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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.

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

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

3

21 CFR 866.5065 - Human allotypic marker immunological test system.  

Code of Federal Regulations, 2013 CFR

... Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Immunological Test Systems § 866.5065 Human allotypic marker immunological test...

2013-04-01

4

Immunological Markers of the R4 Protein of Streptococcus agalactiae  

Microsoft Academic Search

This study focuses on immunological markers of R4, an important Streptococcus group B (GBS) protein. The results obtained by using rabbit antisera and purified proteins for antigens in enzyme-linked immunosorbent assay-based experiments provided evidence that R4 possesses two antigenic determinants. One of the deter- minants is shared with the alpha-like protein 3 (Alp3) of GBS, was named R4\\/Alp3 common, and

Johan A. Maeland; Lars Bevanger; Randi Valsoe Lyng

2005-01-01

5

[Contribution of immunology and molecular biology].  

PubMed

Recent technical advances in immunology and molecular genetics have allowed to better delineate Ewing sarcoma among other small round cell tumors of bone and soft tissues. Ewing cells present with a characteristic translocation t (11;22) (q23-24; q11-12) shared with neuroepithelioma. They express a series of cell-surface antigens associated with the neuroectodermal differentiation lineage. These data open new avenues for exploring the origin and the mechanism of transformation of these tumors and to conceive new therapeutical approaches. PMID:3395706

Lipinski, M; Tursz, T

1988-01-01

6

An Immunological Marker of Tolerance to Infection in Wild Rodents  

PubMed Central

Hosts are likely to respond to parasitic infections by a combination of resistance (expulsion of pathogens) and tolerance (active mitigation of pathology). Of these strategies, the basis of tolerance in animal hosts is relatively poorly understood, with especially little known about how tolerance is manifested in natural populations. We monitored a natural population of field voles using longitudinal and cross-sectional sampling modes and taking measurements on body condition, infection, immune gene expression, and survival. Using analyses stratified by life history stage, we demonstrate a pattern of tolerance to macroparasites in mature compared to immature males. In comparison to immature males, mature males resisted infection less and instead increased investment in body condition in response to accumulating burdens, but at the expense of reduced reproductive effort. We identified expression of the transcription factor Gata3 (a mediator of Th2 immunity) as an immunological biomarker of this tolerance response. Time series data for individual animals suggested that macroparasite infections gave rise to increased expression of Gata3, which gave rise to improved body condition and enhanced survival as hosts aged. These findings provide a clear and unexpected insight into tolerance responses (and their life history sequelae) in a natural vertebrate population. The demonstration that such responses (potentially promoting parasite transmission) can move from resistance to tolerance through the course of an individual's lifetime emphasises the need to incorporate them into our understanding of the dynamics and risk of infection in the natural environment. Moreover, the identification of Gata3 as a marker of tolerance to macroparasites raises important new questions regarding the role of Th2 immunity and the mechanistic nature of the tolerance response itself. A more manipulative, experimental approach is likely to be valuable in elaborating this further.

Jackson, Joseph A.; Hall, Amy J.; Friberg, Ida M.; Ralli, Catriona; Lowe, Ann; Zawadzka, Malgorzata; Turner, Andrew K.; Stewart, Alexander; Birtles, Richard J.; Paterson, Steve; Bradley, Janette E.; Begon, Mike

2014-01-01

7

Molecular and Immunological Characteristics of Latex Allergens  

Microsoft Academic Search

Natural rubber latex proteins are a well-recognized cause of type-I allergic reactions that increasingly afflict health-care workers, housekeeping personnel, and other persons using latex gloves or latex products. More than a dozen individual latex allergens have been identified of which eight have received an international nomenclature designation. To study the biochemical and immunological properties in detail, it is desirable to

Heimo Breiteneder; Otto Scheiner

1998-01-01

8

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

9

Human bancroftian filariasis: immunological markers of morbidity and infection.  

PubMed

Induction of host cytokines plays a critical role in infection as well as disease in human filariasis. Measurements of such molecules in plasma could be used as windows of markers both for understanding the pathogenesis of the disease and for identifying markers of morbidity. Eight inflammatory and non-inflammatory host molecules in circulation were quantified in 207 subjects in filariasis endemic area of Orissa, India. IL-6, IL-8, IL-10, TNF-alpha, TNFR-I, TNFR-II, LBP and sICAM-1 were quantified by immunoassays and were analyzed by multivariate exploratory data analysis methods followed by multivariate analysis of variance. Raised levels of IL-6 and IL-8 emerged as markers of acute as well as chronic disease, while increased TNF-alpha was a feature found only in acute filariasis. Decreased sICAM-1 was a feature found only in asymptomatic subjects with filarial infection. There was a dichotomy in plasma levels of two TNF receptors between infected subjects and patients with filarial disease. Since plasma levels of these cytokines are often determined by host genetics, studies on cytokine genetic polymorphisms could offer new insights into the relationship between infection and disease in human lymphatic filariasis. PMID:16839794

Satapathy, Ashok K; Sartono, Erliyani; Sahoo, Prakash K; Dentener, Mieke A; Michael, Edwin; Yazdanbakhsh, Maria; Ravindran, Balachandran

2006-08-01

10

Immunological markers that correlate with protection immunity against tularemia infection.  

PubMed

An efficient immune response to tularemia is dependent on a strong cell-mediated component. We tried to identify markers of cellular immune responses that indicate a vaccine efficacy against tularemia. BALB/c mice were immunized with mutant F. tularensis 15?23A and/or F. tularensis 15 NIIEG strains and then were challenged i.n. with F. tularensis Schu. We compared the influence of F. tularensis antigens (tularinum) in vitro on production of IL-1, IL-5, IL-6, IL-17, IFN-?, and TNF-? by splenocytes obtained from intact mice and mice immunized with mutant F. tularensis 15?23A and/or F. tularensis 15 NIIEG strains. We also compared expression of CD28, CD154, TLR-2, and CD69 markers on CD4 and CD8 T-cells after activation with tularinum in vitro. We found that tularinum-induced CD4(+) T-cells increased TNF-? and IFN-? synthesis and expression of CD69 only in group mice with high degree of post immunization protection against F. tularensis Schu challenge. Estimation of CD69 expression on CD3(+)CD4(+) cells and IFN-?, TNF-? synthesis by CD4(+) T-lymphocytes could be useful for determination protect ability of antitularemia immunity. PMID:24595607

Firstova, Victoria V; Mokrievich, Alexander N; Pavlov, Vitalii M; Gorbatov, Aleksey A; Kombarova, Tatiana I; Biketov, Sergey F; Dyatlov, Ivan A

2014-01-01

11

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

12

Immunological markers predicting outcome in patients with hepatitis C treated with interferon-? and ribavirin  

Microsoft Academic Search

Type 1 (T1) cytokine responses are required for the clearance of hepatitis C virus by cytotoxic T lymphocytes, but can promote liver damage. Interferon-? (IFN?) can be expected to promote T1 cytokine responses, so treatment outcome may depend on the T1\\/T2 cytokine environment and levels of immune activation at baseline. This model was tested by monitoring immunological markers in a

Silvia Lee; Gerry C MacQuillan; Niamh M Keane; James Flexman; Gary P Jeffrey; Martyn AH French; Jean Brochier; Patricia Price

2002-01-01

13

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

14

(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...

15

Update on immunologic and molecular diagnosis of human strongyloidiasis.  

PubMed

Human strongyloidiasis is an intestinal parasitosis that may affect 100 million individuals. However, the prevalence rates of this infection may represent smaller values than the actual data, mainly due to difficulties in its diagnosis. The aim of this study was to update the immunological and molecular methods applied to the diagnosis of human strongyloidiasis. There is a great diversity of techniques used in the diagnosis of this parasitosis, such as immunofluorescence antibody test (IFAT), enzyme-linked immunosorbent assay (ELISA), immunoblotting, luciferase immunoprecipitation system (LIPS), dispstick and polymerase chain reaction (PCR), all with advantages and disadvantages, and with unique features for specific purposes. Considering the magnitude of strongyloidiasis and the importance of early diagnosis, due to the possibility of chronicity and hyperinfection, this study analyzes the different methods currently employed, and demonstrates the necessity of developing innovative methodologies, which also maintain diagnostic accuracy, particularly for regions with limited technological resources. PMID:24686097

Levenhagen, Marcelo A; Costa-Cruz, Julia M

2014-07-01

16

[The gene pool of Belgorod oblast population: the distribution of immunological and biochemical gene markers].  

PubMed

The frequencies of 33 alleles of 12 loci of immunological and biochemical gene markers (ABO, RH, HP, GC, TF, PI, C'3, ACP1, GLO1, PGM1, ESD, and 6-PGD) have been estimated in the indigenous Russian and Ukrainian populations of Belgorod oblast. Differences of the Belgorod population from other populations of Russia with respect to the genetic structure have been determined. It has been found that the frequency distributions of all alleles studied in the Belgorod population are similar to those typical of the genetic structure of Caucasoid populations. PMID:18666560

Lependina, I N; Balanovskaia, E V; Churnosov, M I

2008-04-01

17

Dye-free protein molecular weight markers.  

PubMed

Protein molecular weight markers are widely used in sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and Western blotting. Here, we describe novel protein molecular weight markers in which a prestaining procedure is no longer needed. Green fluorescent protein (GFP) is stable and resistant to denaturing agents/conditions. Various histidine-tagged GFP fusion proteins were overexpressed in Escherichia coli and purified by metal affinity chromatography. The minimal amount of each protein marker needed for analysis in SDS-PAGE and Western blot under visible light was 62.5 and 125 ng, respectively. Under ultraviolet (UV) ray, the minimal amount of each protein marker needed for analysis in SDS-PAGE and Western blot was half of those amounts used under visible light, respectively. Collectively, the accuracy, sensitivity, ease, economy, and flexibility of our strategy may reinforce the application of GFP in molecular biology. PMID:16041708

Chang, Microsugar; Hsu, Hsue-Yin; Lee, Han-Jung

2005-08-01

18

A novel data mining system points out hidden relationships between immunological markers in multiple sclerosis  

PubMed Central

Background Multiple Sclerosis (MS) is a multi-factorial disease, where a single biomarker unlikely can provide comprehensive information. Moreover, due to the non-linearity of biomarkers, traditional statistic is both unsuitable and underpowered to dissect their relationship. Patients affected with primary (PP=14), secondary (SP=33), benign (BB=26), relapsing-remitting (RR=30) MS, and 42 sex and age matched healthy controls were studied. We performed a depth immune-phenotypic and functional analysis of peripheral blood mononuclear cell (PBMCs) by flow-cytometry. Semantic connectivity maps (AutoCM) were applied to find the natural associations among immunological markers. AutoCM is a special kind of Artificial Neural Network able to find consistent trends and associations among variables. The matrix of connections, visualized through minimum spanning tree, keeps non linear associations among variables and captures connection schemes among clusters. Results Complex immunological relationships were shown to be related to different disease courses. Low CD4IL25+ cells level was strongly related (link strength, ls=0.81) to SP MS. This phenotype was also associated to high CD4ROR+ cells levels (ls=0.56). BB MS was related to high CD4+IL13 cell levels (ls=0.90), as well as to high CD14+IL6 cells percentage (ls=0.80). RR MS was strongly (ls=0.87) related to CD4+IL25 high cell levels, as well indirectly to high percentages of CD4+IL13 cells. In this latter strong (ls=0.92) association could be confirmed the induction activity of the former cells (CD4+IL25) on the latter (CD4+IL13). Another interesting topographic data was the isolation of Th9 cells (CD4IL9) from the main part of the immunological network related to MS, suggesting a possible secondary role of this new described cell phenotype in MS disease. Conclusions This novel application of non-linear mathematical techniques suggests peculiar immunological signatures for different MS phenotypes. Notably, the immune-network displayed by this new method, rather than a single marker, might be viewed as the right target of immunotherapy. Furthermore, this new statistical technique could be also employed to increase the knowledge of other age-related multifactorial disease in which complex immunological networks play a substantial role.

2013-01-01

19

[Genetic, molecular, and immunologic aspects of Vibrio cholerae infection].  

PubMed

The deterioration of the economical and social conditions of the majority of the population in the Americas the last 20 years has generated several epidemics of enteric infections in the region, dramatically manifested by the current massive and widespread cholera outbreak. The absence of cholera from the continent for more than 100 years, the worsening environmental conditions, the biological peculiarities of Vibrio cholerae El Tor such as decreased virulence, which generates increased number of carriers, and its improved ability to thrive in the environment are probably responsible for the rapid dissemination of the disease through out the continent. Genetic and molecular studies of the biology of V cholerae have permitted identification of a variety of new virulence factors besides the enterotoxin, and are also helping to unravel the exquisite mechanisms that regulate the expression of these virulence factors in response to different stimuli. Molecular studies of V cholerae chromosomal and plasmid DNA, and of chromosomal and plasmid gene products, with techniques such as DNA hybridization and multilocus enzyme analysis are improving the characterization of V cholerae strains, resulting in progress in understanding their epidemiology in different communities. The non-invasive character of V cholerae infections, epidemiological and immunological studies suggest that the disease and current vaccines fail in providing an effective and long lasting immunity, and that the control of the disease in endemic areas by the use of vaccines may therefore be unfeasible. Similar studies indicate that the provision of safe drinking water, adequate sewage disposal, sufficient nutrition, and education remain the most effective measures for controlling the disease. PMID:8248646

Fica, A E; Cabello, F C

1993-03-01

20

Marker antibody expression stratifies Crohn's disease into immunologically homogeneous subgroups with distinct clinical characteristics  

PubMed Central

BACKGROUND—Perinuclear antineutrophil cytoplasmic antibodies (pANCA) have been detected in a clinically distinct Crohn's disease subpopulation. Antibodies to Saccharomyces cerevisiae (ASCA) have been demonstrated in the majority of patients with Crohn's disease.?AIMS—To examine the relationship between selective marker antibody expression in Crohn's disease and disease onset, location, and clinical behaviour patterns.?METHODS—Sera from 156 consecutive patients with established Crohn's disease were evaluated in a blinded fashion for the presence of ASCA and ANCA. Clinical profiles were generated by investigators blinded to immune marker status.?RESULTS—Using multiple regression analyses, higher ASCA levels were shown to be independently associated with early age of disease onset as well as both fibrostenosing and internal penetrating disease behaviours. Higher ANCA levels were associated with later age of onset and ulcerative colitis-like behaviour. Substratification of the Crohn's disease population using selective ANCA and ASCA expression (high levels of a single marker antibody): (1) distinguished homogeneous subgroups that manifested similar disease location and behaviours; and (2) identified patients with more aggressive small bowel disease.?CONCLUSIONS—The findings suggest that by taking into account the magnitude of the host immune response, Crohn's disease can now be stratified on an immunological basis into more homogeneous clinically distinct subgroups, characterised by greater uniformity among anatomical distribution of disease and disease behaviour.???Keywords: antineutrophil cytoplasmic antibody; anti-Saccharomyces cerevisiae antibody; Crohn's disease; inflammatory bowel disease; ulcerative colitis

Vasiliauskas, E; Kam, L; Karp, L; Gaiennie, J; Yang, H; Targan, S

2000-01-01

21

Molecular markers for diagnosis and prognosis  

Microsoft Academic Search

A plethora of aberrations are associated with progress and outcome for head and neck cancer patients and some have been shown to provide prognostic information independent of the TNM staging system. These findings justify future studies that will harness recent advances in technologies to refine the range of molecular markers available. Important lessons have been learnt during the last two

Max Partridge; Kamis Gaballah; Xiaohong Huang

2005-01-01

22

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.

Esteva, Francisco J; Hortobagyi, Gabriel N

2004-01-01

23

Molecular Prognostic Markers in Colon Cancer  

Microsoft Academic Search

\\u000a Colorectal cancer arises as a consequence of the accumulation of genetic and epigenetic alterations. Significant progress\\u000a has been made to identify the different biomarkers associated with the biological and clinical behaviour of colorectal tumours.\\u000a Several new molecular predictive and prognostic markers have been identified and are now being translated into routine clinical\\u000a practice. One of the challenges is that most

Thomas Winder; Heinz-Josef Lenz

24

Fecal Molecular Markers for Colorectal Cancer Screening  

PubMed Central

Despite multiple screening techniques, including colonoscopy, flexible sigmoidoscopy, radiological imaging, and fecal occult blood testing, colorectal cancer remains a leading cause of death. As these techniques improve, their sensitivity to detect malignant lesions is increasing; however, detection of precursor lesions remains problematic and has generated a lack of general acceptance for their widespread usage. Early detection by an accurate, noninvasive, cost-effective, simple-to-use screening technique is central to decreasing the incidence and mortality of this disease. Recent advances in the development of molecular markers in faecal specimens are encouraging for its use as a screening tool. Genetic mutations and epigenetic alterations that result from the carcinogenetic process can be detected by coprocytobiology in the colonocytes exfoliated from the lesion into the fecal matter. These markers have shown promising sensitivity and specificity in the detection of both malignant and premalignant lesions and are gaining popularity as a noninvasive technique that is representative of the entire colon. In this paper, we summarize the genetic and epigenetic fecal molecular markers that have been identified as potential targets in the screening of colorectal cancer.

Kanthan, Rani; Senger, Jenna-Lynn; Kanthan, Selliah Chandra

2012-01-01

25

[Prognostic value of molecular biologogy and immunologic parameters in human pancreatic carcinoma].  

PubMed

In the present study we investigated the prognostic relevance of molecular and immunological changes in pancreatic carcinoma. 82 tissue specimens of adenocarcinoma of the pancreas were stained immunohistochemically with following factors: p53, p21WAF1, Cyklin D, EGF, EGF-R, cERB-B2, CD95, BCL-2 and Cathepsin D. We further determined the serum levels of sCD44, sCD44v6, neopterin and IL-2R. Except Cyclin D none of the immunohistochemically determined factors had prognostic significance. Interestingly all of the immunological serum parameters were of high prognostic significance. These data demonstrate the prognostic relevance of immunological parameters in human adenocarcinoma of the pancreas and could raise the possibility of an early immunological intervention in pancreatic cancer. PMID:14518215

Gansauge, F; Gansauge, S; Müller, J; Schmid, E; Beger, H G

1998-01-01

26

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

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

2000-01-01

27

Molecular Markers and Marker-Assisted Selection in Rice  

Microsoft Academic Search

The status of rice as a model crop and the sequencing of the indica and japonica genomes have provided breeders with the necessary tools for marker assisted breeding. Simple Sequence Repeat (SSR) markers\\u000a are easily available for any region of the genome, and candidate gene markers are being developed rapidly. The likely targets\\u000a of MAS include yield and agronomic traits,

David J. Mackill

28

[Genetic structure of the Iranian-speaking population of Azerbaijan from data on frequencies of immunologic and biochemical gene markers].  

PubMed

The data on the genetic studies of Iranian-speaking populations from Azerbaijan (Talyshs and Tats) are presented. In these populations gene frequency distributions for the immunological (AB0, MN, Rhesus-D, -C, -E, P, Lewis, and Kell-Chellano) and biochemical (HP, GC, C'3, TF, 6PGD, GLO1, ESD, ACP1, and PGM1) gene markers were determined. Comparison of the genetic structure of the populations examined with the other Iranian-speaking populations (Persians and Kurds from Iran, Ossetins and Tajiks) and Azerbaijanis showed that Iranian-speaking populations from Azerbaijan were more close to Azerbaijanis, than to Iranian-speaking populations inhabiting other world regions. PMID:14714471

Asadova, P Sh; Shne?der, Iu V; Shil'nikova, I N; Zhukova, O V

2003-11-01

29

Immunological and molecular targets of atopic dermatitis treatment.  

PubMed

Atopic dermatitis (AD) is a common, chronic inflammatory skin disease with a highly variable clinical phenotype and heterogeneous pathophysiology. Its pathogenesis is associated with alterations to both the skin barrier and the immune system, which may in turn be influenced by genetic mutations and the patient's environment. Basic and translational research, as well as clinical trials, have helped broaden our knowledge of the molecular mechanisms underlying the development of AD and to identify potential treatment targets and approaches. These include new ways of reducing transepidermal water loss and the shedding of corneocytes, new ways of interacting with established molecular targets (such as histamine receptors and interleukins and other T-cell cytokines), and the identification of new molecular targets (such as toll-like receptors and tight junction proteins). Well-established treatment options such as emollients, corticosteroids and topical calcineurin inhibitors will clearly continue to have a role in treating AD. Among the new agents that could be joining them in the near future are sphinganin (a precursor of ceramides 1 and 3), cannabinoids, highly targeted monoclonal antibodies and subcutaneous immunotherapy. PMID:24720588

Wollenberg, A; Seba, A; Antal, A S

2014-07-01

30

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

31

Major histocompatibility complex class II deficiency in Kuwait: clinical manifestations, immunological findings and molecular profile.  

PubMed

Major Histocompatibility Complex (MHC) class II deficiency is a combined primary immunodeficiency disease that leads to overwhelming and recurrent infections. It was found to account for 19 % of combined immune deficiency cases in the National Primary Immunodeficiency Disorders Registry in Kuwait, a country with high prevalence of consanguinity. We present the clinical, immunologic and molecular features of 11 Kuwaiti patients who presented with MHC class II deficiency between 2004 and 2011. PMID:23143406

Al-Herz, Waleed; Alsmadi, Osama; Melhem, Motasem; Recher, Mike; Frugoni, Francesco; Notarangelo, Luigi D

2013-04-01

32

Evaluation of Soluble CD30 as an Immunologic Marker in Heart Transplant Recipients  

Microsoft Academic Search

CD30 is an immunologic molecule that belongs to the TNF-R superfamily. CD30 serves as a T-cell signal transducing molecule that is expressed by a subset of activated T lymphocytes, CD45RO+ memory T cells. Augmentation of soluble CD30 during kidney transplant rejection has been reported. Our study sought to determine whether the level of sCD30 prior to heart transplant could categorize

C. Spiridon; J. Hunt; M. Mack; J. Rosenthal; A. Anderson; E. Eichhorn; M. Magee; T. Dewey; M. Currier; A. Nikaein

2006-01-01

33

Molecular Serum Markers of Liver Fibrosis  

PubMed Central

Fibrosis is a hallmark histologic event of chronic liver diseases and is characterized by the excessive accumulation and reorganization of the extracellular matrix (ECM). The gold standard for assessment of fibrosis is liver biopsy. As this procedure has various limitations, including risk of patient injury and sampling error, a non-invasive serum marker for liver fibrosis is desirable. The increasing understanding of the pathogenesis of hepatic fibrosis has suggested several markers which could be useful indicators of hepatic fibrogenesis and fibrosis. These markers include serum markers of liver function, ECM synthesis, fibrolytic processes, ECM degradation and fibrogenesis related cytokines. Recently, neo-epitopes, which are post-translational modifications of proteins, have been successfully used in bone and cartilage diseases which are characterized by extensive ECM remodeling. Increasing numbers of studies are being undertaken to identify neo-epitopes generated during liver fibrosis, and which ultimately might be useful for diagnosing and monitoring fibrogenesis. To date, the metalloproteinases generated fragment of collagen I, III, IV and VI have been proven to be elevated in two rat models of fibrosis. This review summarizes the recent efforts that have been made to identify potentially reliable non-invasive serum markers. We used the recently proposed BIPED (Burden of disease, Investigative, Prognostic, Efficacy and Diagnostic) system to characterize potential serum markers and neo-epitope markers that have been identified to date.

Liu, Tianhui; Wang, Xiaoming; Karsdal, Morten A.; Leeming, Diana J.; Genovese, Federica

2012-01-01

34

Predicting quantitative variation within rice germplasm using molecular markers  

Microsoft Academic Search

Diverse Asian rice (Oryza sativa) germplasm has been used to identify associations between various quantitative traits and RAPD molecular markers using multiple regression analysis. This has allowed us to predict for other samples of germplasm their performance for traits such as culm length and number, days to flowering, grain width, and panicle and leaf length using only RAPD marker data.

Parminder S Virk; Brian V Ford-Lloyd; Michael T Jackson; Harpal S Pooni; Tomas P Clemeno; H John Newbury

1996-01-01

35

Molecular markers of serine protease evolution  

PubMed Central

The evolutionary history of serine proteases can be accounted for by highly conserved amino acids that form crucial structural and chemical elements of the catalytic apparatus. These residues display non- random dichotomies in either amino acid choice or serine codon usage and serve as discrete markers for tracking changes in the active site environment and supporting structures. These markers categorize serine proteases of the chymotrypsin-like, subtilisin-like and ?/?-hydrolase fold clans according to phylogenetic lineages, and indicate the relative ages and order of appearance of those lineages. A common theme among these three unrelated clans of serine proteases is the development or maintenance of a catalytic tetrad, the fourth member of which is a Ser or Cys whose side chain helps stabilize other residues of the standard catalytic triad. A genetic mechanism for mutation of conserved markers, domain duplication followed by gene splitting, is suggested by analysis of evolutionary markers from newly sequenced genes with multiple protease domains.

Krem, Maxwell M.; Di Cera, Enrico

2001-01-01

36

Tissue-based molecular markers for renal cell carcinoma.  

PubMed

Since the introduction of targeted therapies in renal cell carcinoma (RCC), more individualized treatment options have become available. Molecular markers might support treatment planning due to more accurate individual risk stratification. Current molecular markers in RCC were reviewed to elucidate clinical impact and future perspectives. An English-language literature review of the Medline database (1990 to September 2010) of published data on tissue-based molecular markers and RCC was undertaken. Histological types, clinical and oncological behaviour are variable in renal masses. Molecular markers offer potential for additional information in tumour detection and diagnosis, prognostic and predictive values, as well as determination of therapeutic targets. Investigations on molecular biomarkers in RCC include hypoxia inducible factor (HIF-?), vascular endothelial growth factor (VEGF), carbonic anhydrase IX (CAIX), mammalian target of rapamycin (mTOR), survivin, B7-H1, p53, matrix metalloproteinases (MMP), Insulin-like growth factor II mRNA-binding protein 3 (IMP3), Ki-67, C-reactive protein (CRP), Vimentin, Fascin, platelet count, hemoglobin level and combinations of these factors. Although some markers offer promising results, utilization in daily practice is compromised due to limited specificity, predictive accuracy and tumour histology variablity. There is an imminent need for novel molecular markers that allow accurate histologic and biologic classification of RCC to improve upon current outcomes. It is very likely that a panel of molecular markers will be used to achieve a sufficient degree of certainty in order to guide clinical decisions. A large concerted effort is required to advance the field of RCC molecular marker through systematic discovery, verification, and validation. PMID:21996985

Rink, M; Chun, F K H; Robinson, B; Sun, M; Karakiewicz, P I; Bensalah, K; Fisch, M; Scherr, D S; Lee, R K; Margulis, V; Shariat, S F

2011-12-01

37

Prognostic Accuracy of Immunologic and Metabolic Markers for Type 1 Diabetes in a High-Risk Population  

PubMed Central

OBJECTIVE To establish and compare the prognostic accuracy of immunologic and metabolic markers in predicting onset of type 1 diabetes in those with high risk in a prospective study. RESEARCH DESIGN AND METHODS A total of 339 subjects from the Diabetes Prevention Trial–Type 1 (DPT-1) parenteral study, who were islet cell antibody (ICA)-positive, with low first-phase insulin response (FPIR) and/or abnormal glucose tolerance at baseline, were followed until clinical diabetes onset or study end (5-year follow-up). The prognostic performance of biomarkers was estimated using receiver operating characteristic (ROC) curve analysis and compared with nonparametric testing of ROC curve areas. Pearson correlation was used to assess the relationship between the markers. RESULTS Individually, insulin autoantibody titer, ICA512A titer, peak C-peptide, 2-h glucose, FPIR, and FPIR/homeostasis model assessment of insulin resistance provided modest but significant prognostic values for 5-year risk with a similar level of area under ROC curve ranging between 0.61 and 0.67. The combination of 2-h glucose, peak C-peptide, and area under the curve C-peptide significantly improved the prognostic accuracy compared with any solitary index (P < 0.05) with an area under ROC curve of 0.76 (95% CI 0.70–0.81). The addition of antibody titers and/or intravenous glucose tolerance test (IVGTT) markers did not increase the prognostic accuracy further (P = 0.46 and P = 0.66, respectively). CONCLUSIONS The combination of metabolic markers derived from the oral glucose tolerance test improved accuracy in predicting progression to type 1 diabetes in a population with ICA positivity and abnormal metabolism. The results indicate that the autoimmune activity may not alter the risk of type 1 diabetes after metabolic function has deteriorated. Future intervention trials may consider eliminating IVGTT measurements as an effective cost-reduction strategy for prognostic purposes.

Xu, Ping; Beam, Craig A.; Cuthbertson, David; Sosenko, Jay M.; Skyler, Jay S.; Krischer, Jeffrey P.

2012-01-01

38

IMMUNOLOGIC MINIMAL RESIDUAL DISEASE DETECTION IN ACUTE LYMPHOBLASTIC LEUKEMIA: A COMPARATIVE APPROACH TO MOLECULAR TESTING  

PubMed Central

The generation of antisera directed against leukocyte differentiation antigens opened the possibility of studying minimal residual disease (MRD) in patients with acute lymphoblastic leukemia (ALL). During the three decades that followed the pioneering studies in this field, great progress has been made in the development of a wide array of monoclonal antibodies and of flow cytometric techniques for rare event detection. This advance was accompanied by an increasingly greater understanding of the immunophenotypic features of leukemic and normal lymphoid cells, and of the antigenic differences that make MRD studies possible. In parallel, molecular methods for MRD detection were established. The systematic application of immunologic and molecular techniques to study MRD in clinical samples has demonstrated the clinical significance of MRD in patients leading to the use of MRD to regulate treatment intensity in many contemporary treatment protocols. In this article, we discuss methodologic issues related to the immunologic monitoring of MRD and the evidence supporting its clinical significance, and compare the advantages and limitations of this approach to those of molecular monitoring of MRD.

Coustan-Smith, Elaine; Campana, Dario

2010-01-01

39

Molecular Markers in Hereditary Breast Cancer.  

National Technical Information Service (NTIS)

We are entering a new era of medicine where genetic markers are going to be used to make clinical management decisions. My long term career goal is to further our understanding of the genetic alterations which characterize human breast cancer in a way tha...

O. I. Olopade

2003-01-01

40

Molecular Markers in Hereditary Breast Cancer.  

National Technical Information Service (NTIS)

We are entering a new era of medicine where genetic markers are going to be used to make clinical management. decisions My long term career goal is to further our understanding of the genetic alterations which characterize human breast cancer in a way tha...

O. I. Olopade

2002-01-01

41

Prognostic histopathological and molecular markers in feline mammary neoplasia.  

PubMed

Feline mammary tumours comprise approximately 11% of feline non-integumentary neoplasms, are more commonly malignant than benign, and carry a poor prognosis attributable to a high probability of local recurrence and metastasis. This review discusses histopathological and molecular markers that could aid in prognostic discrimination, and draws comparisons with studies examining prognostic markers in breast cancer. Tumour grade and mitotic index correlate with survival data and could be useful for prognostication. Although assessment of Ki67 expression might have prognostic potential, further studies are required to corroborate the correlation between expression and clinical outcome. Additional molecular markers that have been investigated for prognostic potential can be grouped according to the 'hallmarks of cancer'. Many studies utilise 'surrogate markers' of clinical outcome, such as correlation with histological grade, to assess the prognostic value of molecular markers, and further investigation is therefore necessary before reaching firm conclusions regarding the prognostic value of some markers. Feline mammary tumours have been proposed as spontaneous models of breast cancer but might only be suitable models for certain molecular sub-types. Compared to humans, cats tend to have a high percentage of mammary tumours which are oestrogen receptor-negative and they might therefore be suitable models for late stage oestrogen receptor-negative breast cancer. The basal-like properties of feline mammary carcinomas offer another avenue for future research in this field of comparative oncology. PMID:22841451

Hughes, K; Dobson, J M

2012-10-01

42

P53 and Expression of Immunological Markers May Identify Early Stage Thyroid Tumors  

PubMed Central

Background. Besides its major role in cell proliferation, DNA repair, and apoptosis, functional p53 protein is involved in the induction of antitumor cytotoxic-T-cell activity against carcinoma cells. We aimed to investigate p53 and immune cell markers utility as diagnostic and prognostic markers of differentiated thyroid cancer (DTC). Methods. ACIS-III system was used to evaluate p53 and immune cell markers including tumor-associated macrophages (TAM); CD68 and tumor-infiltrating lymphocytes (TIL) subsets such as CD3, CD4, CD8, and CD20 in 206 thyroid carcinomas, 105 benign nodules, and 18 normal tissues. Also, TP53 was sequenced in 78 out of 164 patients with papillary thyroid carcinoma. Results. P53 expression was observed more frequently in malignant than in benign lesions (P < 0.0001) and helped discriminate follicular patterned lesions. In addition, p53 was more frequent in smaller (P = 0.0015), unique tumors (P = 0.0286), with thyroiditis (P = 0.0486) and without metastasis at diagnosis (P = 0.0201). TAM was more frequent in P53 negative tumors (P = 0.002). Infiltration of CD8+ TIL was found in 61.7% of P53 positive and 25.6% of P53 negative DTC (P < 0.001). Conclusions. We suggest that p53 and CD8+ TIL immune profile analysis might be useful in DTC.

Marcello, Marjory Alana; Morari, Elaine Cristina; Cunha, Lucas Leite; De Nadai Silva, Aline Carolina; Carraro, Dirce Maria; Carvalho, Andre Lopes; Soares, Fernando Augusto; Vassallo, Jose; Ward, Laura Sterian

2013-01-01

43

Drosophila hematopoiesis: Markers and methods for molecular genetic analysis.  

PubMed

Analyses of the Drosophila hematopoietic system are becoming more and more prevalent as developmental and functional parallels with vertebrate blood cells become more evident. Investigative work on the fly blood system has, out of necessity, led to the identification of new molecular markers for blood cell types and lineages and to the refinement of useful molecular genetic tools and analytical methods. This review briefly describes the Drosophila hematopoietic system at different developmental stages, summarizes the major useful cell markers and tools for each stage, and provides basic protocols for practical analysis of circulating blood cells and of the lymph gland, the larval hematopoietic organ. PMID:24613936

Evans, Cory J; Liu, Ting; Banerjee, Utpal

2014-06-15

44

Ecological proteomics: finding molecular markers that matter.  

PubMed

It is becoming increasingly clear that local adaptation can occur even in the face of high gene flow and limited overall genomic differentiation among populations (reviewed by Nosil et al. 2009). Thus, one important task for molecular ecologists is to sift through genomic data to identify the genes that matter for local adaptation (Hoffmann & Willi 2008; Stapley et al. 2010). Recent advances in high-throughput molecular technologies have facilitated this search, and a variety of approaches can be applied, including those grounded in population genetics [e.g. outlier analysis (Pavlidis et al. 2008)], classical and quantitative genetics [e.g. quantitative trait locus analysis (MacKay et al. 2009)], and cellular and molecular biology [e.g. transcriptomics (Larsen et al. 2011)]. However, applying these approaches in nonmodel organisms that lack extensive genetic and genomic resources has been a formidable challenge. In this issue, Papakostas et al. (2012). demonstrate how one such approach – high-throughput label-free proteomics (reviewed by Gstaiger & Aebersold 2009; Domon & Aebersold 2010) – can be applied to detect genes that may be involved in local adaptation in a species with limited genomic resources. Using this approach, they identified genes that may be implicated in local adaptation to salinity in European whitefish (Coregonus lavaretus L.) and provide insight into the mechanisms by which fish cope with changes in this critically important environmental parameter. PMID:22953332

Dalziel, Anne C; Schulte, Patricia M

2012-07-01

45

Current immunological and molecular biological perspectives on seafood allergy: a comprehensive review.  

PubMed

Seafood is an important component in human diet and nutrition worldwide. However, seafood also constitutes one of the most important groups of foods in the induction of immediate (type I) food hypersensitivity, which significantly impacts the quality of life and healthcare cost. Extensive efforts within the past two decades have revealed the molecular identities and immunological properties of the major fish and shellfish allergens. The major allergen involved in allergy and cross-reactivity among different fish species was identified as parvalbumin while that responsible for shellfish (crustaceans and mollusks) allergy was identified as tropomyosin. The cloning and expression of the recombinant forms of these seafood allergens facilitate the investigation on the detailed mechanisms leading to seafood allergies, mapping of IgE-binding epitopes, and assessment of their allergenicity and stability. Future research focusing on the immunological cross-reactivity and discovery of novel allergens will greatly facilitate the management of seafood allergies and the design of effective and life-long allergen-specific immunotherapies. PMID:23242979

Leung, Nicki Y H; Wai, Christine Y Y; Shu, ShangAn; Wang, Jinjun; Kenny, Thomas P; Chu, Ka Hou; Leung, Patrick S C

2014-06-01

46

MOLECULAR MARKERS OF EARLY CERVICAL NEOPLASIA  

PubMed Central

Pure morphological distinction of high-grade squamous intraepithelial lesions (HSILs) from their mimics can be challenging. Diagnosis can be difficult with nonconventional HSILs associated with a metaplastic phenotype, squamous intraepithelial lesions (SILs) that defy precise classification such as “eosinophilic dysplasias”, and those that overlap with columnar neoplasms, including stratified variants of adenocarcinoma in situ (“SMILE”). Gene expression and protein profiling have identified biomarkers with the potential to decrease diagnostic variability and increase specificity of histological and cytological analysis. Among the ones clinically useful for HSIL detection are p16INK4A and MIB-1 which complement each other, differentiating SIL from normal/atrophic (MIB-1 low) or reactive/immature metaplastic (p16INK4A scattered) epithelium. Additional markers, including ProExTM C, have been proposed but their added value is yet to be established. In the final analysis, biomarkers are most helpful for distinguishing benign immature or atrophic proliferations from HSIL. The distinction of LSIL from HSIL must be made on the hematoxylin and eosin-stained section and should be made with care, given the potential consequences of a diagnosis of CIN2 or CIN3.

Pinto, Alvaro P.; Crum, Christopher P.; Hirsch, Michelle S.

2010-01-01

47

Modeling the Genetic Architecture of Complex Traits With Molecular Markers  

Microsoft Academic Search

Understanding the genetic control of quantitatively inherited traits is fundamental to agricultural, evolutionary and biomedical genetic research. A detailed picture of the genetic architecture of quantitative traits can be elucidated with a well-saturated genetic map of molecular markers. The parameters that quantify the genetic architecture of a trait include the number of individual quantitative trait loci (QTL), their genomic positions,

Rongling Wu; Wei Hou; Yuehua Cui; Hongying Li; Tian Liu; Song Wu; Chang-Xing Ma; Yanru Zeng

2007-01-01

48

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 (Oryzias latipes), 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). Because of the often long latent period between initial contact with certain chemical and physical agents in our environment and subsequent expression of deleterious health or ecological impact, the development of sensitive methods for detecting and estimating early exposure is needed so that necessary interventions can ensue. A promising biological endpoint for detecting early exposure to damaging chemicals is the interaction of these compounds with cellular macromolecules such as Deoxyribonucleic acids (DNA). This biological endpoint assumes significance because it can be one of the critical early events leading eventually to adverse effects (neoplasia) in the exposed organism.

Shugart, L.R.

1990-10-01

49

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

50

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.

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

2013-01-01

51

DNA marker applications to molecular genetics and genomics in tomato.  

PubMed

Tomato is an important crop and regarded as an experimental model of the Solanaceae family and of fruiting plants in general. To enhance breeding efficiency and advance the field of genetics, tomato has been subjected to DNA marker studies as one of the earliest targets in plants. The developed DNA markers have been applied to the construction of genetic linkage maps and the resultant maps have contributed to quantitative trait locus (QTL) and gene mappings for agronomically important traits, as well as to comparative genomics of Solanaceae. The recently released whole genome sequences of tomato enable us to develop large numbers of DNA markers comparatively easily, and even promote new genotyping methods without DNA markers. In addition, databases for genomes, DNA markers, genetic linkage maps and other omics data, e.g., transcriptome, proteome, metabolome and phenome information, will provide useful information for molecular breeding in tomatoes. The use of DNA marker technologies in conjunction with new breeding techniques will promise to advance tomato breeding. PMID:23641178

Shirasawa, Kenta; Hirakawa, Hideki

2013-03-01

52

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

53

Availability and Use of Molecular Microbiological and Immunological Tests for the Diagnosis of Tuberculosis in Europe  

PubMed Central

Introduction Currently only limited data exist regarding the availability and clinical use of molecular and immunological tests for tuberculosis (TB) in the European setting. Methods Web-based survey of Paediatric-Tuberculosis-Network-European-Trialsgroup (ptbnet) and Tuberculosis-Network-European-Trialsgroup (TBnet) members conducted June to December 2013. Both networks comprise clinicians, microbiologists, epidemiologists and researchers predominately based in Europe. Results 191 healthcare professionals from 31 European countries participated. Overall, 26.8% of respondents did not have access to the Xpert MTB/RIF assay; only 44.6% had access to the assay in-house. However, a substantial proportion had access to other commercial and/or non-commercial PCR-based assays for TB (68.8% and 31.8%, respectively). Only 6.4% did not have access to any PCR-based assays for TB. A large proportion of participants with access to the Xpert MTB/RIF assay had used it for the analysis of non-respiratory samples [pleural fluid: 36.5%, gastric aspirates: 34.7%, cerebrospinal fluid: 34.7%, stool samples: 4.3%, blood/serum: 2.6%, ‘other samples’ (which included biopsy/tissue samples, lymph node aspirates, joint aspirates and urine samples): 16.5%]. Regarding interferon-gamma release assays, a greater proportion of respondents had access to the QuantiFERON-TB Gold assay (84.7%) than to the T-SPOT.TB assay (52.2%). Conclusions Both immunological and molecular TB tests are widely available across Europe. The QuantiFERON-TB Gold assay is more widely used than the T-SPOT.TB assay, which may reflect the difficulties of integrating an ELISPOT assay into the routine laboratory setting. Although Xpert MTB/RIF assays are optimised and solely licensed for the analysis of sputum samples, in clinical practice they are commonly used for non-respiratory samples. Further research is needed to establish how current molecular TB tests impact on patient care and outcome in the routine clinical setting.

Tebruegge, Marc; Ritz, Nicole; Koetz, Karsten; Noguera-Julian, Antoni; Seddon, James A.; Welch, Steven B.; Tsolia, Maria; Kampmann, Beate

2014-01-01

54

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

PubMed

Alien species invasion is one of the most important drivers of worldwide environmental change, which may result in environmental degradation, biodiversity loss, and food and water shortage. It may also increase the possibility and severity of natural disasters, and damage international trade and benefits. In last two decades, DNA-based molecular markers were widely used to detect the genetic diversity of invaded alien species. Inter-simple sequence repeat (ISSR) is a microsatellite-based technique, with the superiorities of simple, quick, reliable, and generating higher levels of DNA polymorphism, and being used as a new molecular marker for genetic study. This paper introduced the principles, characteristics and procedures of ISSR, and summarized its applications in studying the genetic structure, genetic diversity, origin, distribution mode, phylogenesis, and breeding features of invasive plants. PMID:17615894

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

2007-04-01

55

Identification of early molecular markers for breast cancer  

Microsoft Academic Search

BACKGROUND: The ductal carcinoma in situ (DCIS) of the mammary gland represents an early, pre-invasive stage in the development of invasive breast carcinoma. Since DCIS is a curable disease, it would be highly desirable to identify molecular markers that allow early detection. Mice transgenic for the WAP-SV40 early genome region were used as a model for DCIS development. Gene expression

Céline Kretschmer; Anja Sterner-Kock; Friederike Siedentopf; Winfried Schoenegg; Peter M Schlag; Wolfgang Kemmner

2011-01-01

56

Persistently high IgA serum levels are a marker of immunological or virological failure of combined antiretroviral therapy in children with perinatal HIV-1 infection  

PubMed Central

Non-expensive and low-complexity surrogate markers for monitoring the response to combined antiretroviral therapy (combined-ART) are needed in poor-resource settings where routine assessment of CD4+ T-lymphocyte count and viral load can not be afforded. We longitudinally evaluated Ig serum levels in 234 HIV-1 infected children receiving combined-ART with ? 3 drugs. Since Ig levels physiologically vary with age, differences at different age periods were evaluated as differences in z-scores calculated using the mean and standard deviation of the normal population for each age period. Data from 17 (7·3%) children with immunological failure and from 54 (23·1%) children with virological failure of combined-ART were compared with data from not-failed children. At baseline children with immunological failure showed higher IgM z-scores (P = 0·042) than children without. After 3–12 months of therapy immunologically failed children displayed higher viral loads (P < 0·0001) and IgA (P = 0·043) z-scores than not-failed children. Similarly, at the same follow-up time, children with virological failure showed lower CD4+ T-lymphocyte percentages (P = 0·005) and higher IgA z-scores (P < 0·0001) than not-failed children. No difference in IgG or IgM z-scores was evidenced between failed and not-failed children after 3–12 months of therapy. In conclusion, IgA serum level is a cheap and low-complexity marker of immunological or virological failure of combined-ART which might be adopted in poor-resource settings.

Chiappini, Elena; Galli, Luisa; Tovo, Pier-Angelo; Gabiano, Clara; de Martino, Maurizio

2005-01-01

57

Persistently high IgA serum levels are a marker of immunological or virological failure of combined antiretroviral therapy in children with perinatal HIV-1 infection.  

PubMed

Non-expensive and low-complexity surrogate markers for monitoring the response to combined antiretroviral therapy (combined-ART) are needed in poor-resource settings where routine assessment of CD4+ T-lymphocyte count and viral load can not be afforded. We longitudinally evaluated Ig serum levels in 234 HIV-1 infected children receiving combined-ART with > or = 3 drugs. Since Ig levels physiologically vary with age, differences at different age periods were evaluated as differences in z-scores calculated using the mean and standard deviation of the normal population for each age period. Data from 17 (7.3%) children with immunological failure and from 54 (23.1%) children with virological failure of combined-ART were compared with data from not-failed children. At baseline children with immunological failure showed higher IgM z-scores (P = 0.042) than children without. After 3-12 months of therapy immunologically failed children displayed higher viral loads (P < 0.0001) and IgA (P = 0.043) z-scores than not-failed children. Similarly, at the same follow-up time, children with virological failure showed lower CD4(+) T-lymphocyte percentages (P = 0.005) and higher IgA z-scores (P < 0.0001) than not-failed children. No difference in IgG or IgM z-scores was evidenced between failed and not-failed children after 3-12 months of therapy. In conclusion, IgA serum level is a cheap and low-complexity marker of immunological or virological failure of combined-ART which might be adopted in poor-resource settings. PMID:15807857

Chiappini, Elena; Galli, Luisa; Tovo, Pier-Angelo; Gabiano, Clara; de Martino, Maurizio

2005-05-01

58

Sublethal toxicity of Roundup to immunological and molecular aspects of Biomphalaria alexandrina to Schistosoma mansoni infection.  

PubMed

The present study was performed to elucidate the cellular mechanisms of Biomphalaria alexandrina snails hemocytes against sublethal concentration (10 mg/L) of herbicide Roundup (48% Glyphosate) and/or Schistosoma mansoni infection during 7 days of exposure. Obtained results indicated that herbicide treatment and/or infection led to significant increase (P<0.05) in total hemocytes count during exposure period. Examination of hemocytes monolayers resulted in observation of 3 morphologically different cell types, round small, hyalinocytes and spreading hemocytes. Spreading hemocytes are the dominant, more responsive and highly phagocytic cell type in all experimental groups. Moreover, the exposure to herbicide, infection or both together led to a significant increase (P<0.05) of in vitro phagocytic activity against yeast cells during 7 days of exposure. In addition, flow cytometric analysis of cell cycle and comet assay, resulted in DNA damage in B. alexandrina hemocytes exposed to herbicide and/or S. mansoni infection when compared to control group. The immunological responses as well as molecular aspects in B. alexandrina snails have been proposed as biomarkers of exposure to environmental pollutants. PMID:21126764

Mohamed, Azza H

2011-05-01

59

Comparison of two assays in the diagnosis of toxoplasmosis: immunological and molecular.  

PubMed

Serological tests for Toxoplasma gondii are inadequate because antibody production either fails or is significantly delayed. This study in eastern Iraq investigated the IgG-avidity ELISA test for detecting recent T. gondii infections among pregnant women and compared immunological methods and PCR as molecular assays in the diagnosis of T. gondii. Serums samples were taken from 130 pregnant women at risk of toxoplasmosis and a control group of 25 women with normal pregnancy. Of 50 IgM- and/or IgG-positive samples, only 15 showed low IgG-avidity antibodies. PCR was performed on 25 selected samples. Toxoplasma DNA was detected in 15/15 IgM-positive with low IgG-avidity and 1/3 IgM-positive with high IgG-avidity. None of the IgM-negative with high IgG-avidity showed any Toxoplasma DNA. ELISA IgG-avidity when used in combination with ELISA IgG/IgM is a valuable assay for the exclusion of ongoing or recently acquired T. gondii infection in pregnant women. PMID:24932933

Hashoosh, D A; Majeed, I A

2014-01-01

60

Molecular and immunological characterization of Tri a 36, a low molecular weight glutenin, as a novel major wheat food allergen.  

PubMed

Wheat is an essential element in our nutrition but one of the most important food allergen sources. Wheat allergic patients often suffer from severe gastrointestinal and systemic allergic reactions after wheat ingestion. In this study, we report the molecular and immunological characterization of a new major wheat food allergen, Tri a 36. The cDNA coding for a C-terminal fragment of Tri a 36 was isolated by screening a wheat seed cDNA expression library with serum IgE from wheat food-allergic patients. Tri a 36 is a 369-aa protein with a hydrophobic 25-aa N-terminal leader peptide. According to sequence comparison it belongs to the low m.w. glutenin subunits, which can be found in a variety of cereals. The mature allergen contains an N-terminal domain, a repetitive domain that is rich in glutamine and proline residues, and three C-terminal domains with eight cysteine residues contributing to intra- and intermolecular disulfide bonds. Recombinant Tri a 36 was expressed in Escherichia coli and purified as soluble protein. It reacted with IgE Abs of ?80% of wheat food-allergic patients, showed IgE cross-reactivity with related allergens in rye, barley, oat, spelt, and rice, and induced specific and dose-dependent basophil activation. Even after extensive in vitro gastric and duodenal digestion, Tri a 36 released distinct IgE-reactive fragments and was highly resistant against boiling. Thus, recombinant Tri a 36 is a major wheat food allergen that can be used for the molecular diagnosis of, and for the development of specific immunotherapy strategies against, wheat food allergy. PMID:22904302

Baar, Alexandra; Pahr, Sandra; Constantin, Claudia; Scheiblhofer, Sandra; Thalhamer, Josef; Giavi, Stavroula; Papadopoulos, Nikolaos G; Ebner, Christof; Mari, Adriano; Vrtala, Susanne; Valenta, Rudolf

2012-09-15

61

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

62

Is interferon-gamma the right marker for bacille Calmette-Gu?rin-induced immune protection? The missing link in our understanding of tuberculosis immunology  

PubMed Central

Bacille Calmette–Guérin (BCG), developed a century ago, is the only licensed tuberculosis (TB) vaccine in use to date. The protective efficacy of BCG against TB varies with no apparent protection in some population, and mechanisms of its immune protection is poorly known, and yet BCG is the most widely used vaccine, with more than 4 billion BCG-vaccinated children globally. BCG is probably the only licensed vaccine currently in use believed to mediate immune protection through the production of interferon (IFN)-? by CD4 T cells, which in turn activates macrophages to kill Mycobacterium tuberculosis (Mtb). Currently, a number of new TB candidate vaccines are in different phases of clinical trial. The majority of these new vaccines are either recombinant forms of BCG or prime boosters of BCG (rBCG) and their immunogenicity is tested using BCG as a benchmark by measuring specific IFN-? produced by CD4+ T cells as a protective immune marker. However, some recent studies that examined mechanisms of immune protection of BCG in animals and humans have reported a lack of correlation between IFN-? production by CD4 cells and BCG-induced immune protection. These studies point to the fact that there is a missing link in our understanding of TB immunology. Conversely, there is emerging evidence that other T cell subsets (gammadelta, ??), CD8+ T cells and natural killer (NK) cells may play a vital role in immune protection against Mtb infection and BCG-induced immune protection. ?? T cells and NK cells, which were considered to be part of the innate immunity in the past, have been shown to develop immunological memory upon re-encounter with the same pathogen. In this paper, the controversy over the role of IFN-? as a marker for protective immunity against TB, and emerging data on the role of ?? T cells, CD8+ and NK cells in TB immunology, will be presented.

Abebe, F

2012-01-01

63

Protamine mRNA as molecular marker for spermatozoa in semen stains.  

PubMed

Cytological detection of spermatozoa with subsequent DNA analysis is the most important biological evidence in sexual crimes when suitable samples are available. Immunological and enzymatic detection of semen-specific proteins may be helpful but cannot replace specific identification of spermatozoa. We have recently shown that detection of cell-specific gene expression can be used to identify menstrual blood. In this paper we demonstrate that the basic nucleoproteins protamine 1 and 2 are suitable markers for spermatozoa because they are exclusively expressed in the haploid genome and that protamine mRNA can be detected in semen stains by the highly sensitive reverse transcriptase-polymerase chain reaction (RT-PCR). With semi-nested PCR, 10-100 spermatozoa are theoretically sufficient to provide positive amplification results, with hot-start PCR at least 100-1,000 cells are required corresponding to an average semen volume of 0.01-0.1 microl. This new method thus allows specific identification of spermatozoa with molecular biology tools and may broaden the spectrum of investigations in the forensic laboratory. PMID:12799737

Bauer, M; Patzelt, D

2003-06-01

64

Molecular marker diversity of SCN-resistant sources in soybean.  

PubMed

Soybean cyst nematode (SCN) (Heterodera glycines Ichinohe; HG) is one of the most destructive pests of soybean (Glycine max (L.) Merr.) in the United States. Over 100 SCN-resistant accessions within the USDA Soybean Germplasm Collection have been identified, but little is known about the genetic diversity of this SCN-resistant germplasm. The objective of this research was to evaluate the genetic variation and determine the genetic relationships among SCN-resistant accessions. One hundred twenty-two genotypes were evaluated by 85 simple sequence repeat (SSR) markers from 20 linkage groups. Non-hierarchical (VARCLUS) and hierarchical (Ward's) clustering were combined with multidimensional scaling (MDS) to determine relationships among tested lines. The 85 SSR markers produced 566 allelic fragments with a mean polymorphic information content (PIC) value of 0.35. The 122 lines were grouped into 7 clusters by 2 different clustering methods and the MDS results consistently corresponded to the assigned clusters. Assigned clusters were dominated by genotypes that possess one or more unique SCN resistance genes and were associated with geographical origins. The results of analysis of molecular variance (AMOVA) showed that the variation differences among clusters and individual lines were significant, but the differences among individuals within clusters were not significant. PMID:17036069

Chen, Yiwu; Wang, Dechun; Arelli, Prakash; Ebrahimi, Mohsen; Nelson, Randall L

2006-08-01

65

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.

Koedrith, Preeyaporn; Seo, Young Rok

2011-01-01

66

Genetic diversity assessment of summer squash landraces using molecular markers.  

PubMed

Plant identification, classification, and genotyping within a germplasm collection are essential elements for establishing a breeding program that enhances the probability of plants with desirable characteristics in the market place. In this study, random amplified polymorphic DNA (RAPD) was used as a molecular tool to assess the diversity and relationship among 20 summer squash (Curcubita pepo L.) landraces traditionally used to treat hypertension and prostate hyperplasia. A total of 10 RAPD primers produced 65 reproducible bands of which 46 (70.77 %) were polymorphic, indicating a large number of genotypes within the summer squash lines. Cluster analysis divided the summer squash germplasm into two groups, one including one landrace and a second containing 19 landraces that could be divided into five sub-groups. Results of this study indicate the potential of RAPD markers for the identification and assessment of genetic variations among squash landraces and provide a number of choices for developing a successful breeding program to improve summer squash. PMID:23666102

Mady, Emad A; Helaly, Alaa Al-Din; Abu El-Hamd, Abdel Naem; Abdou, Arafa; Shanan, Shamel A; Craker, Lyle E

2013-07-01

67

Molecular markers of cell adhesion in ameloblastomas. An update  

PubMed Central

Ameloblastoma is the most common odontogenic tumor of epithelial origin, and though it is of a benign nature, it frequently infiltrates the bone, has a high rate of recurrence and could potentially become malignant. Cellular adhesion potentially plays an important role in the manifestation of these characteristics and in the tumor biology of ameloblastomas. Losses of cell-cell and extracellular matrix adhesion and cohesion are among the first events that occur in the invasion and growth of tumors of epithelial origin. The present review includes a description of the molecules that are involved in cell adhesion as reported for various types of ameloblastomas and discusses the possible roles of these molecules in the biological behaviors of this odontogenic tumor. Knowledge of the complex mechanisms in which these molecules play a role is critical for the research and discovery of future therapeutic targets. Key words:Ameloblastoma, cellular adhesion, molecular markers, cell-cell adhesion, extracellular matrix-cell adhesion.

Gonzalez-Gonzalez, Rogelio; Molina-Frechero, Nelly; Damian-Matsumura, Pablo

2014-01-01

68

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

69

Molecular prognostic markers in pancreatic cancer: a systematic review.  

PubMed

Pancreatic cancer is one of the most lethal tumours of the gastrointestinal tract. The ability to predict which patients would benefit most from surgical intervention and/or chemotherapy would be a great clinical asset. Considerable research has focused on identifying molecular events in pancreatic carcinogenesis, and their correlation with clinicopathological variables of pancreatic tumours and survival. This systematic review examined evidence from published manuscripts looking at molecular markers in pancreatic cancer and their correlation with tumour stage and grade, response to chemotherapy and long-term survival. A literature search was undertaken using PubMed and MEDLINE search engines, using the keywords p53, p21, p16, p27, SMAD4, K-ras, cyclin D1, Bax, Bcl-2, EGFR, EGF, c-erbB2, HB-EGF, TGFbeta, FGF, MMP, uPA, cathepsin, heparanase, E-cadherin, laminins, integrins, TMSF, CD44, cytokines, angiogenesis, VEGF, IL-8, beta-catenin, DNA microarray, and gene profiling. A bewildering number of biomarkers are currently under evaluation. For the most part, the evidence regarding their application as prognostic indicators is conflicting. The advent of gene microarray and mass spectrometric protein profiling offers the potential to examine many different biomarkers simultaneously. This 'protein/gene signature' could revolutionise work in this field and allow researchers to develop accurate and reproducible predictions of survival based on protein or gene profiles. PMID:16146690

Garcea, G; Neal, C P; Pattenden, C J; Steward, W P; Berry, D P

2005-10-01

70

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

71

Prevalence of Anemia and Immunological Markers in HIV-Infected Patients on Highly Active Antiretroviral Therapy in Northeastern Nigeria  

PubMed Central

Background There are conflicting reports on the impact of highly active antiretroviral therapy (HAART) in resolving hematological complications. Whereas some studies have reported improvements in hemoglobin and other hematological parameters resulting in reduction in morbidity and mortality of HIV patients, others have reported no improvement in hematocrit values of HAART-treated HIV patients compared with HAART-naïve patients. Objective This current study was designed to assess the impact of HAART in resolving immunological and hematological complications in HIV patients by comparatively analyzing the results (immunological and hematological) of HAART-naive patients and those on HAART in our environment. Methods A total of 500 patients participated, consisting of 315 HAART-naive (119 males and 196 females) patients and 185 HAART-experienced (67 males and 118 females) patients. Hemoglobin (Hb), CD4+ T-cell count, total white blood count (WBC), lymphocyte percentage, plateletes, and plasma HIV RNA were determined. Results HAART-experienced patients were older than their HAART-naive counterparts. In HAART-naive patients, the incidence of anemia (packed cell volume [PCV] <30%) was 57.5%, leukopenia (WBC < 2.5), 6.1%, and thrombocytopenia < 150, 9.6%; it was, significantly higher compared with their counterparts on HAART (24.3%, 1.7%, and 1.2%, respectively). The use of HAART was not associated with severe anemia. Of HAART-naive patients, 57.5% had a CD4 count < 200 cells/?L in comparison with 20.4% of HAART-experienced patients (P < 0.001). The mean viral load log10 was significantly higher in HAART-naive than in HAART-experienced patients (P < 0.001). Total lymphocyte count < 1.0 was a significant predictor of immunological parameters associated with disease progression, and death in HIV-infected patients. Total lymphocyte count fails to predict CD4 count < 200 cells/?L in our cohort; thus, its use in the management and monitoring of HIV-infected patients in our settings is not reliable.

Denue, Ballah Akawu; Kida, Ibrahim Musa; Hammagabdo, Ahmed; Dayar, Ayuba; Sahabi, Mohammed Abubakar

2013-01-01

72

Genetic diversity analysis of common beans based on molecular markers  

PubMed Central

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

Gill-Langarica, Homar R.; Muruaga-Martinez, Jose S.; Vargas-Vazquez, M.L. Patricia; Rosales-Serna, Rigoberto; Mayek-Perez, Netzahualcoyotl

2011-01-01

73

Genetic characterization of fig tree mutants with molecular markers.  

PubMed

The fig (Ficus carica L.) is a fruit tree of great world importance and, therefore, the genetic improvement becomes an important field of research for better crops, being necessary to gather information on this species, mainly regarding its genetic variability so that appropriate propagation projects and management are made. The improvement programs of fig trees using conventional procedures in order to obtain new cultivars are rare in many countries, such as Brazil, especially due to the little genetic variability and to the difficulties in obtaining plants from gamete fusion once the wasp Blastophaga psenes, responsible for the natural pollinating, is not found in Brazil. In this way, the mutagenic genetic improvement becomes a solution of it. For this reason, in an experiment conducted earlier, fig plants formed by cuttings treated with gamma ray were selected based on their agronomic characteristics of interest. We determined the genetic variability in these fig tree selections, using RAPD and AFLP molecular markers, comparing them to each other and to the Roxo-de-Valinhos, used as the standard. For the reactions of DNA amplification, 140 RAPD primers and 12 primer combinations for AFLP analysis were used. The selections did not differ genetically between themselves and between them and the Roxo-de-Valinhos cultivar. Techniques that can detect polymorphism between treatments, such as DNA sequencing, must be tested. The phenotypic variation of plants may be due to epigenetic variation, necessitating the use of techniques with methylation-sensitive restriction enzymes. PMID:22911583

Rodrigues, M G F; Martins, A B G; Desidério, J A; Bertoni, B W; Alves, M C

2012-01-01

74

Molecular Markers of Lung Cancer in MAYAK Workers  

SciTech Connect

The molecular mechanisms that result in the elevated risk for lung cancer associated with exposure to radiation have not been well characterized. Workers from the MAYAK nuclear enterprise are an ideal cohort in which to study the molecular epidemiology of cancer associated with radiation exposure and to identify the genes targeted for inactivation that in turn affect individual risk for radiation-induced lung cancer. Epidemiology studies of the MAYAK cohort indicate a significantly higher frequency for adenocarcinoma and squamous cell carcinoma (SCC) in workers than in a control population and a strong correlation between these tumor types and plutonium exposure. Two hypotheses will be evaluated through the proposed studies. First, radiation exposure targets specific genes for inactivation by promoter methylation. This hypothesis is supported by our recent studies with the MAYAK population that demonstrated the targeting of the p16 gene for inactivation by promoter methylation in adenocarcinomas from workers (1). Second, genes inactivated in tumors can serve as biomarkers for lung cancer risk in a cancer-free population of workers exposed to plutonium. Support for this hypothesis is based on exciting preliminary results of our nested, case-control study of persons from the Colorado cohort. In that study, a panel of methylation markers for predicting lung cancer risk is being evaluated in sputum samples from incident lung cancer cases and controls. The first hypothesis will be tested by determining the prevalence for promoter hypermethylation of a panel of genes shown to play a critical role in the development of either adenocarcinoma and/or SCC associated with tobacco. Our initial studies on adenocarcinoma in MAYAK workers will be extended to evaluate methylation of the PAX5 {alpha}, PAX5 {beta}, H-cadherin, GATA5, and bone morphogenesis 3B (BMP3B) genes in the original sample set described under Preliminary studies. In addition, studies will be initiated in SCC from workers and controls to identify genes targeted for inactivation by plutonium in this other common histologic form of lung cancer. We will examine methylation of the p16, O{sup 6}-methylguanine-DNA methyl-transferase (MGMT), and death associated protein kinase genes ([DAP-K], evaluated previously in adenocarcinomas) as well as the new genes being assessed in the adenocarcinomas. The second hypothesis will be tested in a cross-sectional study of cancer-free workers exposed to plutonium and an unexposed population. A cohort of 700 cancer-free workers and 700 unexposed persons is being assembled, exposures are being defined, and induced sputum collected at initial entry into the study and approximately 1-year later. Exposed and unexposed persons will be matched by 5-year age intervals and smoking status (current and former). The frequency for methylation of four genes that show the greatest difference in prevalence in tumors from workers and controls will be determined in exfoliated cells within sputum. These studies will extend those in primary tumors to determine whether difference in prevalence for individual or multiple genes are detected in sputum samples from high-risk subjects exposed to plutonium. Follow-up of this cohort offers the opportunity to validate these endpoints and future biomarkers as true markers for lung cancer risk.

Steven A. Belinsky, PhD

2007-02-15

75

The molecular marker of kdr against fenpropathrin in Tetranychus cinnabarinus.  

PubMed

The carmine spider mite, Tetranychus cinnabarinus (Boisduval), is one of the most important pests in agricultural industry. Pyrethroid insecticide has been used to control insects and mites worldwide. However, the intensive use of pyrethroid insecticide resulted in the development of resistance, which has mainly been induced by a variety of point mutations responsible for voltage-gated sodium channel (VGSC) insensitivity and has become the biggest obstacle to sustain the use of pyrethroid insecticide. In this study, we cloned cDNA full length of the para-homologous sodium channel gene from T. cinnabarinus named TC-vgsc. The complete open reading frame of TC-vgsc contains 6,579 nucleotides, encoding 2,193 amino acids. A point mutation, F1538I, was identified from both the DNA and RNA sequences of VGSC in fenpropathrin-resistant strain, which developed approximately 100-folds resistance against fenpropathrin. The result indicated the F1538I kdr mutation underwent DNA mutation events rather than RNA editing. Single nucleotide polymorphisms detection of F1538I mutation from indoor susceptible strain, fenpropathrin-resistant strain, and seven field populations found that this mutation appeared in all the strains (populations), but the frequency of mutation was closely related to the resistance level, with a r2 value of 0.665 (P < 0.05), that is, the higher the resistance level, the larger the mutation frequency. These results demonstrated that the F1538I mutation in the kdr gene can be used as a molecular marker for fenpropathrin-resistance monitoring in field T. cinnabarinus populations. PMID:24498748

Xu, Zhifeng; Shi, Li; Feng, Yaning; He, Lin

2013-12-01

76

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

77

Molecular Markers Reveal Exclusively Clonal Reproduction in Trichophyton rubrum  

PubMed Central

Genotypic variability among 96 Trichophyton rubrum strains which displayed different colony morphologies and were collected from four continents was investigated. Twelve markers representing 57 loci were analyzed by PCR fingerprinting, amplified fragment length polymorphism, and random amplified monomorphic DNA markers. Interestingly, none of the methods used revealed any DNA polymorphism, indicating a strictly clonal mode of reproduction and a strong adaptation to human skin.

Graser, Y.; Kuhnisch, J.; Presber, W.

1999-01-01

78

Heritability of Phenolics in Quercus laevis Inferred Using Molecular Markers  

Microsoft Academic Search

Studies of quantitative inheritance of phenotypes do not generally encompass the range of environmental conditions to which a population may be exposed in a natural setting and are rarely conducted on long-lived species due to the time re- quired for traditional crossing experiments. We used a marker-based method to estimate relatedness with microsatellite markers in a natural population of a

R. Klaper; K. Ritland; T. A. Mousseau; M. D. Hunter

2001-01-01

79

Multiple regression for molecular-marker, quantitative trait data from large F 2 populations  

Microsoft Academic Search

Molecular marker-quantitative trait associations are important for breeders to recognize and understand to allow application in selection. This work was done to provide simple, intuitive explanations of trait-marker regression for large samples from an F2 and to examine the properties of the regression estimators. Beginning with a(- 1,0,1) coding of marker classes and expected frequencies in the F2, expected values,

A. J. Wright; R. P. Mowers

1994-01-01

80

Bulk segregant analysis with molecular markers and its use for improving drought resistance in maize  

Microsoft Academic Search

QTLs with flanking markers showing significant allele frequency differences in the BSA studies will indicate The usual method to locate and compare loci regulat- those traits likely to be important in determining yield ing quantitative traits (QTLs) requires a segregating under drought. population of plants with each one genotyped with molecular markers. However, plants from such segreg- Key words: Bulk

Steve A Quarrie; Vesna Lazic; Dragan Kovacevic ´; Andy Steed; Sofija Pekic

1999-01-01

81

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

82

The use of molecular markers for germplasm management in a French olive collection  

Microsoft Academic Search

With more than 100 accessions, the CBNMP olive collection includes a major part of the French germplasm. We used molecular markers to characterise all accessions and to study genetic relationships between cultivars. Firstly, 497 olive trees were genotyped using 32 RAPD markers. We identified 114 RAPD profiles and detected several cases of mislabelling, synonymy and homonymy. Secondly, for each RAPD

B. Khadari; C. Breton; N. Moutier; J. P. Roger; G. Besnard; A. Bervillé; F. Dosba

2003-01-01

83

Microsatellite Alterations as Molecular Markers in Breast Cancer Progression.  

National Technical Information Service (NTIS)

Breast cancer detection and diagnosis has been limited by the lack of early and accurate markers of disease. Efforts to date have largely relied on insensitive measures such as mammography or breast examination for detection, with conventional histopathol...

S. Sukamar

1998-01-01

84

Microsatellite Alterations as Molecular Markers in Breast Cancer Progression.  

National Technical Information Service (NTIS)

Breast cancer detection and diagnosis has been limited by the lack of early and accurate markers of disease. Efforts to date have largely relied on insensitive measures such as mammography or breast examination for detection, with conventional histopathol...

S. Sukamar

1997-01-01

85

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

86

Molecular markers linked to PPO inhibitor tolerance in soybeans  

US Patent & Trademark Office Database

This invention relates generally to the detection of genetic differences among soybeans. More particularly, the invention relates to soybean quantitative trait loci (QTL) for tolerance to protoporphyrinogen oxidase inhibitors, to soybean plants possessing these QTLs, which map to a novel chromosomal region, and to genetic markers that are indicative of phenotypes associated with protoporphyrinogen oxidase inhibitor tolerance. Methods and compositions for use of these markers in genotyping of soybean and selection are also disclosed.

2014-06-10

87

Molecular characterization of a SCAR marker purportedly linked to seedlessness in grapevine ( Vitis )  

Microsoft Academic Search

Molecular markers associated with seedlessness in grapevine (Vitis vinifera) could be used for early trait selection in breeding programs and provide useful tools for elucidating the molecular mechanisms\\u000a underlying seed abortion. In this study, the sequence fidelity of a previously reported seedlessness-linked Sequence-Characterized\\u000a Amplified Region (SCAR) marker (GenBank accession #AY327513, Yang et al. in Chinese J Agri Biotech 3:13–17, 2006)

Zhijian T. Li; S. A. Dhekney; D. J. Gray

2010-01-01

88

Immunological detection of osteocalcin in meat and bone meal: a novel heat stable marker for the investigation of illegal feed adulteration.  

PubMed

A sandwich ELISA was developed for the detection of bovine meat and bone meal (BMBM) in feed, based on polyclonal rabbit antibodies raised against the synthetic N-terminal amino acid sequence 1-9 (YLDHWLGAP) of bovine osteocalcin. To set up a sandwich ELISA pair, a commercial mouse monoclonal capture antibody binding to a highly conserved epitope in the mid-fragment of the peptide was employed. It is shown that the bone marker osteocalcin is immunologically well detectable in BMBM extracts obtained by a simple EDTA-based procedure even in a sample heated up to 145°C. Furthermore, a genus-specific restriction of the major specificity to cattle and horse was possible. The observed bi-specificity is consistent with theoretical predictions. The assay sensitivity with bovine osteocalcin of 1?ng was sufficient to enable the detection of 0.1% BMBM in compound plant feed or fish meal, for which no cross reaction was observed. In general the quantification of osteocalcin in extracts is possible using a standard curve procedure with pure bovine osteocalcin. PMID:22300169

Kreuz, G; Zagon, J; Broll, H; Bernhardt, C; Linke, B; Lampen, A

2012-01-01

89

Cancer stem cell markers in breast neoplasias: their relevance and distribution in distinct molecular subtypes.  

PubMed

The identification and characterization of cancer stem cells might lead to more effective control of neoplastic disease, by directing therapies to the most aggressive cells. For that reason, the identification of cancer stem cells (CSCs) in breast tumours is one of the priorities in breast cancer research, which has resulted in many studies attempting to identify their presence based on the expression of specific molecular markers. In this review, we describe the main molecular markers that have been identified as being able to recognise CSCs in breast carcinomas, the major molecular pathways that regulate CSCs and their association with the different molecular subtypes. PMID:22562130

Schmitt, Fernando; Ricardo, Sara; Vieira, André Filipe; Dionísio, Maria Rita; Paredes, Joana

2012-06-01

90

Immunological and molecular characterization of the major allergens from lilac and privet pollens overproduced in Pichia pastoris.  

PubMed

The main allergens from privet and lilac pollens, Lig v 1 and Syr v 1, are proteins homologous to Ole e 1 and have been shown to be involved in cross-reactivity. To overproduce the correctly folded Lig v 1 and Syr v 1 allergens and to study their immunological properties in comparison with those of their natural counterparts. The yeast Pichia pastoris was used as an expression system to produce these recombinant allergens. The proteins were isolated by ion-exchange and size-exclusion chromatographies. Amino acid quantifying, Edman degradation, mass spectrometry and circular dichroism were carried out to obtain molecular properties of the recombinant proteins. Anti-Ole e 1 monoclonal and polyclonal antibodies, as well as sera from patients allergic to olive pollen, were used in immunoblotting and ELISA for immunological characterization. Recombinant Lig v 1 and Syr v 1 were secreted at high yield to the extracellular medium of the yeast. The purified proteins displayed the native conformation, as deduced from their spectroscopic properties and binding ability to an IgG monoclonal antibody. The recombinant allergens behaved similarly to their natural counterparts when they were analysed against Ole e 1-specific antibodies. IgE and IgG binding properties of lilac and privet allergens to olive allergic sera and Ole e 1-specific antibodies indicated that these molecules share common B-cell epitopes with Ole e 1. P. pastoris yeast is an appropriate system for the efficient production of Ole e 1-like allergens, which could be used as analogous allergens and predictors of clinical sensitization. PMID:11251633

González, E; Villalba, M; Rodríguez, R

2001-02-01

91

Understanding the molecular determinants driving the immunological specificity of the protective pilus 2a backbone protein of group B streptococcus.  

PubMed

The pilus 2a backbone protein (BP-2a) is one of the most structurally and functionally characterized components of a potential vaccine formulation against Group B Streptococcus. It is characterized by six main immunologically distinct allelic variants, each inducing variant-specific protection. To investigate the molecular determinants driving the variant immunogenic specificity of BP-2a, in terms of single residue contributions, we generated six monoclonal antibodies against a specific protein variant based on their capability to recognize the polymerized pili structure on the bacterial surface. Three mAbs were also able to induce complement-dependent opsonophagocytosis killing of live GBS and target the same linear epitope present in the structurally defined and immunodominant domain D3 of the protein. Molecular docking between the modelled scFv antibody sequences and the BP-2a crystal structure revealed the potential role at the binding interface of some non-conserved antigen residues. Mutagenesis analysis confirmed the necessity of a perfect balance between charges, size and polarity at the binding interface to obtain specific binding of mAbs to the protein antigen for a neutralizing response. PMID:23825940

Nuccitelli, Annalisa; Rinaudo, C Daniela; Brogioni, Barbara; Cozzi, Roberta; Ferrer-Navarro, Mario; Yero, Daniel; Telford, John L; Grandi, Guido; Daura, Xavier; Zacharias, Martin; Maione, Domenico

2013-01-01

92

Understanding the Molecular Determinants Driving the Immunological Specificity of the Protective Pilus 2a Backbone Protein of Group B Streptococcus  

PubMed Central

The pilus 2a backbone protein (BP-2a) is one of the most structurally and functionally characterized components of a potential vaccine formulation against Group B Streptococcus. It is characterized by six main immunologically distinct allelic variants, each inducing variant-specific protection. To investigate the molecular determinants driving the variant immunogenic specificity of BP-2a, in terms of single residue contributions, we generated six monoclonal antibodies against a specific protein variant based on their capability to recognize the polymerized pili structure on the bacterial surface. Three mAbs were also able to induce complement-dependent opsonophagocytosis killing of live GBS and target the same linear epitope present in the structurally defined and immunodominant domain D3 of the protein. Molecular docking between the modelled scFv antibody sequences and the BP-2a crystal structure revealed the potential role at the binding interface of some non-conserved antigen residues. Mutagenesis analysis confirmed the necessity of a perfect balance between charges, size and polarity at the binding interface to obtain specific binding of mAbs to the protein antigen for a neutralizing response.

Nuccitelli, Annalisa; Rinaudo, C. Daniela; Brogioni, Barbara; Cozzi, Roberta; Ferrer-Navarro, Mario; Yero, Daniel; Telford, John L.; Grandi, Guido; Daura, Xavier; Zacharias, Martin; Maione, Domenico

2013-01-01

93

Immunosignaturing can detect products from molecular markers in brain cancer.  

PubMed

Immunosignaturing shows promise as a general approach to diagnosis. It has been shown to detect immunological signs of infection early during the course of disease and to distinguish Alzheimer's disease from healthy controls. Here we test whether immunosignatures correspond to clinical classifications of disease using samples from people with brain tumors. Blood samples from patients undergoing craniotomies for therapeutically naïve brain tumors with diagnoses of astrocytoma (23 samples), Glioblastoma multiforme (22 samples), mixed oligodendroglioma/astrocytoma (16 samples), oligodendroglioma (18 samples), and 34 otherwise healthy controls were tested by immunosignature. Because samples were taken prior to adjuvant therapy, they are unlikely to be perturbed by non-cancer related affects. The immunosignaturing platform distinguished not only brain cancer from controls, but also pathologically important features about the tumor including type, grade, and the presence or absence of O(6)-methyl-guanine-DNA methyltransferase methylation promoter (MGMT), an important biomarker that predicts response to temozolomide in Glioblastoma multiformae patients. PMID:22815729

Hughes, Alexa K; Cichacz, Zbigniew; Scheck, Adrienne; Coons, Stephen W; Johnston, Stephen Albert; Stafford, Phillip

2012-01-01

94

Immunosignaturing Can Detect Products from Molecular Markers in Brain Cancer  

PubMed Central

Immunosignaturing shows promise as a general approach to diagnosis. It has been shown to detect immunological signs of infection early during the course of disease and to distinguish Alzheimer’s disease from healthy controls. Here we test whether immunosignatures correspond to clinical classifications of disease using samples from people with brain tumors. Blood samples from patients undergoing craniotomies for therapeutically naïve brain tumors with diagnoses of astrocytoma (23 samples), Glioblastoma multiforme (22 samples), mixed oligodendroglioma/astrocytoma (16 samples), oligodendroglioma (18 samples), and 34 otherwise healthy controls were tested by immunosignature. Because samples were taken prior to adjuvant therapy, they are unlikely to be perturbed by non-cancer related affects. The immunosignaturing platform distinguished not only brain cancer from controls, but also pathologically important features about the tumor including type, grade, and the presence or absence of O6-methyl-guanine-DNA methyltransferase methylation promoter (MGMT), an important biomarker that predicts response to temozolomide in Glioblastoma multiformae patients.

Hughes, Alexa K.; Cichacz, Zbigniew; Scheck, Adrienne; Coons, Stephen W.; Johnston, Stephen Albert; Stafford, Phillip

2012-01-01

95

A novel method for estimating heritability using molecular markers  

Microsoft Academic Search

Heritability is usually estimated with individuals of known relatedness generated using a controlled breeding programme or through response to selection. In this paper, we use two single-locus VNTR DNA fingerprint markers in conjunction with a maximum likelihood method to infer relatedness among pairs of individuals in a captive population of Pacific chinook salmon (Oncorhynchus tshawytscha). Patterns of relatedness inferred from

TIMOTHY A. MOUSSEAU; KERMIT RITLAND; DANIEL D. HEATH

1998-01-01

96

USING MOLECULAR MARKERS IN STUDY OF RICE GENETIC DIVERSITY  

Microsoft Academic Search

Random amplified polymorphism DNA (RAPD) was used as a DNA fingerprinting technique in rice germplasm evaluation. The high efficiency and random coverage of RADP markers were established to analyse the biodiversity of 72 rice germplasm accessions . We examined the amplification products in both their size and their polymorphism. Correlation matrix was carried out using the Genstat program. Cluster analysis

BUI CHI BUU; NGUYEN THI LANG

97

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

98

The Effects of Water Matrix on Decay of Human Fecal Molecular Markers and Campylobacter spp.  

EPA Science Inventory

Although molecular source tracking for human fecal contamination is used on a wide range of sample types, little is known about comparative decay of proposed molecular markers under different conditions, or correlation with pathogen decay. Our purpose was to measure correlations ...

99

Molecular markers to study competition and diversity of Rhizobium  

Microsoft Academic Search

The research described in this thesis was directed to the development of molecular identification and detection techniques for studying the ecology of Rhizobium, a nitrogen- fixing bacterium of agricultural importance. Competition of inoculant strains with indigenous microbes is a serious problem in agricultural practice and was therefore addressed in this work using the developed tools. Furthermore, various molecular techniques have

A. Sessitsch

1997-01-01

100

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.

Kirk, Heather; Freeland, Joanna R.

2011-01-01

101

Immunological and molecular detection of digenetic infections in different species of Egyptian freshwater snails.  

PubMed

Due to the possibility of utilizing different snails in the combat of Schistosoma in Egypt; it is important to study the role it may play in transmitting other trematodes of medical and veterinary importance. Taking this background into consideration, polymerase chain reaction (PCR) assay was designed to identify trematode species at larval stages in intermediate hosts (cercariae in snails) using a combination of standard and molecular methods. This PCR assay was also applied to naturally infected molluscan in order to assess the use of the procedure for detection. The importance of the present study was to demonstrate the epidemiological situation and application in control. PMID:23697024

Saad, Abdel-Hakim; Varjabedian, Kohar G; Abdel-Gaber, Rewaida A; Hassan, Hany M; Abdel-Halim, Noha T

2013-04-01

102

Comprehensive genetic discrimination of Leonurus cardiaca populations by AFLP, ISSR, RAPD and IRAP molecular markers.  

PubMed

Leonurus cardiaca is well known for its medicinal importance. In this investigation, genotypic characterization of this species from six eco-geographical regions of Iran was evaluated by four molecular techniques (AFLP, RAPD, ISSR and IRAP). A total of 899 polymorphic fragments were detected by used molecular markers (AFLP = 356, RAPD = 325, ISSR = 113 and IRAP = 105) with an overall average polymorphism of 81.24%. Genetic variation calculated using Shannon's Information index (I) and Nei's gene diversity index (H) showed high genetic diversity in studied germplasm. Also, analysis of molecular variance showed high genetic variation among (55%) and within populations (45%). UPGMA dendrogram constructed from combined data of molecular markers distinguished studied populations in accordance with the results obtained by each marker which all individuals were clearly differentiated into two major clusters. The correlation coefficients were statistically significant for all marker systems with the highest correlation between similarity matrixes of RAPD and ISSR markers (r = 0.82). The present results have an important implication for L. cardiaca germplasm characterization, improvement, and conservation. Furthermore, the characterized individuals exhibited a great deal of molecular variation and they seem to have a rich gene pool for breeding programs. PMID:24562682

Khadivi-Khub, Abdollah; Soorni, Aboozar

2014-06-01

103

Use of standard markers and incorporation of molecular markers into breast cancer therapy: Consensus recommendations from an International Expert Panel.  

PubMed

Breast cancer is a heterogeneous disease of different subtypes on the molecular, histopathological, and clinical level. Genomic profiling techniques have led to several prognostic and predictive gene signatures of breast cancer that may further refine outcome prediction, especially in clinically equivocal situations. In particular, the predictive value of today's most important therapeutic targets, ER and HER2, are strongly influenced by the proliferative status of the tumor. Genomic assays are generally performed in a centralized manner, whereas routine pathological evaluation is mostly done on a decentralized basis, making the comparison of these methods difficult. Thus, there remains considerable uncertainty about the use of the new molecular markers in routine clinical decision making and their role in patient selection or stratification for future clinical trials. To address this concern, a group of representatives from breast cancer research groups in the areas of breast pathology, genomic profiling, and clinical trials critically reviewed all available data. Consensus recommendations are made on the practical use of molecular markers in breast cancer management and their incorporation into future clinical trials. PMID:21472705

Kaufmann, Manfred; Pusztai, Lajos

2011-04-15

104

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

105

[The systems of molecular genetic markers under cancer of stomach].  

PubMed

The study was organized to investigate the anomalous methylation of genes NA?1, RASSF1A, MLH1, N33, DAPK, the expression of genes hTERT. metalloproteinase MMP7, MMP9, survivin. COX-2, p53. The activity of telomerase in 106 samples of stomach tumors taken through intra-operation way and 53 samples of stomach tumors taken through endoscopic way and 50 samples of biopsy taken from patients with chronic calculous cholecystitis (comparison group) was analyzed too. These changes can be used as additional markers both in diagnostic of cancer of stomach and dynamic monitoring of operated patients. PMID:24640104

Nemtsova, M V; Bykov, I I; Tchekinova, N V; Zaletaev, D V; Glikhov, A I; Khorobrykh, T V

2013-11-01

106

Improving Selection in Forage, Turf, and Biomass Crops Using Molecular Markers  

Microsoft Academic Search

\\u000a Selection of improved forage, turf, and bioenergy crops is optimized if measuring the phenotype of interest is rapid, inexpensive,\\u000a and repeatable. Phenotyping remains the most difficult issue to resolve for many important traits, including biomass yield,\\u000a abiotic stress tolerance, and long-term persistence. The identification of molecular markers may augment phenotypic selection\\u000a if markers are identified that are closely linked to

E. Charles Brummer; Michael D. Casler

107

Heritability of phenolics in Quercus laevis inferred using molecular markers.  

PubMed

Studies of quantitative inheritance of phenotypes do not generally encompass the range of environmental conditions to which a population may be exposed in a natural setting and are rarely conducted on long-lived species due to the time required for traditional crossing experiments. We used a marker-based method to estimate relatedness with microsatellite markers in a natural population of a long-lived oak, then used this inferred relatedness to examine quantitative genetic variation in the concentration of foliar phenolics. Estimating heritability using this method requires both significant relatedness and variance in relatedness over distance. However, this population did not show significant variance of relatedness, so only the presence of heritability, and its ranking among traits and environments, could be estimated. Seven foliar phenolics showed a significant relationship between phenotypic similarity and relatedness. The significance of this relationship varied among individual phenolic compounds, as well as by season. Genetic factors appeared to have a more measurable influence on the production of secondary compounds early in the season. After leaf expansion, covariance of relatedness and phenotypic variance appear to become less significant. Therefore heritability may vary seasonally for these traits. PMID:11773250

Klaper, R; Ritland, K; Mousseau, T A; Hunter, M D

2001-01-01

108

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

109

Molecular prognostic markers in pancreatic cancer: A systematic review  

Microsoft Academic Search

Pancreatic cancer is one of the most lethal tumours of the gastrointestinal tract. The ability to predict which patients would benefit most from surgical intervention and\\/or chemotherapy would be a great clinical asset. Considerable research has focused on identifying molecular events in pancreatic carcinogenesis, and their correlation with clinicopathological variables of pancreatic tumours and survival. This systematic review examined evidence

G. Garcea; C. P. Neal; C. J. Pattenden; W. P. Steward; D. P. Berry

2005-01-01

110

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

111

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

PubMed Central

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

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

2011-01-01

112

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

PubMed

New source of molecular markers accelerate the efforts in improving cotton fiber traits and aid in developing high-density integrated genetic maps. We developed new markers based on candidate genes and G. arboreum EST sequences that were used for polymorphism detection followed by genetic and physical mapping. Nineteen gene-based markers were surveyed for polymorphism detection in 26 Gossypium species. Cluster analysis generated a phylogenetic tree with four major sub-clusters for 23 species while three species branched out individually. CAP method enhanced the rate of polymorphism of candidate gene-based markers between G. hirsutum and G. barbadense. Two hundred A-genome based SSR markers were designed after datamining of G. arboreum EST sequences (Mississippi Gossypium arboreum??EST-SSR: MGAES). Over 70% of MGAES markers successfully produced amplicons while 65 of them demonstrated polymorphism between the parents of G. hirsutum and G. barbadense RIL population and formed 14 linkage groups. Chromosomal localization of both candidate gene-based and MGAES markers was assisted by euploid and hypoaneuploid CS-B analysis. Gene-based and MGAES markers were highly informative as they were designed from candidate genes and fiber transcriptome with a potential to be integrated into the existing cotton genetic and physical maps. PMID:22315588

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

2011-01-01

113

SEOM clinical guidelines for using molecular markers in clinical practice  

Microsoft Academic Search

Nowadays, treatment selection for most types of cancers is based on anatomical, histological and clinical criteria, which\\u000a are defined by the selection criteria used in registration phase III trials. However, different cancers present distinct molecular\\u000a features, so the current approach results in a lack of specificity of cancer therapy, which is associated with decreased efficacy\\u000a and unnecessary toxicities and costs.

Virginia Arrazubi; Roberto Pazo; Dolores Isla; José Luis Pérez Gracia

2011-01-01

114

Prognostic molecular markers in non-small cell lung cancer  

Microsoft Academic Search

Although TNM stage is the most significant prognostic parameter in lung cancer, additional parameters are required for explaining variability of survival. Hence molecular alterations in lung cancer have been extensively studied. Most prominent among them are alterations in the p53–p21 pathway, controlling the G1\\/S transition. They are the most commonly observed aberrations in non-small cell lung cancer (NSCLC). The results

Jacek Nikli?ski; Wies?awa Nikli?ska; Jerzy Laudanski; El?bieta Chyczewska; Lech Chyczewski

2001-01-01

115

Volatility of organic molecular markers used for source apportionment analysis: measurements and implications for atmospheric lifetime.  

PubMed

Molecular markers are organic species used to define fingerprints for source apportionment of ambient fine particulate matter. Traditionally, these markers have been assumed to be stable in the atmosphere. This work investigates the gas-particle partitioning of eight organic species used as molecular markers in receptor models for biomass burning (levoglucosan), motor vehicles (5?-cholestane, n-hexacosane, n-triacontane, 1,2-benz[a]anthracene, coronene), and meat cooking (cholesterol, oleic acid). Experiments were conducted using a thermodenuder to measure the evaporation of single component particles. The data were analyzed using the integrated volume method to determine saturation concentrations and enthalpies of vaporization for each compound. The results indicate that appreciable quantities (>10%) of most of these markers exist in the gas phase under typical atmospheric conditions. Therefore, these species should be considered semivolatile. Predictions from a chemical kinetics model indicate that gas-particle partitioning has important effects on the atmospheric lifetime of these species. The atmospheric decay of semivolatile compounds proceeds much more rapidly than nonvolatile compounds because gas-phase oxidation induces evaporation of particle-phase material. Therefore, both gas-particle partitioning and chemical reactions need to be accounted for when semivolatile molecular markers are used for source apportionment studies. PMID:23013599

May, Andrew A; Saleh, Rawad; Hennigan, Christopher J; Donahue, Neil M; Robinson, Allen L

2012-11-20

116

Identification of molecular markers of bipolar cells in the murine retina  

PubMed Central

Retinal bipolar neurons serve as relay interneurons that connect rod and cone photoreceptor cells to amacrine and ganglion cells. They exhibit diverse morphologies essential for correct routing of photoreceptor cell signals to specific postsynaptic amacrine and ganglion cells. The development and physiology of these interneurons have not been completely defined molecularly. Despite previous identification of genes expressed in several bipolar cell subtypes, molecules that mark each bipolar cell type still await discovery. In this report, novel genetic markers of murine bipolar cells were found. Candidates were initially generated by using microarray analysis of single bipolar cells and mining of retinal serial analysis of gene expression (SAGE) data. These candidates were subsequently tested for expression in bipolar cells by RNA in situ hybridization. Ten new molecular markers were identified, five of which are highly enriched in their expression in bipolar cells within the adult retina. Double-labeling experiments using probes for previously characterized subsets of bipolar cells were performed to identify the subtypes of bipolar cells that express the novel markers. Additionally, the expression of bipolar cell genes was analyzed in Bhlhb4 knockout retinas, in which rod bipolar cells degenerate postnatally, to delineate further the identity of bipolar cells in which novel markers are found. From the analysis of Bhlhb4 mutant retinas, cone bipolar cell gene expression appears to be relatively unaffected by the degeneration of rod bipolar cells. Identification of molecular markers for the various subtypes of bipolar cells will lead to greater insights into the development and function of these diverse interneurons.

Kim, Douglas S; Ross, Sarah E; Trimarchi, Jeffrey M; Aach, John; Greenberg, Michael E; Cepko, Constance L

2008-01-01

117

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

118

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

119

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

120

An Educational Software for Simulating the Sample Size of Molecular Marker Experiments  

ERIC Educational Resources Information Center

We developed educational software to show graduate students how to plan molecular marker experiments. These computer simulations give the students feedback on the precision of their experiments. The objective of the software was to show students using a hands-on approach how: (1) environmental variation influences the range of the estimates of the…

Helms, T. C.; Doetkott, C.

2007-01-01

121

DEVELOPMENT OF MOLECULAR MARKERS OF RESPONSE TO ASSESS THE SENSITIVITY OF CHILDREN TO ENVIRONMENTAL CHEMICALS  

EPA Science Inventory

Development of Molecular Markers of Response to Assess the Sensitivity of Children to Environmental Chemicals J.Allen, C. Blackman, M. Blaze, D. Delker, D. DeMarini, C. Doerr, R. Grindstaff, S. Hester, C. Jones, A. Kligerman, G. Knapp, M. Kohan, C. Nelson, R. Owen, J. P...

122

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

123

Evaluating the effects of non-neutral molecular markers on phylogeny inference.  

PubMed

Nucleotide substitution models used in molecular phylogenetics do not account for nucleotide sequences evolving under selection, yet selection is rarely tested for. If non-neutral markers violate these models (i.e. non-independence of sites), it is expected that their reconstructed topologies be incongruent with those inferred from neutral ones and conclusions made from those phylogenies should be reexamined. Using rhodopsin as a phylogenetic marker has recently been called into question for exactly this reason. Rhodopsin is assumed to have evolved under strong positive selection for organisms that inhabit similar aquatic environments, making it unsuitable for the phylogenetics of aquatic organisms, but it is unclear what the effects of non-neutrality on phylogeny estimation are. To evaluate potential incongruence of neutral versus non-neutral markers, and the notion that rhodopsin should not be used in the molecular phylogenetics of fishes, a molecular dataset of 78 acanthomorph taxa and sequences from four nuclear, protein coding loci (including rhodopsin), were examined. Only one marker was found to be neutral while the remaining tests, for all other loci, rejected the null hypothesis of neutrality. To evaluate the possible effect(s) of positively versus negatively selected sites, the three non-neutral markers were analyzed to determine the presence of positively and negatively selected codons. To determine congruence in topology among ML trees inferred by individual neutral and non-neutral markers, as well as the combined (concatenated) dataset, tree, comparisons of distances among trees and hypothesis (topology) testing were carried out. Results of the tree distance metrics and topology testing support the notion that neutrality alone does not determine congruence in topology, and those data that are inferred to have evolved under selection should not necessarily be excluded. In addition, the number of sites inferred to have evolved under positive selection does not predict congruence with other markers or the topology inferred with the concatenated dataset. PMID:24558367

Roje, Dawn M

2014-01-01

124

Variety discrimination in pea (Pisum sativum L.) by molecular, biochemical and morphological markers.  

PubMed

The distinctness, uniformity and stability (DUS) requirements involve expensive, space- and time-consuming measurements of morphological traits. Moreover, for a majority of traits, interactions between genotype and environment complicate the evaluation. Molecular markers have a potential to facilitate this procedure, increase the reliability of decisions, and substantially save the time and space needed for experiments. We chose 25 varieties of pea (Pisum sativum L.) from the list of recommended varieties for cultivation in the Czech Republic, and made both a standard classification by 12 morphological descriptors and a classification by biochemical-molecular markers. Two isozyme systems, 10 microsatellite loci, 2 retrotransposons for multilocus inter-retrotransposon amplified polymorphism (IRAP), and 12 retrotransposon-based insertion polymorphism (RBIP) DNA markers were analysed. The main objective of the study was to examine the potential of each method for discrimination between pea varieties. The results demonstrate a high potential and resolving power of DNA-based methods. Superior in terms of high information content and discrimination power were SSR markers, owing to high allelic variation, which was the only biochemical-molecular method allowing clear identification of all varieties. Retrotransposon markers in RBIP format proved to be the most robust and easy to score method, while multilocus IRAP produced informative fingerprint already in a single analysis. Isozyme analysis offered a fast and less expensive alternative. The results showed that molecular identification could be used to assess distinctness and complement morphological assessment, especially in cases where the time frame plays an important role. Currently developed pea marker systems might serve also for germplasm management and genetic diversity studies. PMID:18436990

Smykal, Peter; Horacek, Jiri; Dostalova, Radmila; Hybl, Miroslav

2008-01-01

125

Reconciling patterns of inter-ocean molecular variance from four classes of molecular markers in blue marlin (Makaira nigricans).  

PubMed

Different classes of molecular markers occasionally yield discordant views of population structure within a species. Here, we examine the distribution of molecular variance from 14 polymorphic loci comprising four classes of molecular markers within approximately 400 blue marlin individuals (Makaira nigricans). Samples were collected from the Atlantic and Pacific Oceans over 5 years. Data from five hypervariable tetranucleotide microsatellite loci and restriction fragment length polymorphism (RFLP) analysis of whole molecule mitochondrial DNA (mtDNA) were reported and compared with previous analyses of allozyme and single-copy nuclear DNA (scnDNA) loci. Temporal variance in allele frequencies was nonsignificant in nearly all cases. Mitochondrial and microsatellite loci revealed striking phylogeographic partitioning among Atlantic and Pacific Ocean samples. A large cluster of alleles was present almost exclusively in Atlantic individuals at one microsatellite locus and for mtDNA, suggesting that, if gene flow occurs, it is likely to be unidirectional from Pacific to Atlantic oceans. Mitochondrial DNA inter-ocean divergence (FST) was almost four times greater than microsatellite or combined nuclear divergences including allozyme and scnDNA markers. Estimates of Neu varied by five orders of magnitude among marker classes. Using mathematical and computer simulation approaches, we show that substantially different distributions of FST are expected from marker classes that differ in mode of inheritance and rate of mutation, without influence of natural selection or sex-biased dispersal. Furthermore, divergent FST values can be reconciled by quantifying the balance between genetic drift, mutation and migration. These results illustrate the usefulness of a mitochondrial analysis of population history, and relative precision of nuclear estimates of gene flow based on a mean of several loci. PMID:11380876

Buonaccorsi, V P; McDowell, J R; Graves, J E

2001-05-01

126

Genetic diversity in cultivated carioca common beans based on molecular marker analysis  

PubMed Central

A wide array of molecular markers has been used to investigate the genetic diversity among common bean species. However, the best combination of markers for studying such diversity among common bean cultivars has yet to be determined. Few reports have examined the genetic diversity of the carioca bean, commercially one of the most important common beans in Brazil. In this study, we examined the usefulness of two molecular marker systems (simple sequence repeats – SSRs and amplified fragment length polymorphisms – AFLPs) for assessing the genetic diversity of carioca beans. The amount of information provided by Roger’s modified genetic distance was used to analyze SSR data and Jaccards similarity coefficient was used for AFLP data. Seventy SSRs were polymorphic and 20 AFLP primer combinations produced 635 polymorphic bands. Molecular analysis showed that carioca genotypes were quite diverse. AFLPs revealed greater genetic differentiation and variation within the carioca genotypes (Gst = 98% and Fst = 0.83, respectively) than SSRs and provided better resolution for clustering the carioca genotypes. SSRs and AFLPs were both suitable for assessing the genetic diversity of Brazilian carioca genotypes since the number of markers used in each system provided a low coefficient of variation. However, fingerprint profiles were generated faster with AFLPs, making them a better choice for assessing genetic diversity in the carioca germplasm.

Kupper Cardoso Perseguini, Juliana Morini; Chioratto, Alisson Fernando; Zucchi, Maria Imaculada; Colombo, Carlos Augusto; Carbonell, Sergio Augusto Moraes; Costa Mondego, Jorge Mauricio; Gazaffi, Rodrigo; Franco Garcia, Antonio Augusto; de Campos, Tatiana; de Souza, Anete Pereira; Rubiano, Luciana Benchimol

2011-01-01

127

Isolation of Bacteroides from fish and human fecal samples for identification of unique molecular markers.  

PubMed

Bacteroides molecular markers have been used to identify human fecal contamination in natural waters, but recent work in our laboratory confirmed cross-amplification of several human-specific Bacteroides spp. assays with fecal DNA from fish. For identification of unique molecular markers, Bacteroides from human (n = 4) and fish (n = 7) fecal samples were cultured and their identities were further confirmed using Rapid ID 32A API strips. The 16S rDNA from multiple isolates from each sample was PCR amplified, cloned, and sequenced to identify unique markers for development of more stringent human-specific assays. In human feces, Bacteroides vulgatus was the dominant species (75% of isolates), whereas in tilapia feces, Bacteroides eggerthii was dominant (66%). Bacteroides from grass carp, channel catfish, and blue catfish may include Bacteroides uniformis, Bacteroides ovatus, or Bacteroides stercoris. Phylogenic analyses of the 16S rRNA gene sequences showed distinct Bacteroides groupings from each fish species, while human sequences clustered with known B. vulgatus. None of the fish isolates showed significant similarity to Bacteroides sequences currently deposited in NCBI (National Center for Biotechnology Information). This study expands the current sequence database of cultured fish Bacteroides. Such data are essential for identification of unique molecular markers in human Bacteroides that can be utilized in differentiating fish and human fecal contamination in water samples. PMID:24313449

Kabiri, Leila; Alum, Absar; Rock, Channah; McLain, Jean E; Abbaszadegan, Morteza

2013-12-01

128

A review of molecular pathological markers in vulvar carcinoma: lack of application in clinical practice.  

PubMed

Vulvar carcinoma is a rare female genital neoplasia. Radical surgery, which has been the standard treatment approach, is often accompanied by considerable morbidity. To reduce the incidence of complications there has been a movement toward individualised therapy and less radical surgery. Associated with this, new tumour markers that could serve as prognostic indicators would be of considerable value to guide treatment decision. In this review, a brief update of molecular pathological markers of vulvar carcinomas is provided, and their impact as prognostic markers is addressed. p16, p21, p14, p27, cyclin A, cyclin D1, p53, vascular endothelial growth factor (VEGF), transforming growth factor alpha, HER-2 and epidermal growth factor receptor (EGFR) have been found to be important in the pathogenesis and/or progression of vulvar carcinomas. Furthermore, human papillomavirus, p16, p21, p14, p53, VEGF, CD44v3, CD44v6, CD44v4, CD44v9, CD44v10, HER-2, EGFR, matrix metalloproteinase-12, caspase 3, Bcl-2 and nm23-H1 have been correlated to clinical outcome of patients with vulvar carcinomas. However, due to the relative small number of studies reported for each molecular pathological marker, and the relative small number of vulvar carcinomas included and the lack of multivariate analysis in the majority of these studies, no conclusion regarding the prognostic value of these markers can be drawn. Therefore, the investigated markers have not yet earned a place in standard clinical diagnostics or treatment, and further studies are needed to clarify the clinical value of these markers. PMID:19251952

Knopp, S; Tropè, C; Nesland, J M; Holm, R

2009-03-01

129

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

130

Patterns of genetic architecture for life-history traits and molecular markers in a subdivided species.  

PubMed

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 subdivision for molecular and quantitative traits are concordant, with QST generally exceeding GST. There is no evidence that microsatellites loci are less informative about subdivision for quantitative traits than are allozyme loci. Character-specific comparison of QST and GST support divergent selection pressures among populations for the majority of life-history traits in both coast and mountain regions. The level of within-population variation for molecular markers is uninformative as to the genetic variation maintained for quantitative traits. In D. pulicaria, regional differences in the frequency of sex may contribute to variation in the maintenance of expressed within-population quantitative-genetic variation without substantially impacting diversity at the genic level. These data are compared to an identical dataset for 17 populations of the temporary-pond species, D. pulex. PMID:11681731

Morgan, K K; Hicks, J; Spitze, K; Latta, L; Pfrender, M E; Weaver, C S; Ottone, M; Lynch, M

2001-09-01

131

How do molecular marker patterns of BC change at increasing age of chars?  

NASA Astrophysics Data System (ADS)

Black carbon (BC) is considered to be a relatively stable form of organic carbon. However, previous results have shown that the physical and chemical properties of BC can vary considerably with formation temperature. Thus, to understand the long-term carbon sink potential of BC there is increasing interest to gain more information about i) the conditions under which BC was formed, and ii) the resulting degradability of BC under natural conditions. In a first step, we synthesised chars from two different sources of biomass (chestnut wood, rice straw) under well-defined conditions as model substances to analyse the changes in their molecular structure at increasing formation temperature. Results are presented obtained from a set of laboratory produced char samples pyrolysed at increasing temperatures with a high resolution between 200 and 1000 °C. The chars were characterized by a molecular marker method for pyrogenic carbon quantification, which additionally provides information about the degree of condensation of chars. At temperatures between 275 and 500°C, which typically are observed during wildfires and thus are relevant for natural char formation, the molecular marker pattern of the chars remains almost constant. In a next step, we analysed changes in the molecular marker patterns of chars from a chronosequence, with BC deposited between 0 and 100 years ago. Based on the data obtained from the laboratory char series, we compare changes in the molecular marker patterns of the chars from the chronosequence over time. These results show if less condensed forms of BC are degraded preferentially and more condensed, aromatic backbone of BC becomes enriched in the soils with time of degradation. Our results provide information about the fate of BC in the environment, which has important implications in the context of carbon sequestration strategies.

Schneider, M. P. W.; Hilf, M.; Schmidt, M. W. I.

2009-04-01

132

Molecular characterization of primary gene pool of chickpea based on ISSR markers.  

PubMed

Genetic diversity and relationships within and among members of the primary gene pool of chickpea, including 38 accessions of Cicer arietinum, six of C. reticulatum,, and four of C. echinospermum, were investigated using 31 ISSR markers. The study revealed moderate diversity, detecting 141 fragments, of which 79 (56%) were polymorphic. Averages were 0.125 for polymorphic information content, 0.350 for marker index, and 0.715 for resolving power. The UPGMA dendrogram and the principal coordinate analysis revealed a clear differentiation between wild and cultivated accessions. The clustering pattern did not strictly follow the grouping of accessions by geographic origin but was in good agreement with the pedigree data and the seed type. The study demonstrates that ISSRs provide promising marker tools in revealing genetic diversity and relationships in chickpea and can contribute to efficient identification, conservation, and utilization of germplasm for plant improvement through conventional as well as molecular breeding approaches. PMID:23329257

Choudhary, Pooja; Khanna, Suruchi M; Jain, Pradeep K; Bharadwaj, Chellapilla; Kumar, Jitendra; Lakhera, Pramesh C; Srinivasan, Ramamurthy

2013-04-01

133

Use of molecular markers to compare Fusarium verticillioides pathogenic strains isolated from plants and humans.  

PubMed

Fusarium verticillioides is a pathogen of agriculturally important crops, especially maize. It is considered one of the most important pathogens responsible for fumonisin contamination of food products, which causes severe, chronic, and acute intoxication in humans and animals. Moreover, it is recognized as a cause of localized infections in immunocompetent patients and disseminated infections among severely immunosuppressed patients. Several molecular tools have been used to analyze the intraspecific variability of fungi. The objective of this study was to use molecular markers to compare pathogenic isolates of F. verticillioides and isolates of the same species obtained from clinical samples of patients with Fusarium mycoses. The molecular markers that we used were inter-simple sequence repeat markers (primers GTG5 and GACA4), intron splice site primer (primer EI1), random amplified polymorphic DNA marker (primer OPW-6), and restriction fragment length polymorphism-internal transcribed spacer (ITS) from rDNA. From the data obtained, clusters were generated based on the UPGMA clustering method. The amplification products obtained using primers ITS4 and ITS5 and loci ITS1-5.8-ITS2 of the rDNA yielded fragments of approximately 600 bp for all the isolates. Digestion of the ITS region fragment using restriction enzymes such as EcoRI, DraI, BshI, AluI, HaeIII, HinfI, MspI, and PstI did not permit differentiation among pathogenic and clinical isolates. The inter-simple sequence repeat, intron splice site primer, and random amplified polymorphic DNA markers presented high genetic homogeneity among clinical isolates in contrast to the high variability found among the phytopathogenic isolates of F. verticillioides. PMID:24065642

Chang, S C; Macêdo, D P C; Souza-Motta, C M; Oliveira, N T

2013-01-01

134

Tumor Endothelial Marker Imaging in Melanomas Using Dual-Tracer Fluorescence Molecular Imaging  

PubMed Central

Purpose Cancer-specific endothelial markers available for intravascular binding are promising targets for new molecular therapies. In this study, a molecular imaging approach of quantifying endothelial marker concentrations (EMCI) is developed and tested in highly light-absorbing melanomas. The approach involves injection of targeted imaging tracer in conjunction with an untargeted tracer, which is used to account for nonspecific uptake and tissue optical property effects on measured targeted tracer concentrations. Procedures Theoretical simulations and a mouse melanoma model experiment were used to test out the EMCI approach. The tracers used in the melanoma experiments were fluorescently labeled anti-Plvap/PV1 antibody (plasmalemma vesicle associated protein Plvap/PV1 is a transmembrane protein marker exposed on the luminal surface of endothelial cells in tumor vasculature) and a fluorescent isotype control antibody, the uptakes of which were measured on a planar fluorescence imaging system. Results The EMCI model was found to be robust to experimental noise under reversible and irreversible binding conditions and was capable of predicting expected overexpression of PV1 in melanomas compared to healthy skin despite a 5-time higher measured fluorescence in healthy skin compared to melanoma: attributable to substantial light attenuation from melanin in the tumors. Conclusions This study demonstrates the potential of EMCI to quantify endothelial marker concentrations in vivo, an accomplishment that is currently unavailable through any other methods, either in vivo or ex vivo.

Tichauer, Kenneth M.; Deharvengt, Sophie J.; Samkoe, Kimberley S.; Gunn, Jason R.; Bosenberg, Marcus W.; Turk, Mary-Jo; Hasan, Tayyaba; Stan, Radu V.; Pogue, Brian W.

2014-01-01

135

The application of molecular markers in the study of diversity in acarology: a review.  

PubMed

The application of molecular markers to the study of ticks and mites has recently yielded new insights into their population structures and taxonomic relationships. Ticks have been studied at individual, population and species level. Mites are a more diverse group and those that have been studied to the same degree as the ticks include the Tetranychidae (spider mites), Phytoseiidae (predatory mites) and the Eriophyidae. Population variation has also been studied in the important bee parasitic mite Varroa jacobsoni Oudemans. The methods used to study these organisms have much in common. At the individual level these range from general approaches, such as AFLP, RAPD or DALP, to highly specific microsatellite analysis. Although these markers also work at the population and species level, additional analysis of specific nuclear or mitochondrial genes has been conducted either by RFLP or sequencing. Molecular applications have had particular success in facilitating the identification of taxonomically difficult species, understanding population structures and elucidating phylogenetic relationships. PMID:11345314

Navajas, M; Fenton, B

2000-01-01

136

Immunological principles regulating immunomodulation with biomaterials.  

PubMed

The immune system has evolved to recognize and eliminate pathogens; this recognition relies on the identification of structural molecular patterns within unique tissue microenvironments. Therefore, bioengineers can harness these immunological cues to design materials that modulate innate and adaptive immunity in a controlled manner. This review acts as an immunology primer by focusing on the basic molecular and cellular immunology principles governing immunomodulation with biomaterials. PMID:24342045

Khan, Tarik A; Reddy, Sai T

2014-04-01

137

Genetic analysis of apomixis in Citrus and Poncirus by molecular markers  

Microsoft Academic Search

Propagation of citrus rootstocks depends upon the production of clonal plants from nucellar seedlings. This makes apomixis\\u000a one of the host important traits in breeding programs for citrus rootstocks. The genetic control of apomixis was studied in\\u000a a 50-tree progeny derived from the cross C. volkameriana?P. trifoliata using 69 molecular markers and bulked segregant analysis. The proportion of nucellar seedlings

R. García; M. J. Asíns; J. Forner; E. A. Carbonell

1999-01-01

138

Molecular markers for plant breeding: comparisons of RFLP and RAPD genotyping costs  

Microsoft Academic Search

Three molecular marker protocols, chemiluminescent restriction fragment length polymorphisms (c-RFLPs), radioactivity-based restriction fragment length polymorphisms (r-RFLPs), and randomly amplified DNA polymorphisms (RAPDs) were compared in terms of cost and time efficiency. Estimates of cost of supplies and time requirements were obtained from simulations of maize (Zea mays L.) genotyping experiments utilizing protocols currently in use. The increase in total cost

M. Ragot; D. A. Hoisington

1993-01-01

139

Quantum computations with atoms in optical lattices: Marker qubits and molecular interactions  

SciTech Connect

We develop a scheme for quantum computation with neutral atoms, based on the concept of 'marker' atoms, i.e., auxiliary atoms that can be efficiently transported in state-independent periodic external traps to operate quantum gates between physically distant qubits. This allows for relaxing a number of experimental constraints for quantum computation with neutral atoms in microscopic potential, including single-atom laser addressability. We discuss the advantages of this approach in a concrete physical scenario involving molecular interactions.

Calarco, T. [Institute for Theoretical Physics, University of Innsbruck, and Institute for Quantum Optics and Quantum Information of the Austrian Academy of Sciences, A-6020 Innsbruck (Austria); European Centre for Theoretical Studies in Nuclear Physics and Related Areas, I-38050 Villazzano, TN (Italy); CRS BEC-INFM, Dipartimento di Fisica, Universita di Trento, I-38050 Povo, TN (Italy); Dorner, U.; Zoller, P. [Institute for Theoretical Physics, University of Innsbruck (Austria); Institute for Quantum Optics and Quantum Information of the Austrian Academy of Sciences, A-6020 Innsbruck (Austria); Julienne, P.S.; Williams, C.J. [National Institute of Standards and Technology, Gaithersburg, Maryland 20899-8423 (United States)

2004-07-01

140

Molecular Marker Studies in Riverine Buffaloes, for Characterization and Diagnosis of Genetic Defects  

Microsoft Academic Search

The buffalo is probably the last livestock species to have been domesticated, with many genetic, physiological and behavioural\\u000a traits not yet well understood. Molecular markers have been used for characterizing animals and breeds, diagnosing diseases\\u000a and identifying anatomical and physiological anomalies. RFLP studies showed low heterozygosity, but genomic and oligonucleotide\\u000a probes showed species-specific bands useful for identification of carcass or

B. R. Yadav

141

Mapping of quantitative trait loci affecting Drechslera teres resistance in barley with molecular markers  

Microsoft Academic Search

Resistance loci for seedling-stage resistance to net blotch disease (Drechslera teres) in barley were mapped with molecular markers in an F2 population derived from a cross between the susceptible barley cultivar ‘Arena’ and the resistant Ethiopian landrace ‘Hor\\u000a 9088’. Disease reactions were scored with first and second leaves of 2-week-old plants 7 and 9 days after inoculation with\\u000a a single

K. Richter; J. Schondelmaier; C. Jung

1998-01-01

142

?H2AX: a sensitive molecular marker of DNA damage and repair  

Microsoft Academic Search

Phosphorylation of the Ser-139 residue of the histone variant H2AX, forming ?H2AX, is an early cellular response to the induction of DNA double-strand breaks. Detection of this phosphorylation event has emerged as a highly specific and sensitive molecular marker for monitoring DNA damage initiation and resolution. Further, analysis of ?H2AX foci has numerous other applications including, but not limited to,

L-J Mah; A El-Osta; T C Karagiannis

2010-01-01

143

Development of molecular markers and linkage maps for the Carthamus species C. tinctorius and C. oxyacanthus.  

PubMed

A set of SSR and RFLP markers for safflower (Carthamus tinctorius) and jeweled distaff thistle (C. oxyacanthus) was generated from cDNA and genomic libraries and by mining public and proprietary sequence databases. In total, 1412 PCR-based markers and 75 RFLP markers were screened and polymorphic loci were mapped in an intraspecific F2 population of C. tinctorius and an interspecific BC1 population of C. tinctorius x C. oxyacanthus. The two populations shared one common parent and the resulting linkage maps could be compared for synteny. The level of polymorphism was low in both populations and only 8.2% and 13.7% of the analyzed markers could be mapped in the intraspecific and interspecific maps, respectively. The two maps showed significant colinearity of markers in several regions and an apparent translocation or inversion event on one linkage group. Noticeable segregation distortion was found on one linkage group of the C. tinctorius map and dense clustering of loci occurred on several linkage groups of the C. oxyacanthus map. The two maps represent the first major linkage analysis of Carthamus species. The molecular tools will be useful for a variety of genetic and genomic applications in safflower and its related species and have been used in our laboratory to map a flower color gene in C. tinctorius. PMID:20616858

Mayerhofer, Reinhold; Archibald, Catherine; Bowles, Victoria; Good, Allen G

2010-04-01

144

Molecular Phenotyping of Thyroid Tumors Identifies a Marker Panel for Differentiated Thyroid Cancer Diagnosis  

Microsoft Academic Search

Background  Currently, a large proportion of individuals undergo thyroidectomy as a diagnostic procedure for cancer. The objective of\\u000a this work was to evaluate the molecular phenotype of differentiated thyroid cancer (DTC) and benign thyroid lesions to identify\\u000a molecular markers that allow for accurate thyroid cancer diagnosis.\\u000a \\u000a \\u000a \\u000a Methods  Tissue microarrays consisting of 100 benign and 105 malignant thyroid lesions, plus 24 lymph node

Sam M. Wiseman; Adrienne Melck; Hamid Masoudi; Fariba Ghaidi; Lynn Goldstein; Allen Gown; Steven J. M. Jones; Obi L. Griffith

2008-01-01

145

Multilocus microsatellite signature and identification of specific molecular markers for Leishmania aethiopica  

PubMed Central

Background Leishmaniasis is a clinically and epidemiologically diverse zoonotic disease caused by obligatory, intracellular protozoan parasites of the genus Leishmania. Cutaneous leishmaniasis is the most widely distributed form of the disease characterized by skin lesions. Leishmania aethiopica is considered the predominant etiological agent in Ethiopia. The current study was aimed at developing multilocus microsatellite markers for L. aethiopica isolated from human cutaneous leishmaniasis patients in Ethiopia. Results L. aethiopica parasites for the study were obtained from Ethiopia and laboratory analysis was conducted at The Ohio State University. DNA was extracted from cultured parasites and an internal transcribed spacer located at the ribosomal region of L. aethiopica genomic DNA was PCR amplified for species identification. Microsatellite markers were identified using multilocus microsatellite typing. We generated an enriched genomic library, and using Primer3 software, designed PCR primers to amplify sequences flanking the detected microsatellites. Subsequent screening of the amplified markers for length variations was performed by gel electrophoresis. Using a variety of molecular methods, 22 different microsatellite markers were identified and tested for typing L. aethiopica strains using a number of clinical isolates. Of the 22 markers tested, 5 were polymorphic and showed distinctive multilocus genotypes, classifying them into four clusters. One marker was found to be specific for L. aethiopica, discriminating it from other species of Leishmania. Conclusion Multilocus microsatellite typing using the markers developed in this study could be useful for epidemiological and population genetic studies of strains of L. aethiopica in order to investigate the structure and dynamics of the corresponding natural foci. It could also help to answer specific clinical questions, such as the occurrence of local and diffuse lesions, strain correlates of parasite persistence after subclinical infection and lesion comparisons from patients suffering from L. aethiopica infections.

2013-01-01

146

Molecular markers from different genomic compartments reveal cryptic diversity within glaucophyte species.  

PubMed

Glaucophytes are the least studied of the three major Archaeplastida (Plantae sensu lato) lineages. It has been largely recognized that comprehensive investigations of glaucophyte genetic and species diversity will shed light on the early evolution of photosynthetic eukaryotes. Here we used molecular phylogenetics and genetic distance estimations of diverse molecular markers to explore strain and species diversity within the glaucophyte genera Cyanophora and Glaucocystis. Single gene and concatenated maximum likelihood analyses of markers from three different genetic compartments consistently recovered similar intrageneric genetic groups. Distance analyses of plastid (psbA and rbcL) and mitochondrial (cob and cox1) genes, and the nuclear internal transcribed spacer (ITS) region, revealed substantial genetic divergence between some Cyanophora paradoxa and Glaucocystis nostochinearum strains. The genetic distances estimated between some glaucophyte strains currently considered the same species are similar or greater than divergence values calculated between different species in other unicellular algae, such as certain green algae and diatoms. The analyzed molecular markers are prospective candidates for future studies of species diversity in glaucophytes. Overall, our results unveil previously unrecognized cryptic diversity within Cyanophora and Glaucocystis species. PMID:24680917

Chong, Jasmine; Jackson, Christopher; Kim, Jong Im; Yoon, Hwan Su; Reyes-Prieto, Adrian

2014-07-01

147

Quantification of the effects of molecular marker oxidation on source apportionment estimates for motor vehicles  

NASA Astrophysics Data System (ADS)

Molecular markers are individual organic compounds used in receptor models to apportion fine particulate matter to sources. These models currently assume that molecular markers are chemically stable; however, recent laboratory experiments suggest they may be significantly oxidized on atmospherically relevant time scales. To investigate the effects of photo-oxidation, we extended a 3-D chemical transport model (PMCAMx) to simulate norhopane concentrations over the eastern United States during July 2001. Norhopane is an important molecular marker for motor vehicle exhaust. We examined eight different simulation scenarios, using different combinations of reaction rates and source profiles. The simulations including norhopane oxidation better reproduced the observed spatial patterns of norhopane concentrations than the non-reactive cases. Chemical mass balance (CMB) analysis was performed using the PMCAMx-predicted motor vehicle norhopane and elemental carbon (EC) concentrations to quantify the bias caused by oxidation on source apportionment estimates. Norhopane oxidation caused CMB to underestimate total vehicle OC by 10-50%, with larger biases in rural areas. This underestimation was largely due to changes in the amount of OC apportioned to gasoline vehicles which was reduced by as much as 100%. The OC apportioned to diesel vehicle emissions was relatively insensitive to norhopane reaction. Therefore, oxidation can substantially alter CMB estimates regarding the relative importance of gasoline and diesel vehicle emissions.

Roy, Anirban A.; Wagstrom, Kristina M.; Adams, Peter J.; Pandis, Spyros N.; Robinson, Allen L.

2011-06-01

148

Variability analysis of 'Persian' acid lime tree selections using agronomic and molecular markers.  

PubMed

'Persian' acid lime (PAL) is the most important triploid commercial citrus crop planted in the world. Little is known about the genetic variability of the selections used in Brazil. Therefore, 25 genotypes originating from the PAL, and three control species, Citrus sunki, C. limon, and C. aurantiifolia, were assessed using inter-simple sequence repeat (ISSR) and inter-retrotransposon amplified polymorphism (IRAP) molecular markers and agronomic traits of the fruit. The dendrograms were designed using the mean Euclidean distance for the physicochemical attributes of the fruit (weight, length, diameter, peel color, peel thickness, number of seeds, juice yield, titratable acidity, soluble solids, and ratio) and the Jaccard distances using the data from the ISSR and IRAP molecular markers. In the physicochemical analysis, the genotypes were grouped according to species. The trait that contributed most to the diversity among accessions was the number of seeds. The 17 ISSR primers produced 69 polymorphic bands in the molecular analysis, and the seven IRAP primers generated 30 polymorphic bands. The markers detected polymorphisms within and among the PALs; two groups were formed within the PALs. PMID:24222236

Santos, M G; Passos, O S; Soares Filho, W S; Girardi, E A; Gesteira, A S; Ferreira, C F

2013-01-01

149

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.

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

2010-01-01

150

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

PubMed

Pearl millet is an important component of food security in the semi-arid tropics and is assuming greater importance in the context of changing climate and increasing demand for highly nutritious food and feed. Molecular tools have been developed and applied for pearl millet on a limited scale. However, the existing tool kit needs to be strengthened further for its routine use in applied breeding programs. Here, we report enrichment of the pearl millet molecular linkage map by exploiting low-cost and high-throughput Diversity Arrays Technology (DArT) markers. Genomic representation from 95 diverse genotypes was used to develop a DArT array with circa 7,000 clones following PstI/BanII complexity reduction. This array was used to genotype a set of 24 diverse pearl millet inbreds and 574 polymorphic DArT markers were identified. The genetic relationships among the inbred lines as revealed by DArT genotyping were in complete agreement with the available pedigree data. Further, a mapping population of 140 F(7) Recombinant Inbred Lines (RILs) from cross H 77/833-2 × PRLT 2/89-33 was genotyped and an improved linkage map was constructed by integrating DArT and SSR marker data. This map contains 321 loci (258 DArTs and 63 SSRs) and spans 1148 cM with an average adjacent-marker interval length of 3.7 cM. The length of individual linkage groups (LGs) ranged from 78 cM (LG 3) to 370 cM (LG 2). This better-saturated map provides improved genome coverage and will be useful for genetic analyses of important quantitative traits. This DArT platform will also permit cost-effective background selection in marker-assisted backcrossing programs as well as facilitate comparative genomics and genome organization studies once DNA sequences of polymorphic DArT clones are available. PMID:21476042

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

2011-07-01

151

Basic Immunology  

NSDL National Science Digital Library

Some individuals might blanch at the idea of a "basic" immunology overview, but Professor Vladimir V. Klimov provides just such a resource on this site. As the homepage notes, the site is designed to assist undergraduate students learning about the basics of immunology through essays, images, animations, quizzes, case histories, and external links. Visitors can begin by looking over the "Table of Contents" area, which includes seven complete chapters of information. These chapters include "The Immune Responses", "Effector Activity", and "Functional Organization of the Immune System". While some of the materials on the site require a paid subscription, there's enough free material here to get students on their way to learning more about this field of study.

Klimov, Vladimir V.

152

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).

Bienenstock, J.; Befus, A. D.

1980-01-01

153

Identification of EZH2 as a Molecular Marker for a Precancerous State in Morphologically Normal Breast Tissues  

Microsoft Academic Search

The discovery of molecular markers to detect the precan- cerous state would have profound implications in the prevention of breast cancer. We report that the expression of the Polycomb group protein EZH2increases in histo- logically normal breast epithelium with higher risk of devel- oping cancer. We identify EZH2as a potential marker for detecting preneoplastic lesions of the breast in vivo

Christine Erdmann; Arul M. Chinnaiyan; Sofia D. Merajver; Celina G. Kleer

2006-01-01

154

Molecular Markers (RAPD) Associated with Growth, Yield, and Origin of the Silkworm, Bombyx mori L. in India  

Microsoft Academic Search

To identify the molecular markers associated with growth and yield parameters in silkworm, Bombyx mori, RAPD profiles generated with seven UBC primers for fourteen silkworm stocks, originated from China, Japan, India, and Russia, were statistically analyzed. Stepwise multiple regression analysis establishes significant association of 45 markers with larval span, growth indices and four cocoon yield parameters relevant for silk production

S. N. Chatterjee; A. R. Pradeep

2003-01-01

155

TRACKING FECAL CONTAMINATION WITH BACTEROIDALES MOLECULAR MARKERS: AN ANALYSIS OF THE DYNAMICS OF FECAL CONTAMINATION IN THE TILLAMOOK BASIN, OREGON  

EPA Science Inventory

Although amplification of source-specific molecular markers from Bacteroidales fecal bacteria can identify several different kinds of fecal contamination in water, it remains unclear how this technique relates to fecal indicator measurements in natural waters. The objectives of t...

156

Genomic DNA fingerprinting of indigenous chicken breeds with molecular markers designed on interspersed repeats.  

PubMed

In Italy more than fifty different local breeds of chicken (Gallus gallus L.) are known to have been present in the past. The overall situation is now critical since most of these breeds are becoming extinct or threatened and only a few are subject of conservation plans. The use of molecular markers for the analysis of chicken populations could help in characterizing their genetic variation and preserving them from genetic erosion. valuable and irreplaceable sources of chicken germplasm from indigenous populations of the veneto region were analyzed by means of DNA fingerprinting with molecular markers designed on interspersed mini- and microsatellite repeats. The identification of either among-breed discriminant or breed-specific markers was based on the S-SAP and M-AFLP systems derived from the AFLP technology. Genomic DNA fingerprints were generated in 84 individuals belonging to six local breeds (Ermellinata, Padovana, Pépoi, Polverara, Robusta Lionata and Robusta Maculata) and one commercial line used as reference standard. A number of variation statistics were computed to assess the genetic variability within and relatedness among breeds: the effective number of alleles per locus (n(e)= 1.570), total and single-breed genetic diversity (H(T)= 0.366 and H(S)= 0.209, respectively) and the fixation index (G(ST)= 0.429). The mean genetic similarity coefficients within and between local breeds were 0.769 and 0.628, respectively. Markers useful for the genetic traceability of breeds revealed significant sequence similarities with either genic or intergenic regions of known chromosome position. Sequence tagged site primers were designed for the most discriminant markers in order to develop multiplex non-radioactive genomic PCR assays. Analysis of the population structure along with individual assignment tests successfully identified all breed clusters and subclusters. The vast majority of animals were correctly allocated to their breed of origin, demonstrating the suitability and reliability of the chosen AFLP-derived marker systems for detecting population structure and tracing individual breeds. The local breeds have been preliminarily identified according to sequence-specific SNPs and haplotypes and the polymorphism information content of genomic AFLP-derived markers is reported and critically discussed. PMID:19891738

Soattin, M; Barcaccia, Gianni; Dalvit, C; Cassandro, M; Bittante, G

2009-10-01

157

Molecular markers for variation in spawning date in a hatchery population of rainbow trout (Oncorhynchus mykiss).  

PubMed

We examined the distribution of alleles at 63 microsatellite loci distributed across 29 linkage groups in broodstock females from a commercial population of rainbow trout spawning on different dates throughout the season (August to January). A total of 368 females, 184 and 117 females from each of the tail-ends of the spawning distribution and a subsample of 67 females spawning in the middle, were used to detect marker-trait associations. Twenty-one loci in a subset of genomic regions (RT-5, 7, 8, 10, 12, 14, 15, 22, 23, 24, 25, 29, 30, and 31) were significantly associated with variation in spawning date. Many of these markers localize to regions with known spawning date quantitative trait loci based on previous studies. An individual assignment analysis was used to test how well the molecular data could be used to assign individuals to their correct spawning group, and markers were given a ranking reflecting their contribution to the accuracy of assignment. The top 15 ranked markers were successful at assigning the majority of females to the correct spawning group based on genotype with an average accuracy of 76 %. The most likely genes that could contribute to these differences in spawning date are discussed. Together, these data indicate that the loci could be incorporated into a selection index with phenotype data to increase the accuracy of selection for spawning date. PMID:24114565

Allen, M S; Ferguson, M M; Danzmann, R G

2014-06-01

158

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.

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

2013-01-01

159

Modelling asthma in macaques: longitudinal changes in cellular and molecular markers.  

PubMed

The aim of the present study was to determine whether systemic sensitisation and chronic aeroallergen challenge in macaques replicate the classical and emerging immunology and molecular pathology of human asthma. Macaques were immunised and periodically challenged over 2 yrs with house dust mite allergen. At key time-points, serum, bronchoalveolar lavage (BAL) and bronchial biopsies were assayed for genes, proteins and lymphocyte subpopulations relevant to clinical asthma. Immunisation and periodic airway challenge induced changes in immunoglobulin E, airway physiology and eosinophilia consistent with chronic, dual-phase asthma. Sensitisation increased interleukin (IL)-1? and -6 concentrations in serum, and IL-13 expression in BAL cells. Airway challenge increased: early expression of IL-5, -6, -13 and -19, and eotaxin; and variable late-phase expression of IL-4, -5 and -13, and thymus- and activation-regulated chemokine in BAL cells. CD4+ lymphocytes comprised 30% of the CD3+ cells in BAL, increasing to 50% in the late phase. Natural killer T-cells represented <3% of the CD3+ cells. Corticosteroid treatment reduced serum histamine levels, percentage of CD4+ cells and monocyte-derived chemokine expression, while increasing CD3+ and CD8+ cells in BAL. Sensitisation and periodic aeroallergen challenge of cynomolgus macaques results in physiological, cellular, molecular and protein phenotypes, and therapeutic responses observed in human asthma, providing a model system useful in target and biomarker discovery, and translational asthma research. PMID:20650997

Ayanoglu, G; Desai, B; Fick, R B; Grein, J; de Waal Malefyt, R; Mattson, J; McClanahan, T; Olmstead, S; Reece, S P; Van Scott, M R; Wardle, R L

2011-03-01

160

Molecular and biologic markers of progression in monoclonal gammopathy of undetermined significance to multiple myeloma.  

PubMed

Multiple myeloma (MM) is a malignant plasma cell dyscrasia localized in the bone marrow. Recent studies have shown that MM is preceded in virtually all cases by a premalignant state called monoclonal gammopathy of undetermined significance (MGUS). This review focuses on non-IgM MGUS and its progression to MM. Although certain clinical markers of MGUS progression have been identified, it currently is not possible to accurately determine individual risk of progression. This review focuses on the various biologic and molecular markers that could be used to determine the risk of MM progression. A better understanding of the pathogenesis will allow us to define the biological high-risk precursor disease and, ultimately, to develop early intervention strategies designed to delay and prevent full-blown MM. PMID:20958231

Mailankody, Sham; Mena, Esther; Yuan, Constance M; Balakumaran, Arun; Kuehl, W Michael; Landgren, Ola

2010-12-01

161

Evaluation of pharmaceuticals and personal care products as water-soluble molecular markers of sewage.  

PubMed

We examined the utility of 13 pharmaceuticals and personal care products (PPCPs) as molecular markers of sewage contamination in riverine, groundwater, and coastal environments. The PPCPs were crotamiton, ibuprofen, naproxen, ketoprofen, fenoprofen, mefenamic acid, thymol, triclosan, propyphenazone, carbamazepine, diethyltoluamide, ethenzamide, and caffeine. Measurements in 37 Japanese rivers showed positive correlations of riverine flux of crotamiton (r2 = 0.85), carbamazepine (r2 = 0.84), ibuprofen (r2 = 0.73), and mefenamic acid (r2 = 0.67) with the population in the catchments. In three surveys in the Tamagawa estuary, crotamiton, carbamazepine, and mefenamic acid behaved conservatively across seasons within a salinity range of 0.4-29 per thousand, suggesting their utility as molecular markers in coastal environments. Removal of ketoprofen and naproxen in the estuary was ascribed to photodegradation. Ibuprofen and thymol were removed from estuarine waters in summer by microbial degradation. Triclosan was removed by a combination of microbial degradation, photodegradation, and adsorption. These results were consistent with those of river water incubated for 8 d at 25 degrees C in the dark in order to examine the effects of biodegradation and photodegradation. Crotamiton was detected in groundwater from the Tokyo metropolitan area (12 out of 14 samples), suggesting wastewater leakage from decrepit sewers. Carbamazepine, ketoprofen, and ibuprofen (5/14), caffeine (4/14), and diethyltoluamide (3/14) were also detected in the groundwater, whereas the other carboxylic and phenolic PPCPs were not detected and were thought to be removed during their passage through soil. All the data demonstrated the utility of crotamiton and carbamazepine as conservative markers in freshwater and coastal environments. We recommend combining these conservative markers with labile PPCPs to detect inputs of poorly treated sewage. PMID:18800500

Nakada, Norihide; Kiri, Kentaro; Shinohara, Hiroyuki; Harada, Arata; Kuroda, Keisuke; Takizawa, Satoshi; Takada, Hideshige

2008-09-01

162

Molecular Markers of Epithelial-to-Mesenchymal Transition Are Associated with Tumor Aggressiveness in Breast Carcinoma  

PubMed Central

BACKGROUND: Epithelial-to-mesenchymal transition (EMT) is a transient process occurring during developmental stages and carcinogenesis, characterized by phenotypic and molecular alterations, resulting in increased invasive and metastatic capabilities of cancer cells and drug resistance. Moreover, emerging evidence suggests that EMT is associated with increased enrichment of cancer stem-like cells in neoplastic tissues. We interrogated the molecular alterations occurring in breast cancer using proposed EMT markers such as E-cadherin, vimentin, epidermal growth factor receptor (EGFR), platelet-derived growth factor (PDGF) D, and nuclear factor ?B (NF-?B) to decipher their roles in the EMT and breast cancer progression. METHODS: Fifty-seven invasive ductal adenocarcinomas of the breast were assessed for the expression of E-cadherin, vimentin, EGFR, NF-?B, and PDGF-D using immunohistochemical analysis. Tumors were categorized into three groups: A (ER+, and/or PR+, HER-2/neu-), B (ER+, and/or PR+, HER-2/neu+), and C (triple-negative: ER-, PR-, and HER-2/neu-). Immunostained slides were microscopically evaluated and scored using intensity (0, 1+, 2+, and 3+) and percentage of positive cells, and data were statistically analyzed. RESULTS: Membranous E-cadherin was positive in all 57 cases (100%), whereas cytoplasmic E-cadherin was predominantly positive in groups B and C compared with group A (21%, 7%, and 0%, respectively). All group A cases were negative for vimentin and EGFR. There was statistically significant increased expression of vimentin (P < .0002), EGFR (P < .0001), and NF-?B (P < .02) in triple-negative cases when compared with groups A and B. CONCLUSIONS: Vimentin, EGFR, and NF-?B were significantly increased in triple-negative tumors, which is consistent with the aggressiveness of these tumors. These markers could be useful as markers for EMT in breast cancers and may serve as predictive markers for designing customized therapy in the future.

Sethi, Seema; Sarkar, Fazlul H; Ahmed, Quratulain; Bandyopadhyay, Sudeshna; Nahleh, Zeina A; Semaan, Assaad; Sakr, Wael; Munkarah, Adnan; Ali-Fehmi, Rouba

2011-01-01

163

Source apportionment of primary and secondary organic aerosols using positive matrix factorization (PMF) of molecular markers  

NASA Astrophysics Data System (ADS)

Monthly average ambient concentrations of more than eighty particle-phase organic compounds, as well as total organic carbon (OC) and elemental carbon (EC), were measured from March 2004 through February 2005 in five cities in the Midwestern United States. A multi-variant source apportionment receptor model, positive matrix factorization (PMF), was applied to explore the average source contributions to the five sampling sites using molecular markers for primary and secondary organic aerosols (POA, SOA). Using the molecular makers in the model, POA and SOA were estimated for each month at each site. Three POA factors were derived, which were dominated by primary molecular markers such as EC, hopanes, steranes, and polycyclic aromatic hydrocarbons (PAHs), and which represented the following POA sources: urban primary sources, mobile sources, and other combustion sources. The three POA sources accounted for 57% of total average ambient OC. Three factors, characterized by the presence of reaction products of isoprene, ?-pinene and ?-caryophyllene, and displaying distinct seasonal trends, were consistent with the characteristics of SOA. The SOA factors made up 43% of the total average measured OC. The PMF-derived results are in good agreement with estimated SOA concentrations obtained from SOA to tracer yield estimates obtained from smog chamber experiments. A linear regression comparing the smog chamber yield estimates and the PMF SOA contributions had a regression slope of 1.01 ± 0.07 and an intercept of 0.19 ± 0.10 ?g OC m -3 (adjusted R2 of 0.763, n = 58).

Zhang, YuanXun; Sheesley, Rebecca J.; Schauer, James J.; Lewandowski, Michael; Jaoui, Mohammed; Offenberg, John H.; Kleindienst, Tadeusz E.; Edney, Edward O.

164

Maximizing genetic differentiation in core collections by PCA-based clustering of molecular marker data.  

PubMed

Developing genetically diverse core sets is key to the effective management and use of crop genetic resources. Core selection increasingly uses molecular marker-based dissimilarity and clustering methods, under the implicit assumption that markers and genes of interest are genetically correlated. In practice, low marker densities mean that genome-wide correlations are mainly caused by genetic differentiation, rather than by physical linkage. Although of central concern, genetic differentiation per se is not specifically targeted by most commonly employed dissimilarity and clustering methods. Principal component analysis (PCA) on genotypic data is known to effectively describe the inter-locus correlations caused by differentiation, but to date there has been no evaluation of its application to core selection. Here, we explore PCA-based clustering of marker data as a basis for core selection, with the aim of demonstrating its use in capturing genetic differentiation in the data. Using simulated datasets, we show that replacing full-rank genotypic data by the subset of genetically significant PCs leads to better description of differentiation and improves assignment of genotypes to their population of origin. We test the effectiveness of differentiation as a criterion for the formation of core sets by applying a simple new PCA-based core selection method to simulated and actual data and comparing its performance to one of the best existing selection algorithms. We find that although gains in genetic diversity are generally modest, PCA-based core selection is equally effective at maximizing diversity at non-marker loci, while providing better representation of genetically differentiated groups. PMID:23178877

van Heerwaarden, Joost; Odong, T L; van Eeuwijk, F A

2013-03-01

165

Determination of specific molecular markers of biomass burning in lake sediments  

NASA Astrophysics Data System (ADS)

Fire influences regional to global atmospheric chemistry and climate. Molecular markers of biomass burning archived in lake sediments are becoming increasingly important in paleoenvironmental reconstruction and may help determine interactions between climate and fire activity. One group of these molecular markers is the monosaccharide anhydrides levoglucosan, mannosan and galactosan. Several aerosol studies and recent ice core research use these compounds as a marker for biomass burning, but studies from lake sediment cores are rare. Previous sediment methods used gas chromatography - mass spectrometry and required derivatization of samples. Here, we present a high performance anion exchange chromatography-mass spectrometry method to allow separation and detection of the three monosaccharide anhydrides in lake sediments with implications for reconstructing past biomass burning events. We validated the method by quantifying levoglucosan, mannosan and galactosan in selected sediment core samples from Lake Kirkpatrick, New Zealand. The freeze-dried, milled and homogenized sediment samples were first extracted with methanol by pressurized solvent extraction, pre-concentrated and finally separated and analyzed by high performance anion exchange chromatography-mass spectrometry. We compared these isomers with macroscopic charcoal concentrations, as charcoal is a well-known proxy for biomass burning. In addition, we applied the method to a sediment core from Lake Petén Itzá, Guatemala to prove the suitability of these markers for reconstructing biomass burning history over the entire Holocene. In the Lake Kirkpatrick samples, levoglucosan, mannosan and galactosan concentrations significantly correlate with macroscopic charcoal concentrations. The three isomers are present in samples without any macroscopic charcoal, and may reflect the presence of microscopic charcoal. Levoglucosan/mannosan and levoglucosan/(mannosan+galactosan) ratios differ between samples with high macroscopic charcoal concentrations and samples without any charcoal. These ratios may help determine not only when fires occurred, but also past changes in the primary burned vegetation. However, the possibility that these isomer ratios help differentiate changes in burned vegetation needs further evaluation. The preliminary results of the Lake Petén Itzá samples demonstrate the occurrence of all three molecular markers in the entire core, covering the past approximately 10,000 years. The three monosaccharide anhydrides levoglucosan, mannosan and galactosan may be an additional tool for reconstructing past fire events over decadal to millennial time scales in sediment cores.

Kirchgeorg, Torben; Schüpbach, Simon; Kehrwald, Natalie; McWethy, David; Barbante, Carlo

2014-05-01

166

Transcript profiling and identification of molecular markers for early microspore embryogenesis in Brassica napus.  

PubMed

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

2007-05-01

167

Molecular and serum markers in hepatocellular carcinoma: predictive tools for prognosis and recurrence.  

PubMed

With increased understanding of cancer biology, a multitude of pathological, genetic, and molecular events that drive hepatocarcinogenesis, including angiogenesis, invasion, and metastasis, has been identified. Lately, they are being aggressively evaluated due to challenges involved in establishing early diagnosis, optimizing therapy for cancer inducing hepatotrophic viruses, minimizing the emergence of new tumors, and preventing recurrence after surgical resection or liver transplantation. This comprehensive review examines and critiques the evidence from published manuscripts reporting various tissue and serum biomarkers involved in hepatocellular carcinoma. These markers not only help in prediction of prognosis or recurrence, but may also assist in deciding appropriate modality of therapy and represent novel targets for potential therapeutic agents. PMID:21680198

Singhal, Ashish; Jayaraman, Muralidharan; Dhanasekaran, Danny N; Kohli, Vivek

2012-05-01

168

Transcriptome analysis of Capsicum annuum varieties Mandarin and Blackcluster: assembly, annotation and molecular marker discovery.  

PubMed

Next generation sequencing technologies have proven to be a rapid and cost-effective means to assemble and characterize gene content and identify molecular markers in various organisms. Pepper (Capsicum annuum L., Solanaceae) is a major staple vegetable crop, which is economically important and has worldwide distribution. High-throughput transcriptome profiling of two pepper cultivars, Mandarin and Blackcluster, using 454 GS-FLX pyrosequencing yielded 279,221 and 316,357 sequenced reads with a total 120.44 and 142.54Mb of sequence data (average read length of 431 and 450 nucleotides). These reads resulted from 17,525 and 16,341 'isogroups' and were assembled into 19,388 and 18,057 isotigs, and 22,217 and 13,153 singletons for both the cultivars, respectively. Assembled sequences were annotated functionally based on homology to genes in multiple public databases. Detailed sequence variant analysis identified a total of 9701 and 12,741 potential SNPs which eventually resulted in 1025 and 1059 genotype specific SNPs, for both the varieties, respectively, after examining SNP frequency distribution for each mapped unigenes. These markers for pepper will be highly valuable for marker-assisted breeding and other genetic studies. PMID:24125952

Ahn, Yul-Kyun; Tripathi, Swati; Kim, Jeong-Ho; Cho, Young-Il; Lee, Hye-Eun; Kim, Do-Sun; Woo, Jong-Gyu; Cho, Myeong-Cheoul

2014-01-10

169

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

170

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

171

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.

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

2014-01-01

172

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.

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

2014-01-01

173

Molecular Marker Differences Relate to Developmental Position and Subsets of Mesodiencephalic Dopaminergic Neurons  

PubMed Central

The development of mesodiencephalic dopaminergic (mdDA) neurons located in the substantia nigra compacta (SNc) and ventral tegmental area (VTA) follow a number of stages marked by distinct events. After preparation of the region by signals that provide induction and patterning, several transcription factors have been identified, which are involved in specifying the neuronal fate of these cells. The specific vulnerability of SNc neurons is thought to root in these specific developmental programs. The present study examines the positions of young postmitotic mdDA neurons to relate developmental position to mdDA subset specific markers. MdDA neurons were mapped relative to the neuromeric domains (prosomeres 1-3 (P1-3), midbrain, and hindbrain) as well as the longitudinal subdivisions (floor plate, basal plate, alar plate), as proposed by the prosomeric model. We found that postmitotic mdDA neurons are located mainly in the floorplate domain and very few in slightly more lateral domains. Moreover, mdDA neurons are present along a large proportion of the anterior/posterior axis extending from the midbrain to P3 in the diencephalon. The specific positions relate to some extent to the presence of specific subset markers as Ahd2. In the adult stage more of such subsets specific expressed genes are present and may represent a molecular map defining molecularly distinct groups of mdDA neurons.

Smits, Simone M.; von Oerthel, Lars; Hoekstra, Elisa J.; Burbach, J. Peter H; Smidt, Marten P.

2013-01-01

174

Molecular Markers for Biomass Traits: Association, Interaction and Genetic Divergence in Silkworm Bombyx mori  

PubMed Central

Improvement of high yielding, disease resistant silkworm strains became imminent to increase production of silk, which is a major revenue earner for sericulturists. Since environment interacts with phenotype, conventional breeding did not result in commendable yield improvement in synthetic strains of silkworm, Bombyx mori. Identification of DNA markers associated with different economically important biomass traits and its introgression could assist molecular breeding and expression of stabilized high yielding characters, but genetic basis of most quantitative traits in silkworm is poorly understood due to its polygenic control. Correlation analysis (R = 0.9) revealed significant interrelation among biomass traits viz., larval duration (TLD), larval weight (LWT), cocoon weight (CWT), shell weight (SWT), shell ratio (SR) and floss content. PCR using inter simple sequence repeat (ISSR) primers revealed 92% polymorphism among 14 tropical and temperate strains of B. mori, with average diversity index of 0.747. Stepwise multiple regression analysis (MRA) selected 35 ISSR markers positively or negatively correlated with different biomass traits, illustrated polygenic control. ISSR marker 830.81050bp was significantly associated with LWT, CWT, SWT, SR and floss content, indicated its pleiotropic role. Two ISSR markers, 835.51950bp and 825.9710bp showed significant association with floss content and TLD. These markers were segregated in F2 generation and Chi-square test confirmed (?2 = ~45; P < 0.05) its genetic contribution to the associated biomass traits. Strains, with both positively and negatively correlated markers, had intermediate mean value for biomass traits (eg. SWT = 0.17 ± 0.014 g in GNM and Moria) indicated interaction of loci in natural populations. Low yielding Indian strains grouped together by Hierarchical clustering. Chinese and Japanese strains were distributed in the periphery of ALSCAL matrix indicated convergence of genetic characters in Indian strains. Average genetic distance between Chinese strains and Indian strains (0.193) significantly (P < 0.01) varied from that between Chinese and Japanese strains. Interaction of loci and allelic substitutions induced phenotypic plasticity in temperate B. mori populations on tropic adaptation in India. These outcomes show possibility to combine favorable alleles at different QTL to increase larval, cocoon and shell weight.

Pradeep, Appukuttannair R; Jingade, Anuradha H; Urs, Raje S

2007-01-01

175

Molecular Markers for Biomass Traits: Association, Interaction and Genetic Divergence in Silkworm Bombyx mori.  

PubMed

Improvement of high yielding, disease resistant silkworm strains became imminent to increase production of silk, which is a major revenue earner for sericulturists. Since environment interacts with phenotype, conventional breeding did not result in commendable yield improvement in synthetic strains of silkworm, Bombyx mori. Identification of DNA markers associated with different economically important biomass traits and its introgression could assist molecular breeding and expression of stabilized high yielding characters, but genetic basis of most quantitative traits in silkworm is poorly understood due to its polygenic control. Correlation analysis (R = 0.9) revealed significant interrelation among biomass traits viz., larval duration (TLD), larval weight (LWT), cocoon weight (CWT), shell weight (SWT), shell ratio (SR) and floss content. PCR using inter simple sequence repeat (ISSR) primers revealed 92% polymorphism among 14 tropical and temperate strains of B. mori, with average diversity index of 0.747. Stepwise multiple regression analysis (MRA) selected 35 ISSR markers positively or negatively correlated with different biomass traits, illustrated polygenic control. ISSR marker 830.8(1050bp) was significantly associated with LWT, CWT, SWT, SR and floss content, indicated its pleiotropic role. Two ISSR markers, 835.5(1950bp) and 825.9(710bp) showed significant association with floss content and TLD. These markers were segregated in F(2) generation and Chi-square test confirmed (chi(2) = ~45; P < 0.05) its genetic contribution to the associated biomass traits. Strains, with both positively and negatively correlated markers, had intermediate mean value for biomass traits (eg. SWT = 0.17 +/- 0.014 g in GNM and Moria) indicated interaction of loci in natural populations. Low yielding Indian strains grouped together by Hierarchical clustering. Chinese and Japanese strains were distributed in the periphery of ALSCAL matrix indicated convergence of genetic characters in Indian strains. Average genetic distance between Chinese strains and Indian strains (0.193) significantly (P < 0.01) varied from that between Chinese and Japanese strains. Interaction of loci and allelic substitutions induced phenotypic plasticity in temperate B. mori populations on tropic adaptation in India. These outcomes show possibility to combine favorable alleles at different QTL to increase larval, cocoon and shell weight. PMID:19662204

Pradeep, Appukuttannair R; Jingade, Anuradha H; Urs, Raje S

2007-01-01

176

At3g08030 transcript: a molecular marker of seed ageing  

PubMed Central

Background and Aims Prolonged storage generally reduces seed viability and vigour, although the rate of deterioration varies among species and environmental conditions. Here, we suggest a possible ageing molecular marker: At3g08030 mRNA. At3g08030 is a member of the DUF642 highly conserved family of cell-wall-associated proteins that is specific for spermatophytes. Methods At3g08030 expression was performed by RT-PCR and qRT-PCR analysis in seed samples differing in their rate of germination and final germination following a matrix priming and/or controlled deterioration (rapid ageing) treatment. Key Results The At3g08030 gene transcript was present during the entire Arabidopsis thaliana plant life cycle and in seeds, during maturation, the ripening period and after germination. Matrix priming treatment increased the rate of germination of control seeds and seeds aged by controlled deterioration. Priming treatments also increased At3g08030 expression. To determine whether the orthologues of this gene are also age markers in other plant species, At3g08030 was cloned in two wild species, Ceiba aesculifolia and Wigandia urens. As in A. thaliana, the At3g08030 transcript was not present in aged seeds of the tested species but was present in recently shed seeds. A reduction in germination performance of the aged seeds under salt stress was determined by germination assays. Conclusions At3g08030 mRNA detection in a dry seed lot has potential for use as a molecular marker for germination performance in a variety of plant species.

Garza-Caligaris, Luz Elena; Avendano-Vazquez, Aida Odette; Alvarado-Lopez, Sandra; Zuniga-Sanchez, Esther; Orozco-Segovia, Alma; Perez-Ruiz, Rigoberto V.; Gamboa-deBuen, Alicia

2012-01-01

177

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.

2012-01-01

178

Transcriptome survey of Patagonian southern beech Nothofagus nervosa (= N. Alpina): assembly, annotation and molecular marker discovery  

PubMed Central

Background Nothofagus nervosa is one of the most emblematic native tree species of Patagonian temperate forests. Here, the shotgun RNA-sequencing (RNA-Seq) of the transcriptome of N. nervosa, including de novo assembly, functional annotation, and in silico discovery of potential molecular markers to support population and associations genetic studies, are described. Results Pyrosequencing of a young leaf cDNA library generated a total of 111,814 high quality reads, with an average length of 447 bp. De novo assembly using Newbler resulted into 3,005 tentative isotigs (including alternative transcripts). The non-assembled sequences (singletons) were clustered with CD-HIT-454 to identify natural and artificial duplicates from pyrosequencing reads, leading to 21,881 unique singletons. 15,497 out of 24,886 non-redundant sequences or unigenes, were successfully annotated against a plant protein database. A substantial number of simple sequence repeat markers (SSRs) were discovered in the assembled and annotated sequences. More than 40% of the SSR sequences were inside ORF sequences. To confirm the validity of these predicted markers, a subset of 73 SSRs selected through functional annotation evidences were successfully amplified from six seedlings DNA samples, being 14 polymorphic. Conclusions This paper is the first report that shows a highly precise representation of the mRNAs diversity present in young leaves of a native South American tree, N. nervosa, as well as its in silico deduced putative functionality. The reported Nothofagus transcriptome sequences represent a unique resource for genetic studies and provide a tool to discover genes of interest and genetic markers that will greatly aid questions involving evolution, ecology, and conservation using genetic and genomic approaches in the genus.

2012-01-01

179

Angelman syndrome: three molecular classes identified with chromosome 15q11q13-specific DNA markers.  

PubMed

Angelman syndrome (AS) and Prader-Willi syndrome (PWS) share a cytogenetic deletion of chromosome 15q11q13. To determine the extent of deletion in AS we analyzed the DNA of 19 AS patients, including two sib pairs, with the following chromosome 15q11q13--specific DNA markers: D15S9-D15S13, D15S17, D15S18, and D15S24. Three molecular classes were identified. Class I showed a deletion of D15S9-D15S13 and D15S18; class II showed a deletion of D15S9-D15S13; and in class III, including both sib pairs, no deletion was detected. These molecular classes appear to be identical to those observed in PWS. High-resolution cytogenetic data were available on 16 of the patients, and complete concordance between the presence of a cytogenetic deletion and a molecular deletion was observed. No submicroscopic deletions were detected. DNA samples from the parents of 10 patients with either a class I or a class II deletion were available for study. In seven of the 10 families, RFLPs were informative as to the parental origin of the deletion. In all informative families, the deleted chromosome 15 was observed to be of maternal origin. This finding is in contrast to the paternal origin of the deletions in PWS and is currently the only molecular difference observed between the two syndromes. PMID:1971993

Knoll, J H; Nicholls, R D; Magenis, R E; Glatt, K; Graham, J M; Kaplan, L; Lalande, M

1990-07-01

180

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

181

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

182

The semidwarf gene, sd-1, of rice ( Oryza sativa L.). II. Molecular mapping and marker-assisted selection  

Microsoft Academic Search

To establish the location of the semidwarf gene, sd-1, the anthocyanin activator (A), purple node (Pn), purple auricle (Pau), and the isozyme locus, EstI-2, in relation to DNA markers on the molecular linkage map of rice, 20 RFLP markers, previously mapped to the central region of chromosome 1 (McCouch et al. 1988), were mapped onto an F2 population derived from

Y. G. Cho; M. Y. Eun; S. R. McCouch; Y. A. Chae

1994-01-01

183

Determination of genetic structure of germplasm collections: are traditional hierarchical clustering methods appropriate for molecular marker data?  

PubMed

Despite the availability of newer approaches, traditional hierarchical clustering remains very popular in genetic diversity studies in plants. However, little is known about its suitability for molecular marker data. We studied the performance of traditional hierarchical clustering techniques using real and simulated molecular marker data. Our study also compared the performance of traditional hierarchical clustering with model-based clustering (STRUCTURE). We showed that the cophenetic correlation coefficient is directly related to subgroup differentiation and can thus be used as an indicator of the presence of genetically distinct subgroups in germplasm collections. Whereas UPGMA performed well in preserving distances between accessions, Ward excelled in recovering groups. Our results also showed a close similarity between clusters obtained by Ward and by STRUCTURE. Traditional cluster analysis can provide an easy and effective way of determining structure in germplasm collections using molecular marker data, and, the output can be used for sampling core collections or for association studies. PMID:21472410

Odong, T L; van Heerwaarden, J; Jansen, J; van Hintum, T J L; van Eeuwijk, F A

2011-07-01

184

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

185

Molecular cloning, expression and immunological characterisation of Pas n 1, the major allergen of Bahia grass Paspalum notatum pollen.  

PubMed

Bahia grass, Paspalum notatum, is a clinically important subtropical grass with a prolonged pollination season from spring to autumn. We aimed to clone and characterise the major Bahia grass pollen allergen, Pas n 1. Grass pollen-allergic patients presenting to a tertiary hospital allergy clinic were tested for IgE reactivity with Bahia grass pollen extract by skin prick testing, ImmunoCAP, ELISA and immunoblotting. Using primers deduced from the N-terminal peptide sequence of a group 1 allergen of Bahia grass pollen extract separated by two-dimensional gel electrophoresis, the complete Pas n 1 cDNA was obtained by rapid amplification of cDNA ends and cloned. Biological relevance of recombinant Pas n 1 expressed in Escherichia coli was assessed by serum IgE reactivity and basophil activation. Twenty-nine of 34 (85%) consecutive patients presenting with grass pollen allergy were skin prick test positive to Bahia grass pollen. The Pas n 1 cDNA has sequence homology with the beta-expansin 1 glycoprotein family and is more closely related to the maize pollen group 1 allergen (85% identity) than to ryegrass Lol p 1 or Timothy grass Phl p 1 (64 and 66% identity, respectively). rPas n 1 reacted with serum IgE in 47 of 55 (85%) Bahia grass pollen-allergic patients, activated basophils and inhibited serum IgE reactivity with the 29 kDa band of Bahia grass pollen extract. In conclusion the cDNA for the major group 1 allergen of the subtropical Bahia grass pollen, Pas n 1, was identified and cloned. rPas n 1 is immunologically active and is a valuable reagent for diagnosis and specific immunotherapy of grass pollen allergy. PMID:18817975

Davies, Janet M; Mittag, Diana; Dang, Thanh D; Symons, Karen; Voskamp, Astrid; Rolland, Jennifer M; O'Hehir, Robyn E

2008-12-01

186

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.

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

2014-01-01

187

Association of molecular markers with cold tolerance and green period in zoysiagrass (Zoysia Willd.)  

PubMed Central

Cold tolerance and the green period are key traits in the breeding of zoysiagrass (Zoysia Willd.). Identification of molecular markers associated with cold tolerance and the green period of zoysiagrass will contribute to efficient selection of elite cultivars. These two traits were measured in 96 zoysiagrass accessions in 2004 and 2005–2006, respectively. The mapping population was screened with 29 pairs of simple sequence repeat (SSR) primers and 54 pairs of sequence-related amplified polymorphism (SRAP) primers. A multi-loci in silico mapping approach implemented with an empirical Bayes method was applied for association mapping of cold tolerance and green period. We detected 254 SSR polymorphic loci and 338 SRAP polymorphic loci, among which three SSR loci (Xgwm131-3B-187, Xgwm469-6D-194 and Xgwm234-5B-244) and one SRAP locus (Me11Em7-406) were significantly associated with cold tolerance with effect values of 57.83%, 38.05%, 36.92% and 37%, respectively. Three SSR loci (Xgwm132-6B-225, Xgwm111-7D-34 and Xgwm102-2D-97) and two SRAP loci (Me19Em5-359 and Me16Em8-483) were significantly associated with the green period with effect values of 79.54%, 62.59%, 99.04%, 49.01% and 82.57%. These markers will be useful for genetic improvement of the cold tolerance and green period of zoysiagrass by marker-assisted breeding.

Guo, Hai-Lin; Xuan, Ji-Ping; Liu, Jian-Xiu; Zhang, Yuan-Ming; Zheng, Yi-Qi

2012-01-01

188

Species boundaries of Astreopora corals (Scleractinia, Acroporidae) inferred by mitochondrial and nuclear molecular markers.  

PubMed

The genus Astreopora is a small but ancestral group in Acroporidae, which is one of the most diverse and dominant families of scleractinian coral in Indo-Pacific reefs. We estimated the species boundaries of Astreopora corals using two molecular markers: a mitochondrial non-coding region and a nuclear ribosomal 5.8S region. Seven species (59 specimens) commonly observed around Japan (Astreopora expansa, A. gracilis, A. incrustans, A. listeri, A. myriophthalma, A. cf. suggesta, and Astreopora sp.1) were investigated, and we observed no genetic divergence in the mitochondrial marker, suggesting that these species are closely related, consistent with a species complex or recent divergence, although genotyping by the marker is not so sensitive. In the nuclear 5.8S region, 121 clones consisted of six species were divided into the four major genetic groups. Although there were no monophyletic clades, the two dominant species A. myriophthalma and A. gracilis rarely shared the same haplotypes, suggesting that gene flow is limited between them. However, A. incrustans frequently shared the same haplotypes with A. gracilis although the distributions do not overlap. We found that the ancestral genus Astreopora in Acroporidae shows less genetic variation than traditionally identified morphospecies. Although further research on fertilization rate among these species is required to determine if there are reproductive barriers, the low level of genetic diversification in this genus hints that some ecological differences among acroporid corals play a role in the evolution of scleractinian corals, considering that the other members of this family, Acropora and Montipora, are highly diversified. PMID:23915155

Suzuki, Go; Nomura, Keiichi

2013-08-01

189

Transcriptome analysis in Concholepas concholepas (Gastropoda, Muricidae): mining and characterization of new genomic and molecular markers.  

PubMed

The marine gastropod Concholepas concholepas, locally known as the "loco", is the main target species of the benthonic Chilean fisheries. Genetic and genomic tools are necessary to study the genome of this species in order to understand the molecular basis of its development, growth, and other key traits to improve the management strategies and to identify local adaptation to prevent loss of biodiversity. Here, we use pyrosequencing technologies to generate the first transcriptomic database from adult specimens of the loco. After trimming, a total of 140,756 Expressed Sequence Tag sequences were achieved. Clustering and assembly analysis identified 19,219 contigs and 105,435 singleton sequences. BlastN analysis showed a significant identity with Expressed Sequence Tags of different gastropod species available in public databases. Similarly, BlastX results showed that only 895 out of the total 124,654 had significant hits and may represent novel genes for marine gastropods. From this database, simple sequence repeat motifs were also identified and a total of 38 primer pairs were designed and tested to assess their potential as informative markers and to investigate their cross-species amplification in different related gastropod species. This dataset represents the first publicly available 454 data for a marine gastropod endemic to the southeastern Pacific coast, providing a valuable transcriptomic resource for future efforts of gene discovery and development of functional markers in other marine gastropods. PMID:21867972

Cárdenas, Leyla; Sánchez, Roland; Gomez, Daniela; Fuenzalida, Gonzalo; Gallardo-Escárate, Cristián; Tanguy, Arnaud

2011-09-01

190

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

191

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

192

Efficacy, safety, and selection of molecular markers of drug resistance by two ACTs in Mali.  

PubMed

We conducted a randomized single-blinded trial comparing the efficacy and safety of artesunate (AS) + amodiaquine (AQ, 3 days) versus AS (3 days) + sulfadoxine-pyrimethamine (SP, single dose) versus AS monotherapy (5 days) in Southern Mali. Uncomplicated malaria cases were followed for 28 days. Molecular markers of drug resistance were determined. After identification of recrudescences by genotyping, both artemisinin-based combination therapies (ACTs) reached nearly 100% efficacy at Day 14 and Day 28 versus 98.3% and 96.5% for AS, respectively (P > 0.05). AS + SP significantly selected DHFR and DHPS mutations associated with sulfadoxine and pyrimethamine resistance (P < 0.001), and AS + AQ equally selected PfCRT and PfMDR1 point mutations associated with chloroquine and AQ resistance (P < 0.001). No significant adverse event attributable to any of the study drugs was found. The ACTs were efficacious and safe, but the selection of markers for resistance to the partner drugs raises concerns over their lifespan in areas of intense malaria transmission. PMID:18337343

Djimdé, Abdoulaye A; Fofana, Bakary; Sagara, Issaka; Sidibe, Bakary; Toure, Sekou; Dembele, Demba; Dama, Souleymane; Ouologuem, Dinkorma; Dicko, Alassane; Doumbo, Ogobara K

2008-03-01

193

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

194

2007 EORTC-NCI-ASCO Annual Meeting: Molecular Markers in Cancer  

PubMed Central

The recent EORTC-NCI-ASCO Annual Meeting on ‘Molecular Markers in Cancer’ was held on 15–17 November 2007 in Brussels, Belgium. It was the largest meeting to date and marked the first year in which the American Association of Clinical Oncology (ASCO) joined in the efforts of the European Organisation for Research and Treatment of Cancer (EORTC) and the National Cancer Institute (NCI) in organizing this annual event. More than 300 clinicians, pathologists, laboratory scientists and representatives from regulatory agencies and the pharmaceutical industry came together for three days of intense discussion, debate and reflection on the latest biomarker therapeutic discoveries, strategies and clinical applications. The poster discussion sessions featured 79 research abstracts. The three most outstanding abstracts, all authored by young female researchers, were selected for presentation during the main meeting sessions. Highlights of each scientific session are presented.

Lukan, C

2008-01-01

195

Triazole-based Zn(2+)-specific molecular marker for fluorescence bioimaging.  

PubMed

Fluorescence bioimaging potential, both in vitro and in vivo, of a yellow emissive triazole-based molecular marker has been investigated and demonstrated. Three different kinds of cells, viz Bacillus thuringiensis, Candida albicans, and Techoma stans pollen grains were used to investigate the intracellular zinc imaging potential of 1 (in vitro studies). Fluorescence imaging of translocation of zinc through the stem of small herb, Peperomia pellucida, having transparent stem proved in vivo bioimaging capability of 1. This approach will enable in screening cell permeability and biostability of a newly developed probe. Similarly, the current method for detection and localization of zinc in Gram seed sprouts could be an easy and potential alternative of the existing analytical methods to investigate the efficiency of various strategies applied for increasing zinc-content in cereal crops. The probe-zinc ensemble has efficiently been applied for detecting phosphate-based biomolecules. PMID:24725748

Sinha, Sougata; Mukherjee, Trinetra; Mathew, Jomon; Mukhopadhyay, Subhra K; Ghosh, Subrata

2014-04-25

196

UHRF1 is a novel molecular marker for diagnosis and the prognosis of bladder cancer  

PubMed Central

Background: Bladder cancer is the second most common cancer of the urinary system. Early diagnosis of this tumour and estimation of risk of future progression after initial transuretherial resection have a significant impact on prognosis. Although there are several molecular markers for the diagnosis and prognosis for this tumour, their accuracy is not ideal. Previous reports have shown that UHRF1 (ubiquitin-like with PHD and ring-finger domains 1) is essential for cellular proliferation. In this study, we examined whether UHRF1 can be a novel molecular marker of bladder cancer. Methods: We performed real-time TaqMan quantitative reverse transcription–PCR and immunohistochemistry to examine expression levels of UHRF1 in bladder and kidney cancers. Results: Significant overexpression of UHRF1 was observed in bladder cancer. The overexpression was correlated with the stage and grade of the cancer. Although UHRF1 expression in muscle-invasive cancer was greater than in non-invasive (pTa) or superficially invasive (pT1) cancers, UHRF1 could still be detected by immunohistochemistry in these early-stage cancers. Overexpression of UHRF1 in bladder cancer was associated with increased risk of progression after transurethral resection. High expression of UHRF1 in kidney cancer was also observed. But the increased levels of UHRF1 in kidney cancer were less significant compared with those in bladder cancer. Conclusion: Our result indicates that an immunohistochemistry-based UHRF1 detection in urine sediment or surgical specimens can be a sensitive and cancer-specific diagnostic and/or prognosis method, and may greatly improve the current diagnosis based on cytology.

Unoki, M; Kelly, J D; Neal, D E; Ponder, B A J; Nakamura, Y; Hamamoto, R

2009-01-01

197

Understanding the pathogenesis of psoriasis, psoriatic arthritis, and autoimmunity via a fusion of molecular genetics and immunology  

Microsoft Academic Search

The goal of my laboratory is to understand the molecular genetics basis of the inflammatory skin disease psoriasis and associated\\u000a psoriatic arthritis. In performing these studies my colleagues and I have begun to identify common pathways leading to autoimmunity\\u000a as well, because some of the defective pathways leading to autoimmunity are the same in different autoimmune diseases. Some\\u000a of these

Anne M. Bowcock

2005-01-01

198

Molecular markers from three organellar genomes unravel complex taxonomic relationships within the coralline algal genus Chiharaea (Corallinales, Rhodophyta).  

PubMed

The use of molecular markers in taxonomic studies has become a standard practice in biology. However, consensus on which markers to use at the species level is lacking because evolutionary lineages show differences in divergence rates between organellar genomes. Ideally, researchers use multiple lines of evidence when first describing a species, such as the incorporation of several molecular markers from varied genomes (mitochondrion, plastid and nucleus). This study examined species boundaries in the red algal genus Chiharaea. We used five molecular markers, with at least one marker from each genome, coupled with thorough morphological analyses. We recognized three species in Chiharaea (C.americana, C. rhododactyla sp. nov., C. silvae) and two forms (C. americana f. americana and C. americana f. bodegensis (H.W. Johansen) stat. nov.). For C. americana f. americana and C. americana f. bodegensis differentiation based on morphological data was reflected in the plastid-encoded large subunit of RuBisCO (rbcL), but was not concordant with either the mitochondrial cytochrome c oxidase subunit 1 (COI-5P) or nuclear internal transcribed spacer (ITS) sequence data. We suggest that this discordance is indicative of ongoing hybridization and introgression between populations of C. americana f. americana and C. americana f. bodegensis. In addition, we used a PCR assay with ITS specific primers to amplify multiple ITS variants for collections assignable to C. americana indicating that there is genetic variability within ITS copies most likely due to introgression, crossing over and/or the retention of ancestral variants. PMID:23467004

Hind, Katharine R; Saunders, Gary W

2013-05-01

199

Survivin as a prognostic/predictive marker and molecular target in cancer therapy.  

PubMed

Evasion from apoptotic cell death is reported to be a pivotal mechanism by which tumor cells acquire resistance to therapeutic treatment. Targeting the apoptotic pathways may constitute a promising strategy to counteract therapy resistance and to re-sensitize cancer cells. Expression of survivin, the smallest and structurally unique member of the inhibitor of apoptosis protein (IAP) family, has been shown to be associated with poor clinical outcome, more aggressive clinicopathologic features and resistance to both, conventional chemo and radiation therapy. Moreover, survivin detection in cancer tissue, in circulating tumor cells and in patient's serum has prognostic and predictive relevance and may display a prerequisite for marker based molecular therapies. Indeed, due to its universal over expression in malignant tissue, and its prominent role at disparate networks of cellular division, intracellular signaling, apoptosis and adaption to unfavorable surroundings, survivin has been shown to be a suitable target for a targeted therapy. The applicability of survivindriven strategies in clinical practice is currently under investigation as the first survivin antagonists (small molecule inhibitors, antisense oligonucleotides and immunotherapy) successfully entered phase I/II trials. Taken together, these data provide a rationale for the implementation of both, survivin as a molecular diagnostic tool and survivin targeted therapies, within future clinical practice. PMID:22680927

Rödel, F; Sprenger, T; Kaina, B; Liersch, T; Rödel, C; Fulda, S; Hehlgans, S

2012-01-01

200

Transcriptomic molecular markers for screening human colon cancer in stool and tissue.  

PubMed

There is a need for sensitive and specific diagnostic molecular markers that can be used to monitor early patterns of gene expression in non-invasive exfoliated colonocytes shed in the stool, and in situ in adenoma-carcinoma epithelium of the colon. RNA-based detection methods are more comprehensive than either DNA-, protein- or methylation-based screening methods. By routinely and systematically being able to perform quantitative gene expression studies on these samples using less than ten colon cancer genes selected by the enormous resources of the National Cancer Institute's Cancer Genome Anatomy Project, we were able to monitor changes at various stages in the neoplastic process, allowing for reliable diagnostic screening of colon cancer particularly at the early, pre-malignant stages. Although the expression of some of the genes tested in tissue showed less variability in normal or cancerous patients than in stool, the stool by itself is suitable for screening. Thus, a transcriptomic approach using stool or tissue samples promises to offer more sensitivity and specificity than currently used molecular screening methods for colon cancer. A larger prospective clinical study utilizing stool and tissue samples derived from many control and colon cancer patients, to allow for a statistically valid analysis, is now urgently required to determine the true sensitivity and specificity of the transcriptomic screening approach for this preventable cancer. PMID:17726236

Ahmed, Farid E; Vos, Paul; iJames, Stephanie; Lysle, Donald T; Allison, Ron R; Flake, Gordon; Sinar, Dennis R; Naziri, Wade; Marcuard, Stefan P; Pennington, Rodney

2007-01-01

201

[Genetic polymorphism of flax Linum usitatissimum based on use of molecular cytogenetic markers].  

PubMed

Using a set of approaches based on the use of molecular cytogenetic markers (DAPI/C-banding, estimation of the total area of DAPI-positive regions in prophase nuclei, FISH with 26S and 5S rDNA probes) and the microsatellite (SSR-PCR) assay, we studied genomic polymorphism in 15 flax (Linum usitatissimum L.) varieties from different geographic regions belonging to three directions of selection (oil, fiber, and intermediate flaxes) and in the k-37 x Viking hybrid. All individual chromosomes have been identified in the karyotypes of these varieties on the basis of the patterns of differential DAPI/C-banding and the distribution of 26S and 5S rDNA, and idiograms of the chromosomes have been generated. Unlike the oil flax varieties, the chromosomes in the karyotypes of the fiber flax varieties have, as a rule, pericentromeric and telomeric DAPI-positive bands of smaller size, but contain larger intercalary regions. Two chromosomal rearrangements (chromosome 3 inversions) were discovered in the variety Luna and in the k-37 x Viking hybrid. In both these forms, no colocalization of 26S rDNA and 5S rDNA on the satellite chromosome was detected. The SSR assay with the use of 20 polymorphic pairs of primers revealed 22 polymorphic loci. Based on the SSR data, we analyzed genetic similarity of the flax forms studied and constructed a genetic similarity dendrogram. The genotypes studied here form three clusters. The oil varieties comprise an independent cluster. The genetically related fiber flax varieties Vita and Luna, as well as the landrace Lipinska XIII belonging to the intermediate type, proved to be closer to the oil varieties than the remaining fiber flax varieties. The results of the molecular chromosomal analysis in the fiber and oil flaxes confirm their very close genetic similarity. In spite of this, the combined use of the chromosomal and molecular markers has opened up unique possibilities for describing the genotypes of flax varieties and creating their genetic passports. PMID:21446184

Rachinskaia, O A; Lemesh, V A; Muravenko, O V; Iurkevich, O Iu; Guzenko, E V; Bol'sheva, N L; Bogdanova, M V; Samatadze, T E; Popov, K V; Malyshev, S V; Shostak, N G; Heller, K; Khotyleva, L V; Zelenin, A V

2011-01-01

202

High throughput genome-specific and gene-specific molecular markers for erucic acid genes in Brassica napus (L.) for marker-assisted selection in plant breeding.  

PubMed

A single base change in the Bn-FAE1.1 gene in the A genome and a two-base deletion in the Bn-FAE1.2 gene in the C genome produce the nearly zero content of erucic acid observed in canola. A BAC clone anchoring Bn-FAE1.1 from a B. rapa BAC library and a BAC clone anchoring Bn-FAE1.2 from a B. oleracea BAC library were used in this research. After sequencing the gene flanking regions, it was found that the dissimilarity of the flanking sequences of these two FAE1 homologs facilitated the design of genome-specific primers that could amplify the corresponding genome in allotetraploid B. napus. The two-base deletion in the C genome gene was detected as a sequence-characterized amplified region (SCAR) marker. To increase the throughput, one genome-specific primer was labeled with four fluorescence dyes and combined with 20 different primers to produce PCR products with different fragment sizes. Eventually, a super pool of 80 samples was detected simultaneously. This dramatically reduces the cost of marker detection. The single base change in the Bn-FAE1.1 gene was detected as single nucleotide polymorphic (SNP) marker with an ABI SNaPshot kit. A multiplexing primer set was designed by adding a polyT to the 5' primer end to increase SNP detection throughput through sample pooling. Furthermore, the Bn-FAE1.1 and Bn-FAE1.2 were integrated into the N8 and N13 linkage groups of our previously reported high-density sequence-related amplified polymorphism (SRAP) map, respectively. There were 124 SRAP markers in a N8 bin in which the Bn-FAE1.1 gene-specific SCAR marker was located and 46 SRAP markers in a N13 bin into which the Bn-FAE1.2 SNP marker was integrated. These three kinds of high throughput molecular markers have been successfully implemented in our canola/rapeseed breeding programs. PMID:18633592

Rahman, Mukhlesur; Sun, Zudong; McVetty, Peter B E; Li, Genyi

2008-10-01

203

Diversity of long-chain toxins in Tityus zulianus and Tityus discrepans venoms (Scorpiones, Buthidae): molecular, immunological, and mass spectral analyses.  

PubMed

In Venezuela, stings by Tityus zulianus scorpions produce cardiorespiratory arrest, whereas envenoming by Tityus discrepans involves gastrointestinal/pancreatic complications, suggesting structural and/or functional differences. We sought to compare their toxin repertoires through immunological, molecular, and mass spectral analyses. First, in vivo tests showed that neutralization of T. zulianus venom toxicity by the anti-T. discrepans antivenom was not complete. To compare T. discrepans and T. zulianus long-chain (sodium channel-active) toxins, their most toxic Sephadex G-50 fractions, TdII and TzII, were subjected to acid-urea PAGE, which showed differences in composition. Amplification of toxin-encoding mRNAs using a leader peptide-based oligonucleotide rendered cDNAs representing twelve T. discrepans and two T. zulianus distinct toxin transcripts, including only one shared component, indicating divergence between T. zulianus and T. discrepans 5' region-encoded, toxin signal peptides. A 3'-UTR polymorphism was also noticed among the transcripts encoding shared components Tz1 and Td4. MALDI-TOF MS profiling of TdII and TzII produced species-specific spectra, with seven of the individual masses matching those predicted by cDNA sequencing. Phylogenetic analysis showed that the unique T. zulianus transcript-encoded sequence, Tz2, is structurally related to Tityus serrulatus and Centruroides toxins. Together with previous reports, this work indicates that T. zulianus and T. discrepans toxin repertoires differ structurally and functionally. PMID:16356783

Borges, Adolfo; García, Carmen C; Lugo, Elizabeth; Alfonzo, Marcelo J; Jowers, Michael J; Op den Camp, Huub J M

2006-01-01

204

High molecular weight microtubule-associated proteins from pig brain are immunologically related to human erythrocyte membrane proteins spectrin, ankyrin, proteins 4.1 and 4.2.  

PubMed

The microtubule-associated proteins MAPs 1 and 2 from pig brain have been found to react with antibodies directed against human ankyrin and spectrin, respectively (Bennett and Davis, 1981; Davis and Bennett, 1982). In a complementary approach we have prepared antibodies against MAP1 alpha. MAP1 gamma and MAP2 purified from pig brain and tested their reactivity with human erythrocyte membrane proteins. Anti-MAP1 alpha was shown to react with alpha and beta-spectrin and with protein 4.1; anti-MAP1 gamma reacted with alpha-spectrin and ankyrin and with a 60 K peptide which copurified with human spectrin. Finally anti-MAP2 was specific for beta-spectrin and protein 4.2. The biological function of protein 4.2 is still unknown but details on the interactions between ankyrin, spectrin and protein 4.1 and their role in mediating the linkage of oligomeric actin on the erythrocyte membrane are well documented. The present results, which demonstrate extended immunological analogies between pig brain high molecular weight MAPs and human erythrocyte membrane proteins, may reflect the presence, in the two families of proteins, of similar functionally important epitopes. PMID:3159450

Hill, A M; Cassoly, R; Chetrite, G; Pantaloni, D

1985-01-01

205

Ribosomal DNA as molecular markers and their applications in the identification of fish parasites (Platyhelminthes: Monogenea) from India  

PubMed Central

The development of molecular techniques for taxonomic analysis of monogenean parasites has led to a great increase for proper identification and factualness. These molecular techniques, in particular the use of molecular markers, have been used to identify and validate the monogenean parasites. Although, improvements in marker detection systems particularly of elements of rDNA like 18S, ITS and 28S used in monogeneans parasites have enabled great advances to be made in recent years in India. However, the molecular sequence analysis and phylogenetic relationships among the parasitic helminthes is unconventional in India. Many workers have been always questioned the validity of Indian species of monogeneans and emphasized the need to ascertain the status of species from Indian fish. Here we would like to provide additional resolution for the interpretation of use of molecular markers in study of monogeneans in India. This review provides an overview of current stage of studies in India that have been used in applying molecular techniques to monogenean.

Chaudhary, Anshu; Verma, Chandni; Singh, Hridaya Shanker

2014-01-01

206

[Molecular and immunological approach to hematological disease: detection and analysis of intracellular modified nucleosides by flow cytometry].  

PubMed

Modified nucleosides are components of ribosomal RNA (rRNA), transfer RNA (tRNA) and messenger RNA (mRNA). 1-methyladenosine and pseudouridine are members of those modified nucleosides. The urinary concentration of 1-methyladenosine and pseudouridine of cancer patients are higher than that of healthy controls, and those compounds were reduced after effective chemotherapy. Thus those compounds might be expected to use as tumor markers. In this study cellular origin of 1-methyladenosine and pseudouridine were analysed about two tumor cell lines (HUT-102, THP-1), peripheral blood lymphocytes (PBL) from healthy adult and PBL under the phytohemagglutinin stimulation, by flow cytometric analysis and immunofluorescent staining of cellular RNA using monoclonal antibodies specific for 1-methyladenosine (AMA) and pseudouridine (APU). Both 1-methyladenosine and pseudouridine were detected in more than 90% of tumor cells above the thresholds of flow cytometric detection (Spectrum III, Ortho). The PBL under the PHA stimulation also tended to take the same way of the tumor cell lines, whereas few of the PBL contained 1-methyladenosine above the thresholds. According to the DNA analysis of those cell lines, high contents of the modified nucleosides in the cell might follow DNA synthesis, this leads to one reason for high levels of the urinary excretion of the modified nucleosides in cancer patient. PMID:2402080

Hoshino, A; Honda, I; Ishimori, A; Itoh, K; Mizugaki, M; Nose, M

1990-07-01

207

A panel of tumor markers, calreticulin, annexin A2, and annexin A3 in upper tract urothelial carcinoma identified by proteomic and immunological analysis  

PubMed Central

Background Upper tract urothelial carcinoma (UTUC) is a tumor with sizable metastases and local recurrence. It has a worse prognosis than bladder cancer. This study was designed to investigate the urinary potential tumor markers of UTUC. Methods Between January 2008 and January 2009, urine was sampled from 13 patients with UTUC and 20 healthy adults. The current study identified biomarkers for UTUC using non-fixed volume stepwise weak anion exchange chromatography for fractionation of urine protein prior to two-dimensional gel electrophoresis. Results Fifty five differential proteins have been determined by comparing with the 2-DE maps of the urine of UTUC patients and those of healthy people. Western blotting analysis and immunohistochemistry of tumor tissues and normal tissues from patients with UTUC were carried out to further verify five possible UTUC biomarkers, including zinc-alpha-2-glycoprotein, calreticulin, annexin A2, annexin A3 and haptoglobin. The data of western blot and immunohistochemical analysis are consistent with the 2-DE data. Combined the experimental data in the urine and in tumor tissues collected from patients with UTUC, the crucial over-expressed proteins are calreticulin, annexin A2, and annexin A3. Conclusions Calreticulin, annexin A2, and annexin A3 are very likely a panel of biomarkers with potential value for UTUC diagnosis.

2014-01-01

208

Molecular markers predictive of the capacity of expanded human articular chondrocytes to form stable cartilage in vivo  

Microsoft Academic Search

Objective. To establish a model and associated molecular markers for monitoring the capacity of in vitro-expanded chondrocytes to generate stable carti- lage in vivo. Methods. Adult human articular chondrocytes (AHAC) were prepared by collagenase digestion of samples obtained postmortem and were expanded in monolayer. Upon passaging, aliquots of chondrocyte suspensions were either injected intramuscularly into nude mice, cultured in agarose,

Francesco Dell'Accio; Cosimo De Bari; Frank P. Luyten

2001-01-01

209

Molecular Markers for Detection and Differentiation of Plasmodium falciparum and Plasmodium vivax in Human Blood Samples by Pyrosequencing  

PubMed Central

PCR amplification coupled with pyrosequencing was used to measure molecular markers that could be used to detect and differentiate Plasmodium falciparum and Plasmodium vivax in human blood samples. The detection rates were in agreement with the results of Giemsa-stained film microscopy, which is the current gold standard for detection. This method provides an exciting alternative for malaria diagnosis.

Lulitanond, Viraphong; Intapan, Pewpan M.; Tantrawatpan, Chairat; Sankuntaw, Nipaporn; Sanpool, Oranuch; Janwan, Penchom

2012-01-01

210

Prevalence, Morphologic Features and Proliferation Indices of Breast Carcinoma Molecular Classes Using Immunohistochemical Surrogate Markers  

PubMed Central

There is dearth of studies that provide a practical working formulation of breast cancer gene expression analysis for the surgical pathologist. ER, PR, HER2 were used as surrogate markers to classify 205 breast carcinomas into molecular classes. Ki-67 labeling index was calculated using an image analysis system. The data was analyzed for molecular class prevalence, and inter-relationships amongst morphologic parameters, Ki-67 index, and molecular classes. Of the 205 tumors, 113 (55%) were classified as luminal A (strong ER+, HER2 negative), 34 (17%) as luminal B (weak to moderate ER+, HER2 negative), 32 (15%) as triple negative (negative for ER/PR and HER2), 8 (4%) as ERBB2 (negative for ER/PR but HER2+), 10 (5%) as luminal A-HER2 hybrid (strong ER+ and HER2+), and 8 (4%) as luminal B-HER2 hybrid (weak to moderate ER+ and HER2+). The average Ki-67 index was lowest in luminal A (15.8%), intermediate for ERBB2 (27.8%) and highest for triple negative tumors (>50%). Multivariate logistic regression analyses found the following associations: ERBB2 tumors with apocrine differentiation (p=0.0031); Triple negative tumors with high Ki-67 index (p<0.0001) and CK5 positivity (p<0.0001); HER2 negative-low receptor positive tumors (luminal B) with increased lymph node involvement (p=0.0141). The immunohistologic criteria were validated on a different set of 359 cases treated with neoadjuvant chemotherapy, which showed a pathologic complete response predominantly in ERBB2 and triple negative tumors. Immunohistochemistry is a reliable surrogate tool to classify breast carcinoma according to the gene expression profile classification.

Bhargava, Rohit; Striebel, Joan; Beriwal, Sushil; Flickinger, John C.; Onisko, Agnieszka; Ahrendt, Gretchen; Dabbs, David J.

2009-01-01

211

Laboratory studies of oxidation of primary emissions: Oxidation of organic molecular markers and secondary organic aerosol production  

NASA Astrophysics Data System (ADS)

Particulate matter (PM) is solid particles and liquid droplets of complex composition suspended in the atmosphere. In 1997, the National Ambient Air Quality Standards (NAAQS) for PM was modified to include new standards for fine particulate (particles smaller than 2.5mum, PM2.5) because of their association with adverse health effects, mortality and visibility reduction. Fine PM may also have large impacts on the global climate. Chemically, fine particulate is a complex mixture of organic and inorganic material, from both natural and anthropogenic sources. A large fraction of PM2.5 is organic. The first objective was to investigate heterogeneous oxidation of condensed-phase molecular markers for two major organic source categories, meat-cooking emissions and motor vehicle exhaust. Effective reaction rate constants of key molecular markers were measured over a range of atmospherically relevant experimental conditions, including a range of concentrations and relative humidities, and with SOA condensed on the particles. Aerosolized meat grease was reacted with ozone to investigate the oxidation of molecular markers for meat-cooking emissions. Aerosolized motor oil, which is chemically similar to vehicle exhaust aerosol and contains the molecular markers used in source apportionment, was reacted with the hydroxyl radical (OH) to investigate oxidation of motor vehicle molecular markers. All molecular markers of interest - oleic acid, palmitoleic acid, and cholesterol for meat-cooking emissions, and hopanes and steranes for vehicle exhaust - reacted at rates that are significant for time scales on the order of days assuming typical summertime oxidant concentrations. Experimental conditions influenced the reaction rate constants. For both systems, experiments conducted at high relative humidity (RH) had smaller reaction rate constants than those at low RH. SOA coating slowed the reaction rate constants for meat-cooking markers, but had no effect on the oxidation of vehicle markers. Aerosol composition is a key influence on reaction rate constants, perhaps more significant than external influences. Alkenoic acid concentrations in the meat grease particles appear to influence cholesterol oxidation rates. Also, the reaction rate constants for new motor oil were faster than those of the more viscous used motor oil. The measured reaction rate constants were used to oxidize source profiles that were subsequently run in the Chemical Mass Balance (CMB) model. Oxidizing the molecular markers in the meat-cooking profile led to unrealistically high meat-cooking aerosol contributions to the total organic carbon (OC), often more than 100%. This suggests that there is either unaccounted for sources of meat-cooking molecular markers in the ambient samples, or there is some property of atmospheric aerosols that significantly inhibits reaction that was not captured in this study. Oxidation of motor vehicle profiles led to both higher estimates of total vehicle OC and a quadrupling of gasoline OC, while the diesel contribution changed very little. The increase in gasoline OC changes gasoline vehicle emissions from a relatively minor source to a major one. Thus, oxidation of molecular markers can have a significant impact on receptor model predictions. The second objective was to investigate SOA formation from the photo-oxidation of whole diesel exhaust. Diluted exhaust from a diesel engine was photo-oxidized in a smog chamber to investigate SOA production. Photochemical oxidation rapidly produced significant SOA, almost doubling the organic aerosol contribution of primary emissions after several hours of processing. Less than 10% of the SOA mass could be explained using a SOA model and the measured oxidation of known precursors, such as light aromatics. However, the ultimate yield of SOA is uncertain because it is sensitive to treatment of particle and vapor losses to the chamber walls. Aerosol Mass Spectrometer (AMS) mass spectra reveal that the organic aerosol becomes progressively more oxidized throughout the experiments. The data provide str

Weitkamp, Emily A.

212

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

213

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

214

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

215

Distinct immunologic effects of different intravenous iron preparations on monocytes  

PubMed Central

Background Iron deficiency contributes to anaemia in patients with chronic kidney disease. I.v. iron is therefore widely used for anaemia treatment, although it may induce oxidative stress and activate monocytes. Different i.v. iron preparations are available, but interestingly their substance-specific immunologic effects are poorly studied. Methods We analysed the effect of iron sucrose, ferric carboxymaltose, iron isomaltoside 1000, low-molecular-weight iron dextran and ferumoxytol on classical, intermediate and nonclassical monocyte biology. We therefore stimulated in vitro mature monocytes and haematopoietic CD34+ stem cells during their differentiation into monocytes with different concentrations (0.133, 0.266, 0.533 mg/mL) of i.v. iron preparations. Alterations of monocyte subset distribution, expression of surface markers (CD86, CCR5, CX3CR1), as well as production of pro-inflammatory cytokines (TNF-?, IL-1?) and reactive oxygen species were measured using flow cytometry. Additionally, we analysed phagocytosis and antigen presentation capacity. Results We found specific immunologic effects after stimulation with iron sucrose which were not induced by the other iron preparations. Iron sucrose activated monocyte subsets leading to significantly increased CD86 expression. Simultaneously CD16 and CX3CR1 expression and monocytic phagocytosis capacity were decreased. Additionally, differentiation of monocytes from haematopoietic CD34+ stem cells was almost completely abolished after stimulation with iron sucrose. Conclusions Our findings demonstrate that specific immunologic effects of distinct i.v. iron preparations exist. The clinical relevance of these findings requires further investigation.

Fell, Lisa H.; Zawada, Adam M.; Rogacev, Kyrill S.; Seiler, Sarah; Fliser, Danilo; Heine, Gunnar H.

2014-01-01

216

Analysis of Segregation Distortion of Molecular Markers in F 2 Population of Rice  

Microsoft Academic Search

A genetic linkage map comprising 148 SSR markers loci was constructed using an F2 population consisting of 90 lines derived from a sub-specific cross between a japonica variety Nipponbare and an indica variety Guangluai-4. The F2 population showed high significantly distorted segregations. Among these SSR markers, 49 markers (33.11%) showed the genetics distortion(P<0.05). Of them, 36 markers deviated toward male

Bing ZHAO; Qi-Ming DENG; Qi-Jun ZHANG; Jie-Qin LI; Shao-Ping YE; Yong-Shu LIANG; Yong PENG; Ping LI

2006-01-01

217

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

218

Swine in Immunologic Research.  

National Technical Information Service (NTIS)

Swine are uniquely suited for certain types of immunologic investigations. In particular, study of the process of immunologic maturation of baby pigs has been revealing. Pigs have little serum gamma-globulin at birth. They normally acquire large quantitie...

D. Segre

1965-01-01

219

Poor weaning transition average daily gain in pigs is not correlated with pathological or immunological markers of enteric disease during a porcine reproductive and respiratory syndrome virus outbreak.  

PubMed

Previous research suggests that enteric disease and poor gut health interact to decrease pig performance. Our objective was to determine if light birth weight pigs or those from the bottom 10th percentile of transition ADG (tADG) have a higher incidence of pathogen presence or enteric lesions than heavier or faster-growing contemporaries. A total of 1,500 pigs were weighed at birth and divided into 5 birth weight (BRW) categories: <1, 1 to 1.25, 1.26 to 1.5, 1.51 to 1.75, and >1.76 kg. At weaning, 1,054 random pigs were moved to a commercial wean-to-finish barn. Pigs were weighed individually at 0 and 3 wk postweaning. Transition ADG was calculated as the ADG between wk 0 and 3 postweaning. One pig from each of the 10th, 30th, and 70th percentiles of tADG was used to create 1 set of 3 pigs with the same litter size and from the same parity sow. Forty pigs from each of the 3 tADG percentiles were matched for sex, litter size, and sow parity but not BRW to create 20 matched sets of 60 pigs. This allowed for the main effects of BRW and tADG to be studied as a 5 × 3 factorial design. At 3 and 22 wk postweaning, pigs were euthanized for organ system tissue evaluation. Lung, lymph node, and digesta were analyzed for presence of pathogens and for severity of microscopic lesions (0 = not present, 1 = present, with slight erosion, 2 = present, with moderate erosion, and 3 = present and severe erosion). Data were analyzed using PROC GENMOD and GLIMMIX, where pig served as the experimental unit. The fixed effects were BRW and tADG and the random effects were pen and set. There were no BRW × tADG interactions (P = 0.16). There was no correlation (P = 0.12) between tADG and pathogen presence at either 3 or 22 wk postweaning. Incidence and severity of microscopic lesions in the large intestine at 3 wk postweaning decreased linearly with increasing tADG (P = 0.01). Lesion incidence and severity were also affected (P < 0.04) by tADG at 22 wk postweaning, with greater stomach incidence in the 10th percentile. Birth weight affected (P = 0.02) haemolytic Escherichia coli and Salmonella spp. B (includes Salmonella typhimurium) isolation at 3 wk postweaning as well as Brachyspira spp. isolation at 22 wk postweaning (P = 0.05) but in mixed directions. There were no effects (P = 0.21) of BRW or tADG on serum or ileum mucosa immune markers. In summary, it is apparent from this research that neither BRW nor tADG are likely causes of pathogen or lesion incidence. PMID:24867935

Jones, C K; Madson, D M; Main, R G; Gabler, N K; Patience, J F

2014-06-01

220

Comparative analyses of mitochondrial and nuclear genetic markers for the molecular identification of Rhipicephalus spp.  

PubMed

The genus Rhipicephalus (Acari: Ixodidae) comprises a large number of vectors of pathogens of substantial medical and veterinary concern; however, species identification based solely on morphological features is often challenging. In the present study, genetic distance within selected Rhipicephalus species (i.e., Rhipicephalus bursa, Rhipicephalus guilhoni, Rhipicephalus muhsamae, Rhipicephalus sanguineus sensu lato and Rhipicephalus turanicus), were investigated based on molecular and phylogenetic analyses of fragments of the mitochondrial 16S, 12S and cytochrome c oxidase subunit 1 (cox1) genes, as well as of the whole sequences of the ribosomal internal transcribed spacer-2 (ITS-2) region. Mean values of inter-specific genetic distance (e.g., up to 12.6%, 11.1% and 15.2%), as well as of intra-specific genetic distance (e.g., 0.9%, 0.9% and 1%), calculated using the Kimura-2 parameter substitution model with uniform rates among sites for 16S, 12S and cox1 genes, respectively, confirmed the differentiation of the rhipicephaline species herein examined. The molecular identification was also supported by the distinct separation of species-specific clades inferred from the phylogenetic analyses of all mitochondrial sequences. Conversely, little interspecific divergence was detected amongst ribosomal ITS-2 sequences (i.e., up to 2.8%) for species belonging to the R. sanguineus complex, which resulted in the ambiguous placement of selected R. sanguineus s.l. and R. turanicus sequences in the corresponding phylogenetic tree. Results from this study confirm the suitability of mtDNA markers for the reliable identification of ticks within the Rhipicephalus genus and provide a framework for future studies of taxonomy, speciation history and evolution of this group of ticks. PMID:24103336

Latrofa, Maria S; Dantas-Torres, Filipe; Annoscia, Giada; Cantacessi, Cinzia; Otranto, Domenico

2013-12-01

221

New STS molecular markers for assessment of genetic diversity and DNA fingerprinting in hop (Humulus lupulus L.).  

PubMed

Molecular markers have been increasingly used in genetic studies of crop species for their applicability in breeding programs. In this work, we report on the development of new sequence-tagged site (STS) markers based on sequence information from several identified hop (Humulus lupulus L.) genes. We demonstrate the usefulness of these STS markers and compare them to SSRs for identifying hop genotypes and estimating genetic diversity in a collection of 68 hop cultivars from around the world. We found 3 individual gene variants (A, B, C) of the chs_H1 gene in this collection. The most frequent gene variant, B (AJ304877), was not detected in Mt. Hood, Glacier, and Horizon (US) cultivars. Gene variant A came from an American germplasm through wild hops. We found length polymorphism in intron 1 of the chs2 gene, and 4 different amplified markers were detected in PCRs. The chs3 gene was found in only one third of the cultivars. None of the variants of the studied CHS genes were found in Humulus japonicus. We detected 5 major gene variants of DNA-binding protein in the collection of H. lupulus cultivars and 2 others in H. japonicus. We also found 3 individual gene variants of an endochitinase gene. The distribution of gene variants did not correlate with any resistance. We proved that developed STS markers can be successfully used for the analysis of genetic diversity and can substitute and supplement SSR markers in hop. PMID:17546067

Patzak, Josef; Vrba, Lukás; Matousek, Jaroslav

2007-01-01

222

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.

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

2014-01-01

223

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.

Diaz-Cano, Salvador J.

2012-01-01

224

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

225

The androgen receptor as a surrogate marker for molecular apocrine breast cancer subtyping.  

PubMed

The Androgen Receptor (AR) is a potential prognostic marker and therapeutic target in breast cancer. We evaluated AR protein expression in high-risk breast cancer treated in the adjuvant setting. Tumors were subtyped into luminal (ER+/PgR±/AR±), molecular apocrine (MAC, [ER-/PgR-/AR+]) and hormone receptor negative carcinomas (HR-negative, [ER-/PgR-/AR-]). Subtyping was evaluated with respect to prognosis and to taxane therapy. High histologic grade (p < 0.001) and increased proliferation (p = 0.001) more often appeared in MAC and HR-negative than in luminal tumors. Patients with MAC had outcome comparable to the luminal group, while patients with HR-negative disease had increased risk for relapse and death. MAC outcome was favorable upon taxane-containing treatment; this remained significant upon multivariate analysis for overall survival (HR 0.31, 95%CI 0.13-0.74, interaction p = 0.035) and as a trend for time to relapse (p = 0.15). In conclusion, AR-related subtyping of breast cancer may be prognostic and serve for selecting optimal treatment combinations. PMID:24703723

Lakis, Sotiris; Kotoula, Vassiliki; Eleftheraki, Anastasia G; Batistatou, Anna; Bobos, Mattheos; Koletsa, Triantafyllia; Timotheadou, Eleni; Chrisafi, Sofia; Pentheroudakis, George; Koutras, Angelos; Zagouri, Flora; Linardou, Helena; Fountzilas, George

2014-06-01

226

Identification of molecular markers for DNA barcoding in the Aphidiinae (Hym. Braconidae).  

PubMed

Reliable identification of Aphidiinae species (Braconidae) is a prerequisite for conducting studies on aphid-parasitoid interactions at the community level. However, morphological identification of Aphidiinae species remains problematic even for specialists and is almost impossible with larval stages. Here, we compared the efficiency of two molecular markers [mitochondrial cytochrome c oxydase I (COI) and nuclear long wavelength rhodopsin (LWRh)] that could be used to accurately identify about 50 species of Aphidiinae that commonly occur in aphid-parasitoid networks in northwestern Europe. We first identified species on a morphological basis and then assessed the consistency of genetic and morphological data. Probably because of mitochondrial introgression, Aphidius ervi and A. microlophii were indistinguishable on the basis of their COI sequences, whereas LWRh sequences discriminated these species. Conversely, because of its lower variability, LWRh failed to discriminate two pairs of species (Aphidius aquilus, Aphidius salicis, Lysiphlebus confusus and Lysiphlebus fabarum). Our study showed that no unique locus but a combination of two genes should be used to accurately identify members of Aphidiinae. PMID:22004100

Derocles, Stephane A P; LE Ralec, Anne; Plantegenest, Manuel; Chaubet, Bernard; Cruaud, Corinne; Cruaud, Astrid; Rasplus, Jean-Yves

2012-03-01

227

Conservation of wild animals by assisted reproduction and molecular marker technology.  

PubMed

Wild animals are an integral component of the ecosystem. Their decimation due to abrupt natural calamities or due to gradual human intervention would be disastrous to the ecosystem and would alter the balance in nature between various biotic components. Such an imbalance could have an adverse effect on the ecosystem. Therefore, there is an urgent need to put an end to the ever increasing list of endangered species by undertaking both in situ and ex situ conservation using tools of modern biology, to ascertain the degree of genetic variation and reproductive competence in these animals. This review highlights the development and use of molecular markers such as microsatellites, minisatellites, mitochondrial control region, cytochrome b and MHC loci to assess the genetic variation in various Indian wild animals such as the lion, tiger, leopard and deer. The review also presents data on the semen profile of the big cats of India. Reproductive technologies such as cryopreservation of semen and artificial insemination in big cats are also highlighted. PMID:15255374

Shivaji, S; Kholkute, S D; Verma, S K; Gaur, Ajay; Umapathy, G; Singh, Anju; Sontakke, Sadanand; Shailaja, K; Reddy, Anuradha; Monika, S; Sivaram, V; Jyotsna, B; Bala, Satyare; Ahmed, M Shakeel; Bala, Aruna; Chandrashekar, B V N; Gupta, Sandeep; Prakash, Surya; Singh, Lalji

2003-07-01

228

Molecular characterization of sour orange (Citrus aurantium) accessions and their relatives using SSR and SRAP markers.  

PubMed

Citrus production with its many varieties is of importance since it provides economically important products for Turkish exports. Sour orange is a rootstock commonly used for propagating the different scion varieties. Knowledge of the genetic diversity of the rootstock accessions would be useful in order to improve citrus breeding programs. We studied genetic relationships and diversity of 51 accessions of sour orange (Citrus aurantium) and their relatives using SSR (simple sequence repeat) and SRAP (sequence-related amplified polymorphism) molecular markers. Twenty-one SRAP primer combinations were tested on these accessions and relatives, producing 167 polymorphic fragments, with a mean of 8.0 and a mean polymorphism information content value of 0.47. Seventeen SSR primers also produced 30 polymorphic fragments, with a mean of 1.4 per primer and a mean polymorphism information content value of 0.39. The unweighted pair-group method with arithmetic average analysis using combined SSR and SRAP data showed a similarity range from 0.71 to 1.00 among the accessions. In the cluster analysis, sour orange relatives were indicated as a separate group from sour orange. 'Macrophylla' and 'Mexican lime' were the accessions most distinct (0.71) from the others. We conclude that genetic diversity in these sour orange accessions is lower and some of them were identical. PMID:23079821

Polat, I; Kacar, Y A; Yesiloglu, T; Uzun, A; Tuzcu, O; Gulsen, O; Incesu, M; Kafa, G; Turgutoglu, E; Anil, S

2012-01-01

229

Development of genomic SSR markers and molecular characterization of magnaporthe oryzae isolates from wheat in Brazil.  

PubMed

Magnaporthe oryzae, the causal agent of wheat blast, was characterized on a molecular level with 38 newly isolated genomic SSR loci. Among the 31 wheat isolates analyzed, 15 polymorphic loci were detected, with an average of 1.7 alleles per locus, 28.9% of them being highly or reasonably informative. The number of polymorphic loci was higher in isolates from Londrina in the Brazilian state of Paraná and Coromandel in Minas Gerais compared with Goiânia in Goiás and São Borja in Rio Grande do Sul. The rice isolate was clearly different from the wheat isolates, and the size difference in polymorphic SSR loci between one isolate from wheat and one isolate from rice was associated with the number of repeats. Some isolates collected from different states and in different years demonstrated similarities of 100%. The markers developed here are useful for the genetic analysis of M. oryzae isolated from wheat, and isolates representing the variability detected in the field can be used to search for better wheat blast resistance. PMID:24271825

Pereira, Jorge Fernando; Consoli, Luciano; de Souza Bombonatto, Estevon Alexandre; Bonato, Ana Lídia Variani; Maciel, João Leodato Nunes

2014-02-01

230

Analysis of genetic variability and population structure of the endemic medicinal Limonium sinense using molecular markers.  

PubMed

Limonium sinense is an endemic medicinal herb used to treat fever, hemorrhage and other disorders. In the present study, population genetic diversity was elucidated using random amplified polymorphic DNA (RAPD), inter simple sequence repeat (ISSR) and amplified fragment length polymorphism (AFLP) primers. Percentage of polymorphic bands, Nei's gene diversity and Shannon's information index revealed a high level of genetic diversity at species level. The analysis of molecular variance revealed that 69.88% (RAPD), 71.19% (ISSR) and 70.97% (AFLP) of variability were partitioned among individuals within populations, which indicated the coherent trend by Gst (0.3849/0.3577/0.3670). Gene flow number (Nm) was 0.581/0.618/0.612, which indicated that there was a limited gene exchange between populations. The UPGMA clustering results showed that the genetic distance had no significant correlation with geographic distance. These results indicate that these markers were reliable tools for the differentiation and determination of the genetic diversity among the populations of L. sinense and the conservation of existing natural population is necessary. PMID:23506829

Ding, Ge; Zhang, Daizhen; Yu, Yanqiu; Zhao, Lingling; Zhang, Beibei

2013-05-15

231

Efficient Molecular Marker Design Using the MaizeGDB Mo17 SNPs and Indels Track  

PubMed Central

Positional cloning in maize (Zea mays) requires development of markers in the region of interest. We found that primers designed to amplify annotated insertion–deletion polymorphisms of seven base pairs or greater between B73 and Mo17 produce polymorphic markers at a 97% frequency with 49% of the products showing co-dominant fragment length polymorphisms. When the same polymorphisms are used to develop markers for B73 and W22 or Mo17 and W22 mapping populations, 22% and 31% of markers are co-dominant, respectively. There are 38,223 Indel polymorphisms that can be converted to markers providing high-density coverage throughout the maize genome. This strategy significantly increases the efficiency of marker development for fine-mapping in maize.

Settles, A. Mark; Bagadion, Alyssa M.; Bai, Fang; Zhang, Junya; Barron, Brady; Leach, Kristen; Mudunkothge, Janaki S.; Hoffner, Cassandra; Bihmidine, Saadia; Finefield, Erin; Hibbard, Jaime; Dieter, Emily; Malidelis, I. Alex; Gustin, Jeffery L.; Karoblyte, Vita; Tseung, Chi-Wah; Braun, David M.

2014-01-01

232

Analysis of segregation distortion of molecular markers in F2 population of rice.  

PubMed

A genetic linkage map comprising 148 SSR markers loci was constructed using an F2 population consisting of 90 lines derived from a sub-specific cross between a japonica variety Nipponbare and an indica variety Guangluai-4. The F2 population showed high significantly distorted segregations. Among these SSR markers, 49 markers(33.11%) showed the genetics distortion(P<0.05). Of them, 36 markers deviated toward male parent indica GuangLuAi-4 and 13 markers toward heterozygote, but none toward the female parent Nipponbare. It was found that the segregation distortion might be caused by gametophyte and zygote. Since most gametophyte loci and sterility loci were mapped in segregation distortion regions, it indicated that the segregation distortion may be caused by these gametophyte loci and sterility loci. Finally, this research also analyzed the skewed segregation of some markers, which had not been mapped on chromosome. PMID:16722340

Zhao, Bing; Deng, Qi-Ming; Zhang, Qi-Jun; Li, Jie-Qin; Ye, Shao-Ping; Liang, Yong-Shu; Peng, Yong; Li, Ping

2006-05-01

233

Inheritance of citrus nematode resistance and its linkage with molecular markers  

Microsoft Academic Search

Eleven RAPD markers linked to a gene region conferring resistance to citrus nematodes in an intergen-eric backcross family\\u000a were identified. Two sequence- characterized amplified region markers linked to a citrus tristeza virus resistance gene and\\u000a one selected resistance gene candidate marker were evaluated for their association with citrus nematode resistance. A nematode-susceptible\\u000a citrus hybrid, LB6-2 [Clementine mandarin (Citrus reticulata)?Hamlin orange

P. Ling; L. W. Duncan; Z. Deng; D. Dunn; X. Hu; S. Huang; F. G. Gmitter Jr

2000-01-01

234

Application of next-generation sequencing for rapid marker development in molecular plant breeding: a case study on anthracnose disease resistance in Lupinus angustifolius L.  

PubMed Central

Background In the last 30?years, a number of DNA fingerprinting methods such as RFLP, RAPD, AFLP, SSR, DArT, have been extensively used in marker development for molecular plant breeding. However, it remains a daunting task to identify highly polymorphic and closely linked molecular markers for a target trait for molecular marker-assisted selection. The next-generation sequencing (NGS) technology is far more powerful than any existing generic DNA fingerprinting methods in generating DNA markers. In this study, we employed a grain legume crop Lupinus angustifolius (lupin) as a test case, and examined the utility of an NGS-based method of RAD (restriction-site associated DNA) sequencing as DNA fingerprinting for rapid, cost-effective marker development tagging a disease resistance gene for molecular breeding. Results Twenty informative plants from a cross of RxS (disease resistant x susceptible) in lupin were subjected to RAD single-end sequencing by multiplex identifiers. The entire RAD sequencing products were resolved in two lanes of the 16-lanes per run sequencing platform Solexa HiSeq2000. A total of 185 million raw reads, approximately 17 Gb of sequencing data, were collected. Sequence comparison among the 20 test plants discovered 8207 SNP markers. Filtration of DNA sequencing data with marker identification parameters resulted in the discovery of 38 molecular markers linked to the disease resistance gene Lanr1. Five randomly selected markers were converted into cost-effective, simple PCR-based markers. Linkage analysis using marker genotyping data and disease resistance phenotyping data on a F8 population consisting of 186 individual plants confirmed that all these five markers were linked to the R gene. Two of these newly developed sequence-specific PCR markers, AnSeq3 and AnSeq4, flanked the target R gene at a genetic distance of 0.9 centiMorgan (cM), and are now replacing the markers previously developed by a traditional DNA fingerprinting method for marker-assisted selection in the Australian national lupin breeding program. Conclusions We demonstrated that more than 30 molecular markers linked to a target gene of agronomic trait of interest can be identified from a small portion (1/8) of one sequencing run on HiSeq2000 by applying NGS based RAD sequencing in marker development. The markers developed by the strategy described in this study are all co-dominant SNP markers, which can readily be converted into high throughput multiplex format or low-cost, simple PCR-based markers desirable for large scale marker implementation in plant breeding programs. The high density and closely linked molecular markers associated with a target trait help to overcome a major bottleneck for implementation of molecular markers on a wide range of germplasm in breeding programs. We conclude that application of NGS based RAD sequencing as DNA fingerprinting is a very rapid and cost-effective strategy for marker development in molecular plant breeding. The strategy does not require any prior genome knowledge or molecular information for the species under investigation, and it is applicable to other plant species.

2012-01-01

235

Molecular diversity and relationships among Cymbidium goeringii cultivars based on inter-simple sequence repeat (ISSR) markers  

Microsoft Academic Search

Spring orchid (Cymbidium goeringii) is a popular flowering plant species. There have been few molecular studies of the genetic diversity and conservation genetics\\u000a on this species. An assessment of the level of genetic diversity in cultivated spring orchid would facilitate development\\u000a of the future germplasm conservation for cultivar improvement. In the present study, DNA markers of intersimple sequence repeats\\u000a (ISSR)

Hui-Zhong Wang; Zhen-Xing Wu; Jiang-Jie Lu; Nong-Nong Shi; Yan Zhao; Zhi-Tao Zhang; Jun-Jun Liu

2009-01-01

236

Genetic relations among basil taxa ( Ocimum L.) based on molecular markers, nuclear DNA content, and chromosome number  

Microsoft Academic Search

Twenty-eight basil accessions including six Ocimum species and six botanical varieties or cultivars of O. basilicum were studied using molecular markers, nuclear DNA content, and chromosome counting. This is the first study reporting the\\u000a nuclear DNA content in the genus Ocimum. The results supported the existence of more infrageneric groups within the genus. The section Ocimum was further divided into

Klaudija Carovi?-Stanko; Zlatko Liber; Višnja Besendorfer; Branka Javornik; Borut Bohanec; Ivan Kolak; Zlatko Satovic

2010-01-01

237

Microsatellites and RFLP probes from maize are efficient sources of molecular markers for the biomass energy crop Miscanthus  

Microsoft Academic Search

A survey of Gramineae markers was carried out with the aim of developing cost-effective methods for the molecular analysis\\u000a of Miscanthus species. Ten out of twenty Gramineae RFLP probes from ”anchor” sets hybridized well to Miscanthus DNA while all 15 maize probes tested cross-hybridized successfully, showing similar patterns in both species. Cross-taxa\\u000a amplification of maize microsatellite primers was then tested.

P. Hernández; G. Dorado; D. A. Laurie; A. Martín; J. W. Snape

2001-01-01

238

Development of public immortal mapping populations, molecular markers and linkage maps for rapid cycling Brassica rapa and B. oleracea  

Microsoft Academic Search

Publicly available genomic tools help researchers integrate information and make new discoveries. In this paper, we describe\\u000a the development of immortal mapping populations of rapid cycling, self-compatible lines, molecular markers, and linkage maps\\u000a for Brassica rapa and B. oleracea and make the data and germplasm available to the Brassica research community. The B. rapa population consists of 160 recombinant inbred

Federico Luis Iniguez-Luy; Lewis Lukens; Mark W. Farnham; Richard M. Amasino; Thomas C. Osborn

2009-01-01

239

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

240

Evidence for tetrasomic inheritance in a tetraploid Solanum commersonii (+) S. tuberosum somatic hybrid through the use of molecular markers  

Microsoft Academic Search

In order to assess the potential for interspecific recombination between the cultivated Solanum tuberosum (tbr) and the sexually isolated wild species Solanum commersonii (cmm), genetic analysis of a F2 progeny obtained by selfing one tetraploid cmm (+) tbr somatic hybrid was performed through molecular markers. For this purpose,\\u000a the extent of disomic and\\/or tetrasomic inheritance of species-specific RAPD and AFLP

A. Barone; J. Li; A. Sebastiano; T. Cardi; L. Frusciante

2002-01-01

241

Cryptic Diversity within the Major Trypanosomiasis Vector Glossina fuscipes Revealed by Molecular Markers  

PubMed Central

Background The tsetse fly Glossina fuscipes s.l. is responsible for the transmission of approximately 90% of cases of human African trypanosomiasis (HAT) or sleeping sickness. Three G. fuscipes subspecies have been described, primarily based upon subtle differences in the morphology of their genitalia. Here we describe a study conducted across the range of this important vector to determine whether molecular evidence generated from nuclear DNA (microsatellites and gene sequence information), mitochondrial DNA and symbiont DNA support the existence of these taxa as discrete taxonomic units. Principal Findings The nuclear ribosomal Internal transcribed spacer 1 (ITS1) provided support for the three subspecies. However nuclear and mitochondrial sequence data did not support the monophyly of the morphological subspecies G. f. fuscipes or G. f. quanzensis. Instead, the most strongly supported monophyletic group was comprised of flies sampled from Ethiopia. Maternally inherited loci (mtDNA and symbiont) also suggested monophyly of a group from Lake Victoria basin and Tanzania, but this group was not supported by nuclear loci, suggesting different histories of these markers. Microsatellite data confirmed strong structuring across the range of G. fuscipes s.l., and was useful for deriving the interrelationship of closely related populations. Conclusion/Significance We propose that the morphological classification alone is not used to classify populations of G. fuscipes for control purposes. The Ethiopian population, which is scheduled to be the target of a sterile insect release (SIT) programme, was notably discrete. From a programmatic perspective this may be both positive, given that it may reflect limited migration into the area or negative if the high levels of differentiation are also reflected in reproductive isolation between this population and the flies to be used in the release programme.

Choi, Kwang-Shik; Darby, Alistair C.; Causse, Sandrine; Kapitano, Berisha; Hall, Martin J. R.; Steen, Keith; Lutumba, Pascal; Madinga, Joules; Torr, Steve J.; Okedi, Loyce M.; Lehane, Michael J.; Donnelly, Martin J.

2011-01-01

242

Molecular markers of trichloroethylene-induced toxicity in human kidney cells  

SciTech Connect

Difficulties in evaluation of trichloroethylene (TRI)-induced toxicity in humans and extrapolation of data from laboratory animals to humans are due to the existence of multiple target organs, multiple metabolic pathways, sex-, species-, and strain-dependent differences in both metabolism and susceptibility to toxicity, and the lack or minimal amount of human data for many target organs. The use of human tissue for mechanistic studies is thus distinctly advantageous. The kidneys are one target organ for TRI and metabolism by the glutathione (GSH) conjugation pathway is responsible for nephrotoxicity. The GSH conjugate is processed further to produce the cysteine conjugate, S-(1,2-dichlorovinyl)-L-cysteine (DCVC), which is the penultimate nephrotoxic species. Confluent, primary cultures of human proximal tubular (hPT) cells were used as the model system. Although cells in log-phase growth, which are undergoing more rapid DNA synthesis, would give lower LD{sub 50} values, confluent cells more closely mimic the in vivo proximal tubule. DCVC caused cellular necrosis only at relatively high doses (>100 {mu}M) and long incubation times (>24 h). In contrast, both apoptosis and enhanced cellular proliferation occurred at relatively low doses (10-100 {mu}M) and early incubation times (2-8 h). These responses were associated with prominent changes in expression of several proteins that regulate apoptosis (Bcl-2, Bax, Apaf-1, Caspase-9 cleavage, PARP cleavage) and cellular growth, differentiation and stress response (p53, Hsp27, NF-{kappa}B). Effects on p53 and Hsp27 implicate function of protein kinase C, the mitogen activated protein kinase pathway, and the cytoskeleton. The precise pattern of expression of these and other proteins can thus serve as molecular markers for TRI exposure and effect in human kidney.

Lash, Lawrence H. [Department of Pharmacology, Wayne State University School of Medicine, 540 East Canfield Avenue, Detroit, MI 48201 (United States)]. E-mail: l.h.lash@wayne.edu; Putt, David A. [Department of Pharmacology, Wayne State University School of Medicine, 540 East Canfield Avenue, Detroit, MI 48201 (United States); Hueni, Sarah E. [Department of Pharmacology, Wayne State University School of Medicine, 540 East Canfield Avenue, Detroit, MI 48201 (United States); Horwitz, Beth P. [Department of Pharmacology, Wayne State University School of Medicine, 540 East Canfield Avenue, Detroit, MI 48201 (United States)

2005-08-07

243

Molecular markers of Plasmodium falciparum drug resistance in southern highland Rwanda.  

PubMed

In Rwanda, frequent mutations in the pfdhfr and pfdhps genes of Plasmodium falciparum have suggested intense sulfadoxine-pyrimethamine resistance. However, data on pfmdr1 are not available but might be important in the context of the first-line treatment with artemether-lumefantrine. During a survey among 749 children under five years of age in southern highland Rwanda, 104 P. falciparum isolates were obtained. Parasite polymorphisms associated with drug sensitivity were typed including the genes pfdhfr, pfdhps, pfmdr1, and pfcrt. Plasma concentrations of chloroquine and pyrimethamine were measured by ELISA. Treatment with artemether-lumefantrine within the preceding two weeks was stated by 12.5% of the respondents; chloroquine in plasma was detected in 17.6%, pyrimethamine in none. Isolates with pfdhfr triple and pfdhps double/triple mutations occurred in 75% and 93%, respectively; 69% of the isolates comprised pfdhfr/pfdhps quintuple or sextuple mutations associated with high-grade sulfadoxine-pyrimethamine resistance. Pfdhfr L164 was absent. The pfmdr1 pattern revealed more than 50% of the F184 polymorphism and almost 40% of the N86-F184-D1246 allele combination known to be selected in infections reappearing following artemether-lumefantrine treatment. Molecular markers demonstrate intense antifolate drug resistance of P. falciparum in southern Rwanda. The present, first-time data on pfmdr1 alleles from Rwanda reveal a pattern which might reflect a predominance of wild types for some alleles or, alternatively, substantial artemether-lumefantrine pressure on the local parasite population. PMID:21996622

Zeile, Irene; Gahutu, Jean-Bosco; Shyirambere, Cyprien; Steininger, Christian; Musemakweri, Andre; Sebahungu, Fidèle; Karema, Corine; Harms, Gundel; Eggelte, Teunis A; Mockenhaupt, Frank P

2012-01-01

244

Long-range transport of biomass burning emissions based on organic molecular markers and carbonaceous thermal distribution.  

PubMed

Semi-continuous organic carbon (OC), elemental carbon (EC), and organic molecular markers were analyzed using the thermal optical transmittance method at the Gosan supersite (on Jeju Island, Korea), which has been widely used as a regional background site for East Asia. The Carbonaceous Thermal Distribution (CTD) method, which can provide detailed carbon signature characteristics relative to analytical temperature, was used to improve the carbon fractionation of the analytical method. Ground-based measurements were conducted from October 25 to November 5, 2010. During the sampling period, one high OC concentration event and two characteristic periods were observed. Considering the thermal distribution patterns, the relationship between the EC and black carbon (BC) by optical measurements, the backward trajectories, the aerosol optical thickness, the PM10 concentrations from the 316 PM-network sites that were operated by the Ministry of Environment in Korea, and the organic molecular markers, such as levoglucosan, PAHs, and organic acids, we concluded that the event was influenced by long-range transport from biomass burning emissions. This study discusses the CTD analysis with organic molecular marker concentrations, extracts and interprets additional carbon fractions from a semi-continuous data set, and provides knowledge regarding the origin of carbon sources and their behaviors. PMID:23892024

Bae, Min-Suk; Shin, Ju-Seon; Lee, Kwang-Yul; Lee, Kwon-Ho; Kim, Young J

2014-01-01

245

Do Molecular Markers Predict Survival in Non-Small-Cell Lung Cancer?  

Microsoft Academic Search

Patients with non-small-cell lung cancer (NSCLC) survive for variable lengths of time, even when ad- justment is made for pathological stage. Numerous reports suggest that biological markers predict survival in patients undergoing surgery for NSCLC with curative intent, but many of these claims are unconfirmed or conflicting. We postulated that the use of multiple putative markers might provide greater power

TODD M. GREATENS; GLORIA A. NIEHANS; JEFFREY B. RUBINS; JOSE JESSURUN; ROBERT A. KRATZKE; MICHAEL A. MADDAUS; DENNIS E. NIEWOEHNER

1998-01-01

246

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.

2013-01-01

247

Bladder Cancer 2000: Molecular Markers for the Diagnosis of Transitional Cell Carcinoma  

PubMed Central

The search continues for better tumor markers to improve the rate of detection of transitional cell carcinoma (TCC) more quickly in larger populations and to predict the possibility of disease recurrence. Among several new tests currently being screened, telomerase and hyaluronic acid/hyaluronidase (HA/HAase) have shown sensitivity and specificity equal to or better than cytology, and other promising tumor markers are being investigated. Although no marker has yet replaced the need to perform cystoscopy and cytology, the new tests can minimize the cost and difficulty of screening and long-term surveillance of patients who have or are at risk for bladder cancer.

Chao, Debby; Freedland, Stephen J; Pantuck, Allan J; Zisman, Amnon; Belldegrun, Arie S

2001-01-01

248

Inheritance studies of SSR and ISSR molecular markers and phylogenetic relationship of rice genotypes resistant to tungro virus.  

PubMed

Multivariate analyses were performed using 13 morphological traits and 13 molecular markers (10 SSRs and three ISSRs) to assess the phylogenetic relationship among tungro resistant genotypes. For morphological traits, the genotypes were grouped into six clusters, according to D(2) statistic and Canonical vector analysis. Plant height, days to flowering, days to maturity, panicle length, number of spikelet per panicle, number of unfilled grain per panicle and yield were important contributors to genetic divergence in 14 rice genotypes. Based on Nei's genetic distance for molecular studies, seven clusters were formed among the tungro resistant and susceptible genotypes. Mantel's test revealed a significant correlation (r = 0.834*) between the morphological and molecular data. To develop high yielding tungro resistant varieties based on both morphological and molecular analyses, crosses could be made with susceptible (BR10 and BR11) genotypes with low yielding but highly resistant genotypes, Sonahidemota, Kumragoir, Nakuchimota, Khaiyamota, Khairymota and Kachamota. The chi-square analysis for seven alleles (RM11, RM17, RM20, RM23, RM80, RM108 and RM531) of SSR and five loci (RY1, MR1, MR2, MR4 and GF5) of three ISSR markers in F2 population of cross, BR11×Sonahidemota, showed a good fit to the expected segregation ratio (1:2:1) for a single gene model. PMID:23643394

Latif, Mohammad Abdul; Rahman, Mohammad Mahfuzur; Ali, Mohammad Eaqub; Ashkani, Sadegh; Rafii, Mohd Yusop

2013-03-01

249

The genome of the Mediterranean fruitfly ceratitis capitata : Localization of molecular markers by in situ hybridization to salivary gland polytene chromosomes  

Microsoft Academic Search

We hybridized cloned DNA segments to salivary gland polytene chromosomes of the medfly,Ceratitis capitata, and thus established molecular markers for 24 sites on 6 out of 10 autosomal arms. An additional marker identified a medfly repetitive element that hybridizes to approximately 100 autosomal sites as well as a granular network that is thought to represent theX chromosome. Some of the

A. Zacharopoulou; M. Frisardi; C. Savakis; A. S. Robinson; P. Tolias; M. Konsolaki; K. Komitopoulou; F. C. Kafatos

1992-01-01

250

An update of the Courtot × Chinese Spring intervarietal molecular marker linkage map for the QTL detection of agronomic traits in wheat  

Microsoft Academic Search

We made an update of the intervarietal molecular marker linkage map of the wheat genome developed using a doubled-haploid (DH) population derived from the cross between the cultivars 'Courtot' and 'Chinese Spring'. This map was constructed using 187 DH lines and 659 markers. The genome was well covered (more than 95%) except for chromosomes from homoeologous group 4 and chromosomes

P. Sourdille; T. Cadalen; H. Guyomarc'h; J. Snape; M. Perretant; G. Charmet; C. Boeuf; S. Bernard; M. Bernard

2003-01-01

251

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

252

ADAM33 gene silencing by promoter hypermethylation as a molecular marker in breast invasive lobular carcinoma  

PubMed Central

Background ADAM33 protein is a member of the family of transmembrane glycoproteins composed of multidomains. ADAM family members have different activities, such as proteolysis and adhesion, making them good candidates to mediate the extracellular matrix remodelling and changes in cellular adhesion that characterise certain pathologies and cancer development. It was reported that one family member, ADAM23, is down-regulated by promoter hypermethylation. This seems to correlate with tumour progression and metastasis in breast cancer. In this study, we explored the involvement of ADAM33, another ADAM family member, in breast cancer. Methods First, we analysed ADAM33 expression in breast tumour cell lines by RT-PCR and western blotting. We also used 5-aza-2'-deoxycytidine (5azadCR) treatment and DNA bisulphite sequencing to study the promoter methylation of ADAM33 in breast tumour cell lines. We evaluated ADAM33 methylation in primary tumour samples by methylation specific PCR (MSP). Finally, ADAM33 promoter hypermethylation was correlated with clinicopathological data using the chi-square test and Fisher's exact test. Results The expression analysis of ADAM33 in breast tumour cell lines by RT-PCR revealed gene silencing in 65% of tumour cell lines. The corresponding lack of ADAM33 protein was confirmed by western blotting. We also used 5-aza-2'-deoxycytidine (5-aza-dCR) demethylation and bisulphite sequencing methodologies to confirm that gene silencing is due to ADAM33 promoter hypermethylation. Using MSP, we detected ADAM33 promoter hypermethylation in 40% of primary breast tumour samples. The correlation between methylation pattern and patient's clinicopathological data was not significantly associated with histological grade; tumour stage (TNM); tumour size; ER, PR or ERBB2 status; lymph node status; metastasis or recurrence. Methylation frequency in invasive lobular carcinoma (ILC) was 76.2% compared with 25.5% in invasive ductal carcinoma (IDC), and this difference was statistically significant (p = 0.0002). Conclusion ADAM33 gene silencing may be related to the discohesive histological appearance of ILCs. We suggest that ADAM33 promoter methylation may be a useful molecular marker for differentiating ILC and IDC.

2009-01-01

253

Applications of the green fluorescent protein as a molecular marker in environmental microorganisms  

Microsoft Academic Search

In this review, we examine numerous applications of the green fluorescent protein (GFP) marker gene in environmental microbiology research. The GFP and its variants are reviewed and applications in plant–microbe interactions, biofilms, biodegradation, bacterial–protozoan interactions, gene transfer, and biosensors are discussed. Methods for detecting GFP-marked cells are also examined. The GFP is a useful marker in environmental microorganisms, allowing new

D. Errampalli; K. Leung; M. B. Cassidy; M. Kostrzynska; M. Blears; H. Lee; J. T. Trevors

1999-01-01

254

Molecular marker-assisted sex control in half-smooth tongue sole ( Cynoglossus semilaevis)  

Microsoft Academic Search

Half-smooth tongue sole females grow larger and faster than males. An all-female population would be of significant benefit for tongue sole aquaculture. In the present study, a female-specific AFLP marker (CseF305) was isolated from female genomic DNA of the tongue sole and sequenced. One pair of SCAR primers was designed based on the sequences of the female-specific marker. A PCR

Song-Lin Chen; Si-Ping Deng; Hong-Yu Ma; Yong-Sheng Tian; Jian-Yong Xu; Jing-Feng Yang; Qing-Yin Wang; Xiang-Shan Ji; Chang-Wei Shao; Xian-Li Wang; Peng-Fei Wu; Han Deng; Jie-ming Zhai

2008-01-01

255

Immunological and clinical follow up of hepatitis C virus associated cryoglobulinaemic vasculitis  

Microsoft Academic Search

OBJECTIVETo study immunological markers and compare these markers with standard measures for the clinical and immunological follow up of vasculitis activity in hepatitis C virus (HCV) associated cryoglobulinaemic vasculitis (CV).METHODSSerial serum samples from eight patients with newly diagnosed HCV associated CV were followed during interferon ? treatment induced remission of the CV. Vasculitis activity and disease extent were evaluated with

P Lamprecht; F Moosig; A Gause; K Herlyn; E Csernok; H Hansen; W L Gross

2001-01-01

256

Epithelioid Sarcoma and Unclassified Sarcoma with Epithelioid Features: Clinicopathological Variables, Molecular Markers, and a New Experimental Model  

PubMed Central

Background. Epithelioid sarcoma (ES) and unclassified sarcoma with epithelioid features (USEF) are clinically and therapeutically unresolved. We compared ES and USEF patients' clinical behavior, treatment, outcome, and molecular marker expression. Furthermore, preclinical ES study models were developed to enable comprehensive benchside investigations. Patients and Methods. A database of ES and USEF patients (n = 116) treated since 1992 was created. A clinically annotated ES–USEF tissue microarray (TMA) was assayed for tumor-related markers. Newly established human and commercially available ES cell lines were characterized and tested in vivo. Results. ES and USEF patients presenting with localized disease exhibited 22% and 25% local recurrence rates, 35% and 19% nodal metastasis rates, and 41% and 53% distant metastasis rates (median follow-up, 54 months and 39 months, respectively). The 5- and 10-year disease-specific survival rates were 88% and 43% and 52% and 42% (ES and USEF, respectively). TMA immunohistochemistry identified integrase interactor (INI)-1 loss, cancer antigen 125, and p53 nuclear expression as significantly more common in ES than USEF cases. Both cell lines preserved ES morphological and biochemical characteristics in vitro and in vivo; loss of INI-1 was shown to occur in both lines. Conclusions. Enhanced knowledge of ES and USEF clinical behavior, marker expression, and molecular determinants, extended via experimental models, will hopefully accelerate development of urgently needed effective targeted therapies for ES and USEF.

Sakharpe, Aniket; Lahat, Guy; Gulamhusein, Taher; Liu, Ping; Bolshakov, Svetlana; Nguyen, Theresa; Zhang, Pingyu; Belousov, Roman; Young, Eric; Xie, Xianbiao; Rao, Priya; Hornick, Jason L.; Lazar, Alexander J.; Pollock, Raphael E.

2011-01-01

257

Evaluation of chemical, molecular, and traditional markers of fecal contamination in an effluent dominated urban stream.  

PubMed

In this paper we present a quantitative sanitary survey of the Middle Santa Ana River, in southern California, utilizing a variety of source tracking tools, including traditional culture-dependent fecal markers (Enterococcus and Escherichia coli by IDEXX), speciation of enterococci isolates, culture-independent fecal markers (human-specific HF183 Bacteroides and Enterococcus by quantitative polymerase chain reaction, qPCR), and chemical markers of sewage and wastewater (nutrients, enantiomeric fraction (EF) of propranolol and ethylenediaminetetraacetic acid). To facilitate comparison of these different methods, data are interpreted in a loading (i.e., mass per time) framework that enables a quantitative apportionment of fecal markers and nutrients to specific source waters in the Middle Santa Ana River. Multiple lines of evidence support the hypothesis that Enterococcus in the Middle Santa Ana River originates primarily from in situ growth in streambed sediments, not from significant and persistent sources of untreated human waste. The EF of propranolol of tertiary treated wastewater effluent is in the range (0.42 to 0.71) previously reported for raw sewage, making EF of propranolol an unsuitable marker for fecal pollution, at least at this site. The human fecal marker HF183 Bacteroides was detected at a few sites, although not in a source of disinfected and tertiary treated wastewater effluent. Based on the results presented here and prior experience at other sites in southern California, HF183 Bacteroides would appear to be a candidate marker of fecal contamination for inland waters, although more qPCR measurements in disinfected wastewater effluent are needed to account for variations due to treatment plant performance and other factors. More generally, our results support the notion that regrowth of fecal indicator bacteria (FIB) in river sediments may lead to a decoupling between FIB and pathogen concentrations in the water column and thus limit the utility of FIB as an indicator of recreational waterborne illness in inland waters. PMID:20839837

Litton, Rachel M; Ahn, Jong Ho; Sercu, Bram; Holden, Patricia A; Sedlak, David L; Grant, Stanley B

2010-10-01

258

Genetic variation in a wild population of the 'sleep' passion fruit (Passiflora setacea) based on molecular markers.  

PubMed

Little is known about the molecular genetic diversity of most Passiflora species. We used RAPD markers to evaluate the genetic diversity of 24 genotypes of the 'sleep' passion fruit (Passiflora setacea). Twelve primers generated 95 markers, 88% of which were polymorphic. The genetic distance estimated by the complement of the Dice index ranged from 0.29 (among accessions Ps-G1 and Ps-G13) to 0.69 (among accessions Ps-G21 and Ps-G23). Genotype grouping based on the UPGMA algorithm showed considerable variability among genotypes. We conclude that P. setacea has a broad genetic base that could be exploited in breeding programs. PMID:22576831

Cerqueira-Silva, C B M; Santos, E S L; Conceição, L D H C S; Cardoso-Silva, C B; Pereira, A S; Oliveira, A C; Corrêa, R X

2012-01-01

259

Extensive spatial genetic structure revealed by AFLP but not SSR molecular markers in the wind-pollinated tree, Fagus sylvatica.  

PubMed

Studies of fine-scale spatial genetic structure (SGS) in wind-pollinated trees have shown that SGS is generally weak and extends over relatively short distances (less than 30-40 m) from individual trees. However, recent simulations have shown that detection of SGS is heavily dependent on both the choice of molecular markers and the strategy used to sample the studied population. Published studies may not always have used sufficient markers and/or individuals for the accurate estimation of SGS. To assess the extent of SGS within a population of the wind-pollinated tree Fagus sylvatica, we genotyped 200 trees at six microsatellite or simple sequence repeat (SSR) loci and 250 amplified fragment length polymorphisms (AFLP) and conducted spatial analyses of pairwise kinship coefficients. We re-sampled our data set over individuals and over loci to determine the effect of reducing the sample size and number of loci used for SGS estimation. We found that SGS estimated from AFLP markers extended nearly four times further than has been estimated before using other molecular markers in this species, indicating a persistent effect of restricted gene flow at small spatial scales. However, our SSR-based estimate was in agreement with other published studies. Spatial genetic structure in F. sylvatica and similar wind-pollinated trees may therefore be substantially larger than has been estimated previously. Although 100-150 AFLP loci and 150-200 individuals appear sufficient for adequately estimating SGS in our analysis, 150-200 individuals and six SSR loci may still be too few to provide a good estimation of SGS in this species. PMID:17305851

Jump, Alistair S; Peñuelas, Josep

2007-03-01

260

Insights into the phylogeny of sporadotrichid ciliates (Protozoa, Ciliophora: Hypotricha) based on genealogical analyses of multiple molecular markers  

NASA Astrophysics Data System (ADS)

The sporadotrichid ciliates are an especially diverse group. A number of investigators have studied the morphological, morphogenetic, and molecular relationships among members of this group. Despite this, a consistent classification is still lacking and several important questions about the phylogenetic relationships within this group remain unsolved. To improve our understanding of these relationships, we constructed phylogenetic trees using the nucleotide sequences of the small-subunit rRNA (SSrRNA) gene and amino acid sequences of actin I and ?-tubulin. Analyses of SSrRNA gene sequences indicated that: 1) the Sporadotrichida sensu Lynn (2008) and the Oxytrichidae are polyphyletic; 2) the Uroleptus species, which are classified to urostylids, formed a sister group with the oxytrichids; 3) Halteria grandinella, which is grouped morphologically with oligotrich species, clustered within the oxytrichids. These results are congruent with previous studies based on SSrRNA gene sequences. However, the amino acid sequences of actin I and ?-tubulin yielded different topologies. The main results are: 1) in all phylogenetic trees, the genus Oxytricha was paraphyletic; 2) Uroleptus was sister to a subset of Urostyla and Holosticha, albeit with low supporting values; 3) Halteria grandinella was separated distantly from the Oxytrichidae in trees inferred from actin I amino acid sequences but clustered with oligotrichids in the ?-tubulin analysis. The inconsistency among the trees inferred from these different molecular markers may be caused by rapidly accumulated genetic characterizations of ciliates. Further studies with additional molecular markers and sampling of more taxa are expected to better address the relationships among sporadotrichids.

Hu, Xiaoyan; Hu, Xiaozhong; Al-Rasheid, Khaled A. S.; Al-Farraj, Saleh A.; Song, Weibo

2011-01-01

261

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

262

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

263

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

264

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

265

Expression and prognostic role of molecular markers in 99 KIT-positive gastric stromal tumors in Taiwanese  

PubMed Central

AIM: To elucidate the prognostic role and relationship of three molecular markers such as tumor suppressor gene p53, proliferating cell nuclear antigen (PCNA) and Ki-67 in gastric stromal tumor. METHODS: A total of 108 surgically resected gastric smooth muscle tumor specimens were collected from January 1987 to December 1999. Immunohistochemical studies were performed on the paraffin sections of 99 of 108 CD117-positive tumors with antibodies of p53, PCNA, and Ki-67. Immunoreactivity of three molecular markers was recorded by labeling index (LI, %) and was analyzed for clinicopathologic and survival correlation. RESULTS: Of the 99 cases, immunostaining revealed that 52 patients (52.5%) had p53, and 37 patients (37.3%) had Ki-67 immunoreactivity (defined as >10% of LI). All patients (100%) had PCNA immunoreactivity ranging from 12% to 93% of LI, divided into high or low by median. Statistics revealed that LI of three markers positively correlate to each other (P<0.01) and to microscopic tumor mitotic counts (P <0.001). By combination, patients with ?2 markers (positive or high) in tumors had early tumor recurrence (P <0.001) and unfavorable outcome (P <0.001). Univariate analysis indicated that patients with tumor size >5 cm (P =?0.003), tumor mitosis >5/50 HPF (P molecular markers in GISTs. The combination of three factors (p53, tumor size, and tumor mitosis) provides a more powerful prediction of prognosis than any single factor does.

Hu, Tsung-Hui; Chuah, Seng-Kee; Lin, Jui-Wei; Chiu, Yi-Chun; Changchien, Chi-Sin; Wang, Chih-Chi; Chen, Yaw-Sen; Yi, Li-Na; Chiu, King-Wah; Lee, Chuan-Mo

2006-01-01

266

Development of ITS sequence based molecular marker to distinguish, Tribulus terrestris L. (Zygophyllaceae) from its adulterants.  

PubMed

Tribulus terrestris L. (Zygophyllaceae) is one of the highly traded raw drugs and also used as a stimulative food additive in Europe and USA. While, Ayurvedic Pharmacopoeia of India recognizes T. terrestris as Goksura, Tribulus lanuginosus and T. subramanyamii are also traded by the same name raising issues of quality control. The nuclear ribosomal RNA genes and ITS (internal transcribed spacer) sequence were used to develop species-specific DNA markers. The species-specific markers efficiently amplified 295bp for T. terrestris (TT1F and TT1R), 300bp for T. lanuginosus (TL1F and TL1R) and 214bp for T. subramanyamii (TS1F and TS1R). These DNA markers can be used to distinguish T. terrestris from its adulterants. PMID:20083169

Balasubramani, Subramani Paranthaman; Murugan, Ramar; Ravikumar, Kaliamoorthy; Venkatasubramanian, Padma

2010-09-01

267

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.

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

2012-01-01

268

Can neutral molecular markers be used to determine the success of an introduction of a "better" strain into an established population of a biocontrol parasitoid?  

PubMed

Neutral molecular markers are gene sequences where variants are considered to confer no fitness advantage, such as microsatellites and mitochondrial haplotypes. Several types of neutral marker are easy to develop, cheap to use, and have found extensive application for addressing ecological questions. In biocontrol, these markers are used to simplify identification of cryptic species and of prey remains in predators. Here, we address the potential of neutral molecular markers for determining the relative performance of a "superior" strain of a species after release into an already established conspecific population. We used modeling to show that only under very limited conditions can traditional neutral markers be used to demonstrate that beneficial genetic variation was successfully introgressed into the existing population. However, new population genomic methods do make it possible to track alleles at a large number of loci and consequently make it possible to show if alleles from a superior strain spread in an already established conspecific population. PMID:24772526

Stouthamer, Richard; Nunney, Leonard

2014-04-01

269

18F-FDG PET Imaging of Murine Atherosclerosis: Association with Gene Expression of Key Molecular Markers  

PubMed Central

Aim To study whether 18F-FDG can be used for in vivo imaging of atherogenesis by examining the correlation between 18F-FDG uptake and gene expression of key molecular markers of atherosclerosis in apoE?/? mice. Methods Nine groups of apoE?/? mice were given normal chow or high-fat diet. At different time-points, 18F-FDG PET/contrast-enhanced CT scans were performed on dedicated animal scanners. After scans, animals were euthanized, aortas removed, gamma counted, RNA extracted from the tissue, and gene expression of chemo (C-X-C motif) ligand 1 (CXCL-1), monocyte chemoattractant protein (MCP)-1, vascular cell adhesion molecule (VCAM)-1, cluster of differentiation molecule (CD)-68, osteopontin (OPN), lectin-like oxidized LDL-receptor (LOX)-1, hypoxia-inducible factor (HIF)-1?, HIF-2?, vascular endothelial growth factor A (VEGF), and tissue factor (TF) was measured by means of qPCR. Results The uptake of 18F-FDG increased over time in the groups of mice receiving high-fat diet measured by PET and ex vivo gamma counting. The gene expression of all examined markers of atherosclerosis correlated significantly with 18F-FDG uptake. The strongest correlation was seen with TF and CD68 (p<0.001). A multivariate analysis showed CD68, OPN, TF, and VCAM-1 to be the most important contributors to the uptake of 18F-FDG. Together they could explain 60% of the 18F-FDG uptake. Conclusion We have demonstrated that 18F-FDG can be used to follow the progression of atherosclerosis in apoE?/? mice. The gene expression of ten molecular markers representing different molecular processes important for atherosclerosis was shown to correlate with the uptake of 18F-FDG. Especially, the gene expressions of CD68, OPN, TF, and VCAM-1 were strong predictors for the uptake.

Hag, Anne Mette Fisker; Pedersen, Sune Folke; Christoffersen, Christina; Binderup, Tina; Jensen, Mette Munk; J?rgensen, Jesper Tranekjaer; Skovgaard, Dorthe; Ripa, Rasmus Sejersten; Kjaer, Andreas

2012-01-01

270

Molecular characterization of Klebsiella pneumoniae isolated from renal transplanted patients: virulence markers, extended-spectrum ?-lactamases, and genetic relatedness.  

PubMed

The objective was to characterize virulence markers and ?-lactam resistance in Klebsiella pneumoniae isolates from renal transplant patients and to evaluate their genetic relatedness. Two main genetic lineages were detected: 1 carried blaCTX-M-15 not associated to IncFIIA plasmid replicon, which was found on the other lineage not expressing CTX-M-type enzyme. PAI III536 and PAI IICFT073 were detected for the first time in K. pneumoniae in 1 clone, while the siderophore kfu was carried by the other, with only PAI IV536. The molecular data indicate colonization before admission and fuel the discussion on implementation of antibiotherapy before surgery. PMID:24746826

Calhau, Vera; Boaventura, Luísa; Ribeiro, Graça; Mendonça, Nuno; da Silva, Gabriela J

2014-07-01

271

Prevalence of molecular markers of Plasmodium falciparum drug resistance in Dakar, Senegal  

PubMed Central

Background As a result of the widespread resistance to chloroquine and sulphadoxine-pyrimethamine, artemisinin-based combination therapy (ACT) (including artemether-lumefantrine and artesunate-amodiaquine) has been recommended as a first-line anti-malarial regimen in Senegal since 2006. Intermittent preventive treatments with anti-malarial drugs based on sulphadoxine-pyrimethamine are also given to children or pregnant women once per month during the transmission season. Since 2006, there have been very few reports on the susceptibility of Plasmodium falciparum to anti-malarial drugs. To estimate the prevalence of resistance to several anti-malarial drugs since the introduction of the widespread use of ACT, the presence of molecular markers associated with resistance to chloroquine and sulphadoxine-pyrimethamine was assessed in local isolates at the military hospital of Dakar. Methods The prevalence of genetic polymorphisms in genes associated with anti-malarial drug resistance, i.e., Pfcrt, Pfdhfr, Pfdhps and Pfmdr1, and the copy number of Pfmdr1 were evaluated for a panel of 174 isolates collected from patients recruited at the military hospital of Dakar from 14 October 2009 to 19 January 2010. Results The Pfcrt 76T mutation was identified in 37.2% of the samples. The Pfmdr1 86Y and 184F mutations were found in 16.6% and 67.6% of the tested samples, respectively. Twenty-eight of the 29 isolates with the 86Y mutation were also mutated at codon 184. Only one isolate (0.6%) had two copies of Pfmdr1. The Pfdhfr 108N/T, 51I and 59R mutations were identified in 82.4%, 83.5% and 74.1% of the samples, respectively. The double mutant (108N and 51I) was detected in 83.5% of the isolates, and the triple mutant (108N, 51I and 59R) was detected in 75.3%. The Pfdhps 437G, 436F/A and 613S mutations were found in 40.2%, 35.1% and 1.8% of the samples, respectively. There was no double mutant (437G and 540E) or no quintuple mutant (Pfdhfr 108N, 51I and 59R and Pfdhps 437G and 540E). The prevalence of the quadruple mutant (Pfdhfr 108N, 51I and 59R and Pfdhps 437G) was 36.5%. Conclusions Since 2004, the prevalence of chloroquine resistance had decreased. The prevalence of isolates with high-level pyrimethamine resistance is 83.5%. The prevalence of isolates resistant to sulphadoxine is 40.2%. However, no quintuple mutant (Pfdhfr 108N, 51I and 59R and Pfdhps 437G and 540E), which is associated with a high level of sulphadoxine-pyrimethamine resistance, has been identified to date. The resistance to amodiaquine remains moderate.

2012-01-01

272

Molecular Analysis of Local Potato Cultivars from Tenerife Island Using Microsatellite Markers  

Microsoft Academic Search

We have used 19 SSR markers to fingerprint 41 local potato cultivars from 10 locations of Tenerife Island. These varieties represent relicts of the early introductions originating from South America and have been characterised previously morphologically and ecophysiologically. The SSR primers generated a varying degree of polymorphisms. A total of 67 alleles were observed, 12 of them were present in

L. Barandalla; J. I. Ruiz de Galarreta; D. Rios; E. Ritter

2006-01-01

273

A clinical, cytogenetic, FISH and molecular study of supernumerary marker 15 chromosomes  

SciTech Connect

We studied 17 patients with supernumerary marker chromosomes shown by fluorescent in situ hybridization (FISH) with the 15-centromere specific probe pTRA-25 to be 15-derived. Genetic constitution of the marker chromosomes was investigated using FISH, Southern blot analysis and PCR for proximal and distal loci on 15q as well as conventional cytogenetics. Eight of the 17 patients were mentally retarded. Six of the eight carried a de novo marker 15 containing one or two doses of loci known to be in or near the Prader-Willi/Angelman (PWS/AS) region, whereas none of the nine non-retarded patients had duplications of this region, and only two of the eight whose parents were available had a de novo marker. None of the mentally retarded patients had PWS or AS. In two retarded patients (one de novo, one familial) there was no duplication of the PWS/AS region. Uniparental disomy affecting the normal 15 homologs was excluded in 10 of the patients, including all eight with mental retardation.

Dennis, N.R. [Princess Anne Hospital, Southampton (United Kingdom); Crolla, J.A.; Harvey, J.F. [Salisbury District Hospital (United Kingdom)

1994-09-01

274

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

275

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

276

Immunophenotyping of thyroid tumors identifies molecular markers altered during transformation of differentiated into anaplastic carcinoma  

Microsoft Academic Search

BackgroundThe objective of this study was to evaluate the change in the tumor expression profile that occurs during the transformation of differentiated thyroid cancer (DTC) into anaplastic thyroid cancer (ATC) and to evaluate an 8-marker transformation panel previously identified through evaluation of ATCs and their adjacent associated DTCs.

Sam M. Wiseman; Obi L. Griffith; Allen Gown; Blair Walker; Steven J. M. Jones

2011-01-01

277

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

278

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

PubMed

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 sequence. Parents were scored for the presence or absence of individual bands. An average of 6.3 bands and 1.3 polymorphisms for presence/absence were observed per primer between the parents. Thirteen of these primers were used to determine the inheritance of RAPD marker alleles in the resulting progeny and in haploid drones from a daughter queen. Four types of polymorphisms were observed. Polymorphisms for band presence/absence as well as for band brightness were inherited as dominant markers, meeting Mendelian expectations in haploid and diploid progeny. Polymorphisms for fragment-length were also observed. These segregated in a near 1?1 ratio in drone progeny. The last type of polymorphism was manifested as a diploid-specific band. Mixing of amplification products after PCR showed that the diploid-specific band was the result of heteroduplex formation from the DNA of alternate alleles in heterozygotes. In two of the four cases of heteroduplex formation, the alternative alleles were manifested as small fragment-length polymorphisms, resulting in co-dominant markers. This is the first demonstration that a proportion of RAPD markers are not inherited in a dominant fashion. PMID:24197223

Hunt, G J; Page, R E

1992-10-01

279

Predictors of gefitinib outcomes in advanced non-small cell lung cancer (NSCLC): Study of a comprehensive panel of molecular markers  

Microsoft Academic Search

A number of different clinical characteristics and molecular markers related to epidermal growth factor receptor (EGFR) activation have been reported to singly correlate with therapeutic activity of EGFR tyrosine kinase inhibitors (TKIs) in advanced non-small cell lung cancer (NSCLC). This study was designed to evaluate the predictive value on gefitinib outcomes of a comprehensive panel of molecular parameters in advanced

Marcello Tiseo; Giulio Rossi; Marzia Capelletti; Giuliana Sartori; Elena Spiritelli; Alessandro Marchioni; Cecilia Bozzetti; Giuseppe De Palma; Costanza Lagrasta; Nicoletta Campanini; Roberta Camisa; Luca Boni; Vittorio Franciosi; Guido Rindi; Andrea Ardizzoni

2010-01-01

280

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

281

Molecularly imprinted polymer of 5-methyluridine for solid-phase extraction of pyrimidine nucleoside cancer markers in urine.  

PubMed

Normal and modified urinary nucleosides represent potential biomarkers for cancer diagnosis. To selectively extract modified nucleosides, we developed a molecularly imprinted polymer (MIP) of 5-methyluridine as selective material for molecularly imprinted solid-phase extraction (MISPE). The MIPs were obtained from vinyl-phenylboronate ester derivative of the template, acrylamide and pentaerythritol triacrylate co-polymer, and were tested in batch and cartridge experiments with aqueous samples. Our results indicated that the imprinted polymer was selective for pyrimidine nucleosides with a K(d) and a B(max) of 46 microM and 18 micromol/g, respectively. Finally, a MISPE of the most common pyrimidine nucleoside cancer markers in urine sample was realized. PMID:18789867

Jégourel, Damien; Delépée, Raphaël; Breton, Florent; Rolland, Antoine; Vidal, Richard; Agrofoglio, Luigi A

2008-10-01

282

Galectin-3 expression in thyroid fine needle cytology (t-FNAC) uncertain cases: validation of molecular markers and technology innovation.  

PubMed

Thyroid cancer is not very common, accounting for 1-2% of all cancers, with a population incidence of about 0.004%. Currently, the ability to discriminate between follicular adenoma and carcinoma represents the major challenge in preclinical diagnosis of thyroid proliferative lesions. Better discrimination between the two would help avoid unnecessary thyroidectomy and save valuable resources. Over the years, galectin-3 (Gal-3) has been proposed as a diagnostic marker with varied success. In this paper, we used Environmental Scanning Electron Microscopy Immunogold Labelling (ESEM-IGL) to investigate the expression of Gal-3 on Thin-Prep fine needle aspiration cytology (FNAC). We optimized the ESEM-IGL method on thyroid cell lines (RO-82 and FTC-133) comparing our membrane Gal-3 labeling data with Western blot. We evaluated 183 thyroid FNAC from Italian patients with a uncertain pre-surgical diagnosis. ESEM-IGL method marker sensitivity is 71.2%, while specificity is 53.3% and diagnostic efficacy is 61.2%. Our results confirmed that Gal-3 expression is associated with situations of hypertrophy and/or cellular hyperproliferation, pathophysiological situations common both to adenomas and to thyroid carcinomas. The innovation of thyroid FNAC Thin-Prep ESEM-IGL shows the levels of Gal-3 immunolabeling clearly, even through the individual cells of a thyroid nodule. However, Gal-3 alone, as a molecular marker of thyroid cancer, can still have a limited application in pre-surgery diagnosis. PMID:23042505

Papale, F; Cafiero, G; Grimaldi, A; Marino, G; Rosso, F; Mian, C; Barollo, S; Pennelli, G; Sorrenti, S; De Antoni, E; Barbarisi, A

2013-05-01

283

[Molecular markers linked to mono-dominant genic male sterile gene in rapeseed (Brassica napus L.)].  

PubMed

Bulked segregant analysis (BSA) was used to identify randomly amplified polymorphic DNA (RAPD) markers linked to the MS gene in mono-dominant GMS of rapeseed (Brassica napus L.), which was bred by Hybrid Rapeseed Research Center of Shaanxi Province. A total of 300 random 10-mer oligonucleotide primers were screened on the DNA from fertile and sterile bulks. Primer S(243) (5'CTATGCCGAC3') gave identical 1.5 kb DNA polymorphic segment OPU-03(1500) in the bulk S, but not in the bulk F (Fig.2). The DNAs from individual plants of each bulk and from their sister lines, which were generated from the same original crossing, were then screened with the primer S(243), and the same results were obtained (Figs.3,4). Other types of GMS and CMS were analyzed using primer S(243), and the specific 1.5 kb DNA segment was not found (Fig.5). Therefore, the RAPD marker OPU-03(1500) is linked to the mono-dominant GMS trait in rapeseed. This RAPD marker OPU-03(1500) was cloned into a T-easy vector and sequenced. The sequence here obtained was highly homologous to one of the Arabidopsis DNA sequences. According to this DNA conserved region in different species, we designed a pair of specific primers P1 (5'ATGTCGCTGAGGCCG-AGCAC3') and P2 (5'GGCACACTGTCACG-ATCCTTGG3') and amplified only one specific 2.3 kb DNA fragment in each bulk. There are two mutant loci between the two DNA fragments after sequencing. We designed another pair of specific primers P3 (5'CTCCAGCAGCAGCAGC-AGCCT3') and P4 (5'GCAGGAATGAGAA-CCGTAGG3') according to the DNA sequence at the mutant loci. A specific DNA segment was amplified only in the fertile line but not in the sterile line using the primers P3 and P4 (Fig.6). Therefore the RAPD marker were converted into SCAR marker. Moreover, the SCAR marker detection method was improved (Fig.7). PMID:17075173

Wang, Dao-Jie; Guo, Ai-Guang; Li, Dian-Rong; Tian, Jian-Hua

2006-10-01

284

Use of molecular and ultrastructural markers to evaluate stage conversion of Toxoplasma gondii in both the intermediate and definitive host.  

PubMed

Toxoplasma gondii has a complex life cycle involving definite (cat) and intermediate (all warm blooded animals) hosts. This gives rise to four infectious forms each of which has a distinctive biological role. Two (tachyzoite and merozoite) are involved in propagation within a host and two (bradyzoite and sporozoite) are involved in transmission to new hosts. The various forms can be identified by their structure, host parasite relationship and distinctive developmental processes. In the present in vivo study, the various stages have been evaluated by electron microscopy and immunocytochemistry using a panel of molecular markers relating to surface and cytoplasmic molecules, metabolic iso-enzymes and secreted proteins that can differentiate between tachyzoite, bradyzoite and coccidian development. Tachyzoites were characterised as being positive for surface antigen 1, enolase isoenzyme 2, lactic dehydrogenase isoenzyme 1 and negative for bradyzoite antigen 1. In contrast, bradyzoites were negative for SAG1 but positive for BAG1, ENO1 and LDH2. When stage conversion was followed in brain lesion at 10 and 15 days post-infection, tachyzoites were predominant but a number of single intermediate organisms displaying tachyzoite and certain bradyzoite markers were observed. At later time points, small groups of organisms displaying only bradyzoite markers were also present. A number (9) of dense granule proteins (GRA1-8, NTPase) have also been identified in both tachyzoites and bradyzoites but there were differences in their location during parasite development. All the dense granule proteins extensively label the parasitophorous vacuole during tachyzoite development. In contrast the tissue cyst wall displays variable staining for the dense granule proteins, which also expresses an additional unique cyst wall protein. The molecular differences could be identified at the single cell stage consistent with conversion occurring at the time of entry into a new cell. These molecular differences were reflected in the structural differences in the parasitophorous vacuoles observed by electron microscopy. Stage conversion to enteric (coccidian) development was limited to the enterocytes of the cat small intestine. Although no specific markers were available, this form of development can be identified by the absence of specific tachyzoite (SAG1) and bradyzoite (BAG1) markers although the isoenzymes ENO2 and LHD1 were expressed. There was also a significant difference in the expression of the dense granule proteins. The coccidian stages and merozoites only expressed two (GRA7 and NTPase) of the nine dense granule proteins and this was reflected in significant differences in the structure of the parasitophorous vacuole. The coccidian stages also undergo conversion from asexual to sexual development. The mechanism controlling this process is unknown but does not involve any change in the host cell type or parasitophorous vacuole and may be pre-programmed, since the number of asexual cycles was self-limiting. In conclusion, it was possible using a combination of molecular markers to identify tachyzoite, bradyzoite and coccidian development in tissue sections. PMID:15003495

Ferguson, D J P

2004-03-01

285

21 CFR 866.5160 - Beta-globulin immunolog-ical test system.  

Code of Federal Regulations, 2010 CFR

...2009-04-01 2009-04-01 false Beta-globulin immunolog-ical test system...Immunological Test Systems § 866.5160 Beta -globulin immunolog-ical test system. (a) Identification. A beta -globulin immunological test...

2009-04-01

286

21 CFR 866.5160 - Beta-globulin immunolog-ical test system.  

Code of Federal Regulations, 2010 CFR

...2010-04-01 2010-04-01 false Beta-globulin immunolog-ical test system...Immunological Test Systems § 866.5160 Beta -globulin immunolog-ical test system. (a) Identification. A beta -globulin immunological test...

2010-04-01

287

Tumor Angiogenic Marker Expression Levels during Tumor Growth: Longitudinal Assessment with Molecularly Targeted Microbubbles and US Imaging  

PubMed Central

Purpose: To evaluate the use of molecularly targeted microbubbles (MBs) and ultrasonography (US) in the noninvasive assessment of the level of expression of three angiogenic markers, ?v?3 integrin, endoglin, and vascular endothelial growth factor receptor (VEGFR) 2, on tumor vascular endothelial cells in vivo during tumor growth. Materials and Methods: All procedures using laboratory animals were approved by the Institutional Administrative Panel on Laboratory Animal Care. Binding specificity of three types of targeted MBs (MBIntegrin, MBEndoglin, MBVEGFR2) was tested in cell culture under flow shear stress conditions. In vivo targeted contrast material–enhanced US imaging signal using the three MB types was measured at three tumor stages (small, medium, large) in three subcutaneous cancer xenografts (breast, ovarian, pancreatic cancer) in mice (n = 54). In vivo US imaging signal was correlated with ex vivo angiogenic marker expression. Significant differences were evaluated by using the Student t, analysis of variance, Wilcoxon, and Tukey Honest Significant Difference tests. Results: Cell attachment of all three MB types was significantly (P = .016) higher compared with control MBs, and this attachment could be significantly (P = .026) decreased by blocking antibodies. Angiogenic marker–expressing cells bound significantly (P = .003) more targeted MBs than negative control cells, and MB attachment significantly (P < .001) correlated with marker expression levels on cells (? = 0.87). In early stage breast and ovarian cancers, in vivo targeted contrast-enhanced US demonstrated significantly (P ? .04) higher endoglin expression than both ?v?3 integrin and VEGFR2 expression, whereas in early stage pancreatic cancer, marker expressions were not significantly different (P ? .07). There was good correlation (? ? 0.63; P ? .05) between in vivo targeted contrast-enhanced US imaging signals using the three MB types and ex vivo immunoblotting results regarding expression levels of the three angiogenic markers. Immunofluorescence confirmed expression of ?v?3 integrin, endoglin, and VEGFR2 on tumor vascular endothelial cells. Conclusion: Targeted contrast-enhanced US imaging allows noninvasive in vivo assessment of the expression levels of ?v?3 integrin, endoglin, and VEGFR2, which vary during tumor growth in subcutaneous cancer xenografts. © RSNA, 2011 Supplemental material: http://radiology.rsna.org/lookup/suppl/doi:10.1148/radiol.10101079/-/DC1

Deshpande, Nirupama; Ren, Ying; Foygel, Kira; Rosenberg, Jarrett

2011-01-01

288

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.

2013-01-01

289

Molecular Markers in the Identification of Some Early Flowering Curcuma L. (Zingiberaceae) Species  

Microsoft Academic Search

In this paper, isozymes have been used for the first time as tools to aid identification of someCurcuma L. species that are still taxonomically confused. These markers were employed to confirm the taxonomic identification and to distinguish the taxa analysed; the results were used to describe the relationship within the early-flowering group. Twenty-one isozymes were initially tested; out of these,

PIMCHAI APAVATJRUT; SOMBOON ANUNTALABHOCHAI; PUANGPEN SIRIRUGSA; CHIARA ALISI

1999-01-01

290

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

291

[Immunology of non-Hodgkin lymphomas].  

PubMed

Cytological and kinetic immunological homogeneity is typical of such lymphomas. Their cytogenesis is broadly connected to the development and differentiation of lymphocytes. It is mainly a question of proliferating B lymphocytes of which the monoclonal membrane receptors are tumoral markers. The final stage of B lymphocyte differentiation is the lymphoplasmacellular proliferation involving monoclonal Ig secretion and consequently the rarefaction and finally disappearance of surface receptors. PMID:6431332

Ricci, C; Cascio, G; Bellone, G; Borio, T; Novarini, M; Riposio, A; Bozzone, D

1983-05-12

292

Networks in immunology  

NASA Astrophysics Data System (ADS)

In this note we present a minireview of the idiotypic network in immunology and we study a very simple model for this network. We discuss some of the similarities of this model with spin glasses and neural networks.

Parisi, Giorgio

1989-12-01

293

Molecular biological markers and micrometastasis in resected non-small-cell lung cancer  

Microsoft Academic Search

Objectives: Recent advances in molecular biology and genetics have created new diagnostic and treatment possibilities in clinical oncology.\\u000a We evaluated the usefulness of molecular biological factors in primary tumor and micrometastasis in the bone marrow and pathological\\u000a negative (pN0) lymph nodes as prognostic parameters in non-small-cell lung cancer (NSCLC) patients.Methods: Pathological specimens were collected from 129 NSCLC patients to analyze

Toshihiro Osaki; Tsunehiro Oyama; Masaaki Inoue; Chun-Dong Gu; Mantaro Kodate; Masayasu Aikawa; Tetsuya So; Makiko Mizukami; Tetsuya Mitsudomi; Kosei Yasumoto

2001-01-01

294

Seminal molecular markers as a non-invasive diagnostic tool for the evaluation of spermatogenesis in non-obstructive azoospermia.  

PubMed

Non-obstructive azoospermia (NOA) is currently evaluated by the use of conventional histopathological methods. In some cases, focal spermatogenesis is present in the testes of patients with NOA which may be almost undetectable by routine histopathological examinations. Application of molecular markers in semen to predict the spermatogenesis status in the testis will emphasize the probability of finding sperm in NOA testis through further search using TESE or mTESE. Detection of germ cell-specific transcripts in semen is a signal of germ cells present in the testis. In this study, we used molecular methods to evaluate spermatogenesis status in azoospermic men. Semen samples were collected from 203 men with azoospermia. Total RNA was extracted from the semen precipitates. First-strand complementary deoxyribonucleic acid (cDNA) was synthesized by reverse transcriptase then, (RT)-PCRs were carried out using primers for testis stage-specific genes (DAZ, AKAP4, PRM1, and PRM2). Testicular tissue biopsies were used for evaluating spermatogenesis status in testis. Histopathological examination and LH, FSH, and testosterone level measurements (chemiluminescence assay) were performed. The presence of DAZ and PRM2 transcripts in semen significantly indicated the presence of spermatogonia and spermatids in the testicular tissues. Absence of all four markers in semen confirmed the histopathological results corresponding to sertoli cell only syndrome (SCO). Although TESE should not be excluded solely on this criteria, using PRM1, PRM2, AKAP4, and DAZ transcripts in semen would provide a non-invasive molecular diagnostic tool to better counsel patients before undergoing TESE. PMID:21548847

Aslani, Ferial; Modarresi, Mohammad Hossein; Soltanghoraee, Haleh; Akhondi, Mohammad Mehdi; Shabani, Ashraf; Lakpour, Niknam; Sadeghi, Mohammad Reza

2011-08-01

295

Generation of expressed sequence tags under cadmium stress for gene discovery and development of molecular markers in chickpea.  

PubMed

Chickpea is the world's third most important legume crop and belongs to Fabaceae family but suffered from severe yield loss due to various biotic and abiotic stresses. Development of modern genomic tools such as molecular markers and identification of resistant genes associated with these stresses facilitate improvement in chickpea breeding towards abiotic stress tolerance. In this study, 1597 high-quality expressed sequence tags (ESTs) were generated from a cDNA library of variety Pusa 1105 root tissue after cadmium (Cd) treatment. Assembly of ESTs resulted in a total of 914 unigenes of which putative homology was obtained for 38.8 % of unigenes after BLASTX search. In terms of species distribution, majority of sequences found similarity with Medicago truncatula followed by Glycine max, Vitis vinifera and Populus trichocarpa and Pisum sativum sequences. Functional annotation was assigned using Blast2Go, and the Gene Ontology (GO) terms were categorized into biological process, molecular function and cellular component. Approximately 10.83 % of unigenes were assigned at least one GO term. Moreover, in the distribution of transcripts into various biological pathways, 20 of the annotated transcripts were assigned to ten pathways in KEGG database. A majority of the genes were found to be involved in sulphur and nitrogen metabolism. In the quantitative real-time PCR analysis, five of the transcription factors and three of the transporter genes were found to be highly expressed after Cd treatment. Besides, the utility of ESTs was demonstrated by exploiting them for the development of 83 genic molecular markers including EST-simple sequence repeats and intron targeted polymorphism that would assist in tagging of genes related to metal stress for future prospects. PMID:24414095

Gaur, Rashmi; Bhatia, Sabhyata; Gupta, Meetu

2014-07-01

296

Rapid development of molecular markers by next-generation sequencing linked to a gene conferring phomopsis stem blight disease resistance for marker-assisted selection in lupin (Lupinus angustifolius L.) breeding.  

PubMed

Selection for phomopsis stem blight disease (PSB) resistance is one of the key objectives in lupin (Lupinus angustifolius L.) breeding programs. A cross was made between cultivar Tanjil (resistant to PSB) and Unicrop (susceptible). The progeny was advanced into F(8) recombinant inbred lines (RILs). The RIL population was phenotyped for PSB disease resistance. Twenty plants from the RIL population representing disease resistance and susceptibility was subjected to next-generation sequencing (NGS)-based restriction site-associated DNA sequencing on the NGS platform Solexa HiSeq2000, which generated 7,241 single nucleotide polymorphisms (SNPs). Thirty-three SNP markers showed the correlation between the marker genotypes and the PSB disease phenotype on the 20 representative plants, which were considered as candidate markers linked to a putative R gene for PSB resistance. Seven candidate markers were converted into sequence-specific PCR markers, which were designated as PhtjM1, PhtjM2, PhtjM3, PhtjM4, PhtjM5, PhtjM6 and PhtjM7. Linkage analysis of the disease phenotyping data and marker genotyping data on a F(8) population containing 187 RILs confirmed that all the seven converted markers were associated with the putative R gene within the genetic distance of 2.1 CentiMorgan (cM). One of the PCR markers, PhtjM3, co-segregated with the R gene. The seven established PCR markers were tested in the 26 historical and current commercial cultivars released in Australia. The numbers of "false positives" (showing the resistance marker allele band but lack of the putative R gene) for each of the seven PCR markers ranged from nil to eight. Markers PhtjM4 and PhtjM7 are recommended in marker-assisted selection for PSB resistance in the Australian national lupin breeding program due to its wide applicability on breeding germplasm and close linkage to the putative R gene. The results demonstrated that application of NGS technology is a rapid and cost-effective approach in development of markers for molecular plant breeding. PMID:23086512

Yang, Huaan; Tao, Ye; Zheng, Zequn; Shao, Di; Li, Zhenzhong; Sweetingham, Mark W; Buirchell, Bevan J; Li, Chengdao

2013-02-01

297

The new molecular markers DDIT3, STT3A, ARG2 and FAM129A are not useful in diagnosing thyroid follicular tumors  

Microsoft Academic Search

Preoperative characterization of thyroid follicular lesions is challenging. Fine-needle aspiration specimens cannot differentiate follicular carcinomas from benign follicular neoplasias. Recently, promising markers have been detected using modern molecular techniques. We conducted a retrospective study to confirm the usefulness of immunohistochemical staining for the protein markers, DDIT3, STT3A (ITM1), ARG2 and FAM129A (C1orf24) in separating benign and malignant thyroid follicular lesions.

Eva Sigstad; Elisabeth Paus; Trine Bjøro; Aasmund Berner; Krystyna Kotanska Grøholt; Lars H Jørgensen; Manuel Sobrinho-Simões; Ruth Holm; David J Warren

2012-01-01

298

Molecular mapping of hybrid necrosis genes Ne1 and Ne2 in hexaploid wheat using microsatellite markers.  

PubMed

Hybrid necrosis is the gradual premature death of leaves or plants in certain F1 hybrids of wheat (Triticum aestivum L.), and it is caused by the interaction of two dominant complementary genes Ne1 and Ne2 located on chromosome arms 5BL and 2BS, respectively. To date, molecular markers linked to these genes have not been identified and linkage relationships of the two genes with other important genes in wheat have not been established. We observed that the F1 hybrids from the crosses between the bread wheat variety 'Alsen' and four synthetic hexaploid wheat (SHW) lines (TA4152-19, TA4152-37, TA4152-44, and TA4152-60) developed at the International Maize and Wheat Improvement Center (CIMMYT) exhibited hybrid necrosis. This study was conducted to determine the genotypes of TA4152-60 and Alsen at the Ne1 and Ne2 loci, and to map the genes using microsatellite markers in backcross populations. Genetic analysis indicated that Alsen has the genotype ne1ne1Ne2Ne2 whereas the SHW lines have Ne1Ne1ne2ne2. The microsatellite marker Xbarc74 was linked to Ne1 at a genetic distance of 2.0 cM on chromosome arm 5BL, and Xbarc55 was 3.2 cM from Ne2 on 2BS. Comparison of the genetic maps with the chromosome deletion-based physical maps indicated that Ne1 lies in the proximal half of 5BL, whereas Ne2 is in the distal half of 2BS. Genetic linkage analysis showed that Ne1 was about 35 cM proximal to Tsn1, a locus conferring sensitivity to the host selective toxin Ptr ToxA produced by the tan spot fungus. The closely linked microsatellite markers identified in this study can be used to genotype parental lines for Ne1 and Ne2 or to eliminate the two hybrid necrosis genes using marker-assisted selection. PMID:16518615

Chu, C-G; Faris, J D; Friesen, T L; Xu, S S

2006-05-01

299

Molecular Diversity Assessment Using Sequence Related Amplified Polymorphism (SRAP) Markers in Vicia faba L.  

PubMed Central

Sequence-related amplified polymorphism (SRAP) markers were used to assess the genetic diversity and relationship among 58 faba bean (Vicia faba L.) genotypes. Fourteen SRAP primer combinations amplified a total of 1036 differently sized well-resolved peaks (fragments), of which all were polymorphic with a 0.96 PIC value and discriminated all of the 58 faba bean genotypes. An average pairwise similarity of 21% was revealed among the genotypes ranging from 2% to 65%. At a similarity of 28%, UPGMA clustered the genotypes into three main groups comprising 78% of the genotypes. The local landraces and most of the Egyptian genotypes in addition to the Sudan genotypes were grouped in the first main cluster. The advanced breeding lines were scattered in the second and third main clusters with breeding lines from the ICARDA and genotypes introduced from Egypt. At a similarity of 47%, all the genotypes formed separated clusters with the exceptions of Hassawi 1 and Hassawi 2. Group analysis of the genotypes according to their geographic origin and type showed that the landraces were grouped according to their origin, while others were grouped according to their seed type. To our knowledge, this is the first application of SRAP markers for the assessment of genetic diversity in faba bean. Such information will be useful to determine optimal breeding strategies to allow continued progress in faba bean breeding.

Alghamdi, Salem S.; Al-Faifi, Sulieman A.; Migdadi, Hussein M.; Khan, Muhammad Altaf; El-Harty, Ehab H.; Ammar, Megahed H.

2012-01-01

300

Assessment of molecular diversity at QTLs for preharvest sprouting resistance in wheat using microsatellite markers.  

PubMed

Breeding for preharvest sprouting (PHS) resistance is of great interest in wheat-growing areas where high rainfall occurs during grain ripening and harvest. We have characterized 32 wheat accessions using 33 microsatellite markers flanking PHS quantitative trait loci (QTLs) previously identified on group 3, 4, 5, and 6 chromosomes of hexaploid wheat. A total of 229 alleles, with an average of 6.94 alleles per marker, were observed among the 32 wheat lines. The polymorphic information content (PIC) was estimated and ranged between 0.25 and 0.90, with an average of 0.67. A cluster analysis revealed 3 main clusters and 3 singlet wheat lines, which is in agreement with pedigree-based relationships, seed coat colour, and origin. Canadian wheat accessions were subdivided into 4 sub-clusters based on pedigree and wheat classes. Grouping of preharvest sprouting germplasm into clusters was consistent with cluster-specific allele diversity observed in the PHS-resistant lines AUS1408, Red-RL4137, White-RL4137, and Kenya321. The implications of these findings in white wheat breeding for PHS tolerance are discussed. PMID:18438441

Fofana, Bourlaye; Humphreys, Gavin; Rasul, Golam; Cloutier, Sylvie; Somers, Daryl

2008-05-01

301

Molecular Diversity Assessment Using Sequence Related Amplified Polymorphism (SRAP) Markers in Vicia faba L.  

PubMed

Sequence-related amplified polymorphism (SRAP) markers were used to assess the genetic diversity and relationship among 58 faba bean (Vicia faba L.) genotypes. Fourteen SRAP primer combinations amplified a total of 1036 differently sized well-resolved peaks (fragments), of which all were polymorphic with a 0.96 PIC value and discriminated all of the 58 faba bean genotypes. An average pairwise similarity of 21% was revealed among the genotypes ranging from 2% to 65%. At a similarity of 28%, UPGMA clustered the genotypes into three main groups comprising 78% of the genotypes. The local landraces and most of the Egyptian genotypes in addition to the Sudan genotypes were grouped in the first main cluster. The advanced breeding lines were scattered in the second and third main clusters with breeding lines from the ICARDA and genotypes introduced from Egypt. At a similarity of 47%, all the genotypes formed separated clusters with the exceptions of Hassawi 1 and Hassawi 2. Group analysis of the genotypes according to their geographic origin and type showed that the landraces were grouped according to their origin, while others were grouped according to their seed type. To our knowledge, this is the first application of SRAP markers for the assessment of genetic diversity in faba bean. Such information will be useful to determine optimal breeding strategies to allow continued progress in faba bean breeding. PMID:23211669

Alghamdi, Salem S; Al-Faifi, Sulieman A; Migdadi, Hussein M; Khan, Muhammad Altaf; El-Harty, Ehab H; Ammar, Megahed H

2012-01-01

302

[Serological and molecular genetic markers of hepatitis C virus in infected donors].  

PubMed

The frequency of hepatitis C virus (HCV) markers was determined in donors; the spectrum and activity of specific antibodies (anti-HCV), the distribution of virus genotypes, and HCV RNA concentrations were studied in virus carrier donors. The activity of antibodies in HCV RNA-negative donors was significantly lower than that in HCV RNA-positive donors (p < or = 0.001). There was a statistically significant difference in antibody activities in donors infected with genotype 1b as compared with those infected with genotype 3a (p < 0.001). However, no correlation was found between the concentration of a virus genome and the activity of specific antibodies. The risk for obtaining infected blood donations was determined during plasma screening by enzyme immunoassay (EIA). Our investigations have indicated that the frequency of serological window period donations is one case per 74750 test plasma units and that of HCV RNA-positive donations with low antibody positivity coefficients, which are frequently detectable as seronegative during screening for laboratory errors, is one case per 37375 test units. A combination of EIA and polymerase chain reaction has shown to minimize the risk of contamination of donor plasma with HCV markers. PMID:21260994

Zubkova, N V; Filatova, E V; Zubov, S V

2010-01-01

303

Molecular markers to characterize the hermaphroditic reproductive system of the planarian Schmidtea mediterranea  

PubMed Central

Background The freshwater planarian Schmidtea mediterranea exhibits two distinct reproductive modes. Individuals of the sexual strain are cross-fertilizing hermaphrodites with reproductive organs that develop post-embryonically. By contrast, individuals of the asexual strain reproduce exclusively by transverse fission and fail to develop reproductive organs. These different reproductive strains are associated with distinct karyotypes, making S. mediterranea a useful model for studying germline development and sexual differentiation. Results To identify genes expressed differentially between these strains, we performed microarray analyses and identified >800 genes that were upregulated in the sexual planarian. From these, we characterized 24 genes by fluorescent in situ hybridization (FISH), revealing their expression in male germ cells or accessory reproductive organs. To identify additional markers of the planarian reproductive system, we also used immuno- and fluorescent lectin staining, identifying several antibodies and lectins that labeled structures associated with reproductive organs. Conclusions Collectively, these cell-type specific markers will enable future efforts to characterize genes that are important for reproductive development in the planarian.

2011-01-01

304

Molecular Characterization of Cultivated Bromeliad Accessions with Inter-Simple Sequence Repeat (ISSR) Markers  

PubMed Central

Bromeliads are of great economic importance in flower production; however little information is available with respect to genetic characterization of cultivated bromeliads thus far. In the present study, a selection of cultivated bromeliads was characterized via inter-simple sequence repeat (ISSR) markers with an emphasis on genetic diversity and population structure. Twelve ISSR primers produced 342 bands, of which 287 (~84%) were polymorphic, with polymorphic bands per primer ranging from 17 to 34. The Jaccard’s similarity ranged from 0.08 to 0.89 and averaged ~0.30 for the investigated bromeliads. The Bayesian-based approach, together with the un-weighted paired group method with arithmetic average (UPGMA)-based clustering and the principal coordinate analysis (PCoA), distinctly grouped the bromeliads from Neoregelia, Guzmania, and Vriesea into three separately clusters, well corresponding with their botanical classifications; whereas the bromeliads of Aechmea other than the recently selected hybrids were not well assigned to a cluster. Additionally, ISSR marker was proven efficient for the identification of hybrids and bud sports of cultivated bromeliads. The findings achieved herein will further our knowledge about the genetic variability within cultivated bromeliads and therefore facilitate breeding for new varieties of cultivated bromeliads in future as well.

Zhang, Fei; Ge, Yaying; Wang, Weiyong; Yu, Xinying; Shen, Xiaolan; Liu, Jianxin; Liu, Xiaojing; Tian, Danqing; Shen, Fuquan; Yu, Yongming

2012-01-01

305

Molecular Characterization of Cultivated Bromeliad Accessions with Inter-Simple Sequence Repeat (ISSR) Markers.  

PubMed

Bromeliads are of great economic importance in flower production; however little information is available with respect to genetic characterization of cultivated bromeliads thus far. In the present study, a selection of cultivated bromeliads was characterized via inter-simple sequence repeat (ISSR) markers with an emphasis on genetic diversity and population structure. Twelve ISSR primers produced 342 bands, of which 287 (~84%) were polymorphic, with polymorphic bands per primer ranging from 17 to 34. The Jaccard's similarity ranged from 0.08 to 0.89 and averaged ~0.30 for the investigated bromeliads. The Bayesian-based approach, together with the un-weighted paired group method with arithmetic average (UPGMA)-based clustering and the principal coordinate analysis (PCoA), distinctly grouped the bromeliads from Neoregelia, Guzmania, and Vriesea into three separately clusters, well corresponding with their botanical classifications; whereas the bromeliads of Aechmea other than the recently selected hybrids were not well assigned to a cluster. Additionally, ISSR marker was proven efficient for the identification of hybrids and bud sports of cultivated bromeliads. The findings achieved herein will further our knowledge about the genetic variability within cultivated bromeliads and therefore facilitate breeding for new varieties of cultivated bromeliads in future as well. PMID:22754348

Zhang, Fei; Ge, Yaying; Wang, Weiyong; Yu, Xinying; Shen, Xiaolan; Liu, Jianxin; Liu, Xiaojing; Tian, Danqing; Shen, Fuquan; Yu, Yongming

2012-01-01

306

Novel Molecular Tumor Cell Markers in Regional Lymph Nodes and Blood Samples from Patients Undergoing Surgery for Non-Small Cell Lung Cancer  

PubMed Central

Introduction Recent evidence suggests that microscopic lymph node metastases and circulating tumor cells may have clinical importance in lung cancer. The purpose of this study was to identify new molecular markers for tumor cells in regional lymph nodes (LNs) and peripheral blood (PB) from patients with non-small cell lung cancer (NSCLC). Methods Candidate markers were selected based on digital transcript profiling and previous literature. KRT19, CEACAM5, EPCAM, DSG3, SFTPA, SFTPC and SFTPB mRNA levels were initially validated by real-time reverse transcription PCR-based quantification in 16 NSCLC tumors and 22 LNs and 12 PB samples from individuals without known cancer. Five of the candidate markers were selected for secondary validation by quantification in parallel tumor biopsies, regional LNs and PB samples from 55 patients undergoing surgery for NSCLC. LN and PB marker status were compared to clinicopathological patient data. Results All selected markers except DSG3 were present at high levels in the primary tumors and at very low or non-detectable levels in normal LNs and PB in the first round of validation, indicating a potential for detecting tumor cells in NSCLC patients. The expression profiles of KRT19, CEACAM5, DSG3, SFTPA and SFTPC mRNA were confirmed in the larger group during the secondary validation. Using the highest normal LN level of each marker as threshold, 39 (71%) of the 55 patients had elevated levels of at least one marker in regional LNs. Similarly, 26 (47%) patients had elevated levels of at least one marker in PB. A significantly higher number of patients with adenocarcinomas had positive LN status for these markers, compared with other histological types (P?=?0.004). Conclusions Several promising molecular tumor cell markers in regional LNs and PB were identified, including the new SFTPA and SFTPC mRNAs. Clinical follow-up in a larger cohort is needed to elucidate their prognostic value.

Nordgard, Oddmund; Singh, Gurpartap; Solberg, Steinar; J?rgensen, Lars; Halvorsen, Ann Rita; Smaaland, Rune; Brustugun, Odd Terje; Helland, Aslaug

2013-01-01

307

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

National Technical Information Service (NTIS)

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...

W. F. Rogge G. R. Cass L. M. Hildemann M. A. Mazurek B. R. T. Simoneit

1992-01-01

308

Molecular Markers for Prostate Cancer Risk Stratification from Multiple Ultrasound-Guided Biopsies.  

National Technical Information Service (NTIS)

This goal of this project is to design and test a novel method for isolating cells from transrectal ultrasound-guided prostate cancer biopsy cores as they are extracted in the clinic and to do so in a manner that permits molecular characterization down to...

J. Hicks

2013-01-01

309

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.

2012-01-01

310

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.

2014-01-01

311

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

312

Transgene-specific and event-specific molecular markers for characterization of transgenic papaya lines resistant to Papaya ringspot virus.  

PubMed

The commercially valuable transgenic papaya lines carrying the coat protein (CP) gene of Papaya ringspot virus (PRSV) and conferring virus resistance have been developed in Hawaii and Taiwan in the past decade. Prompt and sensitive protocols for transgene-specific and event-specific detections are essential for traceability of these lines to fulfill regulatory requirement in EU and some Asian countries. Here, based on polymerase chain reaction (PCR) approaches, we demonstrated different detection protocols for characterization of PRSV CP-transgenic papaya lines. Transgene-specific products were amplified using different specific primer pairs targeting the sequences of the promoter, the terminator, the selection marker, and the transgene, and the region across the promoter and transgene. Moreover, after cloning and sequencing the DNA fragments amplified by adaptor ligation-PCR, the junctions between plant genomic DNA and the T-DNA insert were elucidated. The event-specific method targeting the flanking sequences and the transgene was developed for identification of a specific transgenic line. The PCR patterns using primers designed from the left or the right flanking DNA sequence of the transgene insert in three selected transgenic papaya lines were specific and reproducible. Our results also verified that PRSV CP transgene is integrated into transgenic papaya genome in different loci. The copy number of inserted T-DNA was further confirmed by real-time PCR. The event-specific molecular markers developed in this investigation are crucial for regulatory requirement in some countries and intellectual protection. Also, these markers are helpful for prompt screening of a homozygote-transgenic progeny in the breeding program. PMID:19526355

Fan, Ming-Jen; Chen, Shu; Kung, Yi-Jung; Cheng, Ying-Huey; Bau, Huey-Jiunn; Su, Tien-Tsai; Yeh, Shyi-Dong

2009-12-01

313

Association of molecular markers in Plasmodium falciparum crt and mdr1 with in vitro chloroquine resistance: a Philippine study.  

PubMed

Specific mutations in the pfcrt and pfmdr1 genes have been reported to be associated with chloroquine-resistant falciparum malaria parasites worldwide. These genetic markers are considered to be useful tools for the elucidation of several aspects of the epidemiology of drug resistant malaria. In this study, Plasmodium falciparum isolates from three distinct areas of the Philippines were analyzed for drug-resistance-associated genetic mutations, and their association with the in vitro chloroquine (CQ) response. Two novel pfcrt 72-76 allelic types, CVMDT and SVMDT, were detected. The frequency of the pfcrt K76T mutation in the isolates that were successfully tested for in vitro CQ susceptibility was found to be 100% in Kalinga, 80% in Palawan, and 87% in Mindanao. The frequency of the pfmdr1 N86Y mutation was 39% in Kalinga, 35% in Palawan, and 93% in Mindanao isolates. No mutations were found at positions 1042 and 1246 of pfmdr1. However, there were no significant associations found between polymorphisms in these genes and in vitro CQ susceptibility. The results of this study indicate that mutations in pfcrt and pfmdr1 are not predictive of in vitro CQ resistance in Philippine isolates and may therefore not be suitable as molecular markers for surveillance. PMID:19567229

Hatabu, Toshimitsu; Iwagami, Moritoshi; Kawazu, Shin-ichiro; Taguchi, Nao; Escueta, Aleyla D; Villacorte, Elena A; Rivera, Pilarita T; Kano, Shigeyuki

2009-06-01

314

Molecular diversity and relationships among Cymbidium goeringii cultivars based on inter-simple sequence repeat (ISSR) markers.  

PubMed

Spring orchid (Cymbidium goeringii) is a popular flowering plant species. There have been few molecular studies of the genetic diversity and conservation genetics on this species. An assessment of the level of genetic diversity in cultivated spring orchid would facilitate development of the future germplasm conservation for cultivar improvement. In the present study, DNA markers of intersimple sequence repeats (ISSR) were identified and the ISSR fingerprinting technique was used to evaluate genetic diversity in C. goeringii cultivars. Twenty-five ISSR primers were selected to produce a total of 224 ISSR loci for evaluation of the genetic diversity. A wide genetic variation was found in the 50 tested cultivars with Nei's gene diversity (H = 0.2241) and 93.75% of polymorphic loci. Fifty cultivars were unequivocally distinguished based on ISSR fingerprinting. Cultivar-specific ISSR markers were identified in seven of 50 tested cultivars. Unweighted pair-group mean analysis (UPGMA) and principal coordinates analysis (PCA) grouped them into two clusters: one composed the cultivars mainly from Japan, and the other contained three major subclusters mainly from China. Two Chinese subclusters were generally consistent with horticultural classification, and the third Chinese subcluster contained cultivars from various horticultural groups. Our results suggest that the ISSR technique provides a powerful tool for cultivar identification and establishment of genetic relationships of cultivars in C. goeringii. PMID:19085060

Wang, Hui-Zhong; Wu, Zhen-Xing; Lu, Jiang-Jie; Shi, Nong-Nong; Zhao, Yan; Zhang, Zhi-Tao; Liu, Jun-Jun

2009-07-01

315

[Identification and analysis of the specific molecular marker associated with fertile maintenance of cytoplasmic male sterility cauliflower].  

PubMed

Analysis of RAPD (Randomly Amplification Polymorphic DNA) was performed between cytoplasmic male sterility line and its maintainer line of cauliflower. Totally 2160 detectable bands were obtained by RAPD using 406 10-bp random primers. Averagely, 5 to 10 bands were produced per primer. Among all the primers only the amplification of primer S2121 was polymorphic in two lines. A 934-bp specific band was only detected in maintainer line. After cloning and sequencing, specific primers were designed to transform the RAPD marker to PCR marker, which was named S2121(900). To identify the specificity of S2121(900), southern dot blotting was performed. To further identify its specificity, individual plant and candidate materials testing were also performed. All these results indicated that the S2121(900) was specific. It can be used to screen the maintainer lines of cauliflower in early stage. Analysis of the sequence suggested that this fragment was high homologous with the part sequences of mitochondrial genome in Brassica napus and Arabidopsis thaliana. So we supposed the S2121(900) may also derive from mitochondrial genome. Our results here offer new clues for explaining the molecular mechanism of cytoplasic male sterility of cauliflower in other way. PMID:16944598

Wang, Chun Guo; Li, Hui; Song, Wen Qin

2006-06-01

316

[Incomplete congruence between morphobiological characters and sex-specific molecular markers in Pacific salmons: 1. Analysis of discrepancy in five species of the genus Oncorhynchus].  

PubMed

The congruence between molecular markers, identifying the presence of the Y chromosome, and secondary sexual characters was examined in Asian populations of five Pacific salmon species: pink salmon (Oncorhynchus gorbuscha), chum salmon (O. keta), sockeye salmon (O. nerka), chinook salmon (O. tschawytsha), and sima (O. masou). It was demonstrated that in all species examined, the presence or absence of sex-specific molecular markers was to a considerable degree congruent with secondary sexual characters, but in some cases, an incongruence was found. These findings suggested that the mechanism underlying this phenomenon was similar or identical in all species examined. Possible genetic and physiological explanations of this phenomenon are discussed. PMID:20795502

Brykov, Vl A; Kukhlevski?, A D; Podlesnykh, A V

2010-07-01

317

Molecular Markers in Sex Hormone Pathway Genes Associated with the Efficacy of Androgen-Deprivation Therapy for Prostate Cancer  

PubMed Central

Although most advanced prostate cancer patients respond to androgen-deprivation therapy (ADT), the efficacy is widely variable. We investigated whether the host genetic variations in sex hormone pathway genes are associated with the efficacy of ADT. A cohort of 645 patients with advanced prostate cancer treated with ADT was genotyped for 18 polymorphisms across 12 key genes involved in androgen and estrogen metabolism. We found that after adjusting for known risk factors in multivariate Cox regression models, AKR1C3 rs12529 and AR-CAG repeat length remained significantly associated with prostate cancer-specific mortality (PCSM) after ADT (P?0.041). Furthermore, individuals carrying two unfavorable genotypes at these loci presented a 13.7-fold increased risk of PCSM compared with individuals carrying zero (P<0.001). Our results identify two candidate molecular markers in key genes of androgen and estrogen pathways associated with PCSM after ADT, establishing the role of pharmacogenomics in this therapy.

Yu, Chia-Cheng; Huang, Shu-Pin; Lee, Yung-Chin; Huang, Chao-Yuan; Liu, Chia-Chu; Hour, Tzyh-Chyuan; Huang, Chun-Nung; You, Bang-Jau; Chang, Ta-Yuan; Huang, Chun-Hsiung; Bao, Bo-Ying

2013-01-01

318

Use of BRAF V600E as a Molecular Marker in Aggressive Colorectal Cancer.  

PubMed

Aim: to compare the immunoexpression of BRAF V600E among stage of colorectal cancer. Methods: this was a cross sectional, and retrospective study involving Dukes' stage A, B, and C colorectal carcinoma, each with 15 cases. Immunohistochemistry was performed in paraffin-embedded specimens of tumor mass for the assessment of BRAF V600E. The proportion differences of immunoexpression of BRAF V600E among Dukes' stage A, B, and C were tested using Chi-Square test. Results: the result of positive BRAF V600E immunoexpression (moderately to strongly positive) in Dukes' stage A, B, and C were found in 1 of 15 cases, 4 of 15 cases and 13 of 15 cases respectively. BRAF V600E immunoexpression was statistically significant more frequent in Dukes' stage C (p<0,001, Chi-Square test). Conclusion: positive BRAF V600E immunoexpression could be used as a marker of aggresive colorectal carcinoma. PMID:25053682

Hernowo, Bethy S; Ariyanni, Fenny; Suryanti, Sri; Hassan, Abdul H

2014-04-01

319

Molecular complementation of a genetic marker in Dictyostelium using a genomic DNA library.  

PubMed Central

We constructed a partial Sau3A Dictyostelium genomic DNA library in a shuttle vector that replicates extrachromosomally in Dictyostelium cells. This library was used to complement Dictyostelium strain HPS400, which lacks thymidylate synthase activity and requires exogenous thymidine for growth. We have used a modified high-frequency transformation protocol that allows the introduction of the library into a sufficient number of Dictyostelium cells to select complementing plasmids. Using this approach, we have isolated a gene (Thy1) that complements the thymidine growth requirement of HPS400. The gene encodes a 1.2-kilobase RNA and the derived amino acid sequence shows no homology to thymidylate synthase, a protein highly conserved throughout evolution, or any other protein sequence in the data base examined. Thy1 provides an important selectable marker for transforming Dictyostelium cells. In addition, this work suggests that it will be possible to isolate genes that are essential for developmental processes in Dictyostelium by complementation. Images

Dynes, J L; Firtel, R A

1989-01-01

320

Molecular complementation of a genetic marker in Dictyostelium using a genomic DNA library.  

PubMed

We constructed a partial Sau3A Dictyostelium genomic DNA library in a shuttle vector that replicates extrachromosomally in Dictyostelium cells. This library was used to complement Dictyostelium strain HPS400, which lacks thymidylate synthase activity and requires exogenous thymidine for growth. We have used a modified high-frequency transformation protocol that allows the introduction of the library into a sufficient number of Dictyostelium cells to select complementing plasmids. Using this approach, we have isolated a gene (Thy1) that complements the thymidine growth requirement of HPS400. The gene encodes a 1.2-kilobase RNA and the derived amino acid sequence shows no homology to thymidylate synthase, a protein highly conserved throughout evolution, or any other protein sequence in the data base examined. Thy1 provides an important selectable marker for transforming Dictyostelium cells. In addition, this work suggests that it will be possible to isolate genes that are essential for developmental processes in Dictyostelium by complementation. PMID:2813371

Dynes, J L; Firtel, R A

1989-10-01

321

Molecular characterization of Fusarium oxysporum f. melongenae by ISSR and RAPD markers on eggplant.  

PubMed

Fusarium oxysporum f. melongenae is a major soil-borne pathogen of eggplant (Solanum melongena). ISSR and RAPD markers were used to characterize Fusarium oxysporum f. melongenae isolates collected from eggplant fields in southern Turkey. Those isolates were not pathogenic to tomato. Pathogens were identified by their morphology, and their identity was confirmed by PCR amplification using the specific primer PF02-3. The isolates were classified into groups on the basis of ISSR and RAPD fingerprints, which showed a level of genetic specificity and diversity not previously identified in Fusarium oxysporum f. melongenae, suggesting that genetic differences are related to the pathogen in the Mediterranean region. The primers selected to characterize Fusarium oxysporum f. melongenae may be used to determine genetic differences and pathogen virulence. This study is the first to characterize eggplant F. oxysporum species using ISSR and RAPD. PMID:20390339

Baysal, O; Siragusa, M; Gumrukcu, E; Zengin, S; Carimi, F; Sajeva, M; Teixeira da Silva, Jaime A

2010-06-01

322

South American camelid illegal traffic detection by means of molecular markers.  

PubMed

South American camelids comprise the wild species guanaco and vicuña and their respective domestic relatives llama and alpaca. The aim of the present study was to determine by DNA analysis to which of these species belong a herd of camelids confiscated from a llama breeder but alleged to be alpacas by the prosecution, and to evaluate the usefulness of mitochondrial and autosomal DNA markers to solve judicial cases involving camelid taxa. Cytochrome b and cytochrome oxidase I mitochondrial genes and 7 STR were analyzed in 25 confiscated samples. Mitochondrial results were inconclusive because 18 of the sequestered samples presented haplotypes that corresponded to the guanaco haplogroup and the remaining seven belonged to a vicuña linage. Microsatellite data of casework samples and llama reference samples revealed different genetic profiles by the presence of private alleles at two microsatellites suggesting that the confiscated animals could be alpaca, or at least alpaca hybrids instead of pure llama. PMID:21982877

Di Rocco, F; Posik, D M; Ripoli, M V; Díaz, S; Maté, M L; Giovambattista, G; Vidal-Rioja, L

2011-11-01

323

Molecular hierarchy of mammary differentiation yields refined markers of mammary stem cells.  

PubMed

The partial purification of mouse mammary gland stem cells (MaSCs) using combinatorial cell surface markers (Lin(-)CD24(+)CD29(h)CD49f(h)) has improved our understanding of their role in normal development and breast tumorigenesis. Despite the significant improvement in MaSC enrichment, there is presently no methodology that adequately isolates pure MaSCs. Seeking new markers of MaSCs, we characterized the stem-like properties and expression signature of label-retaining cells from the mammary gland of mice expressing a controllable H2b-GFP transgene. In this system, the transgene expression can be repressed in a doxycycline-dependent fashion, allowing isolation of slowly dividing cells with retained nuclear GFP signal. Here, we show that H2b-GFP(h) cells reside within the predicted MaSC compartment and display greater mammary reconstitution unit frequency compared with H2b-GFP(neg) MaSCs. According to their transcriptome profile, H2b-GFP(h) MaSCs are enriched for pathways thought to play important roles in adult stem cells. We found Cd1d, a glycoprotein expressed on the surface of antigen-presenting cells, to be highly expressed by H2b-GFP(h) MaSCs, and isolation of Cd1d(+) MaSCs further improved the mammary reconstitution unit enrichment frequency to nearly a single-cell level. Additionally, we functionally characterized a set of MaSC-enriched genes, discovering factors controlling MaSC survival. Collectively, our data provide tools for isolating a more precisely defined population of MaSCs and point to potentially critical factors for MaSC maintenance. PMID:23580620

dos Santos, Camila O; Rebbeck, Clare; Rozhkova, Elena; Valentine, Amy; Samuels, Abigail; Kadiri, Lolahon R; Osten, Pavel; Harris, Elena Y; Uren, Philip J; Smith, Andrew D; Hannon, Gregory J

2013-04-30

324

Snord 3A: A Molecular Marker and Modulator of Prion Disease Progression  

PubMed Central

Since preventive treatments for prion disease require early identification of subjects at risk, we searched for surrogate peripheral markers characterizing the asymptomatic phases of such conditions. To this effect, we subjected blood mRNA from E200K PrP CJD patients and corresponding family members to global arrays and found that the expression of Snord3A, a non-coding RNA transcript, was elevated several times in CJD patients as compared to controls, while asymptomatic carriers presented intermediate Snord3A levels. In the brains of TgMHu2ME199K mice, a mouse model mimicking for E200K CJD, Snord 3A levels were elevated in an age and disease severity dependent manner, as was the case for brains of these mice in which disease was exacerbated by copper administration. Snord3A expression was also elevated in scrapie infected mice, but not in PrP0/0 mice, indicating that while the expression levels of this transcript may reflect diverse prion etiologies, they are not related to the loss of PrPC’s function. Elevation of Snord3A was consistent with the activation of ATF6, representing one of the arms of the unfolded protein response system. Indeed, SnoRNAs were associated with reduced resistance to oxidative stress, and with ER stress in general, factors playing a significant role in this and other neurodegenerative conditions. We hypothesize that in addition to its function as a disease marker, Snord3A may play an important role in the mechanism of prion disease manifestation and progression.

Cohen, Eran; Avrahami, Dana; Frid, Kati; Canello, Tamar; Levy Lahad, Ephrat; Zeligson, Sharon; Perlberg, Shira; Chapman, Joab; Cohen, Oren S.; Kahana, Esther; Lavon, Iris; Gabizon, Ruth

2013-01-01

325

Using msa-2b as a molecular marker for genotyping Mexican isolates of Babesia bovis.  

PubMed

Variable merozoite surface antigens of Babesia bovis are exposed glycoproteins having a role in erythrocyte invasion. Members of this gene family include msa-1 and msa-2 (msa-2c, msa-2a(1), msa-2a(2) and msa-2b). To determine the sequence variation among B. bovis Mexican isolates using msa-2b as a genetic marker, PCR amplicons corresponding to msa-2b were cloned and plasmids carrying the corresponding inserts were purified and sequenced. Comparative analysis of nucleotide and deduced amino acid sequences revealed distinct degrees of variability and identity among the coding gene sequences obtained from 16 geographically different Mexican B. bovis isolates and a reference strain. Clustal-W multiple alignments of the MSA-2b deduced amino acid sequences performed with the 17 B. bovis Mexican isolates, revealed the identification of three genotypes with a distinct set each of amino acid residues present at the variable region: Genotype I represented by the MO7 strain (in vitro culture-derived from the Mexico isolate) as well as RAD, Chiapas-1, Tabasco and Veracruz-3 isolates; Genotype II, represented by the Jalisco, Mexico and Veracruz-2 isolates; and Genotype III comprising the sequences from most of the isolates studied, Tamaulipas-1, Chiapas-2, Guerrero-1, Nayarit, Quintana Roo, Nuevo Leon, Tamaulipas-2, Yucatan and Guerrero-2. Moreover, these three genotypes could be discriminated against each other by using a PCR-RFLP approach. The results suggest that occurrence of indels within the variable region of msa-2b sequences can be useful markers for identifying a particular genotype present in field populations of B. bovis isolated from infected cattle in Mexico. PMID:19931189

Genis, Alma D; Perez, Jocelin; Mosqueda, Juan J; Alvarez, Antonio; Camacho, Minerva; Muñoz, Maria de Lourdes; Rojas, Carmen; Figueroa, Julio V

2009-12-01

326

Classification of genetic variation for cadmium tolerance in Bermudagrass [Cynodon dactylon (L.) Pers.] using physiological traits and molecular markers.  

PubMed

Cadmium (Cd) is one of the most toxic pollutants that caused severe threats to animal and human health. Bermudagrass is a dominant species in Cd contaminated soils, which can prevent Cd flow and spread. The objectives of this study were to determine the genetic variations in major physiological traits related to Cd tolerance in six populations of Bermudagrass collected from China, and to examine the genetic diversity and relationships among these accessions that vary in Cd tolerance using molecular markers. Plants of 120 accessions (116 natural accessions and 4 commercial cultivars) were exposed to 0 (i.e. control) or 1.5 mM CdSO4·8/3H2O for 3 weeks in hydroponic culture. Turf quality, transpiration rate, chlorophyll content, leaf water content and growth rate showed wide phenotypic variation. The membership function method was used to comprehensively evaluate Cd-tolerance. According to the average subordinate function value, four accessions were classified as the most tolerant genotypes and four accessions as Cd-sensitive genotypes. The trend of Cd tolerance among the six studied populations was as follows: Hunan > South China > North China > Central China > West South China and Xinjiang population. Phylogenetic analysis revealed that the majority of accessions from the same or adjacent regions were clustered into the same groups or subgroups, and the accessions with similar cadmium tolerance displayed a close phylogenetic relationship. Screening genetically diverse germplasm by combining the physiological traits and molecular markers could prove useful in developing Cd-tolerant Bermudagrass for the remediation of mill tailings and heavy metal polluted soils. PMID:24804624

Xie, Yan; Luo, Hongji; Hu, Longxing; Sun, Xiaoyan; Lou, Yanhong; Fu, Jinmin

2014-08-01

327

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.

2012-01-01

328

Assessing molecular and morpho-agronomical diversity and identification of ISSR markers associated with fruit traits in quince (Cydonia oblonga).  

PubMed

Quince is a deciduous tree known to the countries around the Mediterranean since antiquity. Nowadays, quince is used as an ornamental plant, and as a rootstock for pear trees, with its fruit being appreciated mainly for production of jam and sweets rather than for raw consumption. Quince leaves contain compounds with antioxidant, antimicrobial and anticancerous properties that have been the focus of recent research on pharmaceutical and medical uses as well as for food preservatives. An orchard has been established in Greece, composed of quince varieties (Cydonia oblonga, N = 49) collected from different sites of the country (mainly from home gardens), constituting a unique quince gene bank collection for southeast Europe. We made a phenotypic analysis using 26 morphological plus seven agronomical descriptors coupled with molecular techniques in order to examine the genetic diversity within the collection. Principal component analysis using the 33 descriptors identified 10 components explaining the existence of more than 70% of the total variation. Subsequent cluster analysis classified most of the previously identified productive varieties of the quince orchard in the same clade of a dendrogram. Molecular analysis generated by 13 inter-simple sequence repeat primers amplified 139 bands, including 109 polymorphic bands, indicating a level of polymorphism of 79%; mean gene diversity was calculated to be 0.309. Using stepwise multiple regression analysis, a number of markers significantly associated with fire blight susceptibility, yield, mean fruit weight, citric acid content, soluble solid content, and fruit drop were identified. Hence, data extracted by multiple regression analysis could be useful in marker-assisted breeding programs, especially when no previous genetic information is available. PMID:22095599

Ganopoulos, I; Merkouropoulos, G; Pantazis, S; Tsipouridis, C; Tsaftaris, A

2011-01-01

329

Expression of oxysterol binding protein isoforms in opisthorchiasis-associated cholangiocarcinoma: a potential molecular marker for tumor metastasis.  

PubMed

Oxysterols are oxygenated derivatives of cholesterol generated by enzymatic reactions mediated by cytochrome P450 family enzymes or by inflammation-associated non-enzymatic reactions. Oxysterol binding proteins (OSBPs) are cytosolic high affinity receptors for oxysterols. We previously found that OSBPL-8 is upregulated in liver fluke (Opisthorchis viverrini)-induced hamster cholangiocarcinoma (CCA). Our aims were to determine the expression patterns of OSBP isoforms in human CCA tissues and to evaluate whether OSBPs could be used as molecular markers for the identification of blood-borne CCA metastasis. Expression levels of OSBP1, OSBP2, OSBPL-7 and OSBPL-8 in CCA tissues were detected using qRT-PCR and immunohistochemistry. Expression of OSBPs at mRNA level in the blood of CCA patients was also investigated. We confirmed increased expression of OSBPL-8 in O. viverrini -induced hamster CCA tissues. Moreover, increased expression of OSBP1, OSBP2, OSBPL-7 and OSBPL-8 was seen in human CCA tissues. Notably, a significant increased level of OSBPL-7 mRNA was observed in tumor compared to non-tumor liver tissue. Immunohistochemistry supported the mRNA results, in that OSBPL-7 protein was over-expressed in cancer cells and hepatocytes but not in normal biliary cells and surrounding inflammatory cells. Interestingly, in our preliminary results, significantly higher levels of OSBP2 and OSBPL-7 mRNA were seen in blood samples from CCA patients than in healthy controls. These results suggest that OSBP2 and OSBPL-7 might serve as molecular markers for the identification of CCA metastasis in the bloodstream. PMID:21763455

Loilome, Watcharin; Wechagama, Pairoj; Namwat, Nisana; Jusakul, Apinya; Sripa, Banchob; Miwa, Masanao; Kuver, Rahul; Yongvanit, Puangrat

2012-03-01

330

Dormancy in white-grained wheat: Progress towards identification of genes and molecular markers  

Microsoft Academic Search

Preharvest sprouting limits the consistent production of high quality wheat in many regions of the world. Improvements in\\u000a tolerance from the introduction of better grain dormancy at, or near, harvest-ripeness would be expected to have a significant\\u000a impact on the incidence and severity of sprouting. Genetic and molecular investigations have provided new evidence for the\\u000a presence of dormancy genes on

Daryl Mares; Kolumbina Mrva; Mui-Keng Tan; Peter Sharp

2002-01-01

331

Development of a molecular marker for specific detection of Fusarium oxysporum f. sp. cubense race 4  

Microsoft Academic Search

Fusarium oxysporum f. sp. cubense is the causal agent of Panama disease of banana. A rapid and reliable diagnosis is the foundation of integrated disease management\\u000a practices in commodity crops. For this diagnostic purpose, we have developed a reliable molecular method to detect Foc race\\u000a 4 isolates in Taiwan. By PCR amplification, the primer set Foc-1\\/Foc-2 derived from the sequence

Ying-Hong Lin; Jing-Yi Chang; En-Tzu Liu; Chih-Ping Chao; Jenn-Wen Huang; Pi-Fang Linda Chang

2009-01-01

332

Molecular Markers and Changes of Computed Tomography Appearance in Lung Adenocarcinoma with Ground-glass Opacity  

Microsoft Academic Search

Background: High-resolution computed tomography (HRCT) of lung adenocarcinoma at early stage shows pure ground-glass opacity (GGO) and most cases of pure GGO remain stable during follow-up. There is no consensus on the strategy for follow-up. Identification of the molecular mechanisms that are associated with the natural history of lung adenocarci- noma should provide useful information. Methods: Twenty-three lung adenocarcinomas that

Yukihiro Yoshida; Akiko Kokubu; Kenji Suzuki; Hidehiko Kuribayashi; Koji Tsuta; Yoshihiro Matsuno; Masahiko Kusumoto; Yae Kanai; Hisao Asamura; Setsuo Hirohashi; Tatsuhiro Shibata

2007-01-01

333

High-resolution mapping of the Brassica napus Rfp restorer locus using Arabidopsis -derived molecular markers  

Microsoft Academic Search

The two forms of cytoplasmic male sterility (CMS) native to the oilseed rape or canola species Brassica napus, nap and pol, have novel features that may provide insight into the molecular mechanisms through which CMS\\/nuclear restorer systems evolve.\\u000a One such feature is the finding that the distinct nuclear restorer genes for the two systems represent different alleles or\\u000a haplotypes of

Nataša Formanová; Rachel Stollar; Rachel Geddy; Laetitia Mahé; Martin Laforest; Benoit S. Landry; Gregory G. Brown

2010-01-01

334

Molecular phylogeny of Old World swifts (Aves: Apodiformes, Apodidae, Apus and Tachymarptis) based on mitochondrial and nuclear markers.  

PubMed

We provide a molecular phylogeny for Old World swifts of genera Apus and Tachymarptis (tribe Apodini) based on a taxon-complete sampling at the species level. Phylogenetic reconstructions were based on two mitochondrial (cytochrome b, 12S rRNA) and three nuclear markers (introns of fibrinogen and glyceraldehyde 3-phosphate dehydrogenase plus anonymous marker 12884) while the myoglobin intron 2 did not show any intergeneric variation or phylogenetic signal among the target taxa at all. In contrast to previous hypotheses, the two genera Apus and Tachymarptis were shown as reciprocally monophyletic in all reconstructions. Apus was consistently divided into three major clades: (1) East Asian clade of A. pacificus and A. acuticauda, (2) African-Asian clade of A. caffer, A. batesi, A. horus, A. affinis and A. nipalensis, (3) African-Palearctic clade of eight currently accepted species among which sequences of A. apus and A. pallidus clustered in a terminal crown clade. Phylogenetic signal of all four nuclear markers was extremely shallow within and among species of tribe Apodini and even among genera, such that intra- and intergeneric relationships of Apus, Tachymarptis and Cypsiurus were poorly resolved by nuclear data alone. Four species, A. pacificus, A. barbatus, A. affinis and A. caffer were consistently found to be paraphyletic with respect to their closest relatives and possible taxonomic consequences are discussed without giving particular recommendations due to limitations of sampling. Incomplete mitochondrial lineage sorting with cytochrome-b haplotypes shared among species and across large geographic distances was observed in two species pairs: A. affinis/A. nipalensis and A. apus/A. pallidus. Mitochondrial introgression caused by extant or past gene flow was ruled out as an explanation for the low interspecific differentiation in these two cases because all nuclear markers appeared to be highly unsorted among Apus species, too. Apparently, the two extant species pairs originated from very recent dispersal and/or speciation events. The currently accepted superspecies classification within Apus was not supported by our results. PMID:22361213

Päckert, Martin; Martens, Jochen; Wink, Michael; Feigl, Anna; Tietze, Dieter Thomas

2012-06-01

335

What's New in Immunology?  

PubMed Central

Since 1950, immunology has developed with such rapidity as an interdisciplinary science that even those within the field have difficulty keeping adequately informed. For this reason it is important that those who are closer to the subject, wherever possible, apply recent advances to the practice of medicine in general and primary care in particular. This paper describes a limited number of recent advances in the field of cellular immunology and immunodeficiency diseases. Above all, it attempts to relate the practical significance of these discoveries to the care of the patient by the primary care physician.

Armstrong, W. D.

1975-01-01

336

Immunologically Mediated Dementias  

PubMed Central

Although most dementias are due to neurodegenerative or vascular disease, it is important to diagnose immunologically mediated dementias quickly because they can be both rapidly progressive and readily treatable. They usually affect function of limbic and cortical structures, but subcortical involvement can also occur. Because of the variety of symptoms and the rapid course, these dementias present a particular challenge to the clinician and may require evaluation and intervention in the inpatient setting. Diagnostic workup typically reveals evidence of an autoimmune process and, in some cases, cancer. In contrast to the neurodegenerative processes, many of the immunologically mediated dementias respond to immunomodulatory therapy.

Rosenbloom, Michael H.; Smith, Sallie; Akdal, Gulden; Geschwind, Michael D.

2009-01-01

337

Novel solution-phase immunoassays for molecular analysis of tumor markers.  

PubMed

at 3 x 10(9) M(-1) and a step-wise binding process with PSA-free MAB. Thus, this solution-phase quantitative ECL immunoassay allowed measurement of the affinity of serum PSAs with their MABs and screening of PSAs based upon their affinity to MABs. Unlike other immunoassays, this immunoassay demonstrated one-step rapid analysis while simultaneously eliminating immobilization, separation and washing steps and detected PSA at a level of 1.7 pg mL(-1), which is 1000-fold more sensitive than current PSA immunoassays. Furthermore, single-molecule (SM) phosphorescence microscopy was developed to detect single serum PSA-free and PSA-complex molecules in solution with no use of antibody showing that PSA-free molecules diffused faster than PSA-complex molecules in solution. This finding is consistent with ECL measurements and implies the possibility of screening individual analytes in a complex mixture using their distinct SM diffusion distance. This is the first report describing the detection of single protein molecules labeled with a metal-complex using phosphorescence microscopy and also the screening of serum tumor markers using ECL and SM phosphorescence solution-phase assays. PMID:11534594

Xu, X H; Jeffers, R B; Gao, J; Logan, B

2001-08-01

338

Mutations in p53 as potential molecular markers for human breast cancer.  

PubMed Central

Based on the high incidence of loss of heterozygosity for loci on chromosome 17p in the vicinity of the p53 locus in human breast tumors, we investigated the frequency and effects of mutations in the p53 tumor suppressor gene in mammary neoplasia. We examined the p53 gene in 20 breast cancer cell lines and 59 primary breast tumors. Northern blot analysis, immunoprecipitation, and nucleotide sequencing analysis revealed aberrant mRNA expression, over-expression of protein, and point mutations in the p53 gene in 50% of the cell lines tested. A multiplex PCR assay was developed to search for deletions in the p53 genomic locus. Multiplex PCR of genomic DNA showed that up to 36% of primary tumors contained aberrations in the p53 locus. Mutations in exons 5-9 of the p53 gene were found in 10 out of 59 (17%) of the primary tumors studies by single-stranded conformation polymorphism analysis. We conclude that, compared to amplification of HER2/NEU, MYC, or INT2 oncogene loci, p53 gene mutations and deletions are the most frequently observed genetic change in breast cancer related to a single gene. Correlated to disease status, p53 gene mutations could prove to be a valuable marker for diagnosis and/or prognosis of breast neoplasia. Images

Runnebaum, I B; Nagarajan, M; Bowman, M; Soto, D; Sukumar, S

1991-01-01

339

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

340

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

341

Population genetic structure and trait associations in forest savory using molecular, morphological and phytochemical markers.  

PubMed

In this investigation, morphological, phytochemical and ISSR markers were used to estimate the relationships among and within seven populations of white savory (Satureja mutica), belonging to four provinces in Iran. The individuals were phenotypically diverse, which stamen length, corolla length, corolla diameter, calyx length, bract length, inflorescence length, calyx length and bracteole width were characteristics with the highest variation. Leaf dimensions were in significant correlation with flower and inflorescence characteristics. Chemical compounds of essential oils were found variable in various individuals and all samples were principally composed of phenolic constituents (carvacrol and/or thymol). As a consequence, the plants were classified into two major chemotypes including carvacrol and thymol. A total of 197 band positions were produced by 14 ISSR primers, of which 176 were found polymorphic with 88.91% polymorphism. ISSR genetic similarity values among individuals ranged between 0.45 and 0.94 which was indicative of a high level of genetic variation. Multiple regression analysis (MRA) revealed that phytochemical compositions as dependent variable, showed statistically significant correlation and in association with leaf and flower traits as independent variable, indicating a main role of leaf and flower on production of these compounds. Also, several ISSR fragments were found associated with some morphological traits and phytochemical compositions. The high diversity within and among populations of S. mutica according to different data systems could provide useful information for conservation and selection of cross-parents in breeding programs. PMID:24878369

Khadivi-Khub, Abdollah; Karimi, Ehsan; Hadian, Javad

2014-08-10

342

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.

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

2012-01-01

343

Phenotypic screening and molecular analysis of blast resistance in fragrant rice for marker assisted selection.  

PubMed

Experiments were conducted to identify blast-resistant fragrant genotypes for the development of a durable blast-resistant rice variety during years 2012-2013. The results indicate that out of 140 test materials including 114 fragrant germplasms, 25 differential varieties (DVs) harbouring 23 blast-resistant genes, only 16 fragrant rice germplasms showed comparatively better performance against a virulent isolate of blast disease. The reaction pattern of single-spore isolate of Magnaporthe oryzae to differential varieties showed that Pish, Pi9, Pita-2 and Pita are the effective blast-resistant genes against the tested blast isolates in Bangladesh. The DNA markers profiles of selected 16 rice germplasms indicated that genotype Chinigura contained Pish, Pi9 and Pita genes; on the other hand, both BRRI dhan50 and Bawaibhog contained Pish and Pita genes in their genetic background. Genotypes Jirakatari, BR5, and Gopalbhog possessed Pish gene, while Uknimodhu, Deshikatari, Radhunipagol, Kalijira (3), Chinikanai each contained the Pita gene only. There are some materials that did not contain any target gene(s) in their genetic background, but proved resistant in pathogenicity tests. This information provided valuable genetic information for breeders to develop durable blast-resistant fragrant or aromatic rice varieties in Bangladesh. PMID:24841958

Khan, Mohammad Ashik Iqbal; Sen, Partha Pratim; Bhuiyan, Rejwan; Kabir, Enamul; Chowdhury, Abul Kashem; Fukuta, Yoshimichi; Ali, Ansar; Latif, Mohammad Abdul

2014-05-01

344

Proteomic research in bivalves: towards the identification of molecular markers of aquatic pollution.  

PubMed

Biomonitoring of aquatic environment and assessment of ecosystem health play essential roles in the development of effective strategies for the protection of the environment, human health and sustainable development. Biomarkers of pollution exposure have been extensively utilized in the last few decades to monitor the health of organisms and hence assess environmental status. However, the use of single biomarkers against biotic or abiotic stressors may be limited by the lack of sensitivity and specificity. Therefore, more recently, the search for novel biomarkers has been focused on the application of OMICS methodologies. Environmental proteomics focuses on the analysis of an organism's proteome and the detection of changes in the level of individual proteins/peptides in response to environmental stressors. Proteomics can provide a more robust approach for the assessment of environmental stress and therefore exposure to pollutants. This review aims to summarize the proteomic research in bivalves, a group of sessile and filter feeding organisms that play an important function as "sentinels" of the aquatic environment. A description of the main proteomic methodologies is provided. The current knowledge in bivalves' toxicology, achieved with proteomics, is reported describing the main biochemical markers identified. A brief discussion regarding future challenges in this area of research emphasizing the development of more descriptive gene/protein databases that could support the OMICs approaches is presented. PMID:22579653

Campos, Alexandre; Tedesco, Sara; Vasconcelos, Vitor; Cristobal, Susana

2012-07-19

345

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

346

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.

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

2012-01-01

347

[Proteases from Pseudomonas: immunologic comparison].  

PubMed

We studied 5 strains of Pseudomonas fluorescens, its ability to produce proteolytic enzymes and the antigenic relatedness between P. fluorescens and P. aeruginosa proteases. Cells were grown in tryptic soy broth plus 2% skim milk powder, at 4 C during 5 days. All the proteases acted on gelatin, casein, and showed limited activity on congo redelastin. By zymograms in polyacrylamide gel (PAA), one enzyme responsible of whole enzymatic activity was shown. The extracellular protease of the strain P. fluorescens ATCC 17400 was purified by ammonium sulfate precipitation (60% saturation) and chromatography on DEAE cellulose with ionic strength gradient, and Sephadex G 100. A 181 fold increase in specific activity with a recovery of 21% was obtained. PAA-sodium dodecyl sulfate revealed a single band with a molecular weight of approximately 45,700 +/- 1,000 Daltons. P. fluorescens antiprotease rabbit serum showed by immunodiffusion (ID) and countercurrent immunoelectrophoresis (CIEF) identity pattern of reaction with the homology strains studied. Rabbit sera antielastase and anti-alkaline protease of P. aeruginosa did not exhibit by ID, CIEF and immunoblotting immunological reactivity with antigen (protease) from P. fluorescens; by enzyme linked immunosorbent assay (ELISA), P. aeruginosa antielastase rabbit serum showed a weak response with P. fluorescens protease. These preliminary observations showed analogy in enzymatic functions, such as specificity, between the enzymes produced by phylogenetically related species, but the immunological studies showed very little interspecific homology. PMID:8140333

Monetto de Ledesma, A M

1993-01-01

348

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.

2013-01-01

349

A set of multiplex panels of microsatellite markers for rapid molecular characterization of rice accessions  

PubMed Central

Background This study aimed to analyze the efficiency of three new microsatellite multiplex panels, which were designed to evaluate a total of 16 loci of the rice genome, based on single PCR reactions of each panel. A sample of 548 accessions of traditional upland rice landraces collected in Brazil in the last 25 years was genotyped, a database of allelic frequencies was established, estimates of genetic parameters were performed and analysis of genetic structure of the collection was developed. Results The three panels yielded a combined matching probability of 6.4 × 10-21, polymorphism information content (PIC) of 0.637, and a combined power of exclusion greater than 99.99%. A few samples presented a genetic background of indica rice. The 16 SSR loci produced a total of 229 alleles. Gene diversity values averaged 0.667, and PIC values averaged 0.637. Genetic structure analysis of the collection using a Bayesian approach detected three possible major clusters, with an overall FST value of 0.177. Important inputs on the knowledge about upland rice germplasm differentiations which happened in Brazil in the last few centuries were also achieved and are discussed. Conclusion The three multiplex panels described here represent a powerful tool for rice genetic analysis, offering a rapid and efficient option for rice germplasm characterization. The data gathered demonstrates the feasibility of genotyping extensive germplasm collections using panels of multiplexed microsatellite markers. It contributes to the advancement of research on large scale characterization and management of germplasm banks, as well as identification, protection and assessments of genetic relationship of rice germplasm.

Pessoa-Filho, Marco; Belo, Andre; Alcochete, Antonio AN; Rangel, Paulo HN; Ferreira, Marcio E

2007-01-01

350

Metabolomics and molecular marker analysis to explore pepper (Capsicum sp.) biodiversity.  

PubMed

An overview of the metabolic diversity in ripe fruits of a collection of 32 diverse pepper (Capsicum sp.) accessions was obtained by measuring the composition of both semi-polar and volatile metabolites in fruit pericarp, using untargeted LC-MS and headspace GC-MS platforms, respectively. Accessions represented C. annuum, C. chinense, C. frutescens and C. baccatum species, which were selected based on variation in morphological characters, pungency and geographic origin. Genotypic analysis using AFLP markers confirmed the phylogenetic clustering of accessions according to Capsicum species and separated C. baccatum from the C. annuum-C. chinense-C. frutescens complex. Species-specific clustering was also observed when accessions were grouped based on their semi-polar metabolite profiles. In total 88 semi-polar metabolites could be putatively identified. A large proportion of these metabolites represented conjugates of the main pepper flavonoids (quercetin, apigenin and luteolin) decorated with different sugar groups at different positions along the aglycone. In addition, a large group of acyclic diterpenoid glycosides, called capsianosides, was found to be highly abundant in all C. annuum genotypes. In contrast to the variation in semi-polar metabolites, the variation in volatiles corresponded well to the differences in pungency between the accessions. This was particularly true for branched fatty acid esters present in pungent accessions, which may reflect the activity through the acyl branch of the metabolic pathway leading to capsaicinoids. In addition, large genetic variation was observed for many well-established pepper aroma compounds. These profiling data can be used in breeding programs aimed at improving metabolite-based quality traits such as flavour and health-related metabolites in pepper fruits. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11306-012-0432-6) contains supplementary material, which is available to authorized users. PMID:23335867

Wahyuni, Yuni; Ballester, Ana-Rosa; Tikunov, Yury; de Vos, Ric C H; Pelgrom, Koen T B; Maharijaya, Awang; Sudarmonowati, Enny; Bino, Raoul J; Bovy, Arnaud G

2013-02-01

351

Reproductive immunology: biomarkers of compromised pregnancies  

SciTech Connect

The objective of this paper is to consider several catagories of biomarkers of human pregnancy. The design of the report is to discuss useful and promising markers and techniques. Research gaps, needs, and priorities are also defined. Useful markers are mixed lymphocyte culture reactions, measures of lymphocytotoxic antibodies, histocompatibility (HLA) typing, and immunohematological evaluations. Promising markers are measures of major basic protein and early pregnancy factor, as well as determinations of trophoblast-lymphocyte cross-reactive (TLX) antigens. Promising techniques are flourescence-activated cell-sorter analysis of maternal blood for fetal and extraembryonic tissues and immunotherapy with TLX and other antigens to prevent spontaneous abortion. It is concluded that immunology has much to offer the development of biomarkers of human pregnancy.

Faulk, W.P.; Coulam, C.B.; McIntyre, J.A.

1987-10-01

352

Construction of Brassica B genome synteny groups based on chromosomes extracted from three different sources by phenotypic, isozyme and molecular markers  

Microsoft Academic Search

The three B genomes of Brassica contained in B. nigra, B. carinata and B. juncea were dissected by addition in B. napus. Using phenotypic, isozyme and molecular markers we characterized 8 alien B-genome chromosomes from B. nigra and B. carinata and 7 from B. juncea by constructing synteney groups. The alien chromosomes of the three different sources showed extensive intragenomic

D. Struss; C. F. Quiros; J. Plieske; G. Riibbelen

1996-01-01

353

Ten-Eleven Translocation-2 gene mutations: A potential new molecular marker in malignant gliomas (Review)  

PubMed Central

Alterations of the Ten-Eleven Translocation-2 (TET2) gene in myeloid malignancies and isocitrate dehydrogenase (IDH) gene mutations in gliomas and myeloid malignancies have recently been identified using molecular, comparative genomic hybridization and single nucleotide polymorphism array techniques. The mutations of the TET2 gene have been shown to be mutually exclusive with IDH1/2 mutations in acute myeloid leukemia (AML) and evidence has been found to provide a biochemical basis for the mutual exclusivity of IDH1/2 and TET2 gene mutations. Based on mounting evidence, we aimed to investigate whether TET2 mutations may be identified as novel mutations in malignant gliomas without IDH1/2 mutations, and indicate their possible significance in gliomas.

YU, LEI; QI, SONGTAO

2012-01-01

354

[Molecular markers related to prognosis of acute myeloid leukemia-review].  

PubMed

Numerous genetic abnormalities which can not be identified by cytogenetic detection (e.g., gene mutations, gene expression abnormalities) have been gradually found, which means that the further molecular classification of AML (acute myeloid leukemia) with distinctive prognosis have arrived. For example, mutations of the transcription factor (CCAAT enhancer binding factor alpha, C/EBPalpha) or nucleophosmin-1 (NPM1) may predict better prognosis, whereas partial tandem duplications of the MLL gene (MLL-PTD), internal tandem duplications of FLT3 (FLT3-ITD) or mutations of WT1 gene confer worse prognosis. This review focuses on the features and relationship of these genetic abnormalities, as well as their influence on the prognosis of AML. PMID:19698266

Sun, Chao; Zhang, Su-Jiang; Li, Jian-Yong; Sheng, Yun-Feng

2009-08-01

355

Molecular diversity of Enteromorpha from the coast of Yantai: a dual-marker assessment  

NASA Astrophysics Data System (ADS)

We collected nine Enteromorpha specimens from the coast of Yantai and evaluated their diversity based on analyses of their ITS (internal transcribed spacer) and 5S rDNA NTS (non-transcribed spacer) sequences. The ITS sequences showed slight nucleotide divergences between Enteromorpha linza and Enteromorpha prolifera. In contrast, multiple highly variable regions were found in the ITS region of Enteromorpha flexuosa. In general, there were more variable sites in the NTS region than in the ITS region in the three species. The variations in 5S rDNA NTS sequences indicated that the molecular diversity of Enteromorpha from the coast of Yantai is very high. However, a phylogenetic tree constructed using 5S rDNA NTS sequence data indicated that genetic differences were not directly related to geographical distribution.

Liu, Haiyan; Liu, Zhengyi; Wang, Yinchu; Zhao, Yushan; Qin, Song

2013-11-01

356

From Markers to Molecular Mechanisms: Type 1 Diabetes in the Post-GWAS Era  

PubMed Central

By the year 2000, a draft of the human genome sequence was completed. Millions of single-nucleotide polymorphisms (SNPs) had been deposited into public databases, and high throughput technologies were under development for SNP genotyping. At that time, it was predicted that large case control association studies would provide far better resolution and power than genome-wide linkage studies. Type 1 diabetes was one of the first phenotypes to be examined by genome-wide association studies (GWAS), and to date over 50 genomic regions have been associated with the disease. In general, the great majority of these loci individually contribute a relatively small degree of risk, and most loci lie outside of coding sequences. The identification of molecular mechanisms from these genomic data therefore remains a significant challenge. Here, we summarize genetic candidate, linkage, and association studies of type 1 diabetes and discuss a potential strategy to identify mechanisms of disease from genomic data.

Baxter, Alan G.; Jordan, Margaret A.

2012-01-01

357

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.

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

358

Immunological Treatments for Autism.  

ERIC Educational Resources Information Center

This article discusses research findings that indicate immunological abnormalities in children with autism, including the dysregulation of the immune system, and concludes that there are sufficient data to suggest a role of the immune system in the pathogenesis of autism. Various biological therapies are analyzed, including intravenous…

Gupta, Sudhir

2000-01-01

359

Immunological disbalance in carcinogenesis.  

PubMed

It is postulated a conception of immunological disbalance between carcinogenesis inhibiting and stimulating antibodies (Ab). Inhibiting Ab prevent the carcinogens and estradiol but increase the progesterone penetration into the target cells. And vise versa do stimulating Ab. Inhibiting Ab could be blocked by corresponding antiidiotypic Ab. The processes of carcinogenesis initiation and promotion are intensified when stimulating Ab prevail over inhibiting ones. PMID:24932578

Glushkov, Andrey N

2014-08-01

360

20. Immunologic neuromuscular disorders  

Microsoft Academic Search

Immune-mediated disorders of each of the structural subdivisions of the nervous and neuromuscular system have been described. Despite the immune privilege of the central nervous system, and to a lesser extent the peripheral nervous system, immune dysregulation is not uncommon. Environmental, genetic, and immunologic factors have been postulated to be involved in the development of these disorders. Major immune-mediated neurologic

Tanuja Chitnis; Samia J. Khoury

2003-01-01

361

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

362

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

363

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

364

Purification and characterization of high- and low-molecular-mass isoforms of phosphoenolpyruvate carboxylase from Chlamydomonas reinhardtii. Kinetic, structural and immunological evidence that the green algal enzyme is distinct from the prokaryotic and higher plant enzymes.  

PubMed Central

Phosphoenolpyruvate carboxylase (PEPC) is a key enzyme in the supply of carbon skeletons for the assimilation of nitrogen by green algae. Two PEPC isoforms with respective native molecular masses of 400 (PEPC1) and 650 (PEPC2) kDa have been purified from Chlamydomonas reinhardtii CW-15 cc1883 (Chlorophyceae). SDS/PAGE, immunoblot and CNBr peptide-mapping analyses indicate the presence of the same 100 kDa PEPC catalytic subunit in both isoforms. PEPC1 is a homotetramer, whereas PEPC2 seems to be a complex between the PEPC catalytic subunit and other immunologically unrelated polypeptides of 50-70 kDa. Kinetic analyses indicate that these PEPC isoforms are (1) differentially regulated by pH, (2) activated by glutamine and dihydroxyacetone phosphate and (3) inhibited by glutamate, aspartate, 2-oxoglutarate and malate. These results are consistent with the current model for the regulation of anaplerotic carbon fixation in green algae, and demonstrate that green algal PEPCs are uniquely regulated by glutamine. Several techniques were used to assess the structural relationships between C. reinhardtii PEPC and the higher plant or prokaryotic enzyme. Immunoblot studies using anti-(green algal or higher plant PEPC) IgGs suggested that green algal (C. reinhardtii, Selenastrum minutum), higher plant (maize, banana fruit, tobacco) and prokaryotic (Synechococcus leopoliensis, Escherichia coli) PEPCs have little or no immunological relatedness. Moreover, the N-terminal amino acid sequence of the C. reinhardtii PEPC subunit did not have significant similarity to the highly conserved corresponding region in enzymes from higher plants, and CNBr cleavage patterns of green algal PEPCs were distinct from those of higher plant and cyanobacterial PEPCs. These results point to significant evolutionary divergence between green algal, higher plant and prokaryotic PEPCs.

Rivoal, J; Plaxton, W C; Turpin, D H

1998-01-01

365

Pathogenesis of Ovarian Serous Carcinoma as the Basis for Immunologic Directed Diagnosis and Treatment. Project 1 - Molecular Characterization of Ovarian Serous Tumors Developing Along Different Pathways.  

National Technical Information Service (NTIS)

The purpose of this study is to elucidate the pathogenesis of serous carcinoma by identifying the molecular genetic changes and preferentially expressed genes of different histological types of serous neoplasms. We hypothesize that the development of sero...

R. J. Kurman I. Shih

2003-01-01

366

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

367

Morphological and molecular marker contributions to disentangling the cryptic Hermeuptychia hermes species complex (Nymphalidae: Satyrinae: Euptychiina).  

PubMed

The genus Hermeuptychia is common and widespread through the Americas, from Argentina to the southern United States of America. All eight recognized species within Hermeuptychia are small and brown, with very similar interspecific external morphologies and intraspecifically variable ocelli patterns that render taxonomic identification based on morphology difficult. In our study, we surveyed variability within Hermeuptychia, and evaluated species boundaries based on molecular data (sequences of the 'barcode' mitochondrial DNA COI gene) and morphology (mainly male genitalia), using a phylogenetic approach. We found eight DNA-based and 12 morphological groups in our sampling. Species names were assigned based mainly on comparisons with male genitalia morphology descriptions corresponding to name-bearing type specimens. Morphological and DNA variability were highly congruent, with the exception of group H, the Hermeuptychia cucullina complex. Also, the barcode region showed a clear threshold for intra- and interspecific mean distances around 2%. Based on these results, we circumscribe the species boundaries in the genus Hermeuptychia and discuss conflicts between mitochondrial genes and classic morphological approaches for identifying and delimiting species. Our study revealed cryptic diversity within an ubiquitous genus of Neotropical butterflies. PMID:24034669

Seraphim, N; Marín, M A; Freitas, A V L; Silva-Brandão, K L

2014-01-01

368

Molecular Markers in the Quelccaya Ice Cap, Peru Describe 20th Century Biomass Burning Variability  

NASA Astrophysics Data System (ADS)

Organic geochemical analytical methods were applied to Andean ice core samples, resulting in a multi- molecular biomass burning record spanning 1915 to 2001 AD. The Quelccaya Ice Cap in Peru is situated on the eastern flank of the Andes at 14°S and is well situated to receive aeolian inputs of organic matter derived from Amazonian forest fire events. Compounds of interest, which occur in trace quantities in ice, were recovered by stir bar sorptive extraction and analyzed by gas chromatography/time-of-flight mass spectrometry coupled with thermal desorption. These methods permitted identification and quantitation of numerous biomarkers in sample volumes of as little as 10 ml. At least one wet and dry season sample was analyzed for every year. Observed biomarkers that may be derived from vegetation fires include several polycyclic aromatic hydrocarbons (PAHs), atraric acid, 2-ethylhexyl p-methoxycinnamate, and a range of other aromatic compounds. Abrupt changes in compound abundances were superimposed on decadal variability. Systematic offsets between wet and dry season abundances were not observed, suggesting that the biomass burning signal is not biased by seasonal depositional effects, such as dust delivery. Inputs likely reflect a combination of sources from anthropogenic burning of the Amazon rainforest as well as natural fires related to aridity, and include both high and low elevation vegetation. These compounds and techniques can be applied to older ice in this and other core locations as an independent estimate of aridity.

Makou, M. C.; Thompson, L. G.; Eglinton, T. I.; Montluçon, D. B.

2007-12-01

369

Molecular characterization of Platonia insignis Mart. ("bacurizeiro") using inter simple sequence repeat (ISSR) markers.  

PubMed

Platonia insignis Mart. (Clusiaceae) is widespread throughout the Amazon and adjacent areas. The fruits (known locally as "bacuri") have significant commercial potential, but the species is under threat from agro-industrial expansion. The genetic variability within 72 genotypes of P. insignis belonging to ten populations collected in the Brazilian states of Maranhão and Piauí, and maintained in the germplasm collection of Embrapa Meio-Norte, has been determined, and the organization of genetic diversity within populations, between populations and among geographic groups verified. Eighteen selected inter simple sequence repeat primers allowed amplification of 236 loci of which 221 (93.64%) were polymorphic, indicating a high level of genetic diversity. At the population level, the Shannon and Nei diversity indices ranged from 0.082 to 0.323 and from 0.120 to 0.480, respectively. The global coefficient of genetic differentiation (G(ST)) was 0.4730 indicating that differentiation between populations was significant, a finding that was confirmed by analysis of molecular variance (?(ST) = 0.28). UPGMA cluster analysis revealed that the genotypes could be stratified into groups that were well defined and consistent with those identified in the dendrogram constructed using pair wise ?(ST) values. The high genetic diversity established in this study may facilitate the management and conservation of the germplasm of P. insignis. PMID:23275206

Souza, I G B; Souza, V A B; Lima, P S C

2013-05-01

370

Use of locus-specific AFLP markers to construct a high-density molecular map in barley  

Microsoft Academic Search

By using 25 primer combinations, 563 AFLP markers segregating in a recombinant inbred population (103 lines, F9) derived from L94\\/Vada were generated. The 38 AFLP markers in common to the existing AFLP\\/RFLP combined Proctor\\/Nudinka map,\\u000a one STS marker, and four phenotypic markers with known map positions, were used to assign present AFLP linkage groups to barley\\u000a chromosomes. The constructed high-density

X. Qi; P. Stam; P. Lindhout

1998-01-01

371

Human leucocyte antigens (HLA) and trimellitic anhydride (TMA) immunological lung disease.  

PubMed

Occupational immunological lung disease, due to low molecular weight, reactive chemicals such as trimellitic anhydride (TMA), is an emerging health problem. If there were a marker that was highly predictive of the ability of the immune system to recognize TMA as an allergen, better prevention strategies could be employed with at risk individuals. The purpose of this study is to evaluate whether human leucocyte antigen (HLA) class specificity is associated with the development of late respiratory systemic syndrome (LRSS) or asthma due to immunological sensitivity to trimellitic anhydride (TMA). This is a case control study of 17 individuals with LRSS, 12 with asthma and 22 TMA similarly exposed individuals who did not develop LRSS or asthma. Comparing the sensitized individuals (LRSS or asthma) with the non-sensitized individuals (controls), we found no difference in frequency of any HLA antigen. In summary, the lack of association of HLA antigens with LRSS or asthma due to TMA suggests that these will not be useful markers to identify at risk individuals. PMID:11059949

Grammer, L C; Zeiss, C R; Yarnold, P R; Shaughnessy, M A

2000-10-01

372

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.

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

2013-01-01

373

Immune System Computation and the Immunological Homunculus  

Microsoft Academic Search

Students for the Master of Science degree at the Weizmann Institute of Science are obliged to spend the first year of the\\u000a two-year program doing three-month rotations through three different laboratories in any of the various faculties at the Institute.\\u000a In 1998, Na’aman Kam rotated through my laboratory in the Department of Immunology where he did molecular modeling of an

Irun R. Cohen

2006-01-01

374

Essential concept of transplant immunology for clinical practice.  

PubMed

Our understanding of transplant immunology has advanced from gross allograft rejection to cellular response and to current molecular level. More sensitive assays have been developed to characterize patient sensitization and to detect pre-existing donor-specific antibodies (DSA) in pre-transplant crossmatch. After a transplant, pre-existing or de novo DSA are increasingly monitored to guide clinical management. Therefore, it is important for clinicians to understand the basic concepts and key components of transplant immunology as well as be familiarized with the modern immunological techniques used in kidney transplantation. PMID:24392315

Kumbala, Damodar; Zhang, Rubin

2013-12-24

375

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.

2014-01-01

376

In vitro antimalarial susceptibility and molecular markers of drug resistance in Franceville, Gabon  

PubMed Central

Background Malaria remains a major public health problem, due largely to emergence and widespread P. falciparum drug resistance. WHO recommends artemisinine combination based therapy (ACT) to overcome P. falciparum drug resistance, but reports of declining ACT efficacy have been published. A thorough understanding of the molecular bases of P. falciparum resistance to existing drugs is therefore needed. The aims of this study were to analyze the in vitro sensitivity of P. falciparum field isolates from Franceville, Gabon, to chloroquine (CQ), mefloquine (MF), dihydroartemisinine (DHA) and monodesethylamodiaquine (MDAQ), and to investigate polymorphisms associated with drug resistance. Methods We conducted a cross-sectional study of 53 field isolates. Field isolates sensitivity to CQ, MF, DHA and MDAQ was assessed using the colorimetric DELI test. The Pfmdr1 codons 86 and 1246, Pfcrt (haplotype codon 72 to 76) and the PfATPAse6 codons 110 and 2694 were analysed by PCR-RFLP. Associations between drug sensitivity and parasite gene polymorphisms were evaluated with the Chi square test, and routine hematological parameters were analyzed with Fisher’s exact test implemented with Epinfo software. In all statistical tests, significance was assumed at p<0.05. Results A total of 46 P. falciparum isolates were successfully cultured in vitro and their sensitivity was tested. The proportions of isolates resistant to CQ, MF and MDAQ were 43.5%, 23.4% and 56.5%, respectively. Some isolates (23.9%) had DHA IC50 values higher than 10 nM. The median IC50 values were 71.67 (interquartile range (IQR, 1–438.2), 6.59 (IQR, 0.08-96), 64.79 (IQR, 0.09-448) and 6.45 nM (IQR, 0.09-23) for CQ, MF, MDAQ and DHA, respectively. The strongest correlation between diminished DHA sensitivity and MF resistance was observed (r2=0.73), followed by correlation between diminished DHA sensitivity and CQ resistance. Cross-resistance between CQ and MF was also observed. The prevalence of the 86Y and 1246Y mutations in Pfmdr1, 76T in Pfcrt, and 110A and 2694T in PfATPase6 was respectively 42% and 17.1%, 97.8%, and 0% and 22.2%. Conclusion These high levels of antimalarial drug resistance in Franceville, Gabon, call for reinforced surveillance of drug efficacy.

2012-01-01

377

Processes Underpinning Development and Maintenance of Diversity in Rice in West Africa: Evidence from Combining Morphological and Molecular Markers  

PubMed Central

We assessed the interplay of artificial and natural selection in rice adaptation in low-input farming systems in West Africa. Using 20 morphological traits and 176 molecular markers, 182 farmer varieties of rice (Oryza spp.) from 6 West African countries were characterized. Principal component analysis showed that the four botanical groups (Oryza sativa ssp. indica, O. sativa ssp. japonica, O. glaberrima, and interspecific farmer hybrids) exhibited different patterns of morphological diversity. Regarding O. glaberrima, morphological and molecular data were in greater conformity than for the other botanical groups. A clear difference in morphological features was observed between O. glaberrima rices from the Togo hills and those from the Upper Guinea Coast, and among O. glaberrima rices from the Upper Guinea Coast. For the other three groups such clear patterns were not observed. We argue that this is because genetic diversity is shaped by different environmental and socio-cultural selection pressures. For O. glaberrima, recent socio-cultural selection pressures seemed to restrict genetic diversity while this was not observed for the other botanical groups. We also show that O. glaberrima still plays an important role in the selection practices of farmers and resulting variety development pathways. This is particularly apparent in the case of interspecific farmer hybrids where a relationship was found between pericarp colour, panicle attitude and genetic diversity. Farmer varieties are the product of long and complex trajectories of selection governed by local human agency. In effect, rice varieties have emerged that are adapted to West African farming conditions through genotype × environment × society interactions. The diversity farmers maintain in their rice varieties is understood to be part of a risk-spreading strategy that also facilitates successful and often serendipitous variety innovations. We advocate, therefore, that farmers and farmer varieties should be more effectively involved in crop development.

Maat, Harro; Richards, Paul; Struik, Paul C.

2014-01-01

378

Molecular characterization and genetic relationships among most common identified morphotypes of critically endangered rare Moroccan species Argania spinosa (Sapotaceae) using RAPD and SSR markers  

Microsoft Academic Search

– \\u000a \\u000a • The objective of this work is the molecular characterization of most common identified morphotypes of critically endangered\\u000a rare Moroccan species Argania spinosa.\\u000a \\u000a \\u000a \\u000a \\u000a – \\u000a \\u000a • Eighteen RAPD markers and twenty SSR markers have been assayed in 38 argan tree accessions from the three most commonly\\u000a identified morphotypes: oval, spherical and spindle fruit types.\\u000a \\u000a \\u000a \\u000a \\u000a – \\u000a \\u000a • A total of 140

Khalid Majourhat; Youssef Jabbar; Abdellatif Hafidi; Pedro Martínez-Gómez

2008-01-01

379

Gene expression signatures and molecular markers associated with clinical outcome in locally advanced head and neck carcinoma.  

PubMed

The purpose of this study was to identify molecular markers associated with tumor recurrence and survival in patients with locally advanced head and neck squamous cell carcinoma (HNSCC). We studied the expression profile of 63 pre-treatment tumor biopsies obtained from locally advanced HNSCCs treated with standard treatments. Cluster analysis identified three tumor subtypes associated with significant differences in local recurrence-free survival (LRFS) (P<0.001), progression free-survival (PFS) (P<0.009) and overall survival (OS) (P<0.004). Tumor subtype 1, associated with short LRFS, PFS and OS, showed features of epithelial-mesenchymal transition and undifferentiation. It also overexpressed genes involved in cell adhesion, NF-?B and integrin signalling. Tumor subtype 3, associated with longer LRFS, PFS and OS, showed a high degree of differentiation and overexpressed genes located in chromosomal regions 19q13 and 1q21. Tumor subtype 2, which had an intermediate clinical outcome between subtype 1 and subtype 3, overexpressed genes involved in branching morphogenesis. Finally, we validated the association between gene cluster classification and patient survival using Gene Set Enrichment Analysis and two HNSCC data sets obtained from two independent patient cohorts. In conclusion, we generated a gene prognostic signature associated with survival in locally advanced patients using the expression profile of the pre-treatment tumor biopsy. Independent prospective studies would be necessary to assess if the proposed survival signature could help to guide clinical management of HNSCC. PMID:22696598

Pavón, M A; Parreño, M; Téllez-Gabriel, M; Sancho, F J; López, M; Céspedes, M V; Casanova, I; Lopez-Pousa, A; Mangues, M A; Quer, M; Barnadas, A; León, X; Mangues, R

2012-09-01

380

The potential of molecular markers to improve interventions through the natural history of oesophageal squamous cell carcinoma  

PubMed Central

EC (oesophageal cancer) is one of the ten most frequent and fatal tumours worldwide and ESCC (oesophageal squamous cell carcinoma) accounts for about 80% of the cases. The first symptoms of ESCC arise late during the progression of the disease and, therefore, the diagnosis is usually done in advanced stages. This leads to an inefficient treatment and consequently to a poor prognosis. Thus, a comprehensive knowledge of ESCC biology is of major importance to identify risk factors, especially in high-incidence areas and biomarkers which could enable ESCC prevention and interventions throughout the natural history of the disease. In this review, we present the current knowledge regarding ESCC aetiology as well as the different genetic and epigenetic alterations already described in this tumour. We also discuss how these alterations could be used to anticipate ESCC diagnosis as well as how they can help improving treatment. A molecular natural history of the disease is proposed pointing out potential markers that may improve interventions at different points of ESCC development. Only when the different layers of complexity behind this tumour are elucidated, it will be possible to successfully perform prevention at different levels.

da Costa, Nathalia Meireles; Soares Lima, Sheila Coelho; de Almeida Simao, Tatiana; Ribeiro Pinto, Luis Felipe

2013-01-01

381

The mitochondrial genome of Euphausia superba (Prydz Bay) (Crustacea: Malacostraca: Euphausiacea) reveals a novel gene arrangement and potential molecular markers.  

PubMed

Euphausiid krill are dominant organisms in the zooplankton population and play a central role in marine ecosystems. In this paper, we described the gene organization, gene rearrangement and codon usage in the mitochondrial genome of Euphausia superba Dana 1852 (sampling from Prydz Bay, PB). The mitochondrial genome of E. superba is more than 15,498 bp in length (partial non-coding region was not determined). Translocation of four tRNAs (trnL ( 1 ), trnL ( 2 ), trnW and trnI) and duplication of one tRNA (trnN) were founded in the mitochondrial genome of E. superba when comparing its genome with the pancrustacean ground pattern. To investigate the phylogenetic relationship within Malacostraca, phylogenetic trees based on currently available malacostracan mitochondrial genomes were built with the maximum likelihood and the Bayesian models. All analyses based on nucleotide and amino acid data strongly support the monophyly of Stomatopoda, Penaeidae, Caridea, and Brachyura, which is consistent with previous research. However, the taxonomic position of Euphausiacea within Malacostraca is unstable. From comparing the mitochondrial genome between E. superba (PB) and E. superba (sampling from Weddell Sea, WS), we found that nad2 gene contains maximal variation with 61 segregating sites, following by nad5 gene which has 12 segregating sites. Thus, nad2 and nad5 genes may be used as potential molecular markers to study the inherit diversity among different E. superba groups, which would be helpful to the exploitation and management of E. superba resources. PMID:19578978

Shen, Xin; Wang, Haiqing; Ren, Jianfeng; Tian, Mei; Wang, Minxiao

2010-02-01

382

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

383

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).

2011-01-01

384

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

385

Immunologically mediated dementias  

Microsoft Academic Search

Although most dementias are due to neurodegenerative or vascular disease, it is important to diagnose immunologically mediated\\u000a dementias quickly because they can be both rapidly progressive and readily treatable. They usually affect function of limbic\\u000a and cortical structures, but subcortical involvement can also occur. Because of the variety of symptoms and the rapid course,\\u000a these dementias present a particular challenge

Michael H. Rosenbloom; Sallie Smith; Gulden Akdal; Michael D. Geschwind

2009-01-01

386

Immunology in Pittsburgh.  

PubMed

The University of Pittsburgh School of Medicine has a long tradition of excellence in immunology research and training. Faculty, students, and postdoctoral fellows walk through hallways that are pictorial reminders of the days when Dr. Jonas Salk worked here to develop the polio vaccine, or when Dr. Niels Jerne chaired the Microbiology Department and worked on perfecting the Jerne Plaque Assay for antibody-producing cells. Colleagues and postdoctoral fellows of Professor Salk are still on the faculty of the University of Pittsburgh Medical School as are graduate students of Professor Jerne. A modern research building, the 17 story high Biomedical Science Tower, is a vivid reminder of the day when Dr. Thomas Starzl arrived in Pittsburgh and started building the most prominent solid-organ-transplant program in the world. The immunology research that developed around the problem of graft rejection and tolerance induction trained numerous outstanding students and fellows. Almost 20 yr ago, the University of Pittsburgh founded the University of Pittsburgh Cancer Institute (UPCI) with the renowned immunologist Dr. Ronald Herberman at its helm. This started a number of new research initiatives in cancer immunology and immunotherapy. A large number of outstanding young investigators, as well as several well-established tumor immunologists, were recruited to Pittsburgh at that time. PMID:17337760

Finn, Olivera J; Salter, Russell D

2006-01-01

387

Cosmos-1989 immunology studies  

NASA Technical Reports Server (NTRS)

Evidence from both human and rodent studies has indicated that alterations in immunological parameters occur after space flight. The number of flight experiments has been small, and the full breadth of immunological alterations occurring after space flight remains to be established. Among the major effects on immune responses after space flight that have been reported are: alterations in lymphocyte blastogenesis and natural killer cell activity, alterations in production of cytokines, changes in leukocyte sub-population distribution, and decreases in the ability in the ability of bone marrow cells to respond to colony stimulating factors. Changes have been reported in immunological parameters of both humans and rodents. The significance of these alterations in relation to resistance to infection remains to be established. The current study involved a determination of the effects of flight on Cosmos mission 2044 on leukocyte subset distribution and the sensitivity of bone marrow cells to colony stimulating factor-GM. A parallel study with antiorthostatic suspension was also carried out. The study involved repetition and expa