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1

Colorectal carcinomas with high microsatellite instability: Defining a distinct immunologic and molecular entity with respect to prognostic markers  

Microsoft Academic Search

Molecular analysis of hereditary nonpolyposis colorectal carcinomas (HNPCC) has identified DNA mismatch repair deficiencies with resulting microsatellite instability (MSI) as a pathway of carcinogenesis that appears to be relevant for prognosis, treatment, and possibly prevention. In this study, expression of cell cycle proteins and other known prognostic markers is correlated with the microsatellite status of colorectal cancers (CRC). One hundred

Tina Bocker Edmonston; Kimberly H. Cuesta; Susan Burkholder; Alan Barusevicius; Deborah Rose; Albert J. Kovatich; Bruce Boman; Robert Fry; Richard Fishel; Juan P. Palazzo

2000-01-01

2

Immunological Methods in Molecular Palaeontology  

Microsoft Academic Search

Variable amounts of proteins or protein fragments may survive in fossils for thousands and occasionally millions of years. The quantities are generally too small to determine accurate amino acid sequences, but even these small amounts may be immunologically detectable and may retain useful genetic information. A very sensitive solid phase radioimmunoassay has been used to analyse fossil proteins, particularly albumin

Jerold M. Lowenstein; Gary Scheuenstuhl

1991-01-01

3

21 CFR 866.5065 - Human allotypic marker immunological test system.  

Code of Federal Regulations, 2010 CFR

...marker immunological test system. (a) Identification. A human allotypic marker immunological test system is a device that consists...techniques the inherited human protein allotypic markers...allotypes) in serum and other body fluids. The...

2010-04-01

4

21 CFR 866.5065 - Human allotypic marker immunological test system.  

Code of Federal Regulations, 2010 CFR

...marker immunological test system. (a) Identification. A human allotypic marker immunological test system is a device that consists...techniques the inherited human protein allotypic markers...allotypes) in serum and other body fluids. The...

2009-04-01

5

21 CFR 866.5065 - Human allotypic marker immunological test system.  

Code of Federal Regulations, 2013 CFR

... 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 system. (a)...

2013-04-01

6

Immunological and Molecular Studies of Arboviruses.  

National Technical Information Service (NTIS)

The antigenic relationships within group A arboviruses have been studied by comparison between Sindbiss and WEE and EEE. The comparison was performed on two levels: (1) comparison of immunological activities of the purified whole envelopes; and, (2) compa...

N. Goldblum

1976-01-01

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

Molecular Markers of Hemostatic Activation: Applications in the Diagnosis of Thrombosis and Vascular and Thrombotic Disorders  

Microsoft Academic Search

The recognition of molecular marker events leading to hemostatic and thrombotic disorders and technologic advances in molecular biology and immunology has added a new dimension in the diagnosis of bleeding and thrombotic disorders. Pathophysiologic activation of coagulation, fibrinolysis, kallikrein-kinin system, vascu— lar stress, and intercellular interactions result in the generation of cell\\/process specific markers of a pathophysiologic event. It has

Jawed Fareed; Rodger L. Bick; Debra A. Hoppensteadt; Edward W. Bermes

1995-01-01

9

Microsatellite Markers for Molecular Breeding  

Microsoft Academic Search

Microsatellites are tandem repeats of short sequence motifs that occur ubiquitously in eukaryotic genomes. A key feature of this class of repetitive DNA is an extraordinarily high level of variation among taxa, mainly expressed as a variable copy number of tandem repeats. A multitude of techniques were described that exploit microsatellite variability as molecular markers. Basically, these approaches can be

Kurt Weising; Peter Winter; Bruno Hüttel; GüNter Kahl

1997-01-01

10

Potential of Molecular Markers in Plant Biotechnology  

Microsoft Academic Search

During the last few decades, the use of molecular markers, revealing polymorphism at the DNA level, has been playing an increasing part in plant biotechnology and their genetics studies. There are different types of markers viz. morphological, biochemical and DNA based molecular markers. These DNA based markers are differentiates in two types first non PCR based (RFLP) and second is

P. Kumar; V. K. Gupta; A. K. Misra; D. R. Modi; B. K. Pandey

2009-01-01

11

Molecular and immunological diagnosis of echinococcosis.  

PubMed Central

Echinococcosis is an infectious disease of humans caused by the larval (metacestode) stage of the cestode species Echinococcus granulosus (cystic echinococcosis or hydatid disease) or Echinococcus multilocularis (alveolar echinococcosis or alveolar hydatid disease). Clinical manifestations depend primarily on localization and size of hepatic lesions and may include hepatomegaly, obstructive jaundice, or cholangitis. Prognostically, alveolar echinococcosis is considered similar to liver malignancies, including a lethality rate of 90% for untreated cases. Diagnosis is based on imaging techniques coupled with immunodiagnostic procedures. Antibody detection tests for E. multilocularis have markedly improved with the use of affinity-purified Em2 antigen and recombinant antigen II/3-10 in enzyme immunoassays. Antigens of corresponding quality for E. granulosus are still unavailable. The detection of circulating antigens and immune complexes in the sera of patients with cystic echinococcosis, the demonstration of in vitro lymphocyte proliferation in response to stimulation with Echinococcus antigens, and the discrimination of serum immunoglobulin isotype activity to various Echinococcus antigens in both cystic and alveolar echinococcosis have been suggested for diagnostic purposes as well as for monitoring patients after treatment. New diagnostic molecular tools include DNA probes for Southern hybridization tests and polymerase chain reaction for the amplification of E. multilocularis and E. granulosus species-specific DNA fragments. Images

Gottstein, B

1992-01-01

12

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

13

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

Microsoft Academic Search

OBJECTIVESIn 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.METHODSWith a standardised protocol, the participants of the study were interviewed for work related symptoms, conditions

Jürgen Bünger; Michael Antlauf-Lammers; Thomas G Schulz; Götz A Westphal; Michael M Müller; Peter Ruhnau; Ernst Hallier

2000-01-01

14

An update on the functional molecular immunology (FIMM) database.  

PubMed

Data on the major histocompatibility complex, T-cell epitopes, B-cell epitopes, antigens and diseases are heterogeneous and scattered among different databases and the literature. Since it has become increasingly difficult to obtain an integrated view of functional immune response components, we have developed and updated over several years the Functional molecular IMMunology (FIMM) database (http:// research.i2r.a-star.edu.sg/fimm/). FIMM contains integrated expert-curated data on protein antigens, and on human immunological receptors that recognise and bind them in healthy or disease states. Interfaces with multiple, intuitive query options and query reports provide immunologists with prioritised information that aids data interpretation, vaccine target discovery and immune disease research. PMID:16000010

Schönbach, Christian; Koh, Judice L Y; Flower, Darren R; Brusic, Vladimir

2005-01-01

15

Molecular Marker Discovery and Genetic Map Visualisation  

Microsoft Academic Search

\\u000a The bulk of variation at the nucleotide level is often not visible at the phenotypic level. However, this variation can be\\u000a exploited using molecular genetic marker systems. Molecular genetic markers represent one of the most powerful tools for genome\\u000a analysis and permit the association of heritable traits with underlying genomic variation. Molecular marker technology has\\u000a developed rapidly over the last

Chris Duran; David Edwards; Jacqueline Batley

16

[Erythrophagocytosis a new diagnostic marker of immunologic myocardial damage in ischemic heart disease].  

PubMed

Using data of epidemiological and clinical examination of women of reproductive and menopausal age we studied the processes of erythrophagocytosis (EF) in 46 women with ischemic heart disease (IHD) aged 20-59 years in comparison with a group of healthy individuals. We found that women with IHD had almost 10-fold increase of EF compared with healthy individuals. Therefore determination of EF could be used as laboratory test for detecting autoimmune component of IHD. We also found associations between identified immunological abnormalities and dyslipidemia, in particular elevation of low density lipoprotein cholesterol level which was more pronounced during menopause. EF can serve as an immunological marker of IHD in women. PMID:24090380

Kasumova, F N

2013-01-01

17

Harmonizing Molecular Marker Analyses of Organic Aerosols  

Microsoft Academic Search

Analysis of molecular markers in aerosol samples using GC-MS has become widely used in air pollution studies. There is considerable variability in the analytical details of molecular marker analyses across different research and regulatory groups. These discrepancies result in the use of different methods for the interpretation of source and ambient measurements used in source apportionment and atmospheric particulate studies.

Yuan Xun Zhang; James Jay Schauer; Elizabeth Anne Stone; Yuanhang Zhang; Min Shao; Yongjie Wei; Xianlei Zhu

2009-01-01

18

Prognostic molecular markers in cancer - quo vadis?  

PubMed

Despite the tremendous number of studies of prognostic molecular markers in cancer, only a few such markers have entered clinical practise. The lack of clinical prognostic markers clearly reflects limitations in or an inappropriate approach to prognostic studies. This situation should be of great concern for the research community, clinicians and patients. In the present review, we evaluate immunohistochemical prognostic marker studies in oral squamous cell carcinomas (OSCC) from 2006 to 2012. We comment upon general issues such as study design, assay methods and statistical methods, applicable to prognostic marker studies irrespective of cancer type. The three most frequently studied markers in OSCC are reviewed. Our analysis revealed that most new molecular markers are reported only once. To draw conclusions of clinical relevance based on the few markers that appeared in more than one study was problematic due to between-study heterogeneity. Currently, much valuable tissue material, time and money are wasted on irrelevant studies. PMID:23837466

Søland, Tine M; Brusevold, Ingvild J

2013-07-09

19

(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...

20

MOLECULAR MARKER ANALYSIS OF DEARS SAMPLES  

EPA Science Inventory

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

21

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

22

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

PubMed Central

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

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

2002-01-01

23

Operation of the Molecular Virology and Immunology Laboratory (Georgetown University, Rockville, Maryland). Annual Report October 4, 1983-October 3, 1984.  

National Technical Information Service (NTIS)

Contents: Electron microscope facility (bacterial diseases, allergic diseases, Additional activities); Hepatitis testing laboratory; Molecular virology and immunology (Respiratory Syncytial Virus (RSV), Hepatitis Delta Virus, Woodchuck hepatitis virus, He...

J. L. Gerin

1984-01-01

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

Molecular markers of gliomas: a clinical approach.  

PubMed

Over the last decade, the knowledge on the molecular genetic background of gliomas has dramatically increased. This information provides the basis for the molecular target therapies and molecular tests serve to complement the subjective nature of histopathologic criteria and add useful data regarding response to treatments and prognosis. In particular, the use of loss of heterozygosity (LOH) and methylation specific polymerase chain reaction (PCR) (MSP) based testing of gliomas is already in place and used clinically in several centers. This paper provides a brief overview of these molecular genetic aberrations and discusses the clinical utility, as well as the advantages and disadvantages of such approach. Newly developed molecular techniques, such as LOH testing, fluorescence in situ hybridization (FISH), DNA sequencing and MSP, are currently being employed in assessment of gliomas in some laboratories. However, the clinical use of some markers and the context in which the information obtained should be used are still not entirely understood. Therefore, this paper will focus on validation and implementation of molecular testing in gliomas, with emphasis on LOH on chromosomes 1p, 19q, 17p and 10q and O(6)-methylguanine-DNA methyltransferase (MGMT) methylation status. PMID:16808886

Eoli, M; Silvani, A; Pollo, B; Bianchessi, D; Menghi, F; Valletta, L; Broggi, G; Boiardi, A; Bruzzone, M G; Finocchiaro, G

2006-07-01

26

Molecular and clinical markers of pancreas cancer.  

PubMed

Pancreas cancer has the worst prognosis of any solid tumor but is potentially treatable if it is diagnosed at an early stage. Thus there is critical interest in delineating clinical and molecular markers of incipient disease. The currently available biomarker, CA 19-9, has an inadequate sensitivity and specificity to achieve this objective. Diabetes mellitus, tobacco use, and chronic pancreatitis are associated with pancreas cancer. However, screening is currently only recommended in those with hereditary pancreatitis and genetic syndromes which predispose to cancer. Ongoing work to identify early markers of pancreas cancer consists of high throughput discovery methods including gene arrays and proteomics as well as hypothesis driven methods. While several promising candidates have been identified none has yet been convincingly proven to be better than CA 19-9. New methods including endoscopic ultrasound are improving detection of pancreas cancer and are being used to acquire tissue for biomarker discovery. PMID:21068484

Buxbaum, James L; Eloubeidi, Mohamad A

2010-11-09

27

Molecular Marker Systems for Oenothera Genetics  

PubMed Central

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

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

2008-01-01

28

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

Microsoft Academic Search

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

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

2010-01-01

29

Biological (molecular and cellular) markers of toxicity  

SciTech Connect

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

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

1991-12-15

30

Molecular markers and their use in environmental organic geochemistry  

Microsoft Academic Search

Molecular markers are organic substances that carry information about sources of organic matter or contamination. The source\\/marker relation can be used to indicate the presence of a given source material (qualitative), or, under appropriate conditions, to estimate the amount of a source material (quantitative source apportionment) in the environment. Assemblages of markers can also be used as process probes. In

Robert P. Eganhouse

2004-01-01

31

Advance of molecular marker application in the tobacco research  

Microsoft Academic Search

Tobacco (Nicotiana spp.) is one of the most important commercial crops in the world. During the last two decades, molecular markers have entered the scene of genetic improvement in different fields of agricultural research. The principles and characteristics of several molecular markers such as RFLP, RAPD, AFLP, microsatellites and minisatellites applied in tobacco genetics and breeding were reviewed. The application

X. Z. Liu; H. Y. Zhang

32

Molecular DNA Markers in Phylogeny and Systematics  

Microsoft Academic Search

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

V. V. Grechko

2002-01-01

33

APPLICATION OF MOLECULAR MARKERS FOR CUCUMBER IMPROVEMENT  

Technology Transfer Automated Retrieval System (TEKTRAN)

The historicity of marker development, map construction, and the utility of marker-assisted selection is presented. Experimental results indicate that the identification of marker-trait associations will continue to be extremely expensive and time consuming, but will likely pay large dividends for ...

34

Molecular and immunological characterization of the glycosylated orange allergen Cit s 1  

Microsoft Academic Search

The IgE of sera from patients with a history of allergy to oranges (Citrus sinensis) binds a number of proteins in orange extract, including Cit s 1, a germin-like protein. In the present study, we have analyzed its immunological cross-reactivity and its molecular nature. Sera from many of the patients examined recognize a range of glyco- proteins and neoglycoconjugates containing

Gerald Poltl; Oussama Ahrazem; Katharina Paschinger; M. Dolores Ibanez; Gabriel Salcedo; Iain B. H. Wilson

2007-01-01

35

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

36

Clinical, microbiological, and immunological markers of gingival and periodontal disease induction and progression  

Microsoft Academic Search

The potential impact of periodontal disease, a suspected risk factor for systemic diseases, presents challenges for health promotion and disease prevention strategies. This study examined clinical, microbiological, and immunological factors in a disease model to identify potential biomarkers that may be useful in predicting the onset and severity of both inflammatory and destructive periodontal disease. This project used an historical

David P Cappelli

2002-01-01

37

Modulatory efficacy of green tea polyphenols on glycoconjugates and immunological markers in 4-Nitroquinoline 1-oxide-induced oral carcinogenesis-A therapeutic approach.  

PubMed

Green tea polyphenols (GTP) has been used as a chemopreventive agent world wide against chemically induced cancer. The present study is aimed to understand the therapeutic action of GTP on glycoconjugates and immunological markers in 4-Nitroquinoline 1-oxide (4-NQO)-induced oral cancer over a period of 30 days at 200mg/kg, p.o., Oral cancer was induced by painting 4-NQO for 8 weeks followed by administration of GTP after 22 weeks, for 30 days. Glycoconjugates such as hexose, hexosamine, sialicacid, fucose and mucoprotein were analysed. Expression of glycoconjugates was examined through histology and SDS-PAGE. Immunological markers such as circulating immune complex and mast cell density were studied. Oral cancer-induced animals showed a significant increase in levels of glycoconjugates and its expression, similar to that observed for immunological markers. Treatment with GTP altered the expression of glycoconjugates as well as immunological markers. The results suggest that GTP modulates both the expression of glycoconjugates and immunological markers resulting in regression of oral cancer. PMID:16859662

Srinivasan, Periasamy; Sabitha, Kuruvimalai Ekambaram; Shyamaladevi, Chennam Srinivasulu

2006-06-12

38

Immune Response to Mycobacterium tuberculosis and Identification of Molecular Markers of Disease  

PubMed Central

The complex molecular events that occur within the host during the establishment of a Mycobacterium tuberculosis infection are poorly defined, thus preventing identification of predictive markers of disease progression and state. To identify such molecular markers during M. tuberculosis infection, global changes in transcriptional response in the host were assessed using mouse whole genome arrays. Bacterial load in the lungs, the lesions associated with infection, and gene expression profiling was performed by comparing normal lung tissue to lungs from mice collected at 20, 40, and 100 days after aerosol infection with the H37Rv strain of M. tuberculosis. Quantitative, whole lung gene expression identified signature profiles defining different signaling pathways and immunological responses characteristic of disease progression. This includes genes representing members of the interferon-associated gene families, chemokines and cytokines, MHC, and NOS2, as well as an array of cell surface markers associated with the activation of T cells, macrophages, and dendritic cells that participate in immunity to M. tuberculosis infection. More importantly, several gene transcripts encoding proteins that were not previously associated with the host response to M. tuberculosis infection, and unique molecular markers associated with disease progression and state, were identified.

Gonzalez-Juarrero, Mercedes; Kingry, Luke C.; Ordway, Diane J.; Henao-Tamayo, Marcela; Harton, Marisa; Basaraba, Randall J.; Hanneman, William H.; Orme, Ian M.; Slayden, Richard A.

2009-01-01

39

Immune response to Mycobacterium tuberculosis and identification of molecular markers of disease.  

PubMed

The complex molecular events that occur within the host during the establishment of a Mycobacterium tuberculosis infection are poorly defined, thus preventing identification of predictive markers of disease progression and state. To identify such molecular markers during M. tuberculosis infection, global changes in transcriptional response in the host were assessed using mouse whole genome arrays. Bacterial load in the lungs, the lesions associated with infection, and gene expression profiling was performed by comparing normal lung tissue to lungs from mice collected at 20, 40, and 100 days after aerosol infection with the H37Rv strain of M. tuberculosis. Quantitative, whole lung gene expression identified signature profiles defining different signaling pathways and immunological responses characteristic of disease progression. This includes genes representing members of the interferon-associated gene families, chemokines and cytokines, MHC, and NOS2, as well as an array of cell surface markers associated with the activation of T cells, macrophages, and dendritic cells that participate in immunity to M. tuberculosis infection. More importantly, several gene transcripts encoding proteins that were not previously associated with the host response to M. tuberculosis infection, and unique molecular markers associated with disease progression and state, were identified. PMID:18787176

Gonzalez-Juarrero, Mercedes; Kingry, Luke C; Ordway, Diane J; Henao-Tamayo, Marcela; Harton, Marisa; Basaraba, Randall J; Hanneman, William H; Orme, Ian M; Slayden, Richard A

2008-09-11

40

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

41

Daily urinary neopterin excretion as an immunological marker of disease activity in multiple sclerosis  

Microsoft Academic Search

Summary The aim of this study was to assess neopterin, a marker of and controls, respectively. They also had a greater number of peaks in their serial UNCR measurements than controls interferon gamma (IFN-?) induced macrophage activity, as (P , 0.001 for all patients and P , 0.01 for each group); a possible surrogate marker of inflammation in patients with

Gavin Giovannoni; M. Lai; D. Kidd; J. W. Thorpe; D. H. Miller; A. J. Thompson; G. Keir; M. Feldmann; E. J. Thompson

1997-01-01

42

A genetic map of potato ( Solanum tuberosum ) integrating molecular markers, including transposons, and classical markers  

Microsoft Academic Search

A genetic map of potato (Solanum tuberosum L.) integrating molecular markers with morphological and isozyme markers was constructed using a backcross population of 67 diploid potato plants. A general method for map construction is described that differs from previous methods employed in potato and other outbreeding plants. First, separate maps for the female and male parents were constructed. The female

J. M. E. Jacobs; H. J. Van Eek; P. F. P. Arens; B. Verkerk-Bakker; B. te Lintel Hekkert; H. J. M. Bastiaanssen; A. El-Kharbotly; A. Pereira; E. Jacobsen; W. J. Stiekema

1995-01-01

43

Summary statement: utility of molecular marker testing in thyroid cancer.  

PubMed

The use of molecular markers for thyroid cancer diagnosis, prognosis, and surveillance have been an exciting area of study and change. Recent investigative focus on promising new markers will very likely lead to improvements in the diagnostic utility of fine needle aspiration biopsy (FNAB) in predicting malignancy, as well as provide more accurate prognostic information pre- and postoperatively. The 2010 Annual Meeting of the American Association for Endocrine Surgeons featured a symposium dedicated to molecular marker testing in thyroid cancer and its potential clinical applicability. PMID:21134567

Yip, Linwah; Kebebew, Electron; Milas, Mira; Carty, Sally E; Fahey, Thomas J; Parangi, Sareh; Zeiger, Martha A; Nikiforov, Yuri E

2010-12-01

44

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

45

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

46

Molecular and immunological characterisation of the glycosylated orange allergen Cit s 1  

PubMed Central

The IgE of sera from patients with a history of allergy to oranges (Citrus sinensis) bind a number of proteins in orange extract, including Cit s 1, a germin-like protein. In the present study, we have analysed its immunological cross-reactivity and its molecular nature. Sera from many of the patients examined recognise a range of glycoproteins and neoglycoconjugates containing ?1,2-xylose and core ?1,3-fucose on their N-glycans. These reagents also inhibited the interaction of Cit s 1 with patients’ sera, thus underlining the critical role of glycosylation in the recognition of this protein by patients’ IgE and extending previous data showing that deglycosylated Cit s 1 does not possess IgE epitopes. In parallel, we examined the peptide sequence and glycan structure of Cit s 1 using mass spectrometric techniques. Indeed, we achieved complete sequence coverage of the mature protein as compared to the translation of an expressed sequence tag cDNA clone and demonstrated that the single N-glycosylation site of this protein carries oligosaccharides with xylose and fucose residues. Due to the presumed requirement for multivalency for in vivo allergenicity, our molecular data showing that Cit s 1 is monovalent as regards glycosylation and that the single N-glycan is the target of the IgE response to this protein, therefore, explain the immunological cross-reactive properties of Cit s 1 as well as its equivocal nature as a clinically-relevant allergen.

Poltl, Gerald; Ahrazem, Oussama; Paschinger, Katharina; Ibanez, M. Dolores; Salcedo, Gabriel; Wilson, Iain B. H.

2010-01-01

47

Impact of maternal carrier status on immunologic markers for protection after hepatitis B vaccination in infancy: a meta-analysis.  

PubMed

Better protection against hepatitis B infection in offspring of carrier mothers has been postulated because of a booster effect by close maternal contact. Empirical evidence, however, is inconclusive. Immunologic markers for protection against hepatitis B are anti-HBs ? 10 mIU/ml or response to booster in case anti-HBs had fallen below 10 mIU/ml. The objective of this paper was to asses whether immunologic markers suggest a higher protection after hepatitis B vaccination in offspring of carrier mothers. A systematic review was performed in order to identify all studies in offspring of carrier and non-carrier mothers reporting the proportions of individuals with anti-HBs ? 10 mIU/ml after infant hepatitis B vaccination with a presently recommended dose in children aged 5 years or older or response to a booster dose in case anti-HBs was below 10 mIU/ml. Associations between carrier status and the proportions of anti-HBs ? 10 mIU/ml or booster response were analysed by random effects models with adjustment for age and potential confounders. We identified 19 studies providing proportions of anti-HBs ? 10 mIU/ml with explicit information regarding the maternal carrier status. These studies reported 3245 children of carrier mothers aged up to 20 years and 4602 children of non-carrier mothers aged up to 14 years. Antibody titres ? 10 mIU/ml were detected in 75.8% of children of carrier and 63.6% of non-carrier mothers. A random effects model with adjustment for confounding yielded an odds ratio of 2.43 (95% CI 1.24-4.75) suggesting a markedly higher probability of anti-HBs ? 10 mIU/ml in offspring of carrier compared to non-carrier mothers. The distribution of proportions of individuals with post booster increase of anti-HBs titres ? 10 mIU/ml stratified by age at booster (? 10 years and >10 years) showed no differences between offspring of carrier and non carrier mothers up to the age of 10 years and only marginal differences thereafter. In conclusion the proportions of anti-HBs ? 10 mIU/ml were clearly higher in offspring of carrier mothers years after infant vaccination but there appeared to be no clinically relevant difference in response to booster. It is unclear to which extent higher proportions of breakthrough infections contribute to the higher proportions of protective antibody titres in offspring of carrier mothers. PMID:22885275

Schönberger, Katharina; Riedel, Christina; Rückinger, Simon; Mansmann, Ulrich; Jilg, Wolfgang; von Kries, Rüdiger

2012-08-08

48

Daily urinary neopterin excretion as an immunological marker of disease activity in multiple sclerosis.  

PubMed

The aim of this study was to assess neopterin, a marker of interferon gamma (IFN-gamma) induced macrophage activity, as a possible surrogate marker of inflammation in patients with multiple sclerosis. Urinary neopterin to creatinine ratios (UNCRs) were measured daily in 10 primary progressive (PP). 10 relapsing remitting (RR) and 11 secondary progressive (SP) patients with multiple sclerosis, and 14 normal control (NC) subjects, for periods of up to 12 weeks. After excluding measurements related to infection, the median of the individuals' average UNCRs was significantly higher in patients than in controls (P < 0.001 for all patients and P < 0.01 for each of the three groups of patients); the median UNCRs (and interquartile ranges) were 187 (135-231), 187 (165-277), 218 (164-517) and 134 (97-152) mumol/mol for PP, RR, SP patients and controls, respectively. Similarly, patients had a greater median proportion of days with a UNCR above normal (P < 0.001 for all patients and P < 0.01 for each group); the median percentage (and interquartile ranges) were 16 (6-62), 28 (21-36), 49 (14-86) and 0 (0-6)% for PP, RR, SP patients and controls, respectively. They also had a greater number of peaks in their serial UNCR measurements than controls (P < 0.001 for all patients and P < 0.01 for each group); the means +/- SD peaks/subject/month were: 2.1 +/- 1.8; 3.0 +/- 1.7; 3.3 +/- 2.3 and 0.2 +/- 0.6 for PP, RR, SP patients and controls, respectively. Nine relapses occurred in nine patients during the study, and all were associated with increased neopterin excretion, which tended to be greater than that on days not associated with a relapse. Three of the nine relapses were preceded by an upper respiratory tract infection. In eight out of 13 patients who had infections during the study, increased neopterin excretion was noted for periods of up to 6 weeks post-infection, significantly longer than that which occurred after infections in controls. This confirms infection as a potent inducer of symptomatic and asymptomatic disease activity in mutiple sclerosis, and provides further support of a pivotal role for IFN-gamma in te pathogenesis of mutiple sclerosis. Urinary neopterin excretion is increased in patients with both progressive and relapsing mutiple sclerosis, and therefore has potential as a surrogate marker of the inflammatory component of mutiple sclerosis disease activity. PMID:9055793

Giovannoni, G; Lai, M; Kidd, D; Thorpe, J W; Miller, D H; Thompson, A J; Keir, G; Feldmann, M; Thompson, E J

1997-01-01

49

MOLECULAR MARKERS FOR SEX DETERMINATION IN PAPAYA (CARICA PAPAYA L.)  

Technology Transfer Automated Retrieval System (TEKTRAN)

Molecular markers tightly linked to Sex1, the gene that determines plant sex in papaya (Carica papaya L.), were developed. Three RAPD products have been cloned and a portion of their DNA sequenced. Based on these sequences SCAR primers were synthesized. SCAR T12 and SCAR W11 produce products in h...

50

Acceleration of peanut breeding programs by molecular marker assisted selection  

Technology Transfer Automated Retrieval System (TEKTRAN)

Peanut breeding has played a significant role in yield increases and disease control. Conventional breeding focuses on field selection and phenotypic analysis and it typically takes 12-15 years before a new cultivar can be released. Molecular markers developed from sequencing data can be of great ...

51

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

52

The Effects of Body Acupuncture on Obesity: Anthropometric Parameters, Lipid Profile, and Inflammatory and Immunologic Markers  

PubMed Central

A randomized controlled clinical trial in 196 obese subjects was performed to examine the effectiveness of body acupuncture on body weight loss, lipid profile and immunogenic and inflammatory markers. Subjects received authentic (cases) or sham (controls) acupuncture for 6 weeks in combination with a low-calorie diet. In the following 6 weeks, they received the low-calorie diet alone. Subjects were assessed at the beginning, 6 and 12 weeks later. Heat shock protein (Hsps)-27, 60, 65, 70 antibody titers and high sensitivity C-reactive protein (hs-CRP) levels were also assessed. A significant reduction in measures of adiposity and improvement in lipid profile were observed in both groups, but the levels of anti-Hsp-antibodies decreased in cases only. A reduction in anthropometric and lipid profile in cases were sustained in the second period, however, only changes in lipid profile were observed in the control group. Anti-Hsp-antibodies and hs-CRP levels continued to be reduced in cases but in controls only the reduction in hs-CRP remained. Changes in anthropometric parameters, lipid profile, and anti-Hsp-antibodies were more evident in cases. Body acupuncture in combination with diet restriction was effective in enhancing weight loss and improving dyslipidemia.

Abdi, Hamid; Zhao, Baixiao; Darbandi, Mahsa; Ghayour-Mobarhan, Majid; Tavallaie, Shima; Rahsepar, Amir Ali; Parizadeh, Seyyed Mohammad Reza; Safariyan, Mohammad; Nemati, Mohsen; Mohammadi, Maryam; Abbasi-Parizad, Parisa; Darbandi, Sara; Akhlaghi, Saeed; Ferns, Gordon A. A.

2012-01-01

53

Reviewing and updating the major molecular markers for stem cells.  

PubMed

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

Calloni, Raquel; Cordero, Elvira Alicia Aparicio; Henriques, João Antonio Pêgas; Bonatto, Diego

2013-01-22

54

DNA marker applications to molecular genetics and genomics in tomato  

PubMed Central

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.

Shirasawa, Kenta; Hirakawa, Hideki

2013-01-01

55

Immunological and molecular detection of human immunodeficiency virus in saliva, and comparison with blood testing.  

PubMed

In order to test the detection feasibility of human immunodeficiency virus (HIV) in saliva, a three-method blind screening analysis was conducted. Sixty-eight individuals were studied, comprising 34 HIV carriers and 34 noncarriers (controls) of matched gender and age. An oral examination preceded saliva and blood sampling of studied individuals. All samples were tested blind for HIV by using two immunological methods [Oraquick-compatible enzyme-linked immunosorbent assay (ELISA) and a fluorescent immunoenzymatic method (ELFA)], confirmed by western blotting, and a simple molecular method (polymerase chain reaction amplification of a relatively constant viral DNA region), confirmed by DNA hydridization. Compared with the controls, about twice as many HIV carriers had oral health problems, including periodontal disease. ELFA resulted in 33/34 positives and 34/34 negatives in saliva, while it detected 34/34 positives and 34/34 negatives in blood. ELISA performed even better, with correct assignment of all positives and negatives in both saliva and blood. The PCR method, at three annealing temperatures, surprisingly detected all positive samples, while it gave no false-positive result. In conclusion, the detection of anti-HIV in saliva may achieve accuracy of 97.1-100%, comparable with that in blood. Furthermore, this study suggests that a highly accurate molecular method of HIV detection may be feasible, although the studied carriers had rather homogeneous characteristics. PMID:16776764

Yapijakis, Christos; Panis, Vassilis; Koufaliotis, Nikos; Yfanti, Georgia; Karachalios, Stefanos; Roumeliotou, Anastasia; Mantzavinos, Zacharias

2006-06-01

56

Isolation and identification of Perkinsus olseni from feces and marine sediment using immunological and molecular techniques.  

PubMed

Molecular and immunological probes were used to identify various life stages of Perkinsus olseni, a protozoan parasite of the Manila clam Ruditapes philippinarum, from a marine environment and decomposing clam tissue. Western blotting revealed that the antigenic determinants of the rabbit anti-P. olseni antibody developed in this study were peptides with molecular masses of 55.9, 24.0, and 19.2kDa. Immunofluorescent assay indicated that the rabbit anti-P. olseni IgG was specific to all life stages, including the prezoosporangium, trophozoite, and zoospore. Perkinsus olseni prezoosporangium-like cells were successfully isolated from marine sediment collected from Hwangdo on the west coast of Korea, where P. olseni-associated clam mortality has recurred for the past decade. Purified cells were positively stained with the rabbit anti-P. olseni antibody in an immunofluorescence assay, confirming for the first time the presence of P. olseni in marine sediment. Actively replicating zoospores inside the prezoosporangia were observed in the decomposing clam tissue collected from Hwangdo. P. olseni was also isolated from the feces and pseudofeces of infected clams and confirmed by PCR. The clams released 1-2 prezoosporangia per day through feces. The data suggested that the fecal discharge and decomposition of the infected clam tissue could be the two major P. olseni transmission routes. PMID:20691188

Park, Kyung-Il; Yang, Hyun-Sung; Kang, Hyun-Sil; Cho, Moonjae; Park, Kwang-Jae; Choi, Kwang-Sik

2010-08-04

57

Molecular Methods for Detection of Tumor Markers in Glioblastomas  

Microsoft Academic Search

\\u000a Glioblastoma (grade IV\\/IV astrocytoma), the most malignant type of brain tumor, occurs in all age groups with the highest\\u000a incidence in older patients. Novel therapeutic strategies and molecular assays to follow treatments of suppressible targets\\u000a are urgently needed. Surveys of large numbers of genes in the initial phase of tumor marker identification are currently being\\u000a performed in multi-center studies. Queries

Marie E. Beckner; Mary L. Nordberg

58

Molecular markers in prostate cancer. Part I: predicting lethality  

PubMed Central

Assessing the lethality of 'early,' potentially organ-confined prostate cancer (PCa) is one of the central controversies in modern-day urological clinical practice. Such cases are often considered for radical 'curative' treatment, although active surveillance may be equally appropriate for many men. Moreover, the balance between judicious intervention and overtreatment can be difficult to judge. The patient's age, comorbidities, family history and philosophy of self-health care can be weighed against clinical features such as the palpability of disease, the number and percentage of biopsy cores involved with the disease, histological grade, presenting prostate-specific antigen (PSA) and possible previous PSA kinetics. For many years, scientists and physicians have sought additional molecular factors that may be predictive for disease stage, progression and lethality. Usually, claims for a 'new' unique marker fall short of true clinical value. More often than not, such molecular markers are useful only in multivariate models. This review summarizes relevant molecular markers and models reported up to and including 2008.

Agrawal, Sachin; Dunsmuir, William D.

2009-01-01

59

The immunological synapse and the actin cytoskeleton: molecular hardware for T cell signaling  

Microsoft Academic Search

The actin cytoskeleton seems to play two critical roles in the activation of T cells. One of these roles is T cell shape development and movement, including formation of the immunological synapse. The other is the formation of a scaffold for signaling components. This review focuses on the recent convergence of cell biology and immunology studies to explain the role

John A. Cooper

2000-01-01

60

Molecular phylogenetic study of the Iranians based on polymorphic markers.  

PubMed

The application of polymorphic markers in construction of phylogenetic trees has been documented. Five polymorphic markers located in the PAH gene region including PAH-BglII, PAH-PvuII(A), PAH-EcoRI, PAH-MspI and PAH-STR were selected for analysis of phylogenetic relationships of the Iranians with 15 other populations of the world. The lowest genetic distance was observed between the Iranians and populations residing in Adygei (an ethnic group of the Russian Caucasus), Russia and Druze (a Middle Eastern group). However, East Asian populations including Han, Japanese and Cambodians, Khmer or the Oceanians (Melanesian, Nasioi) showed high genetic distance with the Iranians. The data suggested that the Iranians might have relatively close evolutionary history with the populations residing in Russia rather than East Asian populations. This study provided the first new molecular insight into the evolutionary history of the Iranian population. PMID:23073556

Fazeli, Zahra; Vallian, Sadeq

2012-10-13

61

The application of LTR retrotransposons as molecular markers in plants.  

PubMed

Retrotransposons are a major agent of genome evolution. Various molecular marker systems have been developed that exploit the ubiquitous nature of these genetic elements and their property of stable integration into dispersed chromosomal loci that are polymorphic within species. The key methods, SSAP, IRAP, REMAP, RBIP, and ISBP, all detect the sites at which the retrotransposon DNA, which is conserved between families of elements, is integrated into the genome. Marker systems exploiting these methods can be easily developed and inexpensively deployed in the absence of extensive genome sequence data. They offer access to the dynamic and polymorphic, nongenic portion of the genome and thereby complement methods, such as gene-derived SNPs, that target primarily the genic fraction. PMID:22367869

Schulman, Alan H; Flavell, Andrew J; Paux, Etienne; Ellis, T H Noel

2012-01-01

62

Molecular markers of endometrial carcinoma detected in uterine aspirates.  

PubMed

Endometrial cancer (EC) is the most frequent of the invasive tumors of the female genital tract. Although usually detected in its initial stages, a 20% of the patients present with advanced disease. To date, no characterized molecular marker has been validated for the diagnosis of EC. In addition, new methods for prognosis and classification of EC are needed to combat this deadly disease. We thus aimed to identify new molecular markers of EC and to evaluate their validity on endometrial aspirates. Gene expression screening on 52 carcinoma samples and series of real-time quantitative PCR validation on 19 paired carcinomas and normal tissue samples and on 50 carcinoma and noncarcinoma uterine aspirates were performed to identify and validate potential biomarkers of EC. Candidate markers were further confirmed at the protein level by immunohistochemistry and Western blot. We identified ACAA1, AP1M2, CGN, DDR1, EPS8L2, FASTKD1, GMIP, IKBKE, P2RX4, P4HB, PHKG2, PPFIBP2, PPP1R16A, RASSF7, RNF183, SIRT6, TJP3, EFEMP2, SOCS2 and DCN as differentially expressed in ECs. Furthermore, the differential expression of these biomarkers in primary endometrial tumors is correlated to their expression level in corresponding uterine fluid samples. Finally, these biomarkers significantly identified EC with area under the receiver-operating-characteristic values ranging from 0.74 to 0.95 in uterine aspirates. Interestingly, analogous values were found among initial stages. We present the discovery of molecular biomarkers of EC and describe their utility in uterine aspirates. These findings represent the basis for the development of a highly sensitive and specific minimally invasive method for screening ECs. PMID:21207424

Colas, Eva; Perez, Cristina; Cabrera, Silvia; Pedrola, Nuria; Monge, Marta; Castellvi, Josep; Eyzaguirre, Fernando; Gregorio, Jesus; Ruiz, Anna; Llaurado, Marta; Rigau, Marina; Garcia, Marta; Ertekin, Tugçe; Montes, Melania; Lopez-Lopez, Rafael; Carreras, Ramon; Xercavins, Jordi; Ortega, Alicia; Maes, Tamara; Rosell, Elisabet; Doll, Andreas; Abal, Miguel; Reventos, Jaume; Gil-Moreno, Antonio

2011-04-08

63

Identification of early molecular markers for breast cancer  

PubMed Central

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 profiling was carried out on DCIS-bearing mice and control animals. Additionally, a set of human DCIS and invasive mammary tumors were analyzed in a similar fashion. Enhanced expression of these marker genes in human and murine samples was validated by quantitative RT-PCR. Besides, marker gene expression was also validated by immunohistochemistry of human samples. Furthermore in silico analyses using an online microarray database were performed. Results In DCIS-mice seven genes were identified that were significantly up-regulated in DCIS: DEPDC1, NUSAP1, EXO1, RRM2, FOXM1, MUC1 and SPP1. A similar up-regulation of homologues of the murine genes was observed in human DCIS samples. Enhanced expression of these genes in DCIS and IDC (invasive ductal carcinoma) was validated by quantitative RT-PCR and immunohistochemistry. Conclusions By comparing murine markers for the ductal carcinoma in situ (DCIS) of the mammary gland with genes up-regulated in human DCIS-samples we were able to identify a set of genes which might allow early detection of DCIS and invasive carcinomas in the future. The similarities between gene expression in DCIS and invasive carcinomas in our data suggest that the early detection and treatment of DCIS is of utmost relevance for the survival of patients who are at high risk of developing breast carcinomas.

2011-01-01

64

An analysis of 14 molecular markers for monitoring osteoarthritis: segregation of the markers into clusters and distinguishing osteoarthritis at baseline  

Microsoft Academic Search

Objective To investigate the relationships between serum and urinary molecular markers (MM) used to monitor osteoarthritis.Design Forty osteoarthritis patients had blood and urine collected at baseline and 1, 3, 6 and 12 months later. Specimens from 20 controls were obtained twice at a one month interval. The concentration of 14 different markers was determined at each time point and the

I. G Otterness; A. C Swindell; R. O Zimmerer; A. R Poole; M Ionescu; E Weiner

2000-01-01

65

Molecular markers as a tool for population and evolutionary studies of stingless bees  

Microsoft Academic Search

Molecular markers are widely used in biology to address questions related to ecology, genetics and evolution. In bees, molecular studies addressing those issues have focused on Apis and Apis mellifera. Here we describe examples where molecular markers from mtDNA and microsatellite analyses were applied to stingless bees species. The data obtained, although in some cases preliminary, have already proven useful

Maria Cristina Arias; Rute Magalhães Brito; Flávio de Oliveira Francisco; Geraldo Moretto; Favízia Freitas de Oliveira; Daniela Silvestre; Walter Steven Sheppard

2006-01-01

66

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

67

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

PubMed

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. PMID:22861360

Abebe, F

2012-09-01

68

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

PubMed Central

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

2005-01-01

69

Prophage Carriage as a Molecular Epidemiological Marker in Streptococcus pneumoniae  

PubMed Central

The great majority of clinical isolates of Streptococcus pneumoniae carry prophages that may be identified through their hybridization with a DNA probe specific for the pneumococcal lytA gene (M. Ramirez, E. Severina, and A. Tomasz, J. Bacteriol. 181:3618–3625, 1999). We now show that the lytA hybridization pattern of chromosomal SmaI digests is stable for a given strain during extensive serial culturing in the laboratory; the pattern is specific for the strain’s clonal type, as defined by pulsed-field gel electrophoretis (PFGE) pattern, and variations in PFGE subtypes may be explained by changes in the number and chromosomal localization of this prophage(s). These observations indicate that the lytA hybridization pattern may be used as a molecular epidemiological marker that offers additional resolution of the genetic background of S. pneumoniae strains.

Severina, Elena; Ramirez, Mario; Tomasz, Alexander

1999-01-01

70

Mitochondrial DNA as a marker of molecular diversity: a reappraisal.  

PubMed

Over the last three decades, mitochondrial DNA has been the most popular marker of molecular diversity, for a combination of technical ease-of-use considerations, and supposed biological and evolutionary properties of clonality, near-neutrality and clock-like nature of its substitution rate. Reviewing recent literature on the subject, we argue that mitochondrial DNA is not always clonal, far from neutrally evolving and certainly not clock-like, questioning its relevance as a witness of recent species and population history. We critically evaluate the usage of mitochondrial DNA for species delineation and identification. Finally, we note the great potential of accumulating mtDNA data for evolutionary and functional analysis of the mitochondrial genome. PMID:19821901

Galtier, N; Nabholz, B; Glémin, S; Hurst, G D D

2009-10-09

71

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

72

Evaluation of immunological, parasitological and molecular methods for the diagnosis of Schistosoma mansoni infection before and after chemotherapy treatment with praziquantel in experimentally infected Nectomys squamipes  

Microsoft Academic Search

In low endemicity areas of schistosomiasis, the recommended diagnostic method of coprological examination results in an underestimation of infection cases. Alternative diagnostic methods have been developed, such as immunodiagnostic and molecular techniques. In this study we evaluated three methods used in the diagnosis of Schistosoma mansoni infection: parasitological (Kato-Katz), immunological (ELISA) and molecular (real time PCR), and also investigated the

Rosana Gentile; Margareth Maria Lessa Gonçalves; Sócrates Fraga da Costa Neto; Maristella Matos da Costa; Regina Helena Saramago Peralta; José Mauro Peralta

2011-01-01

73

Clinical, Immunological and Molecular Characteristics of 37 Iranian Patients with X-Linked Agammaglobulinemia  

Microsoft Academic Search

Background: X-linked agammaglobulinemia (XLA) is a hereditary immunodeficiency characterized by an early onset of recurrent bacterial infections, a profound deficiency of all immunoglobulin isotypes and a markedly reduced number of peripheral B lymphocytes. Eighty-five percent of the patients with this phenotype have mutations in Bruton’s tyrosine kinase (BTK) gene. Methods: To provide an informative outlook of clinical and immunological manifestations

Asghar Aghamohammadi; Maurilia Fiorini; Mostafa Moin; Nima Parvaneh; Shahram Teimourian; Mehdi Yeganeh; Francesca Goffi; Hirokazu Kanegane; Ali Akbar Amirzargar; Zahra Pourpak; Nima Rezaei; Ali Salavati; Nima Pouladi; Sina Abdollahzade; Luigi D. Notarangelo; Toshio Miyawaki; Alessandro Plebani

2006-01-01

74

World Antimalarial Resistance Network (WARN) III: Molecular markers for drug resistant malaria  

Microsoft Academic Search

Molecular markers for drug resistant malaria represent public health tools of great but mostly unrealized potential value. A key reason for the failure of molecular resistance markers to live up to their potential is that data on the their prevalence is scattered in disparate databases with no linkage to the clinical, in vitro and pharmacokinetic data that are needed to

Christopher V Plowe; Cally Roper; John W Barnwell; Christian T Happi; Hema H Joshi; Wilfred Mbacham; Steven R Meshnick; Kefas Mugittu; Inbarani Naidoo; Ric N Price; Robert W Shafer; Carol H Sibley; Colin J Sutherland; Peter A Zimmerman; Philip J Rosenthal

2007-01-01

75

Molecular markers of endocrine disruption in aquatic organisms.  

PubMed

A wide range of organic contaminant compounds prevalent in the aquatic environment has been shown to exhibit hormone-disrupting activity. The actual potency of such compounds are low compared with endogenous hormones, such as 17beta-estradiol, but may still produce detrimental biological effects. Induced hormone levels are routinely measured using commercial testing kits, though these fail to relate to actual effects. Field and laboratory studies on the biological effects of environmental estrogens have, in the past, largely relied on assays of vitellogenin (vtg) induction in male fish, reduced growth in testes formation, and intersex incidence. Here, we critically review the current and potential application of molecular techniques in assessing the adverse biological reproductive effects of endocrine-disrupting chemicals in aquatic organisms. The role of fish (estrogen, androgen, and progestogen) hormone receptors and invertebrate (ecdysone) hormone receptor, egg production (vtg and chorion) proteins, steroid biosynthesis enzymes (aromatase, sulfotransferase, and hydroxysteroid dehydrogenase), DNA damage, apoptosis, and their potential development as biomarkers are discussed in turn. In each case, the sequences characterized are presented and homologies across species are highlighted. Molecular methods of gauging vtg and zona radiata (ZR) expression and protein concentrations have included immunoassay and reverse transcription polymerase chain reaction (RT-PCR). Suggestions for the isolation for key gene expression products (aromatase, ZR, and vtg, for instance), from a wider range of fish species using degenerate primers, are given. Endocrine disruption in invertebrates has received less attention compared with fish, partly because the knowledge regarding invertebrate endocrinology is limited. Here we review and suggest alternate isolation strategies for key players in the imposex induction process: vitellin (Vn), aromatase, and Ala-Pro-Gly-Trp (APGW) amide neurohormone. Current molecular-level techniques rely on ligand-binding assays, enzyme-linked immunosorbent assay (ELISA), and, more recently, gene expression. In the future, more reliance will be placed on the development of gene expression assays using reporter systems combined with cross-species PCR-based or polyclonal antibody-based assays. We discuss the use of recombinant receptors as a means of primary screening of environmental samples for estrogenicity and antiestrogenicity, which avoids species and seasonal variation in receptor response to ligand binding, a recognized problem of earlier bioassays. Most exciting is the potential that microarray and proteomics approaches have to offer. Such techniques are now used routinely in medical research to identify specific genes and proteins affected by treatment with endocrine disruptors, including estradiol. The technique has yet to be used to screen aquatic organisms, but it has the potential to implicate previously unsuspected estradiol-sensitive genes that may later become molecular markers of endocrine disruption. PMID:12888444

Rotchell, Jeanette M; Ostrander, Gary K

76

APPLICATION OF MOLECULAR MARKER TECHNOLOGIES ON CEREAL CROPS IMPROVEMENT  

Technology Transfer Automated Retrieval System (TEKTRAN)

The use of PCR-based DNA markers has greatly improved the efficiency in mapping agronomic traits. One such DNA marker is SSR or microsatellite. It is multiallelic and capable of detecting higher levels of polymorphism. At the moment, SSR is the most extensively used marker system in both wheat an...

77

Genetic diversity analysis of common beans based on molecular markers.  

PubMed

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. PMID:22215964

Gill-Langarica, Homar R; Muruaga-Martínez, José S; Vargas-Vázquez, M L Patricia; Rosales-Serna, Rigoberto; Mayek-Pérez, Netzahualcoyotl

2011-10-01

78

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

79

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

2012-08-06

80

Immunologic Proliferation Marker Ki-S2 as Prognostic Indicator for Lymph Node-Negative Breast Cancer  

Microsoft Academic Search

Background: Proper treatment of lymph node-negative breast cancer de- pends on an accurate prognosis. To improve prognostic models for this disease, we evaluated whether an im- munohistochemical marker for prolif- erating cells, Ki-S2 (a monoclonal anti- body that binds to a 100-kd nuclear protein expressed in S, G2, and M

Pierre Rudolph; Hans-Jurgen Heidebrecht; Hendrik Bolte; Virgo Ratjen; Bo Baldetorp; Mårten Ferno; Håkan Olsson; Reza Parwaresch

1999-01-01

81

Rabbit antibodies against the low molecular weight folate binding protein from human milk. Use for immunological characterization of human folate binding proteins in an enzyme-linked immunosorbent assay (ELISA)  

Microsoft Academic Search

Antibodies to a low molecular weight folate binding protein isolated from human milk were raised in rabbits and used for development of a two-site enzyme-linked immunosorbent assay (ELISA) for immunological characterization of human folate binding proteins (FBPs). The high and low molecular weight FBPs from human milk were immunologically indistinguishable. Furthermore, the FBPs in human urine and cerebrospinal fluid showed

Mimi Høier-Madsen; Steen Ingemann Hansen; Jan Holm

1987-01-01

82

Immunological and molecular genetic analysis of the cellulase component from Penicillium funiculosum.  

PubMed

Following immunization of rabbits, the antiserum was initially analyzed for antiendoglucanase activity using dot-blot ELISA methods. When compared with the preimmune serum, the antiserum showed strong response even at 25 ng concentration. The specificity of the polyclonal antibodies, raised against the partially purified endoglucanase component of Penicillium funiculosum, was determined by Oüchterlony double diffusion. Rocket electrophoresis confirmed the presence of only two types of antigens in the serum. The two rockets obtained were attributable to endo I and the merging of immunologically identical (but mobility wise different) endo II and endo III. This antibody preparation was used as a probe. The deduced M1 of the cloned E. coli endo I was found to be 58 Kd by Western blotting. PMID:1796811

Sahasrabudhe, N A

1991-10-01

83

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

84

Gordon Research Conference on Molecular and Immunological Aspects of Parasitology Held at New London, New Hampshire on 7-11 Aug 1989.  

National Technical Information Service (NTIS)

The 1989 Gordon Research Conference on Molecular and Immunological Aspects of Parasitology was held at Colby-Sawyer College, New London, NH, August 7-11, 1989. A large amount of new and exciting data was presented and resulted in long and wide ranging dis...

E. R. Pfefferkorn

1990-01-01

85

Molecular Markers of Radiation-related Normal Tissue Toxicity  

PubMed Central

Over the past five decades, those interested in markers of radiation effect have focused primarily on tumor response. More recently, however, the view has broadened to include irradiated normal tissues—markers that predict unusual risk of side-effects, prognosticate during the prodromal and therapeutic phases, diagnose a particular toxicity as radiation-related, and, in the case of bioterror, allow for tissue-specific biodosimetry. Currently, there are few clinically useful radiation-related biomarkers. Notably, levels of some hormones such as thyroid-stimulating hormone (TSH) have been used successfully as markers of dysfunction, indicative of the need for replacement therapy, and for prevention of cancers. The most promising macromolecular markers are cytokines: TGF?, IL-1, IL-6, and TNF? being lead molecules in this class as both markers and targets for therapy. Genomics and proteomics are still in nascent stages and are actively being studied and developed.

Okunieff, Paul; Chen, Yuhchyau; Maguire, David J.; Huser, Amy K.

2009-01-01

86

[Immunological determination of epidermal G2-chalone as a squamous cell marker in lung tumors in rats].  

PubMed

Epidermal G2 chalone was determined in induced rat lung tumors by the double immunodiffusion test or by immunoautoradiography. Epidermal chalone normally contained by keratinized tissues alone was detected in squamous cell lung carcinomas or adenomas with areas of squamous cell differentiation rather than in so-called pure adenocarcinomas. The antigen concentration correlated with the expansion of the areas of squamous cell differentiation. Thus the detection of epidermal G2 chalone can serve as marker of squamous cell metaplasia in the rat lung tissue. PMID:6157440

Okulov, V B; Zabezhinski?, M A

1980-08-01

87

IMMUNOLOGICAL METHODS  

Technology Transfer Automated Retrieval System (TEKTRAN)

Environmental microbiology does not deal with all aspects of immunology or the immune responses per se, but instead adapts immunology-based research technologies or immunoassays for the study of microorganisms and chemical contaminants in association with the environment. The primary immunologic-bas...

88

Molecular markers and conservation of plant species in Latin America: the case of Phaedranassa viridflora (Amaryllidaceae)  

Technology Transfer Automated Retrieval System (TEKTRAN)

Microsatellites are molecular markers with great potential for investigating genetic structure of populations. This information is valuable for generating effective conservation plans. We studied the endemic and endangered Phaedranassa viridiflora (Amaryllidaceae) to show the utility of microsatelli...

89

IDENTIFICATION OF SEX CHROMOSOME MOLECULAR MARKERS USING RAPDS AND FLUORESCENT IN SITU HYBRIDIZATION IN RAINBOW TROUT  

EPA Science Inventory

The goal of this work is to identify molecular markers associated with the sex chromosomes in rainbow trout to study the mode of sex determination mechanisms in this species. Using the RAPD assay and bulked segregant analysis, two markers were identified that generated polymorphi...

90

Mapping Co , a gene controlling the columnar phenotype of apple, with molecular markers  

Microsoft Academic Search

The columnar phenotype is a very valuable genetic resource for apple breeding because of its compact growth form determined by the dominant gene Co. Using bulked segregant analysis combined with several DNA molecular marker techniques to screen the F1 progeny of Spur Fuji × Telamon (heterozygous for Co), 9 new DNA markers (6 RAPD, 1 AFLP and 2 SSRs) linked

Yi-Ke Tian; Cai-Hong Wang; Ji-Shu Zhang; Celia James; Hong-Yi Dai

2005-01-01

91

Molecular markers of anthropogenic activity in sediments of the Havel and Spree Rivers (Germany)  

Microsoft Academic Search

Detailed gas chromatographic\\/mass spectrometric analyses have been applied to sediment samples of the Havel and Spree River, tributaries to the Elbe River, in order to identify specific molecular markers of anthropogenic activities. Despite a wide variety of lipophilic organic compounds from diffuse anthropogenic contamination, a local emission of an industrial point source was reflected by specific markers including halogenated compounds

M. Ricking; J. Schwarzbauer; S. Franke

2003-01-01

92

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

93

Association between molecular markers for beef tenderness and growth traits in Argentinian angus cattle.  

PubMed

Molecular markers for beef tenderness are classic examples of the contribution of genome technology to animal breeding through marker-assisted selection (MAS). Markers on the ?-calpain (CAPN1) and calpastatin (CAST) genes have been extensively evaluated for their association with tenderness. However, little is known about their potential effect on other economically important traits. In this work, the association of molecular markers for beef tenderness with growth traits was evaluated in Angus cattle of Argentina. Expected progeny differences were extracted from the 2008 Angus Sire Summary of Argentina. Information corresponding to 268 influential bulls that had been genotyped for two markers in CAPN1 and two markers in CAST was provided by the Argentine Angus Association. Genotype probabilities were assigned, by segregation analysis, to those bulls in the Sire Summary that had no marker information. Expected progeny differences of 1365 sires were regressed on the number of alleles favouring tenderness at each locus. There was a significant effect of markers on expected progeny differences of birth weight, weaning weight (direct), weight at 18 months and rib eye area. In general, there was a negative effect of alleles favouring tenderness on growth traits. These correlated responses should be taken into account when molecular markers are used in selection schemes that aim to improve beef tenderness. PMID:21554351

Pintos, D; Corva, P M

2011-02-06

94

Identification of tumor markers and differentiation markers for molecular diagnosis of lung adenocarcinoma  

Microsoft Academic Search

To identify tumor markers and differentiation markers for lung adenocarcinoma (AdC), we analysed expression profiles of 14 500 genes against three cases of type II alveolar epithelial cells, bronchiolar epithelial cells, and bronchial epithelial cells, respectively, and 10 cases of AdC cells isolated by laser capture microdissection. Hierarchical clustering analysis indicated that AdC cells and noncancerous lung epithelial cells are

N Nakamura; K Kobayashi; M Nakamoto; T Kohno; H Sasaki; Y Matsuno; J Yokota

2006-01-01

95

Molecular markers for population genetic analyses in the family Psittacidae (Psittaciformes, Aves)  

Microsoft Academic Search

The selection of molecular markers for population studies is an important tool for biodiversity conservation. The fam- ily Psittacidae contains many endangered and vulnerable species and we tested three kinds of molecular markers for their potential use in population studies of five psitacid species: 43 hyacinth macaws (Anodorhynchus hyacinthinus), 42 blue-and-yellow macaws (Ara ararauna), 23 red-and-green macaws (Ara chloroptera), 19

Patrícia J. Faria; Cristina Y. Miyaki

2006-01-01

96

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

2012-02-02

97

Gordon Research Conference on Molecular and Immunological Aspects of Parasitology (1987).  

National Technical Information Service (NTIS)

This conference on Molecular and Biochemical Parasitiology proved to be very popular. The organizers were forced to turn down over 100 applicants in order to limit the size to 135, the maximum allowed. A wide variety of topics were discussed. The identifi...

E. R. Pfefferkorn

1987-01-01

98

Analysis of plant diversity with retrotransposon-based molecular markers  

PubMed Central

Retrotransposons are both major generators of genetic diversity and tools for detecting the genomic changes associated with their activity because they create large and stable insertions in the genome. After the demonstration that retrotransposons are ubiquitous, active and abundant in plant genomes, various marker systems were developed to exploit polymorphisms in retrotransposon insertion patterns. These have found applications ranging from the mapping of genes responsible for particular traits and the management of backcrossing programs to analysis of population structure and diversity of wild species. This review provides an insight into the spectrum of retrotransposon-based marker systems developed for plant species and evaluates the contributions of retrotransposon markers to the analysis of population diversity in plants.

Kalendar, R; Flavell, A J; Ellis, T H N; Sjakste, T; Moisy, C; Schulman, A H

2011-01-01

99

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

NASA Astrophysics Data System (ADS)

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

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

2006-12-01

100

[Non-small cell lung cancer. Subtyping and predictive molecular marker investigations in cytology].  

PubMed

The diagnosis and treatment of non-small cell lung cancer (NSCLC) have been revolutionized over the last few years. Requirements for cytopathologists in lung cancer diagnosis have therefore changed. The general diagnostic category of NSLC is no longer sufficient. In addition cytological specimens need to be evaluated for adequacy regarding predictive marker analyses. Accurate NSCLC subtyping with a distinction of adenocarcinoma from squamous cell carcinoma is crucial for treatment decisions as the subtype will decide on the chemotherapy regimen and the choice of predictive marker analyses for targeted treatment. In the majority of cases, the subtype can be diagnosed by morphology alone. Cytology is equally well suited as biopsy specimens for the assessment of molecular predictive markers. The best results are achieved when both cytology and biopsy specimens are compared to choose the most appropriate specimen for morphological subtyping and molecular testing. In this paper, we discuss special issues of NSCLC subtyping and currently recommended predictive molecular marker analyses. PMID:22711372

Savic, S; Bihl, M P; Bubendorf, L

2012-07-01

101

Molecular subtype is determinant on inflammatory status and immunological profile from invasive breast cancer patients.  

PubMed

Breast cancer consists in a chronic inflammatory disease with multiple biological and clinical behaviors. Based on high throughput technologies data, this disease is currently classified according to the molecular expression of estrogen (ER), progesterone (PR) and human epidermal growth factor (HER-2) receptors. In this study, we defined the inflammatory profile of the main molecular subtypes of breast cancer patients: luminal (ER and PR positive, HER-2 negative), HER-2 enriched (HER-2 positive) and triple negative (ER, PR and HER-2 negative). Cytokines panel was assessed by measurement of TNF-?, TGF-?, IL-1, IL-10 and IL-12 plasmatic levels. Oxidative profile was assessed by determination of lipid peroxidation, total antioxidant capacity of plasma, malondialdehyde levels, carbonyl content and nitric oxide (NO). Clinical data were correlated with inflammatory findings. Our findings demonstrated that patients bearing the luminal subtype displayed high TNF-?, TGF-? and enhanced oxidative stress levels associated with reduced IL-12. HER-2-enriched group exhibited higher levels of TNF-?, IL-12 and TGF-? associated with enhanced oxidative stress. Triple-negative subtype exhibited the most aggressive profile of disease behavior, with reduction in both TNF-? and TGF-?, with high levels of lipid peroxidation and NO. The clinical importance of our findings lies in the fact that the inflammatory status varies in distinct ways due to molecular subtype of breast cancer, opening potential therapeutic targets to future therapies. PMID:22618884

Herrera, A C S A; Panis, C; Victorino, V J; Campos, F C; Colado-Simão, A N; Cecchini, A L; Cecchini, R

2012-05-22

102

Molecular marker analysis of European Setosphaeria turcica populations  

Microsoft Academic Search

Setosphaeria turcica is the causal agent of northern corn leaf blight, a foliar maize disease of worldwide economic importance. In Europe, its severity increases. To investigate the pathogen's population-genetic structure in central Europe, a total of 80 isolates was sampled in Germany, Switzerland, France, Austria, and Hungary and investigated with 52 random amplified polymorphic DNA (RAPD) markers. The mating type

Dorothea S. Borchardt; H. Günter Welz; Hartwig H. Geiger

1998-01-01

103

MYOSIN ISOENZYMES AS MOLECULAR MARKERS FOR MUSCLE PHYSIOLOGY  

Microsoft Academic Search

SUMMARY Myosin is a major component of skeletal muscle and it plays a central role in determining the physiological performance of adult tissue. Developing muscles contain myosin molecules which are different from the adult forms, and these isoenzymes have been found to be characteristic markers of the diverse physiological and pathological states of muscle tissue. The differences between these isoenzymes

ROBERT G. WHALEN

104

Fingerprinting fission yeast: polymorphic markers for molecular genetic analysis of Schizosaccharomyces pombe strains  

Microsoft Academic Search

The fission yeast Schizosaccharomyces pombe is widely used as a model eukaryote for cell and molecular studies but little is known of natural genetic variation in this species. In order to obtain informative molecular markers, imperfect tandem repeats, identified through bioinformatic methods, were tested for length polymorphism in six wild-type strains of Sch. pombe isolated from different substrates and geographical

Ann-Marie Patch; Stephen J. Aves

2007-01-01

105

Development and use of molecular markers to accelerate peanut cultivar development  

Technology Transfer Automated Retrieval System (TEKTRAN)

Close cooperation between conventional plant breeders and molecular geneticists will be needed to efficiently and effectively utilize modern genetic tools in the development of peanut cultivars. We have used this approach at Tifton to develop molecular markers for resistance to the peanut root-knot...

106

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 ...

107

Genetic mutations, molecular markers and future directions in research.  

PubMed

Recent molecular studies have described a number of abnormalities associated with the pathogenesis of thyroid carcinoma. These distinct molecular events are often associated with specific stages of tumor development and may serve as prognostic factors and therapeutic targets. A better understanding of the mechanisms involved in thyroid cancer pathogenesis, will hopefully help translate these discoveries to improved patient care. PMID:23602255

Patel, Kepal N

2013-04-17

108

Molecular and immunological analysis of a polymorphic periplasmic protein of Borrelia burgdorferi.  

PubMed Central

Borrelia burgdorferi is the causative agent of Lyme disease, a tick-borne spirochetosis with a worldwide prevalence. To assist the categorization and typing of fresh isolates from global foci, we have identified a unique species-specific periplasmic protein (P22-A) conserved among all North American and European isolates examined. The gene encoding this antigen was cloned, and the recombinant was used to screen serum collected from experimentally infected animals. Although antibodies were detected in all infected animals at 21 days after inoculation with live, low-passage spirochetes, the response was stronger in other animals that were inoculated with inactivated and lysed bacteria. This result, along with the immune electron microscopy data, suggests P22-A is concentrated in the periplasmic space. The P22-A antigens exhibited size heterogeneity among different isolates, ranging between 20 and 23 kDa, but as a group the P22-A antigens appeared to retain antigenic homogeneity. Thus, P22-A can serve as a structural marker for characterizing new isolates of B. burgdorferi and may prove useful in future serological assays with a mixture of B. burgdorferi-specific antigens. Images

Simpson, W J; Schrumpf, M E; Hayes, S F; Schwan, T G

1991-01-01

109

Biodiversity in Date Palm: Molecular Markers as Indicators  

Microsoft Academic Search

\\u000a Date palm, a tree known only as cultivated and under domestication for thousands of years with a wide range of distinct morphological\\u000a diversity, has been a target of considerable research work, including, e.g. studies on both phenotypic and genetic diversity.\\u000a Most research has focused on cultivar identification, where both types of markers – phenotypic and genetic – have been utilized.

S. Elshibli; H. Korpelainen

110

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

Microsoft Academic Search

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.

Adolfo Borges; Carmen C. García; Elizabeth Lugo; Marcelo J. Alfonzo; Michael J. Jowers

2006-01-01

111

Stimulated proliferative responses in vertically HIV-infected children on HAART correlate with clinical and immunological markers  

PubMed Central

The objective of the study was to investigate the relationship between various CD4+ T cell subsets and the ability of peripheral blood mononuclear cells (PBMC) to proliferate to several stimuli in vertically human immunodeficiency virus type 1 (HIV-1)-infected children. We studied 29 HIV-1-infected children on highly active antiretroviral therapy (HAART) (median duration: 12·3 months). T cell subsets were determined by flow cytometry. Plasma viral load (VL) was quantified using a standardized molecular method. Proliferative responses were evaluated by [3H]-thymidine incorporation. Decreased proliferative responses of PBMC to pokeweed mitogen (PWM) were found for HIV-1-infected children in Centers for Disease Control (CDC) clinical categories B and C when compared to the control group (P < 0·05). Similarly, children with ? 15% CD4+ T cells showed a decrease in proliferative responses to PWM (P < 0·01), anti-CD3 + anti-CD28 (P < 0·01) and phytohaemagglutinin (PHA) (P < 0·05) with respect to the control group and to children with CD4+ T cells ? 25%. Proliferative responses to PWM, anti-CD3+, anti-CD28 and PHA had a statistically significant positive correlation with CD3+/mm3, CD4+/mm3, % CD4 T cells, CD4/CD8 ratio and the percentage of naive T cell subsets (CD4+CD45RO?HLA-DR?, CD4+ CD45RA+ CD62L+, CD4+ CD45RA+), CD4+ CD62L+ and CD4+ T cells co-expressing CD38+ (CD4+ HLA-DR?CD38+, CD4+ CD38+). Moreover, we found a negative correlation between PBMC proliferative responses and % CD8 T cells, memory, memory-activated and activated CD4+ T cell subsets. Lower proliferative responses to PWM (P < 0·01) and PHA (P < 0·01) were associated with higher VL. Our data show that higher proliferative responses to PWM, anti-CD3 + anti-CD28 and PHA are associated with both non-activated and naive CD4+ T cell subsets in HIV-1-infected children on HAART.

RESINO, S; ABAD, M L; NAVARRO, J; BELLON, J M; SANCHEZ-RAMON, S; ANGELES MUNOZ-FERNANDEZ, M

2003-01-01

112

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

PubMed

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

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

2012-09-21

113

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

114

Phenotypic features of circulating leucocytes as immunological markers for clinical status and bone marrow parasite density in dogs naturally infected by Leishmania chagasi  

PubMed Central

Canine visceral leishmaniasis (CVL) manifests itself as a broad clinical spectrum ranging from asymptomatic infection to patent severe disease. Despite relevant findings suggesting changes on lymphocytes subsets regarding the CVL clinical forms, it still remains to be elucidated whether a distinct phenotypic profile would be correlated with degree of tissue parasite density. Herein, we have assessed the correlation between the clinical status as well as the impact of bone marrow parasite density on the phenotypic profile of peripheral blood leucocytes in 40 Brazilian dogs naturally infected by Leishmania chagasi. Our major findings describe the lower frequency of B cells and monocytes as the most important markers of severe CVL. Our main statistically significant findings reveal that the CD8+ T cell subset reflects most accurately both the clinical status and the overall bone marrow parasite density, as increased levels of CD8+ lymphocytes appeared as the major phenotypic feature of asymptomatic disease and dogs bearing a low parasite load. Moreover, enhanced major histocompatibility complex (MHC)-II density as well as a higher CD45RB/CD45RA expression index seems to represent a key element to control disease morbidity. The association between clinical status, bone marrow parasitism and CD8+ T cells re-emphasizes the role of the T cell-mediated immune response in the resistance mechanisms during ongoing CVL. Higher levels of circulating T lymphocytes (both CD4+ and CD8+ T cells) and lower MHC-II expression by peripheral blood lymphocytes seem to be the key for the effective immunological response, a hallmark of asymptomatic CVL.

Reis, A B; Teixeira-Carvalho, A; Giunchetti, R C; Guerra, L L; Carvalho, M G; Mayrink, W; Genaro, O; Correa-Oliveira, R; Martins-Filho, O A

2006-01-01

115

Genotypic diversity, molecular markers and spatial distribution of genets in clonal plants, a literature survey  

Microsoft Academic Search

We present a literature survey of studies using molecular markers to investigate genet diversity and structure in clonal plants.\\u000a The data from 40 studies comprised 45 species of which only two were studied by DNA methods, the rest by isozyme markers.\\u000a Less than one third of the studies provided information about the spatial distribution of individual genets within populations,\\u000a and

Björn Widén; Nils Cronberg; Marie Widén

1994-01-01

116

Predictive and prognostic molecular markers for cancer medicine  

PubMed Central

Over the last 10 years there has been an explosion of information about the molecular biology of cancer. A challenge in oncology is to translate this information into advances in patient care. While there are well-formed routes for translating new molecular information into drug therapy, the routes for translating new information into sensitive and specific diagnostic, prognostic and predictive tests are still being developed. Similarly, the science of using tumor molecular profiles to select clinical trial participants or to optimize therapy for individual patients is still in its infancy. This review will summarize the current technologies for predicting treatment response and prognosis in cancer medicine, and outline what the future may hold. It will also highlight the potential importance of methods that can integrate molecular, histopathological and clinical information into a synergistic understanding of tumor progression. While these possibilities are without doubt exciting, significant challenges remain if we are to implement them with a strong evidence base in a widely available and cost-effective manner.

Mehta, Sunali; Shelling, Andrew; Muthukaruppan, Anita; Lasham, Annette; Blenkiron, Cherie; Laking, George; Print, Cristin

2010-01-01

117

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

118

Development of novel diagnostic and prognostic molecular markers for sporadic colon cancer.  

PubMed

Gene expression studies are informative about changes in colon cancer, increase understanding of the biology of tumorigenesis and aid in developing diagnostic and prognostic markers. In this review, expression techniques used to examine the multistage process of colon cancer are discussed. Many genes have been found to differ in expression between normal and tumorigenic states, as early as the seemingly normal colonic crypts. The clinical usefulness of markers varies with stage, ethnicity and anatomic location of colon cancer. Thus, combinations of markers can be used to develop an approach to molecularly screen and follow the progression of this prevalent cancer. PMID:15934812

Ahmed, Farid E

2005-05-01

119

Molecular characterization of ten cultivars of Canna lilies (Canna Linn.) using PCR based molecular markers (RAPDs and ISSRs)  

Microsoft Academic Search

Molecular markers like RAPD and ISSR were used to study the genomic affinity among 10 cultivars of Canna lilies (Canna linn.). 15 numbers of decamer oligonucleotide primers produced a total of 103 bands out of which 20 were monomorphic and among the polymorphic bands there were 16 unique bands. Three ISSR primers produced 27 bands among which there were 21

Biswabijayinee Patra; Laxmikanta Acharya; Arup Kumar Mukherjee; Manoj Kumar Panda; Pratap Chandra Panda

120

Computational Immunology Meets Bioinformatics: The Use of Prediction Tools for Molecular Binding in the Simulation of the Immune System  

PubMed Central

We present a new approach to the study of the immune system that combines techniques of systems biology with information provided by data-driven prediction methods. To this end, we have extended an agent-based simulator of the immune response, C-ImmSim, such that it represents pathogens, as well as lymphocytes receptors, by means of their amino acid sequences and makes use of bioinformatics methods for T and B cell epitope prediction. This is a key step for the simulation of the immune response, because it determines immunogenicity. The binding of the epitope, which is the immunogenic part of an invading pathogen, together with activation and cooperation from T helper cells, is required to trigger an immune response in the affected host. To determine a pathogen's epitopes, we use existing prediction methods. In addition, we propose a novel method, which uses Miyazawa and Jernigan protein–protein potential measurements, for assessing molecular binding in the context of immune complexes. We benchmark the resulting model by simulating a classical immunization experiment that reproduces the development of immune memory. We also investigate the role of major histocompatibility complex (MHC) haplotype heterozygosity and homozygosity with respect to the influenza virus and show that there is an advantage to heterozygosity. Finally, we investigate the emergence of one or more dominating clones of lymphocytes in the situation of chronic exposure to the same immunogenic molecule and show that high affinity clones proliferate more than any other. These results show that the simulator produces dynamics that are stable and consistent with basic immunological knowledge. We believe that the combination of genomic information and simulation of the dynamics of the immune system, in one single tool, can offer new perspectives for a better understanding of the immune system.

Rapin, Nicolas; Lund, Ole; Bernaschi, Massimo; Castiglione, Filippo

2010-01-01

121

Use of molecular markers to differentiate between commercial strains of the button mushroom Agaricus bisporus.  

PubMed

Agaricus bisporus is an edible basidiomycete cultivated industrially for food production. Different spawn and mushroom producers use genetically related A. bisporus strains frequently marketed as different products. In this paper we show that the use of suitable molecular markers reveals the high level of genetic homology of commercial strains of A. bisporus, and allows, at the same time, to distinguish between them. In the course of this work, a molecular marker potentially linked to the agronomic character 'mushroom weight' has been identified by bulked segregant analysis. PMID:11325552

Ramírez, L; Muez, V; Alfonso, M; García Barrenechea, A; Alfonso, L; Pisabarro, A G

2001-04-20

122

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

123

Molecular characterization and identification of markers for toxic and non-toxic varieties of Jatropha curcas L. using RAPD, AFLP and SSR markers.  

PubMed

Jatropha curcas L., a multipurpose shrub has acquired significant economic importance for its seed oil which can be converted to biodiesel, is emerging as an alternative to petro-diesel. The deoiled seed cake remains after oil extraction is toxic and cannot be used as a feed despite having best nutritional contents. No quantitative and qualitative differences were observed between toxic and non-toxic varieties of J. curcas except for phorbol esters content. Development of molecular marker will enable to differentiate non-toxic from toxic variety in a mixed population and also help in improvement of the species through marker assisted breeding programs. The present investigation was undertaken to characterize the toxic and non-toxic varieties at molecular level and to develop PCR based molecular markers for distinguishing non-toxic from toxic or vice versa. The polymorphic markers were successfully identified specific to non-toxic and toxic variety using RAPD and AFLP techniques. Totally 371 RAPD, 1,442 AFLP markers were analyzed and 56 (15.09%) RAPD, 238 (16.49%) AFLP markers were found specific to either of the varieties. Genetic similarity between non-toxic and toxic verity was found to be 0.92 by RAPD and 0.90 by AFLP fingerprinting. In the present study out of 12 microsatellite markers analyzed, seven markers were found polymorphic. Among these seven, jcms21 showed homozygous allele in the toxic variety. The study demonstrated that both RAPD and AFLP techniques were equally competitive in identifying polymorphic markers and differentiating both the varieties of J. curcas. Polymorphism of SSR markers prevailed between the varieties of J. curcas. These RAPD and AFLP identified markers will help in selective cultivation of specific variety and along with SSRs these markers can be exploited for further improvement of the species through breeding and Marker Assisted Selection (MAS). PMID:18642099

Sudheer Pamidimarri, D V N; Singh, Sweta; Mastan, Shaik G; Patel, Jalpa; Reddy, Muppala P

2008-07-19

124

Application of molecular markers in predicting production quality of cultivated Cistanche deserticola.  

PubMed

We developed a set of molecular markers in Cistanche deserticola Y. C. MA to evaluate the production quality of cultivated C. deserticola individuals. This application utilizes the inter-simple-sequence repeat (ISSR) polymerase chain reaction (PCR) and random amplified polymorphic DNA (RAPD) PCR as molecular markers to determine the echinacoside content in cultivated C. deserticola individuals. The unweighted pair-group method using arithmetic average clustering (UPGMA) confirmed that the combined ISSR and RAPD data could categorize all C. deserticola individuals into three groups according to their respective echinacoside content. The stepwise multiple regression analysis (SMRA) revealed six potential markers associated with echinacoside accumulation in C. deserticola and produced 18 echinacoside-marker prediction models, four of which were successfully used to predict the quality of C. deserticola from Neimenggu. Both clustering and SMRA showed a correlation between the echinacoside content and molecular markers in cultivated C. deserticola. The relative average deviation of prediction (RADP) of the prediction models could be improved by simplifying and adjusting the model. It was found that the RADP value could reach 2.6% after adjustment and the simplified prediction models could successfully predict the quality of cultivated C. deserticola individuals. PMID:20118564

Wu, Yan; Shi, Hai Ming; Bao, Zhong; Wang, Meng Yue; Tu, Peng Fei; Li, Xiao Bo

2010-01-01

125

Highly isotopically depleted isoprenoids: Molecular markers for ancient methane venting  

SciTech Connect

The authors propose that organic compounds found in a Miocene limestone from Marmorito (Northern Italy) are source markers for organic matter present in ancient methane vent systems (cold seeps). The limestone contains high concentrations of the tail-to-tail linked, acyclic C{sub 20} isoprenoid 2,6,11,15-tetramethylhexadecane (crocetane), a C{sub 25} homolog 2,6,10,15,19-pentamethylicosane (PME), and a distinctive glycerol ether lipid containing 3,7,11,15-tetramethylhexadecyl (phytanyl-) moieties. The chemical structures of these biomarkers indicate a common origin from archaea. Their extremely {sup 13}C-depleted isotope compositions ({delta}{sup 13}C {approximately} {minus}108 to {minus}115.6% PDB) suggest that the respective archaea have directly or indirectly introduced isotopically depleted, methane-derived carbon into their biomass. The authors postulate that a second major cluster of biomarkers showing heavier isotope values ({delta}{sup 13}C {approximately} {minus}88%) is derived from sulfate-reducing bacteria (SRB). The observed biomarkers sustain the idea that methanogenic bacteria, in a syntrophic community with SRB, are responsible for the anaerobic oxidation of methane in marine sediments. Marmorito may thus represent a conceivable ancient scenario for methane consumption performed by a defined, two-membered bacterial consortium: (1) archaea that perform reversed methanogenesis by oxidizing methane and producing CO{sub 2} and H{sub 2}; and (2) SRB that consume the resulting H{sub 2}. Furthermore, the respective organic molecules are, unlike other compounds, tightly bound to the crystalline carbonate phase. The Marmorito carbonates can thus be regarded as cold seep microbialites rather than mere antigenic carbonates.

Thiel, V.; Peckmann, J.; Seifert, R.; Wehrung, P.; Reitner, J.; Michaelis, W.

1999-12-01

126

[Molecular markers of hemostasis activation in children with nephrotic syndrome].  

PubMed

Vein and arterial thrombosis is a rather rare but potentially life-threatening complication of nephrotic syndrome (n.s.). None of the specific markers of hypercoagulability state in n.s. have been identified. The aim of the study was to estimate plasma parameters of prothrombic state in children with n.s. Ten children aged from 3 to 10 yrs (mean 5.7 +/- 2.5) with recurrence of n.s. and 10 healthy controls matched for age and sex were studied. In all children with n.s. prothrombin fragments F 1+2, D-dimers (D-d), thrombin-antithrombin III complexes (TAT) and whole blood clotting time thrombin time, prothrombin time, plasma fibrinogen and platelet count were determined in the hypovolemic state (before therapy was started), in the normovolemic state (after plasma expander was used) and in the course of anticoagulation treatment (two week dicumarol therapy). In comparison with healthy controls all children with recurrence of n.s. in the hypovolemic state showed a significant (p < 0.05) increase of D-d (910 vs 500 ng/ml), TAT (14.26 vs 2.6 ng/ml), F 1+2 (5.68 vs 0.79 nmol/l), plasma fibrinogen (592 vs 272 mg/dl), platelet count (632 vs 275 x 10(9)/l) and shortening of WBCT (30.0 vs 35 s). Plasma volume expansion produced by dekstran was followed by a moderate decrease of all parameters. Two-week anticoagulant treatment had no impact on estimated haemostasis parameters. PMID:8649942

Ksiazek, J; Cichocka, E; Lukasiewicz, H; Tekli?ska, E; Wyszy?ska, T

1995-12-01

127

Characterizing genic and nongenic molecular markers: comparison of microsatellites and SNPs.  

PubMed

The implications of transitioning to single nucleotide polymorphism (SNPs) from microsatellite markers (MSs) have been investigated in a number of population genetics studies, but the effect of genomic location on the amount of information each type of marker reveals has not been explored in detail. We developed novel SNP markers flanking 1 kb regions of 13 genic (within gene or <1 kb away from gene) and 13 nongenic (>10 kb from annotated gene) MSs in the threespine stickleback genome to obtain comparable data for both types of markers. We analysed patterns of genetic diversity and divergence on various geographic scales after converting the SNP loci within each genomic region into haplotypes. Marker type (SNP haplotype or MS) and location (genic or nongenic) significantly affected most estimates of population diversity and divergence. Between-lineage divergence was significantly higher in SNP haplotypes (genic and nongenic), however, within-lineage divergence was similar between marker types. Most divergence and diversity measures were uncorrelated between markers, except for population differentiation which was correlated between MSs and SNP haplotypes (both genic and nongenic). Broad-scale population structure and assignment were similarly resolved by both marker types, however, only the MSs were able to delimit fine-scale population structuring, particularly when genic and nongenic markers were combined. These results demonstrate that estimates of genetic variability and differentiation among populations can be strongly influenced by marker type, their genomic location in relation to genes and by the interaction of these two factors. This highlights the importance of having an awareness of the inherent strengths and limitations associated with different molecular tools to select the most appropriate methods for accurately addressing various ecological and evolutionary questions. PMID:23356957

DeFaveri, Jacquelin; Viitaniemi, Heidi; Leder, Erica; Merilä, Juha

2013-01-29

128

Identifying molecular markers associated with classification of genotypes by External Logistic Biplots  

Microsoft Academic Search

For characterization of genetic diversity in genotypes several mo- lecular techniques, usually resulting in a binary data matrix, have been used. Despite the fact that in Cluster Analysis and Principal Coordinates Analysis the interpretation of the variables responsible for grouping is not straightforward, these methods are commonly used to classify genotypes using DNA molecular markers. In this paper, we present

J. R. Demey; José L. Vicente-villardón; M. P. Galindo-villardón; A. Y. Zambrano

2008-01-01

129

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

130

Molecular genetic diversity of Punica granatum L. (pomegranate) as revealed by microsatellite DNA markers  

Technology Transfer Automated Retrieval System (TEKTRAN)

Pomegranate (Punica granatum L.) is one of the oldest known edible fruits and more and more it arouse interest of scientific community given its numerous biological activities. However, information about its genetic resources and characterization using reliable molecular markers are still scarce. In...

131

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…

Helms, T. C.; Doetkott, C.

2007-01-01

132

Use of molecular markers to differentiate between commercial strains of the button mushroom Agaricus bisporus  

Microsoft Academic Search

Agaricus bisporus is an edible basidiomycete cultivated industrially for food production. Different spawn and mushroom producers use genetically related A. bisporus strains frequently marketed as different products. In this paper we show that the use of suitable molecular markers reveals the high level of genetic homology of commercial strains of A. bisporus, and allows, at the same time, to distinguish

Luc??a Ram??rez; V??ctor Muez; Mikel Alfonso; Alberto Garc??a Barrenechea; Leopoldo Alfonso; Antonio G. Pisabarro

2001-01-01

133

Correlation between molecular markers and adaptively significant genetic variation in Bromus tectorum (Poaceae), an inbreedingannual grass  

Microsoft Academic Search

Single sequence repeat (SSR) and amplified fragment length polymorphic (AFLP) molecular marker genotypes in cheatgrass ( Bromus tectorum) were compared to published data on phenotypic variation in seed dormancy, vernalization requirement, and resistance to the pathogen Ustilago bullata. Several features of cheatgrass facilitated this study: it is a recent invader in the western United States, has considerable phenotypic polymorphism, and

A. P. Ramakrishnan; SUSAN E. MEYER; JENNIFER WATERS; MIKEL R. STEVENS; CRAIG E. COLEMAN; DANIEL J. FAIRBANKS

2004-01-01

134

Study of genetic diversity in Chamomile ( Matricaria chamomilla) based on morphological traits and molecular markers  

Microsoft Academic Search

Chamomile is one of the most important medicinal plants in the world trade that has many applications in drug and sanitary industrials. In order to evaluate the genetic diversity of different chamomile landraces based on morphological and molecular markers, 20 landraces were collected from different area of Iran. In addition to that, five populations imported from European were examined. The

M. Solouki; H. Mehdikhani; H. Zeinali; A. A. Emamjomeh

2008-01-01

135

Correlation between molecular markers and adaptively significant genetic variation in Bromus tectorum (Poaceae), an inbreedingannual grass.  

PubMed

Single sequence repeat (SSR) and amplified fragment length polymorphic (AFLP) molecular marker genotypes in cheatgrass (Bromus tectorum) were compared to published data on phenotypic variation in seed dormancy, vernalization requirement, and resistance to the pathogen Ustilago bullata. Several features of cheatgrass facilitated this study: it is a recent invader in the western United States, has considerable phenotypic polymorphism, and is an obligate self-pollinator. Forty self-pollinating lines from four populations common to the three phenotypic data sets were analyzed for molecular genetic variation using seven SSR loci and 31 AFLP loci. We examined correlations between distance matrices using the Mantel test for each pair of studies. The two molecular data sets were significantly correlated (r = 0.636). The AFLP markers often distinguished among several lines with identical SSR genotypes. The AFLP data were also significantly correlated with the phenotypic data (r values from 0.4640 to 0.5658), but the SSR data were much more highly correlated (r values from 0.677 to 0.844). The difference between molecular marker systems was especially notable when an outlier population from Potosi Pass, Nevada, was excluded from the analysis. These results suggest that SSR markers may be good surrogates for phenotypic traits in population genetic studies of strongly inbreeding species such as cheatgrass. PMID:21653434

Ramakrishnan, Alisa P; Meyer, Susan E; Waters, Jennifer; Stevens, Mikel R; Coleman, Craig E; Fairbanks, Daniel J

2004-06-01

136

Identification of Turkish and standard apple rootstocks by morphological and molecular markers  

Microsoft Academic Search

Two local (Vezir-1 and Vezir-2) and two standard (M9 and MM106) clonal apple rootstocks were compared using both mor- phological and molecular markers. International Union for the Protec- tion of New Varieties of Plants criteria were used for morphological evaluation, which did not clearly separate these rootstocks. We tested 47 random decamer primers for random amplified polymorphic DNA analysis; 15

A. Koc; M. Akbulut; E. Orhan; Z. Celik; S. Bilgener; S. Ercisli

2009-01-01

137

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

138

Genetic variability of Fusarium wilt pathogen isolates of chickpea (Cicer arietinum L.) assessed by molecular markers.  

PubMed

Genetic variability among 43 isolates of Fusarium oxysporum f.sp. ciceri, the chickpea wilt pathogen, collected from nine states of India including the four well-characterized races of the pathogen were assessed using the molecular markers, RAPDs and AFLP. Principal coordinate analysis of the similarity index data generated from the molecular marker studies mostly gave three different clusters: Of these two clusters represented race-1 and race-2, and the third cluster consisted of race-3 and race-4 pathogen isolates. In RAPDs a fourth cluster was seen which did not go with any of the four races of the pathogen. The molecular markers established the distinctness of race-1 and race-2 pathogen isolates and the close similarity of pathogen isolates of race-3 with that of race-4. AFLP was found to be more informative as it differentiated more number of the pathogen isolates with the known races with minimum of outliers. The high levels of DNA polymorphism observed with the molecular markers suggest the rapid evolution of new recombinants of the pathogen in the chickpea growing fields. PMID:12617504

Sivaramakrishnan, S; Kannan, Seetha; Singh, S D

2002-01-01

139

Efficacy, Safety, and Selection of Molecular Markers of Drug Resistance by Two ACTs in Mali  

Microsoft Academic Search

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

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

2008-01-01

140

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...

141

QTL mapping and molecular marker analysis for the resistance of rice to ozone.  

PubMed

The resistance of rice to ozone (O3) is a quantitative trait controlled by nuclear genes. The identification of quantitative trait loci (QTL) and analysis of molecular markers of O3 resistance is important for increasing the resistance of rice to O3 stress. QTL associated with the O3 resistance of rice were mapped on chromosomes 1, 7 and 11 using 164 recombinant inbred (RI) lines from a cross between 'Milyang 23' and 'Gihobyeo'. The quantitative trait loci were tightly linked to the markers RG109, C507 and RG1094 and were detected in each of three replications. The association between these markers and O3 resistance in 26 rice cultivars and doubled haploid (DH) populations was analysed. The markers permit the screening of rice germplasm for O3 resistance and the introduction of resistance into elite lines in breeding programs. PMID:15055542

Kim, Kyung-Min; Kwon, Yong-Sham; Lee, Jong-Jun; Eun, Moo-Young; Sohn, Jae-Keun

2004-02-29

142

MOLECULAR MARKERS FOR IDENTIFICATION OF THE HYPERPARASITOIDS DENDROCERUS CARPENTERI AND ALLOXYSTA XANTHOPIS IN LYSIPHLEBUS TESTACEIPES PARASITIZING CEREAL APHIDS  

Technology Transfer Automated Retrieval System (TEKTRAN)

Molecular markers have been developed to detect the presence of primary parasitoids in cereal aphids for use in estimating parasitism rates. However, the presence of secondary parasitoids (hyperparasitoids) may lead to underestimates of primary parasitism rates. Therefore, molecular markers to det...

143

Development of Public Immortal Mapping Populations, Molecular Markers, and Linkage Maps for Rapid Cycling Brassica rapa and B. oleracea  

Technology Transfer Automated Retrieval System (TEKTRAN)

Past research efforts on genetic mapping in Brassica oleracea and Brassica rapa have been disconnected, utilizing separate mapping populations and different sets of molecular markers. Here we present public immortal mapping populations, molecular markers and linkage maps for rapid cycling B. rapa a...

144

Development of new molecular markers for the Colletotrichum genus using RetroCl1 sequences.  

PubMed

A nonautonomous element of 624 bp, called RetroCl1 (Retroelement Colletotrichum lindemuthianum 1), was identified in the plant pathogenic fungus Colletotrichum lindemuthianum. RetroCl1 contains terminal direct repeats (223 bp) that are surrounded by CTAGT sequences. It has a short internal domain of 178 bp and shows characteristics of terminal-repeat retrotransposon in miniature (TRIM) family. We used RetroCl1 sequence to develop molecular markers for the Colletotrichum genus. IRAP (Inter-Retrotransposon Amplified Polymorphism) and REMAP (Retrotransposon-Microsatellite Amplified Polymorphism) markers were used to analyze the genetic diversity of C. lindemuthianum. Fifty-four isolates belonging to different races were used. A total of 45 loci were amplified. The Nei index showed significant differences among the populations divided according to race, indicating that they are structured according to pathotype. No clear correlation between IRAP and REMAP markers with pathogenic characterization was found. C. lindemuthianum has high genetic diversity, and the analysis of molecular variance showed that 51% of variability is found among the populations of different races. The markers were also tested in different Colletotrichum species. In every case, multiple bands were amplified, indicating that these markers can be successfully used in different species belonging to the Colletotrichum genus. PMID:22805830

Dos Santos, Leandro Vieira; de Queiroz, Marisa Vieira; Santana, Mateus Ferreira; Soares, Marcos Antônio; de Barros, Everaldo Gonçalves; de Araújo, Elza Fernandes; Langin, Thierry

2011-10-01

145

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

146

A note on the rationale for estimating genealogical coancestry from molecular markers  

PubMed Central

Background Genetic relatedness or similarity between individuals is a key concept in population, quantitative and conservation genetics. When the pedigree of a population is available and assuming a founder population from which the genealogical records start, genetic relatedness between individuals can be estimated by the coancestry coefficient. If pedigree data is lacking or incomplete, estimation of the genetic similarity between individuals relies on molecular markers, using either molecular coancestry or molecular covariance. Some relationships between genealogical and molecular coancestries and covariances have already been described in the literature. Methods We show how the expected values of the empirical measures of similarity based on molecular marker data are functions of the genealogical coancestry. From these formulas, it is easy to derive estimators of genealogical coancestry from molecular data. We include variation of allelic frequencies in the estimators. Results The estimators are illustrated with simulated examples and with a real dataset from dairy cattle. In general, estimators are accurate and only slightly biased. From the real data set, estimators based on covariances are more compatible with genealogical coancestries than those based on molecular coancestries. A frequently used estimator based on the average of estimated coancestries produced inflated coancestries and numerical instability. The consequences of unknown gene frequencies in the founder population are briefly discussed, along with alternatives to overcome this limitation. Conclusions Estimators of genealogical coancestry based on molecular data are easy to derive. Estimators based on molecular covariance are more accurate than those based on identity by state. A correction considering the random distribution of allelic frequencies improves accuracy of these estimators, especially for populations with very strong drift.

2011-01-01

147

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

2013-01-18

148

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

2013-08-12

149

Molecular and histological markers in urothelial carcinomas of the upper urinary tract.  

PubMed

Urothelial cell carcinomas (UCCs) are one of the most common types of malignancies. Recently, different mechanisms of carcinogenesis, as well as discrepancies in the natural history of urothelial cancers of the bladder and of the upper urinary tract (UUT), have been identified. As a result several teams have focused on specific markers in UUT-UCCs, a very rare type of cancer. This review gives a brief overview on the current markers of interest. Microsatellite instabilities (MSI) are independent molecular makers for prognosis. In addition, MSI can help detect a germline mutation and therefore allows for the detection of possible hereditary cancers. The loss of proteins of the mismatch repair system can also facilitate the detection of a germline mutation but should be followed by DNA sequencing. Epithelial cadherin has been shown to be an independent marker of prognosis, as well as hypoxia-inducible factor-1alpha (HIF-1alpha) and telomerase RNA component. Furthermore HIF-1alpha is significantly associated with the grade and pattern of growth and the telomerase RNA component could possibly also be used in diagnosis. The active form of the L-type amino acid transporter 1 (LAT1) was a significant prognostic marker in univariate analysis only. There are contrasting studies on the significances of p27 and Ki-67 as prognostic markers in UUT-UCCs. MET is a factor that correlates with vascular invasion of invasive cancer and bcl-2 oncoprotein correlates with stage. The ongoing identification of these markers might help to find specific treatments tailored to the molecular pattern of each tumour. Therefore a subgroup of patients with a higher risk of recurrence could be identified as well as patients that could benefit from minimal invasive surgery. PMID:18384628

Eltz, Stephanie; Comperat, Eva; Cussenot, Olivier; Rouprêt, Morgan

2008-04-02

150

Clinical, Immunological, and Molecular Analysis in a Large Cohort of Patients with X-Linked Agammaglobulinemia: An Italian Multicenter Study  

Microsoft Academic Search

A questionnaire-based retrospective clinical and immunological survey was conducted in 73 males with a definite diagnosis of X-linked agammaglobulinemia based on BTK sequence analysis. Forty-four were sporadic and 29 familial cases. At December 2000, the patients' ages ranged from 2 to 33 years; mean age at diagnosis and mean duration of follow-up were 3.5 and 10 years respectively. After the

Alessandro Plebani; Annarosa Soresina; Roberto Rondelli; Giorgio M. Amato; Chiara Azzari; Fabio Cardinale; Gianantonio Cazzola; Rita Consolini; Domenico De Mattia; Grazia Dell'Erba; Marzia Duse; Maurilia Fiorini; Silvana Martino; Baldassarre Martire; Massimo Masi; Virginia Monafo; Viviana Moschese; Luigi D. Notarangelo; Paola Orlandi; Pietro Panei; Andrea Pession; Maria C. Pietrogrande; Claudio Pignata; Isabella Quinti; Vanda Ragno; Paolo Rossi; Antonella Sciotto; Achille Stabile

2002-01-01

151

Molecular genetic diversity of Punica granatum L. (pomegranate) as revealed by microsatellite DNA markers (SSR).  

PubMed

Pomegranate (Punica granatum L.) is one of the oldest known edible fruits and more and more it arouse interest of scientific community given its numerous biological activities. However, information about its genetic resources and characterization using reliable molecular markers are still scarce. In the present study, we report the development of 4 new polymorphic SSR markers. They have been used in addition to 11 SSRs previously published to investigate molecular diversity of 33 P. granatum ecotypes. Based on the multi-locus profiles, twenty-two distinctive genotypes were identified. Globally, quite low genetic diversity has been revealed, as measured by allele richness (2.83 per locus) and heterozygosity (He=0.245; Ho=0.243), reflecting the narrow genetic background of the plant material. Four synonymous groups could be detected involving 15 accessions. Results of ordination and cluster analysis suggested that almost all the Tunisian cultivars share similar genetic background, and are likely derived from a small number of introductions in ancient times. Results issued from this study provide essential information to project a pomegranate core-collection without plant material duplication and for sustainable management of pomegranate landraces at national and international level. Furthermore, these SSR markers are powerful tool for marker assisted selection (MAS) program and for QTL studies. PMID:22123180

Hasnaoui, Nejib; Buonamici, Anna; Sebastiani, Federico; Mars, Messaoud; Zhang, Dapeng; Vendramin, Giovanni G

2011-11-20

152

Identification of candidate molecular markers of nasopharyngeal Carcinoma by tissue microarray and in situ hybridization  

Microsoft Academic Search

To scan differentially expressed genes and to identify candidate molecular markers in nasopharyngeal carcinoma (NPC), we analyzed\\u000a cDNA microarray data by GenMAPP to find specifically expressed genes in NPC and used tissue microarray and in situ hybridization\\u000a techniques to confirm our microarray results. Our cDNA microarray results showed that TSPAN-1 and DPP10 genes were down-expressed\\u000a in NPC, and COX7B and

Shilong XiongQian; Qian Wang; Lei Zheng; Feng Gao; Junling Li

153

Characterization of molecular markers in smoke from residential coal combustion in China  

Microsoft Academic Search

The organic constituents and distributions of molecular markers emitted from a residential coal-stove burning honeycomb coal briquettes were determined in this study. The major organic components emitted directly in smoke particles were polycyclic aromatic hydrocarbons (PAHs), with abundant hydroxy-polycyclic aromatic hydrocarbons (OH-PAHs), i.e., thermally altered derivative compounds from coal combustion, UCM (unresolved complex mixture of branched and cyclic compounds), n-alkanes

Xinhui Bi; Bernd R. T. Simoneit; Guoying Sheng; Jiamo Fu

2008-01-01

154

The GCP molecular marker toolkit , an instrument for use in breeding food security crops  

Microsoft Academic Search

Crop genetic resources carry variation useful for overcoming the challenges of modern agriculture. Molecular markers can facilitate\\u000a the selection of agronomically important traits. The pervasiveness of genomics research has led to an overwhelming number\\u000a of publications and databases, which are, nevertheless, scattered and hence often difficult for plant breeders to access,\\u000a particularly those in developing countries. This situation separates them

Veerle Van Damme; Humberto Gómez-Paniagua; M. Carmen de Vicente

155

?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

156

Functionally associated molecular genetic marker map construction in perennial ryegrass ( Lolium perenne L.)  

Microsoft Academic Search

A molecular marker-based map of perennial ryegrass (Lolium perenne L.) has been constructed through the use of polymorphisms associated with expressed sequence tags (ESTs). A pair-cross between genotypes from a North African ecotype and the cultivar Aurora was used to generate a two-way pseudo-testcross population. A selection of 157 cDNAs assigned to eight different functional categories associated with agronomically important

M. J. Faville; A. C. Vecchies; M. Schreiber; M. C. Drayton; L. J. Hughes; E. S. Jones; K. M. Guthridge; K. F. Smith; T. Sawbridge; G. C. Spangenberg; G. T. Bryan; J. W. Forster

2004-01-01

157

Mosaic small supernumerary marker chromosome 1 at amniocentesis: prenatal diagnosis, molecular genetic analysis and literature review.  

PubMed

We present prenatal diagnosis and molecular cytogenetic analysis of mosaic small supernumerary marker chromosome 1 [sSMC(1)]. We review the literature of sSMC(1) at amniocentesis and chromosome 1p21.1-p12 duplication syndrome. We discuss the genotype-phenotype correlation of the involved genes of ALX3, RBM15, NTNG1, SLC25A24, GPSM2, TBX15 and NOTCH2 in this case. PMID:23933412

Chen, Chih-Ping; Chen, Ming; Su, Yi-Ning; Huang, Jian-Pei; Chern, Schu-Rern; Wu, Peih-Shan; Su, Jun-Wei; Chang, Shun-Ping; Chen, Yu-Ting; Lee, Chen-Chi; Chen, Li-Feng; Pan, Chen-Wen; Wang, Wayseen

2013-08-07

158

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

159

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

160

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

PubMed Central

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

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

2012-01-01

161

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.

162

Development of molecular diagnostic markers for sharpshooters Homalodisca coagulata and Homalodisca liturata for use in predator gut content examinations  

Microsoft Academic Search

To aid in identifying key predators of Proconiini sharpshooter species present in California, we developed and tested molecular diagnostic markers for the glassy-winged sharpshooter, Homalodisca coagulata (Say), and smoke-tree sharpshooter, Homalodisca liturata (Ball) (Homoptera: Cicadellidae). Two different types of markers were compared, those targeting single-copy sequence characterized amplified regions (SCAR) and mitochondrial markers targeting the multicopy cytochrome oxidase subunit genes

Jesse H. de Leon; Valerie Fournier; James R. Hagler; Kent M. Daane

2006-01-01

163

Map order and linkage distances of molecular markers close to the supernodulation ( nts-1 ) locus of soybean  

Microsoft Academic Search

The molecular characteristics of markers in the chromosome region surrounding the supernodulation gene (nts-1) of soybean (Glycine max L. Merr.) were investigated in 187 F2 plants from a cross of G. max cv. Bragg (nts) and G. soja PI468.397 (wild-type nodulation). RFLP marker pUTG-132a, linked tightly (0.7±0.5 cM) to nts-1, was converted to a PCR marker. The polymorphism resides within

A. Kolchinsky; D. Landau-Ellis; P. M. Gresshoff

1997-01-01

164

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...

165

Molecular markers for cancer prognosis and treatment: have we struck gold?  

PubMed

The last decade has witnessed an emerging role for molecular or biochemical markers indicating a specific cellular mechanism or tissue function, often called 'biomarkers'. Biomarkers such as altered DNA, proteins and inflammatory cytokines are critical in cancer research and strategizing treatment in the clinic. In this review we look at the application of biological indicators to cancer research and highlight their roles in cancer detection and treatment. With technological advances in gene expression, genomic and proteomic analysis, biomarker discovery is expanding fast. We focus on some of the predominantly used markers in different types of malignancies, their advantages, and their limitations. Finally we conclude by looking at the future of biomarkers, their utility in the tumorigenic studies, and the progress towards personalized treatment strategies. PMID:22120674

Nowsheen, Somaira; Aziz, Khaled; Panayiotidis, Mihalis I; Georgakilas, Alexandros G

2011-11-25

166

Using molecular markers to characterize productivity in chinese hamster ovary cell lines.  

PubMed

Selection of high producing cell lines to produce maximum product concentration is a challenging and time consuming task for the biopharmaceutical industry. The identification of early markers to predict high productivity will significantly reduce the time required for new cell line development. This study identifies candidate determinants of high productivity by profiling the molecular and morphological characteristics of a panel of six Chinese Hamster Ovary (CHO) stable cell lines with varying recombinant monoclonal antibody productivity levels ranging between 2 and 50 pg/cell/day. We examined the correlation between molecular parameters and specific productivity (qp ) throughout the growth phase of batch cultures. Results were statistically analyzed using Pearson correlation coefficient. Our study revealed that, overall, heavy chain (HC) mRNA had the strongest association with qp followed by light chain (LC) mRNA, HC intracellular polypeptides, and intracellular antibodies. A significant correlation was also obtained between qp and the following molecular markers: growth rate, biomass, endoplasmic reticulum, and LC polypeptides. However, in these cases, the correlation was not observed at all-time points throughout the growth phase. The repeated sampling throughout culture duration had enabled more accurate predictions of productivity in comparison to performing a single-point measurement. Since the correlation varied from day to day during batch cultivation, single-point measurement was of limited use in making a reliable prediction. PMID:24146795

Edros, Raihana Z; McDonnell, Susan; Al-Rubeai, Mohamed

2013-10-17

167

The Important Molecular Markers on Chromosome 17 and Their Clinical Impact in Breast Cancer  

PubMed Central

Abnormalities of chromosome 17 are important molecular genetic events in human breast cancers. Several famous oncogenes (HER2, TOP2A and TAU), tumor suppressor genes (p53, BRCA1 and HIC-1) or DNA double-strand break repair gene (RDM1) are located on chromosome 17. We searched the literature on HER2, TOP2A, TAU, RDM1, p53, BRCA1 and HIC-1 on the Pubmed database. The association of genes with chromosome 17, biological functions and potential significance are reviewed. In breast cancer, the polysomy 17 (three or more) is the predominant numerical aberration. HER2 amplification is widely utilized as molecular markers for trastuzumab target treatment. Amplified TOP2A, TAU and RDM1 genes are related to a significant response to anthracycline-based chemotherapy, taxane or cisplatin, respectively. In contrast, p53, BRCA1 and HIC-1 are important tumor suppressor genes related to breast carcinogenesis. This review focused on several crucial molecular markers residing on chromosome 17. The authors consider the somatic aberrations of chromosome 17 and associated genes in breast cancer.

Zhang, Wei; Yu, Yingyan

2011-01-01

168

Using Molecular Markers to Characterize Productivity in Chinese Hamster Ovary Cell Lines  

PubMed Central

Selection of high producing cell lines to produce maximum product concentration is a challenging and time consuming task for the biopharmaceutical industry. The identification of early markers to predict high productivity will significantly reduce the time required for new cell line development. This study identifies candidate determinants of high productivity by profiling the molecular and morphological characteristics of a panel of six Chinese Hamster Ovary (CHO) stable cell lines with varying recombinant monoclonal antibody productivity levels ranging between 2 and 50 pg/cell/day. We examined the correlation between molecular parameters and specific productivity (qp) throughout the growth phase of batch cultures. Results were statistically analyzed using Pearson correlation coefficient. Our study revealed that, overall, heavy chain (HC) mRNA had the strongest association with qp followed by light chain (LC) mRNA, HC intracellular polypeptides, and intracellular antibodies. A significant correlation was also obtained between qp and the following molecular markers: growth rate, biomass, endoplasmic reticulum, and LC polypeptides. However, in these cases, the correlation was not observed at all-time points throughout the growth phase. The repeated sampling throughout culture duration had enabled more accurate predictions of productivity in comparison to performing a single-point measurement. Since the correlation varied from day to day during batch cultivation, single-point measurement was of limited use in making a reliable prediction.

Edros, Raihana Z.; McDonnell, Susan; Al-Rubeai, Mohamed

2013-01-01

169

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

170

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

171

Evaluation of immunological, parasitological and molecular methods for the diagnosis of Schistosoma mansoni infection before and after chemotherapy treatment with praziquantel in experimentally infected Nectomys squamipes.  

PubMed

In low endemicity areas of schistosomiasis, the recommended diagnostic method of coprological examination results in an underestimation of infection cases. Alternative diagnostic methods have been developed, such as immunodiagnostic and molecular techniques. In this study we evaluated three methods used in the diagnosis of Schistosoma mansoni infection: parasitological (Kato-Katz), immunological (ELISA) and molecular (real time PCR), and also investigated the sensitivity of each technique in the cure determination after treatment with praziquantel using the water rat Nectomys squamipes, a natural reservoir for S. mansoni, as an experimental model. Two infection laboratory experiments were carried out. The first experiment aimed to observe the evolution of the immunological response in the first moments after infection and in the first months after treatment. The second experiment aimed to compare the efficacy of the three diagnostic techniques after infection and after treatment over a more extended time period. In the first experiment, 44% of the infected animals showed IgG reactivity after two weeks of infection, and 94% were positive based on serology 30 days after infection. The serological IgG titers increased just after infection but decreased gradually after treatment. In the second experiment, 89% of the animals showed positive IgG titers 22 days after infection. Only 68% of the animals showed positive results on the coproscopic diagnostic analysis and 79% did so by qPCR, 50 days after infection. Treated animals showed negative results on coproscopy one month after treatment but remained positive by serology even 12 months after treatment, although showing a decline in immunologic reaction after treatment. By qPCR analysis, all animals showed negative results three months after treatment, except for one animal. The parasitosis can be detected by coproscopy only six weeks after infection, and by serology 14 days after infection. The qPCR was a better diagnostic method for confirming the infection cure of S. mansoni. In early infection, this method was less efficient than serology but was slightly more efficient than the Kato-Katz method. We suggest that the methods should be used in low endemic areas as follows: serology should be used in the initial diagnosis in a population with potential positive cases; subsequently, coproscopy should be used in IgG positive cases to confirm the current infection; and qPCR should be used to evaluate the infection cure after treatment and is also a very valuable tool when there are cases showing positive IgG and negative coproscopy. PMID:21458922

Gentile, Rosana; Gonçalves, Margareth Maria Lessa; da Costa Neto, Sócrates Fraga; da Costa, Maristella Matos; Peralta, Regina Helena Saramago; Peralta, José Mauro

2011-03-12

172

[Identification of molecular markers linked to the fertility restoring gene for the CMS Capsicum annuum L].  

PubMed

Bulked segregant analysis method was used to identify random amplified polymorphic DNA (RAPD) markers linked to the fertility restoring gene for the cytoplasmic male sterility (CMS) capsicum annum L. Totally 336 random primers were screened on the DNA samples of restorer and sterile bulks. Primer S418 produced a special band in restorer line. It was about 3000 bp, including two fragments 1515 bp and 1162 bp. Fluorescence in situ hybridization(FISH) indicated the fragment of 1515 bp only existed in restorer line.It was designed to S418(1515). Analysis of the sequence indicated S418(1515) was unknown before. The homology of blastn was less than 40%, however the homology of tBlastx indicated this sequence was high homologous with the part sequences of rice which were distributed on 2,4,7,10 chromosomes. It suggested this sequence might have the similar function with them. This result offered a good foundation to research the molecular mechanism of fertility restoration for CMS capsicum. Based on the sequence, special primers were designed to transform the RAPD marker to PCR marker. The result indicated that these primers could be used to screen the restorer lines from a large quantitive of candidate lines. PMID:16044916

Chang, Cai Tao; Wang, Chun Guo; Chen, Cheng Bin; Wu, Feng; Sun, De Ling

2005-06-01

173

Cyclin D1, a Novel Molecular Marker of Minimal Residual Disease, in Metastatic Neuroblastoma  

PubMed Central

Accurate monitoring of minimal residual disease (MRD) is critical for the management of metastatic neuroblastoma (NB). We evaluated cyclin D1 (CCND1), a cell-cycle control gene, as a novel MRD marker of NB. Using quantitative reverse transcriptase-polymerase chain reaction, we studied CCND1 expression in 133 solid tumors of different histological types, including 39 NB tumors, and examined its potential clinical utility as an early response marker in the bone marrows before and after treatment of 118 stage 4 patients enrolled after induction chemotherapy in an immunotherapy protocol. Based on 40 normal marrow and peripheral blood samples, a CCND1 transcript value greater than the mean + 2 SD was defined as positive. Sensitivity of this assay was one NB cell in 106 normal mononuclear cells. CCND1 transcript levels were high in NB, breast cancer, and Ewing family tumors. Among the NB patients evaluated, early (2.5 months from protocol entry) marrow response was strongly associated with both progression-free (P = 0.0001) and overall survival (P = 0.0006). CCND1 response remained predictive of survival among a subset of 66 patients who had no histological evidence of marrow disease before immunotherapy. We conclude that CCND1 has potential clinical utility as a novel molecular marker of MRD in the bone marrow of patients with metastatic NB.

Cheung, Irene Y.; Feng, Yi; Vickers, Andrew; Gerald, William; Cheung, Nai-Kong V.

2007-01-01

174

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

PubMed

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

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

2009-04-06

175

Identification of candidate molecular markers of nasopharyngeal carcinoma by tissue microarray and in situ hybridization.  

PubMed

To scan differentially expressed genes and to identify candidate molecular markers in nasopharyngeal carcinoma (NPC), we analyzed cDNA microarray data by GenMAPP to find specifically expressed genes in NPC and used tissue microarray and in situ hybridization techniques to confirm our microarray results. Our cDNA microarray results showed that TSPAN-1 and DPP10 genes were down-expressed in NPC, and COX7B and RFC2 genes were over-expressed in NPC. Real-time quantitative reverse transcription-PCR and in situ hybridization (ISH) techniques confirmed that TSPAN-1 and DPP10 genes had only 40.72 and 40.70% positive expression in NPC, but had high positive expression in chronic inflammation of nasopharyngeal mucosa (P < 0.01). However, COX7B and RFC2 genes were high positive rate in NPC (84.24 and 64.53%, respectively) than in normal control tissues. The data suggested that TSPAN-1, DPP10, COX7B and RFC2 genes might be the putative molecular markers of NPC. PMID:21057896

Xiong, Shilong; Wang, Qian; Zheng, Lei; Gao, Feng; Li, Junling

2010-11-05

176

Molecular phylogenetics of New Caledonian Diospyros (Ebenaceae) using plastid and nuclear markers.  

PubMed

To clarify phylogenetic relationships among New Caledonian species of Diospyros, sequences of four plastid markers (atpB, rbcL, trnK-matK and trnS-trnG) and two low-copy nuclear markers (ncpGS and PHYA) were analysed. New Caledonian Diospyros species fall into three clades, two of which have only a few members (1 or 5 species); the third has 21 closely related species for which relationships among species have been mostly unresolved in a previous study. Although species of the third group (NC clade III) are morphologically distinct and largely occupy different habitats, they exhibit little molecular variability. Diospyros vieillardii is sister to the rest of the NC clade III, followed by D. umbrosa and D. flavocarpa, which are sister to the rest of this clade. Species from coastal habitats of western Grande Terre (D. cherrieri and D. veillonii) and some found on coralline substrates (D. calciphila and D. inexplorata) form two well-supported subgroups. The species of NC clade III have significantly larger genomes than found in diploid species of Diospyros from other parts of the world, but they all appear to be diploids. By applying a molecular clock, we infer that the ancestor of the NC clade III arrived in New Caledonia around 9million years ago. The oldest species are around 7million years old and the youngest ones probably much less than 1million years. PMID:23850609

Turner, Barbara; Munzinger, Jérôme; Duangjai, Sutee; Temsch, Eva M; Stockenhuber, Reinhold; Barfuss, Michael H J; Chase, Mark W; Samuel, Rosabelle

2013-07-12

177

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

178

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

PubMed

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

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

2011-06-25

179

Noninvasive Detection and Imaging of Molecular Markers in Live Cardiomyocytes Derived from Human Embryonic Stem Cells  

PubMed Central

Raman microspectroscopy (RMS) was used to detect and image molecular markers specific to cardiomyocytes (CMs) derived from human embryonic stem cells (hESCs). This technique is noninvasive and thus can be used to discriminate individual live CMs within highly heterogeneous cell populations. Principal component analysis (PCA) of the Raman spectra was used to build a classification model for identification of individual CMs. Retrospective immunostaining imaging was used as the gold standard for phenotypic identification of each cell. We were able to discriminate CMs from other phenotypes with >97% specificity and >96% sensitivity, as calculated with the use of cross-validation algorithms (target 100% specificity). A comparison between Raman spectral images corresponding to selected Raman bands identified by the PCA model and immunostaining of the same cells allowed assignment of the Raman spectral markers. We conclude that glycogen is responsible for the discrimination of CMs, whereas myofibril proteins have a lesser contribution. This study demonstrates the potential of RMS for allowing the noninvasive phenotypic identification of hESC progeny. With further development, such label-free optical techniques may enable the separation of high-purity cell populations with mature phenotypes, and provide repeated measurements to monitor time-dependent molecular changes in live hESCs during differentiation in vitro.

Pascut, Flavius C.; Goh, Huey T.; Welch, Nathan; Buttery, Lee D.; Denning, Chris; Notingher, Ioan

2011-01-01

180

Molecular Markers in Patients with Chronic Wounds to Guide Surgical Debridement  

PubMed Central

Chronic wounds, such as venous ulcers, are characterized by physiological impairments manifested by delays in healing, resulting in severe morbidity. Surgical debridement is routinely performed on chronic wounds because it stimulates healing. However, procedures are repeated many times on the same patient because, in contrast to tumor excision, there are no objective biological/molecular markers to guide the extent of debridement. To develop bioassays that can potentially guide surgical debridement, we assessed the pathogenesis of the patients’ wound tissue before and after wound debridement. We obtained biopsies from three patients at two locations, the nonhealing edge (prior to debridement) and the adjacent, nonulcerated skin of the venous ulcers (post debridement), and evaluated their histology, biological response to wounding (migration) and gene expression profile. We found that biopsies from the nonhealing edges exhibit distinct pathogenic morphology (hyperproliferative/hyperkeratotic epidermis; dermal fibrosis; increased procollagen synthesis). Fibroblasts deriving from this location exhibit impaired migration in comparison to the cells from adjacent nonulcerated biopsies, which exhibit normalization of morphology and normal migration capacity. The nonhealing edges have a specific, identifiable, and reproducible gene expression profile. The adjacent nonulcerated biopsies have their own distinctive reproducible gene expression profile, signifying that particular wound areas can be identified by gene expression profiling. We conclude that chronic ulcers contain distinct subpopulations of cells with different capacity to heal and that gene expression profiling can be utilized to identify them. In the future, molecular markers will be developed to identify the nonimpaired tissue, thereby making surgical debridement more accurate and more efficacious.

Brem, Harold; Stojadinovic, Olivera; Diegelmann, Robert F; Entero, Hyacinth; Lee, Brian; Pastar, Irena; Golinko, Michael; Rosenberg, Harvey; Tomic-Canic, Marjana

2007-01-01

181

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

182

The interrelationship of biological marker maturity parameters and molecular yields during contact metamorphism  

SciTech Connect

Jurassic siltstone samples were collected, on a centimeter scale, as a function of increasing distance from a dolerite dyke (Isle of Skye, northwest Scotland). The constant origin and type of the organic matter in this single lithological horizon is indicated by organic petrological observations as well as organic geochemical analyses. Therefore, changes in biological marker distributions, with distance from the dyke contact, can be unequivocally correlated with the thermal influence of the intrusion. The vitrinite reflectance (R[sub 0] Average) values of these samples increase gradually from 0.35% to 3.60% as the dyke contact is approached. Four classical biological marker maturity parameters (20S/(20S + 20R), TA/(TA + MA), C[sub 20]/(C[sub 20] + C[sub 28]), and 22S/(22S + 22R)), have been measured from GCMS analyses of the sample extracts. Changes in these molecular parameters were compared with changes in the concentrations of the individual biological marker compounds, expressed relative to mass of rock extracted. This comparison revealed that these molecular parameters are not governed by the conventional product-reactant relationships (chiral isomerization, aromatization or side-chain cracking reactions) operating solely in the free saturated or aromatic hydrocarbon structures. Release/formation from macromolecular and/or functionalized moieties (hydrocarbon or non-hydrocarbon) followed by compound loss provide an alternative paradigm in all four cases in this particularly thermal regime. Direct chiral isomerization in the free sterane or homohopane cannot, however, be completely ruled out as a contributor to an admixture of processes. Similarly, aromatization in the free hydrocarbon fraction may account for a proportion of the triaromatic steroids. 31 refs., 7 figs.

Bishop, A.N.; Abbott, G.D. (The University, Newcastle upon Tyne (United Kingdom))

1993-08-01

183

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

184

Comparison of anonymous and targeted molecular markers for the estimation of genetic diversity in ex situ conserved Lactuca.  

PubMed

The anonymous marker systems microsatellites (simple sequence repeats), amplified fragment length polymorphisms and sequence-specific amplified polymorphisms were compared with the targeted marker systems sequence-related amplified polymorphisms, target region amplification polymorphisms and nucleotide binding site profiling for their ability to describe the genetic diversity in a selected set of 80 Lactuca accessions. The accessions were also described morphologically, and all characterisation methods were evaluated against the genetic diversity assessed by a panel of three crop experts. The morphological data showed a low level of association with the molecular data, and did not display a consistently better relationship with the experts' assessments in comparison with the molecular data. In general, the diversity described by the targeted molecular markers did not differ markedly from that of the anonymous markers, resulting in only slight differences in performance when related to the expert-based assessments. It was argued that markers targeted to specific gene sequences may still behave as anonymous markers and that the type of marker system used is irrelevant when at low taxonomic levels a clear genetic structure is absent due to intensive breeding activities. PMID:19697006

van Treuren, R; van Hintum, Th J L

2009-08-21

185

Integrating the cell stress response: a new view of molecular chaperones as immunological and physiological homeostatic regulators.  

PubMed

The response of cells to stress was first documented in the 1960s and 1970s and the molecular nature of the families of proteins that subserve this vital response, the molecular chaperones, were identified and subjected to critical study in the period from the late 1980s. This resulted in the rapidly advancing new field of protein folding and its role in cellular function. Emerging at the same time, but initially largely ignored, were reports that molecular chaperones could be released by cells and exist on the outer plasma membrane or in the body fluids. These secreted molecular chaperones were found to have intercellular signalling functions. There is now a growing body of evidence to support the hypothesis that molecular chaperones have properties ascribed to the Roman god Janus, the god of gates, doors, beginnings and endings, whose two faces point in different directions. Molecular chaperones appear to have one set of key functions within the cell and, potentially, a separate set of functions when they exist on the cell surface or in the various fluid phases of the body. Thus, it is a likely hypothesis that secreted molecular chaperones act as an additional level of homeostatic control possibly linking cellular stress to physiological systems such as the immune system. This review concentrates on three key molecular chaperones: Hsp10, Hsp60 and the Hsp70 family for which most information is available. An important consideration is the role that these proteins may play in human disease and in the treatment of human disease. PMID:19830685

Henderson, Brian

2010-01-01

186

Human herpesvirus-7 in Brazilian liver transplant recipients: a follow-up comparison between molecular and immunological assays.  

PubMed

Human herpesvirus-6 and -7 (HHV-6, HHV-7) remain latent after primary infection and can reactivate after transplantation. HHV-6 active infection has been related to some clinical manifestation, but the role of HHV-7 remains unclear. The clinical significance of HHV-7 DNAemia is not completely known and the immune response against HHV-7 has been poorly studied in transplantation. In this study, we investigated HHV-7 DNAemia in liver transplant recipients and evaluated the immunoglobulin (Ig) G and IgM response against HHV-7. A total of 22 adult liver transplant recipients were followed up for 90 days. HHV-7 DNAemia was detected by nested polymerase chain reaction (PCR) in DNA extracted from sera. IgG and IgM detection was performed by immunofluorescent assay using HHV-7-infected cord blood mononuclear cells. A significant virus antibody response was defined as either a positive IgM or a > or =4-fold rise in the virus IgG antibody. All patients had pre-transplant HHV-7-positive serostatus. Nine of 22 (40.9%) patients presented HHV-7 DNAemia during follow-up. All these patients had anti-HHV-7-positive IgM and/or significant increase in IgG titers with concurrent or subsequent DNAemia. In patients without DNAemia and low persistent IgG antibody titers, IgM was not detected. Correlation between nested PCR and IgM detection was statistically significant (P=0.01). Our study indicates that nested PCR in DNA extraction from serum can be useful to detect and monitor HHV-7 active infection in liver transplant recipients. IgM antibody detection also can be useful as a first immunological technique to detect active infection, especially if combined with PCR. PMID:19671120

Peigo, M F; Thomasini, R L; Puglia, A L P; Costa, S C B; Bonon, S H A; Boin, I F S; Leonardi, M; Mota, N G S

2009-08-05

187

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

2008-09-24

188

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

PubMed Central

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

2011-01-01

189

Molecular markers for the detection of the wheat leaf rust resistance gene Lr10 in diverse genetic backgrounds  

Microsoft Academic Search

We recently showed that the Lr10 wheat leaf rust resistance gene cosegregated with the candidate resistance gene Lrk10 which encodes a putative receptor-like kinase. The aim of this study was to develop Lrk10-derived molecular markers for the detection of the Lr10 gene in breeding material. Different subfragments of Lrk10 were tested as RFLP markers for the Lr10 resistance gene. The

Gabriele Schachermayr; Catherine Feuillet; Beat Keller

1997-01-01

190

Development and use of genic molecular markers (GMMs) for construction of a transcript map of chickpea ( Cicer arietinum L.)  

Microsoft Academic Search

A transcript map has been constructed by the development and integration of genic molecular markers (GMMs) including single\\u000a nucleotide polymorphism (SNP), genic microsatellite or simple sequence repeat (SSR) and intron spanning region (ISR)-based\\u000a markers, on an inter-specific mapping population of chickpea, the third food legume crop of the world and the first food legume\\u000a crop of India. For SNP discovery

Neha Gujaria; Ashish Kumar; Preeti Dauthal; Anuja Dubey; Pavana Hiremath; A. Bhanu Prakash; Andrew Farmer; Mangla Bhide; Trushar Shah; Pooran M. Gaur; Hari D. Upadhyaya; Sabhyata Bhatia; Douglas R. Cook; Greg D. May; Rajeev K. Varshney

2011-01-01

191

Prostate cancer molecular markers GSTP1 and hTERT in expressed prostatic secretions as predictors of biopsy results  

Microsoft Academic Search

ObjectivesTo develop noninvasive diagnostic tools for the early detection of prostate cancer (PCa). Current screening for PCa lacks sensitivity and specificity. Two molecular markers, telomerase activity and aberrant methylation of the glutathione S-transferase P1 (GSTP1) promoter, are found in more than 90% of PCa specimens. Additionally, these markers can be detected in bodily fluids such as urine and postprostatic massage

Laura E. Crocitto; Darlynn Korns; Leo Kretzner; Taras Shevchuk; Sarah L. Blair; Timothy G. Wilson; Soroush A. Ramin; Mark H. Kawachi; Steven S. Smith

2004-01-01

192

Use of RAPD and ITE molecular markers in studying the genetic structure of the Crimean population of T. boeoticum Boiss  

Microsoft Academic Search

The influence of ecological factors on variation of random PCR markers (RAPD and inter-MITE polymorphism (IMP) primers) was\\u000a evaluated in two wild Triticum boeoticum populations with contrasting climatic conditions in Crimea. The proportion of variation that undergoes natural selection\\u000a was compared for these two types of molecular markers. The Sapun Mountain and Baidar Valley populations differed significantly\\u000a in 24.7% of

D. Sh. Mallabaeva; A. N. Ignatov; I. A. Sheiko; V. P. Isikov; V. P. Gelyuta; N. G. Boiko; A. A. Seryapin; D. B. Dorokhov

2007-01-01

193

Simple sequence repeat (SSR) markers survey of the cassava (Manihot esculenta Crantz) genome: towards an SSR-based molecular genetic map of cassava  

Microsoft Academic Search

The development of PCR-based, easily automated molecular genetic markers, such as SSR markers, are required for realistic\\u000a cost-effective marker-assisted selection schemes. This paper describes the development and characterization of 172 new SSR\\u000a markers for the cassava genome. The placement of 36 of these markers on the existing RFLP framework map of cassava is also\\u000a reported. Two similar enrichment methods were

P. Stephenson; K. Edwards; S. Melzer; J. Nkumbira; U. Gullberg; K. Apel; M. Gale; J. Tohme; M. Fregene

2001-01-01

194

Molecular analysis of glycinin genes in soybean mutants for development of gene-specific markers.  

PubMed

Soybean mutant lines that differ in 11S glycinin and 7S ?-conglycinin seed storage protein subunit compositions were developed. These proteins have significant influence on tofu quality. The molecular mechanisms underlying the mutant lines are unknown. In this study, gene-specific markers for five of the glycinin genes (Gy1 to Gy5) were developed using three 11S null lines, two A(4) null Japanese cultivars, Enrei and Raiden, and a control cultivar, Harovinton. Whereas gene-specific primers produced the appropriate products in the control cultivar for the Gy1, Gy2, Gy3 and Gy5 genes, they did not amplify in mutants missing the A(1a)B(2), A(2)B(1a), A(1b) B(1b), and A(3)B(4) subunits. However, ecotype targeting induced local lesions in genomes (EcoTILLING) and sequencing analysis revealed that the absence of the A(4) peptide in the mutants is due to the same point mutation as that in Enrei and Raiden. Selection efficiency of the gene-specific primer pairs was tested using a number of breeding lines segregating for the different subunits. Primer pairs specific to each of the Gy1, Gy2, Gy3, and Gy5 genes can be used to detect the presence or absence of amplification in normal or mutant lines. The Gy4 null allele can be selected for by temperature-switch PCR (TS-PCR) for identification of the A(4) (G4) null genotypes. In comparison to protein analysis by SDS-PAGE, gene-specific markers are easier, faster and more accurate for analysis, they do not have to use seed, and can be analyzed at any plant growth stage for marker-assisted selection. PMID:21959908

Jegadeesan, Souframanien; Yu, Kangfu; Woodrow, Lorna; Wang, Yi; Shi, Chun; Poysa, Vaino

2011-09-29

195

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

196

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

SciTech Connect

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

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

1991-12-15

197

Molecular imprinted nanoelectrodes for ultra sensitive detection of ovarian cancer marker.  

PubMed

The relentless discovery of cancer biomarkers demands improved methods for their detection. In this work, we developed protein imprinted polymer on three-dimensional gold nanoelectrode ensemble (GNEE) to detect epithelial ovarian cancer antigen-125 (CA 125), a protein biomarker associated with ovarian cancer. CA 125 is the standard tumor marker used to follow women during or after treatment for epithelial ovarian cancer. The template protein CA 125 was initially incorporated into the thin-film coating and, upon extraction of protein from the accessible surfaces on the thin film, imprints for CA 125 were formed. The fabrication and analysis of the CA 125 imprinted GNEE was done by using cyclic voltammetry (CV), differential pulse voltammetry (DPV) and electrochemical impedance spectroscopy (EIS) techniques. The surfaces of the very thin, protein imprinted sites on GNEE are utilized for immunospecific capture of CA 125 molecules, and the mass of bound on the electrode surface can be detected as a reduction in the faradic current from the redox marker. Under optimal conditions, the developed sensor showed good increments at the studied concentration range of 0.5-400 U mL(-1). The lowest detection limit was found to be 0.5 U mL(-1). Spiked human blood serum and unknown real serum samples were analyzed. The presence of non-specific proteins in the serum did not significantly affect the sensitivity of our assay. Molecular imprinting using synthetic polymers and nanomaterials provides an alternative approach to the trace detection of biomarker proteins. PMID:22265879

Viswanathan, Subramanian; Rani, Chinnakkaruppanan; Ribeiro, Susana; Delerue-Matos, Cristina

2012-01-05

198

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

199

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

200

Photosynthetic and molecular markers of CO?-mediated photosynthetic downregulation in nodulated alfalfa.  

PubMed

Elevated CO? leads to a decrease in potential net photosynthesis in long-term experiments and thus to a reduction in potential growth. This process is known as photosynthetic downregulation. There is no agreement on the definition of which parameters are the most sensitive for detecting CO? acclimation. In order to investigate the most sensitive photosynthetic and molecular markers of CO? acclimation, the effects of elevated CO?, and associated elevated temperature were analyzed in alfalfa plants inoculated with different Sinorhizobium meliloti strains. Plants (Medicago sativa L. cv. Aragón) were grown in summer or autumn in temperature gradient greenhouses (TGG). At the end of the experiment, all plants showed acclimation in both seasons, especially under elevated summer temperatures. This was probably due to the lower nitrogen (N) availability caused by decreased N?-fixation under higher temperatures. Photosynthesis measured at growth CO? concentration, rubisco in vitro activity and maximum rate of carboxylation were the most sensitive parameters for detecting downregulation. Severe acclimation was also related with decreases in leaf nitrogen content associated with declines in rubisco content (large and small subunits) and activity that resulted in a drop in photosynthesis. Despite the sensitivity of rubisco content as a marker of acclimation, it was not coordinated with gene expression, possibly due to a lag between gene transcription and protein translation. PMID:23480453

Sanz-Sáez, Alvaro; Erice, Gorka; Aranjuelo, Iker; Aroca, Ricardo; Ruíz-Lozano, Juan Manuel; Aguirreolea, Jone; Irigoyen, Juan José; Sanchez-Diaz, Manuel

2013-06-24

201

Use of human bronchial epithelial cells (BEAS-2B) to study immunological markers resulting from exposure to PM(2.5) organic extract from Puerto Rico.  

PubMed

Fine particulate air pollutants, mainly their organic fraction, have been demonstrated to be associated with cardiovascular and respiratory health problems. Puerto Rico has been reported to have the highest prevalence of pulmonary diseases (e.g., asthma) in the United States. The aim of this study was to assess, for the first time, the immunological response of human bronchial epithelial cells (BEAS-2B) to organic extracts isolated from airborne particulate matter (PM(2.5)) in Puerto Rico. Organic extracts from PM(2.5) collected throughout an 8-month period (2000-2001) were pooled (composite) in order to perform chemical analysis and biological activity testing. BEAS-2B cells were exposed to PM(2.5) organic extract to assess cytotoxicity, levels of cytokines and relative gene expression of MHC-II, hPXR and CYP3A5. Our findings show that organic PM(2.5) consist of toxic as well as bioactive components that can regulate the secretion of cytokines in BEAS-2B, which could modulate inflammatory response in the lung. Trace element analyses confirmed the presence of metals in organic extracts highlighting the relative high abundance of Cu and Zn in polar organic extracts. Polar organic extracts exhibited dose-dependant toxicity and were found to significantly induce the release of interleukin 6 (IL-6), IL-1beta and IL-7 while significantly inhibiting the secretion of IL-8, G-CSF and MCP-1. Moreover, MHC-II transcriptional activity was up-regulated after 24 h of exposure, whereas PXR and CYP3A5 were down-regulated. This research provides a new insight into the effects of PM(2.5) organic fractions on specific effectors and their possible role in the development of respiratory inflammatory diseases in Puerto Rico. PMID:20026096

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

2009-12-21

202

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

PubMed Central

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

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

2010-01-01

203

Use of human bronchial epithelial cells (BEAS-2B) to study immunological markers resulting from exposure to PM{sub 2.5} organic extract from Puerto Rico  

SciTech Connect

Fine particulate air pollutants, mainly their organic fraction, have been demonstrated to be associated with cardiovascular and respiratory health problems. Puerto Rico has been reported to have the highest prevalence of pulmonary diseases (e.g., asthma) in the United States. The aim of this study was to assess, for the first time, the immunological response of human bronchial epithelial cells (BEAS-2B) to organic extracts isolated from airborne particulate matter (PM{sub 2.5}) in Puerto Rico. Organic extracts from PM{sub 2.5} collected throughout an 8-month period (2000-2001) were pooled (composite) in order to perform chemical analysis and biological activity testing. BEAS-2B cells were exposed to PM{sub 2.5} organic extract to assess cytotoxicity, levels of cytokines and relative gene expression of MHC-II, hPXR and CYP3A5. Our findings show that organic PM{sub 2.5} consist of toxic as well as bioactive components that can regulate the secretion of cytokines in BEAS-2B, which could modulate inflammatory response in the lung. Trace element analyses confirmed the presence of metals in organic extracts highlighting the relative high abundance of Cu and Zn in polar organic extracts. Polar organic extracts exhibited dose-dependant toxicity and were found to significantly induce the release of interleukin 6 (IL-6), IL-1beta and IL-7 while significantly inhibiting the secretion of IL-8, G-CSF and MCP-1. Moreover, MHC-II transcriptional activity was up-regulated after 24 h of exposure, whereas PXR and CYP3A5 were down-regulated. This research provides a new insight into the effects of PM{sub 2.5} organic fractions on specific effectors and their possible role in the development of respiratory inflammatory diseases in Puerto Rico.

Fuentes-Mattei, Enrique, E-mail: enrique.fuentes@upr.ed [Department of Biochemistry, School of Medicine, Medical Sciences Campus, University of Puerto Rico, San Juan (Puerto Rico); Center for Environmental and Toxicological Research, School of Medicine, Medical Sciences Campus, University of Puerto Rico, San Juan (Puerto Rico); Rivera, Evasomary [Department of Biology, Rio Piedras Campus, University of Puerto Rico, San Juan (Puerto Rico); Center for Environmental and Toxicological Research, School of Medicine, Medical Sciences Campus, University of Puerto Rico, San Juan (Puerto Rico); Gioda, Adriana [Department of Biochemistry, School of Medicine, Medical Sciences Campus, University of Puerto Rico, San Juan (Puerto Rico); Center for Environmental and Toxicological Research, School of Medicine, Medical Sciences Campus, University of Puerto Rico, San Juan (Puerto Rico); Department of Chemistry, Pontifical Catholic University of Rio de Janeiro (PUC-Rio), Marques de Sao Vicente street, 225, Gavea, 22453-900, Rio de Janeiro (Brazil); Sanchez-Rivera, Diana; Roman-Velazquez, Felix R. [Department of Chemistry, Mayaguez Campus, University of Puerto Rico, Mayaguez (Puerto Rico); Jimenez-Velez, Braulio D., E-mail: braulio.jimenez@upr.ed [Department of Biochemistry, School of Medicine, Medical Sciences Campus, University of Puerto Rico, San Juan (Puerto Rico); Center for Environmental and Toxicological Research, School of Medicine, Medical Sciences Campus, University of Puerto Rico, San Juan (Puerto Rico)

2010-03-15

204

Polycyclic aromatic hydrocarbons, black carbon, and molecular markers in soils of Switzerland.  

PubMed

Polycyclic aromatic hydrocarbons (PAH) were analysed in 23 soil samples (0-10 cm layer) from the Swiss soil monitoring network (NABO) together with total organic carbon (TOC) and black carbon (BC) concentration, as well as some PAH source diagnostic ratios and molecular markers. The concentrations of the sum of 16 EPA priority PAHs ranged from 50 to 619 microg/kg dw. Concentrations increased from arable, permanent and pasture grassland, forest, to urban soils and were 21-89% lower than median numbers reported in the literature for similar Swiss and European soils. NABO soils contained BC in concentrations from 0.4 to 1.8 mg/g dw, except for two sites with markedly higher levels. These numbers corresponded to 1-6% of TOC and were comparable to the limited published BC data in soil and sediments obtained with comparable analytical methods. The various PAH ratios and molecular markers pointed to a domination of pyrogenically formed PAHs in Swiss soils. In concert, the gathered data suggest the following major findings: (1) gas phase PAHs (naphthalene to fluorene) were long-range transported, cold-condensated at higher altitudes, and approaching equilibrium with soil organic matter (OM); (2) (partially) particle-bound PAHs (phenanthrene to benzo[ghi]perylene) were mostly deposited regionally in urban areas, and not equilibrated with soil OM; (3) Diesel combustion appeared to be a major emission source of PAH and BC in urban areas; and (4) wood combustion might have contributed significantly to PAH burdens in some soils of remote/alpine (forest) sites. PMID:15276719

Bucheli, Thomas D; Blum, Franziska; Desaules, André; Gustafsson, Orjan

2004-09-01

205

Investigation of Molecular Marker Lipids in Alpine Ice Cores Via Stir Bar Sorptive Extraction  

NASA Astrophysics Data System (ADS)

Recently developed analytical techniques were employed to identify and quantify organic molecular markers trapped in high-altitude ice. While various compounds represent potentially useful proxies for biomass burning, vegetation type, atmospheric circulation, and anthropogenic activity, prior attempts to measure organic compounds in ice cores have typically required large volumes of sample material that are incompatible with generation of high-resolution paleoclimate records. We employed stir bar sorptive extraction (SBSE) and thermal desorption (TD), coupled with gas chromatography/time-of-flight mass spectrometry (GC/TOF-MS), to examine the organic content of small quantities (? 30 ml) of ice. To test the utility of the approach, post-industrial ice core samples from the Huascarán and Sajama sites (Andes), the Dasuopu and Puruogangri sites (Tibetan Plateau), and Mt. Kilimanjaro (east Africa) were tested. n-Alkanes, n-alkanoic acids, n-alkyl amides and nitriles, polycyclic aromatic hydrocarbons (PAHs), and various diterpenoids were identified in this suite of cores. These marker compounds suggest inputs from biomass burning, fresh vascular plant material, and anthropogenic activities such as fossil fuel combustion. Differences in distributions of the alkyl amide and nitrile homologues between the different sites suggest a predominantly local or regional supply of organic matter. Pre-industrial samples from the Sajama and Puruogangri ice cores were also analyzed in order to assess the character of biomarker assemblages in the absence of anthropogenic contributions and investigate changes in inputs over time. PAHs and diterpenoids, which may result from biomass burning and were observed in the modern Sajama samples, occurred in two Holocene Sajama samples, but not in a last glacial sample. Enhanced inputs of terrestrial vegetation combustion biomarkers were consistent with periods of enhanced aridity in both cores. This study demonstrates the utility of SBSE, TD, and GC/TOF-MS for isolating organic compounds from small amounts of alpine ice and paves the way for development of high-resolution molecular stratigraphic records from tropical ice cores.

Makou, M. C.; Eglinton, T. I.; Thompson, L. G.; Hughen, K. A.

2005-12-01

206

Molecular markers in patients with chronic wounds to guide surgical debridement.  

PubMed

Chronic wounds, such as venous ulcers, are characterized by physiological impairments manifested by delays in healing, resulting in severe morbidity. Surgical debridement is routinely performed on chronic wounds because it stimulates healing. However, procedures are repeated many times on the same patient because, in contrast to tumor excision, there are no objective biological/molecular markers to guide the extent of debridement. To develop bioassays that can potentially guide surgical debridement, we assessed the pathogenesis of the patients' wound tissue before and after wound debridement. We obtained biopsies from three patients at two locations, the nonhealing edge (prior to debridement) and the adjacent, nonulcerated skin of the venous ulcers (post debridement), and evaluated their histology, biological response to wounding (migration) and gene expression profile. We found that biopsies from the nonhealing edges exhibit distinct pathogenic morphology (hyperproliferative/hyperkeratotic epidermis; dermal fibrosis; increased procollagen synthesis). Fibroblasts deriving from this location exhibit impaired migration in comparison to the cells from adjacent nonulcerated biopsies, which exhibit normalization of morphology and normal migration capacity. The nonhealing edges have a specific, identifiable, and reproducible gene expression profile. The adjacent nonulcerated biopsies have their own distinctive reproducible gene expression profile, signifying that particular wound areas can be identified by gene expression profiling. We conclude that chronic ulcers contain distinct subpopulations of cells with different capacity to heal and that gene expression profiling can be utilized to identify them. In the future, molecular markers will be developed to identify the nonimpaired tissue, thereby making surgical debridement more accurate and more efficacious. PMID:17515955

Brem, Harold; Stojadinovic, Olivera; Diegelmann, Robert F; Entero, Hyacinth; Lee, Brian; Pastar, Irena; Golinko, Michael; Rosenberg, Harvey; Tomic-Canic, Marjana

207

Development of SRAP, SNP and multiplexed SCAR molecular markers for the major seed coat color gene in Brassica rapa L.  

PubMed

Seed coat color inheritance in B. rapa was studied in F(1), F(2), F(3), and BC(1) progenies from a cross of a Canadian brown-seeded variety 'SPAN' and a Bangladeshi yellow sarson variety 'BARI-6'. A pollen effect was found when the yellow sarson line was used as the maternal parent. Seed coat color segregated into brown, yellow-brown and bright yellow classes. Segregation was under digenic control where the brown or yellow-brown color was dominant over bright yellow seed coat color. A sequence related amplified polymorphism (SRAP) marker linked closely to a major seed coat color gene (Br1/br1) was developed. This dominant SRAP molecular marker was successfully converted into single nucleotide polymorphism (SNP) markers and sequence characterized amplification region (SCAR) markers after the extended flanking sequence of the SRAP was obtained with chromosome walking. In total, 24 SNPs were identified with more than 2-kb sequence. A 12-bp deletion allowed the development of a SCAR marker linked closely to the Br1 gene. Using the five-fluorescence dye set supplied by ABI, four labeled M13 primers were integrated with different SCAR primers to increase the throughput of SCAR marker detection. Using multiplexed SCAR markers targeting insertions and deletions in a genome shows great potential for marker assisted selection in plant breeding. PMID:17846742

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

2007-09-05

208

alpha-Naphthyl acetate esterase activity--a cytochemical marker for T lymphocytees. Correlation with immunologic studies of normal tissues, lymphocytic leukemias, non-Hodgkin's lymphomas, Hodgkin's disease, and other lymphoproliferative disorders.  

PubMed Central

Cytochemical identification of T lymphocytes on the basis of alpha-naphthyl acetate esterase (NAE) activity was compared with immunologic markers for cell suspensions and/or cryostat sections of 113 specimens. Nonneoplastic tissues (peripheral blood, lymph nodes, spleens, tonsils, thymus, and pleural fluid) and specimens from various lymphoproliferative disorders, including acute and chronic lymphocytic leukemia, lymphosarcoma cell leukemia, hairy cell leukemia, non-Hodgkin's lymphomas of B-and T-cell types, and Hodgkin's disease, were evaluated. T (E-rosetting) cells demonstrated several patterns of NAE reactivity: 1) a strong globular reaction product, the most specific pattern for T-cell identification, 2) granular cytoplasmic staining, or 3) no reactivity. B lymphocytes revealed a granular pattern of NAE staining, were devoid of enzyme, or, in rare instances, exhibited strong NAE activity. Percentages of lymphoid cells with strong (globular) NAE activity closely paralleled T-cell (E-rosette) values in the majority of cases, with the best correlations observed for peripheral blood studies. However, discordant results were noted for some neoplastic and nonneoplastic tissues, including cases of T-cell lymphoma or leukemia. Markedly discrepant results were noted for thymic lymphocytes, most of which revealed E-rosette formation and weak or absent NAE activity. Lymph nodes involved by Hodgkin's disease demonstrated a heterogeneous pattern of staining in E-rosetting cells and in Reed-Sternberg variants. Cryostat section studies of reactive lymph nodes and nodular lymphomas demonstrated strong NAE staining in lymphoid cells of T-cell (interfollicular, internodular) areas, with little or no positivity in follicles or nodules (B-cell areas). NAE staining patterns further suggested that T cells comprise part of the follicular cuff and possibly represent a minor population of some neoplastic nodules. Although NAE determinations do not represent a consistently reliable alternative to immunologic methods for T-cell identification, this easily applicable cytochemical marker is complementary to other techniques in assessing neoplastic or nonneoplastic tissues, particularly cryostat sections. (Am J Pathol 97:17--42, 1979). Images Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 Figure 6 Figure 7 Figure 8 Figure 9 Figure 10 Figure 11 Figure 12 Figure 13

Pinkus, G. S.; Hargreaves, H. K.; McLeod, J. A.; Nadler, L. M.; Rosenthal, D. S.; Said, J. W.

1979-01-01

209

Basic concepts in glioma immunology.  

PubMed

Glioblasotmas are the most common primary central nervous system tumor and typically have a dismal prognosis. Immunotherapy has been a promising experimental treatment. Understanding brain tumor immunobiology is critical to designing glioblasotma immunotherapies. In this chapter, we review aspects of basic immunology and neuro-immunology. The antigenic underpinnings of brain tumor immunotherapy including glioma-associated and glioma-specific antigens are discussed. Finally, the molecular and cellular facets of glioma-mediated immunosuppression are outlined. The role of multiple cell types (glioma cells, glioma-infiltrating monocytes, regulatory T cells and myeloid derived suppressor cells) in mediating local and systemic immunosuppression in glioma patients is evaluated. PMID:22639158

Parney, Ian F

2012-01-01

210

Molecular cloning, expression and immunological properties of LiD1, a protein from the dermonecrotic family of Loxosceles intermedia spider venom.  

PubMed

The present report describes the identification and molecular characterization of LiD1, a protein expressed in the venom gland of the brown spider Loxosceles intermedia. LiD1 belongs to a family of proteins with dermonecrotic activity and members of this family have been found in spiders from the genus Loxosceles. The necrotic lesions caused by this group of proteins may lead to serious socio-economic problems such as surgical tissue reconstitution and even patient death. LiD1 was cloned using a cDNA library constructed from the venom gland of L. intermedia and antibodies against proteins with dermonecrotic activity isolated from the crude venom of this spider. The amino acid sequence deduced from the cDNA revealed a mature protein of approximately 31 kDa, with a pI of 7.37. The cDNA also revealed the existence of a signal peptide, a propeptide and also an untranslated 3' region with 218 nucleotides. LiD1 was expressed as a protein fused with beta-galactoside protein using the vector pBK-CMV, resulting in the recombinant protein recLiD1 with important immunological properties. recLiD1 was strongly recognised by anti-dermonecrotic antibodies and was also able to generate reactive antibodies against native dermonecrotic proteins isolated from the venom of L. intermedia. PMID:12457881

Kalapothakis, Evanguedes; Araujo, Simone Costa; de Castro, Cibele Soares; Mendes, Thais Melo; Gomez, Marcus Vinícius; Mangili, Oldemir C; Gubert, Ida C; Chávez-Olórtegui, Carlos

2002-12-01

211

Nicotine alters the expression of molecular markers of endocrine disruption in zebrafish.  

PubMed

Nicotine, a drug of abuse, has been reported to have many adverse effects on the developing nervous system. In rodents, chronic nicotine exposure inhibits estrogen-mediated neuroprotection against cerebral ischemia in females suggesting that nicotine could disrupt endocrine targets. Zebrafish have been used as a model system for examining mechanisms underlying nicotinic effects on neuronal development. Here, using zebrafish embryos, we demonstrate that nicotine alters the expression of the validated endocrine disruption (ED) biomarkers, vitellogenin (vtg 1 and vtg 2) and cytochrome p450 aromatase (cyp19a1a and cyp19a1b) at the transcriptional level. Increased expression of three of these molecular markers (vtg 1, vtg 2 and cyp19a1b) in response to 17?-estradiol (E2) was more pronounced in 48hpf (hours post-fertilization) embryos than in the 24hpf embryos. While 24hpf embryos were non-responsive in this regard to 25?M nicotine, a similar exposure of the 48hpf embryos for 24h significantly down-regulated the expression of all four ED biomarker genes indicating that nicotine's anti-estrogenic effects are detectable in the 48hpf zebrafish embryos. These results provide direct molecular evidence that nicotine is an endocrine disruptor in zebrafish. PMID:22922325

Kanungo, Jyotshna; Cuevas, Elvis; Guo, Xiaoqing; Lopez, Aida G; Ramirez-Lee, Manuel A; Trickler, William; Paule, Merle G; Ali, Syed F

2012-08-24

212

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

213

Leishmania AFLP: paving the way towards improved molecular assays and markers of diversity.  

PubMed

Diversity, phylogenetic, and population genetic studies of the genus Leishmania, causative agent of leishmaniasis, nowadays generally involve multilocus microsatellite and multilocus sequence typing. Even though these are well established and useful applications, amplified fragment length polymorphisms (AFLP) can provide complementary information. In addition, as the technique essentially probes the entire genome at random, without prior sequence knowledge, it is ideally suited as a screening tool for molecular markers linked with biological and clinical traits. We developed an AFLP protocol adapted to the Leishmania genome, tested its repeatability, and validated it on a panel of samples from the Leishmania donovani complex previously analyzed by multiple molecular tests. The technique proved highly reproducible, and showed that genetic relationships between L. donovani strains generally reflect geographic distance. Four main groups were identified: Leishmania infantum, African L. donovani, Indian L. donovani, and a mixed group consisting of L. donovani from India and Africa. Results were highly congruent with previous analyses on essentially the same sample set, indicating that the developed assay produces trustworthy data. This opens possibilities for application in studies of speciation and population dynamics. Moreover, it allows random screening of the entire Leishmania genome for linkage with biological and clinical parasite properties, such as fitness, drug resistance, and disease profile. PMID:21439405

Odiwuor, Samwel; Vuylsteke, Marnik; De Doncker, Simonne; Maes, Ilse; Mbuchi, Margaret; Dujardin, Jean-Claude; Van der Auwera, Gert

2011-03-23

214

Molecular markers associated with outcome and metastasis in human pancreatic cancer  

PubMed Central

Background Pancreatic ductal adenocarcinoma (PDAC) is a heterogeneous cancer in which differences in survival rates might be related to a variety in gene expression profiles. Although the molecular biology of PDAC begins to be revealed, genes or pathways that specifically drive tumour progression or metastasis are not well understood. Methods We performed microarray analyses on whole-tumour samples of 2 human PDAC subpopulations with similar clinicopathological features, but extremely distinct survival rates after potentially curative surgery, i.e. good outcome (OS and DFS?>?50?months, n?=?7) versus bad outcome (OS?molecular markers in pancreatic cancer as their expression seems to be related with prognosis.

2012-01-01

215

Identification and grouping of mycoplasmalike organisms associated with grapevine yellows and clover phyllody diseases based on immunological and molecular analyses.  

PubMed Central

Immunofluorescent staining, dot blot hybridization, PCR, random amplified polymorphic DNA (RAPD) markers, and restriction fragment length polymorphism wee used to study the genetic relatedness among mycoplasmalike organisms (MLOs) associated with several geographically diverse grapevine yellows diseases (CA1, CH1, SA1, and SA2 from Bologna, Italy; GYU from Udine, Italy; GYR from Rome, Italy; and GYG from Germany). The relationship between these and MLOs associated with clover phyllody diseases in Italy (CPhB and CPhC) and Canada (CPhCa) was also examined. Two monoclonal antibodies reacted with MLOs of GYU-, CPhB-, and CPhC-infected periwinkles. Dot blot hybridization with two cloned GYU DNA fragments, GYD-1 and GYD-2 inserts, showed that both hybridized with DNAs of GYU-, CPhB-, and CPhC-infected periwinkles but not with those of GYR and CPhCa. In addition, GYD-1 insert hybridized with DNAs of CA1, CH1, SA1, SA2, and GYG. Three primer pairs were developed in PCR experiments for this study. By using primer set GYD2P1F and GYD2P1R, a 600-bp DNA fragment was amplified only when DNAs from GYU-, CPhB-, and CPhC-infected plants were used as templates. With the primer pair GYD2P1F and GYD2P2R, a 550-bp DNA fragment was amplified from GYU, CPhB, CPhC, and GYG. The primer pair GYD1P1F and GYD1P2R, on the other hand, could amplify all isolates, although the patterns of PCR products were not identical for all isolates.(ABSTRACT TRUNCATED AT 250 WORDS) Images

Chen, K H; Credi, R; Loi, N; Maixner, M; Chen, T A

1994-01-01

216

Immunological identification of a high molecular weight protein as a condidate for the product of the Duchenne muscular dystrophy gene  

SciTech Connect

An oligopeptide was synthesized based on translation of the nucleotide sequence of the putative exon region of clone pERT87-25 from the gene for Duchenne muscular dystrophy. Immunization of rabbits with this oligopeptide induced the formation of antibodies directed against a protein present in human, rat, and rabbit skeletal muscle. This protein, which is missing in the skeletal muscle of two patients with Duchenne muscular dystrophy, has a molecular mass of {approx}320-420 kDa and is clearly different from the putative Duchenne muscular dystrophy-related protein nebulin. The data suggest that this 320-420-kDa protein is produced by the Duchenne muscular dystrophy gene.

Kao, L.; Krstenansky, J.; Mendell, J.; Rammohan, K.W.; Gruenstein, E. (Univ. of Cincinnati College of Medicine, OH (USA))

1988-06-01

217

Molecular Profiling of Conjunctival Epithelial Side-Population Stem Cells: Atypical Cell Surface Markers and Sources of a Slow-Cycling Phenotype  

PubMed Central

PURPOSE Side-population (SP) cells isolated from limbal and conjunctival epithelia derive from cells that are slow cycling in vivo, a known feature of tissue stem cells. The purpose of this study was to define the molecular signature of the conjunctival SP cells and identify markers and signaling pathways associated with the phenotype of these cells. METHODS Overnight cultures of freshly isolated human conjunctival epithelial cells stained with Hoechst 33342 were sorted by flow cytometry into SP and non-SP cohorts. Isolated RNA was processed for microarray analysis using a commercial oligonucleotide spotted array. Results were validated at the gene and protein levels by quantitative PCR and immunologic methods. Data mining methods were used to identify cellular processes relevant for stem cell function. RESULTS Comparative analyses of transcripts expression based on present and absent software calls across four replicate experiments identified 16,993 conjunctival epithelial transcripts including 10,266 unique known genes of ~24,000 represented in the array. Of those genes, 1254 and 363 were overexpressed (>2-fold) or underexpressed (<0.5-fold), respectively, in the SP. The overexpressed set included genes coding for proteins that have been associated with (1) embryonic development and/or stem cell self renewal (MSX, MEIS, ID, Hes1, and SIX homeodomain genes); (2) cell survival (e.g., CYP1A1 to degrade aromatic genotoxic compounds); (3) cycling rate (e.g., DUSPs and Pax6 to foster slow cycling); and (4) genes whose expression is not typical in epithelia (e.g., CD62E). CONCLUSIONS The molecular signature of conjunctival SP cells is consistent with a stem cell phenotype. Their gene expression patterns underpin slow cycling and plasticity, features associated with tissue stem cells. The results provide valuable insights for the preservation and/or expansion of epithelial stem cells.

Akinci, M. A. Murat; Turner, Helen; Taveras, Maria; Barash, Alex; Wang, Zheng; Reinach, Peter; Wolosin, J. Mario

2009-01-01

218

Prognostic molecular markers for planning adjuvant chemotherapy trials in Dukes' B colorectal cancer patients: how much evidence is enough?  

Microsoft Academic Search

The benefit of postoperative adjuvant chemotherapy in patients with Dukes' B colorectal cancer is still uncertain and its routine use is not recommended. Prognostic biomarkers may be useful for identifying high-risk patients with resected, node-negative disease, and this stratification may represent an innovative strategy for designing adjuvant chemotherapy trials. Featured prognostic molecular markers can be divided into the following categor-

F. Graziano; S. Cascinu

2003-01-01

219

DEVELOPMENT OF MOLECULAR DIAGNOSTIC MARKERS FOR HOMALODISCA SHARPSHOOTERS PRESENT IN CALIFORNIA TO AID IN THE IDENTIFICATION OF KEY PREDATORS  

Technology Transfer Automated Retrieval System (TEKTRAN)

The aim of the present study was to develop molecular diagnostic markers to identify key predators of Homalodisca sharpshooter species present in California, H coagulata (Glassy-winged Sharpshooter, GWSS) and H liturata (Smoke-tree Sharpshooter, STSS). RAPD-PCR DNA fmgerprinting of several sharpshoo...

220

Complete chloroplast genome of Oncidium Gower Ramsey and evaluation of molecular markers for identification and breeding in Oncidiinae  

Microsoft Academic Search

BACKGROUND: Oncidium spp. produce commercially important orchid cut flowers. However, they are amenable to intergeneric and inter-specific crossing making phylogenetic identification very difficult. Molecular markers derived from the chloroplast genome can provide useful tools for phylogenetic resolution. RESULTS: The complete chloroplast genome of the economically important Oncidium variety Onc. Gower Ramsey (Accession no. GQ324949) was determined using a polymerase chain

Fu-Hui Wu; Ming-Tsair Chan; De-Chih Liao; Chen-Tran Hsu; Yi-Wei Lee; Henry Daniell; Melvin R Duvall; Choun-Sea Lin

2010-01-01

221

Development of Public Immortal Mapping Populations, Molecular Markers and Linkage Maps for Rapid Cycling Brassica rapa and B. oleracea  

Technology Transfer Automated Retrieval System (TEKTRAN)

In this study we describe public immortal mapping populations of self-compatible lines, molecular markers, and linkage maps for Brassica rapa and B. oleracea. We propose that these resources are valuable reference tools for the Brassica community. The B. rapa population consists of 150 recombinant...

222

In search of the Kumamoto oyster Crassostrea sikamea (Amemiya, 1928) based on molecular markers: is the natural resource at stake?  

Microsoft Academic Search

A cornerstone in conserving wildlife is to resolve taxonomic uncertainties over organisms so that conservationists can define\\u000a the entity that should be conserved. This is the case for two closely related Crassostrea oysters inhabiting the Ariake Sea (Kyushu, Japan) in sympatry, the kumamoto oyster C. sikamea and Pacific oyster C. gigas, where molecular markers have shed light on their taxonomic

Masashi Sekino

2009-01-01

223

MOLECULAR MAPPING OF HYBRID NECROSIS GENES NE1 AND NE2 IN HEXAPLOID WHEAT USING MICROSATELLITE MARKERS  

Technology Transfer Automated Retrieval System (TEKTRAN)

Hybrid necrosis is the gradual pre-mature death of leaves or plants in certain F1 hybrids of wheat, 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...

224

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

EPA Science Inventory

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

225

The estimation of genetic relationships using molecular markers and their efficiency in estimating heritability in natural populations  

PubMed Central

Molecular marker data collected from natural populations allows information on genetic relationships to be established without referencing an exact pedigree. Numerous methods have been developed to exploit the marker data. These fall into two main categories: method of moment estimators and likelihood estimators. Method of moment estimators are essentially unbiased, but utilise weighting schemes that are only optimal if the analysed pair is unrelated. Thus, they differ in their efficiency at estimating parameters for different relationship categories. Likelihood estimators show smaller mean squared errors but are much more biased. Both types of estimator have been used in variance component analysis to estimate heritability. All marker-based heritability estimators require that adequate levels of the true relationship be present in the population of interest and that adequate amounts of informative marker data are available. I review the different approaches to relationship estimation, with particular attention to optimizing the use of this relationship information in subsequent variance component estimation.

Thomas, Stuart C

2005-01-01

226

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.

227

Purification, location, and immunological characterization of the iron-regulated high-molecular-weight proteins of the highly pathogenic yersiniae.  

PubMed Central

We have previously shown that under iron limitation, different Yersinia species synthesize new polypeptides. Two of them, the high-molecular-weight proteins (HMWPs), are expressed only by the highly pathogenic strains. In the present study, the HMWPs from Y. enterocolitica serovar O:8 were purified by gel filtration, and specific antibodies were obtained. Using these antibodies, we show that the two polypeptides were synthesized de novo during iron starvation and that they were found essentially in the bacterial outer membrane fractions, although the majority of the molecules were not exposed on the cell surface. We also demonstrate that the two proteins had common epitopes and that the HMWPs of the high-virulence-phenotype species Y. pestis, Y. pseudotuberculosis, and Y. enterocolitica serovar O:8 (a strain different from the one used to purify the proteins) are antigenically related. The less pathogenic and nonpathogenic strains did not exhibit cross-reacting material, suggesting that these strains do not synthesize even an altered form of the HMWPs. Images

Carniel, E; Antoine, J C; Guiyoule, A; Guiso, N; Mollaret, H H

1989-01-01

228

Molecular cloning and immunological characterization of the gamma polypeptide, a small protein associated with the Na,K-ATPase  

PubMed Central

The gamma subunit of the Na,K-ATPase is a small membrane protein that copurifies with the alpha and beta subunits of the enzyme. Strong evidence that the gamma subunit is a component of the Na,K-ATPase comes from studies indicating that the subunit is involved in forming the site for cardiac glycoside binding. We have isolated and characterized the cDNAs coding the gamma subunit from several species. The gamma subunit is a highly conserved protein consisting of 58 amino acids with a molecular weight of 6500. Hydropathy analysis reveals the presence of a single hydrophobic domain that is sufficient to cross the membrane. There are no sites for N-linked glycosylation. Northern blot analysis revealed that the gamma subunit mRNA is expressed in a tissue-specific fashion and is present in all tissues characterized. gamma-specific antibodies have been used to verify that the sequenced protein is the same protein labeled by [3H]nitroazidobenzoyl-ouabain (NAB-ouabain), and that this protein, the gamma subunit of the Na,K-ATPase, has a distribution pattern along nephron segments that is identical with the alpha subunit. In addition, coimmunoprecipitation of the alpha, beta and gamma subunits demonstrate specific association of the subunits. These results are consistent with the notion that the gamma subunit is specifically associated with and may be an important component of the Na,K-ATPase.

1993-01-01

229

Effects of ibuprofen on molecular markers of cartilage and synovium turnover in patients with knee osteoarthritis  

PubMed Central

Objective: The aim of this study was to evaluate the effect of ibuprofen on the urinary excretion of C-terminal crosslinking telopeptide of type II collagen (CTX-II) and urinary glucosyl galactosyl pyridinoline (Glc-Gal-PYD), two new molecular markers of cartilage and synovial tissue metabolism, respectively, in patients with knee osteoarthritis (OA). Methods: We studied 201 patients with knee pain and radiographic evidence of knee OA who were on treatment with non-steroidal anti-inflammatory drugs (NSAIDs) prior to study initiation. After an initial screening visit, patients were withdrawn from their pre-study NSAID and, following a flare of their OA symptoms, were randomised to ibuprofen (2400 mg/day) or placebo. Urinary CTX-II and Glc-Gal-PYD levels were measured at time of randomisation (baseline) and after 4–6 weeks of treatment. Results: After 4 to 6 weeks, urinary CTX-II (+17%, p = 0.023) and Glc-Gal-PYD (+10%, p = 0.020) increased significantly from baseline in the placebo group whereas marginal or no increase was observed in the ibuprofen group (CTX-II +2%, NS and Glc-Gal-PYD +4%, p = 0.045). For urinary CTX-II, the difference in the change from baseline between placebo and ibuprofen treated groups was significant (13%, p = 0.017). At baseline, urinary levels of CTX-II and Glc-Gal-PYD were higher in patients with knee swelling (n = 127) than in those without (n = 74) (p<0.02 for both markers). When patients were stratified according to presence or absence of knee swelling at baseline, the increases over 4–6 weeks of urinary CTX-II and Glc-Gal-PYD in the placebo group were restricted to patients with knee swelling (+22% from baseline, p = 0.001 and +12%, p = 0.011, for urinary CTX-II and Glc-Gal-PYD respectively). In patients with knee swelling who were treated with ibuprofen this increase was not observed and the difference from placebo was significant for urinary CTX-II (p = 0.014). Conclusion: In patients with a flare of knee OA, specifically in patients with evidence of joint inflammation documented by knee swelling, there was a significant increase in markers reflecting cartilage and synovium metabolism that could partly be prevented by high doses of ibuprofen. These data suggest that patients with a flare of knee OA are characterised by increased cartilage and synovial tissue degradation, which may be partly prevented by high doses of NSAIDs.

Gineyts, E; Mo, J; Ko, A; Henriksen, D; Curtis, S; Gertz, B; Garnero, P; Delmas, P

2004-01-01

230

Development and use of genic molecular markers (GMMs) for construction of a transcript map of chickpea (Cicer arietinum L.).  

PubMed

A transcript map has been constructed by the development and integration of genic molecular markers (GMMs) including single nucleotide polymorphism (SNP), genic microsatellite or simple sequence repeat (SSR) and intron spanning region (ISR)-based markers, on an inter-specific mapping population of chickpea, the third food legume crop of the world and the first food legume crop of India. For SNP discovery through allele re-sequencing, primer pairs were designed for 688 genes/expressed sequence tags (ESTs) of chickpea and 657 genes/ESTs of closely related species of chickpea. High-quality sequence data obtained for 220 candidate genic regions on 2-20 genotypes representing 9 Cicer species provided 1,893 SNPs with an average frequency of 1/35.83 bp and 0.34 PIC (polymorphism information content) value. On an average 2.9 haplotypes were present in 220 candidate genic regions with an average haplotype diversity of 0.6326. SNP2CAPS analysis of 220 sequence alignments, as mentioned above, provided a total of 192 CAPS candidates. Experimental analysis of these 192 CAPS candidates together with 87 CAPS candidates identified earlier through in silico mining of ESTs provided scorable amplification in 173 (62.01%) cases of which predicted assays were validated in 143 (82.66%) cases (CGMM). Alignments of chickpea unigenes with Medicago truncatula genome were used to develop 121 intron spanning region (CISR) markers of which 87 yielded scorable products. In addition, optimization of 77 EST-derived SSR (ICCeM) markers provided 51 scorable markers. Screening of easily assayable 281 markers including 143 CGMMs, 87 CISRs and 51 ICCeMs on 5 parental genotypes of three mapping populations identified 104 polymorphic markers including 90 markers on the inter-specific mapping population. Sixty-two of these GMMs together with 218 earlier published markers (including 64 GMM loci) and 20 other unpublished markers could be integrated into this genetic map. A genetic map developed here, therefore, has a total of 300 loci including 126 GMM loci and spans 766.56 cM, with an average inter-marker distance of 2.55 cM. In summary, this is the first report on the development of large-scale genic markers including development of easily assayable markers and a transcript map of chickpea. These resources should be useful not only for genome analysis and genetics and breeding applications of chickpea, but also for comparative legume genomics. PMID:21384113

Gujaria, Neha; Kumar, Ashish; Dauthal, Preeti; Dubey, Anuja; Hiremath, Pavana; Bhanu Prakash, A; Farmer, Andrew; Bhide, Mangla; Shah, Trushar; Gaur, Pooran M; Upadhyaya, Hari D; Bhatia, Sabhyata; Cook, Douglas R; May, Greg D; Varshney, Rajeev K

2011-03-08

231

DNA Alterations in the Plasma and Serum of Cancer Patients: A Molecular Tumor Marker  

Microsoft Academic Search

SummaryConventional serum tumor markers are soluble glycoproteins that have proven clinically useful for the initial diagnosis as well as the follow-up in multiple tumor entities. However, a number of tumors lack known tumor markers or the tumor markers are characterized by either low sensitivity or specificity. The detection of disseminated tumor cells in the blood by reverse transcriptase polymerase chain

C. Goessl; R. Heicappell; K. Miller

2000-01-01

232

rpoB gene as a novel molecular marker to infer phylogeny in Planctomycetales.  

PubMed

The 16S rRNA gene has been used in the last decades as a gold standard for determining the phylogenetic position of bacteria and their taxonomy. It is a well conserved gene, with some variations, present in all bacteria and allows the reconstruction of genealogies of microorganisms. Nevertheless, this gene has its limitations when inferring phylogenetic relationships between closely related isolates. To overcome this problem, DNA-DNA hybridization appeared as a solution to clarify interspecies relationships when the sequence similarity of the 16S rRNA gene is above 97 %. However, this technique is time consuming, expensive and laborious and so, researchers developed other molecular markers such as sequencing of housekeeping or functional genes for accurate determination of bacterial phylogeny. One of these genes that have been used successfully, particularly in clinical microbiology, codes for the beta subunit of the RNA polymerase (rpoB). The rpoB gene is sufficiently conserved to be used as a molecular clock, it is present in all bacteria and it is a mono-copy gene. In this study, rpoB gene sequencing was applied to the phylum Planctomycetes. Based on the genomes of 19 planctomycetes it was possible to determine the correlation between the rpoB gene sequence and the phylogenetic position of the organisms at a 95-96 % sequence similarity threshold for a novel species. A 1200-bp fragment of the rpoB gene was amplified from several new planctomycetal isolates and their intra and inter-species relationships to other members of this group were determined based on a 96.3 % species border and 98.2 % for intraspecies resolution. PMID:23904187

Bondoso, Joana; Harder, Jens; Lage, Olga Maria

2013-08-01

233

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

PubMed Central

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

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

2009-01-01

234

Confirmation of cross-fertilization using molecular markers in ornamental passion flower hybrids.  

PubMed

Several interspecific Passiflora hybrids are produced in the northern hemisphere for the ornamental plant market. In Brazil, production of passion flower hybrids is limited to the introgression of genes into the main cultivated species, yellow passion fruit, to be used as rootstocks. Confirmation of hybridization in the initial developmental stage is important for breeding perennial and sub-perennial plants, such as passion flowers, reducing time and costs in plant stock maintenance. In order to obtain F? hybrids with ornamental potential, four species of Passiflora (P. alata, P. gardneri, P. gibertii, and P. watsoniana) from the Active Germplasm Bank at UESC were hybridized. Flower buds, in pre-anthesis, of the genitors were previously protected, and the female buds were emasculated. To confirm hybridization, the genomic DNA of the genitor species and the supposed hybrids was extracted and RAPD primers were used to obtain molecular markers and select passion flower interspecific hybrids. Eight primers were used to confirm hybrids derived from P. gardneri with P. alata, P. watsoniana with P. alata, P. watsoniana with P. gardneri, and P. gardneri with P. gibertii; 75, 50, 45, and 46% of the informative bands, respectively, confirmed the hybrid nature of these plants. The RAPD technique was effective in the early identification of hybrids; this will be useful for development of hybrid Passiflora progeny. PMID:21264815

Conceição, L D H C S; Belo, G O; Souza, M M; Santos, S F; Cerqueira-Silva, C B M; Corrêa, R X

2011-01-11

235

Screening of Molecular Virulence Markers in Staphylococcus aureus and Pseudomonas aeruginosa Strains Isolated from Clinical Infections  

PubMed Central

Staphylococcus (S.) aureus and Pseudomonas (Ps.) aeruginosa are two of the most frequently opportunistic pathogens isolated in nosocomial infections, responsible for severe infections in immunocompromised hosts. The frequent emergence of antibiotic-resistant S. aureus and Ps. aeruginosa strains has determined the development of new strategies in order to elucidate the different mechanisms used by these bacteria at different stages of the infectious process, providing the scientists with new procedures for preventing, or at least improving, the control of S. aureus and Ps. aeruginosa infections. The purpose of this study was to characterize the molecular markers of virulence in S. aureus and Ps. aeruginosa strains isolated from different clinical specimens. We used multiplex and uniplex PCR assays to detect the genes encoding different cell-wall associated and extracellular virulence factors, in order to evaluate potential associations between the presence of putative virulence genes and the outcome of infections caused by these bacteria. Our results demonstrate that all the studied S. aureus and Ps. aeruginosa strains synthesize the majority of the investigated virulence determinants, probably responsible for different types of infections.

Cotar, Ani-Ioana; Chifiriuc, Mariana-Carmen; Dinu, Sorin; Bucur, Marcela; Iordache, Carmen; Banu, Otilia; Dracea, Olguta; Larion, Cristina; Lazar, Veronica

2010-01-01

236

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

PubMed Central

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

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

2010-01-01

237

Diagnostic value of molecular markers in chloroquine-resistant falciparum malaria in Southern Mauritania.  

PubMed

Despite its diminishing efficacy because of increased resistance, chloroquine remains the primary antimalarial agent in many endemic areas. Evidence is mounting that point mutations on the Pfcrt and possibly the Pfmdr1 genes are conferring plasmodial resistance to chloroquine. In 1998, atypically strong rainfalls led to an increased activity of falciparum malaria in Mauritania that affected non-endemic regions bordering the Saharan desert. An in vivo study on chloroqine resistance was combined with studies for molecular markers of drug resistance. Detection of Pfmdr1-76-tyrosine showed an increased odds ratio (2.91) for resistance (P = 0.0195). However, by use of this codon alone, sensitivity for detection of resistance was 60.6%, and specificity was 65.3%. In comparison, detection of the K76T mutation at Pfcrt showed a very high sensitivity (100%) while specificity remained relatively low (65.4%). For the combination of mutations on both genes, the odds ratio for detection of resistance increased to 5.31 (P = 0.0005). Here, sensitivity was again decreased to 60.6% while specificity increased to 76.9%. The results of this study suggest that detection of Pfcrt T76 can be applied for predicting chloroquine resistance in epidemiologic settings with sufficiently high sensitivity to make it an attractive alternative to time- and labor-consuming in vivo trials. Additional testing for Pfmdr Y76 provides increased specificity to this approach. PMID:12479542

Jelinek, T; Aida, A O; Peyerl-Hoffmann, G; Jordan, S; Mayor, A; Heuschkel, C; el Valy, A O; von Sonnenburg, F; Christophel, E M

2002-11-01

238

Characterization of prenatally assessed de novo small supernumerary marker chromosomes by molecular cytogenetics.  

PubMed

Small supernumerary marker chromosomes (sSMC) are structurally abnormal chromosomes that cannot be identified or characterized unambiguously by conventional banding cytogenetics alone, and they are generally equal in size or smaller than a chromosome 20 of the same metaphase spread. sSMC are reported in 0.043% of newborn infants and 0.075% of prenatal cases. Molecular cytogenetics is necessary to characterize the origin of an sSMC, and many highly sophisticated approaches are available throughout the literature for their comprehensive description. However, because in a prenatal diagnostic laboratory such techniques are not available, I suggest here a straightforward scheme to characterize at least the sSMC's chromosomal origin as quickly as possible. Based on this scheme, it is possible to compare the actual present case with similar cases from the literature, which are summarized on http://www.med.uni-jena.de/fish/sSMC/00START.htm./ For a more wide-ranging sSMC characterization, a specialized laboratory should be contacted, e.g., my laboratory. PMID:18425469

Liehr, Thomas

2008-01-01

239

Regulatory T cells and dendritic cells in transplantation tolerance: molecular markers and mechanisms.  

PubMed

Transplantation tolerance can be induced in adult rodents using monoclonal antibodies against coreceptor or costimulation molecules on the surface of T cells. There are currently two well-characterized populations of T cells, demonstrating regulatory capacity: the "natural" CD4+CD25+ T cells and the interleukin (IL)-10-producing Tr1 cells. Although both types of regulatory T cells can induce transplantation tolerance under appropriate conditions, it is not clear whether either one plays any role in drug-induced dominant tolerance, primarily due to a lack of clear-cut molecular or functional markers. Similarly, although dendritic cells (DCs) can be pharmacologically manipulated to promote tolerance, the phenotype of such populations remains poorly defined. We have used serial analysis of gene expression (SAGE) with 29 different T-cell and antigen-presenting cell libraries to identify gene-expression signatures associated with immune regulation. We found that independently derived, regulatory Tr1-like clones were highly concordant in their patterns of gene expression but were quite distinct from CD4+CD25+ regulatory T cells from the spleen. DCs that were treated with the tolerance-enhancing agents IL-10 or vitamin D3 expressed a gene signature reflecting a functional specification in common with the most immature DCs derived from embryonic stem cells. PMID:14617201

Cobbold, Stephen P; Nolan, Kathleen F; Graca, Luis; Castejon, Raquel; Le Moine, Alain; Frewin, Mark; Humm, Susan; Adams, Elizabeth; Thompson, Sara; Zelenika, Diana; Paterson, Alison; Yates, Stephen; Fairchild, Paul J; Waldmann, Herman

2003-12-01

240

Sensitivity of molecular marker-based CMB models to biomass burning source profiles  

NASA Astrophysics Data System (ADS)

To assess the contribution of sources to fine particulate organic carbon (OC) at four sites in North Carolina, USA, a molecular marker chemical mass balance model (MM-CMB) was used to quantify seasonal contributions for 2 years. The biomass burning contribution at these sites was found to be 30-50% of the annual OC concentration. In order to provide a better understanding of the uncertainty in MM-CMB model results, a biomass burning profile sensitivity test was performed on the 18 seasonal composites. The results using reconstructed emission profiles based on published profiles compared well, while model results using a single source test profile resulted in biomass burning contributions that were more variable. The biomass burning contribution calculated using an average regional profile of fireplace emissions from five southeastern tree species also compared well with an average profile of open burning of pine-dominated forest from Georgia. The standard deviation of the results using different source profiles was a little over 30% of the annual average biomass contributions. Because the biomass burning contribution accounted for 30-50% of the OC at these sites, the choice of profile also impacted the motor vehicle source attribution due to the common emission of elemental carbon and polycyclic aromatic hydrocarbons. The total mobile organic carbon contribution was less effected by the biomass burning profile than the relative contributions from gasoline and diesel engines.

Sheesley, Rebecca J.; Schauer, James J.; Zheng, Mei; Wang, Bo

241

Biochemical and immunological properties of urinary angiotensinase A and dipeptidylaminopeptidase IV. Their use as markers in patients with renal cell injury.  

PubMed

Dipeptidyl peptidase IV (EC 3.4.14.5) and angiotensinase A (EC 4.4.11.7) were purified to homogeneity from pooled urine concentrate of patients with renal damage, using ultrafiltration, ammonium sulphate precipitation, lectin affinity chromatography, FPLC-ion-exchange(Mono-Q-)chromatography, and FPLC-gel filtration (Superdex). Based on the specific enzyme activity of the starting material, dipeptidyl peptidase IV was enriched 1629 fold, angiotensinase A 1183 fold. The relative molecular masses, Michaelis constants and isoelectric points were determined. Negative staining of the purified enzymes revealed globular proteins (5-7 nm). Antisera raised against dipeptidyl peptidase IV and angiotensinase A reacted specifically with tubular and, in the case of anti-angiotensinase A sera, with tubular and glomerular structures. In addition, urinary membrane vesicles of proximal tubule origin were eluted with the void volume (Superdex-gel filtration), indicating heavy epithelial cell disintegration. Both soluble tissue enzymes (dipeptidyl peptidase IV, angiotensinase A) and vacuolar blebs shed from epithelia contribute to proteinuria, as was shown in patients with glomerulonephritis, interstitial nephritis, diabetic nephropathy and, for angiotensinase A, in patients with essential arterial hypertension. PMID:1362894

Scherberich, J E; Wiemer, J; Schoeppe, W

1992-10-01

242

Localization of the rice stripe disease resistance gene, Stv-bi, by graphical genotyping and linkage analyses with molecular markers  

Microsoft Academic Search

We used graphical genotyping and linkage analyses with molecular markers to determine the chromosomal location of the rice\\u000a stripe disease resistance gene, Stv-b\\u000a \\u000a \\u000a \\u000a i\\u000a \\u000a . The stripe resistance gene from the indica rice (Oryza sativa) cv ‘Modan’ was introgressed into several Japanese rice varieties. We found 4 RFLP markers in ‘Modan’, five susceptible parental\\u000a rice varieties (‘Norin No. 8’, ‘Sachihikari’,

Y. Hayano-Saito; T. Tsuji; K. Fujii; K. Saito; M. Iwasaki; A. Saito

1998-01-01

243

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

PubMed Central

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

Zhang, Shouan; Gao, Muqiang; Zaitlin, David

2012-01-01

244

CD44 as a molecular marker to screen cancer stem cells in hypopharyngeal cancer.  

PubMed

Abstract Conclusions: The CD44(+) cells have a stronger proliferative capacity and higher tumorigenic potential than the CD44(-) cells, which suggests that the cancer stem cells of hypopharyngeal cancer may exist in the CD44(+) tumor cell population. Therefore, we propose that CD44 is an important biological marker to screen cancer stem cells of hypopharyngeal cancer. Objectives: To study the significance of CD44 as a molecular marker for screening cancer stem cells in hypopharyngeal cancer. Methods: The CD44 expression levels in the hypopharyngeal cancer cell line FaDu were analyzed using flow cytometry. To investigate the biological significance of the CD44(+) population, we sorted the CD44(+) and CD44(-) cell populations by using magnetic-associated cell sorting (MACS) technology. After the separation, the purity of the CD44(+) cells was determined using flow cytometry. The MTT method was used to detect the different proliferation capabilities of the CD44(+) and CD44(-) cells in vitro. The tumorigenicity of the CD44(+) and CD44(-) cells was determined by injecting CD44(+) or CD44(-) cells (1 × 10(6) and 1 × 10(5)) into the body of NOD/SCID mice. Results: Some (21.1 ± 1.56)% of the hypopharyngeal cancer cell line FaDu cells expressed CD44. The CD44(+) population was efficiently sorted by MACS, and after separation, the purity of the CD44(+) cells was (99.4 ± 0.29)%. The MTT assay indicated that the sorted CD44(+) cells had a stronger proliferative capacity than the CD44(-) cells. The tumorigenicity study showed that all the mice injected with 1 × 10(6) CD44(+) cells developed tumors (8/8), half the mice injected with 1 × 10(6) CD44(-) cells developed tumors (4/8), 1 of the 8 mice injected with 1 × 10(5) CD44(+) cells developed tumors (12.5%), but none of the mice injected with 1 × 10(5) CD44(-) cells developed any tumors (0/8). At the same concentration, the difference in tumorigenic rates between the CD44(+) and CD44(-) groups was statistically significant (Fisher's exact test, p < 0.05). Furthermore, the CD44(+) group had a shorter incubation period than the CD44(-) group. In addition, the average tumor volume of the CD44(+) group was (2017.81 ± 538.50) mm(3); however, the average tumor volume of the CD44(-) group was (1153.25 ± 503.18) mm(3). The difference was statistically significant (t = 2.67, p < 0.05). PMID:23837451

Shen, Chenling; Xiang, Mingliang; Nie, Chen; Hu, Haixia; Ma, Yan; Wu, Hao

2013-07-09

245

Interpopulation congruence in Chinese Primula ovalifolia revealed by chemical and molecular markers using essential oils and ISSRs.  

PubMed

The chemical composition of the essential oils of five natural populations of P. ovalifolia from central and southwest China and their interpopulation variability were first analyzed by using GC-MS. Twenty-two essential oil compounds were obtained, in which eighteen ones were identified and characterized representing 95%-96% of the oil composition. Three main chemotypes, i.e., the methyl-acetyl-hydroquinone-rich, hydroquinone-rich, and acetyl-hydroquinone-rich chemotypes, were then differentiated, corresponding to the three groups obtained from the cluster analysis based on the essential oil composition percentages. Genetic variations among the five populations were also investigated using the Inter-Simple Sequence Repeats (ISSR) markers. Finally, the Mantel test showed that there was a significant correlation between two distance matrices based on the chemical compounds of essential oils and ISSR markers, confirming the congruence of interpopulation relationships in the P. ovalifolia revealed by the chemical and molecular markers PMID:12622227

Nan, Peng; Peng, Shaolin; Shi, Suhua; Ren, Hai; Yang, Ji; Zhong, Yang

246

Molecular cytogenetic study of supernumerary marker chromosomes in an unselected group of children  

SciTech Connect

We report on an unselected group of 24 children with small supernumerary marker chromosomes, found in a large sample of 34,910 consecutive newborns karyotyped at birth. Sixteen of these were available for reexamination. With the use of in situ hybridization with {alpha}-satellite centromere probes and satellite III, ribosomal and {beta}-satellite DNA probes, we have characterized these markers. In 14 of the 16 cases we have been able to determine the chromosomal origin of the marker. Twelve of the markers are derived from the acrocentric chromosomes. Of these 12 markers, 4 are derived from chromosome 14, 4 from chromosome 22, 3 from chromosome 15 and one is from either chromosome 13 or 21. Ten of these markers were initially ascertained with the satellite III DNA probe, taking advantage of the fact that satellite III DNA is found in the centromeric region of the following chromosomes: 1, 5, 9, 13, 14, 15, 16, 20, 21, 22, and Y. Two markers were derived from chromosomes 4 and 8. The origin of the last 2 markers could not be determined with the techniques employed. Only one of these children is psychometrically retarded and has a peculiar appearance. Unfortunately we were not able to determine the origin of the marker in her case. All other children developed normally. 54 refs., 1 fig., 3 tabs.

Gravholt, C.H. [Aarhus Univ. Hospital, Risskov (Denmark); Friedrich, U. [Aarhus Univ. (Denmark)

1995-03-13

247

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

NASA Astrophysics Data System (ADS)

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

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

2010-05-01

248

Identifying and Characterizing Alternative Molecular Markers for the Symbiotic and Free-Living Dinoflagellate Genus Symbiodinium  

PubMed Central

Dinoflagellates in the genus Symbiodinium are best known as endosymbionts of corals and other invertebrate as well as protist hosts, but also exist free-living in coastal environments. Despite their importance in marine ecosystems, less than 10 loci have been used to explore phylogenetic relationships in this group, and only the multi-copy nuclear ribosomal Internal Transcribed Spacer (ITS) regions 1 and 2 have been used to characterize fine-scale genetic diversity within the nine clades (A–I) that comprise the genus. Here, we describe a three-step molecular approach focused on 1) identifying new candidate genes for phylogenetic analysis of Symbiodinium spp., 2) characterizing the phylogenetic relationship of these candidate genes from DNA samples spanning eight Symbiodinium clades (A–H), and 3) conducting in-depth phylogenetic analyses of candidate genes displaying genetic divergences equal or higher than those within the ITS-2 of Symbiodinium clade C. To this end, we used bioinformatics tools and reciprocal comparisons to identify homologous genes from 55,551 cDNA sequences representing two Symbiodinium and six additional dinoflagellate EST libraries. Of the 84 candidate genes identified, 7 Symbiodinium genes (elf2, coI, coIII, cob, calmodulin, rad24, and actin) were characterized by sequencing 23 DNA samples spanning eight Symbiodinium clades (A–H). Four genes displaying higher rates of genetic divergences than ITS-2 within clade C were selected for in-depth phylogenetic analyses, which revealed that calmodulin has limited taxonomic utility but that coI, rad24, and actin behave predictably with respect to Symbiodinium lineage C and are potential candidates as new markers for this group. The approach for targeting candidate genes described here can serve as a model for future studies aimed at identifying and testing new phylogenetically informative genes for taxa where transcriptomic and genomics data are available.

Pochon, Xavier; Putnam, Hollie M.; Burki, Fabien; Gates, Ruth D.

2012-01-01

249

Molecular markers in management of ex situ PGR-a case study.  

PubMed

Worldwide germplasm collections contain about 7.4 million accessions of plant genetic resources for food and agriculture. One of the 10 largest ex situ genebanks of our globe is located at the Leibniz Institute of Plant Genetics and Crop Plant Research in Gatersleben, Germany. Molecular tools have been used for various gene bank management practices including characterization and utilization of the germplasm. The results on genetic integrity of longterm- stored gene bank accessions of wheat (self-pollinating) and rye (open-pollinating) cereal crops revealed a high degree of identity for wheat. In contrast, the out-pollinating accessions of rye exhibited shifts in allele frequencies. The genetic diversity of wheat and barley germplasm collected at intervals of 40 to 50 years in comparable geographical regions showed qualitative rather than a quantitative change in diversity. The inter- and intraspecific variation of seed longevity was analysed and differences were detected. Genetic studies in barley, wheat and oilseed rape revealed numerous QTL, indicating the complex and quantitative nature of seed longevity. Some of the loci identified were in genomic regions that co-localize with genes determining agronomic traits such as spike architecture or biotic and abiotic stress response. Finally, a genome-wide association mapping analysis of a core collection of wheat for flowering time was performed using diversity array technology (DArT) markers. Maker trait associations were detected in genomic regions where major genes or QTL have been described earlier. In addition, new loci were also detected, providing opportunities to monitor genetic variation for crop improvement. PMID:23107922

Börner, Andreas; Khlestkina, Elena K; Chebotar, Sabina; Nagel, Manuela; Arif, Mian Abdur Rehman; Neumann, Kerstin; Kobiljski, Borislav; Lohwasser, Ulrike; Röder, Marion S

2012-11-01

250

Comparison between genetic and physical maps in Zea mays L. of molecular markers linked to resistance against Diatraea spp  

Microsoft Academic Search

In the pachytene stage, chromosomes are maximally extended and can easily be distinguished. Therefore, by applying fluorescence in situ hybridization (FISH) to pachytene chromosomes, it is possible to generate a high-resolution physical map of chromosome 9 in maize. Molecular markers (umc105a on the short arm of chromosome 9, csu145a on the long arm) were used that flank quantitative trait loci

M. Sadder; G. Weber

2002-01-01

251

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

Microsoft Academic Search

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

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

1994-01-01

252

Identification of molecular markers linked to Pm13, an Aegilops longissima gene conferring resistance to powdery mildew in wheat  

Microsoft Academic Search

RFLP, RAPD, STS and DDRT-PCR techniques were applied to find molecular markers linked to Pm13, an Aegilops longissima gene conferring resistance to powdery mildew in wheat. The experimental strategy was based on the differential comparison\\u000a of DNAs from common wheat and from common wheat\\/Ae. longissima recombinant lines carrying short segments of the 3S\\u000a l\\u000a S chromosome arm containing the Pm13

A. Cenci; R. D’Ovidio; O. A. Tanzarella; C. Ceoloni; E. Porceddu

1999-01-01

253

Identification of a novel mitochondrial genome type and development of molecular markers for cytoplasm classification in radish ( Raphanus sativus L.)  

Microsoft Academic Search

Plant mitochondrial genomes have complex configurations resulting from the multipartite structures and highly rearranged substoichiometric\\u000a molecules created by repetitive sequences. To expedite the reliable classification of the diverse radish (Raphanus sativus L.) cytoplasmic types, we have developed consistent molecular markers within their complex mitochondrial genomes. orf138, a gene responsible for Ogura male-sterility, was detected in normal cultivars in the form

Sunggil Kim; Heerae Lim; Kang-Hee Cho; Soon-Kee Sung; Dae-Geun Oh; Ki-Taek Kim

2007-01-01

254

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

255

Sequence based polymorphic (SBP) marker technology for targeted genomic regions: its application in generating a molecular map of the Arabidopsis thaliana genome  

PubMed Central

Background Molecular markers facilitate both genotype identification, essential for modern animal and plant breeding, and the isolation of genes based on their map positions. Advancements in sequencing technology have made possible the identification of single nucleotide polymorphisms (SNPs) for any genomic regions. Here a sequence based polymorphic (SBP) marker technology for generating molecular markers for targeted genomic regions in Arabidopsis is described. Results A ~3X genome coverage sequence of the Arabidopsis thaliana ecotype, Niederzenz (Nd-0) was obtained by applying Illumina's sequencing by synthesis (Solexa) technology. Comparison of the Nd-0 genome sequence with the assembled Columbia-0 (Col-0) genome sequence identified putative single nucleotide polymorphisms (SNPs) throughout the entire genome. Multiple 75 base pair Nd-0 sequence reads containing SNPs and originating from individual genomic DNA molecules were the basis for developing co-dominant SBP markers. SNPs containing Col-0 sequences, supported by transcript sequences or sequences from multiple BAC clones, were compared to the respective Nd-0 sequences to identify possible restriction endonuclease enzyme site variations. Small amplicons, PCR amplified from both ecotypes, were digested with suitable restriction enzymes and resolved on a gel to reveal the sequence based polymorphisms. By applying this technology, 21 SBP markers for the marker poor regions of the Arabidopsis map representing polymorphisms between Col-0 and Nd-0 ecotypes were generated. Conclusions The SBP marker technology described here allowed the development of molecular markers for targeted genomic regions of Arabidopsis. It should facilitate isolation of co-dominant molecular markers for targeted genomic regions of any animal or plant species, whose genomic sequences have been assembled. This technology will particularly facilitate the development of high density molecular marker maps, essential for cloning genes based on their genetic map positions and identifying tightly linked molecular markers for selecting desirable genotypes in animal and plant breeding experiments.

2012-01-01

256

MOLECULAR MARKERS RUN ON A TEST PANEL: A DATA SOURCE FOR THE COTTON COMMUNITY  

Technology Transfer Automated Retrieval System (TEKTRAN)

Unlike other major crops such as soybean and corn, cotton has no coordinated public marker database. Cotton Incorporated (CI) has identified the need for more markers and a database as critical action points. The Mid South Area Genomics Laboratory in cooperation with scientists from the Crop Genetic...

257

Supernumerary marker 15 chromosomes: a clinical, molecular and FISH approach to diagnosis and prognosis  

Microsoft Academic Search

Seventeen patients presenting with either de novo or familial supernumerary marker (mar) 15 chromosomes were shown by fluorescent in situ hybridization techniques (FISH) to have markers derived from and composed entirely of chromosome 15 material. Using a combination of conventional cytogenetics, FISH, Southern blotting and multiplex polymerase chain reaction (PCR) methods, it was possible to sub-classify the 17 mar(15)s into

John A. Crolla; John F. Harvey; Fiona L. Sitch; Nick R. Dennis

1995-01-01

258

Molecular-marker-facilitated investigations of quantitative trait loci in maize  

Microsoft Academic Search

Restriction fragment length polymorphisms have become powerful tools for genetic investigations in plant species. They allow a much greater degree of genome saturation with neutral markers than has been possible with isozymes or morphological loci. A previous investigation employed isozymes as genetic markers to infer the location of genetic factors influencing the expression of quantitative traits in the maize population:

M. D. Edwards; T. Helentjaris; S. Wright; C. W. Stuber

1992-01-01

259

Molecular markers linked to genes for specific rust resistance and indeterminate growth habit in common bean  

Microsoft Academic Search

Bulked segregant analysis was utilized to identify random amplified polymorphic DNA (RAPD) markers linked to genes for specific resistance to a rust pathotype and indeterminate growth habit in an F2 population from the common bean cross PC-50 (resistant to rust and determinate growth habit) × Chichara 83-109 (susceptible to rust and indeterminate growth habit). Six RAPD markers were mapped in

Soon O. Park; Dermot P. Coyne; James M. Bokosi; James R. Steadman

1999-01-01

260

MOLECULAR MARKERS RUN ON A TEST PANEL: A DATA SOURCE FOR THE COTTON COMMUNITY  

Technology Transfer Automated Retrieval System (TEKTRAN)

Unlike other major crops such as soybean and corn, cotton has no coordinated public marker database. Cotton Incorporated (CI) has identified the need for more markers and a database as critical action points. The Mid South Area Genomics Laboratory in cooperation with scientists from the Crop Genet...

261

Molecular identification of tropical tasar silkworm (Antheraea mylitta) ecoraces with RAPD and SCAR markers.  

PubMed

The tropical tasar silkworm, Antheraea mylitta, has several ecoraces, 10 of which are commercially exploited for the production of tasar silk. These ecoraces are identified by morphological markers that are greatly influenced by photoperiod, humidity, altitude, and host plants. The DNA markers, random amplification of polymorphic DNA (RAPD), and sequence-characterized amplified region (SCAR) are identified to complement the existing morphological markers. Seven RAPD bands are selected that identify 8 of the 10 ecoraces. These identified RAPD fragments are sequenced and primers are designed for SCAR markers. Of the seven sets of primers, a single primer pair produced polymorphic SCAR bands that diagnose 5 of the 10 ecoraces. All 10 ecoraces are identified by the use of RAPD and SCAR markers together. PMID:16648996

Saha, Monalee; Kundu, S C

2006-04-29

262

Construction of intersubspecific molecular genetic map of lentil based on ISSR, RAPD and SSR markers.  

PubMed

Lentil (Lens culinaris ssp. culinaris), is a self-pollinating diploid (2n = 2x = 14), cool-season legume crop and is consumed worldwide as a rich source of protein (~24.0%), largely in vegetarian diets. Here we report development of a genetic linkage map of Lens using 114 F(2) plants derived from the intersubspecific cross between L 830 and ILWL 77. RAPD (random amplified polymorphic DNA) primers revealed more polymorphism than ISSR (intersimple sequence repeat) and SSR (simple sequence repeat) markers. The highest proportion (30.72%) of segregation distortion was observed in RAPD markers. Of the 235 markers (34 SSR, 9 ISSR and 192 RAPD) used in the mapping study, 199 (28 SSRs, 9 ISSRs and 162 RAPDs) were mapped into 11 linkage groups (LGs), varying between 17.3 and 433.8 cM and covering 3843.4 cM, with an average marker spacing of 19.3 cM. Linkage analysis revealed nine major groups with 15 or more markers each and two small LGs with two markers each, and 36 unlinked markers. The study reported assigning of 11 new SSRs on the linkage map. Of the 66 markers with aberrant segregation, 14 were unlinked and the remaining 52 were mapped. ISSR and RAPD markers were found to be useful in map construction and saturation. The current map represents maximum coverage of lentil genome and could be used for identification of QTL regions linked to agronomic traits, and for marker-assisted selection in lentil. PMID:23271013

Gupta, Mamta; Verma, Bhawna; Kumar, Naresh; Chahota, Rakesh K; Rathour, Rajeev; Sharma, Shyam K; Bhatia, Sabhyata; Sharma, Tilak R

2012-12-01

263

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

2013-03-21

264

DEVELOPMENT OF MOLECULAR DIAGNOSTIC MARKERS FOR GLASSY-WINGED AND SMOKETREE SHARPSHOOTERS FOR USE IN PREDATOR GUT CONTENT EXAMINATIONS Project Leaders  

Microsoft Academic Search

To aid in identifying key predators of Proconiini sharpshooter species present in California, we developed and tested molecular diagnostic markers for the glassy-winged sharpshooter Homalodisca coagulata (Say) and smoke-tree sharpshooter Homalodisca liturata (Ball) (Homoptera: Cicadellidae: Proconiini). Two different types of markers were compared, those targeting single-copy sequence characterized amplified regions (SCAR) and mitochondrial markers targeting the multi-copy cytochrome oxidase subunit

Jesse H. de León; James Hagler; Valerie Fournier; Kent Daane

265

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

266

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

267

Microsatellite primed-PCR to select molecular markers for Tuber species  

Microsoft Academic Search

The direct microsatellite-primed PCR and the RAMPO techniques were applied to detect inter-specific polymorphisms in Tuber species and to select species specific fragments. A T. borchii marker was identified and specific primers were selected.

Antonella Amicucci; Chiara Guidi; Lucia Potenza; Vilberto Stocchi

2002-01-01

268

A consensus linkage map for molecular markers and quantitative trait loci associated with economically important traits in melon (Cucumis melo L.)  

Technology Transfer Automated Retrieval System (TEKTRAN)

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 ...

269

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

Microsoft Academic Search

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

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

1999-01-01

270

Epidemiology of tuberculosis immunology.  

PubMed

Immunological impairment plays a major role in the epidemiology of TB. Globally, the most common causes of immunological impairment are malnutrition, diabetes, HIV/AIDS, aging, and smoking. With the notable exception of HIV, each factor leads to relatively mild immunological impairment in individuals. However, as these conditions affect a significant proportion of the population, they contribute substantially to the incidence of TB at a global scale. Understanding immunological impairment is central to understanding the global TB pandemic, and vital to the development of effective disease control strategies. PMID:23468101

Fox, G J; Menzies, D

2013-01-01

271

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

272

Method for mapping a partial lethal-factor locus on a molecular-marker linkage map of a backcross and doubled-haploid population  

Microsoft Academic Search

Distorted segregation has been repeatedly observed in various plant species in molecular-marker linkage mapping where distant\\u000a crosses were made. It may be caused by a partial lethal-factor acting in the filial generations. A method is presented for\\u000a estimating the recombination values between a partial lethal-factor locus and a linked molecular marker and the relative viability\\u000a or fertilization ability of zygotes

R. Cheng; A. Kleinhofs; Y. Ukai

1998-01-01

273

Molecular Markers of Lung Cancer in Workers from the MAYAK Nuclear Enterprise: Final Report.  

National Technical Information Service (NTIS)

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...

S. A. Belinsky V. Telnov

2007-01-01

274

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

2012-03-22

275

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

276

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

277

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

278

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

279

Immunological mechanisms of vaccination  

Microsoft Academic Search

Vaccines represent one of the greatest triumphs of modern medicine. Despite the common origins of vaccinology and immunology more than 200 years ago, the two disciplines have evolved along such different trajectories that most of the highly successful vaccines have been made empirically, with little or no immunological insight. Recent advances in innate immunity have offered new insights about the

Rafi Ahmed; Bali Pulendran

2011-01-01

280

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

281

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

282

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

PubMed Central

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

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

2007-01-01

283

Identification of single-copy orthologous genes between Physalis and Solanum lycopersicum and analysis of genetic diversity in Physalis using molecular markers.  

PubMed

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

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

2012-11-16

284

Genetic diversity in wild species of passion fruit (Passiflora trintae) based on molecular markers.  

PubMed

In spite of the importance of and the considerable variability observed in Passiflora (Passifloraceae), little is known about the genetic diversity of most of the species of this genus. We evaluated the genetic diversity by RAPD markers in 18 genotypes of Passiflora trintae. The 15 primers generated 112 markers, 84% of which were polymorphic. The genetic distance estimated by the complement of the Dice index (average dissimilarity = 0.30) and genotype grouping based on the UPGMA algorithm showed low variability among genotypes. More attention should be given to the study and conservation of the biodiversity of this economically important genus. PMID:21038298

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

2010-10-26

285

HPV-Associated Head and Neck Cancer: Molecular and Nano-Scale Markers for Prognosis and Therapeutic Stratification  

PubMed Central

Over the last 10 years, it has become clear that patients with head and neck cancer can be stratified into two distinct subgroups on the basis of the etiology of their disease. Patients with human papillomavirus-related cancers have significantly better survival rates and may necessitate different therapeutic approaches than those with tobacco and/or alcohol related cancers. This review discusses the various biomarkers currently in use for identification of patients with HPV-positive cancers with a focus on the advantages and limitations of molecular and nano-scale markers.

Kimple, Adam J.; Torres, Alexandra D.; Yang, Robert Z.; Kimple, Randall J.

2012-01-01

286

Molecular characterization of the marker chromosome associated with cat eye syndrome  

SciTech Connect

Cat eye syndrome (CES) is associated with a supernumerary bisatellited marker chromosome which is derived from duplicated regions of 22pter-22q11.2. In this study the authors have used dosage and RFLP analyses on 10 CES patients with marker chromosomes, by using probes to five loci mapped to 22q11.2. The sequences recognized by the probes D22S9, D22S43, and D22S57 are in four copies in all patients, but the sequences at the more distal loci, D22S36 and D22S75, are duplicated only in some individuals. D22S36 is present in three copies in some individuals, and D22S75 is present in two copies in the majority of cases. Only three individuals have a duplication of the most distal locus examined (D22S75), and these individuals have the largest marker chromosomes identified in this study. From the dosage analysis it was found that the marker chromosomes are variable in size and can be asymmetric in nature. There is no obvious correlation between the severity of the phenotype and the size of the duplication. The distal boundary of the CES critical region (D22S36) is proximal to that of DiGeorge syndrome, a contiguous-gene-deletion syndrome of 22q11.2. 35 refs., 3 figs., 2 tabs.

Mears, A.J.; McDermid, H.E. (Univ. of Alberta, Edmonton (Canada)); Duncan, A.M.V. (Queen's Univ. and Kingston General Hospital, Ontario (Canada)); Budarf, M.L.; Emanuel, B.S.; Sellinger, B. (Children's Hospital of Philadelphia, PA (United States)); Siegel-Bartelt, J. (Hospital for Sick Children, Toronto (Canada)); Greenberg, C.R. (Children's Hospital, Winnipeg (Canada))

1994-07-01

287

Molecular markers in circulating tumour cells from metastatic colorectal cancer patients.  

PubMed

The prognosis of metastatic cancer patients is still largely affected by treatment failure, mainly due to drug resistance. The hypothesis that chemotherapy might miss circulating tumour cells (CTCs) and particularly a subpopulation of more aggressive, stem-like CTCs, characterized by multidrug resistance, has been recently raised. We investigated the prognostic value of drug resistance and stemness markers in CTCs from metastatic colorectal cancer patients treated with oxaliplatin (L-OHP) and 5-fluoruracil (5-FU) based regimens. Forty patients with metastatic colorectal cancer were enrolled. CTCs were isolated from peripheral blood and analysed for the expression of aldheyde dehydrogenase 1 (ALDH1), CD44, CD133 (used as markers of stemness), multidrug resistance related protein 5 (MRP5 used as marker of resistance to 5-FU and L-OHP) and survivin (used as a marker of apoptosis resistance). CTCs were found in 27/40 (67%) patients. No correlation was found between the expression of either CD44 and CD133 in CTCs and the outcome of patients, while a statistically significant shorter progression-free survival was found in patients with CTCs positive for the expression of ALDH1, survivin and MRP5. These results support the idea that isolating survivin and MRP5+ CTCs may help in the selection of metastatic colorectal cancer patients resistant to standard 5-FU and L-OHP based chemotherapy, for which alternative regimens may be appropriate. PMID:20597995

Gazzaniga, Paola; Gradilone, Angela; Petracca, Arianna; Nicolazzo, Chiara; Raimondi, Cristina; Iacovelli, Roberto; Naso, Giuseppe; Cortesi, Enrico

2010-08-01

288

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

289

GLOBAL EXPRESSION PROFILING AS A ROOL TO DEVELOP MOLECULAR MARKERS LINKED TO HERBICIDE STRESS IN ARABIDOPSIS  

EPA Science Inventory

Herbicide drift (unintentional physical movement from target to off-target plants) is a cause of crop loss in US. Low-dose, high-potency herbicides that have short environmental persistence times constrain efforts to develop or identify metabolite or biochemical markers of exposu...

290

Use of Novel Technologies to Identify and Investigate Molecular Markers for Ovarian Cancer Screening and Prevention.  

National Technical Information Service (NTIS)

The purpose of this study is to identify novel genes that encode proteins that can be used to detect ovarian cancer before it spreads outside the ovary and becomes incurable. The goal is to assemble a panel of known and novel ovarian tumor markers that ma...

N. D. Urban

2001-01-01

291

Use of Novel Technologies to Identify and Investigate Molecular Markers for Ovarian Cancer Screening and Prevention.  

National Technical Information Service (NTIS)

The purpose of this study is to identify novel genes that encode proteins that can be used to detect ovarian cancer before it spreads outside the ovary and becomes incurable. The goal is to assemble a panel of known and novel ovarian tumor markers that ma...

N. Urban

2000-01-01

292

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

293

Predicting the biologic behavior of ductal carcinoma in situ: An analysis of molecular markers  

Microsoft Academic Search

Background. Ductal carcinoma in situ (DCIS) of the breast encompasses a heterogeneous group of noninvasive cancers that now represents 19% of new breast cancer cases. Optimal treatment remains controversial. We undertook this study to characterize the relationship between angiogenic markers and the biologic behavior of various DCIS phenotypes. Methods. We performed histolopathologic review and immunohistochemistry for p53, vascular endothelial growth

Tina J. Hieken; Miguel Farolan; Stephen D'Alessandro; Josè M. Velasco

2001-01-01

294

Identification from Public Data of Molecular Markers of Adenocarcinoma Characteristic of the Site of Origin  

Microsoft Academic Search

Patients presenting with metastatic adenocarcinoma of unknown origin are a common clinical problem. Their optimal management and therapy are facilitated by identification of the primary site, yet histologically these tumors are almost identical. Better tumor markers are needed to enable the assignment of metastases to likely sites of origin. In this study, hierarchical clustering of public serial analysis of gene

Jayne L. Dennis; J. Keith Vass; Ernst C. Wit; W. Nicol Keith; Karin A. Oien

2002-01-01

295

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

296

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

Microsoft Academic Search

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

Greg J. Hunt; Robert E. Page

1992-01-01

297

Molecular pathology in basal cell cancer with p53 as a genetic marker  

Microsoft Academic Search

Human basal cell cancer (BCC) has unique growth characteristics with virtual inability to metastasize. We investigated clonality and genetic progression using p53 mutations as marker. Sampling was done through microdissection of frozen immunohistochemically stained 16 ?m slices of tumors. From 11 BCC tumors 78 samples were analysed. Direct DNA sequencing of exons 5 – 8 was performed, haplotypes were determined

Fredrik Pontén; Cecilia Berg; Afshin Ahmadian; Zhi-Ping Ren; Monica Nistér; Joakim Lundeberg; Mathias Uhlén; Jan Pontén

1997-01-01

298

Genetic Diversity and Molecular Markers in Introduced and Thai Native Apple Snails (Pomacea and Pila)  

Microsoft Academic Search

The genetic diversity and species-diagnostic markers in the introduced apple snail, Pomacea canaliculata and in the native Thai apple snails; Pila ampullacea, P. angelica, P. pesmei, and P. polita, were investigated by restriction analysis of COI and are reported for the first time. Twenty- one composite haplotypes showing non-overlapping distributions among species were found. Genetic heterogeneity analysis indicated significant differences

Bungorn Thaewnon-ngiw; Sirawut Klinbunga; Nitsri Sangduen; Nitaya Lauhachinda; Piamsak Menasveta

2004-01-01

299

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

300

Linkage mapping of the Mediterranean cypress, Cupressus sempervirens, based on molecular and morphological markers.  

PubMed

Gene mapping for a Cupressus species is presented for the first time. Two linkage maps for the Mediterranean cypress (Cupressus sempervirens) varieties, C. sempervirens var. horizontalis and C. sempervirens var. pyramidalis, were constructed following the pseudo-testcross mapping strategy and employing RAPD, SCAR and morphological markers. A total of 427 loci (425 RAPDs, two SCARs) representing parents and F(1) progeny were screened for polymorphism with 32 random decamer and two SCAR primers. A morphological marker defined as "crown form" was also included. Of 274 polymorphic loci, the 188 that presented Mendelian inheritance formed the mapping dataset. Of these loci, 30% were mapped into seven linkage groups for the horizontalis (maternal) and four linkage groups for the pyramidalis (paternal) map. The putative "crown form" locus was included in a linkage group of both maps. The horizontalis and the pyramidalis maps covered 160.1 and 144.5 cM, respectively, while genome length was estimated to be 1696 cM for the former variety and 1373 cM for the latter. The four RAPD markers most tightly linked to crown form were cloned and converted to SCARs. Each of the cloned RAPD markers yielded two to three different sequences behaving as co-migrating fragments. Two SCAR markers, SC-D05(432) and SC-D09(667), produced amplified bands of the expected sizes and maintained linkage with the appropriate phenotype, but to a lesser extent compared to their original RAPD counterparts. These linkage maps represent a first step towards the localization of QTLs and genes controlling crown form and other polygenic traits in cypress. PMID:21948752

Manescu, C; Hamamouch, N; Maios, C; Harfouche, A; Doulis, A G; Aravanopoulos, F A

2011-08-30

301

Molecular Diversity in Ukrainian Melon Collection as Revealed by AFLP and Microsatellite Markers  

Technology Transfer Automated Retrieval System (TEKTRAN)

Thirty-eight melon accessions, which are of primary breeding importance in the Ukraine, were analyzed for diversity. These collections represent a major non-US and non-west Europe source of melon germplasm that have not yet been subjected to molecular characterization. Molecular diversity was esti...

302

Applications of molecular markers and DNA sequences in identifying fungal pathogens of cool season grain legumes  

Technology Transfer Automated Retrieval System (TEKTRAN)

Molecular techniques have now been widely applied in many disciplines of biological sciences including fungal identification in microbial ecology and plant pathology. In plant pathology, it is now common to use molecular techniques to identify and study plant pathogens of many agronomic and horticul...

303

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

304

Survey of Paramecium duboscqui using three markers and assessment of the molecular variability in the genus Paramecium.  

PubMed

The genus Paramecium (phylum Ciliophora) is one of the best-known among protozoa. Nevertheless, the knowledge on the diversity and distribution of species within this genus was remarkably scarce until recent times. In the last years a constantly growing amount of data has formed, especially on the distribution of species and the characterization of molecular markers. Much effort has been made on detecting clades inside each morphospecies, which could suggest the presence of sibling species complexes as in the famous case of Paramecium aurelia. In this work we present new data on Paramecium duboscqui, one of the morphospecies that have not yet been surveyed employing DNA sequences as markers. We obtained data from nine strains sampled around the world, using the three most commonly employed markers (18S rRNA gene, ITS1-5.8S-ITS2 and COI gene sequences). Moreover, we compared our results with those already available for other Paramecium species, and performed phylogenetic analyses for the entire genus. We also expanded the knowledge on the ITS2 secondary structure and its usefulness in studies on Paramecium. Our approach, that considers the data of all the species together, highlighted some characteristic patterns as well as some ambiguities that should be further investigated. PMID:22982632

Boscaro, Vittorio; Fokin, Sergei I; Verni, Franco; Petroni, Giulio

2012-09-13

305

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

306

Development of Molecular Markers for Detecting Genetic Relationships Within and Among Six Egyptian Buffalo Locations  

Microsoft Academic Search

Genetic variations was detected in Egyptian buffaloes at six locations; El-Behira (Be), El-Sharkia (Sh), El-Menofia (Me), Kafr El-Sheikh (Kf), El-Menia (Mn) and Sohag (So). Ten individuals from each location were blood sampled. SDS-protein and esterase markers were used to detect the genetic variations within the six studied location. SDS-protein profiles showed lower percentage of polymorphism (21.5%) than esterase profiles (45.7%)

A. H. Atta; E. S. Ahmed; M. H. Sadek; A. A. Amin

2009-01-01

307

Identification of Brassica oleracea monosomic alien chromosome addition lines with molecular markers reveals extensive gene duplication  

Microsoft Academic Search

Chromosomes of Brassica oleracea (2n=18) were dissected from the resynthesized amphidiploid B. napus Hakuran by repeated backcrosses to B. campestris (2n=20), creating a series of monosomic alien chromosome addition line plants (2n=21). Using morphological, isozyme and restriction fragment length polymorphism markers (RFLPs), 81 putative loci were identified. Of nine possible synteny groups, seven were represented in the 25 monosomic addition

J. Mitchell McGrath; Carlos F. Quiros; John J. Harada; Benoit S. Landry

1990-01-01

308

Establishment of molecular markers and linkage groups in two F 2 populations of Upland cotton  

Microsoft Academic Search

Two F2 populations of cotton (Gossypium hirsutum L.) from the crosses of HS46 x MARCABUCAG8US-1-88 (MAR) and HS46 x Pee Dee 5363 (PD5363) were characterized for restriction fragment length polymorphisms (RFLPs) using DNA probes. Seventy-three probe\\/enzyme combinations were used in the HS46 x MAR population analysis, which resulted in 42 informative polymorphic fragments. These 42 moleclar markers represented 26 polymorphic

Z. W. Shappley; J. N. Jenkins; C. E. Watson; A. L. Kahler; W. R. Meredith

1996-01-01

309

Genetic diversity of wild coffee ( Coffea arabica L.) using molecular markers  

Microsoft Academic Search

Genetic diversity was studied using RAPD markers among119 coffee (Coffea arabica L.) individuals representing 88 accessions derived from spontaneous and subspontaneous trees in Ethiopia, the primary centre\\u000a of species diversity, six cultivars grown locally in Ethiopia, and two accessions derived from the genetic populations Typica\\u000a and Bourbon, spread in the 18th century, which gave rise to the most currently grown

F. Anthony; B. Bertrand; O. Quiros; A. Wilches; P. Lashermes; J. Berthaud; A. Charrier

2001-01-01

310

Molecular characterization of eight Indian Snakehead species (Pisces: Perciformes Channidae) using RAPD markers  

Microsoft Academic Search

Murrels (Perciformes; Channidei; Channidae) are unique group of freshwater air breathing fishes having a confined distribution\\u000a to African and Asian continents. The phylogenetic relationship among eight Channid species viz.\\u000a Channa aurantimaculata, Channa bleheri, Channa diplogramma, Channa gachua, Channa marulius, Channa punctatus, Channa stewartii and Channa striatus were investigated using RAPD markers. Eight random oligodecamers viz. OPAC03, OPAC05, OPAC07, OPAC09, OPAC19,

Ajaz Ali Bhat; M. A. Haniffa; P. R. Divya; A. Gopalakrishnan; M. James Milton; Raj Kumar; Bilal Ahmad Paray

311

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

Microsoft Academic Search

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

DAIZABURO SHIZUKA; BRUCE E. LYON

2008-01-01

312

The Porcine Immunology and Nutrition Resource Database  

Technology Transfer Automated Retrieval System (TEKTRAN)

Diverse genomics-based databases have been developed to facilitate research with human and rodent models. Current porcine gene databases, however, lack the nutritional and immunological orientation and robust annotation to design effective molecular tools to study relevant pig models. To address t...

313

A 33 kDa molecular marker of sperm acrosome differentiation and maturation in the tammar wallaby (Macropus eugenii).  

PubMed

This study was undertaken to identify potential molecular markers of acrosomal biogenesis and post-testicular maturation in marsupials, using the tammar wallaby as a model species. A two-step sperm extraction procedure yielded two protein extracts of apparent acrosomal origin and a tail extract. The extracts were analysed by SDS-PAGE under reducing conditions. Several prominent polypeptide bands (45, 38 and 33 kDa) appeared common to both acrosomal extracts. Antiserum raised against the 33 kDa polypeptide from the inner acrosomal membrane matrix (IAMM) extract showed immunoreactivity with 45, 38 and 33 kDa polypeptides in both acrosomal extracts, indicating that the 33 kDa polypeptide was related to the proteins in the 45 and 38 kDa bands. Therefore, the antiserum was used as a molecular probe. Indirect immuno-fluorescence indicated that the acrosome was the major location of the 33 kDa polypeptide. This contention was confirmed by ultrastructural study: immunogold labelling indicated that the 33 kDa polypeptide associated with acrosomal matrix components throughout acrosomal development in the testes and throughout post-testicular maturation in the epididymis. The label clearly delineated the changing morphology of the maturing marsupial acrosome. This is the first study to use immunocytochemical techniques to chart testicular and post-testicular development of any sperm organelle in a marsupial. As a result of this study, a 33 kDa molecular marker of marsupial acrosome differentiation and maturation has been identified. It may be possible to chart similar events in other marsupial species and identify opportunities for manipulating fertility. PMID:10645248

Wade, M A; Lin, M

1999-09-01

314

Immunologic Studies in Sarcoidosis.  

National Technical Information Service (NTIS)

Studies have been concerned with investigating immunologic function in sarcoidosis, specifically mechanisms related to hypergammaglobulinemia. The studies indicate that in vitro incubation of peripheral blood mononuclear cells (PBMC) from approximately on...

J. D. Stobo

1977-01-01

315

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

316

Immunology Devices Panel  

Center for Biologics Evaluation and Research (CBER)

... of marketed and investigational in vitro devices for use in clinical laboratory medicine including oncology, immunology, and allergy and makes ... More results from www.fda.gov/advisorycommittees/committeesmeetingmaterials/medicaldevices

317

Immunology Taught by Humans  

PubMed Central

After a half-century of mouse-dominated research, human immunology is making a comeback. Informed by mouse studies and powered by new techniques, human immune research is both advancing disease treatment and providing new insights into basic biology.

Davis, Mark M.

2013-01-01

318

Immunology of pregnancy  

Microsoft Academic Search

Pregnancy is a unique event in which a genetically and immunologically foreign fetus usually survives to full term without\\u000a apparent rejection by the mother's immune system. Over the past decade, more information has been gathered to provide insight\\u000a into the complex immunological mechanisms that allow the fetus to grow and survive in most cases. Whereas the maternal-fetal\\u000a interface was once

Jill A. Poole; Henry N. Claman

2004-01-01

319

IMMUNOLOGIC INCOMPETENCE OF IMMUNOLOGICALLY RUNTED ANIMALS  

PubMed Central

1. Adult (A x C57Bl/1)F1 hybrids regularly show runt disease when injected with adult spleen cells from A strain donors. This also occurs when A strain spleen cells are administered to adult C3H mice made tolerant of A strain tissue in the neonatal period. 2. Mice undergoing the graft versus host reaction fail to form antibodies to an intraperitoneal challenge of T2 bacteriophage. This phenomenon was observed well before any of the other overt signs of runting had occurred. Further, inhibition of antibody production to T2 phage by graft versus host reaction initiated at an interval following antigenic stimulation is demonstrated. 3. The basis for the immunologic incompetence of the host with respect to T2 phage is presumed to be the attack of immunologically competent donor cells on the lymphoid cells of the recipient. 4. The failure of the injected parent strain cells to respond to the antigen used may imply immunologic commitment of these cells.

Blaese, R. Michael; Martinez, Carlos; Good, Robert A.

1964-01-01

320

Immunological methods of component selection and recovery  

US Patent & Trademark Office Database

The invention involves an immunological method of separating specifically-targeted cells or molecular structures from a mixed population under conditions which minimize damage to the cellular structure or the molecular integrity. The method is based upon the specific interaction of a label and an antibody directed against the label and the ability of a competitor to inhibit the interaction between the label and the antibody.

Lund; Garry (Edmonton, CA); Wegmann, deceased; Thomas (late of Edmonton, CA); Mosmann; Timothy (Edmonton, CA)

1996-05-21

321

Prognostic value of molecular markers and cytogenetic alterations that characterize breast cancer precursor lesions (Review)  

PubMed Central

The understanding of the molecular mechanisms that underlie all stages of tumor progression in breast cancer (BC) represents an important goal in the biomedical research of this disease, particularly for the identification of more specific targeted therapies. In this context, BC preinvasive and precursor lesions represent a major dilemma. These lesions are well characterized under the phenotypic and genotypic profile, but it is not clear if they represent obligatory passages of a multistep process determining breast cancer evolution. In fact, the numerous cytogenetic and molecular alterations identified are not always representative of the progression into invasive phenotypes.

DI BONITO, MAURIZIO; CANTILE, MONICA; DE CECIO, ROSSELLA; LIGUORI, GIUSEPPINA; BOTTI, GERARDO

2013-01-01

322

Low molecular weight proteinuria in diabetic children--a marker of early diabetic nephropathy?  

PubMed

Twenty-four hour urine specimens of 67 diabetic children aged 1-17 years without any renal manifestations were examined by SDS-polyacrylamide gel electrophoresis (SDS-PAGE). The excretion of high molecular weight, i.e. glomerular proteins was compared to that of low molecular weight, i.e. tubular proteins corresponding to more or less than 68,000 daltons. The glomerulo-tubular protein ratio (GTPR) obtained was significantly lower in diabetic patients compared with 30 healthy children of the same age and showed a linear decrease with longer duration of diabetes. PMID:3991556

Wartha, R; Nebinger, D; Gekle, D

1985-01-01

323

Chromosomal regions associated with segregation distortion of molecular markers in F 2 ?, backcross, doubled haploid, and recombinant inbred populations in rice ( Oryza sativa L.)  

Microsoft Academic Search

Chromosomal regions associated with marker segregation distortion in rice were compared based on six molecular linkage maps.\\u000a Mapping populations were derived from one interspecific backcross and five intersubspecific (indica?\\/?japonica) crosses, including two F2 populations, two doubled haploid (DH) populations, and one recombinant inbred (RI) population. Mapping data for each population\\u000a consisted of 129–629 markers. Segregation distortion was determined based on

Y. Xu; L. Zhu; J. Xiao; N. Huang; S. R. McCouch

1997-01-01

324

Associations between anther-culture response and molecular markers on chromosomes 2H, 3H and 4H of barley (Hordeum vulgare L.)  

Microsoft Academic Search

Segregation distortion is a common phenomenon among anther-culture-derived plants and it has been suggested that the distorted\\u000a areas may contain genes affecting survival in anther-culture. Segregation of 111 markers was checked in an androgenetic barley\\u000a (Hordeum vulgare L.) progeny and a linkage map was constructed. Thirty one progeny lines were tested for their anther-culture ability and\\u000a associations between molecular markers

Outi M. Manninen

2000-01-01

325

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

Microsoft Academic Search

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

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

2009-01-01

326

Immunological and molecular analysis of B lymphocytes in low-grade MALT lymphoma of the stomach. Are there any useful markers for predicting outcome after Helicobacter pylori eradication?  

Microsoft Academic Search

Background:\\u000a Background:   Although Helicobacter pylori eradication is effective in treating low-grade gastric mucosa-associated lymphoid tissue (MALT) lymphoma, the condition in\\u000a some patients deteriorates even after the eradication. Therefore, it is important to predict the disease outcome before starting\\u000a H. pylori eradication. We investigated the usefulness of flow cytometry, quantifying CD19- and CD20-positive B lymphocytes in MALT lymphoma\\u000a tissue, for predicting

Yumi Matsushima; Yoshikazu Kinoshita; Hirokazu Fukui; Toru Maekawa; Shujiro Yazumi; Akihiko Okada; Hiroshi Nakase; Chiharu Kawanami; Masahiro Iwano; Kimio Hashimoto; Zenju Takeda; Kazuichi Okazaki; Tsutomu Chiba

2002-01-01

327

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

328

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

2012-12-04

329

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

2012-05-18

330

Identification of Paramecium bursaria syngens through molecular markers--comparative analysis of three loci in the nuclear and mitochondrial DNA.  

PubMed

This is the first attempt to resolve the phylogenetic relationship between different syngens of Paramecium bursaria and to investigate at a molecular level the intraspecific differentiation of strains originating from very distant geographical locations. Herein we introduce a new collection of five P. bursaria syngens maintained at St Petersburg State University, as the international collection of syngens was lost in the 1960s. To analyze the degree of speciation within Paramecium bursaria, we examined 26 strains belonging to five different syngens from distant and geographically isolated localities using rDNA (ITS1-5.8S-ITS2-5'LSU) fragments, mitochondrial cytochrome c oxidase subunit I (COI), and H4 gene fragments. It was shown that P. bursaria strains of the same syngens cluster together in all three inferred molecular phylogenies. The genetic diversity among the studied P. bursaria strains based on rDNA sequences was rather low. The COI divergence of Paramecium bursaria was also definitely lower than that observed in the Paramecium aurelia complex. The nucleotide sequences of the H4 gene analyzed in the present study indicate the extent of genetic differences between the syngens of Paramecium bursaria. Our study demonstrates the diagnostic value of molecular markers, which are important tools in the identification of Paramecium bursaria syngens. PMID:22154394

Greczek-Stachura, Magdalena; Potekhin, Alexey; Przybo?, Ewa; Rautian, Maria; Skoblo, Inna; Tarcz, Sebastian

2011-12-09

331

Molecular typing of wine yeast strains Saccharomyces bayanus var. uvarum using microsatellite markers  

Microsoft Academic Search

The Saccharomyces bayanus var. uvarum yeasts are associated with spontaneous fermentation of must. Some strains were shown to be enological yeasts of interest in different winemaking processes. The molecular typing of S. bayanus var. uvarum at the strain level has become significant for wine microbiologists. Four microsatellite loci were defined from the exploration of genomic DNA sequence of S. bayanus

I. Masneuf-Pomarède; C. Le Jeune; P. Durrens; M. Lollier; M. Aigle; D. Dubourdieu

2007-01-01

332

Required techniques and useful molecular markers in the neuropathologic diagnosis of neurodegenerative diseases  

Microsoft Academic Search

Modern neuropathologic methods and molecular biology have lead to increased understanding of neurodegenerative disorders and biologically based classifications of these disorders. The purpose of this review is to discuss neuropathologic methods that are useful in the characterization of neurodegenerative disorders, with emphasis on disorders of late life that present with dementia or movement disorders. A diagnostic algorithm is suggested for

Dennis W. Dickson

2005-01-01

333

Evolutionary dynamics of molecular markers during local adaptation: a case study in Drosophila subobscura  

Microsoft Academic Search

BACKGROUND: Natural selection and genetic drift are major forces responsible for temporal genetic changes in populations. Furthermore, these evolutionary forces may interact with each other. Here we study the impact of an ongoing adaptive process at the molecular genetic level by analyzing the temporal genetic changes throughout 40 generations of adaptation to a common laboratory environment. Specifically, genetic variability, population

Pedro Simões; Marta Pascual; Josiane Santos; Michael R Rose; Margarida Matos

2008-01-01

334

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

335

Upregulation of HMGA2 in thyroid carcinomas: a novel molecular marker to distinguish between benign and malignant follicular neoplasias.  

PubMed

The identification of molecular markers allowing to differentiate between benign and malignant thyroid tumors remains a diagnostic challenge. Herein, we have used the expression of the high mobility group protein gene HMGA2 and its protein, respectively, as a possible marker detecting malignant growth of thyroid tumors. HMGA2 belongs to the high mobility group proteins, i.e. small, highly charged DNA-binding proteins. While HMGA2 is highly expressed in most embryonic tissues, its expression in adult tissues is very low. However, a reactivation of HMGA2 expression has been described for various malignant tumors and often correlates with the aggressiveness of the tumors. The aim of this study was to investigate whether the HMGA2 expression can be used to detect malignant thyroid tumors. RNA from 64 formalin-fixed paraffin-embedded thyroid tissues including normal tissue (n = 3), thyroiditis (n = 2), and follicular adenomas (n = 19) as well as follicular (n = 9), papillary (n = 28), and anaplastic (n = 3) carcinomas was reverse transcribed. Finally, real-time quantitative RT-PCR was performed. Expression differences of up to 400-fold were detected between benign and malignant thyroid tumors. Based on HMGA2 expression alone, it was possible to distinguish between benign and malignant thyroid tissues with a sensitivity of 95.9% and a specificity of 93.9%. There was a highly significant (P < 0.001) difference with histology of the tumors being the gold standard between the benign lesions and malignant tumors. Our results show that even as a stand-alone marker HMGA2 expression has a high potential to improve diagnoses of follicular neoplasms of the thyroid. PMID:17943974

Belge, Gazanfer; Meyer, Anke; Klemke, Markus; Burchardt, Käte; Stern, Corinna; Wosniok, Werner; Loeschke, Siegfried; Bullerdiek, Jörn

2008-01-01

336

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

2010-10-20

337

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

PubMed

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

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

2006-09-01

338

Genetic diversity of Cercospora kikuchii isolates from soybean cultured in Argentina as revealed by molecular markers and cercosporin production.  

PubMed

Leaf blight and purple seed, caused by the fungal pathogen Cercospora kikuchii (Matsumoto & Tomoyasu) M. W. Gardner are very important diseases of soybean (Glycine max L. Merr.) in Argentina. The aims of this work were: (a) to confirm and to assess the genetic variability among C. kikuchii isolates collected from different soybean growing areas in Santa Fe province using inter simple sequence repeats (ISSR) markers and sequence information from the internal transcribed spacer (ITS) region of rDNA and (b) to analyze the cercosporin production of the regional C. kikuchi isolates in order to assess whether there was any relationship between the molecular profiles and the toxin production. Isolates from different regions in Santa Fe province were studied. The sequence of the ITS regions showed high similarity (99-100%) to the GenBank sequences of C. kikuchii BRCK179 (accession number AY633838). The ISSR markers clustered all the isolates into many groups and cercosporin content was highly variable among isolates. No relationship was observed between ITS region, ISSR groups and origin or cercosporin content. The high degree of genetic variability and cercosporin production among isolates compared in this study characterizes a diverse population of C. kikuchii in the region. PMID:20835913

Lurá, María Cristina; Latorre Rapela, María Gabriela; Vaccari, María Celia; Maumary, Roxana; Soldano, Anabel; Mattio, Mónica; González, Ana María

2010-09-12

339

Lunx Is a Superior Molecular Marker for Detection of Non-Small Lung Cell Cancer in Peripheral Blood  

PubMed Central

The clinical management of non-small cell lung cancer (NSCLC) would benefit greatly by a test that was able to detect small amounts of NSCLC in the peripheral blood. In this report, we used a novel strategy to enrich tumor cells from the peripheral blood of 24 stage I to IV NSCLC patients and determined expression levels for six cancer-associated genes (lunx, muc1, KS1/4, CEA, CK19, and PSE). Using thresholds established at three standard deviations above the mean observed in 15 normal controls, we observed that lunx (10 of 24, 42%), muc1 (5 of 24, 21%), and CK19 (5 of 24, 21%) were overexpressed in 14 of 24 (58%) peripheral blood samples obtained from NSCLC patients. Patients who overexpressed either KS1/4 (n = 2) or PSE (n = 1) also overexpressed either lunx or muc1. Of patients with presumed curable and resectable stage I to II disease (n = 7), at least one marker was overexpressed in three (43%) patients. In advanced stage III to IV patients (n = 17), at least one marker was overexpressed in 11 patients (65%). These results provide evidence that circulating tumor cells can be detected in NSCLC patients by a high throughput molecular technique. Further studies are needed to determine the clinical relevance of gene overexpression.

Mitas, Michael; Hoover, Loretta; Silvestri, Gerard; Reed, Carolyn; Green, Mark; Turrisi, Andrew T.; Sherman, Carol; Mikhitarian, Kaidi; Cole, David J.; Block, Mark I.; Gillanders, William E.

2003-01-01

340

An enhanced molecular marker based genetic map of perennial ryegrass (Lolium perenne) reveals comparative relationships with other Poaceae genomes.  

PubMed

A molecular-marker linkage map has been constructed for perennial ryegrass (Lolium perenne L.) using a one-way pseudo-testcross population based on the mating of a multiple heterozygous individual with a doubled haploid genotype. RFLP, AFLP, isoenzyme, and EST data from four collaborating laboratories within the International Lolium Genome Initiative were combined to produce an integrated genetic map containing 240 loci covering 811 cM on seven linkage groups. The map contained 124 codominant markers, of which 109 were heterologous anchor RFLP probes from wheat, barley, oat, and rice, allowing comparative relationships between perennial ryegrass and other Poaceae species to be inferred. The genetic maps of perennial ryegrass and the Triticeae cereals are highly conserved in terms of synteny and colinearity. This observation was supported by the general agreement of the syntenic relationships between perennial ryegrass, oat, and rice and those between the Triticeae and these species. A lower level of synteny and colinearity was observed between perennial ryegrass and oat compared with the Triticeae, despite the closer taxonomic affinity between these species. It is proposed that the linkage groups of perennial ryegrass be numbered in accordance with these syntenic relationships, to correspond to the homoeologous groups of the Triticeae cereals. PMID:11962626

Jones, Elizabeth S; Mahoney, Natalia L; Hayward, Michael D; Armstead, Ian P; Jones, J Gilbert; Humphreys, Mervyn O; King, Ian P; Kishida, Tsugutoshi; Yamada, Toshihiko; Balfourier, François; Charmet, Gilles; Forster, John W

2002-04-01

341

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

PubMed Central

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

2011-01-01

342

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

343

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

2011-11-04

344

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

345

Molecular epidemiology and virulence markers of Salmonella Infantis isolated over 25years in São Paulo State, Brazil.  

PubMed

Infection of humans and animals caused by Salmonella is a major public health problem worldwide. Among the more than 2500 serovars, S. Infantis has been one of the 15 most isolated serovars in the world. Despite its clinical importance, little is known about the molecular characteristics of S. Infantis strains from Brazil. The aims of this study were to type S. Infantis isolates of this country and to assess their pathogenic potential. The molecular epidemiology of 35 S. Infantis strains, isolated from human sources (25) and food items (10) between 1984 and 2009 in São Paulo State, Brazil, were investigated using ERIC-PCR, PFGE and MLST. Furthermore, the presence of some virulence markers from Salmonella pathogenicity islands (SPIs) SPI-1 and SPI-2 and from the virulence plasmid was assessed by PCR. Using ERIC-PCR, 34 S. Infantis strains exhibited a high genetic similarity (?93.7%) and using PFGE, 32 strains exhibited a similarity ?80.6%. Additionally, MLST showed a high clonal similarity among strains that all presented the same ST32. Thirty-two isolates under investigation contained the virulence markers invA, sopB, sopD, sipA, sipD, ssaR, sifA, flgK, fljB and flgL. In conclusion, the S. Infantis strains studied were genetically similar, suggesting that a prevalent subtype has been causing disease and food contamination during a 25year period in São Paulo State, an important metropolitan region in Brazil. Furthermore, the contamination between strains from food items and sick humans indicates that better control measures for S. Infantis may be needed in this country. PMID:23860124

Almeida, Fernanda; Pitondo-Silva, André; Oliveira, Maria Aparecida; Falcão, Juliana Pfrimer

2013-07-13

346

The usefulness of molecular techniques to assess the presence of Aeromonas spp. harboring virulence markers in foods.  

PubMed

A total of 78 raw and 123 processed and ready-to-eat retail food samples were used to assess the presence of motile Aeromonas spp. harboring virulence genes (cytotoxic enterotoxin and hemolysin genes) using a recently described PCR method in comparison with the conventional cultivation method based on the use of Ampicillin-Dextrin Agar (ADA) medium. With the ADA-based method, 65/201 (32.3%) samples showed presumptive Aeromonas spp. colonies whereas the PCR method revealed the presence of Aeromonas spp. harboring the targeted virulence genes in 51/201 (25.4%) of the tested samples. The rate of contaminated samples and the presence of pathogenic Aeromonas were significantly lower with both methods for processed than in case of raw samples. A polyphasic identification approach including biochemical and molecular techniques was applied to a selection of 34 PCR-positive presumptive Aeromonas isolates. Following fatty acid methyl ester (FAME) analysis and amplified fragment length polymorphism (AFLP) fingerprinting, a total of 33 isolates (97%) could be identified to the DNA hybridization group (HG) level. The majority of these isolates belonged to the species Aeromonas hydrophila HG3 (50%) and Aeromonas veronii biovar sobria (HG8/10) (38%). Molecular characterization of PCR amplicons obtained from these strains by PCR-Restriction Fragment Length Polymorphism (PCR-RFLP) fingerprinting and PCR-Amplicon Sequence Analysis (PCR-ASA) allowed classification of all strains in a known PCR-RFLP and PCR-ASA type. In conclusion, the current findings demonstrate that the combined use of PCR-based virulence marker detection, PCR-RFLP and PCR-ASA offers a rapid, sensitive, and specific system to assess the presence and prevalence of Aeromonas spp. harboring virulence markers in food samples. PMID:15193799

Bin Kingombe, César I; Huys, Geert; Howald, Denise; Luthi, Elisabeth; Swings, Jean; Jemmi, Thomas

2004-07-15

347

Major molecular markers in pancreatic ductal adenocarcinoma and their roles in screening, diagnosis, prognosis, and treatment.  

PubMed

Pancreatic cancer is notorious for its late presentation, early and aggressive local invasion, metastatic potential, and poor outcome. It presents at a clinically advanced stage that precludes the possibility of surgical resection in most cases and shows constitutive resistance to chemotherapy and radiotherapy in others. As a result, mortality from this disease parallels its incidence rates.Recent breakthroughs in the molecular biology of pancreatic cancer have assisted in translational research, giving hope for individualized therapy and better disease management. Molecular biology tools are guiding early diagnosis, the assessment of prognosis, and isolation of novel, more effective therapeutic targets.This review discusses the signature mutations of pancreatic cancer, implications of these mutations to pancreatic cancer biology, their linked pathways, and recent advances in their understanding as biomarkers as diagnostic, prognostic, and therapeutic tools in dealing with this disease. PMID:21673535

Singh, Puneet; Srinivasan, Radhika; Wig, Jai Dev

2011-07-01

348

Uses of molecular markers for understanding modern and historical ecosystems (Invited)  

NASA Astrophysics Data System (ADS)

Information on current and historical population sizes and movements is important for understanding many aspects of ecosystem ecology such as responses to climate change. Such information can be surprisingly difficult to acquire, but can be estimated from clues contained in an organism’s DNA. Recent revolutions in molecular genetics, including direct sequencing and efficient mutation-detection methods, enable extraction of sequence information from even very small or ancient specimens. Furthermore, theoretical advances such as coalescent theory and molecular assignments are providing powerful tools to unlock secrets about changes in numbers, distributions and movements. Combination of these approaches with other types of data promises to provide especially useful insights into modern and paleoecosystems. I will provide examples of these applications from recent studies in ornithology.

Friesen, V. L.

2010-12-01

349

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

350

Molecular breeding in the genus Musa: a strong case for STMS marker technology  

Microsoft Academic Search

Musa species are among the tallest monocotyledons and include major food-producing species. The principal cultivars, derived\\u000a from two major species Musa acuminata (‘A’ genome) and Musa balbisiana (‘B’ genome), are polyploid hybrids (mainly AAA, AAB\\u000a and ABB triploids), medium to highly sterile, parthenocarpic and clonally propagated. Bananas and plantains are crops to which\\u000a molecular breeding is expected to have a

D. Kaemmer; D. Fischer; R. L. Jarret; F.-C. Baurens; A. Grapin; D. Dambier; J.-L. Noyer; C. Lanaud; G. Kahl; P. J. L. Lagoda

1997-01-01

351

Molecular and genetic markers of follicular-cell thyroid cancer: etiology and diagnostic and therapeutic opportunities.  

PubMed

Thyroid cancer has an increasing incidence in the US population and worldwide, with 95% of the cancers being of follicular cell origin-papillary, follicular, or anaplastic thyroid carcinomas. Both follicular and papillary thyroid cancers portend good survival rates, with estimated 5-year survival amongst differentiated thyroid cancer approaching 97%. On the other hand, the median survival for a patient with anaplastic thyroid carcinoma is measured in months. Despite the optimistic survival rates for papillary and follicular thyroid carcinoma, a subset of this population demonstrates resistance to radioactive iodine, and a proclivity for more aggressive tumors with higher rates of recurrence and metastasis.As there is an increased understanding of the molecular etiology of thyroid cancer, there is also a new interest in alternative treatment methods for those nonresponsive to typical treatment. Multiple signaling pathways have been identified, including the mitogen activated protein kinase pathway, as crucial to thyroid tumor formation and progression. Additionally, particular oncogenes have been identified as prevalent in anaplastic thyroid carcinoma and thought to be involved in the transformation from differentiated to anaplastic histology.We review the current literature and evidence describing the molecular and genetic etiology of non-medullary (follicular cell derived) thyroid carcinomas including papillary, follicular, and anaplastic thyroid carcinoma. Additionally, we evaluate the current literature on emerging and established therapies of molecular and genetic targets in these cancers. PMID:23288646

Goyal, Neerav; Setabutr, Dhave; Abdulghani, Junaid; Goldenberg, David

2013-01-01

352

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

PubMed

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

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

2011-08-04

353

Immunological memory is associative  

SciTech Connect

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

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

1996-12-31

354

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

PubMed

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

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

2012-05-01

355

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

356

Molecular characterization of Syrian date palm cultivars using plasmid-like DNA markers.  

PubMed

Date palm (Phoenix dactylifera L.) is one of the most important domesticated fruit trees in the Near East and North African countries. This tree has been, for several decades, in serious threat of being completely destroyed by the "Bayoud" disease caused by Fusarium oxysporum f. sp. albedinis. In this study, 18 Syrian date palm cultivars and four male trees were analyzed according to the identity of mitochondrial plasmid-like DNAs. A PCR strategy that employs plasmid-like DNAs-specific primer pair was used. These primers amplify a product of either 373-bp or 265-bp that corresponds to the S-(Bayoud-susceptible) or the R-plasmid (Bayoud-resistant), respectively. Generated data revealed that only six cultivars ('Medjool', 'Ashrasi', 'Gish Rabi', 'Khineze', and yellow- and red-'Kabkab') have the S-plasmid, suggesting their susceptibility to the fusariosis, while the remaining 12 cultivars and the four male trees contain the R-plasmid, suggesting their resistance to the fusariosis. The PCR process applied here has been proved efficient for the rapid screening for the presence of the S and R DNAs in Syrian date palm. PCR markers developed in this study could be useful for the screening of date palm lines growing in the field. The availability of such diagnostic tool for plasmid characterization in date palm would also be of great importance in establishing propagation and breeding programs of date palm in Syria. PMID:22568006

Haider, N; Nabulsi, I

2012-02-01

357

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

2012-05-02

358

Melanoma antigen gene family A as a molecular marker of gastric and colorectal cancers.  

PubMed

The present study aimed to evaluate the role of melanoma antigen family A (MAGEA) in gastric and colorectal cancer cell lines and clinical tissue samples. we used 10 gastric and 9 colorectal cancer cell lines, 20 early-stage and 21 advanced-stage gastric cancer tissues, 20 colon adenomas and 19 colorectal cancer tissues. Real-time RT-PCR assay was used for the determination of MAGEA mRNA levels. Western blot analysis and immunohistochemistry were used for the determination of MAGEA protein levels in cell lines and tissues, respectively. Gastric and colorectal cancer cell lines showed variable mRNA expression levels of MAGEA. The MAGEA protein was detected in 30% of gastric cancer cell lines and in 22.2% of colorectal cancer cell lines. There was a high correlation between mRNA and protein expression. Regarding the clinical samples, MAGEA expression was noted in 25, 28.6 and 31.6%, respectively in early-stage, advanced-stage gastric cancer tissues and colon adenocarcinoma, but was negative in the adjacent normal tissues of the stomach and colon as well as colon adenoma. These results indicate that MAGEA is involved in the carcinogenesis of gastric and colorectal cancer and, therefore, can be used as a diagnostic marker to predict these cancers. PMID:23673898

Lee, Tae-Bum; Lim, Sung-Chul; Moon, Young-Sook; Choi, Cheol-Hee

2013-05-14

359

Genetic diversity and molecular markers in introduced and Thai native apple snails (Pomacea and Pila).  

PubMed

The genetic diversity and species-diagnostic markers in the introduced apple snail, Pomacea canaliculata and in the native Thai apple snails; Pila ampullacea, P. angelica, P. pesmei, and P. polita, were investigated by restriction analysis of COI and are reported for the first time. Twenty-one composite haplotypes showing non-overlapping distributions among species were found. Genetic heterogeneity analysis indicated significant differences between species (P < 0.0001) and within P. pesmei (P < 0.0001) and P. angelica (P < 0.0004). No such heterogeneity was observed in Pomacea canaliculata (P > 0.0036 as modified by the Bonferroni procedure), P. ampullacea (P = 0.0824-1.000) and P. polita (P = 1.0000). A neighbor-joining tree based on genetic distance between pairs of composite haplotypes differentiated all species and indicated that P. angelica and P. pesmei are closely related phylogenetically. In addition, the 16S rDNA of these species was cloned and sequenced. A species-specific PCR for P. canaliculata was successfully developed with a sensitivity of detection of approximately 50 pg of the target DNA template. The amplification of genomic DNA (50 pg and 25 ng) isolated from the fertilized eggs, and juveniles (1, 7, and 15 d after hatching) of Pomacea canaliculata was also successful, and suggested that Pomacea canaliculata and Pila species can be discriminated from the early stages of development. PMID:15469739

Thaewnon-ngiw, Bungorn; Klinbunga, Sirawut; Phanwichien, Kantimanee; Sangduen, Nitsri; Lauhachinda, Nitaya; Menasveta, Piamsak

2004-07-31

360

Molecular typing of, and distribution of genetic markers among, Burkholderia cepacia complex isolates from Brazil.  

PubMed

PCR tests were used to assign genomovar status to 39 non-cystic fibrosis (non-CF) and 11 CF Burkholderia cepacia complex isolates from patients in hospitals in Recife, Brazil. Non-CF isolates were assigned to genomovar IIIA (71.8%), genomovar I (15.4%), B. vietnamiensis (7.7%), and B. multivorans (5.1%). CF isolates were assigned to genomovar IIIA (18.2%), B. vietnamiensis (18.2%), and genomovar I (9.1%). Six CF isolates sharing recA PCR-restriction fragment length polymorphism (RFLP) and randomly amplified polymorphic DNA (RAPD) patterns could not be assigned to a genomovar. 16S rDNA sequence obtained from these isolates indicated a closest relationship to B. anthina, but the recA sequence was equally divergent from several genomovars. PCR screening indicated the presence of cblA in only two isolates, whereas the B. cepacia epidemic strain marker was found in 22 of 28 genomovar IIIA isolates. A type III secretion gene was detected in all but genomovar I isolates. RAPD and PCR-RFLP assays, targeting both recA and fliC, indicated a large amount of genetic variability among the isolates, with many novel patterns being observed. Nine genomovar IIIA isolates from different non-CF patients and clinical sources had identical genotypes, indicating the presence of a common clone. PMID:12958239

Detsika, Maria G; Corkill, John E; Magalhães, Marcelo; Glendinning, Kerry J; Hart, C Anthony; Winstanley, Craig

2003-09-01

361

Molecular Typing of, and Distribution of Genetic Markers among, Burkholderia cepacia Complex Isolates from Brazil  

PubMed Central

PCR tests were used to assign genomovar status to 39 non-cystic fibrosis (non-CF) and 11 CF Burkholderia cepacia complex isolates from patients in hospitals in Recife, Brazil. Non-CF isolates were assigned to genomovar IIIA (71.8%), genomovar I (15.4%), B. vietnamiensis (7.7%), and B. multivorans (5.1%). CF isolates were assigned to genomovar IIIA (18.2%), B. vietnamiensis (18.2%), and genomovar I (9.1%). Six CF isolates sharing recA PCR-restriction fragment length polymorphism (RFLP) and randomly amplified polymorphic DNA (RAPD) patterns could not be assigned to a genomovar. 16S rDNA sequence obtained from these isolates indicated a closest relationship to B. anthina, but the recA sequence was equally divergent from several genomovars. PCR screening indicated the presence of cblA in only two isolates, whereas the B. cepacia epidemic strain marker was found in 22 of 28 genomovar IIIA isolates. A type III secretion gene was detected in all but genomovar I isolates. RAPD and PCR-RFLP assays, targeting both recA and fliC, indicated a large amount of genetic variability among the isolates, with many novel patterns being observed. Nine genomovar IIIA isolates from different non-CF patients and clinical sources had identical genotypes, indicating the presence of a common clone.

Detsika, Maria G.; Corkill, John E.; Magalhaes, Marcelo; Glendinning, Kerry J.; Hart, C. Anthony; Winstanley, Craig

2003-01-01

362

Inheritance and identification of molecular markers associated with a novel dwarfing gene in barley  

PubMed Central

Background Dwarfing genes have widely been used in barley breeding program. More than 30 types of dwarfs or semidwarfs have been reported, but a few has been exploited in barley breeding because pleiotropic effects of dwarfing genes cause some undesired traits. The plant architecture of newly discovered dwarfing germplasm "Huaai 11" consisted of desirable agronomic traits such as shortened stature and early maturity. Genetic factor controlling the plant height in dwarf line Huaai 11 was investigated. Results The Huaai 11 was crossed with tall varieties Monker, Mpyt, Zhenongda 3, Zaoshu 3, Advance, Huadamai 1, Huadamai 6, Hyproly and Ris01508. All the F1 plants displayed tall trait. Both tall and dwarf plants appeared in all the F2 populations with a 3:1 segregation ratio, suggesting that dwarfism of Huaai 11 is controlled by a single recessive gene, btwd1. Allelism test indicated that this dwarfing gene in the Huaai 11 is nonallelic with the gene br, uzu, sdw1 and denso. Using a double haploid population derived from a cross of Huadamai 6 and Huaai 11 and SSR markers the novel dwarfing gene was mapped onto the long arm of chromosome 7H, and closely linked to Bmac031 and Bmac167 with genetic distance of 2.2 cM. Conclusion Huaai 11 is a new source of dwarf for broadening the genetic base of dwarfism. This dwarf source was controlled by a recessive dwarfing gene btwd1, was mapped onto the long arm of chromosome 7H.

2010-01-01

363

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

364

New Molecular Markers for the Distal End of the T-Complex and Their Relationships to Mutations Affecting Mouse Development  

PubMed Central

Many mutations affecting mouse development have been mapped to the t-complex of mouse chromosome 17. We have obtained 17 cosmid clones as molecular markers for this region by screening a hamster-mouse chromosome 17 and 18 cell hybrid cosmid library with mouse-specific repetitive elements and mapping positive clones via t-haplotype vs. C3H restriction fragment length polymorphism (RFLP) analysis. Twelve of the clones mapping distal to Leh66B in t-haplotypes are described here. Using standard RFLP analysis or simple sequence length polymorphism between t-haplotypes, exceptional partial t-haplotypes and nested sets of inter-t-haplotype recombinants, five cosmids have been mapped in or around In(17)3 and seven in the most distal inversion In17(4). More precise mapping of four of the cosmids from In(17)4 shows that they will be useful in the molecular identification of some of the recessive lethals mapped to the t-complex: two cosmids map between H-2K and Crya-1, setting a distal limit in t-haplotypes for the position of the t(w5) lethal, one is inseparable from the t(w12) lethal, and one maps distal to tf near the t(0)(t(6)) lethal and cld.

Ebersole, T.; Lai, F.; Artzt, K.

1992-01-01

365

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

PubMed

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

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

2010-12-01

366

Current therapeutic options and novel molecular markers in skull base chordomas.  

PubMed

Chordomas are extremely rare tumours. They arise in the spheno-occipital region in 35% of cases. Chordomas usually present benign histopathological features but often exhibit a malignant clinical behaviour. Radical surgical removal and high-dose radiation therapy seem to be effective in tumour control and to improve survival rate. Despite the advancements in microsurgical techniques and the development of radiation therapies, clival chordomas still represent a challenge. Nevertheless it appears that chordomas that have been resected to the same extent and that received post-operative radiotherapy might exhibit different rates of regrowth. This result supports the hypothesis that the recurrence rate of chordomas might be dependent on biological variables other than the extent of resection and the post-operative radiotherapy. Genetic and molecular studies on oncogenesis of chordomas are still limited, but they represent the basis for the development of molecular targeted therapies. We present a review of the current knowledge about skull base chordomas biology, therapeutic options and related clinical outcome. PMID:22006091

Gagliardi, Filippo; Boari, Nicola; Riva, Paola; Mortini, Pietro

2011-10-18

367

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

PubMed

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

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

2012-06-04

368

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

369

Circulating cell-free DNA: an up-coming molecular marker in exercise physiology.  

PubMed

The phenomenon of circulating cell-free DNA (cfDNA) concentrations is of importance for many biomedical disciplines including the field of exercise physiology. Increases of cfDNA due to exercise are described to be a potential hallmark for the overtraining syndrome and might be related to, or trigger adaptations of, immune function induced by strenuous exercise. At the same time, exercise provides a practicable model for studying the phenomenon of cfDNA that is described to be of pathophysiological relevance for different topics in clinical medicine like autoimmune diseases and cancer. In this review, we are summarizing the current knowledge of exercise-based acute and chronic alterations in cfDNA levels and their physiological significance. The effects of acute exercise on cfDNA concentrations have been investigated in resistance exercises and in continuous, stepwise and interval endurance exercises of different durations. cfDNA concentrations peaked immediately after acute exercise and showed a rapid return to baseline levels. Typical markers of skeletal muscle damage (creatine kinase, uric acid, C-reactive protein) show delayed kinetics compared with the cfDNA peak response. Exercise parameters such as intensity, duration or average energy expenditure do not explain the extent of increasing cfDNA concentrations after strenuous exercise. This could be due to complex processes inside the human organism during and after physical activity. Therefore, we hypothesize composite effects of different physiological stress parameters that come along with exercise to be responsible for increasing cfDNA concentrations. We suggest that due to acute stress, cfDNA levels increase rapidly by a spontaneous active or passive release mechanism that is not yet known. As a result of the rapid and parallel increase of cfDNA and lactate in an incremental treadmill test leading to exhaustion within 15-20 minutes, it is unlikely that cfDNA is released into the plasma by typical necrosis or apoptosis of cells in acute exercise settings. Recently, rapid DNA release mechanisms of activated immune-competent cells like NETosis (pathogen-induced cell death including the release of neutrophil extracellular traps [NETs]) have been discovered. cfDNA accumulations might comprise a similar kind of cell death including trap formation or an active release of cfDNA. Just like chronic diseases, chronic high-intensity resistance training protocols induced persistent increases of cfDNA levels. Chronic, strenuous exercise protocols, either long-duration endurance exercise or regular high-intensity workouts, induce chronic inflammation that might lead to a slow, constant release of DNA. This could be due to mechanisms of cell death like apoptosis or necrosis. Yet, it has neither been implicated nor proven sufficiently whether cfDNA can serve as a marker for overtraining. The relevance of cfDNA with regard to overtraining status, performance level, and the degree of physical exhaustion still remains unclear. Longitudinal studies are required that take into account standardized and controlled exercise, serial blood sampling, and large and homogeneous cohorts of different athletic achievement. Furthermore, it is important to establish standardized laboratory procedures for the measurement of genomic cfDNA concentrations by quantitative real-time polymerase chain reaction (PCR). We introduce a new hypothesis based on acute exercise and chronic exposure to stress, and rapid active and passive chronic release of cfDNA fragments into the circulation. PMID:22694348

Breitbach, Sarah; Tug, Suzan; Simon, Perikles

2012-07-01

370

Study of the evolutionary relationships among Limonium species (Plumbaginaceae) using nuclear and cytoplasmic molecular markers.  

PubMed

The genus Limonium, due to the patchiness of the natural habitats of its species as well as the high frequency of hybridization and polyploidy and the possibility of reproduction by apomixis, provides an example of all the principal mechanisms of rapid speciation of plants. As an initial study of evolution in this genus, we have analyzed intra- and interspecific variability in 17 species from section Limonium, the largest in the genus, based on RFLPs of cpDNA and nuclear rDNA ITS sequences. In the cpDNA analysis, 21 restriction enzymes were used, resulting in 779 fragments, 490 of which were variable and 339 parsimony informative. L. furfuraceum exhibited two relatively divergent cpDNA haplotypes. The relationships found among the species based on cpDNA restriction fragments were coincident using different methods of phylogenetic analysis. Due to the presumed reticulate evolution in the genus Limonium, the comparison of these results with data from the nuclear DNA was necessary; ITS sequences were analyzed. The final alignment contained 488 characters, of which 198 were variable and 156 parsimony informative. Two relatively divergent ITS types were present at the intraindividual level in L. delicatulum, a triploid species. Each type was related to ITS from different groups of diploid Limonium species, one with a base haploid chromosome number n = 8 (represented by L. cossonianum) and the other with n = 9 (represented by L. minutum). The different phylogenetic inference methods used for the analysis of ITS sequences rendered very similar topologies. In general, the relationships among the species studied were coincident with those obtained with the chloroplast genome. Both nuclear and cytoplasmic markers support the polyphyly of section Limonium, with at least two species, L. narbonense and L. vulgare, clearly divergent from the rest. Moreover, the remaining subsections into which section Limonium is currently divided seem to be artificial. PMID:10679157

Palacios, C; Rosselló, J A; González-Candelas, F

2000-02-01

371

Ceramide galactosyltransferase (UGT8) is a molecular marker of breast cancer malignancy and lung metastases  

PubMed Central

Background: It was shown recently on the level of gene expression that UGT8, coding UDP-galactose:ceramide galactosyltransferase, is one of six genes whose elevated expression correlated with a significantly increased the risk of lung metastases in breast cancer patients. In this study primary tumours and their lung metastases as well as breast cancer cell lines were analysed for UGT8 expression at the protein level. Methods: Expression of UGT8 in breast cancer tissue specimens and breast cancer cell lines was analysed using IHC, real-time PCR and Western blotting. Results: Comparison of the average values of the reaction intensities (IRS scale) showed a significant difference in UGT8 expression between (1) primary and metastatic tumours (Mann–Whitney U, P<0.05), (2) tumours of malignancy grades G3 and G2 (Mann–Whitney U, P<0.01) as well as G3 and G1 (Mann–Whitney U, P<0.001) and (3) node-positive and node-negative tumours (Mann–Whitney U, P<0.001). The predictive ability of increased expression of UGT8 was validated at the mRNA level in three independent cohorts of breast cancer patients (721). Similarly, breast cancer cell lines with the ‘luminal epithelial-like' phenotype did not express or weakly expressed UGT8, in contrast to malignant, ‘mesenchymal-like,' cells forming metastases in nude mice. Conclusion: Our data suggest that UGT8 is a significant index of tumour aggressiveness and a potential marker for the prognostic evaluation of lung metastases in breast cancer.

Dziegiel, P; Owczarek, T; Plazuk, E; Gomulkiewicz, A; Majchrzak, M; Podhorska-Okolow, M; Driouch, K; Lidereau, R; Ugorski, M

2010-01-01

372

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

PubMed Central

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

2012-01-01

373

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

374

A molecular marker for cell guidance information in the axolotl embryo.  

PubMed

Previous studies from this laboratory suggested that the elongation of the pronephric duct (PND) in the axolotl Ambystoma mexicanum is directed by an adhesion gradient along the migrating cells' substratum. We have also shown that cranial neural crest (CNC) cells are able to follow the PND guidance information, for which these cells serve as useful probes (S.L. Zackson and M.S. Steinberg, (1986) Dev. Biol. 117, 342-353). These experiments allow the construction of a map of the cell guidance information. This map is presumed to reflect a molecular prepattern representing the distribution of a cell guidance associated molecule (CGAM) responsible for the ensuing pattern of cell migration. We refer to this proposal as the molecular prepattern hypothesis. In this paper we describe and identify a candidate CGAM displaying a localization pattern corresponding closely with our map of the PND/CNC guidance information on the embryonic flank. This candidate CGAM is also found to be abundant on the posterior neural tube, an embryonic region not previously explored for PND/CNC guidance information. The latter observation has provided the opportunity for an independent test of the correlation between the presence of this molecule in an embryonic region and the ability of that region to direct cell migration. We have found that grafted CNC cells do indeed migrate upon the strongly labeling posterior neural tube in preference to the neighboring poorly labeling presomitic mesoderm. We identify this candidate CGAM as the cell surface enzyme alkaline phosphatase. Possible roles for alkaline phosphatase in directing embryonic cell migrations are discussed. PMID:3378673

Zackson, S L; Steinberg, M S

1988-06-01

375

Molecular identification of the hybrid between the catfish species Pseudoplatystoma corruscans and Pseudoplatystoma reticulatum using a set of eight microsatellite markers.  

PubMed

This study distinguished hybrids of surubim or pintado Pseudoplatystoma corruscans and cachara Pseudoplatystoma reticulatum from pure strains using a set of eight microsatellite markers and population assignment methods. Applications of this molecular tool range from certification of hybrid-free breeders in restocking conservation programmes to the identification of fish products lacking traditional morphological characteristics. PMID:23991882

Cardoso de Carvalho, D; Seerig, A S; Dos Santos Alves Figueiredo Brasil, B; Vieira Crepaldi, D; Aparecida Andrade de Oliveria, D

2013-07-30

376

Evaluation of molecular markers for discriminating Gonaterocerus morrilli: A biological control agent imported from the origin of the glassy-winged sharpshooter  

Technology Transfer Automated Retrieval System (TEKTRAN)

We examined the utility of molecular markers for discriminating between two very closely related species, Gonatocerus morrilli (Howard) (imported from Texas) and G. walkerjonesi S. Triapitsyn (native to California), to determine whether post-release G. morrilli specimens could be detected and discri...

377

A systematic review and meta-analysis of evidence for correlation between molecular markers of parasite resistance and treatment outcome in falciparum malaria  

Microsoft Academic Search

BACKGROUND: An assessment of the correlation between anti-malarial treatment outcome and molecular markers would improve the early detection and monitoring of drug resistance by Plasmodium falciparum. The purpose of this systematic review was to determine the risk of treatment failure associated with specific polymorphisms in the parasite genome or gene copy number. METHODS: Clinical studies of non-severe malaria reporting on

Stéphane Picot; Piero Olliaro; Frédérique de Monbrison; Anne-Lise Bienvenu; Ric N Price; Pascal Ringwald

2009-01-01

378

DEVELOPMENT OF MOLECULAR DIAGNOSTIC MARKERS FOR SHARPSHOOTERS HOMALODISCA COAGULATA AND H. LITURATA (HOMOPTERA: CICADELLIDAE: PROCONIINI) FOR USE IN PREDATOR GUT CONTENT EXAMINATIONS  

Technology Transfer Automated Retrieval System (TEKTRAN)

To aid in identifying key predators of Proconiini sharpshooter species present in California, we developed and tested molecular diagnostic markers for the glassy-winged sharpshooter (GWSS) Homalodisca coagulata (Say) and smoke-tree sharpshooter (STSS) Homalodisca liturata (Ball) (Homoptera: Cicadell...

379

VALIDATION OF A SIMPLIFIED METHOD FOR USING MOLECULAR MARKERS TO PREDICT SULFADOXINE-PYRIMETHAMINE TREATMENT FAILURE IN AFRICAN CHILDREN WITH FALCIPARUM MALARIA  

Microsoft Academic Search

Surveillance of molecular markers for key mutations in Plasmodium falciparum dihydrofolate reductase (DHFR) and dihydropteroate synthetase (DHPS) has been proposed as a means of predicting sulfadoxine\\/ pyrimethamine (SP) treatment outcomes in Africa. This study assessed the association between DHFR and DHPS mutations and standardized clinical outcomes in children treated with SP for uncomplicated malaria in Kampala, Uganda. Two mutations (DHFR

DANIEL KYABAYINZE; ADITHYA CATTAMANCHI; MOSES R. KAMYA; PHILIP J. ROSENTHAL; GRANT DORSEY

2003-01-01

380

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

381

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

382

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

383

Immunological Treatments for Autism  

Microsoft Academic Search

Several investigators, including ourselves, have reported significant changes in various immune responses in children with autism. These changes demonstrate dysregulation of the immune system (deficiency in some components of the immune system and excesses in others). In addition, certain genes in the major histocompatibility complex (that regulates immune responses) appear to be involved in autism. Based upon immunological abnormalities, various

Sudhir Gupta

2000-01-01

384

The immunologic revolution: photoimmunology.  

PubMed

UV radiation targets the skin and is a primary cause of skin cancer (both melanoma and nonmelanoma skin cancer). Exposure to UV radiation also suppresses the immune response, and UV-induced immune suppression is a major risk factor for skin cancer induction. The efforts of dermatologists and cancer biologists to understand how UV radiation exposure suppresses the immune response and contributes to skin cancer induction led to the development of the subdiscipline we call photoimmunology. Advances in photoimmunology have generally paralleled advances in immunology. However, there are a number of examples in which investigations into the mechanisms underlying UV-induced immune suppression reshaped our understanding of basic immunological concepts. Unconventional immune regulatory roles for Langerhans cells, mast cells, and natural killer T (NKT) cells, as well as the immune-suppressive function of lipid mediators of inflammation and alarmins, are just some examples of how advances in immunodermatology have altered our understanding of basic immunology. In this anniversary issue celebrating 75 years of cutaneous science, we provide examples of how concepts that grew out of efforts by immunologists and dermatologists to understand immune regulation by UV radiation affected immunology in general. PMID:22170491

Ullrich, Stephen E; Byrne, Scott N

2011-12-15

385

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

2012-10-10

386

Reproductive immunology: biomarkers of compromised pregnancies.  

PubMed Central

The objective of this paper is to consider several categories 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 fluorescence-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

1987-01-01

387

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

388

Molecular prognostic markers for adult acute myeloid leukemia with normal cytogenetics  

PubMed Central

Acute myeloid leukemia (AML) is a heterogenous disorder that results from a block in the differentiation of hematopoietic progenitor cells along with uncontrolled proliferation. In approximately 60% of cases, specific recurrent chromosomal aberrations can be identified by modern cytogenetic techniques. This cytogenetic information is the single most important tool to classify patients at their initial diagnosis into three prognostic categories: favorable, intermediate, and poor risk. Currently, favorable risk AML patients are usually treated with contemporary chemotherapy while poor risk AML patients receive allogeneic stem cell transplantation if suitable stem cell donors exist. The largest subgroup of AML patients (~40%) have no identifiable cytogenetic abnormalities and are classified as intermediate risk. The optimal therapeutic strategies for these patients are still largely unclear. Recently, it is becoming increasingly evident that it is possible to identify a subgroup of poorer risk patients among those with normal cytogenic AML (NC-AML). Molecular risk stratification for NC-AML patients may be possible due to mutations of NPM1, FLT3, MLL, and CEBP? as well as alterations in expression levels of BAALC, MN1, ERG, and AF1q. Further prospective studies are needed to confirm if poorer risk NC-AML patients have improved clinical outcomes after more aggressive therapy.

Gregory, Tara K; Wald, David; Chen, Yichu; Vermaat, Johanna M; Xiong, Yin; Tse, William

2009-01-01

389

A prescription for human immunology.  

PubMed

Inbred mice have been an extremely successful tool for basic immunology, but much less so as models of disease. Thus, to maximize the use of immunologic approaches to improve human health, we need more strategically directed efforts in human immunology. This would also open up new opportunities for basic research. PMID:19100694

Davis, Mark M

2008-12-19

390

Complete chloroplast genome of Oncidium Gower Ramsey and evaluation of molecular markers for identification and breeding in Oncidiinae  

PubMed Central

Background Oncidium spp. produce commercially important orchid cut flowers. However, they are amenable to intergeneric and inter-specific crossing making phylogenetic identification very difficult. Molecular markers derived from the chloroplast genome can provide useful tools for phylogenetic resolution. Results The complete chloroplast genome of the economically important Oncidium variety Onc. Gower Ramsey (Accession no. GQ324949) was determined using a polymerase chain reaction (PCR) and Sanger based ABI sequencing. The length of the Oncidium chloroplast genome is 146,484 bp. Genome structure, gene order and orientation are similar to Phalaenopsis, but differ from typical Poaceae, other monocots for which there are several published chloroplast (cp) genome. The Onc. Gower Ramsey chloroplast-encoded NADH dehydrogenase (ndh) genes, except ndhE, lack apparent functions. Deletion and other types of mutations were also found in the ndh genes of 15 other economically important Oncidiinae varieties, except ndhE in some species. The positions of some species in the evolution and taxonomy of Oncidiinae are difficult to identify. To identify the relationships between the 15 Oncidiinae hybrids, eight regions of the Onc. Gower Ramsey chloroplast genome were amplified by PCR for phylogenetic analysis. A total of 7042 bp derived from the eight regions could identify the relationships at the species level, which were supported by high bootstrap values. One particular 1846 bp region, derived from two PCR products (trnHGUG -psbA and trnFGAA-ndhJ) was adequate for correct phylogenetic placement of 13 of the 15 varieties (with the exception of Degarmoara Flying High and Odontoglossum Violetta von Holm). Thus the chloroplast genome provides a useful molecular marker for species identifications. Conclusion In this report, we used Phalaenopsis. aphrodite as a prototype for primer design to complete the Onc. Gower Ramsey genome sequence. Gene annotation showed that most of the ndh genes inOncidiinae, with the exception of ndhE, are non-functional. This phenomenon was observed in all of the Oncidiinae species tested. The genes and chloroplast DNA regions that would be the most useful for phylogenetic analysis were determined to be the trnHGUG-psbA and the trnFGAA-ndhJ regions. We conclude that complete chloroplast genome information is useful for plant phylogenetic and evolutionary studies in Oncidium with applications for breeding and variety identification.

2010-01-01

391

Teasing out the best molecular marker in the AKT/MTOR pathway in HNSCC patients  

PubMed Central

Objectives No reliable molecular biomarker is currently available for clinical application in the management of head and neck cancer patients. The AKT/MTOR pathway is activated in 90-100% of HNSCC and could be promising biomarkers closely linked to cancer incidence. Methods Oral mucosa from non-cancer patients were compared to HNSCC tumors and junctional zone mucosa. The candidate biomarkers MTOR, AKT, 4EBP1, and S6 kinase, signaling components upstream and downstream of MTOR that appear dysregulated in HNSCC were evaluated using immunohistochemistry (IHC) and western blot. Results Expression of phosphorylated AKT and phosphorylated MTOR were significantly higher in cancer patient tumors compared to non-cancer oral mucosa samples (p=0.004 and p=0.026 respectively) by western. pMTOR and p4EBP1 expression were higher in patient junctional zones compared to tumors (p=0.017 and p=0.022 respectively) and no difference in p-AKT or p-S6 expression in HNSCC patients' junctional zone compared to tumors. IHC demonstrated p-MTOR expression was 81.9% sensitive and 100% specific in differentiating cancer from non-cancer mucosa, while p-4EBP1 expression by IHC was only 50.0% sensitive and 95.5% specific in differentiating normal mucosa from HNSCC (p<0.01). Conclusions Phosphorylated MTOR appears to be a reliable biomarker by both western (p=0.026) and IHC in human head and neck cancer (p<0.001). Moreover, phosphorylated AKT, which is immediately upstream of MTOR, is a potential biomarker that should be further studied. Clinical trials with MTOR inhibitors are being evaluated for HNSCC, and selecting patients that are likely to respond to these inhibitors requires identifying and validating predictive biomarkers of response.

Clark, Cheryl; Shah, Shivang; Herman-Ferdinandez, Lilantha; Ekshyyan, Oleksandr; Abreo, Fleurette; Rong, Xiaohua; McLarty, Jerry; Lourie, Aubrey; Milligan, Edward J.; Nathan, Cherie-Ann O.

2010-01-01

392

Hypodiploid multiple myeloma is characterized by more aggressive molecular markers than non-hyperdiploid multiple myeloma  

PubMed Central

Multiple myeloma can be categorized into hyperdiploid or non-hyperdiploid myeloma based on the number of chromosomes found in the tumor clone. Among the non-hyperdiploid myelomas, the hypodiploid subtype has the most aggressive clinical phenotype, but the genetic differences between groups are not completely defined. In order to understand the genetic background of hypodiploid multiple myeloma better, we compared the genomic (array-based comparative genomic hybridization) and transcriptomic (gene expression profiling) background of 49 patients with hypodiploid myeloma with 50 other non-hyperdiploid and 125 hyperdiploid myeloma patients. There were significant chromosomal and gene expression differences between hyperdiploid patients and non-hyperdiploid and hypodiploid patients. Non-hyperdiploid and hypodiploid patients shared most of the chromosomal abnormalities; nevertheless a subset of these abnormalities, such as monosomies 13, 14 and 22, was markedly increased in hypodiploid patients. Furthermore, deletions of 1p, 12p, 16q and 17p, all associated with poor outcome or progression in multiple myeloma, were significantly enriched in hypodiploid patients. Molecular risk-stratification indices reinforce the worse prognosis associated with hypodiploid multiple myeloma compared with non-hyperdiploid multiple myeloma. Gene expression profiling clustered hypodiploid and non-hyperdiploid subgroups closer than hyperdiploid myeloma but also highlighted the up-regulation of CCND2, WHSC1/MMSET and FGFR3 in the hypodiploid subtype. In summary, hypodiploid multiple myeloma is genetically similar to non-hyperdiploid multiple myeloma but characterized by a higher prevalence of genetic alterations associated with poor outcome and disease progression. It is provocative to hypothesize that hypodiploid multiple myeloma is an advanced stage of non-hyperdiploid multiple myeloma.

Van Wier, Scott; Braggio, Esteban; Baker, Angela; Ahmann, Gregory; Levy, Joan; Carpten, John D.; Fonseca, Rafael

2013-01-01

393

Molecular Markers of Injury in Kidney Biopsy Specimens of Patients with Lupus Nephritis  

PubMed Central

Prediction of prognosis in patients who have lupus nephritis is inadequate, limiting individualization of potentially toxic therapy. Advances in tissue molecular techniques offer new approaches to study mechanisms underlying kidney injury, and add to prognostic information gleaned from biopsy specimens. Analysis of mRNA expression in formalin-fixed, paraffin-embedded renal biopsy specimens is limited by both quantity and quality of RNA, requiring RNA pre-amplification, which can introduce bias. Accordingly, we developed a new technique for RNA extraction from human kidney formalin fixed paraffin embedded biopsy specimens, and used Taqman low-density arrays Applied Biosystems, Carlsbad, CA to simultaneously measure 48 mRNAs in duplicate, in a single biopsy. We extracted mRNA from more than 150 blocks to determine the quantity and vintage of biopsy tissue suitable for analysis using this protocol. We then used Taqman low-density arrays to identify suitable housekeeping genes in lupus nephritis. Finally, we measured expression of 48 mRNA transcripts in archived lupus biopsy specimens (n = 54). We identified that the mRNA levels of three transcripts (MMP7, EGF, COL1A1) relate to pathological indices of kidney injury and kidney function at the time of biopsy; these were associated with parallel changes in expression of these proteins. This new method for measurement of kidney biopsy mRNA expression has enabled us to identify tissue biomarkers of kidney damage and function, and potentially can increase the information yielded from diagnostic kidney biopsy specimens to improve tailoring of therapy.

Reich, Heather N.; Landolt-Marticorena, Carol; Boutros, Paul C.; John, Rohan; Wither, Joan; Fortin, Paul R.; Yang, Stuart; Scholey, James W.; Herzenberg, Andrew M.

2011-01-01

394

Validation of molecular markers for resistance among Pakistani chickpea germplasm to races of Fusarium oxysporum f. sp. ciceris  

Technology Transfer Automated Retrieval System (TEKTRAN)

DNA markers in chickpea have been identified against different races of Fusarium oxysporum f.sp. ciceris (Foc), but validation of these markers is essential for their effective use in resistant breeding. In view of this, different simple sequence repeats (SSR) markers were analysed in Pakistani ger...

395

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

2009-05-04

396

Centromeric association of small supernumerary marker chromosomes with their sister-chromosomes detected by three dimensional molecular cytogenetics  

PubMed Central

Background Small supernumerary marker chromosomes (sSMC) are detected in 0.043% of general population and can be characterized for their chromosomal origin, genetic content and shape by molecular cytogenetic approaches. Even though recently progress was achieved towards genotype-phenotype-correlations of sSMC, nothing is known on the influence that an additional derivative extra chromosome has on the nuclear architecture. Results Here we present the first three-dimensional interphase fluorescence in situ hybridization (FISH) studies for the nuclear architecture of sSMC. It could be shown that sSMC derived from chromosomes 15, 16 or 18 preferentially colocalized with one of their corresponding sister chromosomes. This was true in B- and T-lymphocytes as well as in skin fibroblasts. Additionally, a case with a complex sSMC with a karyotype 47,XY,+der(18)t(8;18)(8p23.2 ~ 23.1;18q11.1) was studied. Here the sSMC co-localized with one homologous chromosome 8 instead of 18. Conclusion Overall, there is a kind of "attraction" between an sSMC and one of its homologous sister chromosomes. This seems to be transmitted by the euchromatic part of the sSMC rather than its heterochromatic one.

2012-01-01

397

Characterization of the vasa gene in the Chinese mitten crab Eriocheir sinensis: a germ line molecular marker.  

PubMed

The vasa gene first identified in Drosophila encodes an ATP-dependent RNA helicase belonging to the DEAD-box family and is specifically expressed in germ line cells. In this study a full-length vasa gene homolog from the Chinese mitten crab (Eriocheir sinensis) was characterized, comprising of 2369 bp nucleotides with an open reading frame of 1866 bp encoding 621 amino acids. The putative protein was shown to contain eight conserved motifs belonging to the DEAD-box protein family and two zinc-finger domains (CCHC) and a Q-motif. Its sequence showed high similarity to vasa homologs of other species. The E. sinensis vasa (Es-vasa) mRNA expression was specific to the gonad and its temporal expression in the ovary and testes were significantly different between various developmental periods. By real-time qPCR analysis, Es-vasa mRNA transcripts were at the highest levels during periods of rapid development in the gonads (stage III-2 in ovaries and spermatocyte stage in testes) and gradually decreased as the gonads matured. In conclusion, we first identified the vasa gene from Chinese mitten crab. The specificity and pattern of Es-vasa expression in gonads indicates that it may be used as molecular marker for germ line in E. sinensis. PMID:22562064

Wang, Qun; Fang, Di-An; Sun, Jiang-Lin; Wang, Yang; Wang, Juan; Liu, Li-Hua

2012-05-03

398

On the cellular and molecular regulatory transcriptional mechanisms and responsive putative pathways to inflammatory oxidative stress revisited: current immunological breakthroughs and views at a glance.  

PubMed

Responses to oxidative stress are generally regulated by redox-responsive transcription factors (TFs). The abrupt variation in the partial pressure of oxygen (pO2) constitutes a regulatory mechanism. Such TFs forming an integral part of those putative pathways are hypoxia-inducible factor-1?(HIF)-1?and nuclear factor-?B (NF-?B), both are sufficiently tuned to govern such a specific response. Reactive species are produced during this transition and the antioxidant defense system controls their production. Oxidative stress occurs when there is imbalance between the production and removal of reactive species. Evidence exists showing that enhancement of the antioxidant defense system can reduce markers of oxidative stress. Recognition of reactive species and redox-mediated modifications as signals may open up a field of cell regulation via targeted control of TFs and hence can providea novel way of controlling diseases. This synopsis summates the major cutting-edge research work in the field of oxidative stress, and surgically identifies common and unique pathways involved with oxidative stress as means of regulatory elements governing TFs. PMID:23363382

Haddad, John J

2013-08-01

399

Effective rate constants and uptake coefficients for the reactions of organic molecular markers (n-alkanes, hopanes, and steranes) in motor oil and diesel primary organic aerosols with hydroxyl radicals.  

PubMed

Hydroxyl radical (OH) uptake by organic aerosols, followed by heterogeneous oxidation, happens nearly at the collision frequency. Oxidation complicates the use of organic molecular markers such as hopanes for source apportionment, since receptor models assume markers are stable during transport. We report the oxidation kinetics of organic molecular markers (C(25)-C(32) n-alkanes, hopanes and steranes) in motor oil and primary organic aerosol emitted from a diesel engine at atmospherically relevant conditions inside a smog chamber. A thermal desorption aerosol gas chromatograph/mass spectrometer (TAG) and Aerodyne high resolution time-of-flight aerosol mass spectrometer (HR-ToF-AMS) were used to measure the changes in molecular comosition and bulk primary organic aerosol. From the measured changes in molecular composition, we calculated effective OH rate constants, effective relative rate constants, and effective uptake coefficients for molecular markers. Oxidation rates varied with marker volatility, with more volatile markers being oxidized at rates much faster than could be explained from heterogeneous oxidation. This rapid oxidation can be explained by significant gas-phase OH oxidation that dominates heterogeneous oxidation, resulting in overall oxidation lifetimes of 1 day or less. Based on our results, neglecting oxidation of molecular markers used for source apportionment could introduce significant error, since many common markers such as norhopane appear to be semivolatile under atmospheric conditions. PMID:19943648

Lambe, Andrew T; Miracolo, Marissa A; Hennigan, Christopher J; Robinson, Allen L; Donahue, Neil M

2009-12-01

400

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

PubMed

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

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

2010-11-30

401

Molecular characterization of the SCAR markers tightly linked to the Tm2 locus of the genus Lycopersicon  

Microsoft Academic Search

The Tm-2 gene and its alleles conferring tomato mosaic virus resistance in tomato originate from Lycopersicon peruvianum, a wild relative of tomato. DNA fragments of several RAPD markers tightly linked with the Tm-2 locus in tomato were successfully cloned and sequenced. Subsequently, the 24-mer oligonucleotide primer pairs of the SCAR\\u000a markers corresponding to the RAPD markers were designed based on

Sobir; T. Ohmori; M. Murata; F. Motoyoshi

2000-01-01

402

Combining molecular-marker and chemical analysis of Capparis decidua (Capparaceae) in the Thar Desert of Western Rajasthan (india).  

PubMed

The Thar Desert, a very inhospitable place, accommodates only plant species that survive acute drought, unpredictable precipitation, and those can grow in the limited moisture of sandy soils. Capparis decidua is among one of the few plants able to grow well under these conditions. This species is highly exploited and has been naturally taken, as local people use it for various purposes like food, timber and fuel, although, no management or conservation efforts have been established. The present study was conducted in this arid area of Western Rajasthan (India) with the aim to obtain preliminary molecular information about this group of plants. We evaluated diversity among 46 samples of C. decidua using chemical parameters and random amplified polymorphic DNA (RAPD) markers. Fourteen chemical parameters and eight minerals (total 22 variables) of this species fruits were estimated. A total of 14 RAPD primers produced 235 band positions, of which 81.27% were polymorphic. Jaccard's similarity coefficients for RAPD primers ranged from 0.34 to 0.86 with a mean genetic similarity of 0.50. As per observed coefficient of variation, NDF (Neutral Detergent Fiber) content was found to be the most variable trait followed by starch and soluble carbohydrate. The Manhattan dissimilarity coefficient values for chemical parameters ranged between 0.02-0.31 with an average of 0.092. The present study revealed a very low correlation (0.01) between chemical parameters and RAPD-based matrices. The low correlation between chemical- and RAPD-based matrices indicated that the two methods were different and highly variable. The chemical-based diversity will assist in selection of nutritionally rich samples for medicinal purpose, while genetic diversity to face natural challenges and find sustainable ways to promote conservation for future use. PMID:23894984

Kumar, Sushil; Sharma, Ramavtar; Kumar, Vinod; Vyas, Govind K; Rathore, Abhishek

2013-03-01

403

Extended tricyclic terpanes: molecular markers in lower Jurassic synrift lacustrine black mudstones of the Hartford basin, Connecticut  

SciTech Connect

The East Berlin Formation (lowest Jurassic, Hartford basin, Connecticut) is distinctive for its six cyclic black and gray lacustrine mudstone units. The black mudstones are each about a meter thick and were deposited in subtropical, thermally stratified, oligomictic lakes, the youngest of which (lakes 3 through 6) were large enough to flood most of the basin and attained water depths of several tens of meters. From a fresh roadcut 8 km north of Middletown, organic-rich black mudstones of lakes 3, 4 and 6 were analyzed for biological markers. In each case, the saturate fraction predominates, making up 69-75% of the total solvent extract. The n-alkanes in turn dominate the saturate fraction, with a maximum at C/sub 20/ and extending to at least C/sub 37/. There are also extended homologous series of alkylcyclohexanes, alkylbenzenes, and branched-chain alkanes. The methylphenanthrene indices of these samples range from 0.99 to 1.12, indicating middle to late oil window maturity levels. The absence of aromatic steroids, except for the C/sub 20/ and C/sub 21/ triaromatics, confirms the high maturity. The most striking feature of these samples is the presence of a series of extended tricyclic terpanes from C/sub 20/ to at least C/sub 46/. Hopanes are not detectable in the mudstones of lakes 4 and 6. In lake 3, hopanes are present, but only in about the same concentration as the high molecular-weight tricyclics. The samples are depleted in hopanes in part because of the elevated maturity level. There is no evidence for biodegradation.

Kruge, M.A.; Hubert, J.F.; Akes, J.; Meriney, J.

1989-03-01

404

Cross sectional and longitudinal surveys of canine enteric coronavirus infection in kennelled dogs: a molecular marker for biosecurity.  

PubMed

Previous studies have suggested that kennelled dogs are more likely to test positive for CECoV than household pets. Here we describe both cross sectional and longitudinal studies in two rescue kennels and two boarding kennels, together with molecular diagnostics, to provide a new insight into the epidemiology of CECoV. Prevalence of CECoV in the cross sectional studies tended to be higher in the rescue kennels (13.8% and 33.3%) than the boarding kennels (5.3% and 13.5%). In each kennel, type I CECoV was more prevalent than type 2 CECoV. The mean quantity of type I detected was equivalent to 6.3 × 10(8)gc/gm (range=5 × 10(6), 8.5 × 10(11)), compared to 1.3 × 10(8)gc/gm (range = 3 × 10(6), 2.4 × 10(10)) for type II. In one rescue shelter where dogs were followed longitudinally, infection was significantly associated with accommodation block as well as the length of stay (increased risk of CECoV per week in residence of × 1.9). Of those animals sampled on two or more occasions, none tested positive on arrival, and 54.5% later shed CECoV, suggesting that infection may have been acquired within the kennel. Shedding patterns and sequence analysis suggested both types I and II CECoV were maintained in this population by a combination of introductions into the shelter and within-shelter transmission. The findings suggest that some kennel environments may be important in maintaining CECoV infection in the population. We also propose that the diversity of viruses like CECoV in these populations may provide a novel surrogate marker for the success of biosecurity. PMID:22543007

Stavisky, Jenny; Pinchbeck, Gina; Gaskell, Rosalind M; Dawson, Susan; German, Alexander J; Radford, Alan D

2012-04-21

405

Prognostic and Predictive Value of Baseline and Posttreatment Molecular Marker Expression in Locally Advanced Rectal Cancer Treated With Neoadjuvant Chemoradiotherapy  

SciTech Connect

Purpose: To evaluate expression of a panel of molecular markers, including p53, p21, MLH1, MSH2, MIB-1, thymidylate synthase, epidermal growth factor receptor (EGFR), and tissue vascular endothelial growth factor (VEGF), before and after treatment in patients treated with neoadjuvant chemoradiotherapy for locally advanced rectal cancer, to correlate the constitutive profile and dynamics of expression with pathologic response and outcome. Methods and Materials: Expression of biomarkers was evaluated by immunohistochemistry in tumor samples from 91 patients with clinical Stage II and III rectal cancer treated with preoperative pelvic radiotherapy (50 Gy) plus concurrent 5-fluorouracil by continuous intravenous infusion. Results: A pathologic complete remission was observed in 14 patients (15.4%). Patients with MLH1-positive tumors had a higher pathologic complete response rate (24.3% vs. 9.4%; p = 0.055). Low expression of constitutive p21, absence of EGFR expression after chemoradiotherapy, and high Dworak's tumor regression grade (TRG) were significantly associated with improved disease-free survival and overall survival. A high MIB-1 value after chemoradiotherapy was significantly associated with worse overall survival. Multivariate analysis confirmed the prognostic value of constitutive p21 expression as well as EGFR expression and MIB-1 value after chemoradiotherapy among patients not achieving TRG 3-4. Conclusions: In our study, we observed the independent prognostic value of EGFR expression after chemoradiotherapy on disease-free survival. Moreover, our study suggests that a constitutive high p21 expression and a high MIB-1 value after neoadjuvant chemoradiotherapy treatment could predict worse outcome in locally advanced rectal cancer.

Bertolini, Federica [Division of Medical Oncology, Department of Oncology and Hematology, University of Modena and Reggio Emilia, Modena (Italy)]. E-mail: bertolini.federica@policlinico.mo.it; Bengala, Carmelo [Division of Medical Oncology, Department of Oncology and Hematology, University of Modena and Reggio Emilia, Modena (Italy); Losi, Luisa [Department of Pathology and Legal Medicine, University of Modena and Reggio Emilia, Modena (Italy); Pagano, Maria [Division of Medical Oncology, Department of Oncology and Hematology, University of Modena and Reggio Emilia, Modena (Italy); Iachetta, Francesco [Division of Medical Oncology, Department of Oncology and Hematology, University of Modena and Reggio Emilia, Modena (Italy); Dealis, Cristina [Division of Medical Oncology, Department of Oncology and Hematology, University of Modena and Reggio Emilia, Modena (Italy); Jovic, Gordana [Division of Medical Oncology, Department of Oncology and Hematology, University of Modena and Reggio Emilia, Modena (Italy); Depenni, Roberta [Division of Medical Oncology, Department of Oncology and Hematology, University of Modena and Reggio Emilia, Modena (Italy); Zironi, Sandra [Division of Medical Oncology, Department of Oncology and Hematology, University of Modena and Reggio Emilia, Modena (Italy); Falchi, Anna Maria [Division of Radiation Therapy, Department of Oncology and Hematology, University of Modena and Reggio Emilia, Modena (Italy); Luppi, Gabriele [Division of Medical Oncology, Department of Oncology and Hematology, University of Modena and Reggio Emilia, Modena (Italy); Conte, Pier Franco [Division of Medical Oncology, Department of Oncology and Hematology, University of Modena and Reggio Emilia, Modena (Italy)

2007-08-01

406

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

Microsoft Academic Search

Magnaporthe grisea, the blast fungus is one of the main pathological threats to finger millet crop worldwide. A systematic search for the blast\\u000a resistance gene analogs was carried out, using functional molecular markers. Three-fourths of the recognition-dependent disease\\u000a resistance genes (R-genes) identified in plants encodes nucleotide binding site (NBS) leucine-rich repeat (LRR) proteins. NBS-LRR homologs have\\u000a only been isolated on

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

2011-01-01

407

Characterization of a Resistance Locus ( Pfs-1 ) to the Spinach Downy Mildew Pathogen ( Peronospora farinosa f. sp. spinaciae ) and Development of a Molecular Marker Linked to Pfs-1  

Microsoft Academic Search

Irish, B. M., Correll, J. C., Feng, C., Bentley, T., and de los Reyes, B. G. 2008. Characterization of a resistance locus (Pfs-1) to the spinach downy mildew pathogen (Peronospora farinosa f. sp. spinaciae) and develop- ment of a molecular marker linked to Pfs-1. Phytopathology 98:894-900. Downy mildew is a destructive disease of spinach worldwide. There have been 10 races

B. M. Irish; J. C. Correll; C. Feng; T. Bentley; B. G. de los Reyes

2008-01-01

408

Chromosomal regions associated with segregation distortion of molecular markers in F2, backcross, doubled haploid, and recombinant inbred populations in rice (Oryza sativa L.).  

PubMed

Chromosomal regions associated with marker segregation distortion in rice were compared based on six molecular linkage maps. Mapping populations were derived from one interspecific backcross and five inter-subspecific (indica/japonica) crosses, including two F2 populations, two doubled haploid (DH) populations, and one recombinant inbred (RI) population. Mapping data for each population consisted of 129-629 markers. Segregation distortion was determined based on chi-square analysis (P < 0.01) and was observed at 6.8-31.8%, of the mapped marker loci. Marker loci associated with skewed allele frequencies were distributed on all 12 chromosomes. Distortion in eight chromosomal regions bracketed previously identified gametophyte (ga) or sterility genes (S). Distortion in three other chromosomal regions was found only in DH populations, where japonica alleles were over-represented, suggesting that loci in these regions may be associated with preferential regeneration of japonica genotypes during anther culture. Three additional clusters of skewed markers were observed in more than one population in regions where no gametophytic or sterility loci have previously been reported. A total of 17 segregation distortion loci may be po