009) 29752984 Contents lists available at ScienceDirect  

E-print Network

Molecular Immunology 46 (2009) 2975­2984 Contents lists available at ScienceDirect Molecular Immunology journal homepage: www.elsevier.com/locate/molimm Linear IgE-epitope mapping and comparative, USA c Department of Pediatric Pneumology and Immunology, University Children's Hospital Charité

Ronquist, Fredrik

13

03-390 Molecular and Cellular Immunology (9 units) 2009 Instructors (Office hours by appointment)  

E-print Network

03-390 Molecular and Cellular Immunology (9 units) ­ 2009 Instructors (Office hours by appointment: kvasilev@cmu.edu Text: Immunology: A Short Course. 6e. Richard Coico and Geoffrey Sunshine. 2009. Wiley Description: This course offers the student a comprehensive view of modern immunology at the molecular

Murphy, Robert F.

14

Immunological tissue markers in the diagnosis of testicular cancer  

Microsoft Academic Search

Immunohistochemistry greatly contributes to the accuracy of the diagnosis in testicular germ cell tumors (TGCT). Human chorionic gonadotropin (HCG) and alphafetoprotein (AFP) are the most used markers in testicular cancer, where the immunostaining is positive in non-seminomatous TGCT. Pure seminoma does not produce these proteins but some are combined with syncytiotrophoblastic cells which elaborate HCG, producing elevated HCG serum levels

A. de Matteis; F. Silverio

1987-01-01

15

Postdoctoral Research Position in Molecular Immunology A post-doctoral research position in Molecular Immunology is available in the Liu lab at  

E-print Network

dendritic cell and monocyte biology. We combine physiological, cellular methods and genetic tools with small in Molecular Immunology is available in the Liu lab at Columbia University Medical Center (CUMC) to study and solid background in molecular biology and immunology. Expertise in retroviral vector or experience

Symington, Lorraine S.

16

Significance of Immunologic Markers in the Diagnosis of Lymphoma  

Microsoft Academic Search

The malignant lymphomas with indolent course present numerous diagnostic controversies, the frequent involvement of viral etiopathogeny, which can be followed up serologically, making these lymphomas an ideal topic for further study. The phenotypical and genetic heterogenity of the lymphomas make it difficult to elucidate the molecular mechanisms which concur in initiation and growth of these neoplasms. Therefore, the classification, diagnosis

M. Sathiya; K. Muthuchelian

17

Molecular Immunology 44 (2007) 13741383 Genome-wide survey of the gene expression response  

E-print Network

Molecular Immunology 44 (2007) 1374­1383 Genome-wide survey of the gene expression response as the interest for compara- tive and evolutionary immunology has motivated the edification of a substantial body of knowledge in fish immunology (Iwama and Nakanishi, 1996). Hence, the activity of non-specific immu- nity

Bernatchez, Louis

18

Graduate Division of Biological and Biomedical Sciences Program in Immunology and Molecular Pathogenesis  

Microsoft Academic Search

Program of Study The Program in Immunology and Molecular Pathogenesis (IMP) at Emory University offers interdisciplinary training in molecular and cellular immunology and the role of the immune system in the pathogenesis of infectious disease. Students in the IMP Program have a unique opportunity to study all aspects of pathogenesis using a spectrum of cutting-edge molecular and cellular techniques. Faculty

Kathy Smith

19

MOLECULAR MARKER ANALYSIS OF DEARS SAMPLES  

EPA Science Inventory

Source apportionment based on organic molecular markers provides a promising approach for meeting the Detroit Exposure and Aerosol Research Study (DEARS) objective of comparing source contributions between community air monitoring stations and various neighborhoods. Source appor...

20

(ISEA) MOLECULAR MARKER ANALYSIS OF DEARS SAMPLES  

EPA Science Inventory

Source apportionment based on organic molecular markers provides a promising approach for meeting the Detroit Exposure and Aerosol Research Study (DEARS) objective of comparing source contributions between community air monitoring stations and various neighborhoods. Source appor...

21

Molecular markers applied to plant tissue culture  

Microsoft Academic Search

Summary  The last decade has witnessed successful applications of plant tissue culture techniques in several crops. During that same\\u000a period, studies in plant molecular genetics have also grown exponentially. Molecular markers (isozymes, RFLPs, and PCR-based\\u000a markers such as RAPDs) are now used to study many of the current limitations of tissue culture. They have been used to investigate\\u000a mechanisms that underlie

Sylvie Cloutier; Benoit S. Landry

1994-01-01

22

Prenatal immunologic predictors of postpartum depressive symptoms: a prospective study for potential diagnostic markers.  

PubMed

In postpartum depression (PPD), immunologic changes have been proposed to be involved in the disease pathology. The study evaluates the regulation of the innate and adaptive immune response over the course of late pregnancy and postpartum period and their association with the development of postpartum depressive symptoms. Furthermore, prenatal immunologic markers for a PPD were investigated. Hundred pregnant women were included. At 34th and 38th week of pregnancy as well as 2 days, 7 weeks and 6 months postpartum, immune parameters (neopterin, regulatory T cells, CXCR1, CCR2, MNP1 and CD11a) were measured by flow cytometry/ELISA, and the psychopathology was evaluated. We found that regulatory T cells were significantly increased prenatal (p = 0.011) and postnatal (p = 0.01) in mothers with postnatal depressive symptoms. The decrease in CXCR 1 after delivery was significantly higher in mother with postnatal depressive symptoms (p = 0.032). Mothers with postnatal depressive symptoms showed already prenatal significantly elevated neopterin levels (p = 0.049). Finally, regulatory T cells in pregnancy strongly predict postnatal depressive symptoms (p = 0.004). The present study revealed that prenatal and postnatal immunologic parameters are associated with postpartum depressive symptoms in mothers. In addition, we found immune markers that could eventually be the base for a biomarker set that predicts postnatal depressive symptoms already during pregnancy. PMID:24595743

Krause, Daniela; Jobst, Andrea; Kirchberg, Franka; Kieper, Susann; Härtl, Kristin; Kästner, Ralph; Myint, Aye-Mu; Müller, Norbert; Schwarz, Markus J

2014-10-01

23

Molecular markers in pediatric neuro-oncology  

PubMed Central

Pediatric molecular neuro-oncology is a fast developing field. A multitude of molecular profiling studies in recent years has unveiled a number of genetic abnormalities unique to pediatric brain tumors. It has now become clear that brain tumors that arise in children have distinct pathogenesis and biology, compared with their adult counterparts, even for those with indistinguishable histopathology. Some of the molecular features are so specific to a particular type of tumors, such as the presence of the KIAA1549-BRAF fusion gene for pilocytic astrocytomas or SMARCB1 mutations for atypical teratoid/rhabdoid tumors, that they could practically serve as a diagnostic marker on their own. Expression profiling has resolved the existence of 4 molecular subgroups in medulloblastomas, which positively translated into improved prognostication for the patients. The currently available molecular markers, however, do not cover all tumors even within a single tumor entity. The molecular pathogenesis of a large number of pediatric brain tumors is still unaccounted for, and the hierarchy of tumors is likely to be more complex and intricate than currently acknowledged. One of the main tasks of future molecular analyses in pediatric neuro-oncology, including the ongoing genome sequencing efforts, is to elucidate the biological basis of those orphan tumors. The ultimate goal of molecular diagnostics is to accurately predict the clinical and biological behavior of any tumor by means of their molecular characteristics, which is hoped to eventually pave the way for individualized treatment. PMID:23095836

Ichimura, Koichi; Nishikawa, Ryo; Matsutani, Masao

2012-01-01

24

Prognostic molecular markers in early breast cancer  

PubMed Central

A multitude of molecules involved in breast cancer biology have been studied as potential prognostic markers. In the present review we discuss the role of established molecular markers, as well as potential applications of emerging new technologies. Those molecules used routinely to make treatment decisions in patients with early-stage breast cancer include markers of proliferation (e.g. Ki-67), hormone receptors, and the human epidermal growth factor receptor 2. Tumor markers shown to have prognostic value but not used routinely include cyclin D1 and cyclin E, urokinase-like plasminogen activator/plasminogen activator inhibitor, and cathepsin D. The level of evidence for other molecular markers is lower, in part because most studies were retrospective and not adequately powered, making their findings unsuitable for choosing treatments for individual patients. Gene microarrays have been successfuly used to classify breast cancers into subtypes with specific gene expression profiles and to evaluate prognosis. RT-PCR has also been used to evaluate expression of multiple genes in archival tissue. Proteomics technologies are in development. PMID:15084231

Esteva, Francisco J; Hortobagyi, Gabriel N

2004-01-01

25

Molecular tools for marker-assisted breeding of buffelgrass  

E-print Network

The increasing availability of molecular tools is facilitating marker-assisted selection (MAS) in plant improvement programs. The objectives of this research were to: 1) populate the framework buffelgrass genome map with additional molecular markers...

Jessup, Russell William

2005-11-01

26

Immunologic biomarkers in relation to exposure markers of PCBs and dioxins in Flemish adolescents (Belgium).  

PubMed Central

In this study, we investigated 17- to 18-year-old boys and girls to determine whether changes in humoral or cellular immunity or respiratory complaints were related to blood serum levels of polychlorinated biphenyls (PCBs) and dioxin-like compounds after lifetime exposure in Flanders (Belgium). We obtained blood samples from and administered questionnaires to 200 adolescents recruited from a rural area and two urban suburbs. Physicians recorded medical history and respiratory diseases. We measured immunologic biomarkers such as differential blood cell counts, lymphocyte phenotypes, and serum immunoglobulins. As biomarkers of exposure, we determined the serum concentrations of PCBs (PCB 138, PCB 153, and PCB 180) and dioxin-like compounds [chemical-activated luciferase expression (CALUX) bioassay]. The percentages of eosinophils and natural killer cells in blood were negatively correlated with CALUX toxic equivalents (TEQs) in serum (p = 0.009 and p = 0.05, respectively). Increased serum CALUX TEQs resulted in an increase in serum IgA levels (p = 0.05). Furthermore, levels of specific IgEs (measured by radioallergosorbent tests) of cat dander, house dust mite, and grass pollen were also significantly and negatively associated with the CALUX TEQ, with odds ratios (ORs) equal to 0.63 [95% confidence interval (CI), 0.42-0.96], 0.68 (0.5-0.93), and 0.70 (0.52-0.95), respectively. In addition, reported allergies of the upper airways and past use of antiallergic drugs were negatively associated with CALUX TEQs, with ORs equal to 0.66 (0.47-0.93) and 0.58 (0.39-0.85), respectively. We found a negative association between IgGs and marker PCBs in serum (p = 0.009). This study shows that immunologic measurements and respiratory complaints in adolescents were associated with environmental exposure to polyhalogenated aromatic hydrocarbons (PHAHs). The negative correlation between PHAHs and allergic responses in adolescents suggested that exposure may entail alterations in the immune status. PMID:12055051

Van Den Heuvel, Rosette L; Koppen, Gudrun; Staessen, Jan A; Hond, Elly Den; Verheyen, Geert; Nawrot, Tim S; Roels, Harry A; Vlietinck, Robert; Schoeters, Greet E R

2002-01-01

27

The role of molecular markers and marker assisted selection in breeding for organic agriculture  

Microsoft Academic Search

Plant geneticists consider molecular marker assisted selection a useful additional tool in plant breeding programs to make\\u000a selection more efficient. Standards for organic agriculture do not exclude the use of molecular markers as such, however for\\u000a the organic sector the appropriateness of molecular markers is not self-evident and is often debated. Organic and low-input\\u000a farming conditions require breeding for robust

E. T. Lammerts van Bueren; G. Backes; H. de Vriend; H. Østergård

2010-01-01

28

Molecular Marker Systems for Oenothera Genetics  

PubMed Central

The genus Oenothera has an outstanding scientific tradition. It has been a model for studying aspects of chromosome evolution and speciation, including the impact of plastid nuclear co-evolution. A large collection of strains analyzed during a century of experimental work and unique genetic possibilities allow the exchange of genetically definable plastids, individual or multiple chromosomes, and/or entire haploid genomes (Renner complexes) between species. However, molecular genetic approaches for the genus are largely lacking. In this study, we describe the development of efficient PCR-based marker systems for both the nuclear genome and the plastome. They allow distinguishing individual chromosomes, Renner complexes, plastomes, and subplastomes. We demonstrate their application by monitoring interspecific exchanges of genomes, chromosome pairs, and/or plastids during crossing programs, e.g., to produce plastome–genome incompatible hybrids. Using an appropriate partial permanent translocation heterozygous hybrid, linkage group 7 of the molecular map could be assigned to chromosome 9·8 of the classical Oenothera map. Finally, we provide the first direct molecular evidence that homologous recombination and free segregation of chromosomes in permanent translocation heterozygous strains is suppressed. PMID:18791241

Rauwolf, Uwe; Golczyk, Hieronim; Meurer, Jorg; Herrmann, Reinhold G.; Greiner, Stephan

2008-01-01

29

Biological (molecular and cellular) markers of toxicity  

SciTech Connect

Several molecular and cellular markers of genotoxicity were adapted for measurement in the Medaka (Oryzias latipes), and were used to describe the effects of treatment of the organism with diethylnitrosamine (DEN). NO{sup 6}-ethyl guanine adducts were detected, and a slight statistically significant, increase in DNA strand breaks was observed. These results are consistent with the hypothesis that prolonged exposure to high levels of DEN induced alkyltransferase activity which enzymatically removes any O{sup 6}-ethyl guanine adducts but does not result in strand breaks or hypomethylation of the DNA such as might be expected from excision repair of chemically modified DNA. Following a five week continuous DEN exposure with 100 percent renewal of DEN-water every third day, the F values (DNA double strandedness) increased considerably and to similar extent in fish exposed to 25, 50, and 100 ppM DEN. This has been observed also in medaka exposed to BaP.

Shugart, L.R.; D'Surney, S.J.; Gettys-Hull, C.; Greeley, M.S. Jr.

1991-12-15

30

Health complaints and immunological markers of exposure to bioaerosols among biowaste collectors and compost workers  

PubMed Central

OBJECTIVES—In a cross sectional study, work related health complaints and diseases of 58 compost workers and 53 biowaste collectors were investigated and compared with 40 control subjects. Levels of specific IgG antibodies to moulds and bacteria were measured as immunological markers of exposure to bioaerosols.?METHODS—With a standardised protocol, the participants of the study were interviewed for work related symptoms, conditions of exposure to bioaerosols at their workplaces, exposure to bioaerosols from other sources, atopic diseases, and smoking habits. They were clinically examined by physicians specialised in occupational medicine. Also, concentrations of specific IgG antibodies against antigens of moulds and actinomycetes occurring regularly at these workplaces were measured and compared with the health complaints of the workers.?RESULTS—Compost workers had significantly more symptoms and diseases of the airways (p=0.003) and the skin (p=0.02) than the control subjects. Health complaints of biowaste collectors did not differ significantly from those of the control group. Subjects with atopic diseases were underrepresented in the compost workers (p=0.003). Significantly increased antibody concentrations against fungi and actinomycetes were measured in workers at composting plants. The concentrations in biowaste collectors did not differ significantly from those in the control subjects. A significant association between the diseases and increased antibody concentrations were found in the compost workers.?CONCLUSION—The high exposure to bioaerosols of compost workers is significantly associated with a higher frequency of health complaints and diseases as well as higher concentrations of specific antibodies against moulds and actinomycetes. A healthy worker effect is indicated by the underrepresentation of atopic diseases among the compost workers compared with biowaste collectors and the control group.???Keywords: exposure to bioaerosols; organic dust; IgG antibodies; moulds; actinomycetes PMID:10854498

Bunger, J.; Antlauf-Lammers, M.; Schulz, T.; Westphal, G.; Muller, M.; Ruhnau, P.; Hallier, E.

2000-01-01

31

Molecular Immunology 38 (2001) 10291037 Asymmetric ligand recognition by the activating natural killer cell  

E-print Network

Molecular Immunology 38 (2001) 1029�1037 Review Asymmetric ligand recognition by the activating in complex patterns of inhibitory and activating isoforms on overlapping, but distinct, subsets of NK cells cells, but subsequently found on macrophages and a variety of T cell types. NKG2D ligands in rodents

Strong, Roland K.

32

Molecular DNA Markers in Phylogeny and Systematics  

Microsoft Academic Search

The review considers data on the use of the main evolutionary markers (ribosomal, mitochondrial, and RAPD markers; dispersed and tandem repeats). Some circumstances impending analysis of these data are discussed.

V. V. Grechko

2002-01-01

33

HST.176 Cellular and Molecular Immunology, Fall 2002  

E-print Network

Covers cells and tissues of the immune system, lymphocyte development, the structure and function of antigen receptors, the cell biology of antigen processing and presentation including molecular structure and assembly of ...

Pillai, Shiv

34

Resolution-associated molecular patterns (RAMP): RAMParts defending immunological homeostasis?  

PubMed Central

The resolution of inflammation is central to the maintenance of good health and immune homeostasis. Recently, several intracellular stress proteins have been described as having extracellular properties that are anti-inflammatory or favour the resolution of inflammation. We propose that these molecules should be defined as resolution-associated molecular patterns (RAMPs). RAMPs are released at times of cellular stress and help to counterbalance the inflammatory effects of pathogen-associated (PAMPs) and damage-associated (DAMPs) molecular patterns. We propose that heat shock protein 10 (HSP10), ?B-crystallin (?BC), HSP27 and binding immunoglobulin protein (BiP) should be considered founding members of the RAMP family. A greater understanding of RAMP biology may herald the development of novel immunotherapies. PMID:21671907

Shields, A M; Panayi, G S; Corrigall, V M

2011-01-01

35

Serum Polyfluoroalkyl Concentrations, Asthma Outcomes, and Immunological Markers in a Case–Control Study of Taiwanese Children  

PubMed Central

Background: Per?uorinated compounds (PFCs) are ubiquitous pollutants. Experimental data suggest that they may be associated with adverse health outcomes, including asthma. However, there is little supporting epidemiological evidence. Methods: A total of 231 asthmatic children and 225 nonasthmatic controls, all from northern Taiwan, were recruited in the Genetic and Biomarkers study for Childhood Asthma. Structure questionnaires were administered by face-to-face interview. Serum concentrations of 11 PFCs and levels of immunological markers were also measured. Associations of PFC quartiles with concentrations of immunological markers and asthma outcomes were estimated using multivariable regression models. Results: Nine PFCs were detectable in most children (? 84.4%), of which perfluorooctane sulfonate (PFOS) was the most abundant (median serum concentrations of 33.9 ng/mL in asthmatics and 28.9 ng/mL in controls). Adjusted odds ratios for asthma among those with the highest versus lowest quartile of PFC exposure ranged from 1.81 (95% CI: 1.02, 3.23) for the perfluorododecanoic acid (PFDoA) to 4.05 (95% CI: 2.21, 7.42) for perfluorooctanic acid (PFOA). PFOS, PFOA, and subsets of the other PFCs were positively associated with serum IgE concentrations, absolute eosinophil counts (AEC), eosinophilic cationic protein (ECP) concentrations, and asthma severity scores among asthmatics. Conclusions: This study suggests an association between PFC exposure and juvenile asthma. Because of widespread exposure to these chemicals, these findings may be of potential public health concern. PMID:23309686

Dong, Guang-Hui; Tung, Kuan-Yen; Tsai, Ching-Hui; Liu, Miao-Miao; Wang, Da; Liu, Wei; Jin, Yi-He; Hsieh, Wu-Shiun; Chen, Pau-Chung

2013-01-01

36

Autoimmunity-related immunological serum markers and survival in a tertiary care cohort of adult patients with epilepsy.  

PubMed

We evaluated mortality in relation to a panel of autoimmunity-related immunological serum markers in adult patients with epilepsy (PWE), seen in 1996-1997 at the Department of Neurology, Oulu University Hospital in Finland. Blood samples were drawn from 968 volunteers, and baseline measurements included serum immunoglobulins (IgG, IgA, and IgM), and the following antibodies: anticardiolipin, antinuclear, antimitochondrial, antigliadin (IgA and IgG classes), IgA tissue transglutaminase, and IgA endomysial. Hazard ratios (HR) for all-cause mortality in PWE with abnormal immunological markers relative to 413 patients with normal findings were evaluated with adjustment for confounders during a follow-up of nine years. Borderline statistically significant associations were found only for elevated IgA (HR 2.09, 95% CI 0.99-4.42) and for having two or more abnormal antibody titers (HR 1.58, 95% CI 0.98-2.56). The findings of this exploratory study suggested that elevated serum IgA might be associated with excess mortality in PWE. PMID:25257831

Nevalainen, Olli; Auvinen, Anssi; Ansakorpi, Hanna; Raitanen, Jani; Isojärvi, Jouko

2014-11-01

37

Practical immunology  

SciTech Connect

This book covers the advances in contemporary molecular and cellular immunology which have provided the experimentalist with tools of unparalleled reproducibility and precision. Techniques for the propagation and manipulation of cells, genes and gene products have a central place in the new edition, reflecting their role in modern immunology.

Hudson, L. (St. George's Hospital Medical School, London (GB)); Hay, F.C. (Middlesex Hospital, London (UK))

1989-01-01

38

Marker Assisted Selection (MAS) for chickpea Fusarium oxysporum wilt resistant genotypes using PCR based molecular markers.  

PubMed

The exploration of genetically superior accessions is the key source of germplasm conservation and potential breeding material for the future. To meet the demand of better yielding chickpea cultivars in Pakistan the present study was organized to select more stable and resistant lines from indigenous as well as exotic chickpea germplasm obtained from Plant Genetic Resource Institute (PGRI), National Agricultural Research Centre, Islamabad, Pakistan. For the identification and evaluation of chickpea wilt resistant lines against Fusarium oxysporum f. sp. ciceris (Schlechtends), the germplasm was tested in the field for the selection of wilt resistant lines and the PCR based molecular markers were investigated to use Marker Assisted Selection (MAS) for selection of the desirable cultivars. In field trial, 70 % accessions were resistant to wilt disease, while the remaining 30 % have shown susceptibility to the disease. A total of 5 RAPD and 15 SSR markers were screened for molecular based characterization of wilt response. The data of molecular markers were scored by the presence (1) and absence (0) of allele and subjected to statistical analysis. The analysis was based on coefficient of molecular similarity using UPGMA and sorted the germplasm into two groups based on disease response. Among the total used RAPD/SSR primers, only TA194 SSR marker showed linkage to wilt resistant locus at 85 % probability. The linkage of a marker was reconfirmed by receiver operating characteristic curve. The use of the sorted wilt resistant genotypes through SSR marker TA194 can make available ample prospect in MAS breeding for yield improvement of the crop in Pakistan. PMID:25017202

Ahmad, Zakia; Mumtaz, Abdul Samad; Ghafoor, Abdul; Ali, Amjad; Nisar, Mohammad

2014-10-01

39

Molecular markers in bladder cancer: a critical appraisal.  

PubMed

The diagnosis of both primary and recurrent bladder tumors currently relies upon the urine cytology and cystoscopy. Neither of these diagnostic tools is completely accurate. Prognostication of bladder cancer is largely based on pathologic tumor grade and stage. Over the past 2 decades, there is accumulating evidence that like many other cancers, bladder cancer, too, has a distinct molecular signature that separates it from other cancers and normal bladder tissue. Bladder tumors of different grades and stages even possess unique, and specific genotypic and phenotypic characteristics. Although recognition of several of these molecular alterations is possible by analyzing tumor tissue, urine, and serum samples, few if any of these "molecular markers" for bladder cancer are widely used in clinical practice. These markers include some that can be applied during the diagnostic work-up of symptoms (e.g., hematuria), those under surveillance for recurrence of superficial disease and forecasting long-term prognosis, or response to chemotherapy. In this review of molecular markers for bladder cancer, effectiveness of markers in each of these categories that are identifiable in the urine of patients with bladder cancer was examined. Many of the diagnostic markers appear to hold an advantage over urine cytology in terms of sensitivity, especially for the detection of low-grade superficial tumors. However, most markers tend to be less specific than cytology, yielding more false-positives. This result is more commonly observed in patients with concurrent bladder inflammation or other benign bladder conditions. Although there are several candidate markers for assessing prognosis or response to chemotherapy, studies of large patient populations are lacking. Further studies involving larger numbers of patients are required to determine their accuracy and widespread applicability in guiding treatment of bladder cancer. PMID:16818187

Konety, Badrinath R

2006-01-01

40

Biological (molecular and cellular) markers of toxicity  

SciTech Connect

The overall objective of this study is to evaluate the use of the small aquarium fish, Japanese Medaka, as a predictor of potential genotoxicity following exposure to carcinogens. This will be accomplished by quantitatively investigating the early molecular events associated with genotoxicity of various tissues of Medaka subsequent to exposure of the organism to several known carcinogens, such as diethylnitrosamine (DEN) and benzo(a)pyrene (BaP). 11 refs., 1 fig., 1 tab.

McCarthy, J.F.

1990-04-01

41

Prognostically Important Molecular Markers in Cytogenetically Normal Acute Myeloid Leukemia  

PubMed Central

Cytogenetically normal acute myeloid leukemia (CN-AML) is a heterogeneous disease with variable clinical outcomes. Emerging data has identified molecular markers that provide additional prognostic information to better classify these patients into those with a more favorable prognosis and those with an unfavorable prognosis who may require more aggressive or investigational therapies. Markers such as mutations in nucleophosmin 1 gene and CCAAT/enhancer binding protein alpha gene have been associated with a more favorable prognosis in CN-AML. In contrast, FMS-related tyrosine kinase 3 mutations, partial tandem duplication of mixed-lineage leukemia gene and overexpression of brain and acute leukemia, cytoplasmic gene are associated with inferior clinical outcomes. In this article, the authors discuss the classical clinical features of AML and the importance of cytogenetics that predict prognosis in AML. They review the best-described molecular markers in CN-AML and their significance to clinical decision making in CN-AML. PMID:21522052

Lin, Tara L.; Smith, B. Douglas

2014-01-01

42

RESEARCH ARTICLE Uncloaking a cryptic, threatened rail with molecular markers  

E-print Network

RESEARCH ARTICLE Uncloaking a cryptic, threatened rail with molecular markers: origins Black Rail lives under dense marsh vegetation, is rarely observed, flies weakly and has a highly disjunct distribution. The largest population of rails is found in 8­10 large wetlands in San Francisco Bay

Beissinger, Steven R.

43

Pathological, immunological and biochemical markers of subchronic arsenic toxicity in rats.  

PubMed

Subchronic exposure to arsenic in rats was investigated to identify sensitive indicators of subclinical toxicity in rats. Immunological, pathological, and biochemical bioindicators were examined in rats exposed to arsenic in their drinking water. Juvenile male Wistar rats were allocated to four treatment groups receiving 0, 0.4, 4, and 40 ppm of arsenite in drinking water for 18 wks. Besides daily monitoring for clinical signs of adverse health effects, clinical biochemistry, B-cell-mediated and innate immune responses, plus gross, and histopathology were examined. In vitro tests of oxidative damage to basic cellular constituents, lipids, proteins, and nucleic acids, were measured using thiobarbituric acid reacting substances (TBARS) assays, protein carbonyl formation, and 8-hydroxydeoxyguanosine (8-OHdG), respectively. Clinical changes in the rats were limited to decreased feed and water intake in the high- (40 ppm) dose group (P < 0.05), however, growth rate was not affected. Serum biochemical changes occurred in blood urea nitrogen, K(+) , Cl(-) , and alanine aminotransferase (ALT) from arsenic exposure. Immunotoxicity was evident through a dose-dependent suppression of the secondary antibody-mediated response to a T-cell-dependent antigen, keyhole limpet hemocyanin (KLH). Histopathology of the liver revealed marked fatty infiltration and vacuolization particularly evident in periacinar hepatocytes. This pattern of toxicopathology in the high-exposure group may be related to the significantly higher (P < 0.05) oxidative stress, demonstrated through lipid peroxidation (TBARS assay) in the rats exposed to 40 ppm arsenite. The present study revealed that young, growing rats exposed to arsenic for 18 wks tolerated exposures up to 4 ppm. At higher doses, there was evidence of hepatotoxicity, humoral immunity was compromised, and an adverse effect on hepatic organelle and cell membranes was evident through a dose dependent increased in oxidative stress. PMID:20725942

Nain, Sukhbir; Smits, Judit E G

2012-03-01

44

Prospects of molecular markers in Fusarium species diversity.  

PubMed

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 focuses of various molecular-based techniques employed to study the diversity of Fusarium species causing diseases in major food crops. An introduction of fusarial diseases and their mycotoxins and molecular-marker-based methods for detection introduce the concept of marker application. Various well-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 for generation of probes and their use in phylogeny of Fusarium spp. are also presented. The concluding part emphasizes the value of molecular markers for assessing genetic variability and reveals that molecular tools are indispensable for providing information not only of one Fusarium species but on whole fungal community. This will be of extreme value for diagnosticians and researchers concerned with fungal biology, ecology, and genetics. PMID:21494869

Chandra, Nayaka S; Wulff, E G; Udayashankar, A C; Nandini, B P; Niranjana, S R; Mortensen, C N; Prakash, H S

2011-06-01

45

Clinical and Immunological Markers of Dengue Progression in a Study Cohort from a Hyperendemic Area in Malaysia  

PubMed Central

Background With its elusive pathogenesis, dengue imposes serious healthcare, economic and social burden on endemic countries. This study describes the clinical and immunological parameters of a dengue cohort in a Malaysian city, the first according to the WHO 2009 dengue classification. Methodology and Findings This longitudinal descriptive study was conducted in two Malaysian hospitals where patients aged 14 and above with clinical symptoms suggestive of dengue were recruited with informed consent. Among the 504 participants, 9.3% were classified as non-dengue, 12.7% without warning signs, 77.0% with warning signs and 1.0% with severe dengue based on clinical diagnosis. Of these, 37% were misdiagnosed as non-dengue, highlighting the importance of both clinical diagnosis and laboratory findings. Thrombocytopenia, prolonged clotting time, liver enzymes, ALT and AST served as good markers for dengue progression but could not distinguish between patients with and without warning signs. HLA-A*24 and -B*57 were positively associated with Chinese and Indians patients with warning signs, respectively, whereas A*03 may be protective in the Malays. HLA-A*33 was also positively associated in patients with warning signs when compared to those without. Dengue NS1, NS2A, NS4A and NS4B were found to be important T cell epitopes; however with no apparent difference between with and without warning signs patients. Distinction between the 2 groups of patients was also not observed in any of the cytokines analyzed; nevertheless, 12 were significantly differentially expressed at the different phases of illness. Conclusion The new dengue classification system has allowed more specific detection of dengue patients, however, none of the clinical parameters allowed distinction of patients with and without warning signs. While the HLA-A*33 may be predictive marker for development of warning signs; larger studies will be needed to support this findings. PMID:24647042

Rathakrishnan, Anusyah; Klekamp, Benjamin; Wang, Seok Mui; Komarasamy, Thamil Vaani; Natkunam, Santha Kumari; Sathar, Jameela; Azizan, Azliyati; Sanchez-Anguiano, Aurora; Manikam, Rishya; Sekaran, Shamala Devi

2014-01-01

46

Reviewing and Updating the Major Molecular Markers for Stem Cells  

PubMed Central

Stem cells (SC) are able to self-renew and to differentiate into many types of committed cells, making SCs interesting for cellular therapy. However, the pool of SCs in vivo and in vitro consists of a mix of cells at several stages of differentiation, making it difficult to obtain a homogeneous population of SCs for research. Therefore, it is important to isolate and characterize unambiguous molecular markers that can be applied to SCs. Here, we review classical and new candidate molecular markers that have been established to show a molecular profile for human embryonic stem cells (hESCs), mesenchymal stem cells (MSCs), and hematopoietic stem cells (HSCs). The commonly cited markers for embryonic ESCs are Nanog, Oct-4, Sox-2, Rex-1, Dnmt3b, Lin-28, Tdgf1, FoxD3, Tert, Utf-1, Gal, Cx43, Gdf3, Gtcm1, Terf1, Terf2, Lefty A, and Lefty B. MSCs are primarily identified by the expression of CD13, CD29, CD44, CD49e, CD54, CD71, CD73, CD90, CD105, CD106, CD166, and HLA-ABC and lack CD14, CD31, CD34, CD45, CD62E, CD62L, CD62P, and HLA-DR expression. HSCs are mainly isolated based on the expression of CD34, but the combination of this marker with CD133 and CD90, together with a lack of CD38 and other lineage markers, provides the most homogeneous pool of SCs. Here, we present new and alternative markers for SCs, along with microRNA profiles, for these cells. PMID:23336433

Calloni, Raquel; Cordero, Elvira Alicia Aparicio; Henriques, Joao Antonio Pegas

2013-01-01

47

Predictive markers in bladder cancer: Do we have molecular markers ready for clinical use?  

PubMed

Abstract Bladder cancer (BC) is a heterogeneous disease. Approximately 75% of patients present with non-muscle-invasive BC (NMIBC), which has a high recurrence rate and a low but unpredictable progression rate. Conversely, patients with muscle-invasive BC (MIBC) are at high risk for progression and cancer-specific mortality, but, again, disease behavior is unpredictable. To date, risk assessment for tumor recurrence and progression is based on clinico-pathological factors only. A risk assessment calculator that is based on several such parameters is available for NMIBC, but it has been reported to have potential flaws. In the last two decades, great effort has been made to evaluate the prognostic and predictive role of several molecular markers in MIBC and, even more so, in NMIBC, where the need for more precise risk stratification is urgently needed. This review addresses current evidence for the role of several molecular markers easily assessable by immunohistochemical techniques in prognosticating/predicting the outcome of NMIBC and MIBC. To date, because of divergent results among the many studies, no molecular marker has yet entered routine clinical practice; however, some of them (e.g., p53, pRb, p21, and survivin) have proved their predictive value in studies that included a homogeneous patient population on standardized treatment, and, therefore, are probably ready for clinical validation on a larger scale. Even more interesting is the possibility of constructing multimarker panels that could be used in routine clinical practice, as all these markers can easily be evaluated by immunohistochemistry on routine surgical pathology specimens. The molecular markers described herein hold promise for becoming widely available and cost-effective tools for reliable risk assessment, which would represent a great advancement in counseling patients, in selecting them for neoadjuvant and adjuvant treatments, and in determining their eligibility for clinical trials. PMID:25036341

Sanguedolce, Francesca; Bufo, Pantaleo; Carrieri, Giuseppe; Cormio, Luigi

2014-10-01

48

Stabilization of white blood cells and immunologic markers for extended analysis using flow cytometry.  

PubMed

We evaluated whole blood samples drawn from 25 healthy donors and 20 HIV-infected donors into K3EDTA and Cyto-Chex BCT blood collection tubes for CD4, CD8, and CD3 cell counts (HIV Panel). Samples collected in Cyto-Chex BCT were stored at room temperature and tested by 4-color flow cytometry at 6 h, 3 days, and 7 days after isolation for CD4, CD8, and CD3 absolute cell counts/microl and compared with samples collected in K3EDTA tubes and tested at 6 h. Regardless of donor type, the samples collected in Cyto-Chex BCT and tested on day 7 yielded results that were statistically indistinguishable (with correlation coefficients of 0.96 or greater) from samples collected in K3EDTA tubes and tested at 6 h. We conclude that whole blood samples collected in Cyto-Chex BCT are stabilized for their marker phenotype for at least 7 days after phlebotomy. PMID:16214501

Warrino, Dominic E; DeGennaro, Louis J; Hanson, Mary; Swindells, Susan; Pirruccello, Samuel J; Ryan, Wayne L

2005-10-30

49

Modulation of HIV Transmission by Neisseria gonorrhoeae: Molecular and Immunological Aspects  

PubMed Central

Neisseria gonorrhoeae (GC), a major cause of pelvic inflammatory disease, can facilitate HIV transmission. In response to GC infection, genital epithelial cells can produce cytokines, chemokines and defensins to modulate HIV infection and infectivity. GC can also induce the production of cytokines and chemokines in monocytes and modulate T cell activation. In vivo, an increase in the number of endocervical CD4+ T cells has been found in GC-infected women. Additionally, GC appears to modulate HIV-specific immune responses in HIV-exposed sex workers. Interestingly, in vitro, GC exhibits HIV enhancing or inhibitory effects depending on the HIV target cells. This review summarizes molecular and immunological aspects of the modulation of HIV infection and transmission by GC. Future studies using a multi-cellular system or in animal models will offer insight into the mechanisms by which GC increases HIV transmission. PMID:22384840

Jarvis, Gary A.; Chang, Theresa L.

2014-01-01

50

Serum and peritoneal fluid immunological markers in adolescent girls with chronic pelvic pain.  

PubMed

The aim of this study was to determine serum and peritoneal interleukin (IL)-2, IL-4, and monocyte chemotactic protein-1 levels as diagnostic markers of endometriosis in adolescent girls. The design of the study encompassed 50 adolescent girls, aged 13 to 19 years after menarche, with chronic pelvic pain who qualified for diagnostic laparoscopy. The patients were allocated into 2 groups: group I (endometriosis) consisted of subjects with diagnosed endometriosis (n = 33, 66%) and group II (control) whose laparoscopic examinations revealed no evidence of endometriosis (n = 17, 34%). IL-2, IL-4, and Monocyte chemotactic protein 1 concentrations in serum and peritoneal samples were assessed using commercially available human enzyme-linked immunosorbent assay kits. The results were analyzed statistically with the Statistica 8.0 computer software. The value of P < 0.05 was the level of statistical significance. The results in adolescents with endometriosis had significantly higher concentrations of serum IL-4 (3.90 ± 1.58 pg/mL vs. 3.04 ± 1.72 pg/mL; P = 0.04) and peritoneal fluid IL-4 (5.03 ± 8.92 pg/mL vs. 2.74 ± 1.11 pg/mL; P = 0.03), and lower peritoneal fluid IL-2 (92.44 ± 292.75 pg/mL vs. 174.23 ± 389.77 pg/mL; P = 0.01) compared with the control. In a receiver-operating characteristic analysis, serum IL-4 as well as peritoneal fluid IL-2 and IL-4 provided the best discriminative ability between subjects with endometriosis and controls. Using cutoff points for serum IL-4 (3.00 pg/mL), peritoneal fluid IL-2 (21.00 pg/mL) and IL-4 (2.7 pg/mL), relatively high odd ratios were obtained in the prediction of endometriosis in adolescents (3.2; 6.4; 3.3). The Serum IL-4, peritoneal IL-2 and IL-4 provided a good method of discrimination between subjects with endometriosis and controls. PMID:22713164

Drosdzol-Cop, Agnieszka; Skrzypulec-Plinta, Violetta; Stojko, Rafa?

2012-06-01

51

Prognostication in MF: from CBC to cytogenetics to molecular markers.  

PubMed

Myelofibrosis (MF) is a clonal stem cell disorder characterized by ineffective erythropoiesis and extramedullary hematopoiesis leading to progressive bone marrow failure, severe anemia, constitutional symptoms, hepatosplenomegaly, and thrombosis. MF can arise following a history of polycythemia vera (PV) or essential thrombocythemia (ET), or can present de novo as primary myelofibrosis (PMF). The disease course is variable with median survival ranging from months to years. Clinical and biological features such as advanced age, leukocytosis, anemia, transfusion dependence, and elevated inflammatory markers can impact prognosis in patients with PMF. Cytogenetic abnormalities and molecular markers such as JAK2 V617F, ASXL1, and CALR mutations have also been identified as prognostic variables. Several different scoring systems have been developed based on these prognostic factors. In this review, we will discuss the clinical, biological, molecular, and cytogenetic prognostic factors that have been identified in PMF, and the current prognostic models that have been developed to guide treatment decisions. PMID:25189726

Zhou, Amy; Oh, Stephen T

2014-06-01

52

Histopathologic and Molecular Markers of Prognosis and Response to Therapy  

Microsoft Academic Search

The routine pathologic evaluation of breast cancer must yield the histopathologic subtype, precise measurements of tumor size,\\u000a and information regarding surgical margin status and lymph node status. Accurate determination of histopathologic or nuclear\\u000a grade provides valuable additional prognostic information. Three molecular markers are routinely assessed to assist with treatment\\u000a selection: estrogen and progesterone receptors are measured to determine eligibility for

Lajos Pusztai; W. Fraser Symmans

53

Molecular markers for wheat leaf rust resistance gene Lr41  

Microsoft Academic Search

Leaf rust, caused by Puccinia triticina Eriks., is an important foliar disease of common wheat (Triticum aestivum L.) worldwide. Pyramiding several major rust-resistance genes into one adapted cultivar is one strategy for obtaining more\\u000a durable resistance. Molecular markers linked to these genes are essential tools for gene pyramiding. The rust-resistance gene\\u000a Lr41 from T.\\u000a tauschii has been introgressed into chromosome

Xiaochun Sun; Guihua Bai; Brett F. Carver

2009-01-01

54

Molecular Markers, Natural History, and Conservation of Marine Animals  

NSDL National Science Digital Library

Molecular genetic techniques have found broad utility in modern marine ecology, and applications continue to grow. Databases of DNA sequences now permit nonexperts to identify eggs and larval stages of many marine animals that were previously mysteries. Molecular identifications of field-collected organisms and tissues are used to help assess population connectivity, investigate marine food webs, and identify marketed commodities. Advances in technology already include prototype development of in situ robotic instrumentation for sampling and molecular identification of animal larvae. Studies of population connectivity, once limited to a few gene loci, are slowly giving way to new genomic arrays of markers and high-throughput methodologies for scoring genotypes. Population genetic theory is providing new computational techniques to assess patterns of population structure, estimate effective population sizes, and infer aspects of demographic history. In this article I review a subset of recent work in this growing area of molecular marine ecology.

Ronald Burton (Scripps Institution of Oceanography, University of California, San Diego;Marine Biology Research Division)

2009-11-01

55

Molecular and immunological responses of the giant freshwater prawn, Macrobrachium rosenbergii, to the organophosphorus insecticide, trichlorfon.  

PubMed

Trichlorfon is an organophosphorus (OP) insecticide that is used as an agriculture pesticide to destroy insects, a human medicine to combat internal parasites, and an ectoparasiticide in the livestock and aquaculture industries, but which has caused aquatic toxicity in the prawn industry. The aim of this study was to investigate the effects of trichlorfon on molecular and enzymatic processes of the immunological response of the giant freshwater prawn, Macrobrachium rosenbergii, at 0, 0.2, and 0.4mgL(-1) with 0, 3, 6, 12, and 24h of exposure. The total hemocyte count (THC), respiratory bursts (RBs), phenoloxidase (PO) activity, and superoxide dismutase (SOD) activity were examined to evaluate immunological responses and oxidative stress. Results showed that THCs of the prawn exposed to trichlorfon at both concentrations (0.2 and 0.4mgL(-1)) had increased after 12 and 24h; SOD and PO activities had significantly increased at 3h, whereas production of RBs had dramatically increased as oxidative stress at each sampling time after exposure to trichlorfon compared to the control. A potential biomarker of OPs, acetylcholinesterase (AChE) revealed a significant decrease after exposure for 6h, and showed a time-dependent tendency. Immune gene expressions, including prophenoloxidase (proPO), the lipopolysaccharide- and ?-1,3-glucan-binding protein (LGBP), peroxinectin (PE), ?2-macroglubulin (?2M), transglutaminase (TG), and copper, zinc (Cu,Zn)-SOD, of prawns exposed to trichlorfon at 0, 0.2, and 0.4mgL(-1) for 0, 6, and 24h were further evaluated. Expressions of all of the immune genes significantly decreased when prawns were exposed to 0.4mgL(-1) trichlorfon for 24h, and among them, an increase in SOD expression was seen after exposure to 0.4mgL(-1) for 6h. Prawns exposed to trichlorfon within 24h exhibited the decrease of circulating hemocytes, and also the induction of oxidative stress, which caused subsequent damage to DNA formation of immune genes. From these results, we concluded that immunological responses and immune gene expressions of prawn exposed to trichlorfon at 0.4mgL(-1) for 24h were perturbed, thus causing a deficiency in immunity and subsequent increased susceptibility to pathogen infections. PMID:23340335

Chang, Chin-Chyuan; Rahmawaty, Atiek; Chang, Zhong-Wen

2013-04-15

56

Comparison of viro-immunological marker changes between HIV-1 and HIV-2-infected patients in France  

PubMed Central

Background HIV-2 is known to be less pathogenic than HIV-1, although the underlying mechanisms are still debated. We compared the changes over time in viro-immunologic markers in HIV-1 and HIV-2 infected patients living in France during natural history and after initiation of the first Combination of AntiRetroviral Treatment (CART). Method Patients were included in the ANRS CO3 HIV-1 cohort (N=6707) or the ANRS CO5 HIV-2 cohort (N=572). HIV-1 infected patients were matched to HIV-2 patients according to sex, age, HIV transmission group and period of treatment initiation. Changes in markers have been estimated with linear mixed models. Results Analyses were performed for three groups of patients: (1) those with estimated date of contamination (98 HIV-1 and 49 HIV-2 seroincident patients), (2) untreated seroprevalent patients (320 HIV-1 and 160 HIV-2) and (3) those who initiated a first CART (59 HIV-1 and 63 HIV-2). In group 1, CD4 T-cell decreased less rapidly in HIV-2 than HIV-1 patients (?9 vs. ?49 cells/mm3/year, p<10?4). Estimated slopes in untreated group 2 were similar to those estimated in group 1 (?11 vs. ?49 cells/mm3/year, p=0.003). In group 3, baseline CD4 at CART initiation was not different according to the type of infection (269 vs.220 cells/mm3). During the first two months of treatment, CD4 count increased by +59 cells/mm3/month (95% Confidence Interval [CI]=34;84) for HIV-1 and +24 (CI=6;42) for HIV-2. The plasma viral load drop was 3-fold more important in HIV-1 patients: ?1.56 log10/ml/month (CI=?1.83; ? 1.30) vs. ?0.62 (CI=?0.84; ?0.40) among HIV-2 patients (p<10?4). Conclusion Differences between the two infections during natural history are similar to those previously described in Africa. Paradoxically, once treatment is started, response is poorer in HIV-2 patients than in HIV-1 patients. PMID:18301058

Drylewicz, Julia; Matheron, Sophie; Lazaro, Estibaliz; Damond, Florence; Bonnet, Fabrice; Simon, Francois; Dabis, Francois; Brun-Vezinet, Francoise; Chene, Genevieve; Thiebaut, Rodolphe

2008-01-01

57

Molecular biology and immunology for clinicians, 9 pathogenesis of autoimmunity-molecular mimicry.  

PubMed

The immune system generally does an excellent job of differentiating between self and non-self. In so doing, it destroys mutant cells (cells, in essence, becoming non-self) and invaders. In certain circumstances, the immune system breaks down and no longer leaves self alone; this is auto-immunity-the defense system attacks self. In studying these exceptions, some aspects of the magnificent complexity of the immune system and of the molecular biology of life become apparent.Given that evolutionary processes build on prior experience and mechanisms, it is not surprising that human cells have much in common with yeast, and bacteria molecules found in lower organisms resemble, sometimes quite closely, homologous molecules in human cells. Microbes contain molecules resembling those used by mammalian cells, perhaps because some pathogens use or subvert mammalian systems. These similarities may be sufficient to interfere with the immune system's ability to discern between self and non-self. Thus, the immune response to certain components of pathogens may recognize the host, a phenomenon called molecular mimicry. This mechanism may be involved in the pathogenesis of rheumatologic and other immune-mediated diseases. PMID:19078412

Sigal, L H

1999-10-01

58

Molecular markers that predict response to colon cancer therapy.  

PubMed

Progress in the treatment of colon cancer depends on the development of target-based molecules built on an improved understanding of the molecular biology of the disease. Defining end points for chemotherapy resistance is needed as drug resistance develops quickly and patients demonstrate variation in response to chemotherapy. Many techniques that measure a marker's preponderance have been developed including biochemical, immunohistochemical, genomics, proteomics or a combination thereof. However, standardization of these techniques that measure either genes or their protein products is urgently needed. This article reviews several markers (TS,TP, DPD, FT, EGFR, VEGF, CD44v6, TRAIL, microsatellite instability, allelic deletions, oncogenes and suppressor genes [c-myc, Ki-Ras, p53, p21, Topo I, Topo IIalpha, Fos, hMLH1, Bcl-2/Bax and MDR1], MDR-related proteins [Pgp, MRP and LRP], genomic polymorphisms [XPD, ERCC1, GSTP1 and TS 3 -UTR] and COX-;2) that influence DNA metabolism, DNA damage, programmed cell death, the immune or vascular system, or lead to mutations. When combined together and tested by newly developed genomic and proteomic approaches, many of these markers provide a more sensitive indicative predictor of response than when evaluated separately or by older biochemical, immunohistologic or morphologic methods. A global approach involving the simultaneous testing of several predictive multimarkers will provide critical information for improving chemotherapy to alleviate suffering from this disease. PMID:15934813

Ahmed, Farid E

2005-05-01

59

Choosing the right molecular genetic markers for studying biodiversity: from molecular evolution to practical aspects  

Microsoft Academic Search

The use of molecular genetic markers (MGMs) has become widespread among evolutionary biologists, and the methods of analysis\\u000a of genetic data improve rapidly, yet an organized framework in which scientists can work is lacking. Elements of molecular\\u000a evolution are summarized to explain the origin of variation at the DNA level, its measures, and the relationships linking\\u000a genetic variability to the

Chenuil Anne

2006-01-01

60

A molecular marker of artemisinin-resistant Plasmodium falciparum malaria.  

PubMed

Plasmodium falciparum resistance to artemisinin derivatives in southeast Asia threatens malaria control and elimination activities worldwide. To monitor the spread of artemisinin resistance, a molecular marker is urgently needed. Here, using whole-genome sequencing of an artemisinin-resistant parasite line from Africa and clinical parasite isolates from Cambodia, we associate mutations in the PF3D7_1343700 kelch propeller domain ('K13-propeller') with artemisinin resistance in vitro and in vivo. Mutant K13-propeller alleles cluster in Cambodian provinces where resistance is prevalent, and the increasing frequency of a dominant mutant K13-propeller allele correlates with the recent spread of resistance in western Cambodia. Strong correlations between the presence of a mutant allele, in vitro parasite survival rates and in vivo parasite clearance rates indicate that K13-propeller mutations are important determinants of artemisinin resistance. K13-propeller polymorphism constitutes a useful molecular marker for large-scale surveillance efforts to contain artemisinin resistance in the Greater Mekong Subregion and prevent its global spread. PMID:24352242

Ariey, Frédéric; Witkowski, Benoit; Amaratunga, Chanaki; Beghain, Johann; Langlois, Anne-Claire; Khim, Nimol; Kim, Saorin; Duru, Valentine; Bouchier, Christiane; Ma, Laurence; Lim, Pharath; Leang, Rithea; Duong, Socheat; Sreng, Sokunthea; Suon, Seila; Chuor, Char Meng; Bout, Denis Mey; Ménard, Sandie; Rogers, William O; Genton, Blaise; Fandeur, Thierry; Miotto, Olivo; Ringwald, Pascal; Le Bras, Jacques; Berry, Antoine; Barale, Jean-Christophe; Fairhurst, Rick M; Benoit-Vical, Françoise; Mercereau-Puijalon, Odile; Ménard, Didier

2014-01-01

61

Molecular Marker Applications in Oat (Avena Sativa L.) Breeding and Germplasm Diagnostics .  

E-print Network

??The ability to identify germplasm and select traits accurately is fundamental to successful plant breeding. Pedigrees and molecular markers facilitate these processes; however misleading experimental… (more)

Benazir Katarina, Marquez

2014-01-01

62

Breeding for ?-glucan content in elite North American oat (Avena sativa L.) using molecular markers.  

E-print Network

??This dissertation explored genomewide association study (GWAS) and conducted actual breeding program in oat using different selection methods to identify molecular markers and improve beta-glucan… (more)

Asoro, Franco Garcia

2012-01-01

63

Advances in Carcinogenic Metal Toxicity and Potential Molecular Markers  

PubMed Central

Metal compounds such as arsenic, cadmium, chromium, cobalt, lead, mercury, and nickel are classified as carcinogens affecting human health through occupational and environmental exposure. However, the underlying mechanisms involved in tumor formation are not well clarified. Interference of metal homeostasis may result in oxidative stress which represents an imbalance between production of free radicals and the system’s ability to readily detoxify reactive intermediates. This event consequently causes DNA damage, lipid peroxidation, protein modification, and possibly symptomatic effects for various diseases including cancer. This review discusses predominant modes of action and numerous molecular markers. Attention is paid to metal-induced generation of free radicals, the phenomenon of oxidative stress, damage to DNA, lipid, and proteins, responsive signal transduction pathways with major roles in cell growth and development, and roles of antioxidant enzymatic and DNA repair systems. Interaction of non-enzymatic antioxidants (carotenoids, flavonoids, glutathione, selenium, vitamin C, vitamin E, and others) with cellular oxidative stress markers (catalase, glutathione peroxidase, and superoxide dismutase) as well as certain regulatory factors, including AP-1, NF-?B, Ref-1, and p53 is also reviewed. Dysregulation of protective pathways, including cellular antioxidant network against free radicals as well as DNA repair deficiency is related to oncogenic stimulation. These observations provide evidence that emerging oxidative stress-responsive regulatory factors and DNA repair proteins are putative predictive factors for tumor initiation and progression. PMID:22272150

Koedrith, Preeyaporn; Seo, Young Rok

2011-01-01

64

New models and molecular markers in evaluation of developmental toxicity  

SciTech Connect

Mammalian and non-mammalian embryos and embryonic stem cells may be used as models in mechanistic studies and in testing embryotoxicity of compounds. In addition to conventional culture methods, genetic modifications and use of molecular markers offer significant advantages in mechanistic studies as well as in developing new test methods for embryotoxicity. Zebrafish model has been used for a long time and at present several applications are available. It is an easy vertebral non-mammalian model, whose genome is largely known and several genetic modifications are easily constructed to study gene expression or knocked down genes. Fluorescent marker proteins can be used also in zebrafish to indicate gene activation in transgenic models. Chemical genetics approach has been developed using zebrafish model. This is a new approach to screen small molecules that regulate signaling pathways. Embryonic stem cells have been used in mechanistic studies and mouse embryonic stem cell test has been validated to study embryotoxicity in vitro. This method has been improved using quantitative measurements of molecular endpoints by real-time RT-PCR or fluorescent activated cell sorting methods (FACS). Methods facilitating differentiation to several different cell types are available. We have studied preimplantation mouse embryos as a possible model for in vitro testing. In this method, superovulated and in vivo fertilized preimplantation embryos were collected at morula stage and cultured up to blastocysts. The mouse preimplantation culture test was improved by quantitative gene expression measurement using two-step real-time RT-PCR methods. New endpoints improve the tests of in vitro embryotoxicity because subjective assessments are replaced by objective measurements. In addition, automation is possible and less time is needed for analysis. Thus, high throughput screening will come possible to test large numbers of compounds.

Huuskonen, Hannele [National Product Control Agency for Welfare and Health, Chemicals Department, STTV c/o National Public Health Institute, P.O. Box 95, FIN-70701 Kuopio (Finland)]. E-mail: hannele.huuskonen@sttv.fi

2005-09-01

65

Autoantibodies reactive with small ribonucleoprotein antigens: a convergence of molecular biology and clinical immunology.  

PubMed

Autoantibodies to nuclear antigens (ANA) occur in patients with systemic lupus erythematosus (SLE) and other multisystem autoimmune diseases. Although heterogeneous, there are 2 major groups, autoantibodies to DNA and autoantibodies to non-DNA antigens, the latter including ANAs to the soluble or "extractable nuclear antigens" (ENA). This review discusses those ENAs which are ribonucleoproteins (RNPs) consisting of small RNA molecules (80-400 nucleotides) attached to non-histone proteins: these are called small nuclear (sn) or small cytoplasmic (sc) ribonucleoproteins according to their location in the cell and at least some are known to play an important role in nuclear metabolism. ENAs can be immunoprecipitated from crude preparations of nuclei by sera from patients with multisystem autoimmune diseases and, after removal of the associated proteins, the RNA components can be analyzed by gel electrophoresis. This shows 3 main categories of small RNAs: the U group comprising U1-U6 snRNAs, the Ro group comprising small nucleocytoplasmic RNAs, and the La group comprising several species of cellular snRNAs as well as the Ro scRNAs. La, in addition, includes small RNAs encoded by adenovirus (VA I, VA II), Epstein-Barr virus (EBER 1, EBER 2) and vesicular stomatitis virus (leader RNA). In the case of each group, the RNAs themselves are not antigenic but become so when associated with proteins, most of which are uncharacterized. The U snRNAs, located in the nucleus, are transcribed by RNA polymerase II and appear to be involved in the splicing of introns from mRNA. Sera from patients with mixed connective tissue disease (MCTD) react with RNPs containing U1 RNA and sera from patients with SLE react with U RNPs containing U1, U2, U4, U5 and U6 RNAs, collectively known as the Sm antigen. The Ro RNAs are transcribed by RNA polymerase III and have no known function. Sera from patients with primary Sjögren's syndrome and some cases of SLE react with Ro scRNPs. The La RNAs are also transcribed by RNA polymerase III and are located mostly in the nucleus; functionally the protein associated with the La RNAs appears to be important in RNA polymerase III transcription. Sera from patients with primary Sjögren's syndrome react with the heterogeneous group of both cellular and viral RNAs which constitute the La RNP antigen. Sera of patients with SLE, scleroderma, polymyositis and dermatomyositis also react with RNPs relevant to nuclear metabolism and further definition of these RNPs is awaited. Many advances can be expected from the convergence of molecular biology and clinical immunology exemplified by the current studies on ENAs.(ABSTRACT TRUNCATED AT 400 WORDS) PMID:6210367

McNeilage, L J; Whittingham, S; Mackay, I R

1984-09-01

66

The Molecular Immunology of Mucositis: Implications for Evidence-Based Research in Alternative and Complementary Palliative Treatments  

PubMed Central

The terms ‘mucositis’ and ‘stomatitis’ are often used interchangeably. Mucositis, however, pertains to pharyngeal-esophago-gastrointestinal inflammation that manifests as red, burn-like sores or ulcerations throughout the mouth. Stomatitis is an inflammation of the oral tissues proper, which can present with or without sores, and is made worse by poor dental hygiene. Mucositis is observed in a variety of immunosuppressed patients, but is most often consequential to cancer therapy. It appears as early as the third day of intervention, and is usually established by Day 7 of treatment. Mucositis increases mortality and morbidity and contributes to rising health care costs. The precise immune components involved in the etiology of mucositis are unclear, but evidence-based research (EBR) data has shown that applications of granulocyte–macrophage-colony stimulating factor prevent the onset or the exacerbation of oropharyngeal mucositis. The molecular implications of this observation are discussed from the perspective of future developments of complementary and alternative treatments for this condition. It must be emphasized that this article is meant to be neither a review on mucositis and the various treatments for it, nor a discussion paper on its underlying molecular immunology. It is a statement of the implications of EBR for CAM-based interventions for mucositis. It explores and discusses the specific domain of molecular immunology in the context of mucositis and its direct implications for EBR research in CAM-based treatments for mucositis. PMID:16322806

2005-01-01

67

PATTERNS OF GENETIC ARCHITECTURE FOR LIFE-HISTORY TRAITS AND MOLECULAR MARKERS IN A SUBDIVIDED SPECIES  

Microsoft Academic Search

Understanding the utility and limitations of molecular markers for predicting the evolutionary potential of natural populations is important for both evolutionary and conservation genetics. To address this issue, the distribution of genetic variation for quantitative traits and molecular markers is estimated within and among 14 permanent lake populations of Daphnia pulicaria representing two regional groups from Oregon. Estimates of population

Kendall K. Morgan; Justin Hicks; Ken Spitze; Leigh Latta; Michael E. Pfrender; Casse S. Weaver; Marco Ottone; Michael Lynch

2001-01-01

68

Molecular Markers for Discrimination of Benign and Malignant Follicular Thyroid Tumors  

Microsoft Academic Search

Objective: To identify molecular markers useful for the diagnostic discrimination of benign and malignant follicular thyroid tumors. Methods: A panel of thyroid tumors was characterized with expression profiling using cDNA microarrays. A robust algorithm for gene selection was developed to identify molecular markers useful for the classification of heterogeneous tumor classes. The study included tumor tissue specimens from 10 patients

Mårten Fryknäs; Ulrika Wickenberg-Bolin; Hanna Göransson; Mats G. Gustafsson; Theodoros Foukakis; Jia-Jing Lee; Ulf Landegren; Anders Höög; Catharina Larsson; Lars Grimelius; Göran Wallin; Ulf Pettersson; Anders Isaksson

2006-01-01

69

Molecular Evolution and Diversity inBacillus anthracisas Detected by Amplified Fragment Length Polymorphism Markers  

Microsoft Academic Search

Bacillus anthraciscauses anthrax and represents one of the most molecularly monomorphic bacteria known. We have used AFLP (amplified fragment length polymorphism) DNA markers to analyze 78 B. anthracis isolates and six relatedBacillusspecies for molecular variation. AFLP markers are extremely sensitive to even small sequence variation, using PCR and high-resolution electrophoresis to examine restriction fragments. Using this approach, we examined ca.

PAUL KEIM; ABDULAHI KALIF; JAMES SCHUPP; KAREN HILL; STEVEN E. TRAVIS; KARA RICHMOND; DEBRA M. ADAIR; MARTIN HUGH-JONES; CHERYL R. KUSKE; ANDPAUL JACKSON

1997-01-01

70

Protein Molecular Markers for Herbal Natures of Six Traditional Chinese Medicinal Herbs  

Microsoft Academic Search

This article presents a new method of using molecular markers to study the material base of the herbal nature of traditional Chinese medicine (TCM) herbs. The feasibility of using the all-electric ion chromatography to select the appropriate protein molecular markers for studying the herbal nature of TCM herbs is also discussed. In the study, the chromatographic peaks of the total

Wang Hou-wei; Dou Yan-ling; Tian Jing-zhen; Wang Zhen-guo

2008-01-01

71

Molecular Markers and Selection for Complex Traits in Plants: Learning from the Last 20 Years  

Microsoft Academic Search

In the mid-1980s, the development of abundant molecular markers, appropriate statistical pro- cedures, and user-friendly computer software that implemented these statistical procedures permitted the detection of molecular markers associated with quantitative trait loci (QTL) for complex traits. Marker-assisted selection was then proposed as a means of exploiting mark- ers linked to QTL to develop improved cultivars. But while thousands of

Rex Bernardo

2008-01-01

72

Soybean seed lipoxygenase genes: molecular characterization and development of molecular marker assays.  

PubMed

Soybean seeds contain three lipoxygenase (Lox) enzymes that are controlled by separate genes, Lox1, Lox2 and Lox3. Lipoxygenases play a role in the development of unpleasant flavors in foods containing soybean by oxidation of polyunsaturated fatty acids. Null alleles for all three enzymes have been identified, lox1, lox2 and lox3, and are known to be inherited as simple recessive alleles. Previous studies determined that a missense mutation rendered Lox2 inactive; however, the genetic cause of either lox1 or lox3 mutation was not known. The objectives of this study were the molecular characterization of both lox1 and lox3 mutant alleles and the development of molecular markers to accelerate breeding for Lox-free soybean varieties. We identified two independent mutant alleles as the genetic causes of the lack of Lox1 in seeds of two lox1 mutant soybean lines. Similarly, a mutant allele that truncates Lox3 in a lox3 mutant soybean line was identified. Molecular markers were designed and confirmed to distinguish mutant, wild type, and heterozygous individuals for Lox1, Lox2 and Lox3 genes. Genotype and Lox phenotype analysis showed a perfect association between the inheritance of homozygous lox mutant alleles and the lack of Lox activity. Molecular characterization of a seed-lipoxygenase-free soybean line led to the discovery that an induced recombination event within the Lox1 gene was responsible for breaking the tight linkage in repulsion phase between mutant alleles at the Lox1 and Lox2 loci. The molecular resources developed in this work should accelerate the inclusion of the lipoxygenase-free trait in soybean varieties. PMID:20058147

Lenis, Julian M; Gillman, Jason D; Lee, Jeong Dong; Shannon, J Grover; Bilyeu, Kristin D

2010-04-01

73

[Molecular markers in the diagnostics and therapy of urothelial cancer].  

PubMed

Many clinical decisions in the management of bladder cancer would benefit from better and reliable knowledge of individual prognosis. Marker for urothelial cancer can principally be measured in blood, urine and transurethrally resected tissue. In recent years new markers have been identified by new technologies and this opens exiting avenues. Since no single marker gives a clear Yes-or-no prognostic answer but always only a measure of probability, the use of marker systems has so far not gained widespread clinical applications. This will likely change in future. PMID:20959953

Protzel, C; Hakenberg, O W

2010-11-01

74

58th Annual Symposium on Fundamental Cancer Research Discovery, Validation, and Integration of Molecular Markers and Molecular Imaging: Towards Implementation into Clinical Practice  

Cancer.gov

Print This Page 58th Annual Symposium on Fundamental Cancer Research Discovery, Validation, and Integration of Molecular Markers and Molecular Imaging: Towards Implementation into Clinical Practice News & Events

75

Molecular biology and immunology for clinicians 6: antibodies and antigens: terminology, structures, and the humoral immune response.  

PubMed

The immune response that protects us from pathogens and malignancy is directed at the individual constituent molecules of the invading cells, a response specific for discrete sections of each of these molecules. A unique language is used to describe these individual targets, called epitopes or antigenic determinants. Understanding this language is necessary to better appreciate the character of the challenge and the nature, efficiency, and evolution of the response. As we determine the immune mechanisms of many diseases, e.g., autoimmunity due to molecular mimicry, it is crucial that physicians be able to interpret the immunological literature.Proper interpretation of serological testing, e.g., the use of Western blot to confirm/corroborate less specific tests like ELISA, depends in part on a full understanding of how the specificity of antibodies are determined. Novel therapeutic strategies, e.g., use of intravenous gammaglobulin to alter immune control networks, are being developed; only with an appreciation of the humoral immune response can the clinician make use of these new approaches that seek to manipulate the immune system. The terminology used in defining antigens, the molecules that are the target of the immune response, and the structure of immunoglobulins, and how these structures determine and influence function, are reviewed. This paper serves as a start, a "jumping off" point, for further description of the immune response in later papers in this series.To be successfully immersed in or introduced to immunology, it is important to "speak the language." So, consider this a refresher course, not to recall high school Spanish but medical school immunology. PMID:19078228

Sigal, L H

1997-12-01

76

Immunological and molecular polymorphisms of OspC, an immunodominant major outer surface protein of Borrelia burgdorferi.  

PubMed Central

The gene of the immunodominant major protein pC of Borrelia burgdorferi was previously cloned and sequenced (R. Fuchs, S. Jauris, F. Lottspeich, V. Preac-Mursic, B. Wilske, and E. Soutschek, Mol. Microbiol. 6:503-509, 1992). pC is abundantly expressed on the outer surface of B. burgdorferi, as demonstrated by immunoelectron microscopy with monoclonal antibody L22 1F8. Accordingly, pC is renamed OspC, by analogy to the outer surface proteins OspA and OspB. Western immunoblot analysis of 45 B. burgdorferi isolates with monoclonal antibodies revealed that OspC is immunologically heterogeneous. Partial sequence analysis of the ospC gene confirmed the protein heterogeneity at the genetic level. We found that the degree of identity between the ospC partial sequences of five strains representing different OspA serotypes was only 63.3 to 85.4%. Immunological heterogeneity was also observed among representatives of the three newly designated genospecies of B. burgdorferi sensu lato, B. burgdorferi sensu stricto, B. garinii, and group VS461. Heterogeneity was confirmed for B. garinii at the genetic level. The ospC gene was also cloned from strains that did not express OspC, and antibody-reactive OspC was expressed in Escherichia coli. In addition, OspC-expressing variants were obtained from a nonexpressing strain by plating single colonies on solid medium. These findings confirm that the ospC gene is also present in nonexpressing strains. Because OspC is an immunodominant protein for the early immune response in Lyme borreliosis and was effective as a vaccine in an animal model, the immunological and molecular polymorphisms of ospC and OspC have important implications for the development of diagnostic reagents and vaccines. Images PMID:8478108

Wilske, B; Preac-Mursic, V; Jauris, S; Hofmann, A; Pradel, I; Soutschek, E; Schwab, E; Will, G; Wanner, G

1993-01-01

77

Molecular markers in prostate cancer. Part II: potential roles in management  

PubMed Central

Predicting treatment responses in advanced prostate cancer (PCa) currently centres on prostate-specific antigen (PSA) kinetics and on being able to visualize measurable changes in imaging modalities. New molecular markers have emerged as potential diagnostic and prognostic indicators; these were summarized in Part I of this review in the Asian Journal of Andrology. A number of molecular markers are now being used to enhance PCa imaging and staging. However, management options for advanced and hormone-resistant PCa (HRPC) are limited and additional therapeutic options are needed. Molecular markers have been proposed as potential therapeutic targets using gene therapy and immunomodulation. Additionally, markers identified in early PCa and precursor lesions may offer novel targets for chemoprevention and vaccine development. This review summarizes the current advances regarding the roles of these markers in the management of PCa. PMID:19050689

Agrawal, Sachin; Patil, Krishnaji P.; Dunsmuir, William D.

2009-01-01

78

Molecular analysis of silver crucian carp ( Carassius auratus gibelio Bloch) clones by SCAR markers  

Microsoft Academic Search

Random amplified polymorphic DNA (RAPD) molecular markers specific for one, two or three clones have been identified from five gynogenetic clones of silver crucian carp (Carassius auratus gibelio Bloch) using RAPD markers developed earlier. In this study, three RAPD markers (RA1-PA, RA2-EF and RA4-D) produced by Opj-1, and two RAPD DNA fragments (RA3-PAD and RA5-D) produced by Opj-7, were selected

Li Zhou; Yang Wang; Jian-Fang Gui

2001-01-01

79

Molecular marker suggests rapid changes of sex-determining mechanisms in Australian dragon lizards  

E-print Network

Molecular marker suggests rapid changes of sex-determining mechanisms in Australian dragon lizards and W microchromosomes of the Australian central bearded dragon (Pogona vitticeps) to chromosomes of 12

Canberra, University of

80

Molecular Markers Show How Pollen and Seed Dispersal Affect Population Genetic  

E-print Network

485 Molecular Markers Show How Pollen and Seed Dispersal Affect Population Genetic Structure of fragmentation and decreased population sizes is reduced genetic diversity as populations become increasingly. Earlier studies indicated biochemical differentiation of central coast populations from those of Northern

Standiford, Richard B.

81

SEASONAL ABUNDANCE OF ORGANIC MOLECULAR MARKERS IN URBAN PARTICULATE MATTER FROM PHILADELPHIA, PA  

EPA Science Inventory

Organic molecular markers were measured in airborne particulate matter (PM10) from the City of Philadelphia North Broad Street air quality monitoring site to identify the seasonal abundances of key tracer compounds together with their dominant sources. Daily PM10...

82

Quantitative changes in cytological molecular markers during primary medical treatment of breast cancer: A pilot study  

Microsoft Academic Search

Aim: To quantify the changes in biological molecular markers during primary medical treatment in patients with operable breast cancer and to assess their possible relationship with response to treatment.

A. Makris; T. J. Powles; D. C. Allred; S. E. Ashley; P. A. Trott; M. G. Ormerod; M. Dowsett

1999-01-01

83

A review on SNP and other types of molecular markers and their use in animal genetics  

Microsoft Academic Search

During the last ten years, the use of molecular markers, revealing polymorphism at the DNA level, has been playing an increasing part in animal genetics studies. Amongst others, the microsatellite DNA marker has been the most widely used, due to its easy use by simple PCR, followed by a denaturing gel electrophoresis for allele size determination, and to the high

Alain Vignal; Denis Milan; Magali SanCristobal; André Eggen

2002-01-01

84

Kazusa Marker DataBase: a database for genomics, genetics, and molecular breeding in plants  

PubMed Central

In order to provide useful genomic information for agronomical plants, we have established a database, the Kazusa Marker DataBase (http://marker.kazusa.or.jp). This database includes information on DNA markers, e.g., SSR and SNP markers, genetic linkage maps, and physical maps, that were developed at the Kazusa DNA Research Institute. Keyword searches for the markers, sequence data used for marker development, and experimental conditions are also available through this database. Currently, 10 plant species have been targeted: tomato (Solanum lycopersicum), pepper (Capsicum annuum), strawberry (Fragaria × ananassa), radish (Raphanus sativus), Lotus japonicus, soybean (Glycine max), peanut (Arachis hypogaea), red clover (Trifolium pratense), white clover (Trifolium repens), and eucalyptus (Eucalyptus camaldulensis). In addition, the number of plant species registered in this database will be increased as our research progresses. The Kazusa Marker DataBase will be a useful tool for both basic and applied sciences, such as genomics, genetics, and molecular breeding in crops.

Shirasawa, Kenta; Isobe, Sachiko; Tabata, Satoshi; Hirakawa, Hideki

2014-01-01

85

Kazusa Marker DataBase: a database for genomics, genetics, and molecular breeding in plants.  

PubMed

In order to provide useful genomic information for agronomical plants, we have established a database, the Kazusa Marker DataBase (http://marker.kazusa.or.jp). This database includes information on DNA markers, e.g., SSR and SNP markers, genetic linkage maps, and physical maps, that were developed at the Kazusa DNA Research Institute. Keyword searches for the markers, sequence data used for marker development, and experimental conditions are also available through this database. Currently, 10 plant species have been targeted: tomato (Solanum lycopersicum), pepper (Capsicum annuum), strawberry (Fragaria × ananassa), radish (Raphanus sativus), Lotus japonicus, soybean (Glycine max), peanut (Arachis hypogaea), red clover (Trifolium pratense), white clover (Trifolium repens), and eucalyptus (Eucalyptus camaldulensis). In addition, the number of plant species registered in this database will be increased as our research progresses. The Kazusa Marker DataBase will be a useful tool for both basic and applied sciences, such as genomics, genetics, and molecular breeding in crops. PMID:25320561

Shirasawa, Kenta; Isobe, Sachiko; Tabata, Satoshi; Hirakawa, Hideki

2014-09-01

86

Mapping quantitative trait loci using molecular marker linkage maps  

Microsoft Academic Search

High-density restriction fragment length polymorphism (RFLP) and allozyme linkage maps have been developed in several plant species. These maps make it technically feasible to map quantitative trait loci (QTL) using methods based on flanking marker genetic models. In this paper, we describe flanking marker models for doubled haploid (DH), recombinant inbred (RI), backcross (BC), F1 testcross (F1TC), DH testcross (DHTC),

S. J. Knapp; W. C. Bridges; D. Birkes

1990-01-01

87

New sequence-tagged site molecular markers for identification of sex in Distichlis spicata.  

PubMed

Sex-linked molecular markers have become valuable tools for understanding sex ratio evolution and sex-specific physiology in pre-reproductive plants. To develop new accurate methods for sexing Distichlis spicata juveniles and nonflowering individuals, we converted a random amplified polymorphic DNA-polymerase chain reaction marker that co-segregated with the female phenotype into a set of sequence-tagged site markers. We tested the marker pair on known males and females from populations in Oregon and California. A single band was obtained for all female samples but never for males. PMID:21564910

Eppley, Sarah M; O'Quinn, Robin; Brown, Anna L

2009-09-01

88

Immunological markers for tolerance to avian malaria in Hawai`i `Amakihi: new tools for restoring native Hawaiian forest birds?  

USGS Publications Warehouse

We evaluated three assays for non-specific or innate immune capacity to see if measurements were independent of malarial infection and capable of distinguishing malaria-tolerant, low-elevation Hawai?i ?Amakihi from malaria-susceptible, high-elevation ?Amakihi. ?Amakihi were captured at Malama Ki Forest Reserve (20 m), Hakalau Forest National Wildlife Refuge (1800 m), and Upper Waiakea Forest Reserve (1700 m), bled for collection of plasma and packed erythrocytes for malarial diagnostics, and either transported to K?lauea Field Station Aviary and held in captivity for 48 hours for inoculation of wing webs with phytohemagglutinin A (PHA) or released immediately in the field after collection of a blood sample. All birds were tested by polymerase chain reaction (PCR) and microscopy to determine infection status. We found no significant association between malarial infection status and degree of wing web swelling after inoculation with PHA (T = -0.174, df = 13, P = 0.864) and no association between origin of birds from low- and high-elevation populations and degree of wing web swelling (T = 0.113, df = 52, P = 0.911). Infected ?Amakihi from low elevation had significantly higher small molecule plasma antioxidant capacity than uninfected individuals from the same population (T = -2.675, df = 21, P = 0.014), so we limited comparisons to uninfected birds. Uninfected ?Amakihi from low elevations did not differ in small molecule plasma antioxidant capacity from uninfected ?Amakihi from high elevation (T = -0.260, df = 46, P = 0.796). Compared to high-elevation birds, low-elevation ?Amakihi had significantly higher titers of natural antibodies (NAb) as measured by complement-mediated lysis of rabbit erythrocytes (Mann-Whitney U = 27, X2= 32.332, df = 1, P < 0.0001). This innate immunological difference may be related to ability to survive malarial infection and may prove to be important for understanding possible mechanisms for the evolution of disease tolerance in Hawai?i’s native bird species.

Atkinson, Carter T.; Paxton, Eben H.

2013-01-01

89

Advances in the Use of Molecular Markers for Source Apportionment of Atmospheric Organic Aerosols  

NASA Astrophysics Data System (ADS)

Over the past decade, there has been significant effort directed at measuring particle-phase organic compounds in air pollution emission sources and in the atmosphere. A subset of these organic compounds are relatively unique to the emissions from specific air pollution source categories and are believed to be stable enough in the atmosphere to be used as source tracers. To date, studies have been conducted in North America, Asia and Europe in both remote and urbanized locations that have used these organic compound tracers, also called molecular markers, for source attribution studies. The major short-comings of these studies are the uncertainties associated with developing site and season specific molecular marker source profiles and the absence of source fingerprints for secondary organic aerosol. Recent advances in molecular marker chemical analysis methods has lead to two key advances for molecular marker source apportionment efforts: 1) sufficiently large data sets of molecular marker measures have been generated that now allow multivariate receptor models to be used in parallel with chemical mass balance (CMB) models, and 2) compounds that are believed to be predominately associated with secondary organic aerosol (SOA) have been identified and can be routinely analyzed in organic aerosol samples. Given these advances, data sets have been generated that can be used to apportion atmospheric organic aerosols to both primary and secondary organic aerosols without the use of source profiles. Background on molecular markers will be presented along with recent organic aerosol source apportionment results that were obtained using multivariate receptor models to analyze molecular marker data sets obtained in the Midwestern United States. These data sets include a daily time series of molecular marker concentration data from the Midwest Supersite in East St. Louis that spans two years and a monthly average tracer data for a year that were simultaneously obtained in St. Louis, Chicago, Detroit, Indianapolis, Cincinnati, and Bondville. The results of these studies will be presented along with a comparison of the molecular marker source profiles derived from a multivariate receptor models and source testing activities. Such analyses provide insight into the atmospheric stability of these molecular markers and their uniqueness to source categories.

Schauer, J. J.; Sheesley, R. J.; Jaeckels, J. M.

2006-12-01

90

Immunologic mechanisms in Lyme neuroborreliosis: the potential role of autoimmunity and molecular mimicry.  

PubMed

Most of the clinical manifestations of Lyme disease are due to the local presence of the causative agent, Borrelia burgdorferi, in the affected tissues. However, the precise means of tissue damage are not well understood and there is no proof that the organism, live or dead, is always present. An understanding of the complex interaction between the organism, the immune response elicited by the organism, and the host can explain manifestations of the disease and persistence of symptoms and signs after the antibiotic-induced death of the organism. It is possible that dead spirochetes, or fragments thereof may persist and act as a focus of ongoing inflammation. Different immunogenetic types may predispose to different immunologic responses, with distinct clinical outcomes. Vascular changes induced by the infection, either by local infection or the effects of cytokines on the vessel wall, may underlie tissue pathology. Finally, the immune response to B. burgdorferi may elicit the production of antibodies capable of recognizing and damaging or modifying normal host tissues. Only by establishing the mechanisms causing tissue damage in Lyme disease can rational therapeutic strategies be developed. Only by understanding these mechanisms can physicians and patients interpret clinical responses to therapy and accurately appreciate the clinical prognosis. PMID:9166962

Sigal, L H

1997-03-01

91

Markers  

ERIC Educational Resources Information Center

Dry erase whiteboards come with toxic dry erase markers and toxic cleaning products. Dry erase markers labeled "nontoxic" are not free of toxic chemicals and can cause health problems. Children are especially vulnerable to environmental health hazards; moreover, schools commonly have problems with indoor air pollution, as they are more densely…

Healthy Schools Network, Inc., 2011

2011-01-01

92

Applications and Implications of Neutral versus Non-neutral Markers in Molecular Ecology  

PubMed Central

The field of molecular ecology has expanded enormously in the past two decades, largely because of the growing ease with which neutral molecular genetic data can be obtained from virtually any taxonomic group. However, there is also a growing awareness that neutral molecular data can provide only partial insight into parameters such as genetic diversity, local adaptation, evolutionary potential, effective population size, and taxonomic designations. Here we review some of the applications of neutral versus adaptive markers in molecular ecology, discuss some of the advantages that can be obtained by supplementing studies of molecular ecology with data from non-neutral molecular markers, and summarize new methods that are enabling researchers to generate data from genes that are under selection. PMID:21747718

Kirk, Heather; Freeland, Joanna R.

2011-01-01

93

Relative efficiency of morphological characters and molecular markers in the establishment of an apricot core collection.  

PubMed

In order to optimize the management of genetic resources, in most cases a representative sample of the germplasm collections needs to be developed. The establishment of a core collection is thus of major importance either to minimize the cost associated with the management of the associated germplasm or to apply analysis onto representative bases. In order to select a representative core collection among the Tunisian apricot germplasm of 110 accessions large, the Maximization strategy algorithm was used. This algorithm was shown to be the most convenient when using both morphological traits and molecular markers. Three core collections based on morphological characters, molecular markers or the combined data were compared. Our data indicate that both the molecular and the morphological markers have to be considered to obtain a core collection that represents the global diversity of the 110 accessions. Using this method, a subset of 34 selected accessions was found to represent accurately the 110 accessions present in the whole collection (75 to 100% for the morphological characters and 97% of the molecular markers). These results show that the combination of molecular and morphological markers is an efficient way to characterize the apricot core collection and provides an exhaustive coverage for the analyzed diversity on morphological and genetic bases. PMID:23121327

Krichen, L; Audergon, J M; Trifi-Farah, N

2012-10-01

94

Identification of specific molecular markers linked to the rust resistance gene M4 in flax  

Microsoft Academic Search

To identify molecular markers linked to the flax rust-resistance gene M4, RAPD analysis of NM4 (a near-isogenic line containing the M4 gene) and the recurrent parent Bison was performed using 540 decamer primers. The primer OPA18 amplified a specific fragment,\\u000a OPA18432, in the NM4 line. The OPA18432 marker was found to be closely linked to the M4 gene, with a

T. Y. Bo; J. J. Ma; J. X. Chen; T. Y. Miao; W. X. Zhai

2008-01-01

95

Parasite Immunology, 2001: 23: 327344 Immunological genomics of Brugia malayi: filarial genes implicated  

E-print Network

Parasite Immunology, 2001: 23: 327±344 Immunological genomics of Brugia malayi: filarial genes of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University biochemical and immunological data on prominent filarial proteins with the exciting new information provided

Maizels, Rick

96

Molecular and cellular markers of toxicity in the Japanese Medaka @  

SciTech Connect

The Japanese Medaka (Oryzias latipes) has been recommended for use as a model organism to detect carcinogenic, teratogenic, cytotoxic, and genotoxic compounds in aquatic systems. Because a long latent period often occurs between initial contact with deleterious chemicals and subsequent expression of the pathology, we are investigating early biologically-relevant responses that can be used as genotoxicity markers of exposure and effect. This project focuses on the development of genotoxic bioassays and experimental protocols for exposing Japanese Medaka to genotoxic compounds. 21 refs., 8 figs, 2 tabs.

Shugart, L.R.; McCarthy, J.F.; D'Surney, S.J.; Greeley, M.S. Jr.; Hull, C.G.

1990-01-01

97

Genetic diversity of spineless Cereus jamacaru accessions using morphological and molecular markers.  

PubMed

This is the first study to examine the genetic diversity of mandacaru cactus (Cereus jamacaru P. DC.). Plants of spineless mandacaru are commonly found in gardens and parks of urban areas in northeastern Brazil. In addition to exploring their ornamental potential, morphological, and genetic characterization may contribute to the development of plant materials that can be used as a source of macromolecules of potential economic interest. The goal of this study was to estimate the genetic variability of spineless mandacaru accessions using random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) molecular markers, and to characterize their morphology. Ten samples of newly emitted shoots with differentiated areolas and ribs were collected from each accession from the Cactaceous Germplasm Collection of Embrapa Agroindústria Tropical, in Fortaleza, CE. Shoot shape and aspects of spine primordia (presence, location, grouping, and size of spines) were evaluated. The morphological analysis showed that the spineless mandacaru presented spine primordia. Twenty-six RAPD and 15 ISSR primers were polymorphic. A total of 262 markers were obtained, 129 of which were polymorphic. The average polymorphism of ISSR markers was higher than that of RAPD markers. The dendrograms for both analyses showed differentiation between accessions. Nevertheless, the molecular markers detected higher levels of diversity and a different pattern of diversity than those found using morphological markers. The molecular results revealed significant genetic variability both within and between groups. PMID:24222234

Oliveira, F I C; Bordallo, P N; Castro, A C R; Correia, D

2013-01-01

98

Molecular mapping of the immunologic surface of the hCG molecule by monoclonal antibodies (MCA)  

Microsoft Academic Search

The 2-site IRMA-design with MCA is demonstrated to be superior over conventional “l-site”-RIA with polyclonal antibodies since it clearly distinguishes different molecular species of a hormone, especially hCG. Such parallel measurements are considered to be of diagnostic value for screening and therapeutic monitoring of tumor patients who produce freea- and\\/or freeß-subunits early in the course of the disease, or exclusively

S. Schwarz; P. Berger; G. Wick

1984-01-01

99

Molecular markers in the diagnosis of thyroid nodules.  

PubMed

An indeterminate thyroid nodule cytology result occurs about every sixth fine-needle aspiration. These indeterminate nodules harbor a 24% risk of malignancy (ROM); too high to ignore, but driving surgery where most nodules are benign. Molecular diagnostics have emerged to ideally avoid surgery when appropriate, and to trigger the correct therapeutic surgery when indicated, as opposed to an incomplete diagnostic surgery. No current molecular test offers both high sensitivity and high specificity. A molecular diagnostic test with high sensitivity (e.g. Afirma Gene Expression Classifier sensitivity 90%) offers a high Negative Predictive Value when the ROM is relatively low, such as < 30%. Only such tests can "rule-out" cancer. In this setting, a molecularly benign result suggests the same ROM as that of operated cytologically benign nodules (~6%). Thus, clinical observation can replace diagnostic surgery; increasing quality of life and decreasing medical costs. However, its low specificity cannot "rule-in" cancer as a suspicious result has a Positive Predictive Value (PPV) of ~40%, perhaps too low to routinely reflex to definitive cancer surgery. Conversely, high specificity tests (BRAF, RAS, PPAR/PAX-8, RET/PTC, PTEN) offer high PPV results, and only these tests can "rule-in" cancer. Here a positive molecular result warrants definitive therapeutic surgery. However, their low sensitivity cannot "rule-out" cancer and a negative molecular result cannot dissuade diagnostic surgery; limiting their cost-effectiveness. Whether or not there is a useful and cost-effective role to sequentially combine these approaches, or to modify existing approaches, is under investigation. PMID:23525286

Ward, Laura S; Kloos, Richard T

2013-03-01

100

Associations between 25-Hydroxyvitamin D and Immunologic, Metabolic, Inflammatory Markers in Treatment-Naive HIV-Infected Persons: The ANRS CO9 <> Cohort Study  

PubMed Central

Objectives Low 25(OH)D has been associated with dyslipidemia, insulin resistance and inflammation in both general and HIV-infected (mostly treated) populations. We investigated these associations in antiretroviral-naïve HIV-infected persons. Design We measured plasma 25(OH)D, metabolic, immunologic and inflammatory markers in 355 persons (204 Whites, 151 Blacks) at enrollment in the ANRS COPANA cohort. Methods 25(OH)D levels were categorized <10 ng/mL (severe deficiency) and <20 ng/mL (deficiency). Statistical analyses were adjusted for sampling season, ethnicity and the interaction between season and ethnicity. Results 25(OH)D insufficiency (<30 ng/mL), deficiency (<20 ng/mL) and severe deficiency (<10 ng/mL) were highly prevalent (93%, 67% and 24% of patients, respectively). Blacks had significantly lower 25(OH)D than Whites (median: 13 vs. 17 ng/mL, P<0.001), with markedly less pronounced seasonal variation. Smoking and drinking alcohol were associated with having a 25 OHD level<10 ng/mL. In patients with 25(OH)D<10 ng/mL, the proportion of persons with a CD4 count<100/mm3 was higher than in patients with 25(OH)D?10 ng/mL (18.8% vs. 10.7%, P?=?0.04). Persons with 25 OHD<10 ng/mL had higher levels of hsCRP (1.60 mg/L [IQR: 0.59–5.76] vs. 1.27 mg/L [0.58–3,39], P?=?0.03) and resistin (16.81 ng/L [IQR: 13.82–25.74] vs. 11.56 ng/L [IQR: 8.87–20.46], P?=?0.02), and, among Blacks only, sTNFR2 (2.92 ng/mL [2.31–4.13] vs. 2.67 ng/mL, [1.90–3.23], P?=?0.04). The strength and significance of the association between CD4<100/mm3 and 25 OHD<10 ng/mL were reduced after adjustment on sTNFR1, sTNFR2, and hsCRP levels. In multivariate analysis, a CD4 count <100/mm3, resistin concentration and smoking were independently associated with 25(OH)D<10 ng/mL. Conclusions Severe vitamin D deficiency was associated with low CD4 counts and increased markers of inflammation in ARV-naïve HIV-infected persons. PMID:24058636

Legeai, Camille; Vigouroux, Corinne; Souberbielle, Jean-Claude; Bouchaud, Olivier; Boufassa, Faroudy; Bastard, Jean-Philippe; Carlier, Robert; Capeau, Jacqueline; Goujard, Cecile; Meyer, Laurence; Viard, Jean-Paul

2013-01-01

101

Molecular markers in bladder cancer: A critical appraisal  

Microsoft Academic Search

The diagnosis of both primary and recurrent bladder tumors currently relies upon the urine cytology and cystoscopy. Neither of these diagnostic tools is completely accurate. Prognostication of bladder cancer is largely based on pathologic tumor grade and stage. Over the past 2 decades, there is accumulating evidence that like many other cancers, bladder cancer, too, has a distinct molecular signature

Badrinath R. Konety

2006-01-01

102

Molecular imaging of rheumatoid arthritis: emerging markers, tools, and techniques  

PubMed Central

Early diagnosis and effective monitoring of rheumatoid arthritis (RA) are important for a positive outcome. Instant treatment often results in faster reduction of inflammation and, as a consequence, less structural damage. Anatomical imaging techniques have been in use for a long time, facilitating diagnosis and monitoring of RA. However, mere imaging of anatomical structures provides little information on the processes preceding changes in synovial tissue, cartilage, and bone. Molecular imaging might facilitate more effective diagnosis and monitoring in addition to providing new information on the disease pathogenesis. A limiting factor in the development of new molecular imaging techniques is the availability of suitable probes. Here, we review which cells and molecules can be targeted in the RA joint and discuss the advances that have been made in imaging of arthritis with a focus on such molecular targets as folate receptor, F4/80, macrophage mannose receptor, E-selectin, intercellular adhesion molecule-1, phosphatidylserine, and matrix metalloproteinases. In addition, we discuss a new tool that is being introduced in the field, namely the use of nanobodies as tracers. Finally, we describe additional molecules displaying specific features in joint inflammation and propose these as potential new molecular imaging targets, more specifically receptor activator of nuclear factor ?B and its ligand, chemokine receptors, vascular cell adhesion molecule-1, ?V?3 integrin, P2X7 receptor, suppression of tumorigenicity 2, dendritic cell-specific transmembrane protein, and osteoclast-stimulatory transmembrane protein. PMID:25099015

2014-01-01

103

Construction of a genetic linkage map in tetraploid species using molecular markers.  

PubMed Central

This article presents methodology for the construction of a linkage map in an autotetraploid species, using either codominant or dominant molecular markers scored on two parents and their full-sib progeny. The steps of the analysis are as follows: identification of parental genotypes from the parental and offspring phenotypes; testing for independent segregation of markers; partition of markers into linkage groups using cluster analysis; maximum-likelihood estimation of the phase, recombination frequency, and LOD score for all pairs of markers in the same linkage group using the EM algorithm; ordering the markers and estimating distances between them; and reconstructing their linkage phases. The information from different marker configurations about the recombination frequency is examined and found to vary considerably, depending on the number of different alleles, the number of alleles shared by the parents, and the phase of the markers. The methods are applied to a simulated data set and to a small set of SSR and AFLP markers scored in a full-sib population of tetraploid potato. PMID:11238421

Luo, Z W; Hackett, C A; Bradshaw, J E; McNicol, J W; Milbourne, D

2001-01-01

104

Application of genomeceuticals to the molecular and immunological aspects of autism.  

PubMed

Autism is a developmental disease affecting as many as 1 in 300 children and is often characterized as a mental disorder originating in infancy that is associated with self-absorption, inability to interact socially, behavior, and language dysfunction (e.g. echolalia). Current theories indicate an important role of diet in the development of disease. It is thought that, as a result of maldigestion of casein and gluten, opioid-type peptides, or exorphins, are produced. Additionally, because of the time-frame of development of the disease, there has been an association with childhood vaccination. Consequently, prevailing therapies attempt to address these causes in one, or a combination, of three ways: diet restriction (removing casein and gluten); supplementation with exogenous enzymes; and probiotic bacteria. Until recently, none of the therapies addressed the molecular mechanisms that may be at work in the development and progression of autism. This paper presents potential molecular and cellular mechanism related to autism as well as discusses their application to the treatment of the disease through the application of genomeceuticals. Additionally, a link between developmentally associated aberrant immune and inflammatory responses, and autism is suggested and explored. PMID:11461171

Brudnak, M A

2001-08-01

105

Immunology & Pharmacology  

E-print Network

postgraduate courses e.g. M.Sc. courses in Clinical Pharmacology, Immunology, Toxicology, Medicinal Chemistry, Forensic Science, Endocrinology or Information Science. The course is offered by the School of Medical of the School. These are neuropharmacology, toxicology, systems immunology, autoimmunity, inflammation, asthma

Levi, Ran

106

A general mixture model for mapping quantitative trait loci by using molecular markers  

Microsoft Academic Search

In a segregating population a quantitative trait may be considered to follow a mixture of (normal) distributions, the mixing proportions being based on Mendelian segregation rules. A general and flexible mixture model is proposed for mapping quantitative trait loci (QTLs) by using molecular markers. A method is discribed to fit the model to data. The model makes it possible to

R. C. Jansen

1992-01-01

107

A molecular marker-based linkage map of diploid bananas ( Musa acuminata )  

Microsoft Academic Search

A partial molecular linkage map of the Musa acuminata diploid genome is presented. This map is based on 58 RFLP, four isozyme and 28 RAPD markers segregating in an F2 population of 92 individuals. A total of 90 loci was detected, 77 of which were placed on 15 linkage groups while 13 segregated independently. Segregation distortions were shown by 36%

S. Fauré; J. L. Noyer; J. P. Horry; F. Bakry; C. Lanaud; D. Go?zalez de León

1993-01-01

108

Detecting Molecular Signatures of Life on Mars: the Life Marker Chip (lmc) Instrument  

Microsoft Academic Search

In recent years, the rise of interest in planetary exploration and the emergence of Astrobiology as a promising field of research have lead to a number of programmes aiming to develop sensitive instruments for the detection of the molecular signatures of life in extreme environments. An antibody assay-based life detection instrument, the Life Marker Chip (LMC), is currently under development

Mariliza Derveni

2010-01-01

109

Analysis of genetic diversity in Ganoderma population with a novel molecular marker SRAP  

Microsoft Academic Search

Genetic marker technology designed to detect naturally occurring polymorphisms at the DNA level had become an invaluable and revolutionizing tool for both applied and basic studies of fungi. To eliminate the confusion on the taxonomy of Ganoderma strains, in this study, a collection of 31 accessions representative of morphotypes and some unclassified types was used for analyzing molecular diversity using

Shu-Jing Sun; Wei Gao; Shu-Qian Lin; Jian Zhu; Bao-Gui Xie; Zhi-Bin Lin

2006-01-01

110

Molecular marker analysis of Salmonella typhimurium from surface waters, humans, and animals  

Microsoft Academic Search

Salmonella contamination of North Sea water was detected for the first time in 1988 in Germany during routine examinations of bathing areas. Since then, subsequent isolations along the coast have been reported regularly. To define the source of contamination, strains isolated from seawater and rivers were studied by molecular marker methods. Their properties were compared with those of strains originating

I. Graeber; M. A. Montenegro; C. Bunge; U. Boettcher; H. Tobias; E. A. Heinemeyer; R. Helmuth

1995-01-01

111

Molecular Markers and Cotton Genetic Improvement: Current Status and Future Prospects  

PubMed Central

Narrow genetic base and complex allotetraploid genome of cotton (Gossypium hirsutum L.) is stimulating efforts to avail required polymorphism for marker based breeding. The availability of draft genome sequence of G. raimondii and G. arboreum and next generation sequencing (NGS) technologies facilitated the development of high-throughput marker technologies in cotton. The concepts of genetic diversity, QTL mapping, and marker assisted selection (MAS) are evolving into more efficient concepts of linkage disequilibrium, association mapping, and genomic selection, respectively. The objective of the current review is to analyze the pace of evolution in the molecular marker technologies in cotton during the last ten years into the following four areas: (i) comparative analysis of low- and high-throughput marker technologies available in cotton, (ii) genetic diversity in the available wild and improved gene pools of cotton, (iii) identification of the genomic regions within cotton genome underlying economic traits, and (iv) marker based selection methodologies. Moreover, the applications of marker technologies to enhance the breeding efficiency in cotton are also summarized. Aforementioned genomic technologies and the integration of several other omics resources are expected to enhance the cotton productivity and meet the global fiber quantity and quality demands.

Malik, Waqas; Iqbal, Muhammad Zaffar; Ali Khan, Asif; Qayyum, Abdul; Ali Abid, Muhammad; Noor, Etrat; Qadir Ahmad, Muhammad; Hasan Abbasi, Ghulam

2014-01-01

112

NCI-CCI Immunology Branch: Cell & Molecular Biology Section - Yonghzi Karen Cui MD, Ph.D, Biologist  

Cancer.gov

Skip to Main Content CCR Home | About CCR | CCR Intranet Main Navigation Referrals For Patients For Physicians For Prospective Trainees For Scientists News Quick Links Home Referring a Patient Patients and Families Scientific Programs - Immunology Section

113

Biological (molecular and cellular) markers of toxicity. [Oryzias latipes  

SciTech Connect

The objective of this study is to evaluate the use of the Japanese Medaka (Oryzias latipes) as a predictor of genotoxicity following exposure to carcinogens. The early molecular events associated with genotoxicity in Medaka tissues following exposure to known carcinogens will be investigated. The primary endpoint for most small fish carcinogenesis studies is histopathogenic identification of a neoplastic lesion. Such lesions usually occur in the liver, and histogenesis of liver neoplasms in fish is similar to that in rodents. Because of the latent period between initial contact with chemical agents in the environmental and subsequent expression of deleterious effects, development of sensitive assays for detection and estimating early exposure is needed. Carcinogen-induced DNA damage will be assessed as a possible measure of severity of exposure, correlated with activation of liver enzymes. 6 refs., 2 figs., 1 tab.

Shugart, L.R.

1991-04-01

114

Molecular Markers of Influenza B Lineages and Clades  

PubMed Central

Co-circulation of two influenza B virus lineages, B/Yamagata and B/Victoria, has been recognized since the late 1980s. The assessment of the prevalent lineage and the group of viruses in circulation is of importance in order to decide on the vaccine composition and evaluate its efficacy. The molecular characterization of influenza B viruses in circulation has been the aim of this study; this was approached by identifying and locating nucleotide substitutions in the influenza B virus hemagglutinin (HA) and neuraminidase (NA), specific for the lineage and/or clade. By the alignment of 3456 sequences from the influenza GISAID EpiFlu database, a high number of lineage- and group-specific nucleotide positions have been observed in the HA gene, but not in the NA gene. Additionally, an RT-PCR method has been developed, applicable directly to clinical specimens, which amplifies a short HA region that includes a group of unique molecular signatures. Twenty eight influenza B virus-positive respiratory specimens, collected in Tuscany in the seasons 2012–2013 and 2013–2014, were analyzed. The results revealed two clearly distinguishable patterns: one, more frequent, was characterized by all of the nucleotide changes associated with the B/Yamagata lineage (in most cases of Group 2), whereas the other exhibited all of the changes associated with the B/Victoria lineage. It can be concluded that the analysis of this short HA sequence can permit a rapid, highly sensitive determination of influenza B virus lineages and clades. PMID:25412364

Arvia, Rosaria; Corcioli, Fabiana; Pierucci, Federica; Azzi, Alberta

2014-01-01

115

Immunology and Evolution of  

E-print Network

. Immunogenetics. 2. Host-parasite relationships-- Genetic aspects. 3. Microorganisms--Evolution. 4. Antigens. 5--immunology. 2. Evolution, Molecular. 3. Genetics, Population. 4. Immunity--genetics. WC 100 F828i 2002] QR184 .F with Prior Exposure 24 3.3 Infect Hosts with Genetically Variable Resistance 26 3.4 Vary Attachment

Frank, Steven A.

116

Intestinal microflora molecular markers of spleen-deficient rats and evaluation of traditional Chinese drugs  

PubMed Central

AIM: To find a rapid and efficient analysis method of gastrointestinal microflora in Pi-deficient (spleen-deficient) rats and to evaluate traditional Chinese drugs. METHODS: Enterobacterial repetitive intergenic consensus-PCR (ERIC-PCR) based assay was performed to examine changes of intestinal microflora in two Pi-deficienct animal models and to evaluate the efficacy of four traditional Chinese drugs as well as a probiotic recipe and another therapy in Pi-deficient rats. RESULTS: A molecular marker was identified for Pi-deficiency in rats. The pharmacodynamic evaluation system, including identified molecular markers (net integral area and abundance of DNA bands), Shannon’s index for diversity of intestinal microflora, and Sorenson’s pairwise similarity coefficient, was established. The four major clinical recipes of traditional Chinese drugs for Pi-deficiency in rats, especially at their medium dose (equivalence to the clinical dose), produced more pronounced recovery activities in Pi-deficient rats, while higher doses of these recipes did not show a better therapeutic effect but some toxic effects such as perturbation deterioration of intestinal microflora. CONCLUSION: Both fingerprint analysis and identified marker can show Pi-deficiency in rats and its difference after treatment. The identified molecular marker may be applied in screening for the active compounds both in relative traditional Chinese drugs and in pharmacodynamic study of Pi-deficiency in rats. PMID:19437561

Peng, Ying; Wang, Zhuo; Lu, Yuan; Wu, Chun-Fu; Yang, Jing-Yu; Li, Xiao-Bo

2009-01-01

117

Anthropogenic Molecular Markers: Tools to Identify the Sources and Transport Pathways of Pollutants  

USGS Publications Warehouse

The activities of modern civilization have released to the oceans a wide variety of both mobilized natural compounds and synthetic compounds not found prior to modern times. Many of these compounds provide a means of identifying sources of inputs and pathways of movement of chemicals through oceanic ecosystems and serve as molecular markers of human activities. A coastal ocean (Tokyo Bay) and a deep ocean (Deep Water Dump Site 106 in the Western North Atlantic Ocean) example are presented. In the deep ocean study, the correlation between potential sewage marker, i.e. linear alkylbenzenes (LABs), and polychlorinated biphenyls (PCBs) concentrations indicates a contribution of sewage sludge PCBs to the dump site sediments.

Takada, H.; Satoh, F.; Bothner, M. H.; Tripp, B. W.; Johnson, C. G.; Farrington, J. W.

1997-01-01

118

Prognostic Histopathological and Molecular Markers on Prostate Cancer Needle-Biopsies: A Review  

PubMed Central

Prostate cancer is diverse in clinical presentation, histopathological tumor growth patterns, and survival. Therefore, individual assessment of a tumor's aggressive potential is crucial for clinical decision-making in men with prostate cancer. To date a large number of prognostic markers for prostate cancer have been described, most of them based on radical prostatectomy specimens. However, in order to affect clinical decision-making, validation of respective markers in pretreatment diagnostic needle-biopsies is essential. Here, we discuss established and promising histopathological and molecular parameters in diagnostic needle-biopsies. PMID:25243131

Hoogland, A. Marije; Kweldam, Charlotte F.; van Leenders, Geert J. L. H.

2014-01-01

119

A suite of molecular markers for identifying species, detecting introgression and describing population structure in spadefoot toads (Spea spp.).  

PubMed

Two congeneric species of spadefoot toad, Spea multiplicata and Spea bombifrons, have been the focus of hybridization studies since the 1970s. Because complex hybrids are not readily distinguished phenotypically, genetic markers are needed to identify introgressed individuals. We therefore developed a set of molecular markers (amplified fragment length polymorphism, polymerase chain reaction-restriction fragment length polymorphism and single nucleotide polymorphism) for identifying pure-species, F1 hybrids and more complex introgressed types. To do so, we tested a series of markers across both species and known hybrids using populations in both allopatry and sympatry. We retained those markers that differentiated the two pure-species and also consistently identified known species hybrids. These markers are well suited for identifying hybrids between these species. Moreover, those markers that show variation within each species can be used in conjunction with existing molecular markers in studies of population structure and gene flow. PMID:22564443

Pfennig, Karin S; Allenby, Ashley; Martin, Ryan A; Monroy, Anaïs; Jones, Corbin D

2012-09-01

120

Isolation, purification, and immunological activities of a low-molecular-weight polysaccharide from the Lingzhi or Reishi medicinal mushroom Ganoderma lucidum (higher Basidiomycetes).  

PubMed

To obtain a low-molecular-weight polysaccharide with immuno-enhancing activity, hot water extract of Ganoderma lucidum fruit bodies was separated by membrane ultrafiltration, anion exchange, and gel filtration chromatography, and the immunological activities of fractions were assessed on the basis of nitric oxide production by RAW 264.7 macrophages. A novel polysaccharide (TB3-2-2) was successfully isolated and purified. TB3-2-2 is a homogeneous polysaccharide, with a relative molecular weight of 5.11 × 103 Da, identified by high-performance liquid chromatography and was composed of galactose and glucose in a molar ratio of 2:3 determined by high-performance anion exchange chromatography. TB3-2-2 had a carbohydrate content of 99%, as measured using the phenol-sulfuric acid method. Proliferation of mouse spleen lymphocytes and the expression level of interleukin-6 was significantly increased by TB3-2-2. Results indicate that the low-molecular-weight polysaccharide with immunological activity in G. lucidum is worthy of further research and development. PMID:23796222

Zhu, Lina; Luo, Xi; Tang, Qingjiu; Liu, Yanfang; Zhou, Shuai; Yang, Yan; Zhang, Jingsong

2013-01-01

121

Genetic linkage map of peach [Prunus persica (L.) Batsch] using morphological and molecular markers  

Microsoft Academic Search

A genetic linkage map of peach [Prunus persica (L.) Batch] was constructed in order to identify molecular markers linked to economically important agronomic traits that\\u000a would be particularly useful for long-lived perennial species. An intraspecific F2 population was generated from self-pollinating a single F1 plant from a cross between a flat non-acid peach, ‘Ferjalou Jalousia’ and an acid round nectarine

E. Dirlewanger; V. Pronier; C. Parvery; C. Rothan; A. Guye; R. Monet

1998-01-01

122

Isolation of a non-urea-producing sake yeast strain carrying a discriminable molecular marker.  

PubMed

In the fermentation industry, the traceability of microorganisms during the process is important to ensure safety and efficacy. Ethyl carbamate, a group-2A carcinogen, is produced from ethanol and urea during the storage of food/alcoholic beverages. We isolated non-urea-producing sake yeast car1 mutants carrying a discriminable molecular marker, and demonstrated, by the use of PCR assays, that these mutants are useful for traceability analysis and identification during the sake brewing process. PMID:24317072

Kuribayashi, Takashi; Tamura, Hiroyasu; Sato, Keigo; Nabekura, Yoshihito; Aoki, Toshio; Anzawa, Yoshihiko; Katsumata, Kazuaki; Ohdaira, Shunji; Yamashita, Susumu; Kume, Kazunori; Kaneoke, Mitsuoki; Watanabe, Ken-Ichi; Hirata, Dai

2013-01-01

123

Forensic soil DNA analysis using high-throughput sequencing: A comparison of four molecular markers.  

PubMed

Soil analysis, such as mineralogy, geophysics, texture and colour, are commonly used in forensic casework to link a suspect to a crime scene. However, DNA analysis can also be applied to characterise the vast diversity of organisms present in soils. DNA metabarcoding and high-throughput sequencing (HTS) now offer a means to improve discrimination between forensic soil samples by identifying individual taxa and exploring non-culturable microbial species. Here, we compare the small-scale reproducibility and resolution of four molecular markers targeting different taxa (bacterial 16S rRNA, eukaryotic18S rRNA, plant trnL intron and fungal internal transcribed spacer I (ITS1) rDNA) to distinguish two sample sites. We also assess the background DNA level associated with each marker and examine the effects of filtering Operational Taxonomic Units (OTUs) detected in extraction blank controls. From this study, we show that non-bacterial taxa in soil, particularly fungi, can provide the greatest resolution between the sites, whereas plant markers may be problematic for forensic discrimination. ITS and 18S markers exhibit reliable amplification, and both show high discriminatory power with low background DNA levels. The 16S rRNA marker showed comparable discriminatory power post filtering; however, presented the highest level of background DNA. The discriminatory power of all markers was increased by applying OTU filtering steps, with the greatest improvement observed by the removal of any sequences detected in extraction blanks. This study demonstrates the potential use of multiple DNA markers for forensic soil analysis using HTS, and identifies some of the standardisation and evaluation steps necessary before this technique can be applied in casework. PMID:25151602

Young, Jennifer M; Weyrich, Laura S; Cooper, Alan

2014-11-01

124

Biological pathways, candidate genes and molecular markers associated with quality-of-life domains: an update  

PubMed Central

Background There is compelling evidence of a genetic foundation of patient-reported QOL. Given the rapid development of substantial scientific advances in this area of research, the current paper updates and extends reviews published in 2010. Objectives The objective is to provide an updated overview of the biological pathways, candidate genes and molecular markers involved in fatigue, pain, negative (depressed mood) and positive (well-being/happiness) emotional functioning, social functioning, and overall QOL. Methods We followed a purposeful search algorithm of existing literature to capture empirical papers investigating the relationship between biological pathways and molecular markers and the identified QOL domains. Results Multiple major pathways are involved in each QOL domain. The inflammatory pathway has the strongest evidence as a controlling mechanism underlying fatigue. Inflammation and neurotransmission are key processes involved in pain perception and the COMT gene is associated with multiple sorts of pain. The neurotransmitter and neuroplasticity theories have the strongest evidence for their relationship with depression. Oxytocin-related genes and genes involved in the serotonergic and dopaminergic pathways play a role in social functioning. Inflammatory pathways, via cytokines, also play an important role in overall QOL. Conclusions Whereas the current findings need future experiments and replication efforts, they will provide researchers supportive background information when embarking on studies relating candidate genes and/or molecular markers to QOL domains. The ultimate goal of this area of research is to enhance patients’ QOL. PMID:24604075

Sprangers, Mirjam A.G.; Thong, Melissa S.Y.; Bartels, Meike; Barsevick, Andrea; Ordonana, Juan; Shi, Qiuling; Wang, Xin Shelley; Klepstad, Pal; Wierenga, Eddy A.; Singh, Jasvinder A.; Sloan, Jeff A.

2014-01-01

125

Transferability of molecular markers from major legumes to Lathyrus spp. for their application in mapping and diversity studies.  

PubMed

Lathyrus cicera L. (chickling pea) and L. sativus L. (grass pea) have great potential among grain legumes due to their adaptability to inauspicious environments, high protein content and resistance to serious diseases. Nevertheless, due to its past underused, further activities are required to exploit this potential and to capitalise on the advances in molecular biology that enable improved Lathyrus spp. breeding programmes. In this study we evaluated the transferability of molecular markers developed for closely related legume species to Lathyrus spp. (Medicago truncatula, pea, lentil, faba bean and lupin) and tested the application of those new molecular tools on Lathyrus mapping and diversity studies. Genomic and expressed sequence tag microsatellite, intron-targeted amplified polymorphic, resistance gene analogue and defence-related gene markers were tested. In total 128 (27.7 %) and 132 (28.6 %) molecular markers were successfully cross-amplified, respectively in L. cicera and L. sativus. In total, the efficiency of transferability from genomic microsatellites was 5 %, and from gene-based markers, 55 %. For L. cicera, three cleaved amplified polymorphic sequence markers and one derived cleaved amplified polymorphic sequence marker based on the cross-amplified markers were also developed. Nine of those molecular markers were suitable for mapping in a L. cicera recombinant inbred line population. From the 17 molecular markers tested for diversity analysis, six (35 %) in L. cicera and seven (41 %) in L. sativus were polymorphic and discriminate well all the L. sativus accessions. Additionally, L. cicera accessions were clearly distinguished from L. sativus accessions. This work revealed a high number of transferable molecular markers to be used in current genomic studies in Lathyrus spp. Although their usefulness was higher on diversity studies, they represent the first steps for future comparative mapping involving these species. PMID:24203465

Almeida, Nuno Felipe; Trindade Leitão, Susana; Caminero, Constantino; Torres, Ana Maria; Rubiales, Diego; Vaz Patto, Maria Carlota

2014-01-01

126

Molecular marker-based characterization in candidate plus trees of Pongamia pinnata, a potential biodiesel legume  

PubMed Central

Background and aims Pongamia pinnata, a legume tree, has many traditional uses and is a potential biodiesel plant. Despite its importance and the availability of appropriate molecular genetic tools, the full potential of Pongamia is yet to be realized. The objective of this study was to assess genetic diversity among 10 systematically characterized candidate plus trees (CPTs) of P. pinnata from North Guwahati. Methodology The application and informativeness of polymerase chain reaction-based molecular markers [random amplified polymorphic DNA (RAPD), inter-simple sequence repeat (ISSR) and amplified fragment length polymorphism (AFLP)] to assess the genetic variability and relatedness among 10 CPTs of P. pinnata were investigated. Principal results Polymorphism rates of 10.48, 10.08 and 100 % were achieved using 18 RAPD, 12 ISSR and 4 AFLP primer combinations, respectively. Polymorphic information content (PIC) varied in the range 0.33–0.49, 0.18–0.49 and 0.26–0.34 for RAPD, ISSR and AFLP markers, respectively, whereas the corresponding average marker index (MI) values for the above markers were 7.48, 6.69 and 30.75. Based on Nei's gene diversity and Shannon's information index, inter-population diversity (hsp) was highest when compared with intra-population diversity (hpop) and the gene flow (Nm) ranged from a moderate value of 0.607 to a high value of 6.287 for the three DNA markers. Clustering of individuals was not similar when RAPD- and ISSR-derived dendrogram analyses were compared with that of AFLP. The Mantel test cophenetic correlation coefficient was higher for AFLP (r = 0.98) than for ISSR (r = 0.73) and RAPD (r = 0.84). Molecular markers discriminated the individuals efficiently and generated a high similarity in dendrogram topologies derived using unweighted pair-group arithmetic average, although some differences were observed. The three-dimensional scaling by principal coordinate analysis supported the result of clustering. Conclusions Comparing the results obtained with the three DNA markers, AFLP indicated higher efficiency for estimating the levels of genetic diversity and proved to be reliable for fingerprinting, mapping and diversity studies in Pongamia in view of their suitability for energy production purposes. PMID:22476075

Kesari, Vigya; Madurai Sathyanarayana, Vinod; Parida, Ajay; Rangan, Latha

2010-01-01

127

For More Information: http://dbbs.wustl.edu/divprograms/immunology/  

E-print Network

For More Information: http://dbbs.wustl.edu/divprograms/immunology/ To request information: dbbs-info@wustl.edu what is immunology? Immunology is the study of the immune system in health and disease, including. Immunology has a strong foundation in biochemistry, molecular biology and cell biology. Washington University

Stormo, Gary

128

Molecular markers based on LTR retrotransposons BARE - 1 and Jeli uncover different strata of evolutionary relationships in diploid wheats  

Microsoft Academic Search

Molecular markers based on retrotransposon insertions are widely used for various applications including phylogenetic analysis.\\u000a Multiple cases were described where retrotransposon-based markers, namely sequence-specific amplification polymorphism (SSAP),\\u000a were superior to other marker types in resolving the phylogenetic relationships due to their higher variability and informativeness.\\u000a However, the patterns of evolutionary relationships revealed by SSAP may be dependent on the underlying

Fedor A. KonovalovNikolay; Nikolay P. Goncharov; Svetlana Goryunova; Aleksandra Shaturova; Tatyana Proshlyakova; Alexander Kudryavtsev

2010-01-01

129

Morphological versus molecular markers to describe variability in Juniperus excelsa subsp. excelsa (Cupressaceae)  

PubMed Central

Background and aims Juniperus excelsa M.-Bieb. is a major forest element in the mountains of the eastern part of Mediterranean and sub-Mediterranean regions. This study comprises the first morphological investigation covering a large part of the geographical range of J. excelsa and aims to verify the congruency between the morphological results and molecular results of a previous study. Methodology We studied 14 populations sampled from Greece, Cyprus, Ukraine, Turkey and Lebanon, 11 of which have previously been investigated using molecular markers. Three hundred and ninety-four individuals of J. excelsa were examined using nine biometric features characterizing cones, seeds and shoots, and eight derived ratios. Statistical analyses were conducted in order to evaluate the intra- and inter-population morphological variability. Principal results The level of intra-population variability observed did not show any geographical trends. The total variation mostly depended on the ratios of cone diameter/seed width and seed width/seed length. The discrimination analysis, the Ward agglomeration method and barrier analysis results showed a separation of the sampled populations into three main clusters. These results confirmed, in part, the geographical differentiation revealed by molecular markers with a lower level of differentiation and a less clear geographical pattern. The most differentiated populations using both markers corresponded to old, isolated populations in the high altitudes of Lebanon (>2000 m). Moreover, a separation of the northern Turkish population from the southern Turkish populations was observed using both markers. Conclusions Morphological variation together with genetic and biogeographic studies make an effective tool for detecting relict plant populations and also populations subjected to more intensive selection. PMID:22822421

Douaihy, Bouchra; Sobierajska, Karolina; Jasinska, Anna Katarzyna; Boratynska, Krystyna; Ok, Tolga; Romo, Angel; Machon, Nathalie; Didukh, Yakiv; Bou Dagher-Kharrat, Magda; Boratynski, Adam

2012-01-01

130

Immunological detection of small organic molecules in the presence of perchlorates: relevance to the life marker chip and life detection on Mars.  

PubMed

The proposed ExoMars mission, due to launch in 2018, aims to look for evidence of extant and extinct life in martian rocks and regolith. Previous attempts to detect organic molecules of biological or abiotic origin on Mars have been unsuccessful, which may be attributable to destruction of these molecules by perchlorate salts during pyrolysis sample extraction techniques. Organic molecules can also be extracted and measured with solvent-based systems. The ExoMars payload includes the Life Marker Chip (LMC) instrument, capable of detecting biomarker molecules of extant and extinct Earth-like life in liquid extracts of martian samples with an antibody microarray assay. The aim of the work reported here was to investigate whether the presence of perchlorate salts, at levels similar to those at the NASA Phoenix landing site, would compromise the LMC extraction and detection method. To test this, we implemented an LMC-representative sample extraction process with an LMC-representative antibody assay and used these to extract and analyze a model sample that consisted of a Mars analog sample matrix (JSC Mars-1) spiked with a representative organic molecular target (pyrene, an example of abiotic meteoritic infall targets) in the presence of perchlorate salts. We found no significant change in immunoassay function when using pyrene standards with added perchlorate salts. When model samples spiked with perchlorate salts were subjected to an LMC-representative liquid extraction, immunoassays functioned in a liquid extract and detected extracted pyrene. For the same model sample matrix without perchlorate salts, we observed anomalous assay signals that coincided with yellow coloration of the extracts. This unexpected observation is being studied further. This initial study indicates that the presence of perchlorate salts, at levels similar to those detected at the NASA Phoenix landing site, is unlikely to prevent the LMC from extracting and detecting organic molecules from martian samples. PMID:22011057

Rix, Catherine S; Sims, Mark R; Cullen, David C

2011-11-01

131

Screening of rice landraces for salinity tolerance at seedling stage through morphological and molecular markers.  

PubMed

The present investigation was carried out to evaluate 33 rice landrace genotypes for assessment of their salt tolerance at seedling stage. Growth parameters like root length, shoot length and plant biomass were measured after 12 days of exposure to six different levels of saline solution (with electrical conductivity of 4, 6, 8, 10, 12 or 14 dS m (-1)). Genotypes showing significant interaction and differential response towards salinity were assessed at molecular level using 11 simple sequence repeats (SSR) markers, linked with salt tolerance quantitative trait loci. Shoot length, root length and plant biomass at seedling stage decreased with increasing salinity. However, relative salt tolerance in terms of these three parameters varied among genotypes. Out of the 11 SSR markers RM8094, RM336 and RM8046, the most competent descriptors to screen the salt tolerant genotypes with higher polymorphic information content coupled with higher marker index value, significantly distinguished the salt tolerant genotypes. Combining morphological and molecular assessment, four lanraces viz. Gheus, Ghunsi, Kuthiahara and Sholerpona were considered as true salt tolerant genotypes which may contribute in greater way in the development of salt tolerant genotypes in rice. PMID:25320465

Ali, Md Nasim; Yeasmin, Lucina; Gantait, Saikat; Goswami, Rupak; Chakraborty, Somsubhra

2014-10-01

132

[Genetic singularity coefficients of common vetch Vicia sativa L. accessions determined with molecular markers].  

PubMed

Organization and practical application of ex situ collections require estimation of genetic differences between numerous accessions of local cultivars and field weed forms collected from the same ecological and geographical region and similar in their morphophysiological characteristics. A mathematical algorithm for estimating the degree of genetic singularity of a specimen in the system of local gene pool determined with the help of molecular markers is described. The utility of this algorithm is demonstrated by the example of classification of 677 common vetch accessions from the collection of the Vavilov Institute of Plant Industry from 11 ecological-geographic regions of Russia analyzed using AFLP. The proposed classification of accessions is the result of processing the AFLP data by weighting the marker traits based on their frequency in particular regions. This allowed each accession to be characterized according to the ratio of rare and frequent alleles as a genetic singularity coefficient. The proposed method is appropriate for any types of molecular markers. A practical result of its application is the classification of accessions using a five-point score scale, which can be added to descriptors of certificate databases and used for optimization of the work with collections. PMID:19137734

Potokina, E K; Aleksandrova, T G

2008-11-01

133

Molecular and protein markers for clinical decision making in breast cancer: today and tomorrow.  

PubMed

In early breast cancer (eBC), established clinicopathological factors are not sufficient for clinical decision making particularly regarding adjuvant chemotherapy since substantial over- or undertreatment may occur. Thus, novel protein- and molecular markers have been put forward as decision aids. Since these potential prognosis and/or predictive tests differ substantially regarding their methodology, analytical and clinical validation, this review attempts to summarize the essential facts for clinicians. This review focuses on those markers which are the most advanced so far in their development towards routine clinical application, i.e. two protein markers (i.e. uPA/PAI-1 and IHC4) and six molecular multigene tests (i.e. Mammaprint®, Oncotype DX®, PAM50, Endopredict®, the 97-gene genomic grade, and 76 gene Rotterdam signatures). Next to methodological aspects, we summarized the clinical evidences, in particular the main prospective clinical trials which have already been fully recruited (i.e. MINDACT, TAILORx, WSG PLAN B) or are still ongoing (i.e. RxPONDER/SWOG S1007, WSG-ADAPT). Last but not least, this review points out the key elements for clinicians to select one test among the wide panel of proposed assays, for a specific population of patients in term of level of evidence, analytical and clinical validity as well as cost effectiveness. PMID:24138841

Harbeck, Nadia; Sotlar, Karl; Wuerstlein, Rachel; Doisneau-Sixou, Sophie

2014-04-01

134

Identification of novel molecular markers through transcriptomic analysis in human fetal and adult corneal endothelial cells  

PubMed Central

The corneal endothelium is composed of a monolayer of corneal endothelial cells (CECs), which is essential for maintaining corneal transparency. To better characterize CECs in different developmental stages, we profiled mRNA transcriptomes in human fetal and adult corneal endothelium with the goal to identify novel molecular markers in these cells. By comparing CECs with 12 other tissue types, we identified 245 and 284 signature genes that are highly expressed in fetal and adult CECs, respectively. Functionally, these genes are enriched in pathways characteristic of CECs, including inorganic anion transmembrane transporter, extracellular matrix structural constituent and cyclin-dependent protein kinase inhibitor activity. Importantly, several of these genes are disease target genes in hereditary corneal dystrophies, consistent with their functional significance in CEC physiology. We also identified stage-specific markers associated with CEC development, such as specific members in the transforming growth factor beta and Wnt signaling pathways only expressed in fetal, but not in adult CECs. Lastly, by the immunohistochemistry of ocular tissues, we demonstrated the unique protein localization for Wnt5a, S100A4, S100A6 and IER3, the four novel markers for fetal and adult CECs. The identification of a new panel of stage-specific markers for CECs would be very useful for characterizing CECs derived from stem cells or ex vivo expansion for cell replacement therapy. GEO accession number: GSE41616. PMID:23257286

Chen, Yinyin; Huang, Kevin; Nakatsu, Martin N.; Xue, Zhigang; Deng, Sophie X.; Fan, Guoping

2013-01-01

135

Molecular characterization of intra-population variability of Jatropha curcas L. using DNA based molecular markers.  

PubMed

Jatropha curcas L. (Euphorbiaceae) has acquired a great importance as a renewable source of energy with a number of environmental benefits. Very few attempts were made to understand the extent of genetic diversity of J. curcas germplasm. In the present study, efforts were made to analyze the genetic diversity among the elite germplasms of J. curcas, selected on the basis of their performance in field using random amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP) and simple sequence repeats (SSR). The plants were selected on the basis of height, canopy circumference, number of seeds per fruit, weight of 100 seeds, seed yield in grams per plant and oil content. Out of 250 RAPD (with 26 primers), 822 AFLP (with 17 primers) and 19 SSR band classes, 141, 346 and 7 were found to be polymorphic, respectively. The percentage polymorphism among the selected germplasms using RAPD, AFLP and SSR was found to be 56.43, 57.9, and 36.84, respectively. The Jaccard's similarity coefficient was found 0.91, 0.90 and 0.91 through RAPD, AFLP and SSR marker systems, respectively. Principle component analysis (PCA) and dendrogarm analysis of genetic relationship among the germplasm using RAPD, AFLP and SSR data showed a good correlation for individual markers. The germplasm JCC-11, 12, 13, 14 and 15 whose yield found to be high were clustered together in dendrogram and PCA analysis though JCC11 is geographically distinct from others. In overall analysis JCC6 (in RAPD), JCC8 (in AFLP) and JCC 6 and JCC10 (in SSR) were found genetically diverse. Characterization of geographically distinct and genetically diverse germplasms with varied yield characters is an important step in marker assisted selection (MAS) and it can be useful for breeding programs and QTL mapping. PMID:21915629

Mastan, Shaik G; Sudheer, Pamidimarri D V N; Rahman, H; Ghosh, A; Rathore, Mangal S; Ravi Prakash, Ch; Chikara, J

2012-04-01

136

DEVELOPING MOLECULAR GENETIC MAPS First molecular marker map: humans (Botstein et al., 1980)  

E-print Network

. #12;Molecular Mapping 2 ii. Recombinant inbred lines (RI) formed by single seed descent from each F2 of linkage disequilibrium, facilitating mapping. An F1 population from the cross of two inbred lines segregation due to genomic rearrangements. c. Ideally inbred lines--often not possible with outcrossed species

Bhattacharyya, Madan Kumar

137

Molecular Markers Predict Distant Metastases After Adjuvant Chemoradiation for Rectal Cancer  

SciTech Connect

Purpose: The outcomes of adjuvant chemoradiation for locally advanced rectal cancer are nonuniform among patients with matching prognostic factors. We explored the role of molecular markers for predicting the outcome of adjuvant chemoradiation for rectal cancer patients. Methods and Materials: The study included 68 patients with stages II to III rectal adenocarcinoma who were treated with total mesorectal excision and adjuvant chemoradiation. Chemotherapy based on 5-fluorouracil and leucovorin was intravenously administered each month for 6-12 cycles. Radiation therapy consisted of 54 Gy delivered in 30 fractions. Immunostaining of surgical specimens for COX-2, EGFR, VEGF, thymidine synthase (TS), and Raf kinase inhibitor protein (RKIP) was performed. Results: The median follow-up was 65 months. Eight locoregional (11.8%) and 13 distant (19.1%) recurrences occurred. Five-year locoregional failure-free survival (LRFFS), distant metastasis-free survival (DMFS), disease-free survival (DFS), and overall survival (OS) rates for all patients were 83.9%, 78.7%, 66.7%, and 73.8%, respectively. LRFFS was not correlated with TNM stage, surgical margin, or any of the molecular markers. VEGF overexpression was significantly correlated with decreased DMFS (P=.045), while RKIP-positive results were correlated with increased DMFS (P=.025). In multivariate analyses, positive findings for COX-2 (COX-2+) and VEGF (VEGF+) and negative findings for RKIP (RKIP-) were independent prognostic factors for DMFS, DFS, and OS (P=.035, .014, and .007 for DMFS; .021, .010, and <.0001 for DFS; and .004, .012, and .001 for OS). The combination of both COX-2+ and VEGF+ (COX-2+/VEGF+) showed a strong correlation with decreased DFS (P=.007), and the combinations of RKIP+/COX-2- and RKIP+/VEGF- showed strong correlations with improved DFS compared with the rest of the patients (P=.001 and <.0001, respectively). Conclusions: Molecular markers can be valuable in predicting treatment outcome of adjuvant chemoradiation for rectal cancer patients.

Kim, Jun Won; Kim, Yong Bae [Department of Radiation Oncology, Severance Hospital, Yonsei University College of Medicine, Seoul (Korea, Republic of)] [Department of Radiation Oncology, Severance Hospital, Yonsei University College of Medicine, Seoul (Korea, Republic of); Choi, Jun Jeong [Department of Pathology, Severance Hospital, Yonsei University College of Medicine, Seoul (Korea, Republic of)] [Department of Pathology, Severance Hospital, Yonsei University College of Medicine, Seoul (Korea, Republic of); Koom, Woong Sub [Department of Radiation Oncology, Severance Hospital, Yonsei University College of Medicine, Seoul (Korea, Republic of)] [Department of Radiation Oncology, Severance Hospital, Yonsei University College of Medicine, Seoul (Korea, Republic of); Kim, Hoguen [Department of Pathology, Severance Hospital, Yonsei University College of Medicine, Seoul (Korea, Republic of)] [Department of Pathology, Severance Hospital, Yonsei University College of Medicine, Seoul (Korea, Republic of); Kim, Nam-Kyu [Department of Surgery, Severance Hospital, Yonsei University College of Medicine, Seoul (Korea, Republic of)] [Department of Surgery, Severance Hospital, Yonsei University College of Medicine, Seoul (Korea, Republic of); Ahn, Joong Bae [Department of Medical Oncology, Severance Hospital, Yonsei University College of Medicine, Seoul (Korea, Republic of)] [Department of Medical Oncology, Severance Hospital, Yonsei University College of Medicine, Seoul (Korea, Republic of); Lee, Ikjae; Cho, Jae Ho [Department of Radiation Oncology, Severance Hospital, Yonsei University College of Medicine, Seoul (Korea, Republic of)] [Department of Radiation Oncology, Severance Hospital, Yonsei University College of Medicine, Seoul (Korea, Republic of); Keum, Ki Chang, E-mail: kckeum@yuhs.ac [Department of Radiation Oncology, Severance Hospital, Yonsei University College of Medicine, Seoul (Korea, Republic of)

2012-12-01

138

Mitochondrial Telomeres as Molecular Markers for Identification of the Opportunistic Yeast Pathogen Candida parapsilosis  

PubMed Central

Recent studies have demonstrated that a large number of organisms carry linear mitochondrial DNA molecules possessing specialized telomeric structures at their ends. Based on this specific structural feature of linear mitochondrial genomes, we have developed an approach for identification of the opportunistic yeast pathogen Candida parapsilosis. The strategy for identification of C. parapsilosis strains is based on PCR amplification of specific DNA sequences derived from the mitochondrial telomere region. This assay is complemented by immunodetection of a protein component of mitochondrial telomeres. The results demonstrate that mitochondrial telomeres represent specific molecular markers with potential applications in yeast diagnostics and taxonomy. PMID:11923346

Nosek, Jozef; Tomaska, L'ubomir; Rycovska, Adriana; Fukuhara, Hiroshi

2002-01-01

139

Mucosal immunology  

PubMed Central

In this review, we shall highlight some recent advances in mucosal immunology and also those concepts which seem to us to merit more attention than they normally receive. Since we cannot hope to be all inclusive, we recommend the following articles and books to the reader (Tomasi & Bienenstock, 1968; Tomasi & Grey, 1972; Bienenstock, 1974; Heremans, 1974; Mestecky & Lawton, 1974; Lamm, 1976; Tomasi, 1976; Waksman & Ozer, 1976; Porter & Knight, 1977; McGhee, Mestecky & Babb, 1978; Ogra & Dayton, 1979; Befus & Bienenstock, 1980). PMID:7002769

Bienenstock, J.; Befus, A. D.

1980-01-01

140

Towards high-throughput molecular detection of Plasmodium: new approaches and molecular markers  

PubMed Central

Background Several strategies are currently deployed in many countries in the tropics to strengthen malaria control toward malaria elimination. To measure the impact of any intervention, there is a need to detect malaria properly. Mostly, decisions still rely on microscopy diagnosis. But sensitive diagnosis tools enabling to deal with a large number of samples are needed. The molecular detection approach offers a much higher sensitivity, and the flexibility to be automated and upgraded. Methods Two new molecular methods were developed: dot18S, a Plasmodium-specific nested PCR based on the 18S rRNA gene followed by dot-blot detection of species by using species-specific probes and CYTB, a Plasmodium-specific nested PCR based on cytochrome b gene followed by species detection using SNP analysis. The results were compared to those obtained with microscopic examination and the "standard" 18S rRNA gene based nested PCR using species specific primers. 337 samples were diagnosed. Results Compared to the microscopy the three molecular methods were more sensitive, greatly increasing the estimated prevalence of Plasmodium infection, including P. malariae and P. ovale. A high rate of mixed infections was uncovered with about one third of the villagers infected with more than one malaria parasite species. Dot18S and CYTB sensitivity outranged the "standard" nested PCR method, CYTB being the most sensitive. As a consequence, compared to the "standard" nested PCR method for the detection of Plasmodium spp., the sensitivity of dot18S and CYTB was respectively 95.3% and 97.3%. Consistent detection of Plasmodium spp. by the three molecular methods was obtained for 83% of tested isolates. Contradictory results were mostly related to detection of Plasmodium malariae and Plasmodium ovale in mixed infections, due to an "all-or-none" detection effect at low-level parasitaemia. Conclusion A large reservoir of asymptomatic infections was uncovered using the molecular methods. Dot18S and CYTB, the new methods reported herein are highly sensitive, allow parasite DNA extraction as well as genus- and species-specific diagnosis of several hundreds of samples, and are amenable to high-throughput scaling up for larger sample sizes. Such methods provide novel information on malaria prevalence and epidemiology and are suited for active malaria detection. The usefulness of such sensitive malaria diagnosis tools, especially in low endemic areas where eradication plans are now on-going, is discussed in this paper. PMID:19402894

Steenkeste, Nicolas; Incardona, Sandra; Chy, Sophy; Duval, Linda; Ekala, Marie-Therese; Lim, Pharath; Hewitt, Sean; Sochantha, Tho; Socheat, Doung; Rogier, Christophe; Mercereau-Puijalon, Odile; Fandeur, Thierry; Ariey, Frederic

2009-01-01

141

Molecular markers to predict clinical outcome and radiation induced toxicity in lung cancer  

PubMed Central

The elucidation of driver mutations involved in the molecular pathogenesis of cancer has led to a surge in the application of novel targeted therapeutics in lung cancer. Novel oncologic research continues to lead investigators towards targeting personalized tumor characteristics rather than applying targeted therapy to broad patient populations. Several driver genes, in particular epidermal growth factor receptor (EGFR) and ALK fusions, are the earliest to have made their way into clinical trials. The avant-garde role of genomic profiling has led to important clinical challenges when adapting current standard treatments to personalized oncologic care. This new frontier of medicine requires newer biomarkers for toxicity that will identify patients at risk, as well as, new molecular markers to predict and assess clinical outcomes. Thus far, several signature genes have been developed to predict outcome as well as genetic factors related to inflammation to predict toxicity. PMID:24688783

Zaorsky, Nicholas G.; Witek, Matthew; Lu, Bo

2014-01-01

142

Identification of Verbena officinalis based on ITS sequence analysis and RAPD-derived molecular markers.  

PubMed

Verbenae herba is a widely used drug and consists of the aerial parts of Verbena officinalis (Verbenaceae). Until now, the identification has been performed based on morphological and phytochemical analyses, which are not reliable enough to distinguish Verbena officinalis from other relevant species of the genus Verbena. Hence, impurities and adulterants, negatively influencing the therapeutic effect of the drug, may remain undetected. In an attempt to generate an accurate authentication method we used two different DNA-based approaches: comparison of ITS sequences and molecular markers (RAPD). Both approaches generally enabled discrimination of V. officinalis from the rest of the genus despite the intraspecific variation existing within V. officinalis. The application of the two independent methods, supporting each other, increases the security of identification. For better reproducibility and faster analysis, however, a SCAR marker and primers for HRM were derived from the RAPD results. The SCAR marker could distinguish V. officinalis from all other verbena species except its closest relative V. hastata, while discrimination of V. officinalis even from V. hastata was unproblematic with HRM. PMID:19350481

Ruzicka, Joana; Lukas, Brigitte; Merza, Lina; Göhler, Irina; Abel, Gudrun; Popp, Michael; Novak, Johannes

2009-09-01

143

Oligodendrocyte lineage genes (OLIG) as molecular markers for human glial brain tumors  

PubMed Central

The most common primary tumors of the human brain are thought to be of glial cell origin. However, glial cell neoplasms cannot be fully classified by cellular morphology or with conventional markers for astrocytes, oligodendrocytes, or their progenitors. Recent insights into central nervous system tumorigenesis suggest that novel molecular markers might be found among factors that have roles in glial development. Oligodendrocyte lineage genes (Olig1/2) encode basic helix–loop–helix transcription factors. In the rodent central nervous system, they are expressed exclusively in oligodendrocytes and oligodendrocyte progenitors, and Olig1 can promote formation of an chondroitin sulfate proteoglycon-positive glial progenitor. Here we show that human OLIG genes are expressed strongly in oligodendroglioma, contrasting absent or low expression in astrocytoma. Our data provide evidence that neoplastic cells of oligodendroglioma resemble oligodendrocytes or their progenitor cells and may derive from cells of this lineage. They further suggest the diagnostic potential of OLIG markers to augment identification of oligodendroglial tumors. PMID:11526205

Lu, Q. Richard; Park, John K.; Noll, Elizabeth; Chan, Jennifer A.; Alberta, John; Yuk, Dongin; Alzamora, M. Garcia; Louis, David N.; Stiles, Charles D.; Rowitch, David H.; Black, Peter M.

2001-01-01

144

Molecular characterization of Anthurium genotypes by using DNA fingerprinting and SPAR markers.  

PubMed

We characterized single primer amplification reaction (SPAR) molecular markers from 20 genotypes of Anthurium andraeanum Lind., including 3 from commercial varieties and 17 from 2 communities in the State of Espírito Santo, Brazil. Twenty-four SPAR, consisting of 7 random amplified polymorphic DNA and 17 inter-simple sequence repeat markers were used to estimate the genetic diversity of 20 Anthurium accessions. The set of SPAR markers generated 288 bands and showed an average polymorphism percentage of 93.39%, ranging from 71.43 to 100%. The polymorphism information content (PIC) of the random amplified polymorphic DNA primers averaged 0.364 and ranged from 0.258 to 0.490. Primer OPF 06 showed the lowest PIC, while OPAM 14 was the highest. The average PIC of the inter-simple sequence repeat primers was 0.299, with values ranging from 0.196 to 0.401. Primer UBC 845 had the lowest PIC (0.196), while primer UCB 810 had the highest (0.401). By using the complement of Jaccard's similarity index and unweighted pair group method with arithmetic mean clustering, 5 clusters were formed with a cophenetic correlation coefficient of 0.8093, indicating an acceptable clustering consistency. However, no genotype clustering patterns agreed with the morphological data. The Anthurium genotypes investigated in this study are a germplasm source for conservational research and may be used in improvement programs for this species. PMID:25062412

Souza Neto, J D; Soares, T C B; Motta, L B; Cabral, P D S; Silva, J A

2014-01-01

145

Fruit plant germplasm characterisation using molecular markers generated in RAPD and ISSR-PCR.  

PubMed

The genotypes of the strawberry (Fragaria x ananassa), apple (Malus domestica) and Ribes species (R. nigrum, R. rubrum and R. glossularia), maintained in our Institute's collection and used in breeding programs, were screened for DNA markers. Twenty primers for RAPD (among 60 tested) and seven for ISSR (among 10 tested) were chosen as creating polymorphic DNA bands differentiating the investigated genotypes. Based on those identity markers, the genetic distance between genotypes was determined, and their relatedness was estimated. In many cases, both RAPD- and ISSR-based genetic similarity confirmed relatedness connected with biological origin and with the place where the cultivar was developed. However, some diversity connected with the technique used for molecular marker generation was observed. Generally, the similarity values based on ISSR data were higher than those based on RAPD. Parallel study using two data sets seems to enable a reduction in the number of potential mistakes connected with each method's, technical limitations and ensures more precise relatedness determination. PMID:12378239

Korbin, Ma?gorzata; Kuras, Anita; Zurawicz, Edward

2002-01-01

146

Evaluation of genetically modified sugarcane lines carrying Cry 1AC gene using molecular marker techniques.  

PubMed

Five genetically modified insect resistant sugarcane lines harboring the Bt Cry 1AC gene to produce insecticidal proteins were compared with non-transgenic control by using three types of molecular marker techniques namely, RAPD, ISSR and AFLP. These techniques were applied on transgenic and non-transgenic plants to investigate the genetic variations, which may appear in sugarcane clones. This variation might demonstrate the genomic changes associated with the transformation process, which could change important molecular basis of various biological phenomena. Genetic variations were screened using 22 different RAPD primers, 10 ISSR primers and 13 AFLP primer combinations. Analysis of RAPD and ISSR banding patterns gave no exclusive evidence for genetic variations. Meanwhile, the percentage of polymorphic bands was 0.45% in each of RAPD and ISSR, while the polymorphism generated by AFLP analysis was 1.8%. The maximum percentage of polymorphic bands was 1.4%, 1.1% and 5.5% in RAPD, ISSR and AFLP, respectively. These results demonstrate that most transgenic lines showed genomic homogeneity and verified minor genomic changes. Dendrograms revealing the relationships among the transgenic and control plants were developed from the data of each of the three marker types. PMID:23549345

Ismail, Roba M

2013-01-01

147

Molecular Markers Allow to Remove Introgressed Genetic Background: A Simulation Study  

PubMed Central

The maintenance of genetically differentiated populations can be important for several reasons (whether for wild species or domestic breeds of economic interest). When those populations are introgressed by foreign individuals, methods to eliminate the exogenous alleles can be implemented to recover the native genetic background. This study used computer simulations to explore the usefulness of several molecular based diagnostic approaches to recover of a native population after suffering an introgression event where some exogenous alleles were admixed for a few generations. To remove the exogenous alleles, different types of molecular markers were used in order to decide which of the available individuals contributed descendants to next generation and their number of offspring. Recovery was most efficient using diagnostic markers (i.e., with private alleles) and least efficient when using alleles present in both native and exogenous populations at different frequencies. The increased inbreeding was a side-effect of the management strategy. Both values (% of native alleles and inbreeding) were largely dependent on the amount of exogenous individuals entering the population and the number of generations of admixture that occurred prior to management. PMID:23152901

Amador, Carmen; Toro, Miguel Angel; Fernandez, Jesus

2012-01-01

148

Expression of Neuroendocrine Markers in Different Molecular Subtypes of Breast Carcinoma  

PubMed Central

Background. Carcinomas of the breast with neuroendocrine features are incorporated in the World Health Organization classification since 2003 and include well-differentiated neuroendocrine tumors, poorly differentiated neuroendocrine carcinomas/small cell carcinomas, and invasive breast carcinomas with neuroendocrine differentiation. Neuroendocrine differentiation is known to be more common in certain low-grade histologic special types and has been shown to mainly cluster to the molecular (intrinsic) luminal A subtype. Methods. We analyzed the frequency of neuroendocrine differentiation in different molecular subtypes of breast carcinomas of no histologic special type using immunohistochemical stains with specific neuroendocrine markers (chromogranin A and synaptophysin). Results. We found neuroendocrine differentiation in 20% of luminal B-like carcinomas using current WHO criteria (at least 50% of tumor cells positive for synaptophysin or chromogranin A). In contrast, no neuroendocrine differentiation was seen in luminal A-like, HER2 amplified and triple-negative carcinomas. Breast carcinomas with neuroendocrine differentiation presented with advanced stage disease and showed aggressive behavior. Conclusions. We conclude that neuroendocrine differentiation is more common than assumed in poorly differentiated luminal B-like carcinomas. Use of specific neuroendocrine markers is thus encouraged in this subtype to enhance detection of neuroendocrine differentiation and hence characterize the biological and therapeutic relevance of this finding in future studies. PMID:24701575

Wachter, David L.; Hartmann, Arndt; Beckmann, Matthias W.; Fasching, Peter A.; Hein, Alexander; Bayer, Christian M.; Agaimy, Abbas

2014-01-01

149

Management of endocrine disease: clinicopathological classification and molecular markers of pituitary tumours for personalized therapeutic strategies.  

PubMed

Pituitary tumours, the most frequent intracranial tumour, are historically considered benign. However, various pieces of clinical evidence and recent advances in pathological and molecular analyses suggest the need to consider these tumours as more than an endocrinological disease, despite the low incidence of metastasis. Recently, we proposed a new prognostic clinicopathological classification of these pituitary tumours, according to the tumour size (micro, macro and giant), type (prolactin, GH, FSH/LH, ACTH and TSH) and grade (grade 1a, non-invasive; 1b, non-invasive and proliferative; 2a, invasive; 2b, invasive and proliferative and 3, metastatic). In addition to this classification, numerous molecular prognostic markers have been identified, allowing a better characterisation of tumour behaviour and prognosis. Moreover, clinical and preclinical studies have demonstrated that pituitary tumours could be treated by some chemotherapeutic drugs or new targeted therapies. Our improved classification of these tumours should now allow the identification of prognosis markers and help the clinician to propose personalised therapies to selected patients presenting tumours with a high risk of recurrence. PMID:24431196

Raverot, Gerald; Jouanneau, Emmanuel; Trouillas, Jacqueline

2014-04-01

150

Identification of Leaf Rust Resistance Genes in Selected Egyptian Wheat Cultivars by Molecular Markers  

PubMed Central

Leaf rust, caused by Puccinia triticina Eriks., is a common and widespread disease of wheat (Triticum aestivum L.) in Egypt. Host resistance is the most economical, effective, and ecologically sustainable method of controlling the disease. Molecular markers help to determine leaf rust resistance genes (Lr genes). The objective of this study was to identify Lr genes in fifteen wheat cultivars from Egypt. Ten genes, Lr13, Lr19, Lr24, Lr26, Lr34, Lr35 Lr36, Lr37, Lr39, and Lr46, were detected in fifteen wheat cultivars using various molecular markers. The most frequently occurring genes in fifteen Egyptian wheat cultivars were Lr13, Lr24, Lr34, and Lr36 identified in all the cultivars used, followed by Lr26 and Lr35 (93%), Lr39 (66%), Lr37 (53%), and Lr46 (26.6%) of the cultivars, and finally Lr19 was present in 33.3% of cultivars. It is concluded that there was a good variation in Lr genes carried by wheat cultivars commercially grown in Egypt. Therefore, strategies for deploying resistance genes to prolong effective disease resistance are suggested to control wheat leaf rust disease. PMID:24511291

Imbaby, I. A.; Mahmoud, M. A.; Hassan, M. E. M.; Abd-El-Aziz, A. R. M.

2014-01-01

151

Transcriptome profiling and molecular marker discovery in red pepper, Capsicum annuum L. TF68.  

PubMed

Transcriptome from high throughput sequencing-by-synthesis is a good resource of molecular markers. In this study, we present utility of massively parallel sequencing by synthesis for profiling the transcriptome of red pepper (Capsicum annuum L. TF68) using 454 GS-FLX pyrosequencing. Through the generation of approximately 30.63 megabases (Mb) of expressed sequence tag (EST) data with the average length of 375 base pairs (bp), 9,818 contigs and 23,712 singletons were obtained by raw reads assembly. Using BLAST alignment against NCBI non-redundant and a UniProt protein database, 30% of the tentative consensus sequences were assigned to specific function annotation, while 24% returned alignments of unknown function, leaving up to 46% with no alignment. Functional classification using FunCat revealed that sequences with putative known function were distributed cross 18 categories. All unigenes have an approximately equal distribution on chromosomes by aligning with tomato (Solanum lycopersicum) pseudomolecules. Furthermore, 1,536 high quality single nucleotide discrepancies were discovered using the Bukang mature fruit cDNA collection (dbEST ID: 23667) as a reference. Moreover, 758 simple sequence repeat (SSR) motif loci were mined from 614 contigs, from which 572 primer sets were designed. The SSR motifs corresponded to di- and tri- nucleotide motifs (27.03 and 61.92%, respectively). These molecular markers may be of great value for application in linkage mapping and association mapping research. PMID:21706160

Lu, Fu-Hao; Cho, Myeong-Cheoul; Park, Yong-Jin

2012-03-01

152

Multigene assays and molecular markers in breast cancer: systematic review of health economic analyses.  

PubMed

Breast cancer is the most common female cancer and is associated with a significant clinical and economic burden. Multigene assays and molecular markers represent an opportunity to direct chemotherapy only to patients likely to have significant benefit. This systematic review examines published health economic analyses to assess the support for adjuvant therapy decision making. Literature searches of PubMed, the Cochrane Library, and congress databases were carried out to identify economic evaluations of multigene assays and molecular markers published between 2002 and 2012. After screening and data extraction, study quality was assessed using the Quality of Health Economic Studies instrument. The review identified 29 publications that reported evaluations of two assays: Oncotype DX(®) and MammaPrint. Studies of both tests provided evidence that their routine use was cost saving or cost-effective versus conventional approaches. Benefits were driven by optimal allocation of adjuvant chemotherapy and reduction in chemotherapy utilization. Findings were sensitive to variation in the frequency of chemotherapy prescription, chemotherapy costs, and patients' risk profiles. Evidence suggests that multigene assays are likely cost saving or cost-effective relative to current approaches to adjuvant therapy. They should benefit decision making in early-stage breast cancer in a variety of settings worldwide. PMID:23722312

Rouzier, Roman; Pronzato, Paolo; Chéreau, Elisabeth; Carlson, Josh; Hunt, Barnaby; Valentine, William J

2013-06-01

153

Evaluation of hydrogenated resin acids as molecular markers for tire-wear debris in urban environments.  

PubMed

To propose new molecular markers for tire-wear emissions, four dihydroresin acids, that is, 8-isopimaren-18-oic acid (I), 8-pimaren-18-oic acid (II), 13?(H)-abieten-18-oic acid (III), and 13?(H)-abiet-8-en-18-oic acid (IV), were identified and investigated for source specificities, distributions, and environmental stabilities. The absence of I-IV in natural sources and the linear correlations between dihydroresin acids with different skeletons in tires and in environmental samples demonstrated that I-IV are specific markers for synthetic rubbers. The ratio of III + IV to the sum of III + IV plus abietic acid showed the resin acids distribution between different environmental compartments receiving contributions from traffic and natural sources. The physicochemical properties and results of photolysis experiments suggested that I-IV can set lower limits for tire-wear contributions to environmental loads of particulate matter (PM) and polycyclic aromatic hydrocarbons with molecular weight ?202. By comparing III + IV concentrations or (III+IV)/pyrene or (III+IV)/benzo[a]pyrene ratios in tires and those in environmental matrices, the contributions of tire-wear emissions to PM, pyrene, and benzo[a]pyrene were estimated to be 0.68 ± 0.54%, 6.9 ± 4.8%, and 0.37 ± 0.18% in roadside PM and 0.83 ± 0.21%, 0.88 ± 0.52%, and 0.08 ± 0.06% in rooftop PM. PMID:22008013

Kumata, Hidetoshi; Mori, Mika; Takahashi, Sho; Takamiya, Shohei; Tsuzuki, Mikio; Uchida, Tatsuya; Fujiwara, Kitao

2011-12-01

154

Status of potential PfATP6 molecular markers for artemisinin resistance in Suriname  

PubMed Central

Background Polymorphisms within the PfATP6 gene have been indicated as potential molecular markers for artemisinin efficacy. Since 2004, the use of artemisinin combination therapy (ACT) was introduced as first-line treatment of the uncomplicated malaria cases in Suriname. The aim of this research was to determine changes in Suriname in the status of the polymorphic markers in the PfATP6 gene before and after the adoption of the ACT-regimen, particularly of the S769N mutation, which was reported to be associated with in vitro Artemether resistance in the neighboring country French Guiana. Methods The PfATP6 gene from Plasmodium falciparum parasites in Suriname was investigated in 28 samples using PCR amplification and restriction enzyme analysis, to assess and determine the prevalence of potentially interesting single nucleotide polymorphisms. The polymorphisms [L263E; A623E; S769N], which may be associated with the artemisinin resistant phenotype were characterized in parasites from three endemic regions before and after the adoption of the ACT-regimen. In addition, the status of these molecular markers was compared in paired P. falciparum isolates from patients with recurring malaria after controlled ACT. Results All the investigated samples exhibit the wild-type genotype at all three positions; L263, A623, S769. Conclusion All investigated isolates before and after the adoption of the ACT-regimen and independent of endemic region harbored the wild-type genotype for the three investigated polymorphisms. The study revealed that decreased artemisinin susceptibility could occur independent from PfATP6 mutations, challenging the assumption that artemisinin resistance is associated with these mutations in the PfATP6 gene. PMID:22966810

2012-01-01

155

Identification and confirmation of molecular markers and orange flesh color associated with major QTL for high beta-carotene content in muskmelon  

E-print Network

-carotene content, flesh color, and flesh color intensity. Bulk segregent analysis was used with RAPD markers to identify molecular markers associated with high beta-carotene content. Flesh color and flesh color intensity both had significant relationships with beta...

Napier, Alexandra Bamberger

2009-05-15

156

[Abbas et al. 2000] A. K. Abbas, A. H. Lichtman, and J. S. Pober. Cellular and Molecular Immunology. W. B. Saunders Company, 2000.  

E-print Network

Immunology. W. B. Saunders Company, 2000. [Abraham & Malaviya 1997] S. Abraham and R. Malaviya. Mast cells: Round 2. Seminars in Immunology, 12(3):277­292, 2000. [Anderson & Matzinger 2000b] C. C. Anderson and P. Matzinger. Danger: the view from the bottom of the cliff. Seminars in Immunology, 12(3):231­238, 2000

Stepney, Susan

157

Sequence-related amplified polymorphism (SRAP) markers: A potential resource for studies in plant molecular biology(1.).  

PubMed

In the past few decades, many investigations in the field of plant biology have employed selectively neutral, multilocus, dominant markers such as inter-simple sequence repeat (ISSR), random-amplified polymorphic DNA (RAPD), and amplified fragment length polymorphism (AFLP) to address hypotheses at lower taxonomic levels. More recently, sequence-related amplified polymorphism (SRAP) markers have been developed, which are used to amplify coding regions of DNA with primers targeting open reading frames. These markers have proven to be robust and highly variable, on par with AFLP, and are attained through a significantly less technically demanding process. SRAP markers have been used primarily for agronomic and horticultural purposes, developing quantitative trait loci in advanced hybrids and assessing genetic diversity of large germplasm collections. Here, we suggest that SRAP markers should be employed for research addressing hypotheses in plant systematics, biogeography, conservation, ecology, and beyond. We provide an overview of the SRAP literature to date, review descriptive statistics of SRAP markers in a subset of 171 publications, and present relevant case studies to demonstrate the applicability of SRAP markers to the diverse field of plant biology. Results of these selected works indicate that SRAP markers have the potential to enhance the current suite of molecular tools in a diversity of fields by providing an easy-to-use, highly variable marker with inherent biological significance. PMID:25202637

Robarts, Daniel W H; Wolfe, Andrea D

2014-07-01

158

Apportioning black carbon to sources using highly time-resolved ambient measurements of organic molecular markers in Pittsburgh  

Microsoft Academic Search

We present highly time-resolved measurements of organic molecular markers in downtown Pittsburgh, which are used to investigate sources contributing to atmospheric aerosols in the area. Two-hour average concentrations of condensed-phase and semivolatile organic species were measured using a Thermal Desorption Aerosol GC\\/MS (TAG). Concentrations for mobile source markers like hopanes had regular diurnal and day-of-week patterns. Pairing high time-resolved measurements

Andrew T. Lambe; Jennifer M. Logue; Nathan M. Kreisberg; Susanne V. Hering; David R. Worton; Allen H. Goldstein; Neil M. Donahue; Allen L. Robinson

2009-01-01

159

Molecular markers of anti-malarial drug resistance in Lahj Governorate, Yemen: baseline data and implications  

PubMed Central

Background This is an investigation of anti-malarial molecular markers coupled with a therapeutic efficacy test of chloroquine (CQ) against falciparum malaria in an area of unstable malaria in Lahj Governorate, Yemen. The study was aimed at assessment of therapeutic response to CQ and elucidation of baseline information on molecular markers for Plasmodium falciparum resistance against CQ and sulphadoxine/pyrimethamine (SP). Methods Between 2002 and 2003 the field test was conducted according to the standard WHO protocol to evaluate the therapeutic efficacy of CQ in 124 patients with falciparum malaria in an endemic area in Lahj Governorate in Yemen. Blood samples collected during this study were analysed for P. falciparum chloroquine resistance transporter gene (pfcrt)-76 polymorphisms, mutation pfcrt-S163R and the antifolate resistance-associated mutations dihydrofolate reductase (dhfr)-C59R and dihydropteroate synthase (dhps)-K540E. Direct DNA sequencing of the pfcrt gene from three representative field samples was carried out after DNA amplification of the 13 exons of the pfcrt gene. Results Treatment failure was detected in 61% of the 122 cases that completed the 14-day follow-up. The prevalence of mutant pfcrt T76 was 98% in 112 amplified pre-treatment samples. The presence of pfcrt T76 was poorly predictive of in vivo CQ resistance (PPV = 61.8%, 95% CI = 52.7-70.9). The prevalence of dhfr Arg-59 mutation in 99 amplified samples was 5%, while the dhps Glu-540 was not detected in any of 119 amplified samples. Sequencing the pfcrt gene confirmed that Yemeni CQ resistant P. falciparum carry the old world (Asian and African) CQ resistant haplotype CVIETSESI at positions 72,73,74,75,76,220,271, 326 and 371. Conclusion This is the first study to report baseline information on the characteristics and implications of anti-malarial drug resistance markers in Yemen. It is also the first report of the haplotype associated with CQR P. falciparum parasites from Yemen. Mutant pfcrtT76 is highly prevalent but it is a poor predictor of treatment failure in the study population. The prevalence of mutation dhfrArg59 is suggestive of emerging resistance to SP, which is currently a component of the recommended combination treatment of falciparum malaria in Yemen. More studies on these markers are recommended for surveillance of resistance in the study area. PMID:21854642

2011-01-01

160

Multi-marker Solid Tumor Panels Using Next-generation Sequencing to Direct Molecularly Targeted Therapies  

PubMed Central

In contemporary oncology practices there is an increasing emphasis on concurrent evaluation of multiple genomic alterations within the biological pathways driving tumorigenesis. At the foundation of this paradigm shift are several commercially available tumor panels using next-generation sequencing to develop a more complete molecular blueprint of the tumor. Ideally, these would be used to identify clinically actionable variants that can be matched with available molecularly targeted therapy, regardless of the tumor site or histology. Currently, there is little information available on the post-analytic processes unique to next-generation sequencing platforms used by the companies offering these tests. Additionally, evidence of clinical validity showing an association between the genetic markers curated in these tests with treatment response to approved molecularly targeted therapies is lacking across all solid-tumor types. To date, there is no published data of improved outcomes when using the commercially available tests to guide treatment decisions. The uniqueness of these tests from other genomic applications used to guide clinical treatment decisions lie in the sequencing platforms used to generate large amounts of genomic data, which have their own related issues regarding analytic and clinical validity, necessary precursors to the evaluation of clinical utility. The generation and interpretation of these data will require new evidentiary standards for establishing not only clinical utility, but also analytical and clinical validity for this emerging paradigm in oncology practice. PMID:24904755

Marrone, Michael; Filipski, Kelly K; Gillanders, Elizabeth M; Schully, Sheri D; Freedman, Andrew N

2014-01-01

161

Improving the reliability of molecular sexing of birds using a W-specific marker.  

PubMed

Molecular techniques for identifying sex of birds utilize length differences between CHD-Z and CHD-W introns, but in some cases these methods can lead to sexing errors. Here we show that an additional W-specific primer can be used in conjunction with a pre-existing sexing primer pair to dramatically improve the reliability of molecular sexing methods. We illustrate the approach with American coots (Fulica americana), a species with CHD-Z polymorphism that could not be accurately sexed using traditional methods. We developed a reverse primer GWR2 designed to sit within the intron of the W chromosome and amplify a distinctively small DNA fragment that serves as a W-specific marker. Analysis of known-sex individuals indicates that this W-specific primer provides an efficient and reliable protocol to identify the sex of F. americana. The development of such sex-specific primers will likely increase the reliability of molecular sexing methods in other birds as well. Comparisons between CHD-Z alleles of coots and common moorhens (Gallinula chloropus) revealed that CHD-Z polymorphism evolved separately in these two closely related species. We discuss the implications of repeated evolution of CHD-Z polymorphisms among birds. PMID:21586012

Shizuka, Daizaburo; Lyon, Bruce E

2008-11-01

162

IL-32 is a molecular marker of a host defense network in human tuberculosis  

PubMed Central

Tuberculosis is a leading cause of infectious disease–related death worldwide; however, only 10% of people infected with Mycobacterium tuberculosis develop disease. Factors that contribute to protection could prove to be promising targets for M. tuberculosis therapies. Analysis of peripheral blood gene expression profiles of active tuberculosis patients has identified correlates of risk for disease or pathogenesis. We sought to identify potential human candidate markers of host defense by studying gene expression profiles of macrophages, cells that, upon infection by M. tuberculosis, can mount an antimicrobial response. Weighted gene coexpression network analysis revealed an association between the cytokine interleukin-32 (IL-32) and the vitamin D antimicrobial pathway in a network of interferon-?– and IL-15–induced “defense response” genes. IL-32 induced the vitamin D–dependent antimicrobial peptides cathelicidin and DEFB4 and to generate antimicrobial activity in vitro, dependent on the presence of adequate 25-hydroxyvitamin D. In addition, the IL-15–induced defense response macrophage gene network was integrated with ranked pairwise comparisons of gene expression from five different clinical data sets of latent compared with active tuberculosis or healthy controls and a coexpression network derived from gene expression in patients with tuberculosis undergoing chemotherapy. Together, these analyses identified eight common genes, including IL-32, as molecular markers of latent tuberculosis and the IL-15–induced gene network. As maintaining M. tuberculosis in a latent state and preventing transition to active disease may represent a form of host resistance, these results identify IL-32 as one functional marker and potential correlate of protection against active tuberculosis. PMID:25143364

Montoya, Dennis; Inkeles, Megan S.; Liu, Phillip T.; Realegeno, Susan; Teles, Rosane M. B.; Vaidya, Poorva; Munoz, Marcos A.; Schenk, Mirjam; Swindell, William R.; Chun, Rene; Zavala, Kathryn; Hewison, Martin; Adams, John S.; Horvath, Steve; Pellegrini, Matteo; Bloom, Barry R.; Modlin, Robert L.

2014-01-01

163

Identification and characterization of high-molecular-weight glutenin genes in Polish triticale cultivars by PCR-based DNA markers  

Microsoft Academic Search

Molecular markers were used to identify the allele\\/gene composition of complex lociGlu-A1 andGlu-B1 of high-molecular-weight (HMW) glutenin subunits in triticale cultivars. Forty-six Polish cultivars of both winter and spring\\u000a triticale were analysed with 7 PCR-based markers. Amplified DNA fragments of HMW gluteninGlu-1 genes were separated by agarose slab-gel electrophoresis. Differences between all 3 alleles at the locusGlu-A1 [Glu-A1a (encoding Ax1),1b

Boles?aw P. Salmanowicz; Monika Dylewicz

2007-01-01

164

Biological (molecular and cellular) markers of toxicity. Final report, September 15, 1988--September 14, 1991  

SciTech Connect

Several molecular and cellular markers of genotoxicity were adapted for measurement in the Medaka (Oryzias latipes), and were used to describe the effects of treatment of the organism with diethylnitrosamine (DEN). NO{sup 6}-ethyl guanine adducts were detected, and a slight statistically significant, increase in DNA strand breaks was observed. These results are consistent with the hypothesis that prolonged exposure to high levels of DEN induced alkyltransferase activity which enzymatically removes any O{sup 6}-ethyl guanine adducts but does not result in strand breaks or hypomethylation of the DNA such as might be expected from excision repair of chemically modified DNA. Following a five week continuous DEN exposure with 100 percent renewal of DEN-water every third day, the F values (DNA double strandedness) increased considerably and to similar extent in fish exposed to 25, 50, and 100 ppM DEN. This has been observed also in medaka exposed to BaP.

Shugart, L.R.; D`Surney, S.J.; Gettys-Hull, C.; Greeley, M.S. Jr.

1991-12-15

165

A multi-marker molecular signature approach for treatment-specific subgroup identification with survival outcomes.  

PubMed

Delivering on the promise of personalized medicine has become a focus of the pharmaceutical industry as the era of the blockbuster drug is fading. Central to realizing this promise is the need for improved analytical strategies for effectively integrating information across various biological assays (for example, copy number variation and targeted protein expression) toward identification of a treatment-specific subgroup-identifying the right patients. We propose a novel combination of elastic net followed by a maximal ?(2) and semiparametric bootstrap. The combined approaches are presented in a two-stage strategy that estimates patient-specific multi-marker molecular signatures (MMMS) to identify and directly test for a biomarker-driven subgroup with enhanced treatment effect. This flexible strategy provides for incorporation of business-specific needs, such as confining the search space to a subgroup size that is commercially viable, ultimately resulting in actionable information for use in empirically based decision making. PMID:24637498

Li, L; Guennel, T; Marshall, S; Cheung, L W-K

2014-10-01

166

Identification of the sources of primary organic aerosols at urban schools: a molecular marker approach.  

PubMed

Children are particularly susceptible to air pollution and schools are examples of urban microenvironments that can account for a large portion of children's exposure to airborne particles. Thus this paper aimed to determine the sources of primary airborne particles that children are exposed to at school by analyzing selected organic molecular markers at 11 urban schools in Brisbane, Australia. Positive matrix factorization analysis identified four sources at the schools: vehicle emissions, biomass burning, meat cooking and plant wax emissions accounting for 45%, 29%, 16% and 7%, of the organic carbon respectively. Biomass burning peaked in winter due to prescribed burning of bushland around Brisbane. Overall, the results indicated that both local (traffic) and regional (biomass burning) sources of primary organic aerosols influence the levels of ambient particles that children are exposed at the schools. These results have implications for potential control strategies for mitigating exposure at schools. PMID:24842381

Crilley, Leigh R; Qadir, Raeed M; Ayoko, Godwin A; Schnelle-Kreis, Jürgen; Abbaszade, Gülcin; Orasche, Jürgen; Zimmermann, Ralf; Morawska, Lidia

2014-08-01

167

Molecular marker analysis as a guide to the sources of fine organic aerosols  

SciTech Connect

The molecular composition of fine particulate (D{sub p} {ge} 2 {mu}m) organic aerosol emissions from the most important sources in the Los Angeles area has been determined. Likewise, ambient concentration patterns for more than 80 single organic compounds have been measured at four urban sites (West Los Angeles, Downtown Los Angeles, Pasadena, and Rubidoux) and at one remote offshore site (San Nicolas Island). It has been found that cholesterol serves as a marker compound for emissions from charbroilers and other meat cooking operations. Vehicular exhaust being emitted from diesel and gasoline powered engines can be traced in the Los Angeles atmosphere using fossil petroleum marker compounds such as steranes and pentacyclic triterpanes (e.g., hopanes). Biogenic fine particle emission sources such as plant fragments abraded from leaf surfaces by wind and weather can be traced in the urban atmosphere. Using distinct and specific source organic tracers or assemblages of organic compounds characteristic for the sources considered it is possible to estimate the influence of different source types at any urban site where atmospheric data are available.

Rogge, W.F.; Cass, G.R. [California Inst. of Tech., Pasadena, CA (United States); Hildemann, L.M. [Stanford Univ., CA (United States). Dept. of Civil Engineering; Mazurek, M.A. [Brookhaven National Lab., Upton, NY (United States); Simoneit, B.R.T. [College of Oceanography, Oregon State Univ., Corvallis, OR (United States) Environmental Geochemistry Group

1992-07-01

168

Altered Expression of Retinal Molecular Markers in the Canine RPE65 Model of Leber Congenital Amaurosis  

PubMed Central

Purpose. Leber congenital amaurosis (LCA) is a group of childhood-onset retinal diseases characterized by severe visual impairment or blindness. One form is caused by mutations in the RPE65 gene, which encodes the retinal pigment epithelium (RPE) isomerase. In this study, the retinal structure and expression of molecular markers for different retinal cell types were characterized, and differences between control and RPE65 mutant dogs during the temporal evolution of the disease were analyzed. Methods. Retinas from normal and mutant dogs of different ages were examined by immunofluorescence with a panel of 16 different antibodies. Results. Cones and rods were preserved in the mutant retinas, and the number of cones was normal. However, there was altered expression of cone arrestin and delocalization of rod opsin. The ON bipolar cells showed sprouting of the dendritic arbors toward the outer nuclear layer (ONL) and retraction of their axons in the inner nuclear layer (INL). A decreased expression of GABA, and an increased expression of intermediate filament glial markers was also found in the mutant retinas. These changes were more evident in the adult than the young mutant retinas. Conclusions. The structure of the retina is well preserved in the mutant retina, but several molecular changes take place in photoreceptors and in bipolar and amacrine cells. Some of these changes are structural, whereas others reflect a change in localization of the examined proteins. This study provides new information that can be applied to the interpretation of outcomes of retinal gene therapy in animal models and humans. PMID:20671290

Hernandez, Maria; Pearce-Kelling, Susan E.; Rodriguez, F. David; Aguirre, Gustavo D.; Vecino, Elena

2010-01-01

169

Molecular cloning, expression, bioinformatics analysis, and bioactivity of TNFSF13 (APRIL) in the South African clawed frog (Xenopus laevi): a new model to study immunological diseases.  

PubMed

TNFSF13 is one of the tumor necrosis factor (TNF) superfamily members that plays important roles in immune homeostasis and proliferation or apoptosis of certain tumor cell lines. This report describes the development of Xenopus laevis TNFSF13 as a model to study its important role in relation to immunological diseases. In brief, TNFSF13 from Xenopus laevis (designated XlTNFSF13) was first amplified by RT-PCR and rapid amplification of cDNA end (RACE) techniques. Bioinformatics analyses revealed the gene structure, three-dimensional structure, and evolutionary relationships. Real-time quantitative PCR (QPCR) analysis identified the tissue distribution of XlTNFSF13 in the major visceral organs. The recombinant plasmid SUMO-XsTNFSF13 was expressed in E. coli Rosseta (DE3). Subsequently, the recombinant protein purified through Ni-NTA affinity chromatography was analyzed by SDS-PAGE and confirmed by Western blot analysis. Laser scanning confocal microscopy analysis revealed the binding activity of pSUMO-XsTNFSF13 to the surface of B cells. WST-8 assays further indicated that purified XsTNFSF13 could cause the survival/proliferation of B cells. In conclusion, we underscore that as a model organism for human disease, Xenopus laevis has been widely used in molecular biology research. Yet while TNFSF13 research in mammalian, fish (e.g., zebrafish), mouse, and human is widely available, studies in the amphibian species are limited. The latter area of OMICS and integrative biology scholarship is directly informed with the present study, with a view to implications for the future study of human immunological diseases. PMID:23829578

Liu, Xia; Ji, Xue-mei; Du, Xi-ning; Zong, Xi-cui; Liang, Ding-fang; Ma, Li; Wu, Hai-tao; Zhang, Shuang-quan

2013-07-01

170

Use of Human Bronchial Epithelial Cells (BEAS-2B) to Study Immunological Markers Resulting From Exposure to PM2.5 Organic Extract from Puerto Rico  

PubMed Central

Fine particulate air pollutants, mainly their organic fraction, have been demonstrated to be associated with cardiovascular and respiratory health problems. Puerto Rico has been reported to have the highest prevalence of pulmonary diseases (e.g. asthma) in the US. The aim of this study was to assess, for the first time, the immunological response of human bronchial epithelial cells (BEAS-2B) to organic extracts isolated from air-borne particulate matter (PM2.5) in Puerto Rico. Organic extracts from PM2.5 collected throughout an 8-month period (2000-2001) were pooled (composite) in order to perform chemical analysis and biological activity testing. BEAS-2B cells were exposed to PM2.5 organic extract to assess cytotoxicity, levels of cytokines and relative gene expression of MHC-II, hPXR and CYP3A5. Our findings show that organic PM2.5 consist of toxic as well as bioactive components that can regulate the secretion of cytokines in BEAS-2B, which could modulate inflammatory response in the lung. Trace element analyses confirmed the presence of metals in organic extracts highlighting the relative high abundance of Cu and Zn in polar organic extracts. Polar organic extracts exhibited dose-dependant toxicity and were found to significantly induce the release of interleukin 6 (IL-6), IL-1? and IL-7 while significantly inhibiting the secretion of IL-8, G-CSF and MCP-1. Moreover, MHC-II transcriptional activity was up-regulated after 24h of exposure, whereas PXR and CYP3A5 were down-regulated. This research provides a new insight into the effects of PM2.5 organic fractions on specific effectors and their possible role in the development of respiratory inflammatory diseases in Puerto Rico. PMID:20026096

Fuentes-Mattei, Enrique; Rivera, Evasomary; Gioda, Adriana; Sanchez-Rivera, Diana; Roman-Velazquez, Felix R.; Jimenez-Velez, Braulio D.

2010-01-01

171

Diagnosis of Cerebral Toxoplasmosis in AIDS Patients in Brazil: Importance of Molecular and Immunological Methods Using Peripheral Blood Samples  

PubMed Central

Cerebral toxoplasmosis is the most common cerebral focal lesion in AIDS and still accounts for high morbidity and mortality in Brazil. Its occurrence is more frequent in patients with low CD4+ T-cell counts. It is directly related to the prevalence of anti-Toxoplasma gondii antibodies in the population. Therefore, it is important to evaluate sensitive, less invasive, and rapid diagnostic tests. We evaluated the value of PCR using peripheral blood samples on the diagnosis of cerebral toxoplasmosis and whether its association with immunological assays can contribute to a timely diagnosis. We prospectively analyzed blood samples from 192 AIDS patients divided into two groups. The first group was composed of samples from 64 patients with cerebral toxoplasmosis diagnosed by clinical and radiological features. The second group was composed of samples from 128 patients with other opportunistic diseases. Blood collection from patients with cerebral toxoplasmosis was done before or on the third day of anti-toxoplasma therapy. PCR for T. gondii, indirect immunofluorescence, enzyme-linked immunosorbent assay, and an avidity test for toxoplasmosis were performed on all samples. The PCR sensitivity and specificity for diagnosis of cerebral toxoplasmosis in blood were 80% and 98%, respectively. Patients with cerebral toxoplasmosis (89%) presented higher titers of anti-T. gondii IgG antibodies than patients with other diseases (57%) (P < 0.001). These findings suggest the clinical value of the use of both PCR and high titers of anti-T. gondii IgG antibodies for the diagnosis of cerebral toxoplasmosis. This strategy may prevent more invasive approaches. PMID:16207959

Colombo, Fabio A.; Vidal, Jose E.; Oliveira, Augusto C. Penalva de; Hernandez, Adrian V.; Bonasser-Filho, Francisco; Nogueira, Roberta S.; Focaccia, Roberto; Pereira-Chioccola, Vera Lucia

2005-01-01

172

Molecular and immunological characterization of ?'-component (Onc k 5), a major IgE-binding protein in chum salmon roe.  

PubMed

Salmon roe has a high allergic potency and often causes anaphylaxis in Japan. The major allergic protein of salmon roe is ?'-component, which is a 35kDa vitellogenin fragment consisting of two subunits. To elucidate structural information and immunological characteristics, ?'-component and the subunit components were purified from chum salmon (Onchorhincus keta) roe and vitellogenin-encoding mRNA was used to prepare ?'-component subunit-encoding cDNA. This was PCR-amplified, cloned and sequenced and the deduced amino acid sequence compared with partial sequences of ?'-component obtained by peptide mapping. The recombinant ?'-component subunit was produced by bacterial expression in Escherichia coli and its IgE-binding ability was measured by ELISA using the sera of a patient allergic to salmon roe. This was then compared with that of the native ?'-component with and without carboxymethylation. Following successful cloning of the cDNA encoding the ?'-component subunit, 170 amino acid residues were deduced and matched with the amino acid sequences of 121 and 88 residues in the 16kDa and 18kDa subunits, respectively. The sequences of both ?'-component subunits were almost identical, and the predicted secondary structure of the ?'-component showed a high content of ?-pleated sheets and no ?-helices. There was no difference in IgE-binding ability between the native and recombinant ?'-component subunits at the same protein concentration, regardless of carboxymethylation. In conclusion, ?'-component is a homodimer protein composed of two isoform subunits having the same level of IgE-binding ability and, therefore, allergenic identity. PMID:24215907

Shimizu, Yutaka; Kishimura, Hideki; Kanno, Gaku; Nakamura, Atsushi; Adachi, Reiko; Akiyama, Hiroshi; Watanabe, Kazuhiko; Hara, Akihiko; Ebisawa, Motohiro; Saeki, Hiroki

2014-03-01

173

Isolation of molecular markers for salt stress responses in Arabidopsis thaliana.  

PubMed

Characterization of many osmotic stress-induced genes has greatly contributed to the understanding of the physiological responses of plant cells to osmotic stress at the molecular level. In this study we constructed a subtraction library and generated 15 salt stress-inducible ESTs from this library to use as molecular markers that reflect the cellular responses to salt stress responses in Arabidopsis. The sequence analysis showed that 5 salt stress-inducible ESTs were identical to previously identified genes in Arabidopsis, 6 cDNAs were homologous to known genes found in plants as well as yeast, and 4 cDNAs were new genes. To confirm that expression of these clones are induced by salt stress, we carried out Northern blot analysis. When we examined for 15 cDNA clones, they were indeed induced by NaCl treatment. The induction level was variable among these genes ranging from approximately 2-fold to more than 50-fold. Also, Northern blot analysis revealed that these genes can be divided into three different induction patterns: early induction, late induction, and continuous induction. PMID:9339905

Pih, K T; Jang, H J; Kang, S G; Piao, H L; Hwang, I

1997-08-31

174

USING CARBOHYDRATES AS MOLECULAR MARKERS TO DETERMINE THE CONTRIBUTION OF AGRICULTURAL SOIL TO AMBIENT FINE AND COURSE PM  

EPA Science Inventory

Project research optimized the quantification technique for carbohydrates that also allows quantification of other non-polar molecular markers based on using an isotopically labeled internal standard (D-glucose-1,2,3,4,5,6,6-d7) to monitor extraction efficiency, extraction usi...

175

Use of 16S rRNA and rpoB Genes as Molecular Markers for Microbial Ecology Studies  

Microsoft Academic Search

Several characteristics of the 16S rRNA gene, such as its essential function, ubiquity, and evolutionary properties, have allowed it to become the most commonly used molecular marker in microbial ecology. However, one fact that has been overlooked is that multiple copies of this gene are often present in a given bacterium. These intragenomic copies can differ in sequence, leading to

Rebecca J. Case; Yan Boucher; Ingela Dahllof; Carola Holmstrom; W. Ford Doolittle; Staffan Kjelleberg

2007-01-01

176

Transmission of the apomictic mode of reproduction in Pennisetum : co-inheritance of the trait and molecular markers  

Microsoft Academic Search

Apomixis, asexual reproduction through seed, is an obligate mode of reproduction in several species from the genus Pennisetum. Transfer of apomixis to sexual, cultivated pearl millet (P. glaucum) from a wild species P. squamulatum has resulted in an obligate apomictic backcross line with a low, but unknown number, of chromosomes from the wild species. Molecular markers (restriction fragment length polymorphisms

P. Ozias-Akins; E. L. Lubbers; W. W. Hanna; J. W. McNay

1993-01-01

177

Identification of Genetic Factors Contributing to Heterosis in a Hybrid From Two Elite Maize Inbred Lines Using Molecular Markers  

Microsoft Academic Search

The use of molecular markers to identify quantitative trait loci (QTLs) affecting agriculturally important traits has become a key approach in plant genetics-both for understanding the genetic basis of these traits and to help design novel plant improvement programs. In the study reported here, we mapped QTLs (and evaluated their phenotypic effects) associated with seven major traits (including grain yield)

Charles W. Stuber; Stephen E. Lincoln; David W. Wolff; Tim Helentjarisn; Eric S. Lander

178

Congruent Climate?Related Genecological Responses from Molecular Markers and Quantitative Traits for Western White Pine (Pinus monticola)  

Microsoft Academic Search

Analyses of molecular and quantitative genetic data demonstrate the existence of congruent climate?related patterns in western white pine (Pinus monticola). Two independent studies allowed comparisons of amplified fragment length polymorphism (AFLP) markers with quantitative variation in adaptive traits. Principal component analyses were conducted on seedling traits in common gardens collected from 58 sites; principal coordinate analyses were conducted on AFLP

2009-01-01

179

The development of 7E chromosome-specific molecular markers for Thinopyrum elongatum based on SLAF-seq technology.  

PubMed

Thinopyrum elongatum is an important relative of wheat, it is favored by many researchers for the disease resistant genes that exist in its E genome. Some studies have showed that the 7E chromosome of Th. elongatum contains resistance genes related to Fusarium head blight and wheat rust. Therefore, developing 7E chromosome-specific molecular markers linked to resistance genes will provide an important tool for exploring and using the resistant genes of Th. elongatum. In addition, it would greatly contribute in the effort to cultivate disease-resistant wheat varieties. Featured in high throughput, high-accuracy and low-cost, SLAF-seq technology has been widely used in molecular breeding, system evolution, and germplasm resource detection. Based on SLAF-seq, 518 specific fragments on the 7E chromosome of Th. elongatum were successfully amplified. A total of 135 primers were designed according to 135 randomly selected fragments, and 89 specific molecular markers of Th. elongatum were developed, with efficiencies up to 65.9%. These markers were all detected in a variety of materials, and they are all proved to be specific and stable. These markers can be used not only for detecting the 7E chromosome of Th. elongatum but also for providing an important theoretical and practical basis for wheat breeding by marker-assisted selection (MAS). This paper reports the first application of SLAF-seq technology with a high success rate in developing specific molecular markers for Th. elongatum, providing a strong case for the application of this new technology. PMID:23762296

Chen, Shiqiang; Huang, Zefeng; Dai, Yi; Qin, Shuwen; Gao, Yingying; Zhang, Lulu; Gao, Yong; Chen, Jianmin

2013-01-01

180

Microbiology & Immunology DEPARTMENT OF  

E-print Network

Microbiology & Immunology DEPARTMENT OF #12;The Department of Microbiology & Immunology on infectious disease and immunology. The Department publishes M&I, its newsletter, once a year. Highlighting & Immunology Columbia University 701 West 168th St., NY, NY 10032 (212) 305-3647 oj2@columbia.edu #12

Qian, Ning

181

Liver Immunology  

PubMed Central

The liver is the largest organ in the body and is generally regarded by non-immunologists as not having lymphoid function. However, such is far from accurate. This review highlights the importance of the liver as a lymphoid organ. Firstly, we discuss experimental data surrounding the role of liver as a lymphoid organ. The liver facilitates a tolerance rather than immunoreactivity, which protects the host from antigenic overload of dietary components and drugs derived from the gut and is also instrumental to fetal immune tolerance. Loss of liver tolerance leads to autoaggressive phenomena which if are not controlled by regulatory lymphoid populations may lead to the induction of autoimmune liver diseases. Liver-related lymphoid subpopulations also act as critical antigen-presenting cells. The study of the immunological properties of liver and delineation of the microenvironment of the intrahepatic milieu in normal and diseased livers provides a platform to understand the hierarchy of a series of detrimental events which lead to immune-mediated destruction of the liver and the rejection of liver allografts. The majority of emphasis within this review will be on the normal mononuclear cell composition of the liver. However, within this context, we will discus select, but not all, immune mediated liver disease and attempt to place these data in the context of human autoimmunity. PMID:23720323

Bogdanos, Dimitrios P.; Gao, Bin; Gershwin, M. Eric

2014-01-01

182

Molecular analysis of East Anatolian traditional plum and cherry accessions using SSR markers.  

PubMed

We conducted SSR analyses of 59 accessions, including 29 traditional plum (Prunus domestica), 24 sweet cherry (Prunus avium), and 1 sour cherry (Prunus cerasus) selected from East Anatolian gene sources and 3 plum and 2 cherry reference accessions for molecular characterization and investigation of genetic relationships. Eight SSR loci [1 developed from the apricot (UDAp-404), 4 from the peach (UDP96-010, UDP96-001, UDP96-019, Pchgms1) and 3 from the cherry (UCD-CH13, UCD-CH17, UCD-CH31) genome] for plum accessions and 9 SSR loci [5 developed from the cherry (PS12A02, UCD-CH13, UCD-CH17, UCD-CH31, UCD-CH21), 3 from the peach (Pchgms1, UDP96-001, UDP96-005) and 1 from the plum (CPSCT010) genome] for cherry accessions were used for genetic identification. A total of 66 and 65 alleles were obtained in the genetic analyses of 31 plum and 28 cherry accessions, respectively. The number of alleles revealed by SSR analysis ranged from 4 to 14 alleles per locus, with a mean value of 8.25 in plum accessions, and from 5 to 10 alleles per locus with a mean value of 7.2 in cherry accessions. Only one case of synonym was identified among the cherry accessions, while no case of synonym was observed among the plum accessions. Genomic SSR markers used in discrimination of plum and cherry accessions showed high cross-species transferability in the Prunus genus. Because of their appreciable polymorphism and cross species transferability, the SSR markers that we evaluated in this study will be useful for studies involving fingerprinting of cherry and plum cultivars. PMID:24301792

Öz, M H; Vurgun, H; Bakir, M; Büyük, ?; Yüksel, C; Ünlü, H M; Çukadar, K; Karado?an, B; Köse, Ö; Ergül, A

2013-01-01

183

Genetic rearrangements of six wheat-agropyron cristatum 6P addition lines revealed by molecular markers.  

PubMed

Agropyron cristatum (L.) Gaertn. (2n?=?4x?=?28, PPPP) not only is cultivated as pasture fodder but also could provide many desirable genes for wheat improvement. It is critical to obtain common wheat-A. cristatum alien disomic addition lines to locate the desired genes on the P genome chromosomes. Comparative analysis of the homoeologous relationships between the P genome chromosome and wheat genome chromosomes is a key step in transferring different desirable genes into common wheat and producing the desired alien translocation line while compensating for the loss of wheat chromatin. In this study, six common wheat-A. cristatum disomic addition lines were produced and analyzed by phenotypic examination, genomic in situ hybridization (GISH), SSR markers from the ABD genomes and STS markers from the P genome. Comparative maps, six in total, were generated and demonstrated that all six addition lines belonged to homoeologous group 6. However, chromosome 6P had undergone obvious rearrangements in different addition lines compared with the wheat chromosome, indicating that to obtain a genetic compensating alien translocation line, one should recombine alien chromosomal regions with homoeologous wheat chromosomes. Indeed, these addition lines were classified into four types based on the comparative mapping: 6PI, 6PII, 6PIII, and 6PIV. The different types of chromosome 6P possessed different desirable genes. For example, the 6PI type, containing three addition lines, carried genes conferring high numbers of kernels per spike and resistance to powdery mildew, important traits for wheat improvement. These results may prove valuable for promoting the development of conventional chromosome engineering techniques toward molecular chromosome engineering. PMID:24595330

Han, Haiming; Bai, Li; Su, Junji; Zhang, Jinpeng; Song, Liqiang; Gao, Ainong; Yang, Xinming; Li, Xiuquan; Liu, Weihua; Li, Lihui

2014-01-01

184

Genetic Rearrangements of Six Wheat-Agropyron cristatum 6P Addition Lines Revealed by Molecular Markers  

PubMed Central

Agropyron cristatum (L.) Gaertn. (2n?=?4x?=?28, PPPP) not only is cultivated as pasture fodder but also could provide many desirable genes for wheat improvement. It is critical to obtain common wheat–A. cristatum alien disomic addition lines to locate the desired genes on the P genome chromosomes. Comparative analysis of the homoeologous relationships between the P genome chromosome and wheat genome chromosomes is a key step in transferring different desirable genes into common wheat and producing the desired alien translocation line while compensating for the loss of wheat chromatin. In this study, six common wheat–A. cristatum disomic addition lines were produced and analyzed by phenotypic examination, genomic in situ hybridization (GISH), SSR markers from the ABD genomes and STS markers from the P genome. Comparative maps, six in total, were generated and demonstrated that all six addition lines belonged to homoeologous group 6. However, chromosome 6P had undergone obvious rearrangements in different addition lines compared with the wheat chromosome, indicating that to obtain a genetic compensating alien translocation line, one should recombine alien chromosomal regions with homoeologous wheat chromosomes. Indeed, these addition lines were classified into four types based on the comparative mapping: 6PI, 6PII, 6PIII, and 6PIV. The different types of chromosome 6P possessed different desirable genes. For example, the 6PI type, containing three addition lines, carried genes conferring high numbers of kernels per spike and resistance to powdery mildew, important traits for wheat improvement. These results may prove valuable for promoting the development of conventional chromosome engineering techniques toward molecular chromosome engineering. PMID:24595330

Su, Junji; Zhang, Jinpeng; Song, Liqiang; Gao, Ainong; Yang, Xinming; Li, Xiuquan; Liu, Weihua; Li, Lihui

2014-01-01

185

Obtaining 5S rDNA molecular markers for native and invasive Cichla populations (Perciformes – Cichlidae), in Brazil  

E-print Network

ABSTRACT. The 5S rDNA gene is informative and has high conservation rates along the eukaryotic genome, having unique hereditary characteristics. Molecular studies with the 5S rDNA gene have been carried out with several groups, including some species of fish, aiming at solving phylogenetic relationship problems, ancestral patterns and genetic diversity among groups in natural populations. Species of the Cichla genus, introduced in the upper Paraná river basin, present some genetic polymorphisms detected by RAPD and SPAR analyses. These species have been intercrossing and forming viable hybrids, with greater genetic variability. The objective of this work was to standardize the amplification methodology for the non-transcribed regions of 5S rDNA multigenic family of Cichla, and to obtain specific markers for parent species that could also be identified in the hybrids. Sixty-five specimens of Cichla collected from the upper Paraná river and Amazon basins were analyzed. Although molecular markers that could be useful in the identification of hybrids were not obtained, genetic molecular 5S rDNA species-specific markers for Cichla temensis that can be employed to identify of this species, as well population markers that can be useful in population genetic variability studies, were obtained.

Viviane Fátima De Oliveira; Ra Valéria De Oliveira; Alberto José Prioli; Sônia Maria; Alves Pinto Prioli

186

Superior sensitivity of novel molecular imaging probe: simultaneously targeting two types of endothelial injury markers  

PubMed Central

The need remains great for early diagnosis of diseases. The special structure of the eye provides a unique opportunity for noninvasive light-based imaging of fundus vasculature. To detect endothelial injury at the early and reversible stage of adhesion molecule up-regulation, we generated novel imaging agents that target two distinct types of endothelial molecules, a mediator of rolling, P-selectin, and one that mediates firm adhesion, ICAM-1. Interactions of these double-conjugated fluorescent microspheres (MSs) in retinal or choroidal microvasculature were visualized in live animals by scanning laser ophthalmoscopy. The new imaging agents showed significantly higher sensitivity for detection of endothelial injury than singly conjugated MSs (rPSGL-1- or ?-ICAM-1-conjugated), both in terms of rolling (P<0.01) and firm adhesion (P<0.01). The rolling flux of ?-ICAM-1-conjugated MSs did not differ in EIU animals, whereas double-conjugated MSs showed significantly higher rolling flux (P<0.01), revealing that ICAM-1 in vivo supports rolling, once MS interaction with the endothelium is initiated. Double-conjugated MSs specifically detected firmly adhering leukocytes (P<0.01), allowing in vivo quantification of immune response. Antiinflammatory treatment with dexamethasone led to reduced leukocyte accumulation (P<0.01) as well as MS interaction (P<0.01), which suggests that treatment success and resolution of inflammation is quantitatively reflected with this molecular imaging approach. This work introduces novel imaging agents for noninvasive detection of endothelial injury in vivo. Our approach may be developed further to diagnose human disease at a much earlier stage than currently possible.—Sun, D., Nakao, S., Xie, F., Zandi, S., Schering, A., Hafezi-Moghadam, A. Superior sensitivity of novel molecular imaging probe: simultaneously targeting two types of endothelial injury markers. PMID:20103715

Sun, Dawei; Nakao, Shintaro; Xie, Fang; Zandi, Souska; Schering, Alexander; Hafezi-Moghadam, Ali

2010-01-01

187

Glutamine synthetase sequence evolution in the mycobacteria and their use as molecular markers for Actinobacteria speciation  

PubMed Central

Background Although the gene encoding for glutamine synthetase (glnA) is essential in several organisms, multiple glnA copies have been identified in bacterial genomes such as those of the phylum Actinobacteria, notably the mycobacterial species. Intriguingly, previous reports have shown that only one copy (glnA1) is essential for growth in M. tuberculosis, while the other copies (glnA2, glnA3 and glnA4) are not. Results In this report it is shown that the glnA1 and glnA2 encoded glutamine synthetase sequences were inherited from an Actinobacteria ancestor, while the glnA4 and glnA3 encoded GS sequences were sequentially acquired during Actinobacteria speciation. The glutamine synthetase sequences encoded by glnA4 and glnA3 are undergoing reductive evolution in the mycobacteria, whilst those encoded by glnA1 and glnA2 are more conserved. Conclusion Different selective pressures by the ecological niche that the organisms occupy may influence the sequence evolution of glnA1 and glnA2 and thereby affecting phylogenies based on the protein sequences they encode. The findings in this report may impact the use of similar sequences as molecular markers, as well as shed some light on the evolution of glutamine synthetase in the mycobacteria. PMID:19245690

Hayward, Don; van Helden, Paul D; Wiid, Ian JF

2009-01-01

188

Tumor Heterogeneity: Mechanisms and Bases for a Reliable Application of Molecular Marker Design  

PubMed Central

Tumor heterogeneity is a confusing finding in the assessment of neoplasms, potentially resulting in inaccurate diagnostic, prognostic and predictive tests. This tumor heterogeneity is not always a random and unpredictable phenomenon, whose knowledge helps designing better tests. The biologic reasons for this intratumoral heterogeneity would then be important to understand both the natural history of neoplasms and the selection of test samples for reliable analysis. The main factors contributing to intratumoral heterogeneity inducing gene abnormalities or modifying its expression include: the gradient ischemic level within neoplasms, the action of tumor microenvironment (bidirectional interaction between tumor cells and stroma), mechanisms of intercellular transference of genetic information (exosomes), and differential mechanisms of sequence-independent modifications of genetic material and proteins. The intratumoral heterogeneity is at the origin of tumor progression and it is also the byproduct of the selection process during progression. Any analysis of heterogeneity mechanisms must be integrated within the process of segregation of genetic changes in tumor cells during the clonal expansion and progression of neoplasms. The evaluation of these mechanisms must also consider the redundancy and pleiotropism of molecular pathways, for which appropriate surrogate markers would support the presence or not of heterogeneous genetics and the main mechanisms responsible. This knowledge would constitute a solid scientific background for future therapeutic planning. PMID:22408433

Diaz-Cano, Salvador J.

2012-01-01

189

Genetic Introgression and Species Boundary of Two Geographically Overlapping Pine Species Revealed by Molecular Markers  

PubMed Central

Gene introgression and hybrid barriers have long been a major focus of studies of geographically overlapping species. Two pine species, Pinus massoniana and P. hwangshanensis, are frequently observed growing adjacent to each other, where they overlap in a narrow hybrid zone. As a consequence, these species constitute an ideal system for studying genetic introgression and reproductive barriers between naturally hybridizing, adjacently distributed species. In this study, we sampled 270 pine trees along an elevation gradient in Anhui Province, China and analyzed these samples using EST-SSR markers. The molecular data revealed that direct gene flow between the two species was fairly low, and that the majority of gene introgression was intermediated by backcrossing. On the basis of empirical observation, the on-site distribution of pines was divided into a P. massoniana zone, a hybrid zone, and a P. hwangshanensis zone. STRUCTURE analysis revealed the existence of a distinct species boundary between the two pine species. The genetic boundary of the hybrid zone, on the other hand, was indistinct owing to intensive backcrossing with parental species. Compared with P. massoniana, P. hwangshanensis was found to backcross with the hybrids more intensively, consistent with the observation that morphological and anatomical characteristics of trees in the contact zone were biased towards P. hwangshanensis. The introgression ability of amplified alleles varied across species, with some being completely blocked from interspecific introgression. Our study has provided a living example to help explain the persistence of adjacently distributed species coexisting with their interfertile hybrids. PMID:24977711

Dai, Xiaogang; Xu, Jin; Li, Shuxian; Yin, Tongming

2014-01-01

190

Molecular marker analysis of hypoploid regenerants from cultures of barley x Canada wild rye.  

PubMed

Canada wild rye (CWR, Elymus canadensis L., 2n = 4x = 28) is a potential source of genes for disease resistance and environmental tolerance in barley (Hordeum vulgare L., 2n = 2x = 14). Tissue cultures were initiated from immature inflorescences of CWR x 'Betzes' barley hybrids to promote CWR introgression into barley through possible tissue culture induced chromosome breakage and exchange. Among the plants regenerated, some were missing one (2n = 20) or part of one (2n = 20 + telo) chromosome. The objective of this study was to identify the missing chromosome or chromosome arm in these regenerants through the analysis of molecular (RFLP) markers that previously had been mapped in barley. Forty-six hypoploid regenerants that traced to 30 separate explants obtained from 10 interspecific hybrid plants were evaluated. DNA was digested with the restriction enzyme HindIII, Southern blotted, and probed with 39 genomic and cDNA barley clones that identified sequences polymorphic between barley and CWR. Eight of these probes identified band loss patterns that separated the regenerants into two groups. One group, all with barley cytoplasm, were missing a CWR chromosome homoeologous to barley chromosome 3; a second group, all with CWR cytoplasm, were missing a CWR chromosome homoelogous to barley chromosome 7. These results indicated that chromosome elimination in culture was not random. The two cytoplasm groups were further differentiated by probes that identified band shifts. These band shifts were caused by differences in DNA methylation. Key words : Hordeum vulgare, aneuploidy, Elymus canadensis, tissue culture. PMID:18469900

Dahleen, L S

1996-04-01

191

Current Status of Molecular Markers for Early Detection of Sporadic Pancreatic Cancer  

PubMed Central

Pancreatic cancer (PC) is a highly lethal malignancy with near 100% mortality. This is in part due to the fact that most patients present with metastatic or locally advanced disease at the time of diagnosis. Significantly, in nearly 95% of PC patients there is neither an associated family history of PC nor of diseases known to be associated with an increased risk of PC. These groups of patients who comprise the bulk of PC cases are termed as “sporadic PC” in contrast to the familial PC cases that comprise only about 5% of all PCs. Given the insidious onset of the malignancy and its extreme resistance to chemo and radiotherapy, an abundance of research in recent years has focused on identifying biomarkers for the early detection of PC, specifically aiming at the sporadic PC cohort. However, while several studies have established that asymptomatic individuals with a positive family history of PC and those with certain heritable syndromes are candidates for PC screening, the role of screening in identifying sporadic PC is still an unsettled question. The present review attempts to assess this critical question by investigating the recent advances made in molecular markers with potential use in the early diagnosis of sporadic PC- the largest cohort of PC cases worldwide. It also outlines a novel yet simple risk-factor based stratification system that could be potentially employed by clinicians to identify those individuals who at an elevated-risk for the development of sporadic PC and therefore candidates for screening. PMID:20888394

Chakraborty, Subhankar; Baine, Michael J.; Sasson, Aaron R.; Batra, Surinder K.

2010-01-01

192

Molecular markers and imaging tools to identify malignant potential in Barrett's esophagus.  

PubMed

Due to its rapidly rising incidence and high mortality, esophageal adenocarcinoma is a major public health concern, particularly in Western countries. The steps involved in the progression from its predisposing condition, gastroesophageal reflux disease, to its premalignant disorder, Barrett's esophagus, and to cancer, are incompletely understood. Current screening and surveillance methods are limited by the lack of population-wide utility, incomplete sampling of standard biopsies, and subjectivity of evaluation. Advances in endoscopic ablation have raised the hope of effective therapy for eradication of high-risk Barrett's lesions, but improvements are needed in determining when to apply this treatment and how to follow patients clinically. Researchers have evaluated numerous potential molecular biomarkers with the goal of detecting dysplasia, with varying degrees of success. The combination of biomarker panels with epidemiologic risk factors to yield clinical risk scoring systems is promising. New approaches to sample tissue may also be combined with these biomarkers for less invasive screening and surveillance. The development of novel endoscopic imaging tools in recent years has the potential to markedly improve detection of small foci of dysplasia in vivo. Current and future efforts will aim to determine the combination of markers and imaging modalities that will most effectively improve the rate of early detection of high-risk lesions in Barrett's esophagus. PMID:25400987

Bennett, Michael; Mashimo, Hiroshi

2014-11-15

193

Molecular markers and imaging tools to identify malignant potential in Barrett's esophagus  

PubMed Central

Due to its rapidly rising incidence and high mortality, esophageal adenocarcinoma is a major public health concern, particularly in Western countries. The steps involved in the progression from its predisposing condition, gastroesophageal reflux disease, to its premalignant disorder, Barrett’s esophagus, and to cancer, are incompletely understood. Current screening and surveillance methods are limited by the lack of population-wide utility, incomplete sampling of standard biopsies, and subjectivity of evaluation. Advances in endoscopic ablation have raised the hope of effective therapy for eradication of high-risk Barrett’s lesions, but improvements are needed in determining when to apply this treatment and how to follow patients clinically. Researchers have evaluated numerous potential molecular biomarkers with the goal of detecting dysplasia, with varying degrees of success. The combination of biomarker panels with epidemiologic risk factors to yield clinical risk scoring systems is promising. New approaches to sample tissue may also be combined with these biomarkers for less invasive screening and surveillance. The development of novel endoscopic imaging tools in recent years has the potential to markedly improve detection of small foci of dysplasia in vivo. Current and future efforts will aim to determine the combination of markers and imaging modalities that will most effectively improve the rate of early detection of high-risk lesions in Barrett’s esophagus.

Bennett, Michael; Mashimo, Hiroshi

2014-01-01

194

Gene Expression Profiles in Cells of Peripheral Blood Identify New Molecular Markers of Acute Pancreatitis  

PubMed Central

Introduction Blood leukocytes play a major role in mediating local and systemic inflammation during acute pancreatitis. We hypothesize that peripheral blood mononuclear cells (PBMC) in circulation exhibit unique changes in gene expression, and could provide a “reporter” function that reflects the inflammatory response in pancreas of acute pancreatitis. Methods To determine specific changes in blood leukocytes during acute pancreatitis, we studied gene transcription profile of in peripheral blood mononuclear cells (PBMC) in a rat model of experimental pancreatitis (sodium taurocholate). Normal rats, saline controls and a model of septic shock were used as a controls. cRNA obtained from PBMC of each group (n = 3) were applied to Affymetrix rat genome DNA Gene Chip Arrays. Results From the 8,799 rat genes analyzed, 140 genes showed unique significant changes in their expression in PBMC during the acute phase of pancreatitis, but not in sepsis. Among the 140 genes, 57 were upregulated, while 69 were downregulated. Platelet-derived growth factor receptor, prostaglandin E2 receptor and phospholipase D1 are among the top upregulated genes. Others include genes involved in G protein-coupled receptor and TGF-?-mediated signaling pathways, while genes associated with apoptosis, glucocorticoid receptors and even the cholecystokinin receptor are downregulated. Conclusions Microarray analysis in transcriptional profiling of PBMC showed that genes that are uniquely related to molecular and pancreatic function display differential expression in acute pancreatitis. Profiling genes obtained from an easily accessible source during severe pancreatitis may identify surrogate markers for disease severity. PMID:18347268

Bluth, Martin; Lin, Yin-yao; Zhang, Hong; Viterbo, Dominick; Zenilman, Michael

2009-01-01

195

Intraspecific chromosomal and genetic polymorphism in Brassica napus L. detected by cytogenetic and molecular markers.  

PubMed

The application of DNA intercalator 9-aminoacridine allowed us to increase the resolution of chromosome C-banding and DAPI-banding patterns and to investigate chromosomal polymorphism in karyotypes of seven spring and six winter rape varieties. It was shown that the pericentromeric and intercalary C-bands of most of the chromosomes in spring rape were smaller in size and less polymorphic than those of winter rape. More 26S and 5S rDNA sites were found in the winter rape karyotypes than the spring varieties. Separate or colocalized 26S and 5S rDNA sites were revealed on chromosomes 4, 5, 6, 8, 10, 14, 15, 16 and 18. Intervarietal and intravarietal polymorphism of the number and chromosomal localization of rDNA sites were detected. The generalized idiogram of chromosomes of 13 Brassica napus varieties with account of all possibilities of C-banding patterns as well as localization of 26S and 5S rDNA sites were constructed. Polymorphism of the examined molecular and cytogenetic markers as well as the heterozygosis level of FAE1.1 gene controlling erucic acid synthesis in rapeseed was higher in the winter varieties than in the spring ones. The obtained data were in a atisfactory agreement with increased tolerance to environmental stress conditions of winter rape. PMID:24840830

Amosova, Alexandra V; Zemtsova, Lyudmila V; Grushetskaya, Zoya E; Samatadze, Tatiana E; Mozgova, Galina V; Pilyuk, Yadviga E; Volovik, Valentina T; Melnikova, Natalia V; Zelenin, Alexandr V; Lemesh, Valentina A; Muravenko, Olga V

2014-04-01

196

Molecular markers for identifying a new selected variety of Pacific white shrimp Litopenaeus vannamei  

NASA Astrophysics Data System (ADS)

Selective breeding of the Pacific white shrimp Litopenaeus vannamei during the last decade has produced new varieties exhibiting high growth rates and disease resistance. However, the identification of new varieties of shrimps from their phenotypic characters is difficult. This study introduces a new approach for identifying varieties of shrimps using molecular markers of microsatellites and mitochondrial control region sequences. The method was employed to identify a new selected variety, Kehai No. 1 (KH-1), from three representative stocks (control group): Zhengda; Tongwei; and a stock collected from Fujian Province, which is now cultured in mainland China. By pooled genotyping of KH-1 and the control group, five microsatellites showing differences between KH-1 and the control group were screened out. Individual genotyping data confirmed the results from pooled genotyping. The genotyping data for the five microsatellites were applied to the assignment analysis of the KH-1 group and the control group using the partial Bayesian assignment method in GENECLASS2. By sequencing the mitochondrial control regions of individuals from the KH-1 and control group, four haplotypes were observed in the KH-1 group, whereas 14 haplotypes were obtained in the control group. By combining the microsatellite assignment analysis with mitochondrial control region analysis, the average accuracy of identification of individuals in the KH-1 group and control group reached 89%. The five selected microsatellite loci and mitochondrial control region sequences were highly polymorphic and could be used to distinguish new selected varieties of L. vannamei from other populations cultured in China.

Yu, Yang; Zhang, Xiaojun; Liu, Jingwen; Li, Fuhua; Huang, Hao; Li, Yijun; Liu, Xiaolin; Xiang, Jianhai

2014-10-01

197

Molecular Linkage Mapping and Marker-Trait Associations with NlRPT, a Downy Mildew Resistance Gene in Nicotiana langsdorffii  

PubMed Central

Nicotiana langsdorffii is one of two species of Nicotiana known to express an incompatible interaction with the oomycete Peronospora tabacina, the causal agent of tobacco blue mold disease. We previously showed that incompatibility is due to the hypersensitive response (HR), and plants expressing the HR are resistant to P. tabacina at all stages of growth. Resistance is due to a single dominant gene in N. langsdorffii accession S-4-4 that we have named NlRPT. In further characterizing this unique host-pathogen interaction, NlRPT has been placed on a preliminary genetic map of the N. langsdorffii genome. Allelic scores for five classes of DNA markers were determined for 90 progeny of a “modified backcross” involving two N. langsdorffii inbred lines and the related species N. forgetiana. All markers had an expected segregation ratio of 1:1, and were scored in a common format. The map was constructed with JoinMap 3.0, and loci showing excessive transmission distortion were removed. The linkage map consists of 266 molecular marker loci defined by 217 amplified fragment length polymorphisms (AFLPs), 26 simple-sequence repeats (SSRs), 10 conserved orthologous sequence markers, nine inter-simple sequence repeat markers, and four target region amplification polymorphism markers arranged in 12 linkage groups with a combined length of 1062?cM. NlRPT is located on linkage group three, flanked by four AFLP markers and one SSR. Regions of skewed segregation were detected on LGs 1, 5, and 9. Markers developed for N. langsdorffii are potentially useful genetic tools for other species in Nicotiana section Alatae, as well as in N. benthamiana. We also investigated whether AFLPs could be used to infer genetic relationships within N. langsdorffii and related species from section Alatae. A phenetic analysis of the AFLP data showed that there are two main lineages within N. langsdorffii, and that both contain populations expressing dominant resistance to P. tabacina. PMID:22936937

Zhang, Shouan; Gao, Muqiang; Zaitlin, David

2012-01-01

198

Molecular, Immunological, and Biological Characterization of Tityus serrulatus Venom Hyaluronidase: New Insights into Its Role in Envenomation  

PubMed Central

Background Scorpionism is a public health problem in Brazil, and Tityus serrulatus (Ts) is primarily responsible for severe accidents. The main toxic components of Ts venom are low-molecular-weight neurotoxins; however, the venom also contains poorly characterized high-molecular-weight enzymes. Hyaluronidase is one such enzyme that has been poorly characterized. Methods and principal findings We examined clones from a cDNA library of the Ts venom gland and described two novel isoforms of hyaluronidase, TsHyal-1 and TsHyal-2. The isoforms are 83% identical, and alignment of their predicted amino acid sequences with other hyaluronidases showed conserved residues between evolutionarily distant organisms. We performed gel filtration followed by reversed-phase chromatography to purify native hyaluronidase from Ts venom. Purified native Ts hyaluronidase was used to produce anti-hyaluronidase serum in rabbits. As little as 0.94 µl of anti-hyaluronidase serum neutralized 1 LD50 (13.2 µg) of Ts venom hyaluronidase activity in vitro. In vivo neutralization assays showed that 121.6 µl of anti-hyaluronidase serum inhibited mouse death 100%, whereas 60.8 µl and 15.2 µl of serum delayed mouse death. Inhibition of death was also achieved by using the hyaluronidase pharmacological inhibitor aristolochic acid. Addition of native Ts hyaluronidase (0.418 µg) to pre-neutralized Ts venom (13.2 µg venom+0.94 µl anti-hyaluronidase serum) reversed mouse survival. We used the SPOT method to map TsHyal-1 and TsHyal-2 epitopes. More peptides were recognized by anti-hyaluronidase serum in TsHyal-1 than in TsHyal-2. Epitopes common to both isoforms included active site residues. Conclusions Hyaluronidase inhibition and immunoneutralization reduced the toxic effects of Ts venom. Our results have implications in scorpionism therapy and challenge the notion that only neurotoxins are important to the envenoming process. PMID:24551256

Oliveira-Mendes, Bárbara Bruna Ribeiro; do Carmo, Anderson Oliveira; Duarte, Clara Guerra; Felicori, Liza Figueiredo; Machado-de-Ávila, Ricardo Andrez; Chávez-Olórtegui, Carlos; Kalapothakis, Evanguedes

2014-01-01

199

Immunome and venome of Bothrops jararacussu: a proteomic approach to study the molecular immunology of snake toxins.  

PubMed

A combination of anti-bothropic and anti-crotalic sera has been reported to be more effective in neutralizing the effects of Bothrops jararacussu venom than anti-bothropic serum alone. The role of proteins from B. jararacussu venom in the horse immune response was evaluated via the analysis of cross-reactivity with homologous and heterologous sera. Many of the proteins in B. jararacussu venom were identified via 2D gel electrophoresis. Western blots revealed that anti-jararacussu showed higher reactivity to l-aminoxidase (LAOs) and snake venom metalloproteinase, (SVMPs) and weaker reactivity towards Snake venom serine proteases (SVSPs), PLA(2), C-type lectin and cysteine-rich proteins. Anti-jararaca preferentially recognized LAOs, SVMPs and SVSPs. Both of these sera failed to recognize low-molecular weight proteins. Anti-crotalic serum clearly recognized LAOs, C-type lectin, SVSP, cysteine-rich proteins, SVMP and Asp49-PLA(2). The cross-reactivity with anti-PLA(2) revealed the immunoreactivity of these antibodies to proteins with molecular masses in a range that is poorly recognized by other studied anti-sera. Our results suggest that the contribution of anti-crotalic serum to the neutralization of B. jararacussu by may be due to its cross-reactivity with proteins such as C-type lectins, SVSPs, Asp49-PLA(2). These results also reinforce the importance of neutralizing the highly toxic proteins inclusive those with low immunogenicity in commercial antivenom production to obtain a highly protective serum against snake venoms. PMID:20060013

Correa-Netto, Carlos; Teixeira-Araujo, Ricardo; Aguiar, Aniesse Silva; Melgarejo, Aníbal Rafael; De-Simone, Salvatore Giovanni; Soares, Márcia Regina; Foguel, Debora; Zingali, Russolina Benedeta

2010-06-15

200

A genetic map of Asparagus officinalis based on integrated RFLP, RAPD and AFLP molecular markers  

Microsoft Academic Search

An integrated genetic map of the dioecious species Asparagus officinalis L. has been constructed on the basis of RFLP, RAPD, AFLP and isoenzyme markers. The segregation analysis of the polymorphic\\u000a markers was carried out on the progeny of five different crosses between male and female doubled-haploid clones generated\\u000a by anther culture. A total of 274 markers have been organized to

A. Spada; E. Caporali; G. Marziani; P. Portaluppi; F. M. Restivo; F. Tassi; A. Falavigna

1998-01-01

201

Molecular cloning and immunologic characterization of a novel cDNA coding for progesterone-induced blocking factor.  

PubMed

Previous studies from our laboratory showed that the immunomodulatory effects of progesterone are mediated by a 34-kDa protein, named the progesterone-induced blocking factor (PIBF). Lymphocytes of women with threatened abortion fail to produce this factor. Via inducing a Th2 biased cytokine production and blocking of NK activity, PIBF prevents induced pregnancy loss in mice, suggesting that substitution therapy with PIBF could be useful as an alternative treatment of certain forms of recurrent spontaneous abortions. Our study was aimed at mapping the sequence and structure of PIBF coding cDNA and characterizing the encoded protein product. Screening of a human liver cDNA library revealed a 2765-bp clone with a 2271-bp open reading frame. The PIBF1 cDNA encodes a protein of 757 amino acid residues with an 89-kDa predicted molecular mass, which shows no significant amino acid sequence homology with any known protein. PIBF produced via recombinant technique is recognized by the Ab specific for the secreted lymphocyte PIBF Ab, and possesses the biological activities of the secreted lymphocyte PIBF. The full-length PIBF is associated with the nucleus, whereas secretion of shorter forms, such a 34-kDa protein is induced by activation of the cell. The 48-kDa N-terminal part of PIBF is biologically active, and the part of the molecule, responsible for modulating NK activity is encoded by exons 2-4. These data provide an initial step for exploiting the possible diagnostic and therapeutic potential of this immunomodulatory molecule. PMID:14634107

Polgar, Beata; Kispal, Gyula; Lachmann, Margit; Paar, Christian; Nagy, Eszter; Csere, Peter; Miko, Eva; Szereday, Laszlo; Varga, Peter; Szekeres-Bartho, Julia; Paar, Gabriella

2003-12-01

202

21 Molecular Properties and Immunological Reactivity of Arabidopsis EXPB1, a Nonallergenic Homologue of Grass Group 1 Allergens  

PubMed Central

Background Grass group 1 allergens are glyco-proteins of about 30kDa that are highly soluble and profusely released by grass pollen upon hydration. They bind to IgE antibodies that initiate the allergic response causing hay fever, seasonal asthma, and related immune responses in humans. Bermuda grass (Cynodon dactylon; subfamily Chloridoideae) is an important source of seasonal aeroallergens in warm tropical and sub-tropical areas worldwide. Improved approaches to diagnosis and therapy of allergic diseases require a thorough understanding of the structure and epitopes on the allergen molecule that are crucial for the antigen-antibody interaction. In order to understand structural basis of IgE reactivity of group 1 allergen Cyn d1, we have pursued a comparative genomic approach to search for hypoallergenic or non-allergenic homologues. Methods Gene cloning, Protein expression in bacteria, protein structure modeling, IgE reactivity analysis through Immunoblotting. Results EXPB1, an Arabidopsis protein (belonging to the beta expansin multi gene family), showed significant sequence and structural similarity to Cyn d 1. This protein was expressed in E. coli and the recombinant protein did not react with serum IgE from grass pollen allergic patients, suggesting that EXPB1 represented a non-allergenic homologue of grass group 1 allergens. It is proposed that differences in the amino acid sequence are responsible for the difference in the allergenicity profile of the Arabidopsis and grass pollen proteins. Conclusions Our study provides valuable data for further investigations of the molecular basis of allergenicity and cross-reactivity of grass group 1 allergens.

Singh, Mohan; Tiwari, Ruby; Bhalla, Prem

2012-01-01

203

Virtual Immunology: Software for Teaching Basic Immunology  

ERIC Educational Resources Information Center

As immunology continues to evolve, many educational methods have found difficulty in conveying the degree of complexity inherent in its basic principles. Today, the teaching-learning process in such areas has been improved with tools such as educational software. This article introduces "Virtual Immunology," a software program available…

Berçot, Filipe Faria; Fidalgo-Neto, Antônio Augusto; Lopes, Renato Matos; Faggioni, Thais; Alves, Luiz Anastácio

2013-01-01

204

Molecular Mapping and Marker-Assisted Selection of Genes for Septoria Speckled Leaf Blotch Resistance in Barley  

Microsoft Academic Search

Zhong, S., Toubia-Rahme, H., Steffenson, B. J., and Smith, K. P. 2006. Molecular mapping and marker-assisted selection of genes for Septoria speckled leaf blotch resistance in barley. Phytopathology 96:993-999. Septoria speckled leaf blotch (SSLB), caused by Septoria passerinii, has emerged as one of the most important foliar diseases of barley in the Upper Midwest region of the United States. To

Shaobin Zhong; Hala Toubia-Rahme; Brian J. Steffenson; Kevin P. Smith

2006-01-01

205

Identification and localization of molecular markers linked to the Lr 9 leaf rust resistance gene of wheat  

Microsoft Academic Search

Near-isogenic lines (NILs) for the leaf rust resistance gene Lr9 were screened for polymorphisms at the molecular level. RAPD (random amplified polymorphic DNA) primers as well as RFLP (restriction fragment length polymorphism) markers were used. Out of 395 RAPD primers tested, three showed polymorphisms between NILs, i.e., an additional band was found in resistant lines. One of these polymorphic bands

G. Schachermayr; H. Siedler; M. D. Gale; H. Winzeler; M. Winzeler; B. Keller

1994-01-01

206

A conservative region of the mercuric reductase gene (mera) as a molecular marker of bacterial mercury resistance  

PubMed Central

The most common bacterial mercury resistance mechanism is based on the reduction of Hg(II) to Hg0, which is dependent of the mercuric reductase enzyme (MerA) activity. The use of a 431 bp fragment of a conservative region of the mercuric reductase (merA) gene was applied as a molecular marker of this mechanism, allowing the identification of mercury resistant bacterial strains. PMID:24031221

Sotero-Martins, Adriana; de Jesus, Michele Silva; Lacerda, Michele; Moreira, Josino Costa; Filgueiras, Ana Luzia Lauria; Barrocas, Paulo Rubens Guimaraes

2008-01-01

207

Temporal trends of molecular markers associated with artemether-lumefantrine tolerance\\/resistance in Bagamoyo district, Tanzania  

Microsoft Academic Search

BACKGROUND: Development and spread of Plasmodium falciparum resistance to artemisinin-based combination therapy (ACT) constitutes a major threat to recent global malaria control achievements. Surveillance of molecular markers could act as an early warning system of ACT-resistance before clinical treatment failures are apparent. The aim of this study was to analyse temporal trends of established genotypes associated with artemether-lumefantrine tolerance\\/resistance before

M. Malmberg; B. Ngasala; P. E. Ferreira; E. Larsson; I. Jovel; A. Hjalmarsson; M. Petzold; Z. Premji; J. P. Gil; A. Bjorkman; A. Martensson

2013-01-01

208

Cytotoxic effect of eugenol on the expression of molecular markers related to the osteogenic differentiation of human dental pulp cells  

Microsoft Academic Search

The cytotoxic effect of eugenol on the expression of molecular markers related to the osteogenic differentiation of human\\u000a dental pulp cells such as collagen synthesis and the expression of two osteogenesis-related genes, alkaline phosphatase (ALP)\\u000a and bone sialoprotein (BSP), was studied using human dental pulp cells (D824 cells). Cellular growth and survival were decreased\\u000a by treatment of cells with eugenol

Masanori Anpo; Kumiko Shirayama; Takeki Tsutsui

209

Simplified protocol for DNA extraction and amplification of 2 molecular markers to detect and type Giardia duodenalis.  

PubMed

We evaluated the ability of 3 kits: QIAmp® DNA stool mini kit (Qiagen, Hilden, Germany), PureLink PCR Purification®, and PureLink™ Genomic DNA® (Invitrogen, Carlsbad, CA, USA) for DNA extraction, and of 2 molecular markers (heat shock protein [HSP] and ?-giardin genes) for detection and genotyping of Giardia duodenalis stool samples. The detection and typing limits of the markers were determined by the DNA concentration of trophozoites and cysts and were tested in 26 clinical samples. Of the 3 kits tested, the PureLink PCR Purification gave the best results when tested with clinical samples with low, intermediate, and high numbers of cysts. The DNA extracted from trophozoites and cysts was diluted successively in 1:2 ratios until it was no longer possible to observe the amplified product in polyacrylamide gel. Similarly, a suspension of cysts was diluted until no cysts were observed, and then the DNA was extracted. The amount of DNA of trophozoites and cysts for the typing of the parasite was smaller for the HSP marker than for ?-giardin. Combined use of both markers allowed us to detect DNA of Giardia in parasitologically positive samples in a higher percentage (75%) than the results obtained for each marker and in 1 parasitologically negative sample, indicating that this combination increased the potential to accurately detect and genotype this parasite. We also concluded that the HSP marker has a higher limit of detection and typing than the ?-giardin marker and that the DNA extraction method tested for G. duodenalis is simpler and more efficient than those that are currently in use and can be applied on a large scale. PMID:24207076

Uda-Shimoda, Carla Fernanda; Colli, Cristiane Maria; Pavanelli, Mariana Felgueira; Falavigna-Guilherme, Ana Lúcia; Gomes, Mônica Lúcia

2014-01-01

210

Subtracted Diversity Array Identifies Novel Molecular Markers Including Retrotransposons for Fingerprinting Echinacea Species  

PubMed Central

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. PMID:23940565

Olarte, Alexandra; Mantri, Nitin; Nugent, Gregory; Pang, Edwin C. K.

2013-01-01

211

Molecular markers of yolk sac fry development in nine families of lake trout.  

PubMed

Salmonids in certain areas of North America and northern Europe suffer from reproductive disturbances manifested through the death of yolk sac fry. These disturbances are referred to as early mortality syndrome (EMS) in the Great Lakes region and M74 in the Baltic Sea. Both of these syndromes have been associated with reduced concentrations of thiamine in affected females and their eggs. However, large variations in signs and mortality, both within and between the individual syndromes, have been reported. Yolk sac fry mortality (M74) in Atlantic salmon Salmo salar has been shown to be associated with reduced DNA binding of the hypoxia-inducible transcription factor 1 (HIF-1), reduced production of vascular endothelial growth factor (VEGF) protein, decreased capillary density, and down-regulation of adult-type globin gene transcription (which is responsible for the protein part of adult hemoglobin). One of the main effects of all of these changes is reduced oxygen transport to the tissues of affected fry. In this study, the developmental patterns of HIF-1 DNA binding, VEGF protein expression, and adult-type globin gene transcription were analyzed in nine family groups of Lake Michigan lake trout Salvelinus namaycush. The results indicate that HIF-1 DNA binding and globin gene transcription increase from hatch to the end of yolk sac stage. Interindividual and between-family biological variations were detected, especially in VEGF protein expression and globin gene transcription. Our results demonstrate the possibility of using these molecular markers in investigating the etiology of EMS and making comparisons between the mechanisms of different salmonid yolk sac fry mortalities. PMID:20218502

Vuori, Kristiina A; Paavilainen, Tiia; Nikinmaa, Mikko; Czesny, Sergiusz; Rinchard, Jacques

2009-12-01

212

Molecular markers indicate different dynamics of leaves and roots during litter decomposition  

NASA Astrophysics Data System (ADS)

Up to now there is only a poor understanding of the sources contributing to organic carbon in forest soils, especially the contribution of leaves and roots. Studies of the last 2 decades have shown that methods like pyrolysis and CuO oxidation are suitable tools to trace back the main contributors of organic matter in water, sediments and soils. Lignin derived monomers, extractable lipids, cutin and suberin derived compounds have been used frequently for identification of plant material. However, for the selection of suitable biomarker the decomposition patterns and stability of these compounds are of high importance but they are only poorly understood. In this study we focused on following questions: (I) Which compounds are characteristic to identify certain plant parts and plant species? (II) How stable are these compounds during the first 3 years of litter decomposition? We studied the chemical composition of samples from a 3-year litterbag decomposition experiment with roots and leaves of spruce, pine and birch which was done in Finland. Additionally to mass loss, carbon and nitrogen contents, free lipids were extracted; by alkaline hydrolysis non extractable lipids were gained. The extracts were analyzed afterwards by GC-MS, the insoluble residues were analyzed by curie-point Pyrolysis GC-MS. In addition to the identification and quantification of a variety of different compounds and compound ratios we used statistical classification methods to get deeper insights into the patterns of leaf and root-derived biomarkers during litter decomposition. The mass loss was largely different between the litter species and we always observed larger mass loss for leaf-derived litter in comparison to root derived litter. This trend was also observed by molecular analysis. The increase of the ratio of vanillic acid to vanillin was correlated to the mass loss of the samples over time. This shows that the degree of decomposition of plant material was linked with the degree of lignin degradation. Preliminary results show, that we were able to distinguish the different species and plant parts using various approaches, e.g., abundance and patterns of different substances and different ratios of compounds. The polyesters suberin and cutin were particularly useful to differentiate between roots and leaves. We conclude that knowledge of the decomposition patterns of molecular markers will largely improve the identification power of organic matter sources in soils.

Altmann, Jens; Jansen, Boris; Palviainen, Marjo; Kalbitz, Karsten

2010-05-01

213

Biotherapies & Immunology International Master  

E-print Network

Biotherapies & Immunology International Master #12;students the possibility to access to a large knowledge in the field of biotherapies with special focus on immunology. The partners involved in this PIM have a large recognized expertise in Biotherapies and immunology and can offer complementary courses

Arleo, Angelo

214

The potential of hypoxia markers as target for breast molecular imaging - a systematic review and meta-analysis of human marker expression  

PubMed Central

Background Molecular imaging of breast cancer is a promising emerging technology, potentially able to improve clinical care. Valid imaging targets for molecular imaging tracer development are membrane-bound hypoxia-related proteins, expressed when tumor growth outpaces neo-angiogenesis. We performed a systematic literature review and meta-analysis of such hypoxia marker expression rates in human breast cancer to evaluate their potential as clinically relevant molecular imaging targets. Methods We searched MEDLINE and EMBASE for articles describing membrane-bound proteins that are related to hypoxia inducible factor 1? (HIF-1?), the key regulator of the hypoxia response. We extracted expression rates of carbonic anhydrase-IX (CAIX), glucose transporter-1 (GLUT1), C-X-C chemokine receptor type-4 (CXCR4), or insulin-like growth factor-1 receptor (IGF1R) in human breast disease, evaluated by immunohistochemistry. We pooled study results using random-effects models and applied meta-regression to identify associations with clinicopathological variables. Results Of 1,705 identified articles, 117 matched our selection criteria, totaling 30,216 immunohistochemistry results. We found substantial between-study variability in expression rates. Invasive cancer showed pooled expression rates of 35% for CAIX (95% confidence interval (CI): 26-46%), 51% for GLUT1 (CI: 40-61%), 46% for CXCR4 (CI: 33-59%), and 46% for IGF1R (CI: 35-70%). Expression rates increased with tumor grade for GLUT1, CAIX, and CXCR4 (all p < 0.001), but decreased for IGF1R (p < 0.001). GLUT1 showed the highest expression rate in grade III cancers with 58% (45-69%). CXCR4 showed the highest expression rate in small T1 tumors with 48% (CI: 28-69%), but associations with size were only significant for CAIX (p < 0.001; positive association) and IGF1R (p = 0.047; negative association). Although based on few studies, CAIX, GLUT1, and CXCR4 showed profound lower expression rates in normal breast tissue and benign breast disease (p < 0.001), and high rates in carcinoma in situ. Invasive lobular carcinoma consistently showed lower expression rates (p < 0.001). Conclusions Our results support the potential of hypoxia-related markers as breast cancer molecular imaging targets. Although specificity is promising, combining targets would be necessary for optimal sensitivity. These data could help guide the choice of imaging targets for tracer development depending on the envisioned clinical application. PMID:24206539

2013-01-01

215

Linkage mapping of sbm-1 , a gene conferring resistance to pea seed-borne mosaic virus, using molecular markers in Pisum sativum  

Microsoft Academic Search

The location of sbm-1 on the Pisum sativum genetic map was determined by linkage analysis with eight syntenic molecular markers. Analysis of the progeny of two crosses confirmed that sbm-1 is on chromosome 6 and permitted a more detailed map of this chromosome to be constructed. The inclusion of Fed-1 and Prx-3 among the markers facilitated the comparison of our

G. M. Timmerman; T. J. Frew; A. L. Miller; N. F. Weeden; W. A. Jermyn

1993-01-01

216

Construction of cytoplasmic molecular markers distinguishing Danio rerio from Gobiocypris rarus at high identity domains based on MP-PCR strategy and Sybr Green I detection  

Microsoft Academic Search

To distinguish the cytoplasm of Danio rerio from that of Gobiocypris rarus, we cloned G. rarus COXI and constructed cytoplasmic molecular markers at the high identity domains of COXI by mutated primer PCR (MP-PCR for short). Then Sybr Green I was used to detect the single amplicon. As a result, we succeeded in getting the cytoplasmic molecular\\u000a markers, G.M COXI

De-Sheng Pei; Yong-Hua Sun; Zuo-Yan Zhu

2008-01-01

217

Molecular Marker Approach on Characterizing and Quantifying Charcoal in Environmental Media  

NASA Astrophysics Data System (ADS)

Black carbon (BC) is widely distributed in natural environments including soils, sediments, freshwater, seawater and the atmosphere. It is produced mostly from the incomplete combustion of fossil fuels and vegetation. In recent years, increasing attention has been given to BC due to its potential influence in many biogeochemical processes. In the environment, BC exists as a continuum ranging from partly charred plant materials, charcoal residues to highly condensed soot and graphite particles. The heterogeneous nature of black carbon means that BC is always operationally-defined, highlighting the need for standard methods that support data comparisons. Unlike soot and graphite that can be quantified with well-established methods, it is difficult to directly quantify charcoal in geologic media due to its chemical and physical heterogeneity. Most of the available charcoal quantification methods detect unknown fractions of the BC continuum. To specifically identify and quantify charcoal in soils and sediments, we adopted and validated an innovative molecular marker approach that quantifies levoglucosan, a pyrogenic derivative of cellulose, as a proxy of charcoal. Levoglucosan is source-specific, stable and is able to be detected at low concentrations using gas chromatograph-mass spectrometer (GC-MS). In the present study, two different plant species, honey mesquite and cordgrass, were selected as the raw materials to synthesize charcoals. The lab-synthesize charcoals were made under control conditions to eliminate the high heterogeneity often found in natural charcoals. The effects of two major combustion factors, temperature and duration, on the yield of levoglucosan were characterized in the lab-synthesize charcoals. Our results showed that significant levoglucosan production in the two types of charcoal was restricted to relatively low combustion temperatures (150-350 degree C). The combustion duration did not cause significant differences in the yield of levoglucosan in the two charcoals. Interestingly, the low temperature charcoals are undetectable by the acid dichromate oxidation method, a popular soot/charcoal analytical approach. Our study demonstrates that levoglucosan can serve as a proxy of low temperature charcoals that are undetectable using other BC methods. Moreover, our study highlights the limitations of the common BC quantification methods to characterize the entire BC continuum.

Kuo, L.; Herbert, B. E.; Louchouarn, P.

2006-12-01

218

Semi-volatile organic compounds as molecular markers for atmospheric and ecosystem transport  

NASA Astrophysics Data System (ADS)

The use of semi-volatile organic compounds (SOCs) as molecular markers to identify the contributions of regional and long-range atmospheric transport, as well as current and historic sources, and contaminant deposition in remote ecosystems of the Western U.S. was investigated. Trans-Pacific air masses influenced by Siberian biomass burning events had elevated concentrations of polycyclic aromatic hydrocarbons (PAHs) and the historic use pesticides dieldrin and alpha-HCH, while air masses influenced by regional fires in the Pacific Northwestern U.S. had enhanced concentrations of PAHs and the current-use pesticides dacthal and endosulfan. This suggests that previously deposited SOCs, such as pesticides, revolatilize to the atmosphere during forest fires. In addition, forest soils collected from a burned area in the Pacific Northwestern U.S. had significantly lower SOC concentrations (34 to 100 %) than soils collected from an unburned area separated only by a two lane road. This confirms that SOCs re-volatilize and/or degrade from soils and vegetation during the burning process. The chiral signatures of alpha-HCH in air masses at three sites in the Pacific Northwestern U.S. indicated that the boundary layer has a non-racemic alpha-HCH signature likely due to re-volatilization of alpha-HCH from the Pacific Ocean and that the free troposphere is a source of racemic alpha-HCH. Racemic alpha-HCH was also associated with Asian and trans-Pacific air masses. Racemic cis and trans-chlordane in Pacific Northwestern U.S. air masses indicated that U.S. urban areas continue to be a source of chlordane to the atmosphere. The deposition of non-racemic alpha-HCH in seasonal snowpack in continental Western U.S. national park high elevation ecosystems reflected regional transport, while the high latitude, Alaskan national parks were influenced by long-range atmospheric transport of racemic alpha-HCH. The chiral signature of alpha-HCH in fish collected from high elevation and high latitude ecosystems in Western U.S. national parks reflected the chiral signature of the seasonal snowpack in the lake catchment. This indicates that the fish in these ecosystems do not enantioselectively biotransform alpha-HCH. Racemic cis-chlordane was measured in seasonal snowpack and lake sediments in Sequoia National Park due to the high population density surrounding the park and the past use of chlordane as a termiticide in urban areas. Non-racemic cis-chlordane was measured in sediment collected from Rocky Mountain National Park because this park receives chlordane due to re-volatilization from regional agricultural soil.

Genualdi, Susan

219

A high-density molecular map for ryegrass (Lolium perenne) using AFLP markers  

Microsoft Academic Search

AFLP markers have been successfully employed for the development of a high-density linkage map of ryegrass (Lolium\\u000a perenne L.) using a progeny set of 95 plants from a testcross involving a doubled-haploid tester. This genetic map covered 930 cM\\u000a in seven linkage groups and was based on 463 amplified fragment length polymorphism (AFLP) markers using 17 primer pairs,\\u000a three isozymes

P. F. Bert; G. Charmet; P. Sourdille; M. D. Hayward; F. Balfourier

1999-01-01

220

Characterization of the Miiuy Croaker (Miichthys miiuy) Transcriptome and Development of Immune-Relevant Genes and Molecular Markers  

PubMed Central

Background The miiuy croaker (Miichthys miiuy) is an important species of marine fish that supports capture fisheries and aquaculture. At present commercial scale aquaculture of this species is limited due to diseases caused by pathogens and parasites which restrict production and limit commercial value. The lack of transcriptomic and genomic information for the miiuy croaker limits the ability of researchers to study the pathogenesis and immune system of this species. In this study we constructed a cDNA library from liver, spleen and kidney which was sequenced using Illumina paired-end sequencing to enable gene discovery and molecular marker development. Principal Findings In our study, a total of 69,071 unigenes with an average length of 572 bp were obtained. Of these, 45,676 (66.13%) were successfully annotated in public databases. The unigenes were also annotated with Gene Ontology, Clusters of Orthologous Groups and KEGG pathways. Additionally, 498 immune-relevant genes were identified and classified. Furthermore, 14,885 putative simple sequence repeats (cSSRs) and 8,510 putative single nucleotide polymorphisms (SNPs) were identified from the 69,071 unigenes. Conclusion The miiuy croaker (Miichthys miiuy) transcriptome data provides a large resource to identify new genes involved in many processes including those involved in the response to pathogens and diseases. Furthermore, the thousands of potential cSSR and SNP markers found in this study are important resources with respect to future development of molecular marker assisted breeding programs for the miiuy croaker. PMID:24714210

Che, Rongbo; Sun, Yueyan; Sun, Dianqiao; Xu, Tianjun

2014-01-01

221

Virtual immunology: software for teaching basic immunology.  

PubMed

As immunology continues to evolve, many educational methods have found difficulty in conveying the degree of complexity inherent in its basic principles. Today, the teaching-learning process in such areas has been improved with tools such as educational software. This article introduces "Virtual Immunology," a software program available free of charge in Portuguese and English, which can be used by teachers and students in physiology, immunology, and cellular biology classes. We discuss the development of the initial two modules: "Organs and Lymphoid Tissues" and "Inflammation" and the use of interactive activities to provide microscopic and macroscopic understanding in immunology. Students, both graduate and undergraduate, were questioned along with university level professors about the quality of the software and intuitiveness of use, facility of navigation, and aesthetic organization using a Likert scale. An overwhelmingly satisfactory result was obtained with both students and immunology teachers. Programs such as "Virtual Immunology" are offering more interactive, multimedia approaches to complex scientific principles that increase student motivation, interest, and comprehension. PMID:24259333

Berçot, Filipe Faria; Fidalgo-Neto, Antônio Augusto; Lopes, Renato Matos; Faggioni, Thais; Alves, Luiz Anastácio

2013-01-01

222

Identification of Single-Copy Orthologous Genes between Physalis and Solanum lycopersicum and Analysis of Genetic Diversity in Physalis Using Molecular Markers  

PubMed Central

The genus Physalis includes a number of commercially important edible and ornamental species. Its high nutritional value and potential medicinal properties leads to the increased commercial interest in the products of this genus worldwide. However, lack of molecular markers prevents the detailed study of genetics and phylogeny in Physalis, which limits the progress of breeding. In the present study, we compared the DNA sequences between Physalis and tomato, and attempted to analyze genetic diversity in Physalis using tomato markers. Blasting 23180 DNA sequences derived from Physalis against the International Tomato Annotation Group (ITAG) Release2.3 Predicted CDS (SL2.40) discovered 3356 single-copy orthologous genes between them. A total of 38 accessions from at least six species of Physalis were subjected to genetic diversity analysis using 97 tomato markers and 25 SSR markers derived from P. peruviana. Majority (73.2%) of tomato markers could amplify DNA fragments from at least one accession of Physalis. Diversity in Physalis at molecular level was also detected. The average Nei’s genetic distance between accessions was 0.3806 with a range of 0.2865 to 0.7091. These results indicated Physalis and tomato had similarity at both molecular marker and DNA sequence levels. Therefore, the molecular markers developed in tomato can be used in genetic study in Physalis. PMID:23166835

Wei, Jingli; Hu, Xiaorong; Yang, Jingjing; Yang, Wencai

2012-01-01

223

Transcript Profiling and Identification of Molecular Markers for Early Microspore Embryogenesis in Brassica napus1[W][OA  

PubMed Central

Isolated microspores of Brassica napus are developmentally programmed to form gametes; however, microspores can be reprogrammed through stress treatments to undergo appropriate divisions and form embryos. We are interested in the identification and isolation of factors and genes associated with the induction and establishment of embryogenesis in isolated microspores. Standard and normalized cDNA libraries, as well as subtractive cDNA libraries, were constructed from freshly isolated microspores (0 h) and microspores cultured for 3, 5, or 7 d under embryogenesis-inducing conditions. Library comparison tools were used to identify shifts in metabolism across this time course. Detailed expressed sequence tag analyses of 3 and 5 d cultures indicate that most sequences are related to pollen-specific genes. However, semiquantitative and real-time reverse transcription-polymerase chain reaction analyses at the initial stages of embryo induction also reveal expression of embryogenesis-related genes such as BABYBOOM1, LEAFY COTYLEDON1 (LEC1), and LEC2 as early as 2 to 3 d of microspore culture. Sequencing results suggest that embryogenesis is clearly established in a subset of the microspores by 7 d of culture and that this time point is optimal for isolation of embryo-specific expressed sequence tags such as ABSCISIC ACID INSENSITIVE3, ATS1, LEC1, LEC2, and FUSCA3. Following extensive polymerase chain reaction-based expression profiling, 16 genes were identified as unequivocal molecular markers for microspore embryogenesis in B. napus. These molecular marker genes also show expression during zygotic embryogenesis, underscoring the common developmental pathways that function in zygotic and gametic embryogenesis. The quantitative expression values of several of these molecular marker genes are shown to be predictive of embryogenic potential in B. napus cultivars (e.g. ‘Topas’ DH4079, ‘Allons,’ ‘Westar,’ ‘Garrison’). PMID:17384168

Malik, Meghna R.; Wang, Feng; Dirpaul, Joan M.; Zhou, Ning; Polowick, Patricia L.; Ferrie, Alison M.R.; Krochko, Joan E.

2007-01-01

224

Modelling Immunological Memory  

E-print Network

Accurate immunological models offer the possibility of performing highthroughput experiments in silico that can predict, or at least suggest, in vivo phenomena. In this chapter, we compare various models of immunological memory. We first validate an experimental immunological simulator, developed by the authors, by simulating several theories of immunological memory with known results. We then use the same system to evaluate the predicted effects of a theory of immunological memory. The resulting model has not been explored before in artificial immune systems research, and we compare the simulated in silico output with in vivo measurements. Although the theory appears valid, we suggest that there are a common set of reasons why immunological memory models are a useful support tool; not conclusive in themselves.

Garret, Simon; Walker, Joanne; Wilson, William; Aickelin, Uwe

2010-01-01

225

Genetic Stock Identification of Steelhead in the Columbia River Basin: An Evaluation of Different Molecular Markers  

Microsoft Academic Search

Protein genetic markers (allozymes) have been used during the last decade in a genetic stock identification (GSI) program by state and federal management agencies to monitor stocks of steelhead Oncorhynchus mykiss in the Columbia River basin. In this paper we report new data for five microsatellite and three intron loci from 32 steelhead populations in the three upriver evolutionarily significant

Gary A. Winans; Melanie M. Paquin; Donald M. Van Doornik; Bruce M. Baker; Perry Thornton; Dan Rawding; Anne Marshall; Paul Moran; Steven Kalinowski

2004-01-01

226

Evaluation of radiation risk: cytogenetic and molecular markers of low-dose radiation effects  

Microsoft Academic Search

For last 15 years, we have investigated low-dose radiation genetic effects on human populations affected by the Chernobyl accident. Cytogenetic longitudinal investigations showed that radiation markers for cleanup workers remained at an elevated level and had a trend to grow up with time. A dynamic profile of the amount of aberrations confirms that this group has symptoms of the genomic

Sergey Melnov; Pavel Marozik; Tatiana Drozd

227

Isolation of molecular markers for tomato ( L. esculentum ) using random amplified polymorphic DNA (RAPD)  

Microsoft Academic Search

A new DNA polymorphism assay was developed in 1990 that is based on the amplification by the polymerase chain reaction (PCR) of random DNA segments, using single primers of arbitrary nucleotide sequence. The amplified DNA fragments, referred to as RAPD markers, were shown to be highly useful in the construction of genetic maps (“RAPD mapping”). We have now adapted the

R. M. Klein-Lankhorst; A. Vermunt; R. Weide; T. Liharska; P. Zabel

1991-01-01

228

Use of molecular markers in breeding for soluble solids content in tomato — a re-examination  

Microsoft Academic Search

Through earlier breeding efforts, portions of the genome of the wild species Lycopersicon chmielewskii have been introgressed into the cultivated tomato (Rick 1974). These introgressed chromosomal segments have been reported to increase soluble solids in fruit of certain tomato varieties (Rick 1974). Recently, two of the introgressed segments have been identified with RFLP markers and tested for effects on soluble

S. D. Tanksley; J. Hewitt

1988-01-01

229

Patterns of inheritance with RAPD molecular markers reveal novel types of polymorphism in the honey bee  

Microsoft Academic Search

The polymerase chain reaction (PCR) was used to generate random amplified polymorphic DNA (RAPD) from honey bee DNA samples in order to follow the patterns of inheritance of RAPD markers in a haplodiploid insect. The genomic DNA samples from two parental bees, a haploid drone and a diploid queen, were screened for polymorphism with 68 different tennucleotide primers of random

Greg J. Hunt; Robert E. Page

1992-01-01

230

Molecular markers reveal only two mud crab species of genus scylla (brachyura: portunidae) in Indian coastal waters.  

PubMed

The taxonomic ambiguity of the Indian mud crab (genus Scylla de Hann 1833) is still a cause of concern as several papers have been published with misleading identification. This is the first attempt to resolve the taxonomic uncertainty of the mud crab commonly available in Indian coastal waters using molecular genetic markers (ITS-1 and sequencing of COI gene) combined with traditional morphometry. Additionally, we developed a PCR method by which Indian mud crab species can be identified rapidly and effectively. The results clearly indicate that the green morph of the Indian mud crab is Scylla serrata and the brown morph is S. olivacea. The S. serrata commonly mentioned in the literature from India is S. olivacea; the S. tranquebarica noted by many Indian researchers should belong to S. serrata. Caution should be taken when interpreting or implementing the biological, molecular, and aquaculture data in the literature. PMID:24699826

Mandal, Anup; Varkey, Mathews; Sobhanan, Sobha Pindaniyil; Mani, Anjali Kottayil; Gopalakrishnan, Achamveetil; Kumaran, Ganesh; Sethuramalingam, Arulraj; Srinivasan, Pandiarajan; Samraj, Yohannan Chellema Thampi

2014-08-01

231

A Life Marker Chip for the Specific Molecular Identification of Life Experiment  

Microsoft Academic Search

The Specific Molecular Identification of Life Experiment (SMILE) represents the first in-situ attempt to search for a range of molecules in the Martian environment associated with extinct\\/extant life or potential life processes. SMILE will measure specific molecules using electrical and optical transduction techniques in three science subsystems, one of which a molecular receptor array is the subject of this paper.

M. R. Sims; D. C. Cullen; N. P. Bannister; W. D. Grant; R. Jones

2004-01-01

232

A reference consensus genetic map for molecular markers and economically important traits in faba bean (Vicia faba L.)  

PubMed Central

Background Faba bean (Vicia faba L.) is among the earliest domesticated crops from the Near East. Today this legume is a key protein feed and food worldwide and continues to serve an important role in culinary traditions throughout Middle East, Mediterranean region, China and Ethiopia. Adapted to a wide range of soil types, the main faba bean breeding objectives are to improve yield, resistance to biotic and abiotic stresses, seed quality and other agronomic traits. Genomic approaches aimed at enhancing faba bean breeding programs require high-quality genetic linkage maps to facilitate quantitative trait locus analysis and gene tagging for use in a marker-assisted selection. The objective of this study was to construct a reference consensus map in faba bean by joining the information from the most relevant maps reported so far in this crop. Results A combination of two approaches, increasing the number of anchor loci in diverse mapping populations and joining the corresponding genetic maps, was used to develop a reference consensus map in faba bean. The map was constructed from three main recombinant inbreed populations derived from four parental lines, incorporates 729 markers and is based on 69 common loci. It spans 4,602 cM with a range from 323 to 1041 loci in six main linkage groups or chromosomes, and an average marker density of one locus every 6 cM. Locus order is generally well maintained between the consensus map and the individual maps. Conclusion We have constructed a reliable and fairly dense consensus genetic linkage map that will serve as a basis for genomic approaches in faba bean research and breeding. The core map contains a larger number of markers than any previous individual map, covers existing gaps and achieves a wider coverage of the large faba bean genome as a whole. This tool can be used as a reference resource for studies in different genetic backgrounds, and provides a framework for transferring genetic information when using different marker technologies. Combined with syntenic approaches, the consensus map will increase marker density in selected genomic regions and will be useful for future faba bean molecular breeding applications. PMID:24377374

2013-01-01

233

IMMUNOLOGICAL COMPUTATION: THEORY AND APPLICATIONS  

E-print Network

IMMUNOLOGICAL COMPUTATION: THEORY AND APPLICATIONS AUTHORS/AFFILIATIONS: Dipankar Dasgupta Reviews fundamental immunology concepts Presents computational models based on the negative selection From CRC Press About the Book Over the last decade, the field of immunological computation has

Dasgupta, Dipankar

234

Dipeptidase 1: a candidate tumor-specific molecular marker in colorectal carcinoma.  

PubMed

The aim of this study was to identify tumor-specific markers for the detection of rare disseminated colorectal tumor cells in peripheral venous blood and in intra-peritoneal saline lavage samples collected before and after resection of colorectal tumors. Using cDNA micro-array screening, we found dipeptidase 1 (DPEP1) to be highly expressed in colon tumors compared to matched normal mucosa. Relative reverse transcriptase (RT)-PCR showed that DPEP1 was over-expressed by >/=2 fold in colon tumor compared to normal colonic mucosal tissue in 56/68 (82%) patients. Using immunobead RT-PCR, a technique that first enriches for epithelial cells, we found DPEP1 positive cells in intra-peritoneal lavage and venous blood samples from 15/38 (39%) colorectal cancer cases. This is the first report of DPEP1 as a marker for disseminated colon tumor cells. PMID:15145522

McIver, C M; Lloyd, J M; Hewett, P J; Hardingham, J E

2004-06-01

235

Invertebrate Ecological Immunology  

Microsoft Academic Search

Ecological immunology is a rapidly expanding field that examines the causes and consequences of variation in immune function in the context of evolution and of ecology. Millions of invertebrate species rely solely on innate immunity, compared with only 45,000 vertebrate species that rely additionally on an acquired immune system. Despite this difference in diversity, most studies of ecological immunology focus

J. Rolff; M. T. Siva-Jothy

2003-01-01

236

The New Cellular Immunology  

ERIC Educational Resources Information Center

Discusses the nature of the immune response and traces many of the discoveries that have led to the present state of knowledge in immunology. The new cellular immunology is directing its efforts toward improving health by proper manipulation of the immune mechanisms of the body. (JR)

Claman, Henry N.

1973-01-01

237

Immunology of the tonsils  

Microsoft Academic Search

The tonsils are lymphoepithelial structures that provide a protective immunological ring at the openings of both digestive and respiratory tracts. Here, as discussed by Marta Perry and Anthony Whyte, the unique nature of the various human tonsils reveals that they are capable of a variety of complex immunological functions.

Marta Perry; Anthony Whyte

1998-01-01

238

Immunology as Information Processing  

Microsoft Academic Search

This chapter describes the behavior of the immune system from an informationprocessing perspective. It reviews a series of projects conducted at the University of New Mexico and the Santa Fe Institute, which have developed and explored the theme "immunology as information processing." The projects cover the spectrum from serious modeling of real immunological phenomena, such as crossreactive responses in animals

Stephanie Forrest; Steven A. Hofmeyr

2000-01-01

239

16. Immunologic lung disease  

Microsoft Academic Search

This review summarizes the recent advances regarding pathogenesis, diagnosis, and treatment of immunological diseases of the lung. Rather than attempt a comprehensive analysis, we have focused on selected diseases that are of particular relevance to the practicing physician, and the material has been organized according to the dominant immunologic mechanisms underlying the disease. Because of the redundancy that characterizes the

Joseph E. Prince; Farrah Kheradmand; David B. Corry

2003-01-01

240

Development of molecular markers linked to the 'Fiesta' linkage group 7 major QTL for fire blight resistance and their application for marker-assisted selection.  

PubMed

A fire blight resistance QTL explaining 34.3%-46.6% of the phenotypic variation was recently identified on linkage group 7 of apple cultivar 'Fiesta' (F7). However, markers flanking this QTL were AFLP and RAPD markers unsuitable for marker-assisted selection (MAS). Two RAPD markers bracketing the QTL have been transformed into SCAR (sequence-characterized amplified region) markers, and an SSR marker specific for the region was developed. Pedigree analysis of 'Fiesta' with these markers enabled tracking of the F7 QTL allele back to 'Cox's Orange Pippin'. Stability of the effect of this QTL allele in different backgrounds was analyzed by inoculating progeny plants of a cross between 'Milwa', a susceptible cultivar, and '1217', a moderately resistant cultivar, and a set of cultivars that carry or lack the allele conferring increased fire blight resistance. Progenies and cultivars that carried both markers were significantly more resistant than those that did not carry both markers, indicating high stability of the F7 QTL allele in different backgrounds. This stability and the availability of reproducible markers bracketing the QTL make this locus promising for use in MAS. PMID:17632578

Khan, Muhammad A; Durel, Charles-Eric; Duffy, Brion; Drouet, Damien; Kellerhals, Markus; Gessler, Cesare; Patocchi, Andrea

2007-06-01

241

Identification of the IFITM Family as a New Molecular Marker in Human Colorectal Tumors  

Microsoft Academic Search

We analyzed the expression profiles of intestinal adenomas from a new murine familial adenomatous polyposis model (Apc#14\\/+) using suppression subtractive hybridization to identify novel diagnostic markers of colorectal carcinogenesis. We identified 18 candidate genes having increased expression levels in the adenoma. Subsequent Northern blotting, real- time reverse transcription-PCR, and in situ hybridization analysis confirmed their induction in B-catenin-activated epithelial cells

Pauline Andreu; Sabine Colnot; Cecile Godard; Pierre Laurent-Puig; Dominique Lamarque; Axel Kahn; Christine Perret; Beatrice Romagnolo

2006-01-01

242

Self-fertilization in brooding hermaphroditic Caribbean corals: Evidence from molecular markers  

Microsoft Academic Search

The occurrence of self-fertilization in natural populations of hermaphroditic marine invertebrates has seldom been documented. This is in contrast to plant systems where studies of self-fertilization dominate plant mating system literature. Randomly amplified polymorphic DNA markers were used to assess rates of natural self-fertilization in two common hermaphroditic Caribbean corals from the Florida Keys, Favia fragum and Porites astreoides. Rates

Daniel A. Brazeau; Daniel F. Gleason; Michael E. Morgan

1998-01-01

243

Molecular markers linked to white rust resistance in mustard Brassica juncea  

Microsoft Academic Search

White rust, caused by Albugo candida (Pers.) Kuntze, is an economically important disease of Brassica juncea (L.) Czern. and Coss mustard, particularly in India. The most efficient and cost-effective way of protecting mustard plants\\u000a from white rust disease is through genetic resistance. The objective of this study was to identify RAPD markers for white\\u000a rust resistance in an F1-derived doubled-haploid

K. V. Prabhu; D. J. Somers; G. Rakow; R. K. Gugel

1998-01-01

244

Using morphological diagnosis and molecular markers to assess the clonal fidelity of micropropagated Echinacea purpurea regenerants  

Microsoft Academic Search

Both morphological characteristics and amplified fragment length polymorphism (AFLP) markers were used to validate the genetic\\u000a fidelity of 1 080 field-grown Echinacea purpurea plants regenerated from leaf explants of donor T5-9. Morphological diagnosis revealed that 1 067 out of 1 080 regenerants\\u000a were normal, while 13 regenerants were aberrant. AFLP analysis was further performed to assess DNA variations among donor,

S. J. Chuang; C. L. Chen; J. J. Chen; J. M. Sung

2010-01-01

245

Research review: DNA polymerases as molecular markers of the regenerating capacity of hepatocytes  

Microsoft Academic Search

Hepatocyte regeneration has been widely investigated, with the mitotic index and the incorporation of [3H]thymidine being used as regeneration markers. We focused on the induction of DNA replication enzymes, particularly DNA polymerases\\u000a (pol) ?, ?, and ?. Using rat models, we have shown that the activity of pol ? in crude liver extract well represents the regenerating\\u000a capacity of hepatocytes.

Eiji Takeuchi; Yuji Nimura; Shin-ichi Mizuno; Hideaki Suzuki; Shinsuke Iyomasa; Masaki Terasaki; Hiroshi Kuriki; Keiko Tamiya-Koizumi; Shonen Yoshida

1997-01-01

246

Molecular phylogeny of the genus Buteo (Aves: Accipitridae) based on mitochondrial marker sequences  

Microsoft Academic Search

DNA sequences of the mitochondrial nd6 gene and the non-repetitive part of the pseudo-control region (?CR) were isolated from 101 individuals to analyze the phylogenetic relationships among all buzzards of the genus Buteo and other buteonine genera. Comparisons of the two marker sequences indicate that the ?CR evolved two times faster than the nd6 gene. The ?CR proved to be

Martin J. Riesing; Luise Kruckenhauser; Anita Gamauf; Elisabeth Haring

2003-01-01

247

Relationships among fourteen species of Satureja growing wild in Iran detected with molecular markers.  

PubMed

The genus Satureja is an important plant with a number of aromatic and medicinal properties. In this research, the relative efficiencies of amplified fragment length polymorphism (AFLP) and selectively amplified microsatellite polymorphic loci (SAMPL) were used to detect genetic relationships among 14 species of Satureja, growing wild in Iran. Eleven AFLP and 14 SAMPL primer combinations produced 999 and 1142 scorable bands, respectively, all of the fragments of which were found to be polymorphic. The average genetic similarity values based on Jaccard's coefficient were 0.24 and 0.21 for AFLP and SAMPL, respectively, indicating considerable distance and diversity in the studied germplasm. The correlation coefficients were statistically significant between both marker systems (r = 0.89). UPGMA derived from the combined binary data matrices of both markers depicted genetic distinctions among the studied species and clustered them into two main clusters and several groups. S. edmondi showed the maximum distance from other species and was placed into a single main cluster, while the maximum similarity was obtained between S. rechingeri and S. khuzistanica. Our results indicate that both marker systems are suitable for differentiating individuals and species of this genus. PMID:24548629

Hadian, J; Khadivi-Khub, A

2014-09-01

248

Improving the reliability of molecular sexing of birds using a W-specific marker  

Microsoft Academic Search

Molecular techniques for identifying sex of birds utilize length differences between CHD-Z and CHD-W introns, but in some cases these methods can lead to sexing errors. Here we show that an additional W-specific primer can be used in conjunction with a pre-existing sexing primer pair to dramatically improve the reliability of molecular sexing methods. We illustrate the approach with American

DAIZABURO SHIZUKA; BRUCE E. LYON

2008-01-01

249

Protein based molecular markers provide reliable means to understand prokaryotic phylogeny and support Darwinian mode of evolution  

PubMed Central

The analyses of genome sequences have led to the proposal that lateral gene transfers (LGTs) among prokaryotes are so widespread that they disguise the interrelationships among these organisms. This has led to questioning of whether the Darwinian model of evolution is applicable to prokaryotic organisms. In this review, we discuss the usefulness of taxon-specific molecular markers such as conserved signature indels (CSIs) and conserved signature proteins (CSPs) for understanding the evolutionary relationships among prokaryotes and to assess the influence of LGTs on prokaryotic evolution. The analyses of genomic sequences have identified large numbers of CSIs and CSPs that are unique properties of different groups of prokaryotes ranging from phylum to genus levels. The species distribution patterns of these molecular signatures strongly support a tree-like vertical inheritance of the genes containing these molecular signatures that is consistent with phylogenetic trees. Recent detailed studies in this regard on the Thermotogae and Archaea, which are reviewed here, have identified large numbers of CSIs and CSPs that are specific for the species from these two taxa and a number of their major clades. The genetic changes responsible for these CSIs (and CSPs) initially likely occurred in the common ancestors of these taxa and then vertically transferred to various descendants. Although some CSIs and CSPs in unrelated groups of prokaryotes were identified, their small numbers and random occurrence has no apparent influence on the consistent tree-like branching pattern emerging from other markers. These results provide evidence that although LGT is an important evolutionary force, it does not mask the tree-like branching pattern of prokaryotes or understanding of their evolutionary relationships. The identified CSIs and CSPs also provide novel and highly specific means for identification of different groups of microbes and for taxonomical and biochemical studies. PMID:22919687

Bhandari, Vaibhav; Naushad, Hafiz S.; Gupta, Radhey S.

2012-01-01

250

Identification and mapping of molecular markers linked to rust resistance genes located on chromosome 1RS of rye using wheat-rye translocation lines  

Microsoft Academic Search

The short arm of rye (Secale cereale) chromosome 1 has been widely used in breeding programs to incorporate new disease resistance genes into wheat. Using wheat-rye translocation and recombinant lines, molecular markers were isolated and mapped within chromosomal regions of 1RS carrying rust resistance genes Lr26, Sr31, Yr9 from 'Petkus' and SrR from 'Imperial' rye. RFLP markers previously mapped to

R. Mago; W. Spielmeyer; G. Lawrence; E. Lagudah; J. Ellis; A. Pryor

2002-01-01

251

Development of two new molecular markers specific to cytoplasmic male sterility in tuber mustard ( Brassica juncea var. tumida Tsen et Lee)  

Microsoft Academic Search

A novel and stable cytoplasmic male sterility CMS line of tuber mustard has been bred by subsequent backcrosses for 10 years.\\u000a Two specific markers atpA and orf220 were cloned and partially characterized in our previous study (Zhang et al. 2003). In this study, two new molecular markers, orf256 and orf305\\/orf324, have been isolated and identified. The orf256 gene size was found to

Xiao-lin Yu; Qiu-bin Xiao; Jia-shu Cao; Zhu-jun Chen; Yutaka Hirata

2009-01-01

252

Molekulare Marker in der Insektengenetik  

Microsoft Academic Search

Molecular markers in insect genetics. Invention of PCR revolutionized the field of molecular biology in the early 1990ies. Since then, a vast amount of genetic marker systems was introduced and led to the formation of the field of molecular ecology. For the phylogeneticist not primary involved in molecular methods it became difficult to decide which of the many marker systems

W. ARTHOFER

253

Shape-shifting corals: Molecular markers show morphology is evolutionarily plastic in Porites  

PubMed Central

Background Corals are notoriously difficult to identify at the species-level due to few diagnostic characters and variable skeletal morphology. This 'coral species problem' is an impediment to understanding the evolution and biodiversity of this important and threatened group of organisms. We examined the evolution of the nuclear ribosomal internal transcribed spacer (ITS) and mitochondrial markers (COI, putative control region) in Porites, one of the most taxonomically challenging and ecologically important genera of reef-building corals. Results Nuclear and mitochondrial markers were congruent, clearly resolving many traditionally recognized species; however, branching and mounding varieties were genetically indistinguishable within at least two clades, and specimens matching the description of 'Porites lutea' sorted into three genetically divergent groups. Corallite-level features were generally concordant with genetic groups, although hyper-variability in one group (Clade I) overlapped and obscured several others, and Synarea (previously thought to be a separate subgenus) was closely related to congeners despite its unique morphology. Scanning electron microscopy revealed subtle differences between genetic groups that may have been overlooked previously as taxonomic characters. Conclusion This study demonstrates that the coral skeleton can be remarkably evolutionarily plastic, which may explain some taxonomic difficulties, and obscure underlying patterns of endemism and diversity. PMID:19239678

Forsman, Zac H; Barshis, Daniel J; Hunter, Cynthia L; Toonen, Robert J

2009-01-01

254

Prediction of body mass index in mice using dense molecular markers and a regularized neural network.  

PubMed

Bayesian regularization of artificial neural networks (BRANNs) were used to predict body mass index (BMI) in mice using single nucleotide polymorphism (SNP) markers. Data from 1896 animals with both phenotypic and genotypic (12 320 loci) information were used for the analysis. Missing genotypes were imputed based on estimated allelic frequencies, with no attempt to reconstruct haplotypes based on family information or linkage disequilibrium between markers. A feed-forward multilayer perceptron network consisting of a single output layer and one hidden layer was used. Training of the neural network was done using the Bayesian regularized backpropagation algorithm. When the number of neurons in the hidden layer was increased, the number of effective parameters, ?, increased up to a point and stabilized thereafter. A model with five neurons in the hidden layer produced a value of ? that saturated the data. In terms of predictive ability, a network with five neurons in the hidden layer attained the smallest error and highest correlation in the test data although differences among networks were negligible. Using inherent weight information of BRANN with different number of neurons in the hidden layer, it was observed that 17 SNPs had a larger impact on the network, indicating their possible relevance in prediction of BMI. It is concluded that BRANN may be at least as useful as other methods for high-dimensional genome-enabled prediction, with the advantage of its potential ability of capturing non-linear relationships, which may be useful in the study of quantitative traits under complex gene action. PMID:21481292

Okut, Hayrettin; Gianola, Daniel; Rosa, Guilherme J M; Weigel, Kent A

2011-06-01

255

Veterinary Clinical Pathologist Position The Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and  

E-print Network

Veterinary Clinical Pathologist Position The Department of Microbiology, Immunology and Pathology, immunology, molecular diagnostics, and cancer. A large combined residency/PhD program in pathology and experience. Environment Overview The Department of Microbiology, Immunology and Pathology (MIP) has more than

Stephens, Graeme L.

256

Distribution and localization of microsatellites in the Perigord black truffle genome and identification of new molecular markers.  

PubMed

The level of genetic diversity and genetic structure in the Perigord black truffle (Tuber melanosporum Vittad.) has been debated for several years, mainly due to the lack of appropriate genetic markers. Microsatellites or simple sequence repeats (SSRs) are important for the genome organisation, phenotypic diversity and are one of the most popular molecular markers. In this study, we surveyed the T. melanosporum genome (1) to characterise its SSR pattern; (2) to compare it with SSR patterns found in 48 other fungal and three oomycetes genomes and (3) to identify new polymorphic SSR markers for population genetics. The T. melanosporum genome is rich in SSRs with 22,425 SSRs with mono-nucleotides being the most frequent motifs. SSRs were found in all genomic regions although they are more frequent in non-coding regions (introns and intergenic regions). Sixty out of 135 PCR-amplified mono-, di-, tri-, tetra, penta, and hexa-nucleotides were polymorphic (44%) within black truffle populations and 27 were randomly selected and analysed on 139 T. melanosporum isolates from France, Italy and Spain. The number of alleles varied from 2 to 18 and the expected heterozygosity from 0.124 to 0.815. One hundred and thirty-two different multilocus genotypes out of the 139 T. melanosporum isolates were identified and the genotypic diversity was high (0.999). Polymorphic SSRs were found in UTR regulatory regions of fruiting bodies and ectomycorrhiza regulated genes, suggesting that they may play a role in phenotypic variation. In conclusion, SSRs developed in this study were highly polymorphic and our results showed that T. melanosporum is a species with an important genetic diversity, which is in agreement with its recently uncovered heterothallic mating system. PMID:20965267

Murat, C; Riccioni, C; Belfiori, B; Cichocki, N; Labbé, J; Morin, E; Tisserant, E; Paolocci, F; Rubini, A; Martin, F

2011-06-01

257

De novo transcriptome analysis of Hevea brasiliensis tissues by RNA-seq and screening for molecular markers  

PubMed Central

Background The rubber tree, Hevea brasiliensis, is a species native to the Brazilian Amazon region and it supplies almost all the world’s natural rubber, a strategic raw material for a variety of products. One of the major challenges for developing rubber tree plantations is adapting the plant to biotic and abiotic stress. Transcriptome analysis is one of the main approaches for identifying the complete set of active genes in a cell or tissue for a specific developmental stage or physiological condition. Results Here, we report on the sequencing, assembling, annotation and screening for molecular markers from a pool of H. brasiliensis tissues. A total of 17,166 contigs were successfully annotated. Then, 2,191 Single Nucleotide Variation (SNV) and 1.397 Simple Sequence Repeat (SSR) loci were discriminated from the sequences. From 306 putative, mainly non-synonymous SNVs located in CDS sequences, 191 were checked for their ability to characterize 23 Hevea genotypes by an allele-specific amplification technology. For 172 (90%), the nucleotide variation at the predicted genomic location was confirmed, thus validating the different steps from sequencing to the in silico detection of the SNVs. Conclusions This is the first study of the H. brasiliensis transcriptome, covering a wide range of tissues and organs, leading to the production of the first developed SNP markers. This process could be amplified to a larger set of in silico detected SNVs in expressed genes in order to increase the marker density in available and future genetic maps. The results obtained in this study will contribute to the H. brasiliensis genetic breeding program focused on improving of disease resistance and latex yield. PMID:24670056

2014-01-01

258

Aberrant promoter CpG methylation as a molecular marker for disease monitoring in natural killer cell lymphomas.  

PubMed

Natural killer (NK) cell lymphomas lack suitable clonal markers for tumour cell detection, making the monitoring of minimal residual lymphoma difficult. Aberrant promoter CpG methylation occurs frequently in NK cell lymphomas. The objective of this study was to assess the potential of aberrant methylation as a surrogate tumour marker. Twenty-five primary tumours and 105 serial biopsies taken at various time points after treatment were examined using a methylation-specific polymerase chain reaction (MSP) for a panel of genes, comprising p73, p16, hMLH1, RARbeta and p15, previously shown to be methylated in NK cell lymphomas. All samples underwent independent morphological examination, supplemented by immunostaining for CD56 and in-situ hybridization for Epstein-Barr-virus-encoded RNA. Primary tumours showed the frequent methylation of the genes p73 (92%), p16 (71%), hMLH1 (61%), RARbeta (56%) and p15 (48%). MSP results in serial post-treatment biopsies were correlated with clinicopathological findings. Results were concordant in 89 follow-up samples (18 samples, histology positive/MSP positive; 71 samples, histology negative/MSP negative) and discordant in 16. Fifteen samples were histology negative/MSP positive, and tumour involvement was subsequently confirmed (positive re-biopsies or relapses at the same sites), indicating that MSP was more sensitive for minimal lymphoma detection. One sample was histology positive/MSP negative; a subsequent histological review and continuous clinical remission of the patient did not support tumour involvement. Our findings suggest that MSP for aberrantly methylated genes is a potentially valuable molecular marker for detecting either residual or relapsed disease in NK cell lymphoma patients. PMID:12823347

Siu, Lisa L P; Chan, John K C; Wong, Kit F; Choy, Carolyn; Kwong, Yok L

2003-07-01

259

Markers of hemostatic system activation during treatment of deep vein thrombosis with subcutaneous unfractionated or low-molecular weight heparin.  

PubMed

Prothrombin fragments (F1+2), thrombin-antithrombin complexes (TAT) and D-dimers, markers of hemostatic system activation, were measured in 59 consecutive patients with deep vein thrombosis (DVT). Patients were randomly treated either with subcutaneous unfractionated heparin (UH) administered in two to three subcutaneous doses adjusted to activated partial thromboplastin time (APTT) or with low-molecular weight heparin (LMWH) (dalteparin) administered in a fixed dose of 200 IU/kg body weight in one subcutaneous injection daily. Before treatment, F1+2, TAT and D-dimer were above the cut-off level in 27/59 (46%), 34/59 (58%) and all (100%) patients, respectively. Significant associations were observed between F1+2 and TAT (r=.66, P<.001), TAT and D-dimer (r=.36, P<.005) and F1+2 and D-dimer (r=.30, P<.050). On the third day of treatment, F1+2 and TAT significantly decreased to reference values in almost all patients (in 64/66 determinations of both F1+2 and TAT) and remained low on the seventh day of treatment. Compared to pretreatment values, a nonsignificant decrease of D-dimer was noted in both groups, but all values remained above the cut-off value. When markers of hemostatic system activation in the UH and LMWH groups were compared, no significant differences were observed. It was concluded that subcutaneous UH in an APTT-adjusted dose and subcutaneous LMWH in a once-daily weight-adjusted dose controlled these markers of hemostatic system activation in a similar manner. PMID:11927130

Peternel, Polona; Terbizan, Martina; Tratar, Gregor; Bozic, Mojca; Horvat, Dunja; Salobir, Barbara; Stegnar, Mojca

2002-02-01

260

Molecular markers for biodiversity analysis of wildlife animals: a brief review  

Microsoft Academic Search

Los marcadores moleculares constituyen unas herramientas indispensables para determinar la variación genética y la biodiversidad con un alto grado de precisión y reproductibilidad. Dichos marcadores se clasifican principalmente en dos tipos: marcadores mitocondriales y nucleares. Los marcadores de DNA mitocondrial, que se utilizan mucho, son en orden decreciente de secuencias conservadas ADNr 12S < ADNr 16S < citocromo b <

I. A. Arif; H. A. Khan

2009-01-01

261

Yellow lupin (Lupinus luteus L.) transcriptome sequencing: molecular marker development and comparative studies  

PubMed Central

Background Yellow lupin (Lupinus luteus L.) is a minor legume crop characterized by its high seed protein content. Although grown in several temperate countries, its orphan condition has limited the generation of genomic tools to aid breeding efforts to improve yield and nutritional quality. In this study, we report the construction of 454-expresed sequence tag (EST) libraries, carried out comparative studies between L. luteus and model legume species, developed a comprehensive set of EST-simple sequence repeat (SSR) markers, and validated their utility on diversity studies and transferability to related species. Results Two runs of 454 pyrosequencing yielded 205?Mb and 530?Mb of sequence data for L1 (young leaves, buds and flowers) and L2 (immature seeds) EST- libraries. A combined assembly (L1L2) yielded 71,655 contigs with an average contig length of 632 nucleotides. L1L2 contigs were clustered into 55,309 isotigs. 38,200 isotigs translated into proteins and 8,741 of them were full length. Around 57% of L. luteus sequences had significant similarity with at least one sequence of Medicago, Lotus, Arabidopsis, or Glycine, and 40.17% showed positive matches with all of these species. L. luteus isotigs were also screened for the presence of SSR sequences. A total of 2,572 isotigs contained at least one EST-SSR, with a frequency of one SSR per 17.75 kbp. Empirical evaluation of the EST-SSR candidate markers resulted in 222 polymorphic EST-SSRs. Two hundred and fifty four (65.7%) and 113 (30%) SSR primer pairs were able to amplify fragments from L. hispanicus and L. mutabilis DNA, respectively. Fifty polymorphic EST-SSRs were used to genotype a sample of 64?L. luteus accessions. Neighbor-joining distance analysis detected the existence of several clusters among L. luteus accessions, strongly suggesting the existence of population subdivisions. However, no clear clustering patterns followed the accession’s origin. Conclusion L. luteus deep transcriptome sequencing will facilitate the further development of genomic tools and lupin germplasm. Massive sequencing of cDNA libraries will continue to produce raw materials for gene discovery, identification of polymorphisms (SNPs, EST-SSRs, INDELs, etc.) for marker development, anchoring sequences for genome comparisons and putative gene candidates for QTL detection. PMID:22920992

2012-01-01

262

Molecular identification and phylogenetic relationship of green algae, Spirogyra ellipsospora (Chlorophyta) using ISSR and rbcL markers  

PubMed Central

Spirogyra is found in a wide range of habitats, including small stagnant water bodies, rivers, and streams. Spirogyra ellipsospora is common in northern Thailand. Species identification of the Spirogyra species based only on morphological characteristics can be difficult. A reliable and accurate method is required to evaluate genetic variations. This study aims to apply molecular approaches for the identification of S. ellipsospora using microsatellites and rbcL markers. Based on DNA sequencing, the rbcL gene was sequenced and the data was analyzed using the BLAST (Basic Local Alignment Search Tool) program in the NCBI (National Center for Biotechnology Information) database. The sequence of S. ellipsospora from this study revealed definitive identity matches in the range of 99% for the consensus sequences of S. ellipsospora. The 10 primers of ISSR could be amplified by 92 amplification fragments. The DNA fragments and the rbcL sequence data grouped the Spirogyra specimens into two distinct clusters.

Wongsawad, Pheravut; Peerapornpisal, Yuwadee

2014-01-01

263

Molecular identification and phylogenetic relationship of green algae, Spirogyra ellipsospora (Chlorophyta) using ISSR and rbcL markers.  

PubMed

Spirogyra is found in a wide range of habitats, including small stagnant water bodies, rivers, and streams. Spirogyra ellipsospora is common in northern Thailand. Species identification of the Spirogyra species based only on morphological characteristics can be difficult. A reliable and accurate method is required to evaluate genetic variations. This study aims to apply molecular approaches for the identification of S. ellipsospora using microsatellites and rbcL markers. Based on DNA sequencing, the rbcL gene was sequenced and the data was analyzed using the BLAST (Basic Local Alignment Search Tool) program in the NCBI (National Center for Biotechnology Information) database. The sequence of S. ellipsospora from this study revealed definitive identity matches in the range of 99% for the consensus sequences of S. ellipsospora. The 10 primers of ISSR could be amplified by 92 amplification fragments. The DNA fragments and the rbcL sequence data grouped the Spirogyra specimens into two distinct clusters. PMID:25313288

Wongsawad, Pheravut; Peerapornpisal, Yuwadee

2014-11-01

264

[Genetic diversity of Dactylis glomerata germplasm resources detected by Inter-simple Sequence Repeats (ISSRS) molecular markers].  

PubMed

Inter-simple Sequence Repeat (ISSR) molecular markers were used to detect the genetic diversity among 50 materials of Dactylis glomerata collected from China and other countries. Twelve primers produced 101 polymorphic bands, averaged 8.41 bands each primer pair. The average percentage of polymorpgic bands was 86.3.8%, and the range of GS (define) was 0.6116-0.9290, indicating a rich genetic diversity of D. glomerata. Based on the cluster and principal component analyses on the genetic characteristics, D. glomerata could be divided into 5 groups according to the nearest phylogenetic relationship. In most cases, accessions from the same continent were classified into the same group, the accessions from China and the United States belong to the different groups, respectively, indicating the geographical distribution of genetic diversity of D. glomerata. The present paper also discussed collection and conservation of germplasm resources in D. glomerata. PMID:16963418

Zeng, Bing; Zhang, Xin-Quan; Fan, Yan; Lan, Ying; Ma, Xiao; Peng, Yan; Liu, Wei

2006-09-01

265

A computational procedure for functional characterization of potential marker genes from molecular data: Alzheimer's as a case study  

PubMed Central

Background A molecular characterization of Alzheimer's Disease (AD) is the key to the identification of altered gene sets that lead to AD progression. We rely on the assumption that candidate marker genes for a given disease belong to specific pathogenic pathways, and we aim at unveiling those pathways stable across tissues, treatments and measurement systems. In this context, we analyzed three heterogeneous datasets, two microarray gene expression sets and one protein abundance set, applying a recently proposed feature selection method based on regularization. Results For each dataset we identified a signature that was successively evaluated both from the computational and functional characterization viewpoints, estimating the classification error and retrieving the most relevant biological knowledge from different repositories. Each signature includes genes already known to be related to AD and genes that are likely to be involved in the pathogenesis or in the disease progression. The integrated analysis revealed a meaningful overlap at the functional level. Conclusions The identification of three gene signatures showing a relevant overlap of pathways and ontologies, increases the likelihood of finding potential marker genes for AD. PMID:21726470

2011-01-01

266

Identification of Molecular Genetic Markers in Pyrenophora teres f. teres Associated with Low Virulence on 'Harbin' Barley.  

PubMed

ABSTRACT Two isolates of the barley net blotch pathogen (Pyrenophora teres f. teres), one possessing high virulence (0-1) and the other possessing low virulence (15A) on the barley cultivar Harbin, were crossed and the progeny of the mating were isolated. Conidia from cultures of the parent and progeny isolates were used as inoculum to determine the inheritance of virulence in the pathogen. Of the 82 progeny tested, 42 exhibited high virulence and 40 exhibited low virulence on 'Harbin' barley. The data support a model in which a single, major gene controls virulence in P. teres f. teres on this barley cultivar (1:1 ratio; chi(2) = 0.05, P = 0.83). Preparations of DNA were made from parental and progeny isolates, and the DNA was subjected to the random amplified polymorphic DNA (RAPD) technique in a search for molecular genetic markers associated with the virulence phenotype. Five RAPD markers were obtained that were associated in coupling with low virulence. The data indicate that the RAPD technique can be used to tag genetic determinants for virulence in P. teres f. teres. PMID:18944793

Weiland, J J; Steffenson, B J; Cartwright, R D; Webster, R K

1999-02-01

267

Molecular Phylogeny of a tick, Ixodes granulatus (Acari: Ixodidae) based on cytochrome oxidase subunit I (COI) marker  

NASA Astrophysics Data System (ADS)

Identification of a local species of tick, Ixodes granulatus from the family Ixodidae is essential because it has potential to be vector for spotted fever group (SFG) rickettsia and tick thypus. The aim of this study is to portray the relationships among several populations of I. granulatus collected from different species of animal hosts and localities in Peninsular Malaysia. Polymerase Chain Reaction was conducted by amplifying mitochondrial DNA marker, namely cytochrome oxidase subunit I (COI) sequences from 15 individual ticks that attached to five different hosts caught from three different localities. Confirmation of the species identity was accomplished using BLAST program. Neighbor-joining (NJ) and Maximum Parsimony (MP) tree based on COI sequences were constructed by using PAUP 4.0b10 to identify the relationship among species. The result of this study showed a high genetic heterogeneity between I. granulatus and other species of the same genus (7.2-23.7%). Furthermore, a low intraspecific variation was observed among the species of I. granulatus collected from different localities (0-3.7%). This study produced the first establishment of molecular marker for clarifying genetic species variation and diversity of local I. granulatus tick which contribute to the control of tick-borne infections.

Lah, Ernieenor Faraliana Che; Yaakop, Salmah; Ahamad, Mariana; George, Ernna; Nor, Shukor Md

2014-09-01

268

Molecular characterization of a gender-linked DNA marker and a related gene in Mercurialis annua L.  

PubMed

The dioecious Mercurialis annua L. was used as a model plant to study some aspects of the molecular basis of sex determination in plants. We report in this paper the characterization of a previously identified male specific DNA marker, OPB01-1562, from diploid dioecious M. annua. The marker co-segregated with male sex in the progeny of hormonally feminized males. Sequence analysis showed the presence of approximately 0.6 kb retrotransposon-like sequence at its 3' end. Homologous sequences were isolated from diploid female, hexaploid male and monoecious plants. These sequences contained RNaseH and integrase domains of reverse transcriptase and were most similar to pineapple retrotransposon dea1, hence were named M. annua retrotransposon-like sequences (MARL-1 to MARL-5). A 771 bp fragment isolated from a diploid female, named fem771, was homologous to the 5' end of OPB01-1562. Results from DNA blot hybridization suggested OPB01-1562 and fem771 to be from the same locus and MARL-1 from a different one. RNA blot hybridization with OPB01-1562 and MARL-1 detected an approximately 2.8 kb transcript which was expressed strongly in stems and flowers of females but not males. This transcript was named M. annua female expressed (Mafex). Sex linkage of OPB01-1562 and expression of Mafex detected by OPB01-1562 strongly suggested Mafex to be a candidate gene involved in sex determination in M. annua. PMID:16049676

Khadka, Deepak Kumar; Nejidat, Ali; Tal, Moshe; Golan-Goldhirsh, Avi

2005-12-01

269

Immunologic derangement preceding clinical autoimmunity.  

PubMed

Autoantibodies are valuable markers for the recognition of autoimmune diseases. Over the last 25 years, several investigators have consistently shown that autoantibodies precede the clinical onset of cognate diseases by years or decades. This phenomenon, regularly observed in the natural history of autoimmune diseases, indicates that autoimmunity develops through successive stages across a variable period of time until the characteristic manifestations of disease are clinically apparent. Recent evidence indicates that the pre-clinical stages of autoimmune diseases involve a series of immunologic derangements and that this process is dynamic and progressive. During the years preceding clinical disease onset, there is progressive intensification in the humoral autoimmune response, characterized by increases in autoantibody titer, avidity, number of immunoglobulin isotypes, and spread of epitopes and of autoantigens targeted. This scenario is reminiscent of cancer processes that develop slowly by means of progressive stages, and may be interrupted by early detection and therapeutic intervention. Therefore, it might be reasoned that early intervention may be more effective in reverting the less firmly established autoimmune abnormalities at the pre-clinical stage of autoimmunity. With the continuous progress in novel immunologic therapeutic strategies, one can envision the possibility that early intervention at pre-clinical stages may lead to prevention of overt disease development and even cure of the autoimmune disorder. PMID:25228734

Dellavance, A; Coelho Andrade, L E

2014-10-01

270

Sib-parentage testing using molecular markers when parents are unknown.  

PubMed

The formulae for computing the so-called Sib Index using codominant alleles for (1) full-sib and (2) half-sib parentage are given. Hypothesis testing is based on the distribution of conditional likelihood ratio or Bayes' factor. Thresholds for rejecting the null hypothesis and P-values were obtained in function of the number of alleles and their frequency distributions. Simulations showed that a relatively low number of marker systems (e.g. 20) are enough to accept the hypothesis of sib parentage with a reasonable power for usual significance levels, but that a higher number would be necessary if full-sib against half-sib parentage is the contrast to be carried out. The effect of sampling variation on the allele frequencies on power calculations is also analysed. PMID:12354145

García, D; Carleos, C; Parra, D; Cañón, J

2002-10-01

271

The detection of pfcrt and pfmdr1 point mutations as molecular markers of chloroquine drug resistance, Pahang, Malaysia  

PubMed Central

Background Malaria is still a public health problem in Malaysia with chloroquine (CQ) being the first-line drug in the treatment policy of uncomplicated malaria. There is a scarcity in information about the magnitude of Plasmodium falciparum CQ resistance. This study aims to investigate the presence of single point mutations in the P. falciparum chloroquine-resistance transporter gene (pfcrt) at codons 76, 271, 326, 356 and 371 and in P. falciparum multi-drug resistance-1 gene (pfmdr1) at codons 86 and 1246, as molecular markers of CQ resistance. Methods A total of 75 P. falciparum blood samples were collected from different districts of Pahang state, Malaysia. Single nucleotide polymorphisms in pfcrt gene (codons 76, 271, 326, 356 and 371) and pfmdr1 gene (codons 86 and 1246) were analysed by using mutation-specific nested PCR and restriction fragment length polymorphism (PCR-RFLP) methods. Results Mutations of pfcrt K76T and pfcrt R371I were the most prevalent among pfcrt gene mutations reported by this study; 52% and 77%, respectively. Other codons of the pfcrt gene and the positions 86 and 1246 of the pfmdr1 gene were found mostly of wild type. Significant associations of pfcrt K76T, pfcrt N326S and pfcrt I356T mutations with parasitaemia were also reported. Conclusion The high existence of mutant pfcrt T76 may indicate the low susceptibility of P. falciparum isolates to CQ in Peninsular Malaysia. The findings of this study establish baseline data on the molecular markers of P. falciparum CQ resistance, which may help in the surveillance of drug resistance in Peninsular Malaysia. PMID:22853645

2012-01-01

272

Designing a SCAR molecular marker for monitoring Trichoderma cf. harzianum in experimental communities* #  

PubMed Central

Several species of the fungal genus Trichoderma establish biological interactions with various micro- and macro-organisms. Some of these interactions are relevant in ecological terms and in biotechnological applications, such as biocontrol, where Trichoderma could be considered as an invasive species that colonizes a recipient community. The success of this invasion depends on multiple factors, which can be assayed using experimental communities as study models. Therefore, the aim of this work is to develop a species-specific sequence-characterized amplified region (SCAR) marker to monitor the colonization and growth of T. cf. harzianum when it invades experimental communities. For this study, 16 randomly amplified polymorphic DNA (RAPD) primers of 10-mer were used to generate polymorphic patterns, one of which generated a band present only in strains of T. cf. harzianum. This band was cloned, sequenced, and five primers of 20–23 mer were designed. Primer pairs 2F2/2R2 and 2F2/2R3 successfully and specifically amplified fragments of 278 and 448 bp from the T. cf. harzianum BpT10a strain DNA, respectively. Both primer pairs were also tested against the DNA from 14 strains of T. cf. harzianum and several strains of different fungal genera as specificity controls. Only the DNA from the strains of T. cf. harzianum was successfully amplified. Moreover, primer pair 2F2/2R2 was assessed by quantitative real-time polymerase chain reaction (PCR) using fungal DNA mixtures and DNA extracted from fungal experimental communities as templates. T. cf. harzianum was detectable even when as few as 100 copies of the SCAR marker were available or even when its population represented only 0.1% of the whole community. PMID:25367789

Perez, Gabriel; Verdejo, Valentina; Gondim-Porto, Clarissa; Orlando, Julieta; Caru, Margarita

2014-01-01

273

Designing a SCAR molecular marker for monitoring Trichoderma cf. harzianum in experimental communities.  

PubMed

Several species of the fungal genus Trichoderma establish biological interactions with various micro- and macro-organisms. Some of these interactions are relevant in ecological terms and in biotechnological applications, such as biocontrol, where Trichoderma could be considered as an invasive species that colonizes a recipient community. The success of this invasion depends on multiple factors, which can be assayed using experimental communities as study models. Therefore, the aim of this work is to develop a species-specific sequence-characterized amplified region (SCAR) marker to monitor the colonization and growth of T. cf. harzianum when it invades experimental communities. For this study, 16 randomly amplified polymorphic DNA (RAPD) primers of 10-mer were used to generate polymorphic patterns, one of which generated a band present only in strains of T. cf. harzianum. This band was cloned, sequenced, and five primers of 20-23 mer were designed. Primer pairs 2F2/2R2 and 2F2/2R3 successfully and specifically amplified fragments of 278 and 448 bp from the T. cf. harzianum BpT10a strain DNA, respectively. Both primer pairs were also tested against the DNA from 14 strains of T. cf. harzianum and several strains of different fungal genera as specificity controls. Only the DNA from the strains of T. cf. harzianum was successfully amplified. Moreover, primer pair 2F2/2R2 was assessed by quantitative real-time polymerase chain reaction (PCR) using fungal DNA mixtures and DNA extracted from fungal experimental communities as templates. T. cf. harzianum was detectable even when as few as 100 copies of the SCAR marker were available or even when its population represented only 0.1% of the whole community. PMID:25367789

Pérez, Gabriel; Verdejo, Valentina; Gondim-Porto, Clarissa; Orlando, Julieta; Carú, Margarita

2014-11-01

274

DEGREE PROGRAMME BSc (Hons) Immunology  

E-print Network

BSc (Hons) Immunology DEGREE PROGRAMME GUIDE 2013-2014 #12;BSc (Hons) Immunology Introduction - Year 4 Introduction Immunology developed as the study of how the body defends itself against pathogens health and regulating disease have become apparent. As a result, immunology incorporates a wide variety

Levi, Ran

275

Stanford Immunology Graduate Program Handbook  

E-print Network

1 Stanford Immunology Graduate Program Handbook 2013-2014 #12;PhD Program in Immunology 2013-2014 PhD Handbook 2 The PhD Program in Immunology is one of thirteen Stanford Biosciences programs. The goal of the PhD Program in Immunology is to provide outstanding training and education for obtaining

Puglisi, Joseph

276

tostandoutfromthecrowd? NextGen Immunology  

E-print Network

tostandoutfromthecrowd? Doyouwant NextGen Immunology: The Michael Sela Student and Postdoc Program for Excellence in Immunology Become a leader of NextGen Immunology! The immune system, in addition to its, state-of-the-art immunology is now reemerging as the most rapidly evolving multi-disciplinary biological

Shapiro, Ehud

277

Book reviews Evolutionary immunology?  

E-print Network

or biomedical value: carp, earthworms, snails, mosquitoes. (As an aide, why is immunology one of the very few branches of basic biology not to have sought initial understanding from organisms simpler than mam- mals

Read, Andrew

278

Genetic Profiling of the Plasmodium falciparum Population Using Antigenic Molecular Markers  

PubMed Central

About 50% of malaria infections in India are attributed to Plasmodium falciparum but relatively little is known about the genetic structure of the parasite populations. The molecular genotyping of the parasite populations by merozoite surface protein (msp1 and msp2) and glutamate-rich protein (glurp) genes identifies the existing parasite population in the regions which help in understanding the molecular mechanisms involved in the parasite's drive for survival. This study reveals the genetic profile of the parasite population in selected regions across the country with varying degree of endemicity among them. We also report the prevalence of Pfcrt mutations in this parasite population to evaluate the pattern of drug resistance development in them.

Gupta, Purva; Khan, Haris; Raza, Adil; Yadavendu, Veena; Bhatt, R. M.; Singh, Vineeta

2014-01-01

279

The immunological synapse  

Microsoft Academic Search

CHAPTER SUMMARY: T-cell activation requires interaction of T-cell antigen receptors with proteins of the major histocompatibility complex (antigen). This interaction takes place in a specialized cell–cell junction referred to as an immunological synapse. The immunological synapse contains at least two functional domains: a central cluster of engaged antigen receptors and a surrounding ring of adhesion molecules. The segregation of the

Michael L Dustin

2002-01-01

280

Carbohydrate microarrays for the recognition of cross-reactive molecular markers of microbes and host cells  

Microsoft Academic Search

We describe here the development of a carbohydrate-based microarray to extend the scope of biomedical research on carbohydrate-mediated molecular recognition and anti-infection responses. We have demonstrated that microbial polysaccharides can be immobilized on a surface-modified glass slide without chemical conjugation. With this procedure, a large repertoire of microbial antigens (?20,000 spots) can be patterned on a single micro-glass slide, reaching

Shaoyi Liu; Brian J. Trummer; Chao Deng; Aili Wang; Denong Wang

2002-01-01

281

Oranges and lemons: clues to the taxonomy of Citrus from molecular markers.  

PubMed

Go into any grocery store and one is confronted with an array of Citrus fruit: oranges, grapefruit, mandarins (tangerines), lemons and limes. This is rich bounty for the shopper, but taxonomists are perplexed as to how to classify the various kinds of Citrus that have existed since antiquity. Now, thanks to new genetic and molecular biological techniques, the relationships between these fruit are being unraveled and show that there are probably only three true species. PMID:11525837

Moore, G A

2001-09-01

282

Development of a molecular linkage map of pearl millet integrating DArT and SSR markers  

Microsoft Academic Search

Pearl millet is an important component of food security in the semi-arid tropics and is assuming greater importance in the\\u000a context of changing climate and increasing demand for highly nutritious food and feed. Molecular tools have been developed\\u000a and applied for pearl millet on a limited scale. However, the existing tool kit needs to be strengthened further for its routine

A. Supriya; S. Senthilvel; T. Nepolean; K. Eshwar; V. Rajaram; R. Shaw; C. T. Hash; A. Kilian; R. C. Yadav; M. L. Narasu

2011-01-01

283

Predictive molecular markers in metastases to the central nervous system: recent advances and future avenues.  

PubMed

Metastases to the central nervous system (CNS) are common in several cancer types. For most primary tumors that commonly metastasize to the CNS, molecular biomarker analyses are recommended in the clinical setting for selection of appropriate targeted therapies. Therapeutic efficacy of some of these agents has been documented in patients with brain metastases, and molecular testing of CNS metastases should be considered in the clinical setting. Here, we summarize the clinically relevant biomarker tests that should be considered in neurosurgical specimens based on the current recommendations of the European Society of Medical Oncology (ESMO) or the National Comprehensive Cancer Network (NCCN) for the most relevant primary tumor types: lung cancer (EGFR mutations, ALK rearrangement, BRAF mutations), breast cancer (HER2 amplification, steroid receptor overexpression), melanoma (BRAF mutations), and colorectal cancer (RAS mutations). Furthermore, we discuss emerging therapeutic targets including novel oncogenic alterations (ROS1 rearrangements, FGFR1 amplifications, CMET amplifications, and others) and molecular features of the tumor microenvironment (including immune-checkpoint molecules such as CTLA4 and PD-1/PD-L1). We also discuss the potential role of advanced biomarker tests such as next-generation sequencing and "liquid biopsies" for patients with CNS metastases. PMID:25287912

Berghoff, Anna Sophie; Bartsch, Rupert; Wöhrer, Adelheid; Streubel, Berthold; Birner, Peter; Kros, Johan M; Brastianos, Priscilla K; von Deimling, Andreas; Preusser, Matthias

2014-12-01

284

Applicability of molecular markers to determine parasitic infection origins in the animal trade: a case study from Sarcoptes mites in wildebeest.  

PubMed

The development of non-manipulative molecular tools to determine the origin of parasite infections in the animal trade (if infected before their export or import) is of great interest worldwide for both the animal trade industry and for animal welfare. Molecular tools have a wide range of applications, including forensic identification, wildlife preservation and conservation, veterinary public health protection, and food safety. Nonetheless, genetic markers were not reported to detect the source of infection in the animal trade. In this study we tested the applicability of molecular tools to detect the origin of Sarcoptes mite infection of wildebeest imported by the United Arab Emirate (UAE) from Tanzania. Using one multiplex of seven microsatellite markers and control samples from UAE, Kenya and Italy, we demonstrated the usefulness of the multiplex STR-typing as a molecular tool of pivotal interest to help commercialist, authorities, and conservationists, to identify the geographical origin of parasitic infections. PMID:21814832

Alasaad, Samer; Schuster, Rolf K; Gakuya, Francis; Theneyan, Mohamed; Jowers, Michael J; Maione, Sandra; Min, Annarita Molinar; Soriguer, Ramón C; Rossi, Luca

2012-09-01

285

Associations among cytoplasmic molecular markers, gender, and components of fitness in Silene vulgaris, a gynodioecious plant.  

PubMed

It has been suggested that the dynamics of chloroplast DNA (cpDNA) or mitochondrial DNA (mtDNA) genetic markers used in studies of plant populations could be influenced by natural selection acting elsewhere in the genome. This could be particularly true in gynodioecious plants if cpDNA or mtDNA genetic markers are in gametic disequilibrium with genes responsible for sex expression. In order to investigate this possibility, a natural population of the gynodioecious plant Silene vulgaris was used to study associations among mtDNA haplotype, cpDNA haplotype, sex and some components of fitness through seed. Individuals were sampled for mtDNA and cpDNA haplotype as determined using restriction fragment length polymorphism (RFLP) methods, sex (female or hermaphrodite), fruit number, fruit set, seeds/fruit and seed germination. The sex of surviving germinating seeds was also noted. All individuals in the population fell into one of two cytoplasmic categories, designated haplotypes f and g by a unique electrophoretic signature in both the mtDNA and cpDNA. The subset of the population carrying haplotype g included a significantly higher proportion of females when compared with the sex ratio of the subset carrying the f haplotype. Haplotype g had a significantly higher fitness when measured by fruit number, fruit set and seeds/fruit, whereas haplotype f had significantly higher fitness when measured by seed germination. Offspring of individuals carrying haplotype g included a significantly greater proportion of females when compared with offspring of individuals carrying the f haplotype. Other studies of gynodioecious plants have shown that females generally have higher fitness through seed than hermaphrodites, but in this study not all fitness differences between haplotypes could be predicted from differences in haplotype-specific sex ratio alone. Rather, some differences in haplotype-specific fitness were due to differences in fitness between individuals of the same sex, but carrying different haplotypes. The results are discussed with regard to the potential for hitchhiking selection to influence the dynamics of the noncoding regions used to designate the cpDNA and mtDNA haplotypes. PMID:12675832

McCauley, D E; Olson, M S

2003-03-01

286

Expanding Character Sampling for Ciliate Phylogenetic Inference Using Mitochondrial SSU-rDNA as a Molecular Marker  

PubMed Central

Molecular systematics of ciliates, particularly at deep nodes, has largely focused on increasing taxon sampling using the nuclear small subunit rDNA (nSSU-rDNA) locus. These previous analyses have generally been congruent with morphologically-based classifications, although there is extensive non-monophyly at many levels. However, caution is needed in interpreting these results as nSSU-rDNA is just a single molecular marker. Here the mitochondrial small subunit rDNA (mtSSU-rDNA) is evaluated for deep ciliate nodes using the Colpodea as an example. Overall, well-supported nodes in the mtSSU-rDNA and concatenated topologies are well supported in the nSSU-rDNA topology; e.g., the non-monophyly of the Cyrtolophosidida. The two moderately-to well-supported incongruences between the loci are the placement of the Sorogenida and Colpoda aspera. Our analyses of mtSSU-rDNA support the conclusion, originally derived from nSSU-rDNA, that the morphological characters used in taxonomic circumscriptions of the Colpodea represent a mixture of ancestral and derived states. This demonstration of the efficacy of the mtSSU-rDNA will enable phylogenetic reconstructions of deep nodes in the ciliate tree of life to move from a single-locus to a multi-locus approach. PMID:20708960

Dunthorn, Micah; Foissner, Wilhelm; Katz, Laura A.

2012-01-01

287

The evolving role of molecular markers in the diagnosis and management of diffuse glioma.  

PubMed

While the classification of diffuse gliomas has relied on the examination of morphologic features supplemented with techniques such as immunohistochemistry, there is an increasing recognition of substantial biologic diversity within morphologically defined entities. High-throughput technologies, in particular studies that integrate genome-wide data from diverse molecular platforms, increasingly identify the existence of robust and distinct glioma subtypes. While treatment advances and improvement of outcomes for patients with diffuse glioma have been modest, there may be benefit to integrate findings from biologic studies into clinical practice to enhance the precision of treatment for these diseases. Recent examples such as the identification of mutations in IDH1 and IDH2 as an early genetic event that is predominantly in lower-grade gliomas (grades 2 and 3) underscore the importance of molecular discovery leading to the ability to develop subclassifications with prognostic and potentially therapeutic implications. In contrast, glioblastoma (grade 4), the most common and aggressive glioma, typically arises without IDH mutation, supporting the need for different therapeutic approaches. Additional genomic and epigenomic signatures are generally nonoverlapping between IDH-mutant and IDH wild-type diffuse glioma, and despite comparable histopathology, IDH-mutant gliomas can be considered as biologically distinct from IDH wild-type gliomas. In this CCR Focus article, we highlight and summarize the current understanding of recent molecular findings and the relationships of these findings to clinical trials and clinical management. See all articles in this CCR Focus section, "Discoveries, Challenges, and Progress in Primary Brain Tumors." Clin Cancer Res; 20(22); 5601-11. ©2014 AACR. PMID:25398843

Huse, Jason T; Aldape, Kenneth D

2014-11-15

288

Study Of Genetic Diversity Between Grasspea Landraces Using Morphological And Molecular Marker  

NASA Astrophysics Data System (ADS)

Grass pea is a beneficial crop to Iran since it has some major advantageous such as high grain and forage quality, high drought tolerance and medium level of salinity tolerance and a good native germplasm variation which accessible for breeding programs. This study was carried out to evaluate morphological traits of the grass pea landraces using a randomized complete block design with 3 replications at Research Farm of Isfahan University of Technology. To evaluate genetic diversity of 14 grass pea landraces from various locations in Iran were investigated using 32 RAPD & ISJ primers at Biocenter of University of Zabol. Analysis of variance indicated a highly significant differences among 14 grass pea landrace for the morphological traits. Average of polymorphism percentage of RAPD primer was 73.9%. Among used primer, 12 random primers showed polymorphism and a total of 56 different bands were observed in the genotypes. Jafar-abad and Sar-chahan genotypes with similarity coefficient of 66% and Khoram-abad 2 and Khoram-abad 7 genotypes with similarity coefficient of 3% were the most related and the most distinct genotypes, respectively. Fourteen primers out of 17 semi random primers produced 70 polymorphic bands which included 56% of the total 126 produced bands. Genetic relatedness among population was investigated using Jacard coefficient and unweighted pair group mean analysis (UPGMA) algorithm. The result of this research verified possibility of use of RAPD & ISJ markers for estimation of genetic diversity, management of genetic resources and determination of repetitive accessions in grass pea.

Sedehi, Abbasali Vahabi; Lotfi, Asefeh; Solooki, Mahmood

2008-01-01

289

Fasciola hepatica: identification of molecular markers for resistant and susceptible Pseudosuccinea columella snail hosts.  

PubMed

Protein electrophoresis, RAPD-PCR and nuclear rDNA ITS sequencing were performed to search for genetic differences between Pseudosuccinea columella snails susceptible and resistant to Fasciola hepatica infection. Of the 21 enzymatic loci analyzed in both populations, none of them exhibited neither within- or between-group variation. Such an absence of enzyme polymorphism support the hypothesis of selfing as the "prevalent" mating system for this hermaphroditic species. Conversely, the RAPD profiles displayed clear differences between susceptible and resistant isolates for 17 of the 26 primers tested while no within-group variation was detected. rDNA ITS sequence analysis from snails of each isolates showed only two bases that differed between groups accounting for a 0.17% of variation confirming that susceptible and resistant snails belong to the same species. This is the first time that a genetic variation using RAPD markers is demonstrated between susceptible and resistant lymnaeid snails vis-a-vis of F. hepatica infection in absence of experimental selection. PMID:14990314

Gutiérrez, Alfredo; Pointier, Jean-Pierre; Fraga, Jorge; Jobet, Edouard; Modat, Sylvain; Pérez, R T; Yong, Mary; Sanchez, J; Loker, Eric S; Théron, André

2003-01-01

290

Molecular markers reveal infestation dynamics of the bed bug (Hemiptera: Cimicidae) within apartment buildings.  

PubMed

The bed bug, Cimex lectularius L. (Hemiptera: Cimicidae), has experienced an extraordinary global resurgence in recent years, the reasons for which remain poorly understood. Once considered a pest of lower socioeconomic classes, bed bugs are now found extensively across all residential settings, with widespread infestations established in multiapartment buildings. Within such buildings, understanding the population genetic structure and patterns of dispersal may prove critical to the development of effective control strategies. Here, we describe the development of 24 high-resolution microsatellite markers through next generation 454 pyrosequencing and their application to elucidate infestation dynamics within three multistory apartment buildings in the United States. Results reveal contrasting characteristics potentially representative of geographic or locale differences. In Raleigh, NC, an infestation within an apartment building seemed to have started from a single introduction followed by extensive spread. In Jersey City, NJ, two or more introductions followed by spread are evident in two buildings. Populations within single apartments in all buildings were characterized by high levels of relatedness and low levels of diversity, indicative of foundation from small, genetically depauperate propagules. Regardless of the number of unique introductions, genetic data indicate that spread within buildings is extensive, supporting both active and human-mediated dispersal within and between adjacent rooms or apartments spanning multiple floors. PMID:22679860

Booth, Warren; Saenz, Virna L; Santangelo, Richard G; Wang, Changlu; Schal, Coby; Vargo, Edward L

2012-05-01

291

Distribution of Mytilus taxa in European coastal areas as inferred from molecular markers  

NASA Astrophysics Data System (ADS)

The genetic constitution of mussels ( Mytilus spp.) was studied by means of three nuclear (Me 15/16, EF-bis, ITS) and one mtDNA (ND2-COIII) marker on a large European scale. In addition to a sharp cline between Atlantic and Mediterranean M. galloprovincialis, we observed a clear genetic distinction between the Black Sea and Mediterranean populations and a higher incidence of M. trossulus than reported so far in northern European populations. The frequency of M. galloprovincialis nuclear alleles was high along the Iberian Peninsula and decreased abruptly along the French coasts with a high frequency of M. edulis alleles in the Bay of Biscay, The Netherlands, Germany, Iceland, Barents and White Seas, and with little evidence of introgression between the two taxa. M. trossulus alleles were observed in the Baltic Sea and Danish Straits as expected. In addition, occurrence of M. trossulus alleles in cold waters of Iceland, Barents Sea and White Sea is reported for the first time.

Kijewski, T.; ?mietanka, B.; Zbawicka, M.; Gosling, E.; Hummel, H.; Wenne, R.

2011-02-01

292

Molecular Insight of Putative Pathogenicity Markers with ESBL Genes and Lipopolysaccharide in Laribacter hongkongensis.  

PubMed

Laribacter hongkongensis is an emerging bacterial pathogen causing gastroenteritis and traveller's diarrhoea. However, pathogenicity of L. hongkongensis has not yet been properly understood. We therefore, investigated putative pathogenicity markers like elt, est, stx1, stx2, eae, eaf, EAgg, bfpA, Int I, Int II, Int III and cnf respectively in strains received from Queen Mary Hospital, Hong Kong University. Above genes were commonly found among pathogenic member genera of Enterobacteriaceae-causing diarrhoea. Received strains were confirmed microbiologically and by 16S ribosomal RNA (rRNA) sequencing. Cultivability was examined using 23 different commercially available microbial growth media followed by antibiotic susceptibility test, lipopolysaccharide (LPS) extraction and raising antisera in rabbit against heat-killed L. hongkongensis. Moreover, Escherichia coli classification genes chuA, yjaA, TspE4 and extended spectrum beta lactamase (ESBL) genes like TEM, SHV, OXA, CTXM, CTXM1 and CTXM9 were also examined by PCR assay. Results showed the possession of eae, bfpA, Int and CTXM9 respectively for putative virulence. Furthermore, purity of extracted LPS was confirmed by HPLC, and raised serum was found useful in diagnosis of LPS; bacterium thus can be employed for immunodiagnostics. PMID:25154369

Raja, Krishna M; Ghosh, Asit Ranjan

2014-11-01

293

Identification of Molecular Markers Linked to a Pyrenophora teres Avirulence Gene.  

PubMed

ABSTRACT Genetic control of avirulence in the net blotch pathogen, Pyrenophora teres, was investigated. To establish an appropriate study system, a collection of 10 net form (P. teres f. teres) and spot form (P. teres f. maculata) isolates were evaluated on a set of eight barley lines to identify two isolates with differential virulence on an individual host line. Two net form isolates, WRS 1906, exhibiting avirulence on the cv. Heartland, and WRS 1607, exhibiting high virulence, were mated and 67 progeny were isolated and phenotyped for reaction on Heartland. The population segregated in a 1:1 ratio, 34 avirulent to 33 virulent (chi(2) = 0.0, P = 1.0), indicating single gene control of WRS 1906 avirulence on Heartland. Bulked segregant analysis was used to identify six amplified fragment length polymorphism markers closely linked to the avirulence gene (Avr(Heartland)). This work provides evidence that the P. teres-barley pathosystem conforms to the gene-for-gene model and represents an initial step toward map-based cloning of this gene. PMID:18943933

Beattie, Aaron D; Scoles, Graham J; Rossnagel, Brian G

2007-07-01

294

Molecular detection of virulence genes as markers in Pseudomonas aeruginosa isolated from urinary tract infections  

PubMed Central

Catheter associated urinary tract infections by P. aeruginosa are related to variety of complications. Quorum sensing and related circuitry guard its virulence potential. Though P. aeruginosa accounts for an appreciable amount of virulence factors, this organism is highly unstable phenotypically. Thus, genotyping of clinical isolates of P. aeruginosa is of utmost importance for understanding the epidemiology of infection. This may contribute towards development of immunotherapeutic approaches against this multi drug resistant pathogen. Moreover, no epidemiological study has been reported yet on uroisolates of P. aeruginosa. Thus this study was planned to obtain information regarding presence, distribution and rate of occurrence of quorum sensing and some associated virulence genes at genetic level. The profiling of quorum sensing genes lasI, lasR, rhlI, rhlR and virulence genes like toxA, aprA, rhlAB, plcH, lasB and fliC of twelve strains of P. aeruginosa isolated from patients with UTIs was done by direct PCR. The results showed variable distribution of quorum sensing genes and virulence genes. Their percentage occurrence may be specifically associated with different levels of intrinsic virulence and pathogenicity in urinary tract. Such information can help in identifying these virulence genes as useful diagnostic markers for clinical P. aeruginosa strains isolated from UTIs. PMID:25379131

Sabharwal, Neha; Dhall, Shriya; Chhibber, Sanjay; Harjai, Kusum

2014-01-01

295

Retrotransposon-Based Molecular Markers for Analysis of Genetic Diversity within the Genus Linum  

PubMed Central

SSAP method was used to study the genetic diversity of 22 Linum species from sections Linum, Adenolinum, Dasylinum, Stellerolinum, and 46 flax cultivars. All the studied flax varieties were distinguished using SSAP for retrotransposons FL9 and FL11. Thus, the validity of SSAP method was demonstrated for flax marking, identification of accessions in genebank collections, and control during propagation of flax varieties. Polymorphism of Fl1a, Fl1b, and Cassandra insertions were very low in flax varieties, but these retrotransposons were successfully used for the investigation of Linum species. Species clusterization based on SSAP markers was in concordance with their taxonomic division into sections Dasylinum, Stellerolinum, Adenolinum, and Linum. All species of sect. Adenolinum clustered apart from species of sect. Linum. The data confirmed the accuracy of the separation in these sections. Members of section Linum are not as closely related as members of other sections, so taxonomic revision of this section is desirable. L. usitatissimum accessions genetically distant from modern flax cultivars were revealed in our work. These accessions are of utmost interest for flax breeding and introduction of new useful traits into flax cultivars. The chromosome localization of Cassandra retrotransposon in Linum species was determined.

Melnikova, Nataliya V.; Kudryavtseva, Anna V.; Zelenin, Alexander V.; Lakunina, Valentina A.; Yurkevich, Olga Yu.; Speranskaya, Anna S.; Dmitriev, Alexey A.; Krinitsina, Anastasia A.; Belenikin, Maxim S.; Uroshlev, Leonid A.; Snezhkina, Anastasiya V.; Sadritdinova, Asiya F.; Koroban, Nadezda V.; Amosova, Alexandra V.; Samatadze, Tatiana E.; Guzenko, Elena V.; Lemesh, Valentina A.; Savilova, Anastasya M.; Rachinskaia, Olga A.; Kishlyan, Natalya V.; Rozhmina, Tatiana A.; Bolsheva, Nadezhda L.; Muravenko, Olga V.

2014-01-01

296

Echinococcus granulosus tegumental enzymes as in vitro markers of pharmacological damage: a biochemical and molecular approach.  

PubMed

Cystic echinococcosis is a chronic, complex, and neglected disease. Novel therapeutical tools are needed to optimize human treatment. A number of compounds have been investigated, either using in vitro cultured parasites and/or applying in vivo rodent models. Although some of these compounds showed promising activities in vitro, and to some extent also in the rodent models, they have not been translated into clinical applications. Membrane enzyme activities in culture supernatants of treated protoscoleces with calcium modulator drugs and anthelmintic drugs were measured and provided an indication of compound efficacy. This work describes for the first time the detection of alkaline phosphatase, gamma-glutamyl-transpeptidase and acetylcholinesterase activities in supernatants of in vitro treated Echinococcus granulosus protoscoleces. Marked differences on the enzymatic activities in supernatants from drug treated cultures were detected. We demonstrated that those genes that show the highest degree of conservation when compared to orthologs, are constitutively and highly expressed in protoscoleces and metacestodes. Due to high sensibility and the lack of activity in supernatants of intact protoscoleces, gamma-glutamyl-transpeptidase is proposed as the ideal viability marker during in vitro pharmacological studies against E. granulosus protoscoleces. PMID:22609954

Cumino, Andrea C; Nicolao, M Celeste; Loos, Julia A; Denegri, Guillermo; Elissondo, M Celina

2012-12-01

297

[Inheritance analysis and molecular marker selection of genes for wheat spindle streak mosaic disease resistance].  

PubMed

Three wheat spindle streak mosaic viruses (WSSMV) resistant cultivars ('Yining Xiaomai', 'Xu87-633', and 'Xifeng') and one susceptible cultivar ('Zhen9523') were used as parents of 3 crosses in this experiment. WSSMV resistance of the parents, F1, and F2 was evaluated under field condition. Based on the segregation ratios of resistant and susceptible plants in F, and F2 populations, it was deduced that the resistance to WSSMV was dominant and the inheritable factors controlling WSSMV resistance were encoded by the nuclear genome. WSSMV resistances in 'Yining Xiaomai' and 'Xifeng' were controlled by two pairs of alleles, which showed complementary effects. However the resistance in 'Xu-87633' was controlled by a single dominant gene. 266 pairs of SSR primers located on 21 wheat chromosomes were used for polymorphic analysis of the two resistant and the susceptible parents 'Yining Xiaomai' and 'Zhen9523', and 108 of them amplified polymorphic DNA products. By Bulk Segregant Analysis of resistant and susceptible pools, one pair of primer located on chromosome arm 2DS, Xgwm261, were found being linked to WSSMV resistance. The 224 F2 individuals were then amplified with marker Xgwm261. The statistic genetic distance between Xgwm261 and the resistance locus was calculated to be 22.9 cM using the software Mapmaker 3.0. PMID:16078742

Zhang, Qing-Ping; Wang, Xiu-E; Wang, Yao-Nan; Zhao, Yan; Wang, Hai-Yan; Wang, Su-Ling; Chen, Pei-Du

2005-07-01

298

Molecular Characterization of Selected Local and Exotic Cattle Using RAPD Marker  

PubMed Central

In order to develop specific genetic markers and determine the genetic diversity of Bangladeshi native cattle (Pabna, Red Chittagong) and exotic breeds (Sahiwal), randomly amplified polymorphic DNA (RAPD) analysis was performed using 12 primers. Genomic DNA was extracted from 20 cattle (local and exotic) blood samples and extracted DNA was observed by gel electrophoresis. Among the random primers three were matched and found to be polymorphic. Genetic relations between cattle’s were determined by RAPD polymorphisms from a total of 66.67%. Statistical analysis of the data, estimating the genetic distances between cattle and sketching the cluster trees were estimated by using MEGA 5.05 software. Comparatively highest genetic distance (0.834) was found between RCC-82 and SL-623. The lowest genetic distance (0.031) was observed between M-1222 and M-5730. The genetic diversity of Red Chittagong and Sahiwal cattle was relatively higher for a prescribed breed. Adequate diversity in performance and adaptability can be exploited from the study results for actual improvement accruing to conservation and development of indigenous cattle resources. PMID:25049622

Khatun, M. Mahfuza; Hossain, Khondoker Moazzem; Mahbubur Rahman, S. M.

2012-01-01

299

Retrotransposon-Based Molecular Markers for Analysis of Genetic Diversity within the Genus Linum.  

PubMed

SSAP method was used to study the genetic diversity of 22 Linum species from sections Linum, Adenolinum, Dasylinum, Stellerolinum, and 46 flax cultivars. All the studied flax varieties were distinguished using SSAP for retrotransposons FL9 and FL11. Thus, the validity of SSAP method was demonstrated for flax marking, identification of accessions in genebank collections, and control during propagation of flax varieties. Polymorphism of Fl1a, Fl1b, and Cassandra insertions were very low in flax varieties, but these retrotransposons were successfully used for the investigation of Linum species. Species clusterization based on SSAP markers was in concordance with their taxonomic division into sections Dasylinum, Stellerolinum, Adenolinum, and Linum. All species of sect. Adenolinum clustered apart from species of sect. Linum. The data confirmed the accuracy of the separation in these sections. Members of section Linum are not as closely related as members of other sections, so taxonomic revision of this section is desirable. L. usitatissimum accessions genetically distant from modern flax cultivars were revealed in our work. These accessions are of utmost interest for flax breeding and introduction of new useful traits into flax cultivars. The chromosome localization of Cassandra retrotransposon in Linum species was determined. PMID:25243121

Melnikova, Nataliya V; Kudryavtseva, Anna V; Zelenin, Alexander V; Lakunina, Valentina A; Yurkevich, Olga Yu; Speranskaya, Anna S; Dmitriev, Alexey A; Krinitsina, Anastasia A; Belenikin, Maxim S; Uroshlev, Leonid A; Snezhkina, Anastasiya V; Sadritdinova, Asiya F; Koroban, Nadezda V; Amosova, Alexandra V; Samatadze, Tatiana E; Guzenko, Elena V; Lemesh, Valentina A; Savilova, Anastasya M; Rachinskaia, Olga A; Kishlyan, Natalya V; Rozhmina, Tatiana A; Bolsheva, Nadezhda L; Muravenko, Olga V

2014-01-01

300

Molecular characterization and differentiation of five horse breeds raised in Algeria using polymorphic microsatellite markers.  

PubMed

In this study, genetic analyses of diversity and differentiation were performed on five horse breeds raised in Algeria (Barb, Arab-Barb, Arabian, Thoroughbred and French Trotter). All microsatellite markers were highly polymorphic in all the breeds. A total of 123 alleles from 14 microsatellite loci were detected in 201 horses. The average number of alleles per locus was the highest in the Arab-Barb horses (7.86) and lowest in the thoroughbred breed (5.71), whereas the observed and expected heterozygosities per breed ranged from 0.71 (Thoroughbred) to 0.752 (Barb) and 0.71 (Thoroughbred) to 0.77 (Arab-Barb), respectively. The genetic differentiation between the breeds was significant (p < 0.01) based on the infinitesimal model (FST ). Three different approaches for evaluating the genetic relationships were applied. Genetic distances, the factorial correspondence analysis and structure analysis showed that a significant amount of genetic variation is maintained in the native horse populations and the other breeds. The Barb and Arab-Barb breeds seem to be the most genetically related and support the decision to consider the breeds as same population. PMID:24834806

Berber, N; Gaouar, S; Leroy, G; Kdidi, S; Tabet Aouel, N; Saïdi Mehtar, N

2014-10-01

301

[Biological markers in schizophrenia].  

PubMed

Based on a review of the literature, the article deals with the major biological markers of schizophrenia. Recent developments in molecular biology have shown a possible association between schizophrenia and various HLA markers (A1, A2, A9, A10, A28, B27, BW16), and a linkage--in several families--between the disease and some polymorphisms of chromosome 5. On the other hand, chromosome X might also be involved. Neuropathological abnormalities have often been found in the brains of schizophrenics, such as cellular alterations in the basal ganglia and the limbic structures. Investigations by means of CT-scan and Magnetic Resonance Imaging have pointed out an enlargement of cerebral ventricles and/or an atrophy of frontal areas, especially amongst patients with prominent negative symptoms. The dopaminergic hypothesis of schizophrenia reposes on the major following facts: the therapeutic efficiency of neuroleptics (dopaminergic antagonists); a positive correlation between plasma homovanillic acid (metabolite of dopamine) concentration and the severity of schizophrenic illness; a higher density of dopaminergic D2-receptors (revealed by Positron Emission Tomography thanks to specific radioligands), particularly in the striatum; and an abnormal plasmatic growth-hormone response to apomorphine (dopaminergic agonist). Central noradrenergic dysfunctions might also occur in paranoid schizophrenia, as underlined by higher cerebrospinal fluid levels of norepinephrine, and a lack of decrease of plasma 3-methoxy-4-hydroxy-phenylglycol (MHPG, metabolite of norepinephrine) after clonidine (alpha-2-adrenergic agonist) dispensation. Nevertheless, in patients with predominating negative symptoms, this is a trouble in serotoninergic functions which has been suggested. In the field of immunology, some findings such as alteration in lymphocytes populations (T4/T8, CD5), anti-cerebral auto-antibodies, abnormal lymphocytes responses to mitogens, decreased production of interleukin-2, have lead to two main hypotheses: autoimmunity and immunologic incompetence. On the other hand, electrophysiological studies have shown a hypovariability of alpha-rythm on the EEG; a lower amplitude of the component P300 from visual evoked potentials; sleep disorders such as a shorter rapid eye movement sleep latency and a decreased total slow-wave sleep percent; irregular smooth pursuit eyes-movements; an electrodermal response according to either the hyper-responder either the non-responder type. At last, troubles in sensory integration, motor coordination and attention have also been demonstrated. All those many findings outline the heterogeneity of schizophrenic disorders. PMID:8306920

Lembreghts, M; Ansseau, M

1993-01-01

302

Mechanisms and potential molecular markers of early response to combination epigenetic therapy in patients with myeloid malignancies.  

PubMed

Combination epigenetic treatment (EGT) utilizing DNA methyl transferase inhibitors (DNMTi) and histone deacetylase inhibitors (HDACi) may be more efficacious than single agent treatment in myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML). The molecular mechanisms behind the potential clinical efficacy of combination EGT treatment are incompletely understood and the frequently lengthy EGT regimes required to determine clinical response have generated a significant demand for early molecular markers of treatment response. Our study aimed to identify the effect of combination azacitidine (AZA) and panobinostat (LBH589) on expression levels of a panel of genes implicated in the pathogenesis of high-risk MDS or AML in HL-60 cells. We also characterized gene expression profiles in peripheral blood mononuclear (PBMCs) from patients in a recently reported phase Ib/II clinical trial using the combination of AZA and LBH589 and correlated these findings with clinical response to treatment. In vitro analysis demonstrated increased expression of caspase-3, Nor-1, NUR77, p15INK4B and p21WAF1/CIP1 and decreased expression of Bcl?xL in HL-60 cells treated with combination EGT. Analysis of patient samples prior to treatment demonstrated a significant reduction in NUR77 and p21WAF1/CIP1 expression compared to healthy controls. NUR77 and p21WAF1/CIP1 levels were similar between treatment non?responders and responders at screening. Early post first cycle treatment (day 25) analysis demonstrated a significant increase in expression of both NUR77, and p21WAF1/CIP1. A significant increase in NUR77, and p21WAF1/CIP1 together with a trend to increase in p15INK4B first cycle expression was observed in treatment responders compared to non-responders. In summary, combination AZA and LBH589 epigenetic treatment is associated with in vitro and in vivo modulation of genes implicated in the pathogenesis of MDS/AML. Early expression of NUR77 and p21WAF1/CIP1 correlated with clinical response to combination EGT suggesting investigation for potential use as molecular markers of early treatment response may be warranted. PMID:25051119

Liu, H B; Urbanavicius, D; Tan, P; Spencer, A; Dear, A E

2014-10-01

303

Temporal trends of molecular markers associated with artemether-lumefantrine tolerance/resistance in Bagamoyo district, Tanzania  

PubMed Central

Background Development and spread of Plasmodium falciparum resistance to artemisinin-based combination therapy (ACT) constitutes a major threat to recent global malaria control achievements. Surveillance of molecular markers could act as an early warning system of ACT-resistance before clinical treatment failures are apparent. The aim of this study was to analyse temporal trends of established genotypes associated with artemether-lumefantrine tolerance/resistance before and after its deployment as first-line treatment for uncomplicated malaria in Tanzania 2006. Methods Single nucleotide polymorphisms in the P. falciparum multidrug resistance gene 1 (pfmdr1) N86Y, Y184F, D1246Y and P. falciparum chloroquine transporter gene (pfcrt) K76T were analysed from dried blood spots collected during six consecutive studies from children with uncomplicated P. falciparum malaria in Fukayosi village, Bagamoyo District, Tanzania, between 2004–2011. Results There was a statistically significant yearly increase of pfmdr1 N86, 184F, D1246 and pfcrt K76 between 2006–2011 from 14% to 61% (yearly OR = 1.38 [95% CI 1.25-1.52] p < 0.0001), 14% to 35% (OR = 1.17 [95% CI 1.07-1.30] p = 0.001), 54% to 85% (OR = 1.21 [95% CI 1.03-1.42] p = 0.016) and 49% to 85% (OR = 1.33 [95% CI 1.17-1.51] p < 0.0001), respectively. Unlike for the pfmdr1 SNP, a significant increase of pfcrt K76 was observed already between 2004–2006, from 26% to 49% (OR = 1.68 [95% CI 1.17-2.40] p = 0.005). From 2006 to 2011 the pfmdr1 NFD haplotype increased from 10% to 37% (OR = 1.25 [95% CI 1.12-1.39] p < 0.0001), whereas the YYY haplotype decreased from 31% to 6% (OR = 0.73 [95% CI 0.56-0.98] p = 0.018). All 390 successfully analysed samples had one copy of the pfmdr1 gene. Conclusion The temporal selection of molecular markers associated with artemether-lumefantrine tolerance/resistance may represent an early warning sign of impaired future drug efficacy. This calls for stringent surveillance of artemether-lumefantrine efficacy in Tanzania and emphasizes the importance of molecular surveillance as a complement to standard in vivo trials. PMID:23506218

2013-01-01

304

Validity of the bear tapeworm Diphyllobothrium ursi (Cestoda: Diphyllobothriidae) based on morphological and molecular markers.  

PubMed

The bear tapeworm Diphyllobothrium ursi is described based upon the morphology of adult tapeworms recovered from the brown bear (Ursus arctos middendorffi) and larval plerocercoids found in sockeye salmon (Oncorhynchus nerka) from Kodiak Island in Alaska in 1952. However, in 1987 D. ursi was synonymized with Diphyllobothrium dendriticum, and the taxonomic relationship between both species has not subsequently been revised. In this study mitochondrial cytochrome c oxidase subunit 1 gene (cox1) sequences of holotype and paratype D. ursi specimens that had been preserved in a formalin-acetic acid-alcohol solution since the time the species was initially described approximately 60 yr ago were analyzed. Molecular and phylogenetic analysis of the cox1 sequences revealed that D. ursi is more closely related to D. dendriticum than it is to Diphyllobothrium nihonkaiense and Diphyllobothrium latum. In addition to molecular evidence, differences in the life cycle and ecology of the larval plerocercoids between D. ursi and D. dendriticum also suggest that D. ursi is a distinct species, separate from D. dendriticum and D. nihonkaiense, and also possibly from D. latum . PMID:22663179

Yamasaki, Hiroshi; Muto, Maki; Yamada, Minoru; Arizono, Naoki; Rausch, Robert L

2012-12-01

305

Comparative protein profiles: potential molecular markers from spermatozoa of Acipenseriformes (Chondrostei, Pisces).  

PubMed

Sturgeon and paddlefish (Acipenseriformes), the source of roe consumed as caviar, are a unique and commercially valuable group of ancient fishes. In this study, comparative proteomics was used to analyze protein profiles of spermatozoa from five sturgeon species and one paddlefish: Siberian sturgeon (Acipenser baerii), sterlet (A. ruthenus), Russian sturgeon (A. gueldenstaedtii), starry sturgeon (A. stellatus), beluga (Huso huso), and Mississippi paddlefish (Polyodon spathula). Protein profiles of spermatozoa were determined by isoelectric focusing and two-dimensional electrophoresis (2-DE) high-resolution gels. The peptides, previously selected by 2-DE analysis as potentially species-specific, were obtained by "in-gel" tryptic digestion, followed by matrix-associated laser desorption/ionization time-of-flight/mass spectrometry (MALDI-TOF/MS). Among the 23 protein spots selected, 14 were identified as isoforms of enolase B present in all species, but with different isoelectric points or molecular mass. Exceptions were A. ruthenus and H. huso, species with a close phylogenetic relationship. Glycerol-3-phosphate dehydrogenase was detected exclusively in P. spathula. Phosphoglycerate kinase was detected only in A. ruthenus and H. huso, and 3 additional proteins (fructose bisphosphate aldolase A-2, glycogen phosphorylase type IV and glyceraldehyde-3-phosphate dehydrogenase) were found exclusively in A. gueldenstaedtii and H. huso. This study points to the application of proteomics for differential characterization and comparative studies of acipenseriform species at the molecular level. PMID:20869341

Li, Ping; Hulak, Martin; Rodina, Marek; Sulc, Miroslav; Li, Zhi-Hua; Linhart, Otomar

2010-12-01

306

Molecular characterization of the Andean blackberry, Rubus glaucus, using SSR markers.  

PubMed

The species Rubus glaucus, also known as the Andean or "Castilla" blackberry, is one of nine edible species of this genus that grow naturally in Central and South America. In Colombia, this species is the most important of all Rubus species for agricultural and commercial purposes. We used 20 SSRs developed for other Rubus species to characterize 44 Colombian R. glaucus genotypes, collected from eight different departments, and to look for molecular differences between thornless and thorny cultivated blackberries. Eighty-two bands were obtained from 28 loci. The genotypes were classified into eight populations, corresponding to collection sites. The mean number of polymorphic alleles per locus in all populations and genotypes ranged from 1.857 to 2.393. Samples collected from Valle del Cauca, Quindío, Caldas, and Risaralda departments had the highest heterozygosity values. The finding of exclusive bands from R. glaucus genotypes from Valle del Cauca, Quindío, and Caldas demonstrates genetic and molecular differentiation between thorny and thornless Andean blackberries. PMID:22370934

Marulanda, M; López, A M; Uribe, M

2012-01-01

307

Distinctive mitochondrial genome of Calanoid copepod Calanus sinicus with multiple large non-coding regions and reshuffled gene order: Useful molecular markers for phylogenetic and population studies  

Microsoft Academic Search

BACKGROUND: Copepods are highly diverse and abundant, resulting in extensive ecological radiation in marine ecosystems. Calanus sinicus dominates continental shelf waters in the northwest Pacific Ocean and plays an important role in the local ecosystem by linking primary production to higher trophic levels. A lack of effective molecular markers has hindered phylogenetic and population genetic studies concerning copepods. As they

Wang Minxiao; Sun Song; Li Chaolun; Shen Xin

2011-01-01

308

New insights into family relationships within the avian superfamily Sylvioidea (Passeriformes) based on seven molecular markers  

PubMed Central

Background The circumscription of the avian superfamily Sylvioidea is a matter of long ongoing debate. While the overall inclusiveness has now been mostly agreed on and 20 families recognised, the phylogenetic relationships among the families are largely unknown. We here present a phylogenetic hypothesis for Sylvioidea based on one mitochondrial and six nuclear markers, in total ~6.3 kbp, for 79 ingroup species representing all currently recognised families and some species with uncertain affinities, making this the most comprehensive analysis of this taxon. Results The resolution, especially of the deeper nodes, is much improved compared to previous studies. However, many relationships among families remain uncertain and are in need of verification. Most families themselves are very well supported based on the total data set and also by indels. Our data do not support the inclusion of Hylia in Cettiidae, but do not strongly reject a close relationship with Cettiidae either. The genera Scotocerca and Erythrocercus are closely related to Cettiidae, but separated by relatively long internodes. The families Paridae, Remizidae and Stenostiridae clustered among the outgroup taxa and not within Sylvioidea. Conclusions Although the phylogenetic position of Hylia is uncertain, we tentatively support the recognition of the family Hyliidae Bannerman, 1923 for this genus and Pholidornis. We propose new family names for the genera Scotocerca and Erythrocercus, Scotocercidae and Erythrocercidae, respectively, rather than including these in Cettiidae, and we formally propose the name Macrosphenidae, which has been in informal use for some time. We recommend that Paridae, Remizidae and Stenostiridae are not included in Sylvioidea. We also briefly discuss the problems of providing a morphological diagnosis when proposing a new family-group name (or genus-group name) based on a clade. PMID:22920688

2012-01-01

309

Most frequent molecular and immunohistochemical markers present in selected types of brain tumors.  

PubMed

Tumors of brain tissue and meninges create a heterogeneous group with various biological behavior, therapy management and differing prognosis. Some of these do not require treatment, some can be cured by surgery and some are rapidly fatal despite treatment. Despite huge progress in tumor research, innovations in diagnostic tools and therapy, prognosis remains, in case of malignant tumor types, very serious. There has been an increased understanding of molecular abnormalities occurring in primary brain tumors. Genome-wide analyses of tumors have improved the knowledge in tumor biology. The aim of the research is to explain the oncogenesis features thus leading to the use of new therapeutic modalities in order to prolong survival rate of patients and at the same time providing satisfactory life quality. This article offers a short review of the basic genetic alterations present with some histological types of brain tumors. PMID:24968406

Richterová, Romana; Jure?eková, Jana; Evinová, Andrea; Kolarovszki, Branislav; Ben?o, Martin; De Riggo, Július; Sutovský, Juraj; Mahmood, Silvia; Ra?ay, Peter; Dobrota, Dušan

2014-01-01

310

The Transferrin Receptor: A Potential Molecular Imaging Marker for Human Cancer1  

PubMed Central

Abstract Noninvasive imaging of differences between the molecular properties of cancer and normal tissue has the potential to enhance the detection of tumors. Because overexpression of endogenous transferrin receptor (TfR) has been qualitatively described for various cancers and is presumably due to malignant transformation of cells, TfR may represent a suitable target for application of molecular imaging technologies to increase detection of smaller tumors. In the work reported here, investigation into the biology of this receptor using electron microscopy has demonstrated that iron oxide particles targeted to TfR are internalized and accumulate in lysosomal vesicles within cells. Biochemical analysis of the interaction of imaging probes with cells overexpressing the TfR demonstrated that the extent of accumulation, and therefore probe efficacy, is dependent on the nature of the chemical cross-link between transferrin and the iron oxide particle. These data were utilized to design and synthesize an improved imaging probe. Experiments demonstrate that the novel magnetic resonance imaging (MRI) probe is sensitive enough to detect small differences in endogenous TfR expression in human cancer cell lines. Quantitative measurement of TfR overexpression in a panel of 27 human breast cancer patients demonstrated that 74% of patient cancer tissues overexpressed the TfR and that the sensitivity of the new imaging agent was suitable to detect TfR overexpression in greater than 40% of these cases. Based on a biochemical and cell biological approach, these studies have resulted in the synthesis and development of an improved MRI probe with the best in vitro and in vivo imaging properties reported to date. PMID:14965443

Hogemann-Savellano, Dagmar; Bos, Erik; Blondet, Cyrille; Sato, Fuminori; Abe, Tatsuya; Josephson, Lee; Weissleder, Ralph; Gaudet, Justin; Sgroi, Dennis; Peters, Peter J.; Basilion, James P.

2003-01-01

311

Molecular marker and stable carbon isotope analyses of carbonaceous Ambassador uranium ores of Mulga Rock in Western Australia  

NASA Astrophysics Data System (ADS)

Mulga Rock is a multi-element deposit containing uranium hosted by Eocene peats and lignites deposited in inset valleys incised into Permian rocks of the Gunbarrel Basin and Precambrian rocks of the Yilgarn Craton and Albany-Fraser Orogen. Uranium readily adsorbs onto minerals or phytoclasts to form organo-uranyl complexes. This is important in pre-concentrating uranium in this relatively young ore deposit with rare uraninite [UO2] and coffinite [U(SiO4)1-x(OH)4x], more commonly amorphous and sub-micron uranium-bearing particulates. Organic geochemical and compound-specific stable carbon isotope analyses were conducted to identify possible associations of molecular markers with uranium accumulation and to recognize effect(s) of ionizing radiation on molecular markers. Samples were collected from the Ambassador deposit containing low (<200 ppm) to high (>2000 ppm) uranium concentrations. The bulk rock C/N ratios of 82 to 153, Rock-Eval pyrolysis yields of 316 to 577 mg hydrocarbon/g TOC (Hydrogen Index, HI) and 70 to 102 mg CO2/g TOC (Oxygen Index, OI) are consistent with a terrigenous and predominantly vascular plant OM source deposited in a complex shallow water system, ranging from lacustrine to deltaic, swampy wetland and even shallow lake settings as proposed by previous workers. Organic solvent extracts were separated into saturated hydrocarbon, aromatic hydrocarbon, ketone, and a combined free fatty acid and alcohol fraction. The molecular profiles appear to vary with uranium concentration. In samples with relatively low uranium concentrations, long-chain n-alkanes, alcohols and fatty acids derived from epicuticular plant waxes dominate. The n-alkane distributions (C27 to C31) reveal an odd/even preference (Carbon Preference Index, CPI=1.5) indicative of extant lipids. Average ?13C of -27 to -29 ‰ for long-chain n-alkanes is consistent with a predominant C3 plant source. Samples with relatively higher uranium concentrations contain mostly intermediate-length n-alkanes, ketones, alcohols, and fatty acids (C20 to C24) with no preferential distribution (CPI~1). Intermediate length n-alkanes have modest carbon isotope enrichment compared to long-chain n-alkanes. These shorter-chain hydrocarbons are interpreted to represent alteration products. The diversity and relative abundance of ketones in highly mineralised Mulga Rock peats and lignites are not consistent with aerobic and diagenetic degradation of terrigenous OM in oxic environments. Moreover, molecular changes cannot be associated with thermal breakdown due to the low maturity of the deposits. It is possible that the association of high uranium concentrations and potential radiolysis resulted in the oxidation of alcohol functional groups into aldehydes and ketones and breakdown of highly aliphatic macromolecules (i.e. spores, pollen, cuticles, and algal cysts). These phytoclasts are usually considered to be recalcitrant as they evolved to withstand chemical and physical degradation. Previous petrographic analyses show that spores, pollen and wood fragments are preferentially enriched in uranium. Their molecular compositions are feasible sources of short- to intermediate-length n-alkanes that dominate the mineralised peats and lignites.

Jaraula, C.; Schwark, L.; Moreau, X.; Grice, K.; Bagas, L.

2013-12-01

312

Molecular systematics and phylogeography of the tribe Myonycterini (Mammalia, Pteropodidae) inferred from mitochondrial and nuclear markers.  

PubMed

The tribe Myonycterini comprises five fruit bat species of the family Pteropodidae, which are endemic to tropical Africa. Previous studies have produced conflicting results about their interspecific relationships. Here, we performed a comparative phylogeographic analysis based on 148 complete cytochrome b gene sequences from the three species distributed in West Africa and Central Africa (Myonycteris torquata, Lissonycteris angolensis and Megaloglossus woermanni). In addition, we investigated phylogenetic relationships within the tribe Myonycterini, using a matrix including 29 terminal taxa and 7235 nucleotide characters, corresponding to an alignment of two mitochondrial genes and seven nuclear introns. Our phylogenetic analyses confirmed that the genus Megaloglossus belongs to the tribe Myonycterini. Further, the genus Rousettus is paraphyletic, with R. lanosus, sometimes placed in the genus Stenonycteris, being the sister-group of the tribes Myonycterini and Epomophorini. Our phylogeographic results showed that populations of Myonycteris torquata and Megaloglossus woermanni from the Upper Guinea Forest are highly divergent from those of the Congo Basin Forest. Based on our molecular data, we recommended several taxonomic changes. First, Stenonycteris should be recognized as a separate genus from Rousettus and composed of S. lanosus. This genus should be elevated to a new tribe, Stenonycterini, within the subfamily Epomophorinae. This result shows that the evolution of lingual echolocation was more complicated than previously accepted. Second, the genus Lissonycteris is synonymised with Myonycteris. Third, the populations from West Africa formerly included in Myonycteris torquata and Megaloglossus woermanni are now placed in two distinct species, respectively, Myonycteris leptodon and Megaloglossus azagnyi sp. nov. Our molecular dating estimates show that the three phases of taxonomic diversification detected within the tribe Myonycterini can be related to three distinct decreases in tree cover vegetation, at 6.5-6, 2.7-2.5, and 1.8-1.6Ma. Our results suggest that the high nucleotide distance between Ebolavirus Côte d'Ivoire and Ebolavirus Zaire can be correlated with the Plio/Pleistocene divergence between their putative reservoir host species, i.e., Myonycteris leptodon and Myonycteris torquata, respectively. PMID:23063885

Nesi, Nicolas; Kadjo, Blaise; Pourrut, Xavier; Leroy, Eric; Pongombo Shongo, Célestin; Cruaud, Corinne; Hassanin, Alexandre

2013-01-01

313

Detection of self-incompatible oilseed rape plants (Brassica napus L.) based on molecular markers for identification of the class I S haplotype.  

PubMed

The selection of desirable genotypes with recessive characteristics, such as self-incompatible plants, is often difficult or even impossible and represents a crucial barrier in accelerating the breeding process. Molecular approaches and selection based on molecular markers can allow breeders to overcome this limitation. The use of self-incompatibility is an alternative in hybrid breeding of oilseed rape. Unfortunately, stable self-incompatibility is recessive and phenotype-based selection is very difficult and time-consuming. The development of reliable molecular markers for detecting desirable plants with functional self-incompatible genes is of great importance for breeders and allows selection at early stages of plant growth. Because most of these reliable molecular markers are based on discrimination of class I S-locus genes that are present in self-compatible plants, there is a need to use an internal control in order to detect possible PCR inhibition that gives false results during genotyping. In this study, 269 double haploid F2 oilseed rape plants obtained by microspore embryogenesis were used to verify the applicability of an improved PCR assay based on the detection of the class I SLG gene along with an internal control. Comparative analysis of the PCR genotyping results vs. S phenotype analysis confirmed the applicability of this molecular approach in hybrid breeding programs. This approach allows accurate detection of self-incompatible plants via a different amplification profile. PMID:25249779

Havlícková, Lenka; Jozová, Eva; Klíma, Miroslav; Kucera, Vratislav; Curn, Vladislav

2014-09-01

314

Molecular Classification of Prostate Cancer Progression: Foundation for Marker driven-Treatment of Prostate Cancer  

PubMed Central

Recently, many therapeutic agents for prostate cancer (PCa) have been approved that target the androgen receptor and/or the prostate tumor microenvironment. Each of these therapies has modestly increased patient survival. However, if a better understanding as to when in the course of PCa progression specific therapies should be applied, and what biomarkers would indicate when resistance arises, survival due to these therapies would almost certainly improve. Thus, applying the armamentarium of therapeutic agents in the right sequences in the right combination at the right time is a major goal in prostate cancer treatment. For this to occur, an understanding of prostate cancer evolution during progression is required. In this review, we discuss the current understanding of PCa progression, but challenge the prevailing view by proposing a new model of PCa progression, with the goal of improving biologic classification and treatment strategies. We use this model to discuss how integrating clinical and basic understanding of PCa will lead to better implementation of molecularly-targeted therapeutics and improve patient survival. PMID:23811619

Logothetis, Christopher J; Gallick, Gary E.; Maity, Sankar N.; Kim, Jeri; Aparicio, Ana; Efstathiou, Eleni; Lin, Sue-Hwa

2014-01-01

315

Molecular markers to predict outcome to antiangiogenic therapies in colorectal cancer: current evidence and future perspectives.  

PubMed

Angiogenesis is a universal requirement for the growth of solid tumours beyond the limits of oxygen diffusion from the existing vasculature. The expression and function of proangiogenic and antiangiogenic factors are altered in solid malignancies to drive net neoangiogenesis. Vascular endothelial growth factor (VEGF) has been confirmed in several clinical trials as an important therapeutic target in colorectal cancer (CRC) treatment. However, given that the efficacy of antiangiogenic agents appears to be limited to a subset of patients, the identification of who will obtain the greater benefit from this therapy or suffer from specific toxicities and when or for how long they should be administered in the treatment algorithm are major open questions for clinicians and challenges for present and future research. Current evidence indicates some predictive value for particular circulating measures, such as an increase in VEGF, a decrease in vascular endothelial growth factor receptor 2 (VEGFR-2) or circulating endothelial cells, tissue biomarkers, microvessel density, KRAS and BRAF gene mutations or polymorphisms affecting components of the VEGF pathway. Many questions relating to these and other surrogate biomarkers, however, remain unanswered and their clinical usefulness has yet to be proven. This review will focus on the present status of knowledge and future perspectives for developing molecular tools to foresee and monitor antiangiogenic therapy activity in CRC patients. PMID:23510598

Custodio, Ana; Barriuso, Jorge; de Castro, Javier; Martínez-Marín, Virginia; Moreno, Víctor; Rodríguez-Salas, Nuria; Feliu, Jaime

2013-12-01

316

Genetic diversity analysis of Chrysopidae family (Insecta, Neuroptera) via molecular markers.  

PubMed

In entomology, improvement of molecular methods would be beneficial tools for accurate identification and detecting the genetic diversity of insect species to discover a corroborative evidence for the traditional classification based on morphology. The aim of this study was focused on RAPD-PCR method for distinguishing the genetic diversity between eight species of Chrysopidae family. In current research, many specimens were collected in different locations of Tehran province (Iran), between them 24 specimens were identified. The wing venation, male genitalia and other morphological characters were used for identification and also the sexing of species was recognized with study of external genitalia. Then, the DNA was extracted with CTAB method. The RAPD-PCR method was carried out with twenty random primers. The agarose gel electrophoresis was used for separation of the PCR products. Based on electrophoresis results, 133 bands were amplified and between them, 126 bands were poly-morph and others were mono-morph. Also, among the applied primers, the primers OPA02 with 19 bands and OPA03 with 8 bands were amplified the maximum and minimum of bands, respectively. The results showed that 80.35 and 73.21 % of genetic similarity existed between Chrysopa pallens-Chrysopa dubitans, and between the Chrysoperla kolthoffi and Chrysoperla carnea, respectively. The minimum (45.53 %) of genetic similarity was observed between C. kolthoffi and C. dubitans, and the maximum (0.80 %) was seen between C. pallens and C. dubitans. PMID:24973885

Yari, Kheirollah; Mirmoayedi, Alinaghi; Marami, Marzieh; Kazemi, Elham; Kahrizi, Danial

2014-09-01

317

Separation of DNA for molecular markers analysis from leaves of the Vitis vinifera.  

PubMed

In the present study, three DNA extraction procedures were examined to determine which might yield DNA from Grape leaves suitable for molecular analysis for RAPD, SSR. AFLP and etc analysis. The three methods examined were: the miniprep procedure and the modified CTAB for difficult species and protocol CTAB. Only the modified CTAB method consistently yielded DNA suitable for Polymerase Chain Reaction (PCR) amplification, regardless of plant growing conditions or leaf age. The quality and quantity of extracted genomic DNA gained from these methods are deliberated by means UV biophotometer, electrophoresis in 1.2% agarose gel and PCR. In this regard, application chosen for young and mature leaves, the most value of qualified DNA, is extracted from fully expanded leave when PVP was added to the extraction buffer. This same procedure also yielded PCR-amplifiable DNA from various other perennial, woody species and from other fruit species such as apple (Malus domestica), cherry (Prunus avium), peach (Prunuspersica), plum (Prunus domestica). DNA yield from this procedure is high (up to 1 mg g(-1) of leaf tissue). DNA is completely digestible with restriction endonucleases and amplifiable in the Polymerase Chain Reaction (PCR). PMID:18817243

Nazhad, Nafiseh Rigi; Solouki, Mahmood

2008-06-01

318

Immunological memory is associative  

SciTech Connect

The purpose of this paper is to show that immunological memory is an associative and robust memory that belongs to the class of sparse distributed memories. This class of memories derives its associative and robust nature by sparsely sampling the input space and distributing the data among many independent agents. Other members of this class include a model of the cerebellar cortex and Sparse Distributed Memory (SDM). First we present a simplified account of the immune response and immunological memory. Next we present SDM, and then we show the correlations between immunological memory and SDM. Finally, we show how associative recall in the immune response can be both beneficial and detrimental to the fitness of an individual.

Smith, D.J.; Forrest, S. [New Mexico Univ., Albuquerque, NM (United States). Dept. of Computer Science; Perelson, A.S. [Los Alamos National Lab., NM (United States)

1996-12-31

319

The Effect of Unsaturated Fatty Acids on Molecular Markers of Cholesterol Homeostasis in THP-1 Macrophages  

PubMed Central

Background Macrophages derived foam cells are key factors in the maladaptive immune and inflammatory response. Objectives The study of the cholesterol homeostasis and the molecular factor involved in these cells is very important in understanding the process of atherosclerosis and the mechanisms that prevent its occurrence. Materials and Methods This experimental study investigated the effects of c9, t11-Conjugated Linoleic Acid (c9, t11-CLA). Alpha Linolenic Acid (LA), and Eicosapentaenoic Acid (EPA) on the PPAR? and ACAT1 mRNA expression by Real time PCR and cholesterol homeostasis in THP-1 macrophages derived foam cells. Results Incubation of CLA, LA, EPA, and synthetic ligands did not prevent increasing the cellular total cholesterol (TC). Free cholesterol (FC) is increased by Sandoz58-035 (P = 0.024) and decreased by fatty acids and Wy14643 (Pirinixic acid) (P = 0.035). The pattern of distribution of %EC is similar to the EC pattern distribution. The ACAT1 mRNA expression was significantly increased by EPA (P = 0.009), but c9, t11- CLA, LA, Wy14643, and Sandoz58-035 had no significant effect on the mRNA level of ACAT1 expression compared to DMSO(Dimethyl sulfoxide). Discussions In comparison to the control of Wy14643, Sandoz58-035, c9 and t11-CLA, EPA increased the PPAR? mRNA levels (P = 0.024, P = 0.041, P = 0.043, and P = 0.004, respectively), even though, LA had no significant effect on the PPAR? mRNA expression (P = 0.489). Conclusions Variations in the chemical structure of fatty acids can affect their physiological function. PMID:24396573

Zavar Reza, Javad; Nahangi, Hossein; Mansouri, Reza; Dehghani, Ali; Mojarrad, Majid; Fathi, Mohammad; Nikzamir, Abdolrahim; Yekaninejad, Mir Saeed

2013-01-01

320

Population typing of the causal agent of cassava bacterial blight in the Eastern Plains of Colombia using two types of molecular markers  

PubMed Central

Background Molecular typing of pathogen populations is an important tool for the development of effective strategies for disease control. Diverse molecular markers have been used to characterize populations of Xanthomonas axonopodis pv. manihotis (Xam), the main bacterial pathogen of cassava. Recently, diversity and population dynamics of Xam in the Colombian Caribbean coast were estimated using AFLPs, where populations were found to be dynamic, diverse and with haplotypes unstable across time. Aiming to examine the current state of pathogen populations located in the Colombian Eastern Plains, we also used AFLP markers and we evaluated the usefulness of Variable Number Tandem Repeats (VNTRs) as new molecular markers for the study of Xam populations. Results The population analyses showed that AFLP and VNTR provide a detailed and congruent description of Xam populations from the Colombian Eastern Plains. These two typing strategies clearly separated strains from the Colombian Eastern Plains into distinct populations probably because of geographical distance. Although the majority of analyses were congruent between typing markers, fewer VNTRs were needed to detect a higher number of genetic populations of the pathogen as well as a higher genetic flow among sampled locations than those detected by AFLPs. Conclusions This study shows the advantages of VNTRs over AFLPs in the surveillance of pathogen populations and suggests the implementation of VNTRs in studies that involve large numbers of Xam isolates in order to obtain a more detailed overview of the pathogen to improve the strategies for disease control. PMID:24946775

2014-01-01

321

Molecular markers of ionizing radiation-induced gene mutations in mammalian cells.  

PubMed

We have isolated independent Chinese hamster ovary (CHO) cell mutants at the hypoxanthine guanine phosphoribosyltransferase (hprt) locus from untreated, 60Co gamma-ray-exposed, and 212Bi alpha-exposed cells and identified the molecular changes underlying the mutation determined by multiplex polymerase chain reaction (PCR)-based exon deletion analysis. Both the parental CHO-K1 cells and the X-ray-sensitive mutant xrs-5 cells were studied. The radiosensitive xrs-5 cells are defective in DNA double-strand break rejoining ability and in V(D)J recombination, which can be complemented by Ku protein. Of the 71 spontaneous CHO-K1 hprt mutants analyzed, 78% showed no change in exon number or size, 20% showed loss of one to eight exons (partial deletion), and 3% showed loss of all nine hprt exons (total deletion). Exposure of CHO-K1 cells to 6 Gy of gamma rays, which reduced survival levels to 10%, produced a high deletion spectrum with 45% of the 20 mutants analyzed showing a loss of one to eight exons and 30% showing total deletion. Exposure to an equitoxic dose of alpha radiation from 212Bi, a 220Rn daughter, resulted in a spectrum similar to the gamma-ray spectrum in that 75% of the 49 mutants analyzed were deletions. To alpha radiation, however, tended to produce larger intragenic deletions than gamma radiation. Of the 92 spontaneous xrs-5 mutants analyzed for deletions, 43% showed a loss of one to eight exons and 14% showed total deletion. This suggests that, in certain regions of the hprt gene, base alterations can be converted into large deletions and alteration in the Ku protein complex can influence this type of mutational process. Exposure to alpha radiation (10% survival) to xrs-5 cells resulted in a deletion spectrum similar to that seen in CHO-K1 cells. Of the 49 mutants analyzed, 43% showed on change in exon number or size, 16% showed a loss of one to eight exons, and 41% showed total deletion. While the defect in xrs-5 cells has a profound effect on spontaneous mutant spectra, this defect does not appear to affect alpha-induced mutation spectra. PMID:8781403

Hsie, A W; Porter, R C; Xu, Z; Yu, Y; Sun, J; Meltz, M L; Schwartz, J L

1996-05-01

322

A consensus linkage map for molecular markers and Quantitative Trait Loci associated with economically important traits in melon (Cucumis melo L.)  

PubMed Central

Background A number of molecular marker linkage maps have been developed for melon (Cucumis melo L.) over the last two decades. However, these maps were constructed using different marker sets, thus, making comparative analysis among maps difficult. In order to solve this problem, a consensus genetic map in melon was constructed using primarily highly transferable anchor markers that have broad potential use for mapping, synteny, and comparative quantitative trait loci (QTL) analysis, increasing breeding effectiveness and efficiency via marker-assisted selection (MAS). Results Under the framework of the International Cucurbit Genomics Initiative (ICuGI, http://www.icugi.org), an integrated genetic map has been constructed by merging data from eight independent mapping experiments using a genetically diverse array of parental lines. The consensus map spans 1150 cM across the 12 melon linkage groups and is composed of 1592 markers (640 SSRs, 330 SNPs, 252 AFLPs, 239 RFLPs, 89 RAPDs, 15 IMAs, 16 indels and 11 morphological traits) with a mean marker density of 0.72 cM/marker. One hundred and ninety-six of these markers (157 SSRs, 32 SNPs, 6 indels and 1 RAPD) were newly developed, mapped or provided by industry representatives as released markers, including 27 SNPs and 5 indels from genes involved in the organic acid metabolism and transport, and 58 EST-SSRs. Additionally, 85 of 822 SSR markers contributed by Syngenta Seeds were included in the integrated map. In addition, 370 QTL controlling 62 traits from 18 previously reported mapping experiments using genetically diverse parental genotypes were also integrated into the consensus map. Some QTL associated with economically important traits detected in separate studies mapped to similar genomic positions. For example, independently identified QTL controlling fruit shape were mapped on similar genomic positions, suggesting that such QTL are possibly responsible for the phenotypic variability observed for this trait in a broad array of melon germplasm. Conclusions Even though relatively unsaturated genetic maps in a diverse set of melon market types have been published, the integrated saturated map presented herein should be considered the initial reference map for melon. Most of the mapped markers contained in the reference map are polymorphic in diverse collection of germplasm, and thus are potentially transferrable to a broad array of genetic experimentation (e.g., integration of physical and genetic maps, colinearity analysis, map-based gene cloning, epistasis dissection, and marker-assisted selection). PMID:21797998

2011-01-01

323

Molecular Markers Demonstrate that the First Described Multidrug-Resistant Mycobacterium bovis Outbreak Was Due to Mycobacterium tuberculosis  

PubMed Central

We genetically characterized multidrug-resistant Mycobacterium tuberculosis complex strains which caused a nosocomial outbreak of tuberculosis affecting six human immunodeficiency virus (HIV)-positive patients and one HIV-negative staff member (E. Bouvet, E. Casalino, G. Mendoza-Sassi, S. Lariven, E. Vallée, M. Pernet, S. Gottot, and F. Vachon, AIDS 7:1453–1460, 1993). The strains showed all the phenotypic characteristics of Mycobacterium bovis. They presented a high copy number of IS6110, the spacers 40 to 43 in the direct repeat locus, and the mtp40 fragment. They lacked the G-A mutation at position 285 in the oxyR gene and the C-G mutation at position 169 in the pncA gene. These genetic characteristics revealed that these were dysgonic, slow-growing M. tuberculosis strains mimicking the M. bovis phenotype, probably as a consequence of cellular alterations associated with the multidrug resistance. Spoligotyping and IS6110 restriction fragment length polymorphism (RFLP) analysis confirmed that the outbreak was due to a single strain. However, the IS6110 RFLP pattern of the strain isolated from the last patient, diagnosed three years after the index case, differed slightly from the patterns of the other six strains. A model of a possible genetic event is presented to explain this divergence. This study stresses the value of using several independent molecular markers to identify multidrug-resistant tubercle bacilli. PMID:10074511

Gutierrez, M. C.; Galan, J. C.; Blazquez, J.; Bouvet, E.; Vincent, V.

1999-01-01

324

Spatial and Temporal Expression of Molecular Markers and Cell Signals During Normal Development of the Mouse Patellar Tendon  

PubMed Central

Tendon injuries are common clinical problems and are difficult to treat. In particular, the tendon-to-bone insertion site, once damaged, does not regenerate its complex zonal arrangement. A potential treatment for tendon injuries is to replace injured tendons with bioengineered tendons. However, the bioengineering of tendon will require a detailed understanding of the normal development of tendon, which is currently lacking. Here, we use the mouse patellar tendon as a model to describe the spatial and temporal pattern of expression of molecular markers for tendon differentiation from late fetal life to 2 weeks after birth. We found that collagen I, fibromodulin, and tenomodulin were expressed throughout the tendon, whereas tenascin-C, biglycan, and cartilage oligomeric protein were concentrated in the insertion site during this period. We also identified signaling pathways that are activated both throughout the developing tendon, for example, transforming growth factor beta and bone morphogenetic protein, and specifically in the insertion site, for example, hedgehog pathway. Using a mouse line expressing green fluorescent protein in all tenocytes, we also found that tenocyte cell proliferation occurs at highest levels during late fetal life, and declines to very low levels by 2 weeks after birth. These data will allow both the functional analysis of specific signaling pathways in tenocyte development and their application to tissue-engineering studies in vitro. PMID:21939397

Liu, Chia-Feng; Aschbacher-Smith, Lindsey; Barthelery, Nicolas J.; Dyment, Nathaniel; Butler, David

2012-01-01

325

Identification of larval Anisakis spp. (Nematoda: Anisakidae) in Alaska pollock (Theragra chalcogramma) in northern Japan using morphological and molecular markers.  

PubMed

The Alaska pollock, Theragra chalcogramma (Pallas), is an important raw source for surimi and other food products in Japan. However, Alaska pollock caught in the Atlantic and Mediterranean regions has been reported to harbor Anisakis species that pose considerable food safety problems. Here, we identified the third-stage (L3) Anisakis spp. sampled from Alaska pollock caught in northern Japan using a combination of morphological and molecular analyses which included PCR-RFLP and sequencing of the ITS (ITS1-5.8S rDNA-ITS2) region and mtDNA cox2 gene markers. Four Anisakis spp. were confirmed, namely Anisakis simplex (sensu stricto [s.s.]), A. pegreffii, A. brevispiculata, and an Anisakis sp. belonging to the Anisakis Type II group. The identification of 4 different Anisakis spp. occurring in Alaska Pollock, and the identification of A. brevispiculata and an Anisakis sp. (Anisakis Type II) in the northwest Pacific region, are first reports. Anisakis simplex (s.s.) composed the majority of Anisakis spp. in Alaska pollock at 91.0%, followed by A. pegreffii (5.2%), Anisakis sp. (Anisakis Type II) (2.4%), and A. brevispiculata (1.4%). PMID:19413366

Quiazon, K M A; Yoshinaga, T; Santos, M D; Ogawa, K

2009-10-01

326

Basic and clinical immunology  

NASA Technical Reports Server (NTRS)

Progress in immunology continues to grow exponentially every year. New applications of this knowledge are being developed for a broad range of clinical conditions. Conversely, the study of primary and secondary immunodeficiencies is helping to elucidate the intricate mechanisms of the immune system. We have selected a few of the most significant contributions to the fields of basic and clinical immunology published between October 2001 and October 2002. Our choice of topics in basic immunology included the description of T-bet as a determinant factor for T(H)1 differentiation, the role of the activation-induced cytosine deaminase gene in B-cell development, the characterization of CD4(+)CD25(+) regulatory T cells, and the use of dynamic imaging to study MHC class II transport and T-cell and dendritic cell membrane interactions. Articles related to clinical immunology that were selected for review include the description of immunodeficiency caused by caspase 8 deficiency; a case series report on X-linked agammaglobulinemia; the mechanism of action, efficacy, and complications of intravenous immunoglobulin; mechanisms of autoimmunity diseases; and advances in HIV pathogenesis and vaccine development. We also reviewed two articles that explore the possible alterations of the immune system caused by spaceflights, a new field with increasing importance as human space expeditions become a reality in the 21st century.

Chinen, Javier; Shearer, William T.

2003-01-01

327

Logistics of tumor immunology  

Microsoft Academic Search

Summary This article deals with the experimental problems of tumor immunology. It stresses that animal tumors should in their pathogenesis closely reflect the pathogenesis of human cancer because otherwise they may be useless and cloud the issues instead of making useful contributions. Animal tumors for experimental work should be of “spontaneous” origin, metastatie and of low antigenicity. However, the origin

H. Kirchner

1982-01-01

328

Immunology & Human Health.  

ERIC Educational Resources Information Center

This monograph was designed for the high school biology curriculum. The first section reviews the major areas of importance in immunology. Section three contains six instructional activities for the high school classroom and the second section contains teacher's materials for those activities. The activities address for students some of the major…

Dawson, Jeffrey R.; And Others

329

Immunology Research in Israel.  

National Technical Information Service (NTIS)

Research in immunology has developed and flourished greatly in Israel. Initially, research in this area was carried out primarily at the Weizmann Institute of Science, Rehovot. In the late 1960s and 1970s, new academic centers were established for immunol...

C. E. Zomzely-Neurath

1985-01-01

330

Review of Immunological and Immunopathological Findings in Schizophrenia  

Microsoft Academic Search

The involvement of immunological and immunopathological mechanisms in the etiopathogenesis of schizophrenia has been a matter of research, with recently increasing effort. This article reviews the findings focusing on postmortem neuropathology, the blood–brain barrier, antibodies, acute phase proteins, immunocompetent cells, and activation markers of immunocompetent cells. Evidence for the two primarily postulated hypotheses (the infectious hypothesis and the autoimmune hypothesis)

Matthias Rothermundt; Volker Arolt; Thomas A. Bayer

2001-01-01

331

Functional markers based molecular characterization and cloning of resistance gene analogs encoding NBS-LRR disease resistance proteins in finger millet (Eleusine coracana).  

PubMed

Magnaporthe grisea, the blast fungus is one of the main pathological threats to finger millet crop worldwide. A systematic search for the blast resistance gene analogs was carried out, using functional molecular markers. Three-fourths of the recognition-dependent disease resistance genes (R-genes) identified in plants encodes nucleotide binding site (NBS) leucine-rich repeat (LRR) proteins. NBS-LRR homologs have only been isolated on a limited scale from Eleusine coracana. Genomic DNA sequences sharing homology with NBS region of resistance gene analogs were isolated and characterized from resistant genotypes of finger millet using PCR based approach with primers designed from conserved regions of NBS domain. Attempts were made to identify molecular markers linked to the resistance gene and to differentiate the resistant bulk from the susceptible bulk. A total of 9 NBS-LRR and 11 EST-SSR markers generated 75.6 and 73.5% polymorphism respectively amongst 73 finger millet genotypes. NBS-5, NBS-9, NBS-3 and EST-SSR-04 markers showed a clear polymorphism which differentiated resistant genotypes from susceptible genotypes. By comparing the banding pattern of different resistant and susceptible genotypes, five DNA amplifications of NBS and EST-SSR primers (NBS-05(504,) NBS-09(711), NBS-07(688), NBS-03(509) and EST-SSR-04(241)) were identified as markers for the blast resistance in resistant genotypes. Principal coordinate plot and UPGMA analysis formed similar groups of the genotypes and placed most of the resistant genotypes together showing a high level of genetic relatedness and the susceptible genotypes were placed in different groups on the basis of differential disease score. Our results provided a clue for the cloning of finger millet blast resistance gene analogs which not only facilitate the process of plant breeding but also molecular characterization of blast resistance gene analogs from Eleusine coracana. PMID:21116864

Panwar, Preety; Jha, Anand Kumar; Pandey, P K; Gupta, Arun K; Kumar, Anil

2011-06-01

332

Molecular Characterization of c-Abl\\/c-Src Kinase Inhibitors Targeted against Murine Tumour Progenitor Cells that Express Stem Cell Markers  

Microsoft Academic Search

BackgroundThe non-receptor tyrosine kinases c-Abl and c-Src are overexpressed in various solid human tumours. Inhibition of their hyperactivity represents a molecular rationale in the combat of cancerous diseases. Here we examined the effects of a new family of pyrazolo [3,4-d] pyrimidines on a panel of 11 different murine lung tumour progenitor cell lines, that express stem cell markers, as well

Thomas Kruewel; Silvia Schenone; Marco Radi; Giovanni Maga; Astrid Rohrbeck; Maurizio Botta; Juergen Borlak; Maria A. Deli

2010-01-01

333

Cinnamyl-Alcohol Dehydrogenase, a Molecular Marker Specific for Lignin Synthesis: cDNA Cloning and mRNA Induction by Fungal Elicitor  

Microsoft Academic Search

Cinnamyl-alcohol dehydrogenase (CAD; EC 1.1.1.195) catalyzes the final step in a branch of phenylpropanoid synthesis specific for production of lignin monomers. We have isolated a full-length cDNA clone encoding CAD, as a molecular marker specific for lignification, by immunoscreening a lambda gt11 library containing cDNAs complementary to mRNA from elicitor-treated cell cultures of bean (Phaseolus vulgaris L.). The clone comprises

Michael H. Walter; Jacqueline Grima-Pettenati; Claude Grand; Alain M. Boudet; Christopher J. Lamb

1988-01-01

334

Comparative chloroplast genomes of photosynthetic orchids: insights into evolution of the Orchidaceae and development of molecular markers for phylogenetic applications.  

PubMed

The orchid family Orchidaceae is one of the largest angiosperm families, including many species of important economic value. While chloroplast genomes are very informative for systematics and species identification, there is very limited information available on chloroplast genomes in the Orchidaceae. Here, we report the complete chloroplast genomes of the medicinal plant Dendrobium officinale and the ornamental orchid Cypripedium macranthos, demonstrating their gene content and order and potential RNA editing sites. The chloroplast genomes of the above two species and five known photosynthetic orchids showed similarities in structure as well as gene order and content, but differences in the organization of the inverted repeat/small single-copy junction and ndh genes. The organization of the inverted repeat/small single-copy junctions in the chloroplast genomes of these orchids was classified into four types; we propose that inverted repeats flanking the small single-copy region underwent expansion or contraction among Orchidaceae. The AT-rich regions of the ycf1 gene in orchids could be linked to the recombination of inverted repeat/small single-copy junctions. Relative species in orchids displayed similar patterns of variation in ndh gene contents. Furthermore, fifteen highly divergent protein-coding genes were identified, which are useful for phylogenetic analyses in orchids. To test the efficiency of these genes serving as markers in phylogenetic analyses, coding regions of four genes (accD, ccsA, matK, and ycf1) were used as a case study to construct phylogenetic trees in the subfamily Epidendroideae. High support was obtained for placement of previously unlocated subtribes Collabiinae and Dendrobiinae in the subfamily Epidendroideae. Our findings expand understanding of the diversity of orchid chloroplast genomes and provide a reference for study of the molecular systematics of this family. PMID:24911363

Luo, Jing; Hou, Bei-Wei; Niu, Zhi-Tao; Liu, Wei; Xue, Qing-Yun; Ding, Xiao-Yu

2014-01-01

335

Fluorescent whitening agents in Tokyo Bay and adjacent rivers: their application as anthropogenic molecular markers in coastal environments.  

PubMed

Two kinds of stilbene-type fluorescent whitening agents (i.e., DSBP and DAS1), minor components of laundry detergents, were analyzed in surface waters of Tokyo Bay and adjacent rivers and in sewage effluents to examine their usefulness as molecular markers in the marine environment. Sensitive determination using HPLC (high performance liquid chromatography) with fluorescence detection with postcolumn UV radiator was employed. DSBP and DAS1 were found in Tokyo rivers at concentrations of a few microg/L and approximately 1 microg/L, respectively. DSBP and DAS1 were widely distributed in Tokyo Bay waters at concentrations in the range of 0.019-0.264 microg/L and 0.021-0.127 microg/L, respectively. Comparison of these concentrations with those in sewage effluents (DSBP: 8 microg/L and DAS1: 2.5 microg/L on average) yielded sewage dilutions in Tokyo Bay on the order of 10(2). FWAs-salinity diagram in the Tamagawa Estuary showed fairly conservative behaviors of the FWAs with approximately 20% and approximately 10% removal of DSBP and DAS1, respectively. This is thought to be caused by photodegradation. The persistent nature of FWAs and their widespread distribution in coastal environments demonstrates the utility of FWAs in tracing the behavior of water from rivers and sewage outfalls. The DSBP/DAS1 ratio showed a decreasing trend from sewage effluents, to rivers, to Tokyo Bay, indicating selective photodegradation of DSBP. The DSBP/DAS1 ratio is proposed as an index of the degree of photodegradation and residence time and freshness of water mass in coastal environments. PMID:12214649

Hayashi, Yuko; Managaki, Satoshi; Takada, Hideshige

2002-08-15

336

Comparative Chloroplast Genomes of Photosynthetic Orchids: Insights into Evolution of the Orchidaceae and Development of Molecular Markers for Phylogenetic Applications  

PubMed Central

The orchid family Orchidaceae is one of the largest angiosperm families, including many species of important economic value. While chloroplast genomes are very informative for systematics and species identification, there is very limited information available on chloroplast genomes in the Orchidaceae. Here, we report the complete chloroplast genomes of the medicinal plant Dendrobium officinale and the ornamental orchid Cypripedium macranthos, demonstrating their gene content and order and potential RNA editing sites. The chloroplast genomes of the above two species and five known photosynthetic orchids showed similarities in structure as well as gene order and content, but differences in the organization of the inverted repeat/small single-copy junction and ndh genes. The organization of the inverted repeat/small single-copy junctions in the chloroplast genomes of these orchids was classified into four types; we propose that inverted repeats flanking the small single-copy region underwent expansion or contraction among Orchidaceae. The AT-rich regions of the ycf1 gene in orchids could be linked to the recombination of inverted repeat/small single-copy junctions. Relative species in orchids displayed similar patterns of variation in ndh gene contents. Furthermore, fifteen highly divergent protein-coding genes were identified, which are useful for phylogenetic analyses in orchids. To test the efficiency of these genes serving as markers in phylogenetic analyses, coding regions of four genes (accD, ccsA, matK, and ycf1) were used as a case study to construct phylogenetic trees in the subfamily Epidendroideae. High support was obtained for placement of previously unlocated subtribes Collabiinae and Dendrobiinae in the subfamily Epidendroideae. Our findings expand understanding of the diversity of orchid chloroplast genomes and provide a reference for study of the molecular systematics of this family. PMID:24911363

Niu, Zhi-Tao; Liu, Wei; Xue, Qing-Yun; Ding, Xiao-Yu

2014-01-01

337

Studies on the genetic variation of the green unicellular alga Haematococcus pluvialis (Chlorophyceae) obtained from different geographical locations using ISSR and RAPD molecular marker.  

PubMed

Haematococcus pluvialis (Flotow) is a unicellular green alga, which is considered to be the best astaxanthin-producing organism. Molecular markers are suitable tools for the purpose of finding out genetic variations in organisms; however there have been no studies conducted on ISSR or RAPD molecular markers for this organism. The DNA of 10 different strains of H. pluvialis (four strains from Iran, two strains from Finland, one strain from Switzerland and three strains from the USA) was extracted. A genetic similarity study was carried out using 14 ISSR and 12 RAPD primers. Moreover, the molecular weights of the bands produced ranged from 0.14 to 3.4 Kb. The PCA and dendrogram clustered the H. pluvialis strains into various groups according to their geographical origin. The lowest genetic similarity was between the Iran2 and USA2 strains (0.08) and the highest genetic similarity was between Finland1 and Finland2 (0.64). The maximum numbers of bands produced by the ISSR and RAPD primers were 35 and 6 bands, respectively. The results showed that ISSR and RAPD markers are useful for genetic diversity studies of Haematococcus as they showed geographical discrimination. PMID:21441863

Mostafa, Noroozi; Omar, Hishamuddin; Tan, Soon Guan; Napis, Suhaimi

2011-01-01

338

Hematology and immunology studies  

NASA Technical Reports Server (NTRS)

The hematology and immunology program conducted in support of the Apollo missions was designed to acquire specific laboratory data relative to the assessment of the health status of the astronauts prior to their commitment to space flight. A second objective was to detect and identify any alterations in the normal functions of the immunohematologic systems which could be attributed to space flight exposure, and to evaluate the significance of these changes relative to man's continuing participation in space flight missions. Specific changes observed during the Gemini Program formed the basis for the major portion of the hematology-immunology test schedule. Additional measurements were included when their contribution to the overall interpretation of the flight data base became apparent.

Kimzey, S. L.; Fischer, C. L.; Johnson, P. C.; Ritzmann, S. E.; Mengel, C. E.

1975-01-01

339

Analogues in immunology  

Microsoft Academic Search

Summary  A number of immunological functions has been found to be endowed with biological rhythmicity. Variations of peripheral blood\\u000a lymphocytes, immediate and delayed hypersensitivity responses, and reactivity of the immune system to antigenic challenge\\u000a have consistently shown circadian bioperiodicity. By employing a panel of monoclonal antibodies specific for the various lymphocyte\\u000a subsets, we have been able to detect rhythmic variations in

Franco Dammacco; Nicla Campobasso; Edoardo Altomare; Giuseppe Iodice

1984-01-01

340

A High Density Consensus Genetic Map of Tetraploid Cotton That Integrates Multiple Component Maps through Molecular Marker Redundancy Check  

PubMed Central

A consensus genetic map of tetraploid cotton was constructed using six high-density maps and after the integration of a sequence-based marker redundancy check. Public cotton SSR libraries (17,343 markers) were curated for sequence redundancy using 90% as a similarity cutoff. As a result, 20% of the markers (3,410) could be considered as redundant with some other markers. The marker redundancy information had been a crucial part of the map integration process, in which the six most informative interspecific Gossypium hirsutum×G. barbadense genetic maps were used for assembling a high density consensus (HDC) map for tetraploid cotton. With redundant markers being removed, the HDC map could be constructed thanks to the sufficient number of collinear non-redundant markers in common between the component maps. The HDC map consists of 8,254 loci, originating from 6,669 markers, and spans 4,070 cM, with an average of 2 loci per cM. The HDC map presents a high rate of locus duplications, as 1,292 markers among the 6,669 were mapped in more than one locus. Two thirds of the duplications are bridging homoeologous AT and DT chromosomes constitutive of allopolyploid cotton genome, with an average of 64 duplications per AT/DT chromosome pair. Sequences of 4,744 mapped markers were used for a mutual blast alignment (BBMH) with the 13 major scaffolds of the recently released Gossypium raimondii genome indicating high level of homology between the diploid D genome and the tetraploid cotton genetic map, with only a few minor possible structural rearrangements. Overall, the HDC map will serve as a valuable resource for trait QTL comparative mapping, map-based cloning of important genes, and better understanding of the genome structure and evolution of tetraploid cotton. PMID:23029214

Blenda, Anna; Fang, David D.; Rami, Jean-Francois; Garsmeur, Olivier; Luo, Feng; Lacape, Jean-Marc

2012-01-01

341

The okra (Abelmoschus esculentus) transcriptome as a source for gene sequence information and molecular markers for diversity analysis.  

PubMed

A combined leaf and pod transcriptome of okra (Abelmoschus esculentus (L.) Moench) has been produced by RNA sequencing and short read assembly. More than 150,000 unigenes were obtained, comprising some 46 million base pairs of sequence information. More than 55% of the unigenes were annotated through sequence comparison with databases. The okra transcriptome sequences were mined for simple sequence repeat (SSR) markers. From 935 non-redundant SSR motifs identified in the unigene set, 199 were chosen for testing in a germplasm set, resulting in 161 polymorphic SSR markers. From this set, 19 markers were selected for a diversity analysis on 65 okra accessions comprising three different species, revealing 58 different genotypes and resulted in clustering of the accessions according to species and geographic origin. The okra gene sequence information and the marker resource are made available to the research community for functional genomics and breeding research. PMID:23299025

Schafleitner, Roland; Kumar, Sanjeet; Lin, Chen-Yu; Hegde, Satish Gajanana; Ebert, Andreas

2013-03-15

342

Application of leftover sample material from waterborne protozoa monitoring for the molecular detection of Bacteroidales and fecal source tracking markers  

EPA Science Inventory

In this study, we examined the potential for detecting fecal bacteria and microbial source tracking markers in samples discarded during the concentration of Cryptosporidium and Giardia using USEPA Method 1623. Recovery rates for different fecal bacteria were determined using sp...

343

Analysis of black carbon molecular markers by two chromatographic methods (GC-FID and HPLC-DAD)  

NASA Astrophysics Data System (ADS)

The analysis of benzenepolycarboxylic acids (BPCA) as a quantitative measure for black carbon (BC) in soil and sediment samples is a well-established method [1, 2]. Briefly, the oxidation of polycondensated BC molecules forms seven molecular markers, which can be assigned to BC, and which subsequently can be quantified by GC-FID (gas chromatography with flame ionization detector). Recently this method has been refined for BC quantification in seawater samples measuring BPCA on HPLC-DAD (High performance liquid chromatography with diode array detector) [3]. However, a systematic comparison of BC as determined by both analytical techniques would be essential to the calculation of global BC budgets, but is lacking. Here we present data for the systematic comparison of the two BPCA methods, both for quantity and quality. We prepared chars under well-defined laboratory conditions. Chestnut hardwood chips and rice straw were pyrolysed at temperatures between 200 and 1000°C under constant N2 stream. The BC contents of the chars have been analysed using the BPCA extraction method followed by either GC-FID or HPLC-DAD quantification [4]. It appears that the GC-FID method yields systematically lower concentrations of BPCA in the chars compared to the HPLC-DAD method. Possible reasons for the observed difference are i) higher losses of sample material during preparation for GC-FID; ii) different quality of the linear regression used for quantification; iii) incomplete derivatisation of B5CA and B6CA, which is needed for GC-FID analysis. In a next step, we will test different derivatisation procedures (methylation with dimethyl sulfate or diazomethane, and silylation) for their influence on the GC-FID results. The aim of this study is to test if black carbon can be quantified in soil, sediment and water samples using one single method - a crucial step when attempting a global BC budget. References: [1] Brodowski, S., Rodionov, A., Haumeier L., Glaser, B., Amelung, W. (2005) Org. Geochem. 36, 1299-1310. [2] Glaser, B., Haumeier, L., Guggenberger, G., Zech, W. (1998) Org. Geochem. 29, 811-819. [3] Dittmar, T. (2008) Org. Geochem. 39. 396-407. [4] Schneider, M.P.W., Hilf, M., Vogt, U.F., Schmidt, M.W.I., Org. Geochem. (submitted)

Schneider, Maximilian P. W.; Smittenberg, Rienk H.; Dittmar, Thorsten; Schmidt, Michael W. I.

2010-05-01

344

A Dense Genetic Map of the Silkworm, Bombyx mori, Covering All Chromosomes Based on 1018 Molecular Markers  

Microsoft Academic Search

A dense linkage map was constructed for the silkworm, Bombyx mori, containing 1018 genetic markers on all 27 autosomes and the Z chromosome. Most of the markers, covering z2000 cM, were randomly amplified polymorphic DNAs amplified with primer-pairs in combinations of 140 commercially available decanucleotides. In addition, eight known genes and five visible mutations were mapped. Bombyx homo- logues of

Yuji Yasukochi

345

Molecular markers associated with the immature fiber (im) gene affecting the degree of fiber cell wall thickening in cotton (Gossypium hirsutum L.).  

PubMed

Cotton fiber fineness and maturity measured indirectly as micronaire (MIC) are important properties of determining fiber grades in the textile market. To understand the genetic control and molecular mechanisms of fiber fineness and maturity, we studied two near isogenic lines, Gossypium hirsutum, Texas Marker-1 wild type (TM-1) and immature fiber (im) mutant showing a significant difference in MIC values. The fibers from im mutant plants were finer and less mature with lower MIC values than those from the recurrent parent, TM-1. A comprehensive fiber property analysis of TM-1 and im mutant showed that the lower MIC of fibers in im mutant was due to the lower degree of fiber cell wall thickening as compared to the TM-1 fibers. Using an F(2) population comprising 366 progenies derived from a cross between TM-1 and im mutant, we confirmed that the immature fiber phenotype present in a mutant plant was controlled by one single recessive gene im. Furthermore, we identified 13 simple sequence repeat markers that were closely linked to the im gene located on chromosome 3. Molecular markers associated with the im gene will lay the foundation to further investigate genetic information required for improving cotton fiber fineness and maturity. PMID:22890806

Kim, Hee Jin; Moon, Hong S; Delhom, Christopher D; Zeng, Linghe; Fang, David D

2013-01-01

346

Analysis of molecular markers associated with powdery mildew resistance genes in peach (Prunus persica (L.) Batsch)xPrunus davidiana hybrids.  

PubMed

A progeny of 77 hybrids issued from a cross between two heterozygous Prunus, peach [P. persica (L.) Batsch] (variety 'Summergrand') and a related species, P. davidiana (clone 1908), was analysed for powdery mildew resistance in five independent experiments. This population was also analysed for its genotype with isoenzyme and RAPD markers in order to map the genes responsible for resistance. A genetic linkage map was generated for each parent. The 'Summergrand' linkage map is composed of only four linkage groups including 15 RAPD markers and covering 83.1 centiMorgans (cM) of the peach nuclear genome, whereas the P. davidiana linkage map contains 84 RAPD markers and one isoenzyme assigned to ten linkage groups and covering 536 cM. Significant associations between molecular markers and powdery mildew resistance were found in each parent. For P. davidiana, one major QTL with a very strong effect and five other QTLs with minor effects were located in different linkage groups. For 'Summergrand', three QTLs for powdery mildew resistance, with minor effects, were also detected. Consequently, evidence is given here that the powdery mildew resistance of P. davidiana clone 1908 and P. persica variety 'Summergrand' is not a monogenic character but is controlled by at least one major gene and several minor genes. PMID:24162425

Dirlewanger, E; Pascal, T; Zuger, C; Kervella, J

1996-10-01

347

Editorial: nanoscience advances in rheumatology and immunology.  

PubMed

Improved understanding of the molecular mechanisms leading to autoimmunity have resulted in advances toward the diagnosis, management, and treatment of rheumatologic diseases. Many of these mechanisms overlap with inflammatory disease states and cancer, where nanoscience is increasingly being applied for pharmacologic and diagnostic purposes [1-6]. Additionally, nanoscience has furthered the study of cellular interactions within the in situ environment, thereby increasing the understanding of these complex, multi-system disorders [1, 7-9]. This Hot Topics review series intends to provide an overview of nanoscience, as it pertains to rheumatology and immunology, highlighting emerging technologies applied to rheumatologic models and with the potential for human use. This mini-series has a particular focus on imaging and drug delivery applications pertinent to autoimmune conditions as well as reviewing the pharmacology, clearance, and biodistribution of nanomaterials in inflammatory conditions and by immune cells. Nanotechnology involves the synthesis and utilization of materials - including but not limited to metals, oxides, lipids, polymers -- in the nanoscale range (1 to 1000 nm). Nanomaterial composition as well as the size, shape, charge, and surface coating contribute to unique nanomaterial characteristics that can be used for a variety of biomedical applications [1, 10]. Each of these independent variables influences the application, biodistribution, metabolism, and as anticipated, bystander toxicity. In the current era of biologic and monoclonal antibody-directed therapy for autoimmune disease, clinical and radiographic markers are becoming less sensitive to detect subtle disease activity, and there is an increasing demand for improved diagnostic imaging techniques and contrast agents. Because of the large surface to volume ratio and ease of functionalization, nanoparticles are particularly well suited for advanced imaging [1, 11] and may fill this gap. In the review by Rogers et al., the authors cite several examples of novel nanoparticle-based imaging strategies to identify inflammation and rheumatic disease in the early, pre-clinical stages and even at the cellular level [7, 12, 13]. Coupled with targeted molecular markers, multimodal nanoparticles carrying larger payloads than traditional contrast materials have the ability to increase the sensitivity and specificity of disease monitoring while retaining the anatomic detail of traditional imaging. In addition to the advantages nanomaterials provide as novel contrast agents in imaging, they can also be utilized in vaccination strategies or as drug carriers for targeted delivery to tissues [1, 14, 15]. This technology may improve upon current treatments or could provide therapies for some rheumatic illness, such as systemic lupus erythematosus or scleroderma, for which there are limited therapeutic options. In the review authored by Henderson and colleagues, a wide range of nanoparticle platforms including varied material composition and conjugated strategies are described as approaches to control the processes of drug release, targeted delivery, and degradation [16-19]. There is precedence for FDA approval of nanoparticle-based drug delivery for the treatment of infection and cancer in humans, and in some instances, this has decreased systemic toxicity while improving efficacy [20]. This same balance between targeted therapy and untoward side effects will need to be applied to medications designed for the rheumatic illnesses as the field advances. Many nanomaterials in the living organism are phagocytized by cells of the reticuloendothelial system, and in particular, these include the monocyte/macrophage cellular lineage [21]. In the review by Song et al., the authors discuss the complex interactions between nanoparticles and immune cells since this interplay can affect particle distribution, clearance, and potentially lead to off-target effects such as immune stimulation. Ultimately, these relationships between nanoparticles and immune system activation versus s

Tarrant, Teresa K

2014-01-01

348

Mathematics and physics Biology Modelling a population Immunology Modelling T cell immunology  

E-print Network

Mathematics and physics Biology Modelling a population Immunology Modelling T cell immunology;Mathematics and physics Biology Modelling a population Immunology Mathematics is a special science! #12;Mathematics and physics Biology Modelling a population Immunology Classical mechanics (Newton) Figure

Wirosoetisno, Djoko

349

Broadening the translational immunology landscape  

PubMed Central

It is just over 5 years since Clinical and Experimental Immunology came under the direction of a new team of Editors and made a concerted effort to refresh its approach to promoting clinical and applied immunology through its pages. There were two major objectives: to foster papers in a field which, at the time, we loosely termed ‘translational immunology’; and to create a forum for the presentation and discussion of immunology that is relevant to clinicians operating in this space. So, how are we doing with these endeavours? This brief paper aims to summarize some of the key learning points and successes and highlight areas in which translational gaps remain. PMID:23121665

Peakman, M

2012-01-01

350

Hematology and immunology studies  

NASA Technical Reports Server (NTRS)

A coordinated series of experiments were conducted to evaluate immunologic and hemotologic system responses of Skylab crewmen to prolonged space flights. A reduced PHA responsiveness was observed on recovery, together with a reduced number of T-cells, with both values returning to normal 3 to 5 days postflight. Subnormal red cell count, hemoglobin concentration, and hematocrit values also returned gradually to preflight limits. Most pronounced changes were found in the shape of red blood cells during extended space missions with a rapid reversal of these changes upon reentry into a normal gravitational environment.

Kimzey, S. L.

1977-01-01

351

Role of the pulmonologist in ordering post-procedure molecular markers in non-small-cell lung cancer: implications for personalized medicine.  

PubMed

In the growing era of personalized medicine for the treatment of non-small-cell lung cancer (NSCLC), it is becoming increasingly important that sufficient quality and quantity of tumor tissue are available for morphologic diagnosis and molecular analysis. As new treatment options emerge that might require more frequent and possibly higher volume biopsies, the role of the pulmonologist will expand, and it will be important for pulmonologists to work within a multidisciplinary team to provide optimal therapeutic management for patients with NSCLC. In this review, we discuss the rationale for individualized treatment decisions for patients with NSCLC, molecular pathways and specific molecular predictors relevant to personalized NSCLC therapy, assay technologies for molecular marker analysis, and specifics regarding tumor specimen selection, acquisition, and handling. Moreover, we briefly address issues regarding racial and socioeconomic disparities as they relate to molecular testing and treatment decisions, and cost considerations for molecular testing and targeted therapies in NSCLC. We also propose a model for an institution-based multidisciplinary team, including oncologists, pathologists, pulmonologists, interventional radiologists, and thoracic surgeons, to ensure adequate material is available for cytological and histological studies and to standardize methods of tumor specimen handling and processing in an effort to provide beneficial, individualized therapy for patients with NSCLC. PMID:24188629

Murgu, Septimiu; Colt, Henri

2013-11-01

352

Complete mitochondrial genomes of Taenia multiceps, T. hydatigena and T. pisiformis: additional molecular markers for a tapeworm genus of human and animal health significance  

PubMed Central

Background Mitochondrial genomes provide a rich source of molecular variation of proven and widespread utility in molecular ecology, population genetics and evolutionary biology. The tapeworm genus Taenia includes a diversity of tapeworm parasites of significant human and veterinary importance. Here we add complete sequences of the mt genomes of T. multiceps, T. hydatigena and T. pisiformis, to a data set of 4 published mtDNAs in the same genus. Seven complete mt genomes of Taenia species are used to compare and contrast variation within and between genomes in the genus, to estimate a phylogeny for the genus, and to develop novel molecular markers as part of an extended mitochondrial toolkit. Results The complete circular mtDNAs of T. multiceps, T. hydatigena and T. pisiformis were 13,693, 13,492 and 13,387 bp in size respectively, comprising the usual complement of flatworm genes. Start and stop codons of protein coding genes included those found commonly amongst other platyhelminth mt genomes, but the much rarer initiation codon GTT was inferred for the gene atp6 in T. pisiformis. Phylogenetic analysis of mtDNAs offered novel estimates of the interrelationships of Taenia. Sliding window analyses showed nad6, nad5, atp6, nad3 and nad2 are amongst the most variable of genes per unit length, with the highest peaks in nucleotide diversity found in nad5. New primer pairs capable of amplifying fragments of variable DNA in nad1, rrnS and nad5 genes were designed in silico and tested as possible alternatives to existing mitochondrial markers for Taenia. Conclusions With the availability of complete mtDNAs of 7 Taenia species, we have shown that analysis of amino acids provides a robust estimate of phylogeny for the genus that differs markedly from morphological estimates or those using partial genes; with implications for understanding the evolutionary radiation of important Taenia. Full alignment of the nucleotides of Taenia mtDNAs and sliding window analysis suggests numerous alternative gene regions are likely to capture greater nucleotide variation than those currently pursued as molecular markers. New PCR primers developed from a comparative mitogenomic analysis of Taenia species, extend the use of mitochondrial markers for molecular ecology, population genetics and diagnostics. PMID:20649981

2010-01-01

353

Immunology, Microbiology & Immunology, and Institute for Immunity, Transplantation & Infection  

E-print Network

of Adipocytokine Leptin in Mucosal Innate Immunity to Amebic Colitis January 24, 2012 Tues, 4pm LKSC 130 RichardImmunology, Microbiology & Immunology, and Institute for Immunity, Transplantation & Infection): A Pivotal Regulator of Innate and Adaptive Immunity February 28, 2012 Tues, 4pm LKSC 130 Ira Mellman

Ford, James

354

Distinctive mitochondrial genome of Calanoid copepod Calanus sinicus with multiple large non-coding regions and reshuffled gene order: Useful molecular markers for phylogenetic and population studies  

PubMed Central

Background Copepods are highly diverse and abundant, resulting in extensive ecological radiation in marine ecosystems. Calanus sinicus dominates continental shelf waters in the northwest Pacific Ocean and plays an important role in the local ecosystem by linking primary production to higher trophic levels. A lack of effective molecular markers has hindered phylogenetic and population genetic studies concerning copepods. As they are genome-level informative, mitochondrial DNA sequences can be used as markers for population genetic studies and phylogenetic studies. Results The mitochondrial genome of C. sinicus is distinct from other arthropods owing to the concurrence of multiple non-coding regions and a reshuffled gene arrangement. Further particularities in the mitogenome of C. sinicus include low A + T-content, symmetrical nucleotide composition between strands, abbreviated stop codons for several PCGs and extended lengths of the genes atp6 and atp8 relative to other copepods. The monophyletic Copepoda should be placed within the Vericrustacea. The close affinity between Cyclopoida and Poecilostomatoida suggests reassigning the latter as subordinate to the former. Monophyly of Maxillopoda is rejected. Within the alignment of 11 C. sinicus mitogenomes, there are 397 variable sites harbouring three 'hotspot' variable sites and three microsatellite loci. Conclusion The occurrence of the circular subgenomic fragment during laboratory assays suggests that special caution should be taken when sequencing mitogenomes using long PCR. Such a phenomenon may provide additional evidence of mitochondrial DNA recombination, which appears to have been a prerequisite for shaping the present mitochondrial profile of C. sinicus during its evolution. The lack of synapomorphic gene arrangements among copepods has cast doubt on the utility of gene order as a useful molecular marker for deep phylogenetic analysis. However, mitochondrial genomic sequences have been valuable markers for resolving phylogenetic issues concerning copepods. The variable site maps of C. sinicus mitogenomes provide a solid foundation for population genetic studies. PMID:21269523

2011-01-01

355

Characterization of Haemaphysalis flava (Acari: Ixodidae) from Qingling subspecies of giant panda (Ailuropoda melanoleuca qinlingensis) in Qinling Mountains (Central China) by morphology and molecular markers.  

PubMed

Tick is one of important ectoparasites capable of causing direct damage to their hosts and also acts as vectors of relevant infectious agents. In the present study, the taxa of 10 ticks, collected from Qinling giant pandas (Ailuropoda melanoleuca qinlingensis) in Qinling Mountains of China in April 2010, were determined using morphology and molecular markers (nucleotide ITS2 rDNA and mitochondrial 16S). Microscopic observation demonstrated that the morphological features of these ticks were similar to Haemaphysalis flava. Compared with other Haemaphysalis species, genetic variations between Haemaphysalis collected from A. m. qinlingensis and H. flava were the lowest in ITS2 rDNA and mitochondrial 16S, with sequence differences of 2.06%-2.40% and 1.30%-4.70%, respectively. Phylogenetic relationships showed that all the Haemaphysalis collected from A. m. qinlingensis were grouped with H. flava, further confirmed that the Haemaphysalis sp. is H. flava. This is the first report of ticks in giant panda by combining with morphology and molecular markers. This study also provided evidence that combining morphology and molecular tools provide a valuable and efficient tool for tick identification. PMID:23894541

Cheng, Wen-yu; Zhao, Guang-hui; Jia, Yan-qing; Bian, Qing-qing; Du, Shuai-zhi; Fang, Yan-qing; Qi, Mao-zhen; Yu, San-ke

2013-01-01

356

Principles of ecological immunology  

PubMed Central

Defending self against nonself is a major problem in a world in which individuals are under constant pressure from parasites that gain fitness benefits at a cost to their host. Defences that have evolved are diverse, and range from behavioural adaptations to physiochemical barriers. The immune defence is a final line of protection and is therefore of great importance. Given this importance, variability in immune defence would seem counterintuitive, yet that is what is observed. Ecological immunology attempts to explain this variation by invoking costs and trade-offs, and in turn proposing that the optimal immune defence will vary over environments. Studies in this field have been highly successful in establishing an evolutionary ecology framework around immunology. However, in order enrich our understanding of this area, it is perhaps time to broaden the focus to include parasites as more than simply elicitors of immune responses. In essence, to view immunity as produced by the host, the environment, and the active involvement of parasites.

Sadd, Ben M; Schmid-Hempel, Paul

2009-01-01

357

Helminths and Immunological Tolerance  

PubMed Central

Current immunosuppression regimens for solid-organ transplantation have shown disappointing efficacy in the prevention of chronic allograft rejection and carry unacceptable risks including toxicity, neoplasia, and life-threatening infection. Achievement of immunological tolerance (long-term antigen unresponsiveness in an immunocompetent host) presents the exciting prospect of freedom from immunosuppression for transplant recipients. It is now 60 years since the first demonstration of immunological tolerance in animal models of transplantation, but translation into routine clinical practice remains elusive. Helminth parasites may provide novel strategies toward achieving this goal. Helminths are remarkably successful parasites: they currently infect more than one quarter of the world’s population. It is now well established that the parasites’ success is the result of active immunomodulation of their hosts’ immune response. Although this primarily secures ongoing survival of the parasites, helminth-induced immunomodulation can also have a number of benefits for the host. Significant reductions in the prevalence of allergy and autoimmune conditions among helminth-infected populations are well recognized and there is now a significant body of evidence to suggest that harmful immune responses to alloantigens may be abrogated as well. Here, we review all existing studies of helminth infection and transplantation, explore the mechanisms involved, and discuss possible avenues for future translation to clinical practice. PMID:24025322

Johnston, Chris J.C.; McSorley, Henry J.; Anderton, Stephen M.; Wigmore, Stephen J.; Maizels, Rick M.

2014-01-01

358

Genetic analysis and molecular characterization of Chinese sesame (Sesamum indicum L.) cultivars using Insertion-Deletion (InDel) and Simple Sequence Repeat (SSR) markers  

PubMed Central

Background Sesame is an important and ancient oil crop in tropical and subtropical areas. China is one of the most important sesame producing countries with many germplasm accessions and excellent cultivars. Domestication and modern plant breeding have presumably narrowed the genetic basis of cultivated sesame. Several modern sesame cultivars were bred with a limited number of landrace cultivars in their pedigree. The genetic variation was subsequently reduced by genetic drift and selection. Characterization of genetic diversity of these cultivars by molecular markers is of great value to assist parental line selection and breeding strategy design. Results Three hundred and forty nine simple sequence repeat (SSR) and 79 insertion-deletion (InDel) markers were developed from cDNA library and reduced-representation sequencing of a sesame cultivar Zhongzhi 14, respectively. Combined with previously published SSR markers, 88 polymorphic markers were used to assess the genetic diversity, phylogenetic relationships, population structure, and allele distribution among 130 Chinese sesame accessions including 82 cultivars, 44 landraces and 4 wild germplasm accessions. A total of 325 alleles were detected, with the average gene diversity of 0.432. Model-based structure analysis revealed the presence of five subgroups belonging to two main groups, which were consistent with the results from principal coordinate analysis (PCA), phylogenetic clustering and analysis of molecular variance (AMOVA). Several missing or unique alleles were identified from particular types, subgroups or families, even though they share one or both parental/progenitor lines. Conclusions This report presented a by far most comprehensive characterization of the molecular and genetic diversity of sesame cultivars in China. InDels are more polymorphic than SSRs, but their ability for deciphering genetic diversity compared to the later. Improved sesame cultivars have narrower genetic basis than landraces, reflecting the effect of genetic drift or selection during breeding processes. Comparative analysis of allele distribution revealed genetic divergence between improved cultivars and landraces, as well as between cultivars released in different years. These results will be useful for assessing cultivars and for marker-assisted breeding in sesame. PMID:24641723

2014-01-01

359

Medical Immunology Campus Erlangen Beteiligte Forschungsverbnde  

E-print Network

Medical Immunology Campus Erlangen Beteiligte Forschungsverbünde: Sonderforschungsbereich 643;Medical Immunology Campus Erlangen Beteiligte Forschungsverbünde: Sonderforschungsbereich 643 Sprecher Klinische Mikrobiologie, Immunologie und Hygiene, Wasserturmstra�e 3-5, 1. Stock #12;Medical Immunology

Fiebig, Peter

360

IMMUNOLOGY PROGRAM DIVISION OF MEDICAL SCIENCES  

E-print Network

IMMUNOLOGY PROGRAM DIVISION OF MEDICAL SCIENCES DISSERTATION ADVISORY COMMITTEE REPORT STUDENT Student: Program: Immunology Dissertation Advisor: Year G.S.A.S.: ADVISORY COMMITTEE: SIGNATURES: 1. Chair: PLEASE RETURN TO PROGRAM ADMINISTRATOR: Immunology Program Administrator Modell Center Harvard Medical

Mekalanos, John

361

42 CFR 493.921 - Diagnostic immunology.  

Code of Federal Regulations, 2012 CFR

... 2012-10-01 false Diagnostic immunology. 493.921 Section 493.921 Public...Subspecialty § 493.921 Diagnostic immunology. The subspecialties under the specialty of immunology for which a program may offer...

2012-10-01

362

42 CFR 493.927 - General immunology.  

Code of Federal Regulations, 2013 CFR

...2013-10-01 2013-10-01 false General immunology. 493.927 Section 493.927 ...Subspecialty § 493.927 General immunology. (a) Program content and frequency...approved for proficiency testing for immunology, the annual program must...

2013-10-01

363

42 CFR 493.921 - Diagnostic immunology.  

Code of Federal Regulations, 2011 CFR

... 2011-10-01 false Diagnostic immunology. 493.921 Section 493.921 Public...Subspecialty § 493.921 Diagnostic immunology. The subspecialties under the specialty of immunology for which a program may offer...

2011-10-01

364

42 CFR 493.921 - Diagnostic immunology.  

Code of Federal Regulations, 2010 CFR

... 2010-10-01 false Diagnostic immunology. 493.921 Section 493.921 Public...Subspecialty § 493.921 Diagnostic immunology. The subspecialties under the specialty of immunology for which a program may offer...

2010-10-01

365

42 CFR 493.921 - Diagnostic immunology.  

Code of Federal Regulations, 2013 CFR

... 2013-10-01 false Diagnostic immunology. 493.921 Section 493.921 Public...Subspecialty § 493.921 Diagnostic immunology. The subspecialties under the specialty of immunology for which a program may offer...

2013-10-01

366

42 CFR 493.927 - General immunology.  

Code of Federal Regulations, 2011 CFR

...2011-10-01 2011-10-01 false General immunology. 493.927 Section 493.927 ...Subspecialty § 493.927 General immunology. (a) Program content and frequency...approved for proficiency testing for immunology, the annual program must...

2011-10-01

367

42 CFR 493.927 - General immunology.  

Code of Federal Regulations, 2012 CFR

...2012-10-01 2012-10-01 false General immunology. 493.927 Section 493.927 ...Subspecialty § 493.927 General immunology. (a) Program content and frequency...approved for proficiency testing for immunology, the annual program must...

2012-10-01

368

42 CFR 493.927 - General immunology.  

Code of Federal Regulations, 2010 CFR

...2010-10-01 2010-10-01 false General immunology. 493.927 Section 493.927 ...Subspecialty § 493.927 General immunology. (a) Program content and frequency...approved for proficiency testing for immunology, the annual program must...

2010-10-01

369

Marker-Assisted Selection  

NSDL National Science Digital Library

A method of selecting desirable individuals in a breeding scheme based on DNA molecular marker patterns instead of, or in addition to, their trait values.A tool that can help plant breeders select more efficiently for desirable crop traits.

370

Immunological mechanisms in specific immunotherapy  

Microsoft Academic Search

Specific immunotherapy (SIT) represents the only curative treatment of allergy and is, therefore, of particular interest for immunological and pharmacological research. The current understanding of immunological mechanisms underlying SIT focuses on regulatory T cells (T regs), which balance Th1 and Th2 effector functions. This ensures that allergens are recognized, but tolerated by the immune system. There is clear evidence that

Carsten B. Schmidt-Weber; Kurt Blaser

2004-01-01

371

Chemokines: immunology's high impact factors  

Microsoft Academic Search

Chemokines facilitate leukocyte migration and positioning as well as other processes such as angiogenesis and leukocyte degranulation. The burgeoning knowledge on chemokines and their receptors has influenced many aspects of immunology, in part because cell migration is intimately related to leukocyte function. This overview assesses the impact that chemokines have had on our understanding of immunology and infectious diseases. These

Charles R. Mackay

2001-01-01

372

Trifluoroleucine resistance as a dominant molecular marker in transformation of strains of Saccharomyces cerevisiae isolated from wine.  

PubMed

The resistance to 5,5,5-trifluoro-DL-leucine, encoded by the dominant allele LEU4-1, was used as a selectable marker to transform laboratory and natural Saccharomyces cerevisiae strains by the lithium acetate procedure. Results of transformation of S. cerevisiae laboratory and wine natural strains showed that trifluoroleucine resistance is a very effective selection marker and can be widely used to transform prototrophic S. cerevisiae strains. The LEU4-1 gene could also be exploited to improve wine flavour, as indicated by the higher isoamyl alcohol content of the transformants compared to the parental strains. PMID:10556716

Bendoni, B; Cavalieri, D; Casalone, E; Polsinelli, M; Barberio, C

1999-11-15

373

Characterization of Broad Spectrum Potato Virus Y Resistance in a Solanum tuberosum ssp. andigena Derived Population and Select Breeding Clones Using Molecular Markers, Grafting, and Field Inoculations  

Microsoft Academic Search

PVY causes yield and quality loss in potato. The Ry\\u000a \\u000a adg\\u000a gene from Solanum tuberosum ssp. andigena has been shown to provide extreme resistance to PVY; defined as resistance against all strains. However, Ry\\u000a \\u000a adg\\u000a gene clones have not been screened against PVYN:O, a newly detected North America strain. Three Ry\\u000a \\u000a adg\\u000a \\u000a -diagnostic molecular markers were tested in tetraploid progeny

Jonathan L. Whitworth; Richard G. Novy; Darren G. Hall; James M. Crosslin; Charles R. Brown

2009-01-01

374

Pediatric allergy and immunology in Brazil.  

PubMed

The subspecialty of pediatric allergy and immunology in Brazil is in its early years and progressing steadily. This review highlights the research developed in the past years aiming to show the characteristics of allergic and immunologic diseases in this vast country. Epidemiologic studies demonstrated the high prevalence of asthma in infants, children, and adolescents. Mortality rates and average annual variation of asthma hospitalization have reduced in all pediatric age groups. Indoor aeroallergen exposure is excessively high and contributes to the high rates of allergy sensitization. Prevalence of food allergy has increased to epidemic levels. Foods (35%), insect stings (30%), and drugs (23%) are the main etiological agents of anaphylaxis in children and adolescents. Molecular diagnosis of primary immunodeficiencies (PID) showed a high incidence of fungal infections including paracoccidioidomycosis in X-linked hyper-IgM syndrome, and the occurrence of BCG adverse reactions or other mycobacterial infections in patients with chronic granulomatous disease. Education in pediatric allergy and immunology is deficient for medical students, but residency programs are effective in training internists and pediatricians for the practice of allergy. The field of PID requires further training. Last, this review is a tribute to Prof. Dr. Charles Naspitz, one of the pioneers of our specialty in Brazil. PMID:23578336

Rosario-Filho, Nelson A; Jacob, Cristina M; Sole, Dirceu; Condino-Neto, Antonio; Arruda, Luisa K; Costa-Carvalho, Beatriz; Cocco, Renata R; Camelo-Nunes, Inês; Chong-Neto, Herberto J; Wandalsen, Gustavo F; Castro, Ana P M; Yang, Ariana C; Pastorino, Antonio C; Sarinho, Emanuel S

2013-06-01

375

Molecular abnormalities in the major psychiatric illnesses: Classification and Regression Tree (CRT) analysis of post-mortem prefrontal markers  

Microsoft Academic Search

Post-mortem specimens from the Stanley Foundation Neuropathology Consortium, which contains matched samples from patients with schizophrenia, bipolar disorder, non-psychotic depression and normal controls (n = 15 per group), have been distributed to many research groups around the world. This paper provides a summary of abnormal markers found in prefrontal cortical areas from this collection between 1997 and 2001. With parametric

M B Knable; B M Barci; J J Bartko; M J Webster; E F Torrey

2002-01-01

376

Hierarchical Analysis of Genetic Structure in Native Fire Ant Populations: Results from Three Classes of Molecular Markers  

PubMed Central

We describe genetic structure at various scales in native populations of the fire ant Solenopsis invicta using two classes of nuclear markers, allozymes and microsatellites, and markers of the mitochondrial genome. Strong structure was found at the nest level in both the monogyne (single queen) and polygyne (multiple queen) social forms using allozymes. Weak but significant microgeographic structure was detected above the nest level in polygyne populations but not in monogyne populations using both classes of nuclear markers. Pronounced mitochondrial DNA (mtDNA) differentiation was evident also at this level in the polygyne form only. These microgeographic patterns are expected because polygyny in ants is associated with restricted local gene flow due mainly to limited vagility of queens. Weak but significant nuclear differentiation was detected between sympatric social forms, and strong mtDNA differentiation also was found at this level. Thus, queens of each form seem unable to establish themselves in nests of the alternate type, and some degree of assortative mating by form may exist as well. Strong differentiation was found between the two study regions using all three sets of markers. Phylogeographic analyses of the mtDNA suggest that recent limitations on gene flow rather than longstanding barriers to dispersal are responsible for this large-scale structure. PMID:9335601

Ross, K. G.; Krieger, MJB.; Shoemaker, D. D.; Vargo, E. L.; Keller, L.

1997-01-01

377

Immunology for physicists  

NASA Astrophysics Data System (ADS)

The immune system is a complex system of cells and molecules that can provide us with a basic defense against pathogenic organisms. Like the nervous system, the immune system performs pattern recognition tasks, learns, and retains a memory of the antigens that it has fought. The immune system contains more than 107 different clones of cells that communicate via cell-cell contact and the secretion of molecules. Performing complex tasks such as learning and memory involves cooperation among large numbers of components of the immune system and hence there is interest in using methods and concepts from statistical physics. Furthermore, the immune response develops in time and the description of its time evolution is an interesting problem in dynamical systems. In this paper, the authors provide a brief introduction to the biology of the immune system and discuss a number of immunological problems in which the use of physical concepts and mathematical methods has increased our understanding.

Perelson, Alan S.; Weisbuch, Gérard

1997-10-01

378

Molecular markers of cartilage breakdown and synovitis at baseline as predictors of structural progression of hip osteoarthritis. The ECHODIAH* Cohort  

PubMed Central

Objective To determine whether systemic markers of bone, cartilage, and synovium can predict structural progression of osteoarthritis (OA). Methods Patients with painful hip OA were treated with diacerein or placebo in a multicentre, prospective, double blind, 3?year follow up trial. The following information was collected at entry: demographics, characteristics of hip OA, and 10 markers: N?propeptides of collagen types I and III, cartilage oligomeric matrix protein, YKL?40, hyaluronan (sHA), matrix metalloproteinases?1 and ?3, C reactive protein, C?terminal crosslinking telopeptides of collagen types I and II (uCTX?II). Radiographs were obtained at entry and every year. Structural progression was defined as a joint space decrease ?0.5?mm or requirement for total hip replacement. Grouped survival analysis was performed with time to structural progression as dependent variable, and clinical data, radiographic findings, treatment groups (diacerein versus placebo), and markers as explanatory measures. Results In the 333 patients in whom all markers were measured, high functional impairment, a joint space width <2?mm, and lateral migration of the femoral head at baseline increased the risk of progression, but diacerein had a protective effect (relative risk?=?0.75; 95% confidence interval (CI) 0.54 to 0.96). In addition, patients in whom uCTX?II and sHA were in the upper tertile had a relative risk of progression of 3.73 (95% CI 2.48 to 5.61) compared with patients with markers in the two lower tertiles. Conclusion In this large cohort, combined measurements of uCTX?II and sHA were a new predictor of the structural progression of hip OA. PMID:16322084

Mazieres, B; Garnero, P; Gueguen, A; Abbal, M; Berdah, L; Lequesne, M; Nguyen, M; Salles, J-P; Vignon, E; Dougados, M

2006-01-01

379

Immunology of melanoma.  

PubMed

It can be safely said that human melanomas are immunogenic. Virtually all the major principles of "tumor immunology" have been experimentally established in this model. It is now amply clear that melanoma cells display multiple antigens and peptide epitopes that are targetable by the host immune system and that patients with melanoma are capable of responding to these antigens and epitopes serologically as well as through the cell-mediated mechanisms. The immune responses against melanoma are, however, subject to regulation by the regulatory processes within the immune system itself and melanoma cells can resort to overt evasive activities. Indeed, the intrinsic as well as the extrinsic mechanisms within the immune system that are designed to control the magnitude as well as the duration of immune responses at times act as constraints against generating a robust and long-lasting antimelanoma response and melanoma cells are capable of using all the tricks (eg, downregulation of targetable molecules, elaboration of immunosuppressive cytokines) available to living organisms so as to evade immune recognition and destruction. As a result, the immune system often fails to protect the host against melanoma development and progression. The cumulative knowledge over the years on melanoma-associated antigens and epitopes, on methods of immunization, and on technologies for generating melanoma antigen-specific T cells, natural or engineered, have led to the development of immunotherapeutic strategies with "melanoma vaccines" and with T-cell-based adoptive immunotherapy for melanoma. Although these strategies have not been uniformly successful in all cases, durable complete regressions of metastatic melanoma can at times be obtained with active specific immunization or adoptive cell therapy. There is reason for hope that continued research in the field is likely to improve the outcome of melanoma immunotherapy: the ultimate goal of tumor immunology. PMID:23438379

Mukherji, Bijay

2013-01-01

380

Comparative Assessment of Lymph Node Micrometastasis in Cervical, Endometrial and Vulvar Cancer: Insights on the Real Time qRT-PCR Approach versus Immunohistochemistry, Employing Dual Molecular Markers  

PubMed Central

To address the value of qRT-PCR and IHC in accurately detecting lymph node micrometastasis in gynecological cancer, we performed a systematic approach, using a set of dual molecular tumor-specific markers such as cytokeratin 19 (CK19) and carbonic anhydrase 9 (CA9), in a series of 46 patients (19 with cervical cancer, 18 with endometrial cancer, and 9 with vulvar cancer). A total of 1281 lymph nodes were analyzed and 28 were found positive by histopathology. Following this documentation, 82 lymph nodes, 11 positive and 71 negative, were randomly selected and further analyzed both by IHC and qRT-PCR for CK19 and CA9 expression. All 11 (100%) expressed CK19 by IHC, while only 6 (54.5%) expressed CA9. On the contrary, all the histologically negative for micrometastases lymph nodes were also negative by IHC analysis for both markers. The comparative diagnostic efficacy of the two markers using qRT-PCR, however, disclosed that the analysis of the same aliquots of the 82 lymph nodes led to 100% specificity for the CK19 biomarker, while, in contrast, CA9 failed to recapitulate a similar pattern. These data suggest that qRT-PCR exhibits a better diagnostic accuracy compared to IHC, while CK19 displays a consistent pattern of detection compared to CA9. PMID:24527437

Pappa, Kalliopi I.; Rodolakis, Alexandros; Christodoulou, Ioanna; Gazouli, Maria; Markaki, Sofia; Antsaklis, Aris; Anagnou, Nicholas P.

2014-01-01

381

Evaluation of genetic homogeneity in tissue culture regenerates of Jatropha curcas L. using flow cytometer and DNA-based molecular markers.  

PubMed

The present investigation aimed to evaluate the reliability of in vitro propagation methods for elite genotypes of Jatropha curcas L., that maintain genetic integrity of tissue culture (TC) regenerates among two regeneration systems developed through direct shoot bud regeneration using nodal/apical shoot segments (protocol-A) and in vitro-derived leaves (protocol-B) as explants. Random amplified polymorphic DNA (RAPD), intersimple sequence repeat (ISSR), simple sequence repeat (SSR) molecular markers, and flow cytometery (FCM) were employed to evaluate genetic homogeneity in TC-regenerates at different passages of subcultures. RAPD markers showed genetic homogeneity in fifth-generation TC-regenerates of both protocols. ISSR markers showed genetic stability of leaf regenerates (protocol-B) at 10th generation. FCM analysis of TC-regenerates at 10th generation in protocol-B and at 20th generation in both protocols, showed stability of ploidy level. SSR assessment of TC-regenerates at 20th generation in both protocols confirmed genetic homogeneity. The results confirmed the genetic stability of the TC-regenerates and demonstrated the reliability of the regeneration systems developed so far using explants of two different origins, for large-scale multiplication of elite genotypes of Jatropha. PMID:24078186

Rathore, Mangal S; Yadav, P; Mastan, Shaik G; Prakash, Ch R; Singh, A; Agarwal, Pradeep K

2014-01-01

382

Assessment of genetic diversity and variation of Robinia pseudoacacia seeds induced by short-term spaceflight based on two molecular marker systems and morphological traits.  

PubMed

The black locust (Robinia pseudoacacia) is a forest legume that is highly valued as a honey plant and for its wood. We explored the effect of short-term spaceflight on development of R. pseudoacacia seedlings derived from seeds that endured a 15-day flight; the genetic diversity and variation of plants sampled from space-mutagenized seeds were compared to plants from parallel ground-based control seeds using molecular markers and morphological traits. In the morphology analysis, the space-mutagenized group had apparent variation compared with the control group in morphological traits, including plant height, basal diameter, number of branches, branch stipular thorn length, branch stipular thorn middle width, leaflet vertex angle, and tippy leaf vertex angle. Simple sequence repeat (SSR) and sequence-related amplified polymorphism (SRAP) molecular marker analyses showed a slightly higher levels of genetic diversity in the space-mutagenized group compared to the control group. In the SRAP analysis, the space-mutagenized group had 115 polymorphic bands vs 98 in the controls; 91.27% polymorphic loci vs 77.78% in the controls; 1.9127 ± 0.2834 alleles vs 1.7778 ± 0.4174 in the controls; Nei's genetic diversity (h) was 0.2930 ± 0.1631 vs 0.2688 ± 0.1862 in the controls, and the Shannon's information index (I) was 0.4452 ± 0.2177 vs 0.4031 ± 0.2596 in the controls. The number of alleles was significantly higher in the space-mutagenized group. In the SSR analysis, the space-mutagenized group also had more polymorphic bands (51 vs 46), a greater percentage of polymorphic loci (89.47% vs 80.70%); h was also higher (0.2534 ± 0.1533 vs 0.2240 ± 0.1743), as was I (0.3980 ± 0.2069 vs 0.3501 ± 0.2412). These results demonstrated that the range of genetic variation in the populations of R. pseudoacacia increased after spaceflight. It also suggested that the SSR and SRAP markers are effective markers for studying mutations and genetic diversity in R. pseudoacacia. The data provide valuable molecular evidence for the effects of the space environment on R. pseudoacacia and may contribute to future space-breeding programs involving forest trees. PMID:23315806

Yuan, C Q; Li, Y F; Sun, P; Sun, Y H; Zhang, G J; Yang, M S; Zhang, Y Y; Li, Y; Wang, L

2012-01-01

383

Novel method to establish molecular identity using inter-simple sequence repeat markers in cotton (Gossypium hirsutum) cultivars.  

PubMed

Plant molecular identity (ID) is used to describe molecular characteristics of plants, which should contain all of the necessary information. Using inter-simple sequence repeat (ISSR) primers, molecular ID can be described in a way that reflects the polymerase chain reaction (PCR) conditions, annealing temperature, and the bands obtained in PCR amplification. A new complete molecular ID system is described in this study, which can be easily used and expanded to include more information. Using three cotton cultivars, we analyzed the products of PCR with ISSR primers and discussed the strategy for establishing their molecular ID. Using the segmented naming method, we designate the simple names and the full name systems of these three cultivars. PMID:24938605

Zhao, Z-Y; Zhi, M-X; Zhang, Z-Y; Sun, H-L; Liu, Y-S; Li, X-J

2014-01-01

384

Correlation of a priori DCE-MRI and 1H-MRS data with molecular markers in neck nodal metastases: Initial analysis  

PubMed Central

Objectives The aim of the present study is to correlate non-invasive, pretreatment biological imaging (dynamic contrast enhanced-MRI [DCE-MRI] and proton magnetic resonance spectroscopy [1H-MRS]) findings with specific molecular marker data in neck nodal metastases of head and neck squamous cell carcinoma (HNSCC) patients. Materials and Methods Pretreatment DCE-MRI and 1H-MRS were performed on neck nodal metastases of 12 patients who underwent surgery. Surgical specimens were analyzed with immunohistochemistry (IHC) assays for: Ki-67 (reflecting cellular proliferation), vascular endothelial growth factor (VEGF) (the “endogenous marker” of tumor vessel growth), carbonic anhydrase (CAIX), hypoxia inducible transcription factor (HIF-1?), and human papillomavirus (HPV). Additionally, necrosis was estimated based on H&E staining. The Spearman correlation was used to compare DCE-MRI, 1H-MRS, and molecular marker data. Results A significant correlation was observed between DCE-MRI parameter std(kep) and VEGF IHC expression level (rho = 0.81, p = 0.0001). Furthermore, IHC expression levels of Ki-67 inversely correlated with std(Ktrans) and std(ve) (rho = ?0.71; p = 0.004, and rho = ?0.73; p = 0.003, respectively). Other DCE-MRI, 1H-MRS and IHC values did not show significant correlation. Conclusion The results of this preliminary study indicate that the level of heterogeneity of perfusion in metastatic HNSCC seems positively correlated with angiogenesis, and inversely correlated with proliferation. These results are preliminary in nature and are indicative, and not definitive, trends portrayed in HNSCC patients with nodal disease. Future studies with larger patient populations need to be carried out to validate and clarify our preliminary findings. PMID:22366441

Jansen, Jacobus F.A.; Carlson, Diane L.; Lu, Yonggang; Stambuk, Hilda. E.; Moreira, Andre L.; Singh, Bhuvanesh; Patel, Snehal G.; Kraus, Dennis H.; Wong, Richard J.; Shaha, Ashok R.; Shah, Jatin P.; Shukla-Dave, Amita

2012-01-01

385

Genetic variability of oil palm parental genotypes and performance of its' progenies as revealed by molecular markers and quantitative traits.  

PubMed

Studies were conducted to assess the genetic relationships between the parental palms (dura and pisifera) and performance of their progenies based on nine microsatellite markers and 29 quantitative traits. Correlation analyses between genetic distances and hybrids performance were estimated. The coefficients of correlation values of genetic distances with hybrid performance were non-significant, except for mean nut weight and leaf number. However, the correlation coefficient of genetic distances with these characters was low to be used as predicted value. These results indicated that genetic distances based on the microsatellite markers may not be useful for predicting hybrid performance. The genetic distance analysis using UPGMA clustering system generated 5 genetic clusters with coefficient of 1.26 based on quantitative traits of progenies. The genotypes, DP16, DP14, DP4, DP13, DP12, DP15, DP8, DP1 and DP2 belonging to distant clusters and greater genetic distances could be selected for further breeding programs. PMID:21513898

Abdullah, Norziha; Rafii Yusop, Mohd; Ithnin, Maizura; Saleh, Ghizan; Latif, M A

2011-04-01

386

Molecular marker analysis of Helianthus annuus L. 2. Construction of an RFLP linkage map for cultivated sunflower  

Microsoft Academic Search

A detailed linkage map of Helianthus annuus was constructed based on segregation at 234 RFLP loci, detected by 213 probes, in an F2 population of 289 individuals (derived from a cross between the inbred lines HA89 and ZENB8). The genetic markers covered 1380 centiMorgans (cM) of the sunflower genome and were aranged in 17 linkage groups, corresponding to the haploid

S. T. Berry; A. J. Leon; C. C. Hanfrey; P. Challis; A. Burkholz; S. R. Barnes; G. K. Rufener; M. Lee; P. D. S. Caligari

1995-01-01

387

Biochemical and molecular markers for investigating the mode of reproduction in the facultative apomict Poa pratensis L  

Microsoft Academic Search

Isozymes and random amplified polymorphic DNA (RAPD) markers were used for precocious identification of non-maternal plants in progenies of the facultative apomict Poa pratensis. Four progenies obtained from controlled crosses that showed different degrees of apomixis on isozyme analysis of phospho-gluco-isomerases, esterases and peroxidases were chosen for RAPD analysis to generate genomic fingerprints using species-specific primers. At an advanced vegetative

A. Mazzucato; G. Barcaccia; M. Pezzotti; M. Falcinelli

1995-01-01

388

MOLECULAR BIOLOGY INSTITUTE LIST OF CURRENT MEMBERS  

E-print Network

MOLECULAR BIOLOGY INSTITUTE LIST OF CURRENT MEMBERS Adams, John S. Orthopedic Surgery Bajaj, S. Paul Orthopedic Surgery Banerjee, Utpal Molecular, Cell & Developmental Biology Baum, Linda G Orthopedic Surgery Hill, Kent L. Microbiology, Immunology & Molecular Genetics Hirsch, Ann M. Molecular, Cell

Koehler, Carla

389

The golden anniversary of Burnet's clonal selection Immunology and Cell Biology (2008) 86, 15; doi:10.1038/sj.icb.7100145  

E-print Network

EDITORIAL The golden anniversary of Burnet's clonal selection theory Immunology and Cell Biology for the first time the principles that would underlie the era of modern cellular and molecular immunology with immunology and the further testing and development of the clonal selection theory. It is fitting

Cai, Long

390

[Dementias: present situation and future perspectives (II). Biological markers].  

PubMed

In the previous paper, the first one in our trilogy about dementias, we introduce the concept and evaluate the diagnostic methods and the data provided by epidemiological investigation. In this paper we review the different biological diagnostic markers, based, in the first place, on the studies of neuroimage (computerized axial tomography, magnetic resonance, functional neuroimage techniques) and those properly neurophysiological; in the second place, the anatomopathological and physiopathological markers are examined; and, in the third place, those based on the modern genetic investigations. In the absence of an 'univocal biological marker', the current investigation about markers is on the way to the study of abnormal proteins discovered in the brain, of the modifications detected in the cellular metabolism, of the manifestations of the immunologic mechanisms and of the involved inflammatory processes, and is on the way to the advances and proximate perspectives of molecular genetics and animal models. Meanwhile, the diagnostic for the main dementia, due to Alzheimer's disease, is basically a clinic, exclusive and residual one, mainly in its initial stadium. PMID:8548649

Espert, R; Bertolín, J M; Navarro, J F; González, A

1995-01-01

391

Immunological and molecular diagnosis of cysticercosis  

PubMed Central

Cysticercosis, the infection with the larval stage of Taenia solium, is a cause of neurological symptoms including seizures, affecting the quality of life of patients and their families. Diagnosis focuses on brain imaging and serological tests are mostly used as confirmatory tools. Most cases, however, occur in poor endemic areas, where both kinds of diagnostic tools are poorly available. Development of point of care diagnostic tests is one of the most important priorities for cysticercosis researches today. The ideal point of care test would require detection of viable cysticercosis and hopefully identify cases with severe or progressive forms of neurocysticercosis, leading to referral of the patient for specialized medical attention. This manuscript describes the evolution of the serological diagnosis of cysticercosis over time, and the characteristics of the most common currently available tools, their advantages and disadvantages, and their potential use in future diagnostic tests. PMID:23265553

Rodriguez, Silvia; Wilkins, Patricia; Dorny, Pierre

2012-01-01

392

Molecular virology and immunology of HIV infection  

Microsoft Academic Search

Great progress has been made with respect to our understanding of the immunopathogenesis of AIDS and the infectious agent, HIV, that causes the disease. HIV, a human retrovirus with tropism for CD4+ T cells and monocytes, induces a decrease of T-cell counts, T-cell dysfunction, and, ultimately, immunodeficiency. HIV also causes B-cell dysfunction characterized by polyclonal activation, hypergammaglobulinemia, and lack of

Javier Chinen; William T. Shearer

2002-01-01

393

Measurements of organic molecular markers in California using comprehensive 2-Dimensional Gas Chromatograph High-Resolution Time-of-Flight Mass Spectrometry (GCxGC-HRTOF-MS)  

NASA Astrophysics Data System (ADS)

Understanding the sources and transformation processes of organic aerosol requires detailed speciation of organic compounds. Molecular markers specific to individual sources help determine the contribution of each source to organic aerosol emissions. In previous work using one-dimensional gas-chromatograph mass spectrometry (GC/MS), less than 10-20% of the organic fraction has been identified, with a large contribution of unresolved complex mixture (UCM). Two-dimensional gas-chromatograph is a novel technique which provides excellent resolution to separate compounds buried in this complex mixture. In addition to a volatility-based chromatographic separation, compounds are further separated on a second column based on their polarities. Here we report measurements of more than 200 resolved compounds observed on filters collected during CalNex 2010 in Bakersfield and Pasadena, and during a large biomass burning event in the Los Angeles area (Station Fire). High volume filter samples are thermally desorbed in a Gerstel Thermal Desorption System (TDS2) and preconcentrated on a cooled inlet (CIS). The compounds are then analyzed by comprehensive 2-dimensional GC using a Zoex modulator, followed by high-resolution mass spectrometry (Tofwerks). Compound identification is carried out by comparison of retention times with known standards, mass spectral library match, and identification of molecular fragments by exact mass. A wide range of compounds are observed: n-alkanes, polyaromatic hydrocarbons, and oxygenated compounds such as acids, esters and ketones. While levoglucosan was observed in organic aerosol produced during the Station Fire, many other compounds revealed by two-dimensional GC (such as resin acids, lignin pyrolysis products) show elevated signals, suggesting that other molecular markers can provide additional information about aerosol formation processes during biomass burning events.

Chan, A. W.; Isaacman, G. A.; Worton, D. R.; Kreisberg, N. M.; Schilling, K. A.; Craven, J. S.; Metcalf, A. R.; Hersey, S. P.; Rubitschun, C. L.; Lin, Y. H.; Offenberg, J. H.; Surratt, J. D.; Seinfeld, J.; Hering, S. V.; Goldstein, A. H.

2011-12-01

394

Intravenous immunoglobulin (IVIG) therapy for immunologic abortion  

Microsoft Academic Search

Recurrent pregnancy loss associated with immunologic abnormalities has been termed immunologic abortion. Immunologic abortion occurs primarily in women over the age of 30 years and may affect either natural or in-vitro fertilization (IVF)-induced pregnancy. In this article, we review the humoral and cellular immunologic abnormalities that have been associated with this form of recurrent abortion, and we discuss treatment options

Raphael B. Stricker; Alex Steinleitner; Edward E. Winger

2002-01-01

395

Modelling Immunological Memory Simon Garrett1  

E-print Network

5 Modelling Immunological Memory Simon Garrett1 , Martin Robbins1 , Joanne Walker1 , William Wilson. Accurate immunological models offer the possibility of performing high- throughput experiments in silico of immunological memory. We first validate an experimental immunological simulator, developed by the authors

Aickelin, Uwe

396

M&ISummer 2011 Microbiology & Immunology  

E-print Network

M&ISummer 2011 Microbiology & Immunology DEPARTMENT OF #12;04 Message Letter from the Chair 08 AID newsletter from the Department of Mi- crobiology & Immunology. In this inaugural issue, I would like Immunology (CCTI), a cross-departmental initiative that will emphasize transla- tion of basic immunological

Biasutti, Michela

397

Analytic Immunologic Techniques Joseph G. Kunkel  

E-print Network

Chapter 1 Analytic Immunologic Techniques Joseph G. Kunkel I. Introduction Analytic immunologic that are present in a complex mixture and measure their relative or absolute titers at the same time. Immunology may or may not be replaced by mABs. Before investigators embark on using a particular immunologic

Kunkel, Joseph G.

398

Immunology of reactive arthritides.  

PubMed

Reactive arthritis (ReA) and Lyme arthritis together comprise a pair of chronic inflammatory diseases of the joints. Although differing in detail, these relatively rare diseases are related in their immunopathology to the much commoner rheumatoid arthritis (RA), for which they serve as both model and control. The trigger for rheumatoid arthritis is unknown, but for these rarer diseases triggering occurs by certain well-defined bacterial infections. Arthritis is an uncommon outcome of these infections, for reasons unknown, and the development of chronic, as distinct from brief, arthritis is even rarer; again, the reasons are unknown. Not only does knowing the trigger greatly assist us in understanding these diseases, so also does knowing the contrasting pattern of Th1 versus Th2 cytokines observed in RA and ReA. ReA and Lyme arthritis are here considered in the wider setting of infections where chronic morbidity arises first from hypersensitivity, and perhaps finally from autoimmunity, such as occurs in some of the major tropical diseases. The immunology of ReA and Lyme disease is surveyed in detail, concentrating on T cells and including an update on the Lyme vaccine(s). Additional sections deal with the enigma of HLA B27, with epidemiological findings relevant to the chronicity of ReA and to the need for enlarged prospective studies of ReA in the setting of a developing country. PMID:7612222

Burmester, G R; Daser, A; Kamradt, T; Krause, A; Mitchison, N A; Sieper, J; Wolf, N

1995-01-01

399

Introduction. Ecological immunology  

PubMed Central

An organism's fitness is critically reliant on its immune system to provide protection against parasites and pathogens. The structure of even simple immune systems is surprisingly complex and clearly will have been moulded by the organism's ecology. The aim of this review and the theme issue is to examine the role of different ecological factors on the evolution of immunity. Here, we will provide a general framework of the field by contextualizing the main ecological factors, including interactions with parasites, other types of biotic as well as abiotic interactions, intraspecific selective constraints (life-history trade-offs, sexual selection) and population genetic processes. We then elaborate the resulting immunological consequences such as the diversity of defence mechanisms (e.g. avoidance behaviour, resistance, tolerance), redundancy and protection against immunopathology, life-history integration of the immune response and shared immunity within a community (e.g. social immunity and microbiota-mediated protection). Our review summarizes the concepts of current importance and directs the reader to promising future research avenues that will deepen our understanding of the defence against parasites and pathogens. PMID:18926970

Schulenburg, Hinrich; Kurtz, Joachim; Moret, Yannick; Siva-Jothy, Michael T.

2008-01-01

400

Immunology of schistosomiasis*  

PubMed Central

This Memorandum, after summarizing the life cycle of the different species of human schistosome, reviews the present knowledge of the immunology of schistosomiasis. Each stage of the parasite contains antigen that may stimulate an immune response. However, at the moment there are no accepted serological in vitro tests that correlate with protection; this develops only after the host has experienced a living infection, which suggests that the stimulation of immunity is due to some metabolic process involving the release of protective antigen. The adult worm, however, seems to be able to escape the immune mechanism of the host. Specific antigens are also released by the eggs, and the immune response against these antigens seems to cause granuloma formation around the egg itself. The granuloma is the main lesion found in schistosomiasis. Evidence for protective immunity in experimental animals and man is reviewed, together with the possible mechanism by which the adult worm escapes the immune response of the host. A review of methods used for the diagnosis of schistosomiasis and a list of recommendations for further research are also included. PMID:4219757

1974-01-01