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1

[Immunological Markers in Organ Transplantation.  

PubMed

The immunological monitoring in organ transplantation is based mainly on the determination of laboratory parameters as surrogate markers of organ dysfunction. Structural damage, caused by alloreactivity, can only be detected by invasive biopsy of the graft, which is why inevitably rejection episodes are diagnosed at a rather progressive stage. New non-invasive specific markers that enable transplant clinicians to identify rejection episodes at an earlier stage, on the molecular level, are needed. The accurate identification of rejection episodes and the establishment of operational tolerance permit early treatment or, respectively, a controlled cessation of immunosuppression. In addition, new prognostic biological markers are expected to allow a pre-transplant risk stratification thus having an impact on organ allocation and immunosuppressive regimen. New high-throughput screening methods allow simultaneous examination of hundreds of characteristics and the generation of specific biological signatures, which might give concrete information about acute rejection, chronic dysfunction as well as operational tolerance. Even though multiple studies and a variety of publications report about important advances on this subject, almost no new biological marker has been implemented in clinical practice as yet. Nevertheless, new technologies, in particular analysis of the genome, transcriptome, proteome and metabolome will make personalised transplantation medicine possible and will further improve the long-term results and graft survival rates. This article gives a survey of the limitations and possibilities of new immunological markers in organ transplantation. PMID:23696203

Beckmann, J H; Heits, N; Braun, F; Becker, T

2013-05-21

2

HIV Molecular Immunology Database  

NSDL National Science Digital Library

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

3

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

E-print Network

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

Manstein, Dietmar J.

4

21 CFR 866.5065 - Human allotypic marker immunological test system.  

Code of Federal Regulations, 2014 CFR

...2014-04-01 2014-04-01 false Human allotypic marker immunological test system...ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES...Immunological Test Systems § 866.5065 Human allotypic marker immunological test...

2014-04-01

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

21 CFR 866.5065 - Human allotypic marker immunological test system.  

Code of Federal Regulations, 2012 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)...

2012-04-01

7

21 CFR 866.5065 - Human allotypic marker immunological test system.  

Code of Federal Regulations, 2011 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)...

2011-04-01

8

MOLECULAR MARKERS IN WILD TURKEY  

E-print Network

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

Latch, Emily K.

9

Immunological and biochemical markers in preeclampsia.  

PubMed

A basic precondition for the development of preeclampsia is the presence of placental trophoblast cells in the maternal blood circulation. On the other hand, while trophoblast cells are present in the blood of all pregnant women, preeclampsia occurs in only 2-5% of them. Evidently, other factors play a crucial role. The aim of this study was to compare a set of selected immunological factors (anti-cardiolipin autoantibodies, trophoblast-induced cell-mediated immunity, C3 and C4 complement components) and biochemical factors (serum immunoglobulins IgA, IgG, IgM) among three groups of women with uncomplicated pregnancy, gestational hypertension, or preeclampsia. Blood samples were taken 2-12h before delivery. In the preeclampsia group, there was a significantly higher number of women positive for anti-cardiolipin autoantibodies, trophoblast-induced cell-mediated immunity was elevated, serum IgG was elevated and C4 complement component was reduced. We conclude that both elevated autoimmune reactivity and the higher immune reactivity to trophoblast may contribute to the onset of preeclampsia. PMID:23131770

Kestlerová, A; Feyereisl, J; Frisová, V; M?churová, A; Š?la, K; Zima, T; B?lá?ek, J; Madar, J

2012-12-01

10

Mathematical Immunology at the molecular, cellular and population scales  

E-print Network

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

Wirosoetisno, Djoko

11

Postdoctoral Research Positions in Mucosal Immunology and Molecular Microbiology  

E-print Network

Postdoctoral Research Positions in Mucosal Immunology and Molecular Microbiology Two post-doctoral research positions are available at the Department of Microbiology and Immunology, Columbia University, New the challenge of working at the interface between Immunology and Microbiology. The selected candidates will work

Symington, Lorraine S.

12

Emerging molecular markers of cancer  

Microsoft Academic Search

Alterations in gene sequences, expression levels and protein structure or function have been associated with every type of cancer. These 'molecular markers' can be useful in detecting cancer, determining prognosis and monitoring disease progression or therapeutic response. But what is the best way to identify molecular markers and can they be easily incorporated into the clinical setting?

David Sidransky

2002-01-01

13

FIMM, a database of functional molecular immunology: update 2002  

Microsoft Academic Search

FIMM database (http:\\/\\/sdmc.krdl.org.sg:8080\\/fimm) contains data relevant to functional molecular immunology, focusing on cellular immunology. It contains fully referenced data on protein antigens, major histocompatibility complex (MHC) molecules, MHC-associated peptides and relevant disease asso- ciations. FIMM has a set of search tools for extraction of information and results are presented as lists or as reports.

Christian Schönbach; Judice L. Y. Koh; Darren R. Flower; Limsoon Wong; Vladimir Brusic

2002-01-01

14

An immunological marker of tolerance to infection in wild rodents.  

PubMed

Hosts are likely to respond to parasitic infections by a combination of resistance (expulsion of pathogens) and tolerance (active mitigation of pathology). Of these strategies, the basis of tolerance in animal hosts is relatively poorly understood, with especially little known about how tolerance is manifested in natural populations. We monitored a natural population of field voles using longitudinal and cross-sectional sampling modes and taking measurements on body condition, infection, immune gene expression, and survival. Using analyses stratified by life history stage, we demonstrate a pattern of tolerance to macroparasites in mature compared to immature males. In comparison to immature males, mature males resisted infection less and instead increased investment in body condition in response to accumulating burdens, but at the expense of reduced reproductive effort. We identified expression of the transcription factor Gata3 (a mediator of Th2 immunity) as an immunological biomarker of this tolerance response. Time series data for individual animals suggested that macroparasite infections gave rise to increased expression of Gata3, which gave rise to improved body condition and enhanced survival as hosts aged. These findings provide a clear and unexpected insight into tolerance responses (and their life history sequelae) in a natural vertebrate population. The demonstration that such responses (potentially promoting parasite transmission) can move from resistance to tolerance through the course of an individual's lifetime emphasises the need to incorporate them into our understanding of the dynamics and risk of infection in the natural environment. Moreover, the identification of Gata3 as a marker of tolerance to macroparasites raises important new questions regarding the role of Th2 immunity and the mechanistic nature of the tolerance response itself. A more manipulative, experimental approach is likely to be valuable in elaborating this further. PMID:25004450

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

2014-07-01

15

An Immunological Marker of Tolerance to Infection in Wild Rodents  

PubMed Central

Hosts are likely to respond to parasitic infections by a combination of resistance (expulsion of pathogens) and tolerance (active mitigation of pathology). Of these strategies, the basis of tolerance in animal hosts is relatively poorly understood, with especially little known about how tolerance is manifested in natural populations. We monitored a natural population of field voles using longitudinal and cross-sectional sampling modes and taking measurements on body condition, infection, immune gene expression, and survival. Using analyses stratified by life history stage, we demonstrate a pattern of tolerance to macroparasites in mature compared to immature males. In comparison to immature males, mature males resisted infection less and instead increased investment in body condition in response to accumulating burdens, but at the expense of reduced reproductive effort. We identified expression of the transcription factor Gata3 (a mediator of Th2 immunity) as an immunological biomarker of this tolerance response. Time series data for individual animals suggested that macroparasite infections gave rise to increased expression of Gata3, which gave rise to improved body condition and enhanced survival as hosts aged. These findings provide a clear and unexpected insight into tolerance responses (and their life history sequelae) in a natural vertebrate population. The demonstration that such responses (potentially promoting parasite transmission) can move from resistance to tolerance through the course of an individual's lifetime emphasises the need to incorporate them into our understanding of the dynamics and risk of infection in the natural environment. Moreover, the identification of Gata3 as a marker of tolerance to macroparasites raises important new questions regarding the role of Th2 immunity and the mechanistic nature of the tolerance response itself. A more manipulative, experimental approach is likely to be valuable in elaborating this further. PMID:25004450

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

2014-01-01

16

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

E-print Network

Postdoctoral Research Position in Molecular Immunology A post-doctoral research position in Molecular Immunology is available in the Liu lab at Columbia University Medical Center (CUMC) to study and solid background in molecular biology and immunology. Expertise in retroviral vector or experience

Symington, Lorraine S.

17

MOLECULAR MARKERS IN RICE BREEDING  

Technology Transfer Automated Retrieval System (TEKTRAN)

Researchers in the USDA/TAES/TAMU Molecular Genetics Laboratory are continuing to develop and analyze markers for several economically important traits in rice. We are presently active in a multi-institute Coordinated Agricultural Project (RiceCAP) funded by the USDA National Research Initiative to ...

18

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

19

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

20

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

E-print Network

AIDS. Author manuscript Page /1 11 Comparison of viro-immunological marker changes between HIV-1 and HIV-2-infected patients in France Drylewicz Julia 1 2 , Matheron Sophie 3 , Lazaro Estibaliz 4 Background HIV-2 is known to be less pathogenic than HIV-1, although the underlying mechanisms are still

Boyer, Edmond

21

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

22

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

E-print Network

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

Murphy, Robert F.

23

Inflammatory and immunological markers in preterm infants: correlation with disease.  

PubMed

Newborn infants often suffer from bacterial and viral infections without presenting typical symptoms. Therefore, reliable methods for detecting and monitoring sepsis in the newborn would be beneficial. In older patients C-reactive protein (CRP) and neopterin have proved useful serum markers of infection and inflammation. Both of these markers are regulated by cytokines, and it has been proposed that cytokines themselves could be used to monitor immune activation and infection. This study has examined the levels of CRP, neopterin, soluble IL-2R, tumour necrosis factor-alpha (TNF-alpha) and interferon-gamma (IFN-gamma) in cord blood samples from both premature and term neonates. Having established reference ranges for these analytes, serial measurements were made in babies requiring intensive care support. The results suggest that in preterm infants the simultaneous measurement of CRP and neopterin, and possibly soluble IL-2R, may provide an accurate early diagnosis of sepsis and may be of use in differentiating between bacterial and viral etiologies. In addition, serial measurement of these markers may help in the early diagnosis of necrotizing enterocolitis (NEC). PMID:8809148

Jurges, E S; Henderson, D C

1996-09-01

24

Molecular biology and immunology of fungal allergens  

Microsoft Academic Search

Fungi are non-chlorophyllus microorganisms, which constitutes the main source of outdoor and indoor allergens. The antigens\\u000a present in the spores and fragments of hyphae induce allergic responses in sensitized patients. The frequently recognized\\u000a fungi associated with asthma include Alternaria, Cladosporium, Aspergillus, and Penicillium. With the advent of molecular\\u000a biology techniques a number of fungal genes encoding relevant allergens have been

Viswanath P. Kurup; Banani Banerjee; Kevin J. Kelly; Jordan N. Fink

2000-01-01

25

Immunological Markers for PML Prediction in MS Patients Treated with Natalizumab  

PubMed Central

Natalizumab (NTZ), a monoclonal antibody recognizing the alpha4 integrin chain, has been approved for the treatment of active multiple sclerosis, but expose to the onset of a rare side effect, progressive multifocal leukoencephalopathy (PML). Estimating the individual risk of PML in NTZ-treated patients is a major challenge, and therapeutic strategies are mainly guided by the overall PML risk assessed by identified risk factors: JC virus (JCV) seropositivity, treatment duration (with peak incidence after 24?months), and the previous use of immunosuppressive therapies. Given that this stratification does not yet allow a precise individual prediction of PML, other predictive markers are needed, and several immunological biomarkers have been described. Quantification of anti-JCV antibody levels may improve individual predictive value, with higher baseline titers indicating increased risk. Other immunological biomarkers such as leukocyte cell membrane markers (CD49d, CD11a, and CD62L), detection of circulating JCV-specific activated T effector memory cells (TEM) or genetic screening have been proposed. In this review, we discuss how recent progress in immunology has paved the way for «new combined monitoring», which will include immunological screening, in NTZ-treated patients. PMID:25601865

Antoniol, Caroline; Stankoff, Bruno

2015-01-01

26

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 PMID:1498767

Gottstein, B

1992-01-01

27

A review: Immunological markers for malignant salivary gland tumors  

PubMed Central

Salivary gland cancers are rare. Around 8 out of 10 salivary gland tumors (80%) are in the parotid. Just fewer than 2 out of 10 salivary gland cancers develop in the other two salivary glands – the submandibular or sublingual glands. Fewer than 1 in 10 cancers start in the minor salivary glands. There are many different types of salivary gland cancers. The most common is mucoepidermoid carcinoma (MEC). Just over 3 out of 10 (25–35%) salivary gland cancers (SGT, SGC) are of this type. The others include adenoid cystic carcinoma (ACC), acinic cell carcinoma, carcinoma ex-pleomorphic adenoma (Ca-PA), polymorphous low grade adenocarcinoma (PLGA) and some newly discovered salivary gland tumors. Because of the infrequency of salivary gland tumors and their complex histopathological diagnosis, it is difficult to exactly predict their clinical course by means of its recurrence, malignant progression or metastasis. Salivary gland tumors always pose problems in diagnosis. This review provides an insight into the recent concepts and immunohistochemical markers to diagnose the malignant salivary gland tumors (SGT), thus guiding the Ear, Nose and Throat specialists, Oral and Maxillofacial Surgeons, General Pathologists and other medical and dental specialists thereby enabling them to make correct diagnosis and provide the appropriate treatment. PMID:25737930

Namboodiripad, P.C. Anila

2014-01-01

28

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

E-print Network

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

Bernatchez, Louis

2007-01-01

29

CHARACTERIZING SAFFLOWER GERMPLASM WITH AFLP MOLECULAR MARKERS  

Technology Transfer Automated Retrieval System (TEKTRAN)

Molecular markers are useful to improve germplasm collection management and for identifying genes for future enhancement and breeding. Safflower (Carthamus tinctorius L.) accessions from the U.S. germplasm collection were characterized using AFLP (Amplified Length Polymorphisms) markers. After DNA e...

30

(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...

31

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...

32

Characterizing Safflower Germplasm with AFLP Molecular Markers  

Technology Transfer Automated Retrieval System (TEKTRAN)

Characterization of safflower (Carthamus tinctorius L.) germplasm with molecular markers is needed to enhance germplasm management and utilization. Amplified Fragment Length Polymorphism (AFLP) analysis was completed in safflower using two selective primer pairs resulting in 102 unambiguous polymor...

33

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

E-print Network

Parasite Immunology, 2001: 23: 327±344 Immunological genomics of Brugia malayi: filarial genes of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, and few markers have yet been established for diagnostic use. In this review, we bring together

Maizels, Rick

34

Glioma biology and molecular markers.  

PubMed

The tumors classified as gliomas include a wide variety of histologies including the more common (astrocytoma, glioblastoma), as well as the less common histologies (oligodendroglioma, mixed oligoastrocytoma, pilocytic astrocytoma). Recent efforts at comprehensive genetic characterization of various primary brain tumor types have identified a number of common alterations and pathways common to multiple tumor types. Common pathways in glioma biology include growth factor receptor tyrosine kinases and their downstream signaling via the MAP kinase cascade or PI3K signaling, loss of apoptosis through p53, cell cycle regulation, angiogenesis via VEGF signaling, and invasion. However, in addition to these common general pathway alterations, a number of specific alterations have been identified in particular tumor types, and a number of these have direct therapeutic implications. These include mutations or fusions in the BRAF gene seen in pilocytic astrocytomas (and gangliogliomas). In oligodendrogliomas, mutations in IDH1 and codeletion of chromosomes 1p and 19q are associated with improved survival with upfront use of combined chemotherapy and radiation, and these tumors also have unique mutations of CIC and FUBP1 genes. Low grade gliomas are increasingly seen to be divided into two groups based on IDH mutation status, with astrocytomas developing through IDH mutation followed by p53 mutation, while poor prognosis low grade gliomas and primary glioblastomas (GBMs) are characterized by EGFR amplification, loss of PTEN, and loss of cyclin-dependent kinase inhibitors. GBMs can be further characterized based on gene expression and gene methylation patterns into three or four distinct subgroups. Prognostic markers in diffuse gliomas include IDH mutation, 1p/19q codeletion, and MGMT methylation, and MGMT is also a predictive marker in elderly patients with glioblastoma treated with temozolomide monotherapy. PMID:25468223

Cohen, Adam L; Colman, Howard

2015-01-01

35

A morphologic and immunologic surface marker study of 299 cases of non-Hodgkin lymphomas and related leukemias.  

PubMed Central

This study relateds the cytologic types of the classification of malignant lymphoma of Lukes and Collins to the results of immunologic surface marker studies as part of a systematic multiparameter study of 299 cases of non-Hodgkin lymphomas. The results support the hypothesis that malignant lymphomas are neoplasms of the immune system and involve the B- and T-cell systems and, rarely, histiocytes. The morphologic features of the cytologic types of Lukes and Collins are predictive of the subtypes of lymphoma and considerably more effective than the immunologic surface marker techniques in identifying homogeneous groups. There are considerable methodologic and interpretive problems that are evaluated in detail. The verification of the B- and T-cell subtypes of the Lukes and Collins classification indicates that the time has come to change from the terminology and classification of lymphomas of the past to a modern immunologic approach. PMID:304674

Lukes, R. J.; Taylor, C. R.; Parker, J. W.; Lincoln, T. L.; Pattengale, P. K.; Tindle, B. H.

1978-01-01

36

Molecular Genetic Markers: Discovery, Applications, Data Storage and Visualisation  

Microsoft Academic Search

Molecular genetic markers represent one of the most powerful tools for the analysis of genomes and enable the association of heritable traits with underlying genomic variation. Molecular marker technology has developed rapidly over the last decade and two forms of sequence based marker, Simple Sequence Repeats (SSRs), also known as microsatellites, and Single Nucleotide Polymorphisms (SNPs) now predominate applications in

Chris Duran; Nikki Appleby; David Edwards; Jacqueline Batley

2009-01-01

37

Immunological response and markers of cell damage in seropositive horses for Toxoplasma gondii.  

PubMed

Toxoplasmosis is an important parasitic disease affecting several species of mammals, but little is known about this disease in horses. This study aimed to investigate the levels of several immunological variables and markers of cell damage in the serum of seropositive horses for Toxoplasma gondii. Sera samples of adult horses from the Santa Catarina State, Brazil used on a previous study were divided into groups according to their antibody levels for T. gondii determined by immunofluorescence assay, i.e. 20 samples from seronegative horses (Group A - control), 20 samples from horses with titers of 1:64 (Group B), 20 samples of horses with titers of 1:256 (Group C), and five samples from horses with titers of 1:1024 (Group D). Positive animals (Groups B, C, and D) had higher levels of immunoglobulins (IgM and IgG), pro-inflammatory cytokines (TNF-?, IFN-?, IL-1, IL-4, and IL-6) and protein C-reactive protein, as well as lower levels of IL-10 (anti-inflammatory cytokine) when compared to seronegative horses (Group A). The nitric oxide levels were also elevated in seropositive horses. Therefore, we have found humoral and cellular immune responses in seropositive horses, and a correlation between high antibody levels and inflammatory mediators. Markers of cell injury by lipid peroxidation (TBARS) and protein oxidation (AOPP) were elevated in animals seropositives for T. gondii when compared to seronegatives. Therefore, seropositive horses to T. gondii can keep active immune responses against the parasite. As a consequence with chronicity of disease, they show cellular lesions that may lead to tissue damage with the appearance of clinical disease. PMID:25555997

Do Carmo, Guilherme M; Da Silva, Aleksandro S; Klauck, Vanderlei; Pazinato, Rafael; Moura, Anderson B; Duarte, Thiago; Duarte, Marta M M F; Bochi, Guilherme V; Moresco, Rafael N; Stefani, Lenita M

2015-02-01

38

Immunological and Biochemical Markers in Oral Carcinogenesis: The Public Health Perspective  

PubMed Central

Oral health is an integral component of general health and well being and a basic human right. Dental public health is probably the most challenging specialty of dentistry. Because of the lack of adequate resources among other factors, many people are likely to suffer from dental diseases. Despite great improvements in the oral health status of populations across the world, the burden and impact of dental diseases are still high. This is particularly true among underprivileged groups in both developed and developing communities. Oral diseases and conditions, including oral cancer, oral manifestations of HIV/AIDS, dental trauma, craniofacial anomalies, and noma, all have broad impacts on health and well-being. Oral cancer, the sixth most common cancer worldwide continues to be most prevalent cancer related to the consumption of tobacco, alcohol and other carcinogenic products. Nevertheless, significant reduction in mortality can be achieved by advances in early diagnosis and implementation of multidisciplinary treatment programs leading to improvement of survivorship and better quality of life. The present study was designed to evaluate the immunologic and biochemical markers in oral carcinogenesis using circulating immune complexes (CIC), copper, iron, and selenium concentrations as assessment endpoints. Study results indicated an increase in CIC and copper levels, and a decrease in iron and selenium concentrations in oral cancer patients compared to controls. The implications of these findings for public health are discussed. PMID:19151437

Khanna, Sunali

2008-01-01

39

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

PubMed

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

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

2002-06-01

40

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

41

Identifying commercially relevant Echinacea species by AFLP molecular markers.  

PubMed

The rising interest in medicinal plants has brought several species of the genus Echinacea to the attention of many scientists. Echinacea angustifolia, E. pallida, and E. purpurea are the most important for their immunological properties, well known and widely used by the native Americans. The three species are easily distinguishable on the basis of their morphological characteristics, but it would be difficult, if not impossible, to distinguish them in commercial preparations of ground, dry plant parts of E. purpurea (the most valuable species for chemotherapeutic properties) mixed with the other two species. Species-specific molecular markers could be useful to address this issue. In the present work, using fresh material collected from cultivated Echinacea spp., AFLP analysis was used to discriminate the three species and to detect species-specific DNA fragments. By using 14 primer combinations it was possible to detect a total of 994 fragments, of which 565 were polymorphic. Overall, 89 fragments were unique to E. purpurea, 32 to E. angustifolia, and 26 to E. pallida. E+CAC/M+AAT or E+CAC/M+AGC alone provided 13, 9, and 4 or 7, 5, and 5 specific fragments for E. purpurea, E. angustifolia, and E. pallida, respectively. A validation trial to confirm the results was carried out on bulked samples of 23 accessions covering most of the genetic diversity of the three species. The results are discussed in terms of practical applications in the field of popular medicine, detecting frauds, and implications for the genus Echinacea. PMID:19935915

Russi, Luigi; Moretti, Chiaraluce; Raggi, Lorenzo; Albertini, Emidio; Falistocco, Egizia

2009-11-01

42

Molecular Marker Systems for Oenothera Genetics  

PubMed Central

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

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

2008-01-01

43

Immunological methods  

Microsoft Academic Search

New technology and techniques for understanding immunology are describes below - including a serum protein quantification system, antibodies to proliferation markers, a human interleuken-10 ELISA and an unmasking reagent.

Brendan Norton

1995-01-01

44

Molecular Immunology 38 (2001) 289302 Germ-line transcripts of the immunoglobulin l JC clusters in the  

E-print Network

Molecular Immunology 38 (2001) 289­302 Germ-line transcripts of the immunoglobulin l J­C clusters al., 1999, for review see Gor- man and Alt, 1998). Strong evidence exists that both rearrangement Science Ltd. All rights reserved. PII: S0161-5890(01)00056-6 #12;H. Engel et al. / Molecular Immunology 38

Benham, Craig J.

45

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

46

The evolution of molecular markers — just a matter of fashion?  

Microsoft Academic Search

In less than half a century, molecular markers have totally changed our view of nature, and in the process they have evolved themselves. However, all of the molecular methods developed over the years to detect variation do so in one of only three conceptually different classes of marker: protein variants (allozymes), DNA sequence polymorphism and DNA repeat variation. The latest

Christian Schlötterer

2004-01-01

47

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

E-print Network

Molecular detection and immunological localization of gill Na /H exchanger in the dogfish (Squalus localization of gill Na /H exchanger in the dogfish (Squalus acanthias). Am J Physiol Regul Integr Comp Physiol dogfish (Squalus acanthias) can make rapid adjustments to gill acid-base transfers to compensate

Evans, David H.

48

HST.176 Cellular and Molecular Immunology, Fall 2002  

E-print Network

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

Pillai, Shiv

49

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

PubMed Central

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

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

2013-01-01

50

c-GAMMA:Comparative Genome Analysis of Molecular Markers  

NASA Astrophysics Data System (ADS)

Discovery of molecular markers for efficient identification of living organisms remains a challenge of high interest. The diversity of species can now be observed in details with low cost genomic sequences produced by new generation of sequencers. A method, called c-GAMMA, is proposed. It formalizes the design of new markers for such data. It is based on a series of filters on forbidden pairs of words, followed by an optimization step on the discriminative power of candidate markers.

Peterlongo, Pierre; Nicolas, Jacques; Lavenier, Dominique; Vorc'h, Raoul; Querellou, Joël

51

Characterizing Safflower Germplasm with AFLP Molecular Markers  

Technology Transfer Automated Retrieval System (TEKTRAN)

Safflower (Carthamus tinctorius L.) accessions from the U.S. germplasm collection were characterized using AFLP (Amplified Length Polymorphisms) markers. Separation and scoring of 392 markers was completed using the Beckman CEQ8000 capillary electrophoresis system. Twelve plants from each of eight...

52

Molecular markers in Tokyo Bay sediments: Sources and distribution  

Microsoft Academic Search

The spatial distribution of different classes of molecular markers in Tokyo Bay sediments, a semi-enclosed system surrounded by one of the most urbanized areas in the world, has been investigated. In order to study the environmental stability of different chemical classes of sewage markers, their isomeric composition was determined in river particulate matter, waste-water influent and surficial sediments. Among the

N. Chalaux; H. Takada; J. M. Bayona

1995-01-01

53

Immunological and molecular targets of atopic dermatitis treatment.  

PubMed

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

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

2014-07-01

54

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. PMID:22787174

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

2012-01-01

55

Molecular markers in the epidemiology and diagnosis of coccidioidomycosis.  

PubMed

The prevalence of coccidioidomycosis in endemic areas has been observed to increase daily. To understand the causes of the spread of the disease and design strategies for fungal detection in clinical and environmental samples, scientists have resorted to molecular tools that allow fungal detection in a natural environment, reliable identification in clinical cases and the study of biological characteristics, such as reproductive and genetic structure, demographic history and diversification. We conducted a review of the most important molecular markers in the epidemiology of Coccidioides spp. and the diagnosis of coccidioidomycosis. A literature search was performed for scientific publications concerning the application of molecular tools for the epidemiology and diagnosis of coccidioidomycosis. The use of molecular markers in the epidemiological study and diagnosis of coccidioidomycosis has allowed for the typing of Coccidioides spp. isolates, improved understanding of their mode of reproduction, genetic variation and speciation and resulted in the development specific, rapid and sensitive strategies for detecting the fungus in environmental and clinical samples. Molecular markers have revealed genetic variability in Coccidioides spp. This finding influences changes in the epidemiology of coccidioidomycosis, such as the emergence of more virulent or antifungal resistant genotypes. Furthermore, the molecular markers currently used to identify Coccidioides immitis and Coccidioides posadasii are specific and sensitive. However, they must be validated to determine their application in diagnosis. This manuscript is part of the series of works presented at the "V International Workshop: Molecular genetic approaches to the study of human pathogenic fungi" (Oaxaca, Mexico, 2012). PMID:24270069

Duarte-Escalante, Esperanza; Frías-De-León, María Guadalupe; Zúñiga, Gerardo; Martínez-Herrera, Erick; Acosta-Altamirano, Gustavo; Reyes-Montes, María Del Rocío

2014-01-01

56

Development and use of molecular markers: past and present.  

PubMed

Abstract Molecular markers, due to their stability, cost-effectiveness and ease of use provide an immensely popular tool for a variety of applications including genome mapping, gene tagging, genetic diversity diversity, phylogenetic analysis and forensic investigations. In the last three decades, a number of molecular marker techniques have been developed and exploited worldwide in different systems. However, only a handful of these techniques, namely RFLPs, RAPDs, AFLPs, ISSRs, SSRs and SNPs have received global acceptance. A recent revolution in DNA sequencing techniques has taken the discovery and application of molecular markers to high-throughput and ultrahigh-throughput levels. Although, the choice of marker will obviously depend on the targeted use, microsatellites, SNPs and genotyping by sequencing (GBS) largely fulfill most of the user requirements. Further, modern transcriptomic and functional markers will lead the ventures onto high-density genetic map construction, identification of QTLs, breeding and conservation strategies in times to come in combination with other high throughput techniques. This review presents an overview of different marker technologies and their variants with a comparative account of their characteristic features and applications. PMID:25430893

Grover, Atul; Sharma, P C

2014-11-28

57

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

PubMed

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

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

2014-10-01

58

Drosophila hematopoiesis: Markers and methods for molecular genetic analysis.  

PubMed

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

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

2014-06-15

59

Biological (molecular and cellular) markers of toxicity  

SciTech Connect

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

McCarthy, J.F.

1990-04-01

60

RESEARCH ARTICLE Uncloaking a cryptic, threatened rail with molecular markers  

E-print Network

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

Beissinger, Steven R.

61

Phylogenetic study of some Aporrectodea species based on molecular markers  

E-print Network

in "Advances in Earthworm Taxonomy V (Annelida: Oligochaeta), T. Pavlicek, P. Cardet, C. Csuzdi, R.C. Le Bayon earthworms play as key organisms in terrestrial ecosystems functioning, the lack of knowledge in phylogenetic earthworm taxonomy has only recently started. Molecular markers, mitochondrial and nucle- ar, are thus

Paris-Sud XI, Université de

62

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

PubMed Central

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

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

2014-01-01

63

CXCL10, MCP-1, and Other Immunologic Markers Involved in Neural Leprosy.  

PubMed

Nerve damage in leprosy can be directly induced by Mycobacterium leprae in the early stages of infection, however, immunomediated mechanisms add gravity to the impairment of neural function in symptomatic periods of the disease. This study investigated the immunohistochemical expression of immunomarkers involved in the pathogenic mechanisms of leprosy nerve damage. These markers selected were CXCL10, CCL2 chemokines and immunomarkers as CD3, CD4, CD8, CD45RA, CD45RO, CD68, HLA-DR, and metalloproteinases 2 and 9 (MMP2 and MMP9) occurring in nerve biopsy specimens collected from leprosy (23) and nonleprosy patients (5) suffering peripheral neuropathy. CXCL10, CCL2, MMP2, and MMP9 immunoreactivities were found in the leprosy nerves but not in nonleprosy samples. Immunolabeling was predominantly found in recruited macrophages and Schwann cells composing the inflammatory cellular population in the leprosy-affected nerves. The immunohistochemical expression of all the markers, but CXCL10, was associated with fibrosis, however, only CCL2 was, independently from the others, associated with this excessive deposit of extracellular matrix. No difference in the frequency of the immunolabeling was detected between the AFB and AFB leprosy subgroups of nerve, exception made to some statistical trend to difference in regard to CD68 and HLA-DR cells in the AFB nerves exhibiting epithelioid granuloma. MMP9 expression associated with fibrosis is consistent with previous results of research group. The findings conveys the idea that CCL2 and CXCL10 chemokines at least in advanced stages of leprosy nerve lesions are not determinant for the establishment of AFB or AFB leprosy lesions, however, CCL2 is associated with macrophage recruitment and fibrosis. PMID:25221954

Medeiros, Mildred F; Rodrigues, Márcia M J; Vital, Robson T; da Costa Nery, José A; Sales, Anna M; de Andrea Hacker, Mariana; Ferreira, Helen; Chimelli, Leila; Sarno, Euzenir N; Antunes, Sérgio L G

2015-03-01

64

Reviewing and Updating the Major Molecular Markers for Stem Cells  

PubMed Central

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

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

2013-01-01

65

[Molecular markers associated to prognosis of melanoma].  

PubMed

Melanoma prognosis is based on histological criteria such as tumor thickness (measured by Breslow index), level of invasion (Clarck's level), presence of ulceration and number of mitoses per mm2. However, these parameters do not provide a precise prognosis in all cases: thin melanomas may develop metastases and thick melanomas may remain focalized for many years. For these reasons, the search for other prognostic factors is still ongoing. Many molecules play a part in the invasiveness and metastatic dissemination of melanoma have now been identified. Expression of these molecules has been studied in primary melanoma and correlated with prognosis. An increase in the number of cells positive for Ki67 (detected by Mib1), cycline A, cycline D, p35, MMp-2, beta1 and beta3 integrins, osteonectin, the presence of an intense inflammatory infiltrate and capillary invasion are considered as factors of poor prognosis as well as the decrease in p16, p27, Melan A and nm23. The significance of CD44 modifications is still controversial. Only a small number of these different proteins has a prognostic value independent of tumor thickness. These results need to be confirmed on larger series of patients. Additional hope is given to new techniques such as the analysis of the genes implied in tumor progression by microarray technique in such a way as to provide a molecular map of each tumor. PMID:14724537

Heenen, M; Laporte, M

2003-11-01

66

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

PubMed Central

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

Jarvis, Gary A.; Chang, Theresa L.

2014-01-01

67

Molecular Markers for Breast Cancer: Prediction on Tumor Behavior  

PubMed Central

Breast cancer is one of the most common cancers with greater than 1,300,000 cases and 450,000 deaths each year worldwide. The development of breast cancer involves a progression through intermediate stages until the invasive carcinoma and finally into metastatic disease. Given the variability in clinical progression, the identification of markers that could predict the tumor behavior is particularly important in breast cancer. The determination of tumor markers is a useful tool for clinical management in cancer patients, assisting in diagnostic, staging, evaluation of therapeutic response, detection of recurrence and metastasis, and development of new treatment modalities. In this context, this review aims to discuss the main tumor markers in breast carcinogenesis. The most well-established breast molecular markers with prognostic and/or therapeutic value like hormone receptors, HER-2 oncogene, Ki-67, and p53 proteins, and the genes for hereditary breast cancer will be presented. Furthermore, this review shows the new molecular targets in breast cancer: CXCR4, caveolin, miRNA, and FOXP3, as promising candidates for future development of effective and targeted therapies, also with lower toxicity. PMID:24591761

Banin Hirata, Bruna Karina; Oda, Julie Massayo Maeda; Losi Guembarovski, Roberta; Ariza, Carolina Batista; de Oliveira, Carlos Eduardo Coral; Watanabe, Maria Angelica Ehara

2014-01-01

68

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. PMID:17095532

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

2010-01-01

69

Molecular markers for wheat leaf rust resistance gene Lr41  

Microsoft Academic Search

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

Xiaochun Sun; Guihua Bai; Brett F. Carver

2009-01-01

70

Molecular markers of pancreatic cancer: development and clinical relevance  

Microsoft Academic Search

Background  The prognosis of pancreatic cancer remains poor, mainly because of its aggressive biological behaviour and late clinical diagnosis,\\u000a which precludes the application of appropriate curative therapies. Therefore, one of the major goals in clinical pancreatology\\u000a is to find molecular markers, specific and sensitive enough to make an early and correct diagnosis of pancreatic cancer, before\\u000a it has disseminated and become

Lucia C. Fry; Klaus Mönkemüller; Peter Malfertheiner

2008-01-01

71

Molecular Markers, Natural History, and Conservation of Marine Animals  

NSDL National Science Digital Library

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

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

2009-11-01

72

De Novo Transcriptome Assembly of Pummelo and Molecular Marker Development  

PubMed Central

Pummelo (Citrus grandis) is an important fruit crop worldwide because of its nutritional value. To accelerate the pummelo breeding program, it is essential to obtain extensive genetic information and develop relative molecular markers. Here, we obtained a 12-Gb transcriptome dataset of pummelo through a mixture of RNA from seven tissues using Illumina pair-end sequencing, assembled into 57,212 unigenes with an average length of 1010 bp. The annotation and classification results showed that a total of 39,584 unigenes had similar hits to the known proteins of four public databases, and 31,501 were classified into 55 Gene Ontology (GO) functional sub-categories. The search for putative molecular markers among 57,212 unigenes identified 10,276 simple sequence repeats (SSRs) and 64,720 single nucleotide polymorphisms (SNPs). High-quality primers of 1174 SSR loci were designed, of which 88.16% were localized to nine chromosomes of sweet orange. Of 100 SSR primers that were randomly selected for testing, 87 successfully amplified clear banding patterns. Of these primers, 29 with a mean PIC (polymorphic information content) value of 0.52 were effectively applied for phylogenetic analysis. Of the 20 SNP primers, 14 primers, including 54 potential SNPs, yielded target amplifications, and 46 loci were verified via Sanger sequencing. This new dataset will be a valuable resource for molecular biology studies of pummelo and provides reliable information regarding SNP and SSR marker development, thus expediting the breeding program of pummelo. PMID:25799271

Liang, Mei; Yang, Xiaoming; Li, Hang; Su, Shiying; Yi, Hualin; Chai, Lijun; Deng, Xiuxin

2015-01-01

73

The Promise of Novel Molecular Markers in Bladder Cancer  

PubMed Central

Bladder cancer is the fourth most common malignancy in the US and is associated with the highest cost per patient. A high likelihood of recurrence, mandating stringent surveillance protocols, has made the development of urinary markers a focus of intense pursuit with the hope of decreasing the burden this disease places on patients and the healthcare system. To date, routine use of markers is not recommended for screening or diagnosis. Interests include the development of a single urinary marker that can be used in place of or as an adjunct to current screening and surveillance techniques, as well identifying a molecular signature for an individual’s disease that can help predict progression, prognosis, and potential therapeutic response. Markers have shown potential value in improving diagnostic accuracy when used as an adjunct to current modalities, risk-stratification of patients that could aid the clinician in determining aggressiveness of surveillance, and allowing for a decrease in invasive surveillance procedures. This review discusses the current understanding of emerging biomarkers, including miRNAs, gene signatures and detection of circulating tumor cells in the blood, and their potential clinical value in bladder cancer diagnosis, as prognostic indicators, and surveillance tools, as well as limitations to their incorporation into medical practice. PMID:25535079

Miremami, Jahan; Kyprianou, Natasha

2014-01-01

74

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

75

Pyrogenic molecular markers: linking PAH with BPCA analysis.  

PubMed

Molecular characterization of pyrogenic organic matter (PyOM) is of great interest to understand the formation and behavior of these increasingly abundant materials in the environment. Two molecular marker methods have often been used to characterize and trace PyOM: polycyclic aromatic hydrocarbon (PAH) and benzenepolycarboxylic acid (BPCA) analysis. Since both methods target pyrogenic polycyclic compounds, we investigated the linkages between the two approaches using chars that were produced under controlled conditions. Rye and maize straws and their analogues charred at 300, 400 and 500 °C, respectively, were thus analyzed with both methods. Moreover, we also measured BPCAs directly on the lipid extracts, on which PAHs were analyzed, and on the respective extraction residues, too. Both methods revealed important features of the chars, in particular the increasing degree of aromatic condensation with increasing highest heating temperature (HTT). The overlap between the two methods was identified in the lipid fraction, where the proportion of benzenetricarboxylic acids (B3CAs) correlated with PAH abundance. The results confirmed the validity and complementarity of the two molecular marker methods, which will likely continue to play a crucial role in PyOM research due to the recent developments of compound-specific PAH and BPCA stable carbon (?(13)C) and radiocarbon ((14)C) isotope methods. PMID:25084061

Wiedemeier, Daniel B; Brodowski, Sonja; Wiesenberg, Guido L B

2015-01-01

76

Molecular marker from pancreatic 'juices' helps identify pancreatic cancer  

Cancer.gov

Researchers at Mayo Clinic have developed a promising method to distinguish between pancreatic cancer and chronic pancreatitis — two disorders that are difficult to tell apart. A molecular marker obtained from pancreatic "juices" can identify almost all cases of pancreatic cancer, their study shows. The findings were being presented at Digestive Disease Week 2013 in Orlando, Fla. Pancreatic cancer and chronic pancreatitis both produce the same signs of disease in the pancreas, such as inflammation, but cancer in the organ is a life-threatening disorder that must be treated immediately and aggressively.

77

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

78

A molecular marker of artemisinin-resistant Plasmodium falciparum malaria  

NASA Astrophysics Data System (ADS)

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

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

2014-01-01

79

Molecular tools for marker-assisted breeding of buffelgrass  

E-print Network

, 2) develop polymerase chain reaction (PCR)-based markers from selected, informative restriction fragment length polymorphism (RFLP) markers on the buffelgrass genome map, and 3) increase marker resolution near the locus conferring apomixis (PApo1...

Jessup, Russell William

2005-11-01

80

Intelligent DNA-based molecular diagnostics using linked genetic markers  

SciTech Connect

This paper describes a knowledge-based system for molecular diagnostics, and its application to fully automated diagnosis of X-linked genetic disorders. Molecular diagnostic information is used in clinical practice for determining genetic risks, such as carrier determination and prenatal diagnosis. Initially, blood samples are obtained from related individuals, and PCR amplification is performed. Linkage-based molecular diagnosis then entails three data analysis steps. First, for every individual, the alleles (i.e., DNA composition) are determined at specified chromosomal locations. Second, the flow of genetic material among the individuals is established. Third, the probability that a given individual is either a carrier of the disease or affected by the disease is determined. The current practice is to perform each of these three steps manually, which is costly, time consuming, labor-intensive, and error-prone. As such, the knowledge-intensive data analysis and interpretation supersede the actual experimentation effort as the major bottleneck in molecular diagnostics. By examining the human problem solving for the task, we have designed and implemented a prototype knowledge-based system capable of fully automating linkage-based molecular diagnostics in X-linked genetic disorders, including Duchenne Muscular Dystrophy (DMD). Our system uses knowledge-based interpretation of gel electrophoresis images to determine individual DNA marker labels, a constraint satisfaction search for consistent genetic flow among individuals, and a blackboard-style problem solver for risk assessment. We describe the system`s successful diagnosis of DMD carrier and affected individuals from raw clinical data.

Pathak, D.K.; Perlin, M.W.; Hoffman, E.P.

1994-12-31

81

Molecular Immunology 46 (2009) 840847 Contents lists available at ScienceDirect  

E-print Network

-mapping, a phage-display library is initially scanned with the antibody; following that, the affinity selected-cell epitopes Nimrod D. Rubinstein, Itay Mayrose, Tal Pupko Department of Cell Research and Immunology, Tel Aviv

Pupko, Tal

82

Genetic diversity assessment of summer squash landraces using molecular markers.  

PubMed

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

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

2013-07-01

83

New models and molecular markers in evaluation of developmental toxicity  

SciTech Connect

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

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

2005-09-01

84

STRATEGIES FOR THE DEVELOPMENT AND IMPLEMENTATION OF MOLECULAR MARKERS IN PLANT BREEDING PROGRAMS.  

Technology Transfer Automated Retrieval System (TEKTRAN)

Molecular markers have been slow to meet expectations, but markers are currently providing real benefits in a number of breeding programs. Improved technologies provide opportunities to increase the usefulness of markers to breeding programs by reducing their costs and labor requirements and by inc...

85

Molecular markers for identifying municipal, domestic and agricultural sources of organic matter in natural waters.  

PubMed

Molecular markers can be used to determine the sources of organic pollution in water. This review summarizes progress made during the last two decades in identifying reliable molecular markers to distinguish pollution from sewage, animal production, and other sources. Two artificial sweeteners, sucralose and acesulfame-K, are sufficiently stable to be molecular markers and easily associated with domestic wastewater. Waste from different animal species may be distinguished by profiling fecal sterols and bile acids. Other markers which have been evaluated, including caffeine, detergent components, and compounds commonly leached from landfills are discussed. PMID:24200048

Harwood, John J

2014-01-01

86

Immunology & Pharmacology  

E-print Network

BSc (Hons) Immunology & Pharmacology DEGREE PROGRAMME GUIDE 2013-2014 #12;BSc (Hons) Immunology & Pharmacology Introduction Degree Aims and Outcomes General Enquiries General Requirements Industrial illnesses and chronic inflammatory diseases. Immunology with pharmacology is therefore concerned primarily

Levi, Ran

87

Associations between immunologic, inflammatory, and oxidative stress markers with severity of depressive symptoms: an analysis of the 2005-2006 National Health and Nutrition Examination Survey.  

PubMed

Previous studies have demonstrated increased levels of serum markers of systemic inflammation and immune system function among individuals with depressive symptoms. Despite these observations, the biological mechanisms behind this association remain elusive. The objective of the present analysis was to examine the individual and joint associations of white blood cell counts, platelet counts, and C-reactive protein with depression severity and to determine whether oxidative stress might mediate these associations. We conducted an analysis of 3867 subjects from the 2005-2006 National Health and Nutritional Examination Survey. Ordinal logistic regression was used to assess associations between three levels of depression symptom severity (as measured by the nine-item Patient Health Questionnaire) and serum C-reactive protein, white blood cell counts, platelet counts, and four surrogate markers of oxidative stress. Covariates included sex, age, smoking status, physical activity, education, poverty to income ratio, as well as medication use and medical conditions influencing inflammation levels. In separate models, the risk of moderate to severe depression was significantly greater in the highest quartiles of CRP (OR=1.84. 95 percent confidence interval (CI)=1.35-2.52), WBC (OR=1.70, CI=1.31-2.19), and platelet counts (OR=1.41, CI=1.13-1.76) after adjusting for basic sociodemographic and behavioral factors. After additional adjustment for medication use and oxidative stress surrogate measures, the highest quartile of WBC counts remained associated with depression (OR=1.60, CI=1.23-2.09). Adjustment for oxidative stress measures did not substantially affect estimated associations of inflammation/immunologic markers. In summary, we observed significantly elevated white blood cell counts among subjects with moderate and severe depression, and oxidative stress and a medical history of inflammatory diseases do not appear to mediate this association. Although limited through its use of cross-sectional data, this is the first analysis to simultaneously consider immunologic and oxidative stress markers. Further research is needed to identify the biological basis for this persistent association. PMID:19853625

Kobrosly, Roni; van Wijngaarden, Edwin

2010-01-01

88

Plasticity of immunological synapses.  

PubMed

TCR engagement with peptide/MHC complexes displayed on the surface of the antigen-presenting cells is the crucial event in developing an adaptive immune response and occurs within specialized signaling areas named immunological synapses. Immunological synapses are diverse both in structure and function and exhibit a strikingly dynamic molecular organization. In this review, we focus on the diversity of immunological synapses and on their plasticity in response to stimulation. We discuss how the study of the adaptable features of immunological synapses can be instrumental to a better understanding of the complex regulation of adaptive immunity. PMID:19960316

Valitutti, Salvatore; Dupré, Loïc

2010-01-01

89

Genetic Diversity Among Wheat Cultivars Using Molecular Markers  

Microsoft Academic Search

The objective of this study was to compare amplified fragment length polymorphism (AFLP), random amplified polymorphic DNA (RAPD), and DNA amplification fingerprinting (DAF) marker systems for estimating genetic diversity among 13 Iranian wheat (Triticum aestivum L.) cultivars through average expected heterozygosity (Hav), sum of effective number of alleles (SENA), and marker index (MI). The AFLP markers had the highest values

Babak Abdollahi Mandoulakani; Ali-Akbar Shahnejat-Bushehri; Badredin Ebrahim Sayed Tabatabaei; Sepideh Torabi; Alireza Mohammadi Hajiabad

2010-01-01

90

T cell subsets and expression of immunological activation markers in the arterial walls of patients with giant cell arteritis.  

PubMed Central

Immunohistochemical features of infiltrating mononuclear cells (MNC) and resident cells were studied in the temporal artery biopsy specimens of 13 patients with histological verified giant cell arteritis (GCA) and in six biopsy specimens from patients with GCA with negative histological findings. Eight temporal artery biopsy specimens from seven patients with unrelated diseases served as controls. In all patients with GCA proved by biopsy an infiltration of T lymphocytes in the arterial wall was observed, most being of the helper/inducer subset. No B lymphocytes, or very few, were seen. Lymphocytes in 10 out of the 13 positive biopsy specimens displayed staining for the class II major histocompatibility complex (MHC) antigen HLA-DR, whereas this was found in only two of eight controls. A minor number of the infiltrating T lymphocytes from seven out of 13 patients with GCA proved by biopsy stained for transferrin receptors, and in six out of the 13 cases they reacted with anti-interleukin 2 receptor antibody. In the arterial wall from all patients with histologically verified GCA we also found an increased number of macrophages, many of them expressing HLA-DR antigens and transferrin receptors. The immunohistochemical pattern of cell phenotypes found in the arterial wall of patients with GCA suggests that the infiltrating T cells are immunologically activated. This finding supports the hypothesis of a predominantly cellular immunological pathogenesis of giant cell arteritis. Images PMID:2962542

Andersson, R; Jonsson, R; Tarkowski, A; Bengtsson, B A; Malmvall, B E

1987-01-01

91

Identification of molecular markers associated with fruit traits in olive and assessment of olive core collection with AFLP markers and fruit traits.  

PubMed

The purpose of this study was to characterize olive core collection with amplified fragment length polymorphism (AFLP) markers and fruit traits and to determine AFLP markers significantly associated with these fruit characters in olive. A total of 168 polymorphic AFLP markers generated by five primer combinations and nine fruit traits were used to characterize relationships between 18 olive cultivars. Although all olive cultivars were discriminated from each other by either AFLP markers (<0.75 similarity level) or fruit traits, clustering based on the AFLP markers and fruit traits was not significantly correlated (r = 0.13). Partial clustering of olive cultivars by AFLP markers according to their geographical origin was observed. Associations of AFLP markers with fruits were determined using a multiple-regression analysis with stepwise addition of AFLP markers. Significant associations between eight AFLP markers and fruit traits were identified. While five AFLP markers demonstrated significant negative correlation with fruit and stone weight, width and length and total polyphenols (P < 0.05), three AFLP markers displayed significant positive correlation with ?-tocopherol and ?-tocopherol (P < 0.01). This is the first report on the association of molecular markers with fruit traits in olive. Molecular markers associated with morphological and agronomic traits could be utilized for the breeding of olive cultivars. However, the association power of these markers needs to be confirmed in larger populations, and highly correlated markers should then be converted to PCR-based DNA markers such as sequence-characterized amplified region markers for better utilization. PMID:25867425

Ipek, M; Seker, M; Ipek, A; Gul, M K

2015-01-01

92

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

PubMed Central

Background There are conflicting reports on the impact of highly active antiretroviral therapy (HAART) in resolving hematological complications. Whereas some studies have reported improvements in hemoglobin and other hematological parameters resulting in reduction in morbidity and mortality of HIV patients, others have reported no improvement in hematocrit values of HAART-treated HIV patients compared with HAART-naïve patients. Objective This current study was designed to assess the impact of HAART in resolving immunological and hematological complications in HIV patients by comparatively analyzing the results (immunological and hematological) of HAART-naive patients and those on HAART in our environment. Methods A total of 500 patients participated, consisting of 315 HAART-naive (119 males and 196 females) patients and 185 HAART-experienced (67 males and 118 females) patients. Hemoglobin (Hb), CD4+ T-cell count, total white blood count (WBC), lymphocyte percentage, plateletes, and plasma HIV RNA were determined. Results HAART-experienced patients were older than their HAART-naive counterparts. In HAART-naive patients, the incidence of anemia (packed cell volume [PCV] <30%) was 57.5%, leukopenia (WBC < 2.5), 6.1%, and thrombocytopenia < 150, 9.6%; it was, significantly higher compared with their counterparts on HAART (24.3%, 1.7%, and 1.2%, respectively). The use of HAART was not associated with severe anemia. Of HAART-naive patients, 57.5% had a CD4 count < 200 cells/?L in comparison with 20.4% of HAART-experienced patients (P < 0.001). The mean viral load log10 was significantly higher in HAART-naive than in HAART-experienced patients (P < 0.001). Total lymphocyte count < 1.0 was a significant predictor of immunological parameters associated with disease progression, and death in HIV-infected patients. Total lymphocyte count fails to predict CD4 count < 200 cells/?L in our cohort; thus, its use in the management and monitoring of HIV-infected patients in our settings is not reliable. PMID:24847174

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

2013-01-01

93

A MOLECULAR MARKER MAP IN KANOTA X OGLE HEXAPLOID OAT (AVENA SP.) ENHANCED BY ADDITIONAL MARKERS AND A ROBUST FRAMEWORK  

Technology Transfer Automated Retrieval System (TEKTRAN)

Molecular mapping of cultivated oats was conducted to update the previous reference map constructed using a recombinant inbred (RI) population derived from Avena byzantina C. Koch cv. 'Kanota' X A. sativa L. cv. 'Ogle.' In the current work, 607 new markers were scored, many on a larger set of RI lin...

94

Molecular and immunological characterization of a novel polymorphic lipoprotein of Borrelia burgdorferi.  

PubMed Central

We describe the cloning, expression, and molecular characterization of a novel polymorphic Borrelia burgdorferi lipoprotein recognized by monoclonal antibody LA7. Sequence analysis revealed an open reading frame encoding a 21,866-Da polypeptide (IpLA7). Comparison with other known proteins indicated sequence similarity between IpLA7 signal peptides and those of other prokaryotic lipoproteins, including the immunodominant B. burgdorferi outer surface proteins OspA, OspB, pC, and OspD. Both natural IpLA-7 and recombinant IpLA-7 could be biosynthetically labeled with [3H]palmitate. Upon solubilization of intact B. burgdorferi with the nonionic detergent Triton X-114, IpLA7 was extracted together with other lipoproteins into the detergent phase. Indirect immunolabeling studies indicated that the epitope recognized by monoclonal antibody LA7 is mainly located in the periplasmic space. Two-dimensional gel electrophoresis and immunoblotting confirmed the calculated acidic pI of 5.7 for IpLA-7. The LA7 gene was shown to be species specific and to be located on the linear chromosome of B. burgdorferi. The analysis of 40 individual spirochetal isolates on the basis of restriction fragment length polymorphisms revealed considerable genotypic heterogeneity of LA7 corresponding to that previously found for ospA. Native IpLA-7 and recombinant IpLA-7 were recognized by immune sera from infected mice as well as some human sera derived from infected but healthy donors and may thus prove useful as an additional marker for the serodiagnosis of Lyme disease. Images PMID:8104894

Wallich, R; Simon, M M; Hofmann, H; Moter, S E; Schaible, U E; Kramer, M D

1993-01-01

95

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

96

Cellular and molecular functions of hepatic stellate cells in inflammatory responses and liver immunology  

PubMed Central

The liver is a central immunological organ. Liver resident macrophages, Kupffer cells (KC), but also sinusoidal endothelial cells, dendritic cells (DC) and other immune cells are involved in balancing immunity and tolerance against pathogens, commensals or food antigens. Hepatic stellate cells (HSCs) have been primarily characterized as the main effector cells in liver fibrosis, due to their capacity to transdifferentiate into collagen-producing myofibroblasts (MFB). More recent studies elucidated the fundamental role of HSC in liver immunology. HSC are not only the major storage site for dietary vitamin A (Vit A) (retinol, retinoic acid), which is essential for proper function of the immune system. This pericyte further represents a versatile source of many soluble immunological active factors including cytokines [e.g., interleukin 17 (IL-17)] and chemokines [C-C motif chemokine (ligand) 2 (CCL2)], may act as an antigen presenting cell (APC), and has autophagy activity. Additionally, it responds to many immunological triggers via toll-like receptors (TLR) (e.g., TLR4, TLR9) and transduces signals through pathways and mediators traditionally found in immune cells, including the Hedgehog (Hh) pathway or inflammasome activation. Overall, HSC promote rather immune-suppressive responses in homeostasis, like induction of regulatory T cells (Treg), T cell apoptosis (via B7-H1, PDL-1) or inhibition of cytotoxic CD8 T cells. In conditions of liver injury, HSC are important sensors of altered tissue integrity and initiators of innate immune cell activation. Vice versa, several immune cell subtypes interact directly or via soluble mediators with HSC. Such interactions include the mutual activation of HSC (towards MFB) and macrophages or pro-apoptotic signals from natural killer (NK), natural killer T (NKT) and gamma-delta T cells (?? T-cells) on activated HSC. Current directions of research investigate the immune-modulating functions of HSC in the environment of liver tumors, cellular heterogeneity or interactions promoting HSC deactivation during resolution of liver fibrosis. Understanding the role of HSC as central regulators of liver immunology may lead to novel therapeutic strategies for chronic liver diseases. PMID:25568859

2014-01-01

97

The molecular marker of kdr against fenpropathrin in Tetranychus cinnabarinus.  

PubMed

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

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

2013-12-01

98

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

Microsoft Academic Search

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

Li Zhou; Yang Wang; Jian-Fang Gui

2001-01-01

99

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. PMID:18506399

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

2009-01-01

100

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

101

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

PubMed Central

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

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

2014-01-01

102

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

PubMed

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

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

2014-09-01

103

Molecular Markers Show How Pollen and Seed Dispersal Affect Population Genetic  

E-print Network

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

Standiford, Richard B.

104

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...

105

Identification of Putative Molecular Markers Associated with Root Traits in Coffea canephora Pierre ex Froehner  

PubMed Central

Coffea canephora exhibit poor root system and are very sensitive to drought stress that affects growth and production. Deeper root system has been largely empirical as better avoidance to soil water limitation in drought condition. The present study aimed to identify molecular markers linked to high root types in Coffea canephora using molecular markers. Contrasting parents, L1 valley with low root and S.3334 with high root type, were crossed, and 134 F1 individuals were phenotyped for root and associated physiological traits (29 traits) and genotyped with 41 of the 320 RAPD and 9 of the 55 SSR polymorphic primers. Single marker analysis was deployed for detecting the association of markers linked to root associated traits by SAS software. There were 13 putative RAPD markers associated with root traits such as root length, secondary roots, root dry weight, and root to shoot ratio, in which root length associated marker OPS1850 showed high phenotypic variance of 6.86%. Two microsatellite markers linked to root length (CPCM13400) and root to shoot ratio (CM211300). Besides, 25 markers were associated with more than one trait and few of the markers were associated with positively related physiological traits and can be used in marker assisted trait selection.

Achar, Devaraja; Awati, Mallikarjuana G.; Udayakumar, M.; Prasad, T. G.

2015-01-01

106

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

107

Molecular Markers Reveal Exclusively Clonal Reproduction in Trichophyton rubrum  

PubMed Central

Genotypic variability among 96 Trichophyton rubrum strains which displayed different colony morphologies and were collected from four continents was investigated. Twelve markers representing 57 loci were analyzed by PCR fingerprinting, amplified fragment length polymorphism, and random amplified monomorphic DNA markers. Interestingly, none of the methods used revealed any DNA polymorphism, indicating a strictly clonal mode of reproduction and a strong adaptation to human skin. PMID:10523582

Gräser, Y.; Kühnisch, J.; Presber, W.

1999-01-01

108

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

109

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

USGS Publications Warehouse

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

Atkinson, Carter T.; Paxton, Eben H.

2013-01-01

110

Targeting the molecular and cellular interactions of the bone marrow niche in immunologic disease.  

PubMed

Recent investigations have expanded our knowledge of the regulatory bone marrow (BM) niche, which is critical in maintaining and directing hematopoietic stem cell (HSC) self-renewal and differentiation. Osteoblasts, mesenchymal stem cells (MSCs), and CXCL12-abundant reticular (CAR) cells are niche components in close association with HSCs and have been more clearly defined in immune cell function and homeostasis. Importantly, cellular inhabitants of the BM niche signal through G protein-coupled surface receptors (GPCRs) for various appropriate immune functions. In this article, recent literature on BM niche inhabitants (HSCs, osteoblasts, MSCs, CAR cells) and their GPCR mechanistic interactions are reviewed for better understanding of the BM cells involved in immune development, immunologic disease, and current immune reconstitution therapies. PMID:24408534

Brozowski, Jaime M; Billard, Matthew J; Tarrant, Teresa K

2014-02-01

111

A comprehensive study on the immunological reactivity of the Hsp90 molecular chaperone.  

PubMed

Periodontitis is a chronic infectious disease, Porphyromonas gingivalis being the most implicated pathogen. In the present study, we investigated the role of P. gingivalis HtpG (PgHtpG), a bacterial ortholog of mammalian Hsp90, in the growth of P. gingivalis and also assessed the immunological cross-reactivity of the members of the Hsp90 family. Antiserum against rat liver Hsp90 potently reacted with yeast Hsp90, called Hsc82, and also weakly with human Hsp90 (hHsp90) and human mitochondrial paralog Trap1, but did not react with PgHtpG, Escherichia coli HtpG, or human endoplasmic reticulum paralog Grp94. Moreover, among 19 monoclonal antibodies raised against hHsp90, nine cross-reacted with yeast Hsc82, and one with human Grp94, but none bound to PgHtpG or E. coli HtpG. Among them, three mAbs that strongly reacted with yeast Hsc82 recognized Asn(291)-Ile(304), a conserved region of the family protein. The polyclonal antibody raised against a peptide, Met(315)-Glu(328), of human Grp94, which corresponded to the conserved region of hHsp90, cross-reacted with hHsp90, but not with other Hsp90-family members. Thus, although mammalian Hsp90 shares some immunological reactivity with yeast Hsc82, human Grp94, and human Trap1, it is considerably distinct from its bacterial ortholog, HtpG. Disruption of the P. gingivalis htpG gene neither affected bacterial survival nor altered the sensitivity of P. gingivalis to various forms of stress. PMID:15632312

Kawano, Toshihiro; Kobayakawa, Takeshi; Fukuma, Yutaka; Yukitake, Hideharu; Kikuchi, Yuichiro; Shoji, Mikio; Nakayama, Koji; Mizuno, Akio; Takagi, Takashi; Nemoto, Takayuki K

2004-11-01

112

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...

113

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. PMID:20683483

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

2011-01-01

114

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 ...

115

No selection on immunological markers in response to a highly virulent pathogen in an Arctic breeding bird  

PubMed Central

In natural populations, epidemics provide opportunities to look for intense natural selection on genes coding for life history and immune or other physiological traits. If the populations being considered are of management or conservation concern, then identifying the traits under selection (or ‘markers’) might provide insights into possible intervention strategies during epidemics. We assessed potential for selection on multiple immune and life history traits of Arctic breeding common eiders (Somateria mollissima) during annual avian cholera outbreaks (summers of 2006, 2007 & 2008). We measured prelaying body condition, immune traits, and subsequent reproductive investment (i.e., clutch size) and survival of female common eiders and whether they were infected with Pasteurella multocida, the causative agent of avian cholera. We found no clear and consistent evidence of directional selection on immune traits; however, infected birds had higher levels of haptoglobin than uninfected birds. Also, females that laid larger clutches had slightly lower immune responses during the prelaying period reflecting possible downregulation of the immune system to support higher costs of reproduction. This supports a recent study indicating that birds investing in larger clutches were more likely to die from avian cholera and points to a possible management option to maximize female survival during outbreaks. PMID:25469158

Legagneux, Pierre; Berzins, Lisha L; Forbes, Mark; Harms, Naomi Jane; Hennin, Holly L; Bourgeon, Sophie; Gilchrist, H G; Bêty, Joël; Soos, Catherine; Love, Oliver P; Foster, Jeffrey T; Descamps, Sébastien; Burness, Gary

2014-01-01

116

A Comparison of Three Molecular Markers for the Identification of Populations of Globodera pallida.  

PubMed

Potato cyst nematodes cost the potato industry substantial financial losses annually. Through the use of molecular markers, the distribution and infestation routes of these nematodes can be better elucidated, permitting the development of more effective preventative methods. Here we assess the ability of three molecular markers to resolve multiple representatives of five Globodera pallida populations as monophyletic groups. Molecular markers included a region of the rbp-1 gene (an effector), a non-coding nuclear DNA region (the ITS region), and a novel marker for G. pallida, a ?3.4 kb non-coding mitochondrial DNA (mtDNA) region. Multiple phylogenetic analysis methods were performed on the three DNA regions separately, and on a data set of these three regions combined. The analyses of the combined data set were similar to that of the sole mtDNA marker; resolving more populations as monophyletic groups, relative to that of the ITS region and rbp-1 gene region. This suggests that individual markers may be inadequate for distinguishing populations of G. pallida. The use of this new non-coding mtDNA marker may provide further insights into the historical distribution of G. pallida, as well as enable the development of more sensitive diagnostic methods. PMID:23482966

Hoolahan, Angelique H; Blok, Vivian C; Gibson, Tracey; Dowton, Mark

2012-03-01

117

Identifying molecular markers associated with stigma characteristics in rice  

Technology Transfer Automated Retrieval System (TEKTRAN)

Stigma characteristics play essential roles in hybrid seed production of rice and marker-assisted breeding plays essential role because they are quantitatively inherited with single-flowered perfect spikelet. Ninety four accessions originated from 47 countries were selected from the USDA rice core c...

118

MOLECULAR MARKER ASSISTED BREEDING FOR DISEASE RESISTANCE IN COMMON BEAN  

Technology Transfer Automated Retrieval System (TEKTRAN)

There have been 40 sequence characterized amplified region (SCAR) markers (http://www.usda.prosser.wsu.edu/miklas/Scartable3.pdf) generated across laboratories that are available for indirect selection of 27 qualitatively and 8 quantitatively expressed genes conditioning resistance to bacterial, fun...

119

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

PubMed Central

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

Kirk, Heather; Freeland, Joanna R.

2011-01-01

120

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

PubMed

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

Khadivi-Khub, Abdollah; Soorni, Aboozar

2014-06-01

121

Molecular markers to study competition and diversity of Rhizobium  

Microsoft Academic Search

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

A. Sessitsch

1997-01-01

122

EVALUATION OF GENETIC DIVERSITY IN SORGHUM GERMPLASM USING MOLECULAR MARKERS  

Technology Transfer Automated Retrieval System (TEKTRAN)

In molecular breeding, there is an increasing demand for the establishment of molecular profiles for each of germplasm accession, so that specific germplasm accession can be selected for various crop breeding purposes. Presently sorghum represents one of the largest germplasm collections, comprisin...

123

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

PubMed Central

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

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

2013-01-01

124

A new set of molecular markers for the genotyping of Babesia bovis isolates.  

PubMed

Babesia bovis is a tick-borne apicomplexan pathogen that remains an important constraint for the development of cattle industries worldwide. The existence of different strains and subpopulations has long been described in this hemoparasite. However, few molecular markers have been reported for strain genotyping and characterization. Minisatellite sequences show high levels of variation and therefore provide excellent tools for both the genotyping and population genetic analysis. In this work we report a set of five molecular markers containing minisatellites that showed a variable degree of polymorphism in several American strains. We have used a bioinformatics approach to search for marker sequences contained in open reading frames. Five genes were chosen and primers were designed in conserved regions flanking the repeat region. Two of the genes were the previously described Bv80/Bb-1 and TRAP. The other three genes were named p200, Antigen 3 and Desmoyokin. Amplification by PCR, sequencing and comparative analysis of 11 strains from Argentina, Brazil, Uruguay, Mexico and USA determined that the tandem repeats varied in number and sequence among the isolates. Genome analysis of the five markers revealed that they were single copy and distributed across the four B. bovis chromosomes. When the new markers were analyzed in an experimental infection, absolute sequence conservation was found, indicating the stability of these markers during the course of infection. These markers were also stable during three syringe passages through calves. The application of this panel of molecular markers could provide new molecular tools for the genotyping of B. bovis isolates and analysis of changes in parasite populations following vaccination. PMID:19251367

Wilkowsky, S E; Moretta, R; Mosqueda, J; Gil, G; Echaide, I; Lía, V; Falcón, A; Florin Christensen, M; Farber, M

2009-04-01

125

Characterization of Italian lentil ( Lens culinaris Medik.) germplasm by agronomic traits, biochemical and molecular markers  

Microsoft Academic Search

Genetic relationships, agronomic, nutritional and technological traits of ten Italian landraces, two improved lines and two\\u000a cultivars of lentil (Lens culinaris Medik.) were investigated using a multi-disciplinary approach. Seed storage proteins, used as biochemical markers, were able\\u000a to detect polymorphisms with variability mainly related to the polypeptide abundance. Microsatellite (SSR) molecular markers\\u000a provided very useful information on genetic variation and

Massimo Zaccardelli; Francesco Lupo; Angela Rosa Piergiovanni; Gaetano Laghetti; Gabriella Sonnante; Maria Gloria Daminati; Francesca Sparvoli; Lucia Lioi

126

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

Microsoft Academic Search

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

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

2008-01-01

127

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

PubMed Central

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 degree of information provided by its large number of alleles per locus. Despite this, a new marker type, named SNP, for Single Nucleotide Polymorphism, is now on the scene and has gained high popularity, even though it is only a bi-allelic type of marker. In this review, we will discuss the reasons for this apparent step backwards, and the pertinence of the use of SNPs in animal genetics, in comparison with other marker types. PMID:12081799

Vignal, Alain; Milan, Denis; SanCristobal, Magali; Eggen, André

2002-01-01

128

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

PubMed

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

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

2013-01-01

129

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

PubMed

The dogfish (Squalus acanthias) can make rapid adjustments to gill acid-base transfers to compensate for internal acidosis/alkalosis. Branchial Na+/H+ exchange (NHE) has been postulated as one mechanism driving the excretion of H+ following acidosis. We have cloned gill cDNA that includes an open reading frame coding for a 770-residue protein most homologous (approximately 71%) to mammalian NHE2. RT-PCR revealed NHE2 transcripts predominantly in gill, stomach, rectal gland, intestine, and kidney. In situ hybridization with an antisense probe against NHE2 in gill sections revealed a strong mRNA signal from a subset of interlamellar and lamellae cells. We developed dogfish-specific polyclonal antibodies against NHE2 that detected a approximately 70-kDa protein in Western blots and immunologically recognized branchial cells having two patterns of protein expression. Cytoplasmic and apical NHE2 immunoreactivity were observed in cells coexpressing basolateral Na+-K+-ATPase. Other large ovoid cells more generally staining for NHE2 also were strongly positive for basolateral H+-ATPase. Gill mRNA levels for NHE2 and H+-ATPase did not change following systemic acidosis (as measured by quantitative PCR 2 h after a 1- or 2-meq/kg acid infusion). These data indicate that posttranslational adjustments of NHE2 and other transport systems (e.g., NHE3) following acidosis may be of importance in the short-term pH adjustment and net branchial H+ efflux observed in vivo. NHE2 may play multiple roles in the gills, involved with H+ efflux from acid-secreting cells, basolateral H+ reabsorption for pHi regulation, and in parallel with H+-ATPase for the generation of HCO3(-) in base-secreting cells. PMID:18094061

Claiborne, James B; Choe, Keith P; Morrison-Shetlar, Alison I; Weakley, Jill C; Havird, Justin; Freiji, Abe; Evans, David H; Edwards, Susan L

2008-03-01

130

Phylogeny of African cichlid fishes as revealed by molecular markers.  

PubMed

The species flocks of cichlid fish in the three great East African Lakes, Victoria, Malawi, and Tanganyika, have arisen in each lake by explosive adaptive radiation. Various questions concerning their phylogeny have not yet been answered. In particular, the identity of the ancestral founder species and the monophyletic origin of the haplochromine cichlids from the East African lakes have not been established conclusively. In the present study, we used the anonymous nuclear DNA marker DXTU1 as a step towards answering these questions. A 280 bp-fragment of the DXTU1 locus was amplified by the polymerase chain reaction from East African lacustrine species, the East African riverine cichlid species Haplochromis bloyeti, H. burtoni and H. sparsidens, and other African cichlids. Sequencing revealed several indels and substitutions that were used as cladistically informative markers to support a phylogenetic tree constructed by the neighbor-joining method. The topology, although not supported by high bootstrap values, corresponds well to the geographical distribution and previous classification of the cichlids. Markers could be defined that: (i) differentiate East African from West African cichlids; (ii) distinguish the riverine and Lake Victoria/Malawi haplochromines from Lake Tanganyika cichlids; and (iii) indicate the existence of a monophyletic Lake Victoria cichlid superflock which includes haplochromines from satellite lakes and East African rivers. In order to resolve further the relationship of East African riverine and lacustrine species, mtDNA cytochrome b and control region segments were sequenced. The mtDNA-based trees support the notion of the monophyly of the Lake Victoria superflock but are ambiguous with respect to the phylogenetic position of the Lake Malawi flock. PMID:9675872

Mayer, W E; Tichy, H; Klein, J

1998-06-01

131

[Immunological safety of transfusion].  

PubMed

Transfusion safety lies on the strict application of measures aimed: at avoiding the occurrence of acute hazards, as far as they can be prevented by e.g. the ABO compatibility for red blood cell concentrates and therapeutic plasma; at reducing the frequency of other acute accidents such as TRALI or post-transfusion GVH (based on the implementation of measures which prove to be largely efficacious though not completely); and at reducing delayed incidents and hazards. The implementation of such immunological safety measures also aim at favoring the transfusion efficacy, in avoiding the lysis of transfused red cells or platelets. Perfect immunological compatibility (match) is impossible because transfused cells expose several hundreds of molecular variants with antigenic properties. Adaptive immunity is largely based upon antigen/antibody conflicts and it predominates in transfusion immunological hazards, but inflammation (as well as other components of innate immunity) is now acknowledged as a major actor of transfusion immunological linked hazards. PMID:25578545

Muller, Jean-Yves; Chiaroni, Jacques; Garraud, Olivier

2015-02-01

132

Molecular and cellular markers of toxicity in the Japanese Medaka @  

SciTech Connect

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

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

1990-01-01

133

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

PubMed Central

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

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

2001-01-01

134

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. PMID:22315588

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

2011-01-01

135

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

PubMed

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

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

2011-01-01

136

Novel molecular, cytotoxical, and immunological study on promising and selective anticancer activity of Mung bean sprouts  

PubMed Central

Background The anticancer and immunomodulatory activity of mung bean sprouts (MBS) and the underlying mechanisms against human cervical and hepatocarcinoma cancer cells were explored. Methods MBS cytotoxicity and MBS-induced anticancer cytokines, TNF-? and IFN-? from cancer cells, and immunological cytokines, IL-4, IFN-?, and IL-10 from peripheral mononuclear cells (PMNC) were assessed by MTS and ELISA assays. Apoptotic cells were investigated by flow cytometry. The expression level of apoptotic genes (Bax, BCL-2, Capsases 7–9) and cell cycle regulatory genes (cyclin D, E, and A) and tumor suppressor proteins (p27, p21, and p53) was assessed by real-time qPCR in the cancer cells treated with extract IC50. Results The cytotoxicity on normal human cells was significantly different from HeLa and HepG2 cells, 163.97 ± 5.73, 13.3 ± 0.89, and 14.04 ± 1.5 mg/ml, respectively. The selectivity index (SI) was 12.44 ± 0.83 for HeLa and 11.94 ± 1.2 for HepG2 cells. Increased levels of TNF-? and IFN-? were observed in the treated HeLa and HepG2 culture supernatants when compared with untreated cells. MBS extract was shown to be an immunopolarizing agent by inducing IFN? and inhibiting IL-4 production by PBMC; this leads to triggering of CMI and cellular cytotoxicity. The extract induced apoptosis, in a dose and time dependent manner, in treated HeLa and HepG2, but not in untreated, cells (P < 0.05). The treatment significantly induced cell cycle arrest in G0/G1 in HeLa cells. The percentage of cells in G0/G1 phase of the treated HeLa cells increased from 62.87 ± 2.1%, in untreated cells, to 80.48 ± 2.97%. Interestingly, MBS IC50 induced the expression of apoptosis and tumor suppressor related genes in both HeLa and HepG2 cells. MBS extract succeeded in inducing cdk-inhibitors, p21, p53, and p27 in HeLa cells while it induced only p53 in HepG2 cells (P < 0.05). This is a clue for the cell type- specific interaction of the studied extract. These proteins inhibit the cyclin-cdk complexes apart from the presence of some other components that might stimulate some cyclins such as cyclin E, A, and D. Conclusion MBS extract was shown to be a potent anticancer agent granting new prospects of anticancer therapy using natural products. PMID:23122182

2012-01-01

137

Mapping the evolutionary twilight zone: molecular markers, populations and  

E-print Network

Departamento de Biologia Geral, ICB, Universidade Federal de Goia´s. Cx.P. 131, 74.001-970 Goia^nia, 2 Laborato, Caixa Postal 15053, 91501-970 Porto Alegre, RS, 5 Departamento de Biologia Geral, ICB, UFMG, Belo Horizonte, MG, 6 Laborato´rio de Biodiversidade Molecular, Departamento de Gene´tica, Instituto de Biologia

Solé-Cava, Antonio M.

138

Molecular markers for breast cancer diagnosis, prognosis and targeted therapy.  

PubMed

Precision medicine involves understanding the molecular drivers unique to an individual patient's cancer so that specific factors may be targeted with the goal of improved patient outcomes. The purpose of this article is to review standard of care and research grade (non-standard of care) biomarkers in breast cancer that may be useful for diagnosis, prognosis and targeted therapy. PMID:25091830

Lang, Julie E; Wecsler, Julie S; Press, Michael F; Tripathy, Debasish

2015-01-01

139

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

PubMed

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

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

2012-11-20

140

Identification of RAPD markers and their use for molecular mapping in pea (Pisum sativum L.).  

PubMed

The RAPD method (Random Amplified Polymorphic DNA) was used for identifying and mapping new molecular markers in pea. RAPD analysis of various cultivars and lines of pea was carried out using 10-mer random primers. The presence of multiple polymorphism between cultivars and lines was revealed; at least one fragment for any given primer was present in the DNA of one form of pea and absent in the DNA of another line or cultivar. To detect molecular markers linked to the genes of chi-15, xa-18 and also to the 12 morphological markers of the L-1238 line, the F2 populations (Chi-15 ? L-1238), (Vio ? L-1238), (Xa-18 ? L-1238), (L-111 ? Chi-15) and (L-84 ? Xa-18) were studied via bulked segregant analysis. DNA molecular analysis of F1 hybrids revealed the presence of parental polymorphic fragments in all of the populations. The study of the F2 plants showed that the obtained fragments are inherited as Mendelian factors. 13 RAPD-markers linked to genes of A/a (flower color), I/i (seed color), Gp/gp (pod color), R/r (seed form), S/s (seeds linkage), and also to genes of Chi-15/chi-15 (leaf color) and Xa-18/xa-18 (leaf color) were discovered. The study of individual plant DNA from the F2 populations allowed us to determine the genetic distances between genes and the RAPD markers linked to them. PMID:12378223

Cheghamirza, Kianoosh; Koveza, Oksana; Konovalov, Fedor; Gostimsky, Sergei

2002-01-01

141

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

PubMed

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 and nitrogen containing substances (4-ethylnitrobenzene, formyl piperidine, acetyl piperidine). In addition to well-known anthropogenic markers various new molecular tracers were detected and are discussed, namely plasticizers (alkylsulfonic acid aryl esters, tributyl and tricresyl phosphates), synthetic fragrances (galaxolide, tonalide, 4-oxoisophorone), additives of personal care products (4-methoxycinnamic acid 2-ethylhexyl ester, benzyl benzoate, dibenzyl ether, benzophenone), occurring due to sewage treatment plant input. PMID:12753838

Ricking, M; Schwarzbauer, J; Franke, S

2003-06-01

142

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

PubMed Central

Narrow genetic base and complex allotetraploid genome of cotton (Gossypium hirsutum L.) is stimulating efforts to avail required polymorphism for marker based breeding. The availability of draft genome sequence of G. raimondii and G. arboreum and next generation sequencing (NGS) technologies facilitated the development of high-throughput marker technologies in cotton. The concepts of genetic diversity, QTL mapping, and marker assisted selection (MAS) are evolving into more efficient concepts of linkage disequilibrium, association mapping, and genomic selection, respectively. The objective of the current review is to analyze the pace of evolution in the molecular marker technologies in cotton during the last ten years into the following four areas: (i) comparative analysis of low- and high-throughput marker technologies available in cotton, (ii) genetic diversity in the available wild and improved gene pools of cotton, (iii) identification of the genomic regions within cotton genome underlying economic traits, and (iv) marker based selection methodologies. Moreover, the applications of marker technologies to enhance the breeding efficiency in cotton are also summarized. Aforementioned genomic technologies and the integration of several other omics resources are expected to enhance the cotton productivity and meet the global fiber quantity and quality demands. PMID:25401149

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

2014-01-01

143

A new set of molecular markers for the genotyping of Babesia bovis isolates  

Microsoft Academic Search

Babesia bovis is a tick-borne apicomplexan pathogen that remains an important constraint for the development of cattle industries worldwide. The existence of different strains and subpopulations has long been described in this hemoparasite. However, few molecular markers have been reported for strain genotyping and characterization. Minisatellite sequences show high levels of variation and therefore provide excellent tools for both the

S. E. Wilkowsky; R. Moretta; J. Mosqueda; G. Gil; I. Echaide; V. Lía; A. Falcón; M. Florin Christensen; M. Farber

2009-01-01

144

Proceedings of the second international symposium on molecular markers in horticulture Acta Horticulturae  

Technology Transfer Automated Retrieval System (TEKTRAN)

The second International Symposium on Molecular Markers in Horticulture was held at the CH2M Hill Alumni Center at Oregon State University (OSU), Corvallis (Oregon, US), from July 29 to August 1st, 2009. This symposium was convened by a scientist at the National Clonal Germplasm Repository (NCGR) of...

145

Land ahead: using genome scans to identify molecular markers of adaptive relevance  

Microsoft Academic Search

Adaptation is back on the research schedules of evolutionists and ecologists. This renewed interest is driven by global change, to which species, in particular arctic and alpine ones, either react by migration or adaptation. In this overview, we give a brief introduction to the use of genome scans along with environmental data to identify molecular markers of adaptive relevance. This

Rolf Holderegger; Doris Herrmann; Bénédicte Poncet; Felix Gugerli; Wilfried Thuiller; Pierre Taberlet; Ludovic Gielly; Delphine Rioux; Sabine Brodbeck; Serge Aubert; Stéphanie Manel

2008-01-01

146

Progression of Hair Cell Ejection and Molecular Markers of Apoptosis in the  

E-print Network

Progression of Hair Cell Ejection and Molecular Markers of Apoptosis in the Avian Cochlea following-dependent apoptotic death in inner ear sensory hair cells. The timing of apoptotic signaling in sensory hair cells- nocytochemical techniques to document the following responses in affected hair cells: T-cell restricted

147

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

148

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

149

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

ERIC Educational Resources Information Center

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

Helms, T. C.; Doetkott, C.

2007-01-01

150

Molecular genetic variation in cultivated peanut cultivars and breeding lines revealed by highly informative SSR markers  

Technology Transfer Automated Retrieval System (TEKTRAN)

Groundnut or peanut (Arachis hypogaea L.) is an economically important crop worldwide as a source of protein and cooking oil, particularly in developing countries. Because of its narrow genetic background and shortage of polymorphic genetic markers, molecular characterization of cultivated peanuts e...

151

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

152

Assessing Cheatgrass (Bromus tectorum) genetic diversity and population structure using RAPD and microsatellite molecular markers  

Technology Transfer Automated Retrieval System (TEKTRAN)

Two molecular marker systems, random amplified polymorphic DNA (RAPD) and microsatellites, were used to evaluate population diversity and differentiation in four northern Nevada Bromus tectorum populations. We found 16 RAPD primers that yielded 165 strong repeatable bands. Of those bands, 60 (35.8%...

153

Molecular markers in the Portuguese Bísaro pig: screening for breed specific microsatellites  

Microsoft Academic Search

SUMMARY - A large number of autochthonous breeds of domestic animals are endangered. The Portuguese indigenous pig breed Bísaro is reduced to a small number of animals mostly restricted to the Trás-os-Montes province. In order to prevent its extinction and preserve genetic variability fast measures are needed. Among molecular markers to assess the genetic variability microsatellites are the most widely

M. C. Guerreiro-Pereira; J. Matos; A. M. Ramos; F. Simões; A. Clemente; T. Rangel-Figueiredo

154

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...

155

MOLECULAR DNA MARKERS UTILIZED TO DISCERN ALFALFA FALL DORMANCY CHECK CULTIVARS  

Technology Transfer Automated Retrieval System (TEKTRAN)

Alfalfa cultivars are difficult to distinguish based upon morphological traits. Only a few morphological traits have been used to describe alfalfa. Molecular markers especially simple sequence repeats (SSR) have not been utilized in alfalfa to characterize alfalfa cultivars. This study was conduct...

156

Molecular markers highlight variation within and among Kentucky bluegrass varieties and accessions  

Technology Transfer Automated Retrieval System (TEKTRAN)

Assessing relationships among germplasm and cultivars of Kentucky bluegrass (Poa pratensis L.) is limited to field evaluations or a small set of molecular markers. To improve the efficiency of characterizing Kentucky bluegrass cultivars and germplasm, this study was designed to develop a larger set...

157

Supplementary Material Paper: Organic molecular markers and signature from wood combustion  

E-print Network

1 Supplementary Material Paper: Organic molecular markers and signature from wood combustion of the particle, and the vaporisation of the non- refractory compounds. One of the most problematic parts mass versus the PM2.5 mass concentration from the TEOM subtracted by the BC mass colored by the nitrate

Meskhidze, Nicholas

158

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...

159

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...

160

Development of molecular genetic markers from a cDNA subtraction library of Frosty Pod inoculated cacao  

Technology Transfer Automated Retrieval System (TEKTRAN)

We have been employing a candidate gene approach to identify molecular markers associated with disease resistance in Theobroma cacao. Candidate genes can be turned into molecular markers using single strand conformation polymorphism (SSCP) analysis. As a novel approach to identifying genes associa...

161

Biomedical wellness monitoring system based upon molecular markers  

NASA Astrophysics Data System (ADS)

We wish to assist caretakers with a sensor monitoring systems for tracking the physiological changes of homealone patients. One goal is seeking biomarkers and modern imaging sensors like stochastic optical reconstruction microscopy (STORM), which has achieved visible imaging at the nano-scale range. Imaging techniques like STORM can be combined with a fluorescent functional marker in a system to capture the early transformation signs from wellness to illness. By exploiting both microscopic knowledge of genetic pre-disposition and the macroscopic influence of epigenetic factors we hope to target these changes remotely. We adopt dual spectral infrared imaging for blind source separation (BSS) to detect angiogenesis changes and use laser speckle imaging for hypertension blood flow monitoring. Our design hypothesis for the monitoring system is guided by the user-friendly, veteran-preferred "4-Non" principles (noninvasive, non-contact, non-tethered, non-stop-to-measure) and by the NIH's "4Ps" initiatives (predictive, personalized, preemptive, and participatory). We augment the potential storage system with the recent know-how of video Compressive Sampling (CSp) from surveillance cameras. In CSp only major changes are saved, which reduces the manpower cost of caretakers and medical analysts. This CSp algorithm is based on smart associative memory (AM) matrix storage: change features and detailed scenes are written by the outer-product and read by the inner product without the usual Harsh index for image searching. From this approach, we attempt to design an effective household monitoring approach to save healthcare costs and maintain the quality of life of seniors.

Ingram, Whitney

2012-06-01

162

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

163

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. PMID:21637550

Küpper Cardoso Perseguini, Juliana Morini; Chioratto, Alisson Fernando; Zucchi, Maria Imaculada; Colombo, Carlos Augusto; Carbonell, Sérgio 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

164

Cytogenetic and molecular markers for detecting Aegilops uniaristata chromosomes in a wheat background.  

PubMed

Aegilops uniaristata has many agronomically useful traits that can be used for wheat breeding. So far, a Triticum turgidum - Ae. uniaristata amphiploid and one set of Chinese Spring (CS) - Ae. uniaristata addition lines have been produced. To guide Ae. uniaristata chromatin transformation from these lines into cultivated wheat through chromosome engineering, reliable cytogenetic and molecular markers specific for Ae. uniaristata chromosomes need to be developed. Standard C-banding shows that C-bands mainly exist in the centromeric regions of Ae. uniaristata but rarely at the distal ends. Fluorescence in situ hybridization (FISH) using (GAA)8 as a probe showed that the hybridization signal of chromosomes 1N-7N are different, thus (GAA)8 can be used to identify all Ae. uniaristata chromosomes in wheat background simultaneously. Moreover, a total of 42 molecular markers specific for Ae. uniaristata chromosomes were developed by screening expressed sequence tag - sequence tagged site (EST-STS), expressed sequence tag - simple sequence repeat (EST-SSR), and PCR-based landmark unique gene (PLUG) primers. The markers were subsequently localized using the CS - Ae. uniaristata addition lines and different wheat cultivars as controls. The cytogenetic and molecular markers developed herein will be helpful for screening and identifying wheat - Ae. uniaristata progeny. PMID:25486537

Gong, Wenping; Li, Guangrong; Zhou, Jianping; Li, Genying; Liu, Cheng; Huang, Chengyan; Zhao, Zhendong; Yang, Zujun

2014-09-01

165

The natural profilin from Russian thistle (Salsola kali) contains a low IgE-binding ability isoform--molecular and immunological characterization.  

PubMed

Chenopodiaceae pollens such as those from Salsola kali and Chenopodium album are important causes of allergy in Mediterranean areas because of the progress of desertification in European countries. Among the various allergenic protein families, profilins constitute a group of pan-allergens that are involved in polysensitization and pollen-food allergy syndrome. Two-dimensional electrophoresis analysis of S. kali profilin highlighted a polymorphic pattern, with several isoforms that have different molecular features (isoelectric point and molecular mass) and immunological features. Two isoforms have been cloned and sequenced. Sal k 4.02 and Sal k 4.03 displayed non-conservative amino acid changes in critical positions of the IgE epitopes. Both isoforms were produced in Escherichia coli and structurally and spectroscopically characterized. Changes in the electrophoretic mobility and in their IgG and IgE immunological behavior were observed in comparison with Che a 2, their counterpart from C. album. The IgE-binding ability of Sal k 4.03 is similar to that of Che a 2, whereas Sal k 4.02 showed a 35% reduction in IgE binding in 86% of patients, suggesting a hypoallergenic character. Three-dimensional modeling allowed us to propose which amino acid residues are involved in those immunological changes based on epitope mapping studies previously performed in other profilins. These profilin isoforms constitute suitable candidates for specific immunotherapy with recombinant allergens. PMID:23043287

Mas, Salvador; Barderas, Rodrigo; Colás, Carlos; Quiralte, Joaquín; Rodríguez, Rosalía; Villalba, Mayte

2012-12-01

166

Molecular and immunological characterization of Babesia gibsoni and Babesia microti heat shock protein-70.  

PubMed

Serological immunoscreening was used to identify a gene encoding heat shock protein-70 from Babesia gibsoni (BgHSP-70) that showed high homology with HSP-70s from other apicomplexan parasites. This gene corresponded to a full-length cDNA containing an open reading frame of 1968 bp predicted to result in a 70-kDa mature protein consisting of 656 amino acids. Analysis of the expression levels of BgHSP-70 indicated elevated transcription from cultured parasites incubated at 40 degrees C for 1 h, but not at 30 degrees C. Interestingly, antiserum raised against recombinant BgHSP-70 protein reacted specifically not only with a 70-kDa protein of B. gibsoni but also with a corresponding native protein of B. microti (BmHSP-70), indicating the high degree of conservation of this protein. The BmHSP-70 gene was then isolated and characterized and the immunoprotective properties of recombinant BgHSP-70 (rBgHSP-70) and rBmHSP-70 were compared in vitro and in vivo. Both proteins had potent mitogenic effects on murine and canine mononuclear cells as evidenced by high proliferative responses and IFN-gamma production after stimulation. Immunization regimes in BALB/c and C57BL/6 mice using rBgHSP-70 and rBmHSP-70 elicited high antibody levels, with concurrent significant reductions in peripheral parasitaemias. Taken together, these results emphasize the potential of HSP-70s as a molecular adjuvant vaccine. PMID:19493212

Terkawi, M Alaa; Aboge, G; Jia, H; Goo, Y-K; Ooka, H; Yamagishi, J; Nishikawa, Y; Yokoyama, N; Igarashi, I; Kawazu, S-I; Fujisaki, K; Xuan, X

2009-06-01

167

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

USGS Publications Warehouse

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

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

1997-01-01

168

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. PMID:20419125

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

2010-01-01

169

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

PubMed

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

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

2012-09-01

170

Molecular phylogeny of elasmobranchs inferred from mitochondrial and nuclear markers.  

PubMed

The elasmobranchs (sharks, rays and skates) being the extant survivors of one of the earliest offshoots of the vertebrate evolutionary tree are good model organisms to study the primitive vertebrate conditions. They play a significant role in maintaining the ecological balance and have high economic value. Due to over-exploitation and illegal fishing worldwide, the elasmobranch stocks are being decimated at an alarming rate. Appropriate management measures are necessary for restoring depleted elasmobranch stocks. One approach for restoring stocks is implementation of conservation measures and these measures can be formulated effectively by knowing the evolutionary relationship among the elasmobranchs. In this study, a total of 30 species were chosen for molecular phylogeny studies using mitochondrial cytochrome c oxidase subunit I, 12S ribosomal RNA gene and nuclear Internal Transcribed Spacer 2. Among different genes, the combined dataset of COI and 12S rRNA resulted in a well resolved tree topology with significant bootstrap/posterior probabilities values. The results supported the reciprocal monophyly of sharks and batoids. Within Galeomorphii, Heterodontiformes (bullhead sharks) formed as a sister group to Lamniformes (mackerel sharks): Orectolobiformes (carpet sharks) and to Carcharhiniformes (ground sharks). Within batoids, the Myliobatiformes formed a monophyly group while Pristiformes (sawfishes) and Rhinobatiformes (guitar fishes) formed a sister group to all other batoids. PMID:24293104

Pavan-Kumar, A; Gireesh-Babu, P; Babu, P P Suresh; Jaiswar, A K; Hari Krishna, V; Prasasd, K Pani; Chaudhari, Aparna; Raje, S G; Chakraborty, S K; Krishna, Gopal; Lakra, W S

2014-01-01

171

Long-term monitoring of molecular markers can distinguish different seasonal patterns of fecal indicating bacteria sources.  

PubMed

Elevated levels of fecal indicator bacteria (FIB) have been observed at Topanga Beach, CA, USA. To identify the FIB sources, a microbial source tracking study using a dog-, a gull- and two human-associated molecular markers was conducted at 10 sites over 21 months. Historical data suggest that episodic discharge from the lagoon at the mouth of Topanga Creek is the main source of bacteria to the beach. A decline in creek FIB/markers downstream from upper watershed development and a sharp increase in FIB/markers at the lagoon sites suggest sources are local to the lagoon. At the lagoon and beach, human markers are detected sporadically, dog marker peaks in abundance mid-winter, and gull marker is chronically elevated. Varied seasonal patterns of FIB and source markers were identified showing the importance of applying a suite of markers over long-term spatial and temporal sampling to identify a complex combination of sources of contamination. PMID:25618519

Riedel, Timothy E; Thulsiraj, Vanessa; Zimmer-Faust, Amity G; Dagit, Rosi; Krug, Jenna; Hanley, Kaitlyn T; Adamek, Krista; Ebentier, Darcy L; Torres, Robert; Cobian, Uriel; Peterson, Sophie; Jay, Jennifer A

2015-03-15

172

Discovery of Molecular Markers to Discriminate Corneal Endothelial Cells in the Human Body  

PubMed Central

The corneal endothelium is a monolayer of hexagonal corneal endothelial cells (CECs) on the inner surface of the cornea. CECs are critical in maintaining corneal transparency through their barrier and pump functions. CECs in vivo have a limited capacity in proliferation, and loss of a significant number of CECs results in corneal edema called bullous keratopathy which can lead to severe visual loss. Corneal transplantation is the most effective method to treat corneal endothelial dysfunction, where it suffers from donor shortage. Therefore, regeneration of CECs from other cell types attracts increasing interests, and specific markers of CECs are crucial to identify actual CECs. However, the currently used markers are far from satisfactory because of their non-specific expression in other cell types. Here, we explored molecular markers to discriminate CECs from other cell types in the human body by integrating the published RNA-seq data of CECs and the FANTOM5 atlas representing diverse range of cell types based on expression patterns. We identified five genes, CLRN1, MRGPRX3, HTR1D, GRIP1 and ZP4 as novel markers of CECs, and the specificities of these genes were successfully confirmed by independent experiments at both the RNA and protein levels. Notably none of them have been documented in the context of CEC function. These markers could be useful for the purification of actual CECs, and also available for the evaluation of the products derived from other cell types. Our results demonstrate an effective approach to identify molecular markers for CECs and open the door for the regeneration of CECs in vitro. PMID:25807145

Yoshihara, Masahito; Ohmiya, Hiroko; Hara, Susumu; Kawasaki, Satoshi; Hayashizaki, Yoshihide; Itoh, Masayoshi; Kawaji, Hideya; Tsujikawa, Motokazu; Nishida, Kohji

2015-01-01

173

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

PubMed Central

Purpose Cancer-specific endothelial markers available for intravascular binding are promising targets for new molecular therapies. In this study, a molecular imaging approach of quantifying endothelial marker concentrations (EMCI) is developed and tested in highly light-absorbing melanomas. The approach involves injection of targeted imaging tracer in conjunction with an untargeted tracer, which is used to account for nonspecific uptake and tissue optical property effects on measured targeted tracer concentrations. Procedures Theoretical simulations and a mouse melanoma model experiment were used to test out the EMCI approach. The tracers used in the melanoma experiments were fluorescently labeled anti-Plvap/PV1 antibody (plasmalemma vesicle associated protein Plvap/PV1 is a transmembrane protein marker exposed on the luminal surface of endothelial cells in tumor vasculature) and a fluorescent isotype control antibody, the uptakes of which were measured on a planar fluorescence imaging system. Results The EMCI model was found to be robust to experimental noise under reversible and irreversible binding conditions and was capable of predicting expected overexpression of PV1 in melanomas compared to healthy skin despite a 5-time higher measured fluorescence in healthy skin compared to melanoma: attributable to substantial light attenuation from melanin in the tumors. Conclusions This study demonstrates the potential of EMCI to quantify endothelial marker concentrations in vivo, an accomplishment that is currently unavailable through any other methods, either in vivo or ex vivo. PMID:24217944

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

2014-01-01

174

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

PubMed

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

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

2014-01-01

175

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

PubMed

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

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

2010-04-01

176

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. PMID:23734874

2013-01-01

177

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

PubMed

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

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

2014-11-01

178

Molecular markers for yellow stem borer Scirpophaga incertulas (Walker) resistance in rice  

Microsoft Academic Search

Breeding for yellow stem borer resistance in rice is difficult owing to the complex genetics of the trait and inherent difficulties\\u000a in screening. Identification of molecular markers linked to the trait would enhance phenotypic evaluation for the trait. An\\u000a F2 population was developed using parents contrasting in their reaction to yellow stem borer resistance. Random Amplified Polymorphic\\u000a DNA (RAPD) analysis,in

A. Selvi; P. Shanmugasundaram; S. Mohan Kumar; J. A. J. Raja

2002-01-01

179

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

Microsoft Academic Search

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

M. Ragot; D. A. Hoisington

1993-01-01

180

Characterization of Italian grasspea ( Lathyrus sativus L.) germplasm using agronomic traits, biochemical and molecular markers  

Microsoft Academic Search

Genetic relationships among 13 grasspea (Lathyrus sativus L.) landraces mainly collected in Southern Italy were assessed using agronomic traits, biochemical and molecular markers.\\u000a Field trials were carried out in two locations and revealed a high influence of field locations on yield, but a low genotype × environment\\u000a interaction. Despite this, the agronomic data obtained provided useful information for the choice of the

Lucia Lioi; Francesca Sparvoli; Gabriella Sonnante; Gaetano Laghetti; Francesco Lupo; Massimo Zaccardelli

2011-01-01

181

Genetic analysis of apomixis in Citrus and Poncirus by molecular markers  

Microsoft Academic Search

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

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

1999-01-01

182

Genetic analysis of adaptation differences between highland and lowland tropical maize using molecular markers  

Microsoft Academic Search

Molecular-marker loci were used to investigate the adaptation differences between highland and lowland tropical maize. An\\u000a F2 population from the cross of two inbred lines independently derived from highland and lowland maize germplasm was developed,\\u000a and extracted F3:4 lines were phenotype in replicated field trials at four thermally diverse tropical testing sites, ranging from lowland to\\u000a extreme highland (mean growing

C. Jiang; G. O. Edmeades; I. Armstead; H. R. Lafitte; M. D. Hayward; D. Hoisington

1999-01-01

183

Phylogenetic analysis in the Festuca-Lolium complex using molecular markers and ITS rDNA  

Microsoft Academic Search

Molecular markers were used to investigate phylogenetic relationships among the eight species of ryegrass (Lolium) and 11 species of fescue (Festuca). RAPD and RFLP analyses were carried out on total bulked DNA from each population. Factorial analysis of a phenetic distance\\u000a matrix yielded three major groups: (1) fine-leaved fescues, (2) broad-leaved fescues and (3) ryegrasses. Six non-coding regions\\u000a of chloroplastic

G. Charmet; C. Ravel; F. Balfourier

1997-01-01

184

Molecular marker assisted selection and pyramiding of two QTLs for fiber strength in upland cotton.  

PubMed

Based on two major QTLs that control high fiber strength which originated from an elite fiber germ-plasm line 7235 (Gossypium hiusutum L.), the efficiency of molecular marker-assisted selection (MAS) was investigated using two populations from pedigree selection and modified backcrossing pyramiding developed for the breeding purpose. Simian 3 (SM3), a widely planted variety in the Yangtze River Valley, and 7235 were used as parents to develop the two populations. In the two major QTLs for fiber strength from 7235, QTLfs-1 could explain more than 30% of the phenotypic variation (PV) in the (7235 x TM-1) F2 population. QTLfs-2 was at first identified in another super quality fiber line HS427-10 from (HS427-10 x TM-1) F2 population with 12.5% of PV explanation,which was further also identified in 7235 line but was non-allelic with QTLfs-1. The result of molecular marker-assisted selection for fiber strength showed that the genetic effect of the QTLfs-1 was stable under different environmental conditions, and its molecular marker-assisted selection showed significant selective efficiency among breeding populations with different genetic backgrounds. QTLfs-2 also showed high selective efficiency in advanced generation populations though its effect was a little lower than the former. When QTLfs-1 was selected simultaneously with 2 molecular markers with known genetic distance, the selection efficiency for the fiber strength was greatly increased. The pyramiding for two QTLs that control high fiber strength by MAS greatly improved the selection efficiency for cotton fiber strength. This report provides a successful example of MAS pyramiding for QTL for favorable traits in breeding programs. PMID:16459656

Guo, Wang-Zhen; Zhang, Tian-Zhen; Ding, Ye-Zhang; Zhu, Yi-Chao; Shen, Xin-Lian; Zhu, Xie-Fei

2005-12-01

185

Comparison of molecular markers to detect fresh sewage in environmental waters.  

PubMed

Human-specific Bacteroides HF183 (HS-HF183), human-specific Enterococci faecium esp (HS-esp), human-specific adenoviruses (HS-AVs) and human-specific polyomaviruses (HS-PVs) assays were evaluated in freshwater, seawater and distilled water to detect fresh sewage. The sewage spiked water samples were also tested for the concentrations of traditional fecal indicators (i.e., Escherichia coli, enterococci and Clostridium perfringens) and enteric viruses such as enteroviruses (EVs), sapoviruses (SVs), and torquetenoviruses (TVs). The overall host-specificity of the HS-HF183 marker to differentiate between humans and other animals was 98%. However, the HS-esp, HS-AVs and HS-PVs showed 100% host-specificity. All the human-specific markers showed >97% sensitivity to detect human fecal pollution. E. coli, enterococci and, C. perfringens were detected up to dilutions of sewage 10(-5), 10(-4) and 10(-3) respectively. HS-esp, HS-AVs, HS-PVs, SVs and TVs were detected up to dilution of sewage 10(-4) whilst EVs were detected up to dilution 10(-5). The ability of the HS-HF183 marker to detect fresh sewage was 3-4 orders of magnitude higher than that of the HS-esp and viral markers. The ability to detect fresh sewage in freshwater, seawater and distilled water matrices was similar for human-specific bacterial and viral marker. Based on our data, it appears that human-specific molecular markers are sensitive measures of fresh sewage pollution, and the HS-HF183 marker appears to be the most sensitive among these markers in terms of detecting fresh sewage. However, the presence of the HS-HF183 marker in environmental waters may not necessarily indicate the presence of enteric viruses due to their high abundance in sewage compared to enteric viruses. More research is required on the persistency of these markers in environmental water samples in relation to traditional fecal indicators and enteric pathogens. PMID:19818987

Ahmed, W; Goonetilleke, A; Powell, D; Chauhan, K; Gardner, T

2009-11-01

186

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

PubMed

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

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

2013-01-01

187

Analysis of molecular marker expression reveals neuronal homology in distantly related arthropods.  

PubMed

Morphological studies suggest that insects and crustaceans of the Class Malacostraca (such as crayfish) share a set of homologous neurons. However, expression of molecular markers in these neurons has not been investigated, and the homology of insect and malacostracan neuroblasts, the neural stem cells that produce these neurons, has been questioned. Furthermore, it is not known whether crustaceans of the Class Branchiopoda (such as brine shrimp) or arthropods of the Order Collembola (springtails) possess neurons that are homologous to those of other arthropods. Assaying expression of molecular markers in the developing nervous systems of various arthropods could resolve some of these issues. Here, we examine expression of Even-skipped and Engrailed, two transcription factors that serve as insect embryonic CNS markers, across a number of arthropod species. This molecular analysis allows us to verify the homology of previously identified malacostracan neurons and to identify additional homologous neurons in malacostracans, collembolans and branchiopods. Engrailed expression in the neural stem cells of a number of crustaceans was also found to be conserved. We conclude that despite their distant phylogenetic relationships and divergent mechanisms of neurogenesis, insects, malacostracans, branchiopods and collembolans share many common CNS components. PMID:10225992

Duman-Scheel, M; Patel, N H

1999-06-01

188

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

PubMed Central

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

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

2014-01-01

189

Immunology Review Topics for 2nd Exam February 27, 2008  

E-print Network

Immunology Review Topics for 2nd Exam February 27, 2008 Molecular and Cellular Immunology Review, but you will not be expected to memorize the order of the genes nor their numbers. #12;Immunology Review discussion of their role in immunology, or to compare and contrast two or more terms. · Allelic Exclusion

Murphy, Robert F.

190

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

PubMed Central

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

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

2010-01-01

191

Molecular markers linked to the blast resistance gene pi-z in oryza sativa for use in marker assisted selection  

Technology Transfer Automated Retrieval System (TEKTRAN)

We have identified DNA markers that cosegregate with the blast resistance gene Pi-z using microsatellite markers found in public databases and degenerate primer pairs based on the P-loop, nucleotide binding site and kinase domain motifs of previously cloned resistance genes. These markers are ploym...

192

Integration of simple sequence repeat (SSR) markers into a molecular linkage map of common bean (Phaseolus vulgaris L.)  

Microsoft Academic Search

Microsatellite or simple sequence repeat (SSR) markers have been successfully used for genomic mapping, DNA fingerprinting, and marker-assisted selection in many plant species. Here we report the first successful assignment of 15 SSR markers to the Phaseolus vulgaris molecular linkage map. A total of 37 SSR primer pairs were developed and tested for amplification and product-length polymor- phism with BAT93

K. Yu; S. J. Park; V. Poysa; P. Gepts

2000-01-01

193

Molecular markers, genetic maps, and QTLs for peanut molecular breeding in peanut  

Technology Transfer Automated Retrieval System (TEKTRAN)

Integration of plant breeding, genetics and genomics promises to foster genetic enhancement leading to increased productivity, oil quality and resistance/tolerance to biotic and abiotic stresses. Recent advances have resulted in the development of genomic resources such as SSR markers, and genetic m...

194

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...

195

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

PubMed Central

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

Douaihy, Bouchra; Sobierajska, Karolina; Jasi?ska, Anna Katarzyna; Boraty?ska, Krystyna; Ok, Tolga; Romo, Angel; Machon, Nathalie; Didukh, Yakiv; Bou Dagher-Kharrat, Magda; Boraty?ski, Adam

2012-01-01

196

Trend of different molecular markers in the last decades for studying human migrations.  

PubMed

Anatomically modern humans are known to have widely migrated throughout history. Different scientific evidences suggest that the entire human population descended from just several thousand African migrants. About 85,000 years ago, the first wave of human migration was out of Africa, that followed the coasts through the Middle East, into Southern Asia via Sri Lanka, and in due course around Indonesia and into Australia. Another wave of migration between 40,000 and 12,000 years ago brought humans northward into Europe. However, the frozen north limited human expansion in Europe, and created a land bridge, "Bering land bridge", connecting Asia with North America about 25,000 years ago. Although fossil data give the most direct information about our past, it has certain anomalies. So, molecular archeologists are now using different molecular markers to trace the "most recent common ancestor" and also the migration pattern of modern humans. In this study, we have studied the trend of molecular markers and also the methodologies implemented in the last decades (2003-2014). From our observation, we can say that D-loop region of mtDNA and Y chromosome based markers are predominant. Nevertheless, mtDNA, especially the D-loop region, has some unique features, which makes it a more effective marker for tracing prehistoric footprints of modern human populations. Although, natural selection should also be taken into account in studying mtDNA based human migration. As per technology is concerned, Sanger sequencing is the major technique that is being used in almost all studies. But, the emergence of different cost-effective-and-easy-to-handle NGS platforms has increased its popularity over Sanger sequencing in studying human migration. PMID:25510397

Kundu, Sharbadeb; Ghosh, Sankar Kumar

2015-02-10

197

Predictive Gene Signatures: Molecular Markers Distinguishing Colon Adenomatous Polyp and Carcinoma  

PubMed Central

Cancers exhibit abnormal molecular signatures associated with disease initiation and progression. Molecular signatures could improve cancer screening, detection, drug development and selection of appropriate drug therapies for individual patients. Typically only very small amounts of tissue are available from patients for analysis and biopsy samples exhibit broad heterogeneity that cannot be captured using a single marker. This report details application of an in-house custom designed GenomeLab System multiplex gene expression assay, the hCellMarkerPlex, to assess predictive gene signatures of normal, adenomatous polyp and carcinoma colon tissue using archived tissue bank material. The hCellMarkerPlex incorporates twenty-one gene markers: epithelial (EZR, KRT18, NOX1, SLC9A2), proliferation (PCNA, CCND1, MS4A12), differentiation (B4GANLT2, CDX1, CDX2), apoptotic (CASP3, NOX1, NTN1), fibroblast (FSP1, COL1A1), structural (ACTG2, CNN1, DES), gene transcription (HDAC1), stem cell (LGR5), endothelial (VWF) and mucin production (MUC2). Gene signatures distinguished normal, adenomatous polyp and carcinoma. Individual gene targets significantly contributing to molecular tissue types, classifier genes, were further characterised using real-time PCR, in-situ hybridisation and immunohistochemistry revealing aberrant epithelial expression of MS4A12, LGR5 CDX2, NOX1 and SLC9A2 prior to development of carcinoma. Identified gene signatures identify aberrant epithelial expression of genes prior to cancer development using in-house custom designed gene expression multiplex assays. This approach may be used to assist in objective classification of disease initiation, staging, progression and therapeutic responses using biopsy material. PMID:25423035

Drew, Janice E.; Farquharson, Andrew J.; Mayer, Claus Dieter; Vase, Hollie F.; Coates, Philip J.; Steele, Robert J.; Carey, Francis A.

2014-01-01

198

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

PubMed

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

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

2011-11-01

199

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

PubMed Central

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

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

2013-01-01

200

Prospective molecular markers for the identification of illegally traded angelsharks (Squatina) and dolphin (Sotalia guianensis).  

PubMed

Endangered angelsharks and a protected dolphin species are illegally traded in Brazil. In this study, we determined prospective molecular markers for detecting these species in the trade of angelshark carcasses and 'dolphin' eyeball amulets. We compiled publicly available as well as new and unpublished cytochrome b (cyt b) DNA sequences for species involved in these trades. These sequences were digested in silico using restriction enzymes. We then described prospective polymerase chain reaction (PCR)-restriction fragment length polymorphism markers for distinguishing between protected species and the species whose trade was legally allowed in these two trade groups. The prospective marker for identifying angelshark carcasses consists of cyt b PCR and digestion by BstXI, BsgI, BspMI, BsrDI, and HaeII restriction enzymes. The prospective marker for identifying eyeball amulets consists of cyt b PCR and digestion by ApoI, BtsI, HindII, BsaAI, BplI, and SspI restriction enzymes. This is the first study to deposit in GenBank cyt b sequences for the angelshark species Squatina argentina, Squatina guggenheim, and Squatina occulta. Moreover, the S. argentina haplotype is the first DNA sequence for this species deposited in GenBank. PMID:25501182

Falcão, L H O; Furtado-Neto, M A A; Maggioni, R; Faria, V V

2014-01-01

201

Molecular markers reveal cryptic sex in the human pathogen Coccidioides immitis.  

PubMed Central

Coccidioides immitis, cause of a recent epidemic of "Valley fever" in California, is typical of many eukaryotic microbes in that mating and meiosis have yet to be reported, but it is not clear whether sex is truly absent or just cryptic. To find out, we have undertaken a population genetic study using PCR amplification, screening for single-strand conformation polymorphisms, and direct DNA sequencing to find molecular markers with nucleotide-level resolution. Both population genetic and phylogenetic analyses indicate that C. immitis is almost completely recombining. To our knowledge, this study is the first to find molecular evidence for recombination in a fungus for which no sexual stage has yet been described. These results motivate a directed search for mating and meiosis and illustrate the utility of single-strand conformation polymorphism and sequencing with arbitrary primer pairs in molecular population genetics. Images Fig. 1 PMID:8570632

Burt, A; Carter, D A; Koenig, G L; White, T J; Taylor, J W

1996-01-01

202

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. PMID:24146795

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

2013-01-01

203

Determination of specific molecular markers of biomass burning in lake sediments  

NASA Astrophysics Data System (ADS)

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

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

2014-05-01

204

Regulation of ubiquitin proteasome pathway molecular markers in response to endurance and resistance exercise and training.  

PubMed

Knowledge on the effects of divergent exercise on ostensibly protein degradation pathways may be valuable for counteracting muscle wasting and for understanding muscle remodelling. This study examined mRNA and/or protein levels of molecular markers of the ubiquitin proteasome pathway (UPP), including FBXO32 (atrogin-1), MURF-1, FBXO40, FOXO1 and FOXO3. Protein substrates of atrogin-1-including EIF3F, MYOG and MYOD1-and of MURF-1-including PKM and MHC-were also measured. Subjects completed 10 weeks of endurance training (ET) or resistance training (RT) followed by a single-bout of endurance exercise (EE) or resistance exercise (RE). Following training, atrogin-1, FBXO40, FOXO1 and FOXO3 mRNA increased independently of exercise mode, whereas MURF-1 mRNA and FOXO3 protein increased following ET only. No change in other target proteins occurred post-training. In the trained state, single-bout EE, but not RE, increased atrogin-1, MURF-1, FBXO40, FOXO1, FOXO3 mRNA and FOXO3 protein. In contrast to EE, FBXO40 mRNA and protein decreased following single-bout RE. MURF-1 and FOXO1 protein levels as well as the protein substrates of atrogin-1 and MURF-1 were unchanged following training and single-bout exercise. This study demonstrates that the intracellular signals elicited by ET and RT result in an upregulation of UPP molecular markers, with a greater increase following ET. However, in the trained state, the expression levels of UPP molecular markers are increased following single-bout EE, but are less responsive to single-bout RE. This suggests that adaptations following endurance exercise training are more reliant on protein UPP degradation processes than adaptations following resistance exercise training. PMID:25104573

Stefanetti, Renae J; Lamon, Séverine; Wallace, Marita; Vendelbo, Mikkel H; Russell, Aaron P; Vissing, Kristian

2014-08-01

205

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.

206

Mucosal immunology  

PubMed Central

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

Bienenstock, J.; Befus, A. D.

1980-01-01

207

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

Microsoft Academic Search

BACKGROUND: Several strategies are currently deployed in many countries in the tropics to strengthen malaria control toward malaria elimination. To measure the impact of any intervention, there is a need to detect malaria properly. Mostly, decisions still rely on microscopy diagnosis. But sensitive diagnosis tools enabling to deal with a large number of samples are needed. The molecular detection approach

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

2009-01-01

208

The immunology of bipolar disorder  

PubMed Central

Bipolar disorder is a psychiatric condition associated with elevated frequency of clinical co-morbidities and cognitive impairment. The neurobiology of bipolar disorder is not completely understood. Recent evidence has implicated immune dysfunction in its physiopathology. Here, we review several data supporting the presence of immunological dysfunction in bipolar disorder: (i) increased frequency of autoimmune diseases; (ii) distinct immune cells profile; (iii) altered/ release of cytokines by stimulated mononuclear cells; (iv) elevated levels of circulating immune markers; and (vi) inflammatory changes in the central nervous system. We also discussed the interplay between immunological dysfunction and neuroprogression in bipolar disorder. PMID:24557044

Barbosa, Izabela Guimarães; Machado-Vieira, Rodrigo; Soares, Jair C; Teixeira, Antonio L

2014-01-01

209

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

PubMed

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

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

2014-01-10

210

Microevolutionary Patterns and Molecular Markers: The Genetics of Geographic Variation in Ascaris suum  

PubMed Central

Molecular markers have been used only rarely to characterize the population genetic structure of nematodes. Published studies have suggested that different taxa may show distinct genetic architectures. Isoenzyme and RAPD markers have been used to investigate geographic variation of Ascaris suum at the level of infrapopulations (nematodes within individual hosts), within localities, and among geographic regions. Independent estimates of genetic differentiation among population samples based on isoenzyme and RAPD data showed similar patterns and substantial correlation. Heterozygote deficiencies within infrapopulations and large values for inbreeding coefficients among infrapopulations suggested that the composition of these populations was not consistent with a model of random recruitment from a large panmictic pool of life-cycle stages. Both isoenzyme and RAPD markers revealed moderate levels of genetic differentiation among samples representing infrapopulations and localities. Of total gene diversity, 9.4% (isoenzyme) and 9.2% (RAPD) was partitioned among infrapopulations. Geographic localities accounted for 7.8% (isoenzyme) and 6.2% (RAPD) of total diversity. Only infrapopulations from the same farm had low levels of differentiation. PMID:19277145

Nadler, S. A.

1996-01-01

211

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

PubMed

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

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

2009-09-01

212

Delimitation of Russula Subgenus Amoenula in Korea Using Three Molecular Markers  

PubMed Central

Distinguishing individual Russula species has been difficult due to extensive phenotypic plasticity and obscure morphological and anatomical discontinuities. Due to highly similar macroscopic features, such as the presence of a red-cap, species identification within the Russula subgenus Amoenula is particularly difficult. Three species of the subgenus Amoneula have been reported in Korea. We used a combination of morphology and three molecular markers, the internal transcribed spacer (ITS), 28S nuclear ribosomal large subunit (LSU), and RNA polymerase II gene (RPB2), for identification and study of the genetic diversity of Russula subgenus Amoenula in Korea. We identified only two species in Korea (R. mariae and R. violeipes); these two species were indistinguishable according to morphology and LSU, but were found to be reciprocally monophyletic species using ITS and RPB2. The markers, ITS, LSU, and RPB2, have been tested in the past for use as DNA barcoding markers, and findings of our study suggest that ITS and RPB2 had the best performance for the Russula subgenus Amoneula. PMID:24493939

Park, Myung Soo; Fong, Jonathan J.; Lee, Hyun; Oh, Seung-Yoon; Jung, Paul Eunil; Min, Young Ju; Seok, Soon Ja

2013-01-01

213

Expression of Neuroendocrine Markers in Different Molecular Subtypes of Breast Carcinoma  

PubMed Central

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

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

2014-01-01

214

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

PubMed Central

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

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

2014-01-01

215

Bladder Carcinoma Data with Clinical Risk Factors and Molecular Markers: A Cluster Analysis  

PubMed Central

Bladder cancer occurs in the epithelial lining of the urinary bladder and is amongst the most common types of cancer in humans, killing thousands of people a year. This paper is based on the hypothesis that the use of clinical and histopathological data together with information about the concentration of various molecular markers in patients is useful for the prediction of outcomes and the design of treatments of nonmuscle invasive bladder carcinoma (NMIBC). A population of 45 patients with a new diagnosis of NMIBC was selected. Patients with benign prostatic hyperplasia (BPH), muscle invasive bladder carcinoma (MIBC), carcinoma in situ (CIS), and NMIBC recurrent tumors were not included due to their different clinical behavior. Clinical history was obtained by means of anamnesis and physical examination, and preoperative imaging and urine cytology were carried out for all patients. Then, patients underwent conventional transurethral resection (TURBT) and some proteomic analyses quantified the biomarkers (p53, neu, and EGFR). A postoperative follow-up was performed to detect relapse and progression. Clusterings were performed to find groups with clinical, molecular markers, histopathological prognostic factors, and statistics about recurrence, progression, and overall survival of patients with NMIBC. Four groups were found according to tumor sizes, risk of relapse or progression, and biological behavior. Outlier patients were also detected and categorized according to their clinical characters and biological behavior. PMID:25866762

Redondo-Gonzalez, Enrique; de Castro, Leandro Nunes; Moreno-Sierra, Jesús; Maestro de las Casas, María Luisa; Vera-Gonzalez, Vicente; Ferrari, Daniel Gomes; Corchado, Juan Manuel

2015-01-01

216

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

PubMed Central

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 9 million years ago. The oldest species are around 7 million years old and the youngest ones probably much less than 1 million years. PMID:23850609

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

2013-01-01

217

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. PMID:21190678

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

2011-01-01

218

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

PubMed

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

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

2007-01-01

219

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

PubMed Central

Background Nothofagus nervosa is one of the most emblematic native tree species of Patagonian temperate forests. Here, the shotgun RNA-sequencing (RNA-Seq) of the transcriptome of N. nervosa, including de novo assembly, functional annotation, and in silico discovery of potential molecular markers to support population and associations genetic studies, are described. Results Pyrosequencing of a young leaf cDNA library generated a total of 111,814 high quality reads, with an average length of 447 bp. De novo assembly using Newbler resulted into 3,005 tentative isotigs (including alternative transcripts). The non-assembled sequences (singletons) were clustered with CD-HIT-454 to identify natural and artificial duplicates from pyrosequencing reads, leading to 21,881 unique singletons. 15,497 out of 24,886 non-redundant sequences or unigenes, were successfully annotated against a plant protein database. A substantial number of simple sequence repeat markers (SSRs) were discovered in the assembled and annotated sequences. More than 40% of the SSR sequences were inside ORF sequences. To confirm the validity of these predicted markers, a subset of 73 SSRs selected through functional annotation evidences were successfully amplified from six seedlings DNA samples, being 14 polymorphic. Conclusions This paper is the first report that shows a highly precise representation of the mRNAs diversity present in young leaves of a native South American tree, N. nervosa, as well as its in silico deduced putative functionality. The reported Nothofagus transcriptome sequences represent a unique resource for genetic studies and provide a tool to discover genes of interest and genetic markers that will greatly aid questions involving evolution, ecology, and conservation using genetic and genomic approaches in the genus. PMID:22747958

2012-01-01

220

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. PMID:22975286

Garza-Caligaris, Luz Elena; Avendaño-Vázquez, Aida Odette; Alvarado-López, Sandra; Zúñiga-Sánchez, Esther; Orozco-Segovia, Alma; Pérez-Ruíz, Rigoberto V.; Gamboa-deBuen, Alicia

2012-01-01

221

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

PubMed Central

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

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

2009-01-01

222

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

PubMed

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

Robarts, Daniel W H; Wolfe, Andrea D

2014-07-01

223

Sequence-related amplified polymorphism (SRAP) markers: A potential resource for studies in plant molecular biology1  

PubMed Central

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

Robarts, Daniel W. H.; Wolfe, Andrea D.

2014-01-01

224

Associations between immunologic, inflammatory, and oxidative stress markers with severity of depressive symptoms: An analysis of the 2005–2006 National Health and Nutrition Examination Survey  

Microsoft Academic Search

Previous studies have demonstrated increased levels of serum markers of systemic inflammation and immune system function among individuals with depressive symptoms. Despite these observations, the biological mechanisms behind this association remain elusive. The objective of the present analysis was to examine the individual and joint associations of white blood cell counts, platelet counts, and C-reactive protein with depression severity and

Roni Kobrosly; Edwin van Wijngaarden

2010-01-01

225

A novel combined 15q11.2 duplication and a bisatellited supernumerary marker derived from chromosome 22: molecular characterization of the marker.  

PubMed

Supernumerary marker chromosomes (SMC) are heterogeneous group of chromosomes which are reported in variable phenotypes. Approximately 70% originate from acrocentric chromosomes. Here we report a couple with recurrent miscarriages and a SMC originating from an acrocentric chromosome. The cytogenetic analysis of the husband revealed a karyotype of 47,XY+marker whereas the wife had a normal karyotype. Analysis of SMC with C-banding showed the presence of a big centromere in the center and silver staining showed prominent satellites on both sides of the marker. Apparently, microarray analysis revealed a 2.1 Mb duplication of 15q11.2 region but molecular cytogenetic analysis by fluorescence in situ hybridization (FISH) with whole chromosome paint (WCP) 15 showed that the SMC is not of chromosome 15 origin. Subsequently, FISH with centromere 22 identified the SMC to originate from chromosome 22 which was also confirmed by WCP 22. Additional dual FISH with centromere 22 and Acro-p-arm probes confirmed the centromere 22 and satellites on the SMC. Further fine mapping of the marker with Bacterial Artificial Chromosome (BAC) clones; two on chromosome 22 and four on chromosome 15 determined the marker to possess only centromere 22 sequences and that the duplication 15 exists directly on chromosome 15. In our study, we had identified and characterized a SMC showing inversion duplication 22(p11.1) combined with a direct tandem duplication of 15q11.2. The possible genotype-phenotype in relation with the two rearrangements is discussed. PMID:24508374

Dutta, Usha R; Vempally, Subhash; Ranganath, Prajnya; Dalal, Ashwin

2014-04-10

226

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

E-print Network

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

Stepney, Susan

227

Five molecular markers reveal extensive morphological homoplasy and reticulate evolution in the Malva alliance (Malvaceae).  

PubMed

The Malva alliance is a well-defined group with extensive morphological homoplasy. As a result, the relationships among the taxa as well as the evolution of morphological traits have remained elusive and the traditional classifications are highly artificial. Using five molecular markers (nuclear ITS, plastid matK plus trnK, ndhF, trnL-trnF, psbA-trnH), we arrived at a phylogenetic hypothesis of this group, the genera Alcea, Althaea and Malvalthaea being studied here for the first time with molecular data. Althaea and, in particular, Lavatera and Malva are highly polyphyletic as currently circumscribed, because their diagnostic characters, the number and degree of fusion of the epicalyx bracts, evolve in a highly homoplasious manner. In contrast, fruit morphology largely agrees with the molecularly delimited groups. Hybrid origins confirmed for the genus Malvalthaea and for Lavatera mauritanica and hybridization in the group of ruderal small-flowered mallows underline the importance of reticulate evolution in shaping the history of this group and complicating the interpretation of morphological evolution. PMID:19026753

Escobar García, Pedro; Schönswetter, Peter; Fuertes Aguilar, Javier; Nieto Feliner, Gonzalo; Schneeweiss, Gerald M

2009-02-01

228

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

PubMed

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

Shizuka, Daizaburo; Lyon, Bruce E

2008-11-01

229

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

PubMed Central

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

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

2014-01-01

230

Genetic approaches for studying myiasis-causing flies: molecular markers and mitochondrial genomics.  

PubMed

"Myiasis-causing flies" is a generic term that includes species from numerous dipteran families, mainly Calliphoridae and Oestridae, of which blowflies, screwworm flies and botflies are among the most important. This group of flies is characterized by the ability of their larvae to develop in animal flesh. When the host is a live vertebrate, such parasitism by dipterous larvae is known as primary myiasis. Myiasis-causing flies can be classified as saprophagous (free-living species), facultative or obligate parasites. Many of these flies are of great medical and veterinary importance in Brazil because of their role as key livestock insect-pests and vectors of pathogens, in addition to being considered important legal evidence in forensic entomology. The characterization of myiasis-causing flies using molecular markers to study mtDNA (by RFLP) and nuclear DNA (by RAPD and microsatellite) has been used to identify the evolutionary mechanisms responsible for specific patterns of genetic variability. These approaches have been successfully used to analyze the population structures of the New World screwworm fly Cochliomyia hominivorax and the botfly Dermatobia hominis. In this review, various aspects of the organization, evolution and potential applications of the mitochondrial genome of myiasis-causing flies in Brazil, and the analysis of nuclear markers in genetic studies of populations, are discussed. PMID:16502089

de Azeredo-Espin, Ana Maria Lima; Lessinger, Ana Cláudia

2006-01-01

231

gammaH2AX: a sensitive molecular marker of DNA damage and repair.  

PubMed

Phosphorylation of the Ser-139 residue of the histone variant H2AX, forming gammaH2AX, 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 gammaH2AX foci has numerous other applications including, but not limited to, cancer and aging research. Quantitation of gammaH2AX foci has also been applied as a useful tool for the evaluation of the efficacy of various developmental drugs, particularly, radiation modifying compounds. This review focuses on the current status of gammaH2AX as a marker of DNA damage and repair in the context of ionizing radiation. Although the emphasis is on gamma-radiation-induced gammaH2AX foci, the effects of other genotoxic insults including exposure to ultraviolet rays, oxidative stress and chemical agents are also discussed. PMID:20130602

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

2010-04-01

232

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

233

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

234

GammaH2AX as a molecular marker of aging and disease.  

PubMed

Double-strand breaks are one of the most critical DNA lesions with respect to cell-death and preservation of genomic integrity. Rapid phosphorylation of the histone variant H2AX at Ser-139 to form gammaH2AX is an early cellular response to DNA double-strand breaks. Visualization of discrete gammaH2AX foci using immunofluorescence-based assays has provided a sensitive and effective method for detecting DSBs which may be implicated in various pathologies including cancer, age-related diseases, chronic inflammatory diseases and ischemia-reperfusion injury. In this review, the potential utility and significance of gammaH2AX as a molecular marker of aging and disease is analysed. PMID:20150765

Mah, Li-Jeen; El-Osta, Assam; Karagiannis, Tom C

2010-02-16

235

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

236

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. PMID:22275966

Lukan, C

2008-01-01

237

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

NASA Astrophysics Data System (ADS)

In recent years, the rise of interest in planetary exploration and the emergence of Astrobiology as a promising field of research have lead to a number of programmes aiming to develop sensitive instruments for the detection of the molecular signatures of life in extreme environments. An antibody assay-based life detection instrument, the Life Marker Chip (LMC), is currently under development by a UK-lead international consortium for the European Space Agency's (ESA) ExoMars rover. This forms part of the joint ESA/NASA Mars exploration programme with the ExoMars Rover currently scheduled for launch in 2018. The organic molecules targeted for Life detection by the LMC are based on an assumption of "Earth-like" Life on Mars -extinct and/or extant. The molecular targets for the LMC have been chosen to represent markers of extinct Life, extant Life, abiotic chemistry (e.g. of meteoritic origin) and mission-borne Earth contamination. The LMC incorporates integrated liquid sample extraction and processing for dry Martian samples, which will be collected from up to 2m below the surface of Mars, where organic molecules, if present, are expected to be better preserved. The core technology of the LMC is a combination of optical evanescent waveguides, micro-fluidics, immuno-microarrays with fluorescent labels and CCD detector readout. Phage display recombinant antibody technology has been employed in order to acquire antibodies against a number of the LMC target molecules. The LMC hardware is currently in a breadboard phase of development. The recombinant antibody development for LMC targets is an on-going project, and testing of Earth-analogue Martian samples has been initiated

Derveni, Mariliza

238

Clinicopathologic factors and molecular markers related to lymph node metastasis in early gastric cancer  

PubMed Central

AIM: To analyze predictive factors for lymph node metastasis in early gastric cancer. METHODS: We analyzed 1104 patients with early gastric cancer (EGC) who underwent a gastrectomy with lymph-node dissection from May 2003 through July 2011. The clinicopathologic factors and molecular markers were assessed as predictors for lymph node metastasis. Molecular markers such as microsatellite instability, human mutL homolog 1, p53, epidermal growth factor receptor (EGFR) and human epidermal growth factor receptor 2 (HER2) were included. The ?2 test and logistic regression analysis were used to determine clinicopathologic parameters. RESULTS: Lymph node metastasis was observed in 104 (9.4%) of 1104 patients. Among 104 cases of lymph node positive patients, 24 patients (3.8%) were mucosal cancers and 80 patients (16.7%) were submucosal. According to histologic evaluation, the number of lymph node metastasis found was 4 (1.7%) for well differentiated tubular adenocarcinoma, 45 (11.3%) for moderately differentiated tubular adenocarcinoma, 36 (14.8%) for poorly differentiated tubular adenocarcinoma, and 19 (8.4%) for signet ring cell carcinoma. Of 690 EGC cases, 77 cases (11.2%) showed EGFR overexpression. HER2 overexpression was present in 110 cases (27.1%) of 406 EGC patients. With multivariate analysis, female gender (OR = 2.281, P = 0.009), presence of lymphovascular invasion (OR = 10.950, P < 0.0001), diameter (? 20 mm, OR = 3.173, P = 0.01), and EGFR overexpression (OR = 2.185, P = 0.044) were independent risk factors for lymph node involvement. CONCLUSION: Female gender, tumor size, lymphovascular invasion and EGFR overexpression were predictive risk factors for lymph node metastasis in EGC. PMID:25593477

Jin, Eun Hyo; Lee, Dong Ho; Jung, Sung-Ae; Shim, Ki-Nam; Seo, Ji Yeon; Kim, Nayoung; Shin, Cheol Min; Yoon, Hyuk; Jung, Hyun Chae

2015-01-01

239

Highly variable microsatellite markers for the fungal and algal symbionts of the lichen Lobaria pulmonaria and challenges in developing biont-specific molecular markers for fungal associations.  

PubMed

The availability of highly variable markers for the partners of a fungal symbiosis enables the integrated investigation of ecological and evolutionary processes at the symbiotic level. In this article we analyze the specificity of the first and to date only microsatellite markers that had been developed for an epiphytic lichen (Lobaria pulmonaria). We used DNA extracts from cultures of the fungal and of the green algal symbionts of L. pulmonaria as well as total DNA extracts from related Lobaria species associated with the same algal partner, and got evidence that five of the previously described microsatellite markers, proposed to be fungus-specific, are indeed alga-specific. Hence, highly variable microsatellite primer sets available for both, the algal and the fungal symbionts of L. pulmonaria are now at our hands, which allow us to investigate so far unexplored biological processes of lichen symbionts, such as codispersal and coevolution. In a broader sense, our work evaluates and discusses the challenges in developing biont-specific molecular markers for fungi forming close associations with other organisms. PMID:20943165

Widmer, Ivo; Dal Grande, Francesco; Cornejo, Carolina; Scheidegger, Christoph

2010-07-01

240

Integration of simple sequence repeat (SSR) markers into a molecular linkage map of common bean (Phaseolus vulgaris L.).  

PubMed

Microsatellite or simple sequence repeat (SSR) markers have been successfully used for genomic mapping, DNA fingerprinting, and marker-assisted selection in many plant species. Here we report the first successful assignment of 15 SSR markers to the Phaseolus vulgaris molecular linkage map. A total of 37 SSR primer pairs were developed and tested for amplification and product-length polymorphism with BAT93 and Jalo EEP558, the parental lines of an F7 recombinant inbred (RI) population previously used for the construction of a common bean molecular linkage map. Sixteen of the SSRs polymorphic to the parental lines were analyzed for segregation and 15 of them were assigned to seven different linkage groups, indicating a widespread distribution throughout the bean genome. Map positions for genes coding for DNAJ-like protein, pathogenesis-related protein 3, plastid-located glutamine synthetase, endochitinase, sn-glycerol-3 phosphate acyltransferase, NADP-dependent malic enzyme, and protein kinase were determined for the first time. Addition of three SSR loci to linkage group B4 brought two separated smaller linkage groups together to form a larger linkage group. Analysis of allele segregation in the F7 RI population revealed that all 16 SSRs segregated in the expected 1:1 ratio. These SSR markers were stable and easy to assay by polymerase chain reaction (PCR). They should be useful markers for genetic mapping, genotype identification, and marker-assisted selection of common beans. PMID:11218079

Yu, K; Park, S J; Poysa, V; Gepts, P

2000-01-01

241

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

2010-03-15

242

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

243

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

PubMed Central

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

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

2010-01-01

244

Department of Microbiology, Immunology and Pathology Akkina Lab Postdoctoral Position  

E-print Network

Department of Microbiology, Immunology and Pathology Akkina Lab ­ Postdoctoral Position Job Description: We are looking for post-doctoral scientists with research experience in the areas of immunology, Palmer et al J Immunol. 190:211-219, 2013). Must have an earned PhD in molecular virology, immunology

Stephens, Graeme L.

245

Comparison of PM2.5 source apportionment using positive matrix factorization and molecular marker-based  

E-print Network

Comparison of PM2.5 source apportionment using positive matrix factorization and molecular marker balance (CMB-MM) modeling on PM2.5 source contributions was conducted for particulate matter measurements 24-h PM2.5 samples collected in July 2001 and January 2002. While for PMF, with elements, ions, five

Zheng, Mei

246

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...

247

Identification of candidate predictive and surrogate molecular markers for dasatinib in prostate cancer: rationale for patient selection and efficacy monitoring  

Microsoft Academic Search

BACKGROUND: Dasatinib is a potent, multi-targeted kinase inhibitor that was recently approved for treatment of chronic myelogenous leukemia resistant to imatinib. To aid the clinical development of dasatinib in prostate cancer, we utilized preclinical models to identify potential molecular markers for patient stratification and efficacy monitoring. RESULTS: Using gene expression profiling, we first identified 174 genes whose expression was highly

Xi-De Wang; Karen Reeves; Feng R Luo; Li-An Xu; Francis Lee; Edwin Clark; Fei Huang

2007-01-01

248

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

Microsoft Academic Search

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

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

2007-01-01

249

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

Microsoft Academic Search

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

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

250

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...

251

Identification of essentially derived varieties with molecular markers: an approach based on statistical test theory and computer simulations  

Microsoft Academic Search

Genetic similarities (GS) based on molecular markers have been proposed as a tool for identification of essentially derived varieties (EDVs). Nevertheless, scientifically reliable criteria for discrimination of EDVs and independently derived varieties with GS estimates are scanty, and implementation into practical breeding has not yet taken place. Our objectives were to (1) assess the influence of chromosome number and length,

M. Heckenberger; M. Bohn; M. Frisch; H. P. Maurer; A. E. Melchinger

2005-01-01

252

Immunology of human schistosomiasis  

PubMed Central

There is a wealth of immunologic studies that have been carried out in experimental and human schistosomiasis that can be classified into three main areas: immunopathogenesis, resistance to reinfection and diagnostics. It is clear that the bulk of, if not all, morbidity due to human schistosomiasis results from immune-response-based inflammation against eggs lodged in the body, either as regulated chronic inflammation or resulting in fibrotic lesions. However, the exact nature of these responses, the antigens to which they are mounted and the mechanisms of the critical regulatory responses are still being sorted out. It is also becoming apparent that protective immunity against schistosomula as they develop into adult worms develops slowly and is hastened by the dying of adult worms, either naturally or when they are killed by praziquantel. However, as with anti-egg responses, the responsible immune mechanisms and inducing antigens are not clearly established, nor are any potential regulatory responses known. Finally, a wide variety of immune markers, both cellular and humoral, can be used to demonstrate exposure to schistosomes, and immunologic measurement of schistosome antigens can be used to detect, and thus diagnose, active infections. All three areas contribute to the public health response to human schistosome infections. PMID:25142505

Colley, D G; Secor, W E

2014-01-01

253

History & Scope of Immunology Program Education and research in Immunology has a 60-year history at the University of  

E-print Network

units of the University of Pennsylvania: College of Arts and Sciences; Medical School; Hospital sciences and with some physical sciences, including chemistry and physics; this breadth of topics provides Faculty Research Seminar · Immunology 601 Molecular Immunology · Immunology 605 Current Topics

Plotkin, Joshua B.

254

Molecular markers of early Parkinson's disease based on gene expression in blood  

PubMed Central

Parkinson's disease (PD) progresses relentlessly and affects five million people worldwide. Laboratory tests for PD are critically needed for developing treatments designed to slow or prevent progression of the disease. We performed a transcriptome-wide scan in 105 individuals to interrogate the molecular processes perturbed in cellular blood of patients with early-stage PD. The molecular multigene marker here identified is associated with risk of PD in 66 samples of the training set comprising healthy and disease controls [third tertile cross-validated odds ratio of 5.7 (P for trend 0.005)]. It is further validated in 39 independent test samples [third tertile odds ratio of 5.1 (P for trend 0.04)]. Insights into disease-linked processes detectable in peripheral blood are offered by 22 unique genes differentially expressed in patients with PD versus healthy individuals. These include the cochaperone ST13, which stabilizes heat-shock protein 70, a modifier of ?-synuclein misfolding and toxicity. ST13 messenger RNA copies are lower in patients with PD (mean ± SE 0.59 ± 0.05) than in controls (0.96 ± 0.09) (P = 0.002) in two independent populations. Thus, gene expression signals measured in blood can facilitate the development of biomarkers for PD. PMID:17215369

Scherzer, Clemens R.; Eklund, Aron C.; Morse, Lee J.; Liao, Zhixiang; Locascio, Joseph J.; Fefer, Daniel; Schwarzschild, Michael A.; Schlossmacher, Michael G.; Hauser, Michael A.; Vance, Jeffery M.; Sudarsky, Lewis R.; Standaert, David G.; Growdon, John H.; Jensen, Roderick V.; Gullans, Steven R.

2007-01-01

255

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. PMID:22925330

2012-01-01

256

Microbiology & Immunology DEPARTMENT OF  

E-print Network

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

Qian, Ning

257

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

PubMed

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

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

2008-12-01

258

Liver Immunology  

PubMed Central

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

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

2014-01-01

259

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

PubMed

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

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

2013-01-01

260

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

PubMed

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

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

2014-01-01

261

Establishment of a proteome profile and identification of molecular markers for mouse spermatogonial stem cells  

PubMed Central

Spermatogonial stem cells (SSCs) are undifferentiated cells that are required to maintain spermatogenesis throughout the reproductive life of mammals. Although SSC transplantation and culture provide a powerful tool to identify the mechanisms regulating SSC function, the precise signalling mechanisms governing SSC self-renewal and specific surface markers for purifying SSCs remain to be clearly determined. In the present study, we established a steady SSC culture according to the method described by Shinohara's lab. Fertile progeny was produced after transplantation of cultured SSCs into infertile mouse testis, and the red fluorescence exhibited by the culture cell membranes was stably and continuously transmitted to the offspring. Next, via advanced mass spectrometry and an optimized proteomics platform, we constructed the proteome profile, with 682 proteins expressed in SSCs. Furthermore bioinformatics analysis showed that the list contained several known molecules that are regulated in SSCs. Several nucleoproteins and membrane proteins were chosen for further exploration using immunofluorescence and RT-PCR. The results showed that SALL1, EZH2, and RCOR2 are possibly involved in the self-renewal mechanism of SSCs. Furthermore, the results of tissue-specific expression analysis showed that Gpat2 and Pld6 were uniquely and highly expressed in mouse testes and cultured SSCs. The cellular localization of PLD6 was further explored and the results showed it was primarily expressed in the spermatogonial membrane of mouse testes and cultured SSCs. The proteins identified in this study form the basis for further exploring the molecular mechanism of self-renewal in SSCs and for identifying specific surface markers of SSCs. PMID:25352495

Zhou, Quan; Guo, Yueshuai; Zheng, Bo; Shao, Binbin; Jiang, Min; Wang, Gaigai; Zhou, Tao; Wang, Lei; Zhou, Zuomin; Guo, Xuejiang; Huang, Xiaoyan

2015-01-01

262

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

PubMed Central

Background Upper tract urothelial carcinoma (UTUC) is a tumor with sizable metastases and local recurrence. It has a worse prognosis than bladder cancer. This study was designed to investigate the urinary potential tumor markers of UTUC. Methods Between January 2008 and January 2009, urine was sampled from 13 patients with UTUC and 20 healthy adults. The current study identified biomarkers for UTUC using non-fixed volume stepwise weak anion exchange chromatography for fractionation of urine protein prior to two-dimensional gel electrophoresis. Results Fifty five differential proteins have been determined by comparing with the 2-DE maps of the urine of UTUC patients and those of healthy people. Western blotting analysis and immunohistochemistry of tumor tissues and normal tissues from patients with UTUC were carried out to further verify five possible UTUC biomarkers, including zinc-alpha-2-glycoprotein, calreticulin, annexin A2, annexin A3 and haptoglobin. The data of western blot and immunohistochemical analysis are consistent with the 2-DE data. Combined the experimental data in the urine and in tumor tissues collected from patients with UTUC, the crucial over-expressed proteins are calreticulin, annexin A2, and annexin A3. Conclusions Calreticulin, annexin A2, and annexin A3 are very likely a panel of biomarkers with potential value for UTUC diagnosis. PMID:24884814

2014-01-01

263

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

PubMed Central

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

Zhang, Shouan; Gao, Muqiang; Zaitlin, David

2012-01-01

264

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

PubMed

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

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

2013-12-01

265

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

Microsoft Academic Search

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

Anne M. Bowcock

2005-01-01

266

26 2011 John Wiley & Sons A/S Immunological Reviews 243/2011 Mary F. Fontana  

E-print Network

26 � 2011 John Wiley & Sons A/S · Immunological Reviews 243/2011 Mary F. Fontana Russell E. Vance/S Immunological Reviews 0105-2896 Summary: Two-signal models have a rich history in immunology. In the classic two of Immunology & Pathogenesis, Department of Molecular & Cell Biology, University of California, Berkeley, CA

Vance,. Russell

267

Genetic variability and geographic typicality of Italian former Prosecco grape variety using PCR-derived molecular markers.  

PubMed

This study uses PCR-derived marker systems to investigate the extent and distribution of genetic variability of 80 Italian Prosecco accessions coming from Prosecco DOC area (north-east area of Italy). The studied samples include genotypes from Veneto and Friuli Venezia Giulia region. In order to verify the varietal identity of the samples, analyses based on 22 SSR loci were performed, and two grape varieties were found: Prosecco tondo and Prosecco lungo. In addition to microsatellite analysis, intra-varietal variability study was performed using AFLP, SAMPL, ISSR, and M-AFLP molecular markers. This molecular approach could discriminate different Prosecco tondo accessions coming from Treviso hills, from Veneto plain, from Friuli Venezia Giulia region, and from Padua hills (Serprina samples). As concerning Prosecco lungo variety, it was possible to discriminate molecularly the accessions from Veneto region and those from Friuli Venezia Giulia region. The molecular analysis allowed a distinction of the Prosecco genotypes on the basis of their geographic origins with plant-specific markers able to differentiate all Prosecco accessions. In this paper, the studied grape variety is termed Prosecco and not Glera (which is the present name) because the sampled vineyards were established many years ago when the name of the variety was Prosecco. PMID:24347297

Meneghetti, Stefano; Costacurta, Angelo; Bavaresco, Luigi; Calo', Antonio

2014-05-01

268

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

PubMed Central

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

Bennett, Michael; Mashimo, Hiroshi

2014-01-01

269

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

NASA Astrophysics Data System (ADS)

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

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

2015-01-01

270

[Exploring genetic diversity in Dioscorea zingiberensis by amplified fragment length polymorphism molecular markers].  

PubMed

Amplified fragment length polymorphism (AFLP) was used to study 30 individuals from 5 wild populations of Dioscorea zingiberensis for the first time. A total of 14 698 bands were detected with 9 pairs of AFLP primers and 12 686 of them were polymorphic. On the average each primer combination could be used to detect 230 polymorphic bands and account for 85.92% of total genetic diversity at species level. Shannonos index of diversity (I) was 0.3656-/+0.1721, and Nei's gene diversity (H) was 0.2322-/+0.2200 at the species level. The result of genetic variance analysis showed the coefficient of genetic differentiation (Gst) was 0.4827 at species level, it indicated there were certain degree of genetic differentiation in five Dioscorea zingiberensis populations. The gene flow (Nm) among populations of D. zingiberensis was 0.5358. The data were analyzed using unweighted pair group method, basing on arithmetic averages (UPGMA) bootstrap analysis. Cluster analyses were performed by using NTSYSpc version 2.11F and Popgene 1.32 software. The results showed that the genetic differentiation of 5 wild populations of D. zingiberensis was abundant, and 5 wild populations of D. zingiberensis could be clustered by the distance of the position basically. The AFLP molecular marker was used to identify the genetic differences of different populations of Dioscorea zingiberensis. PMID:17675758

Li, Yong-Hui; Li, Xiang-Min

2007-08-01

271

Tracking neuronal marker expression inside living differentiating cells using molecular beacons  

PubMed Central

Monitoring gene expression is an important tool for elucidating mechanisms of cellular function. In order to monitor gene expression during nerve cell development, molecular beacon (MB) probes targeting markers representing different stages of neuronal differentiation were designed and synthesized as 2'-O-methyl RNA backbone oligonucleotides. MBs were transfected into human mesencephalic cells (LUHMES) using streptolysin-O-based membrane permeabilization. Mathematical modeling, simulations and experiments indicated that MB concentration was equal to the MB in the transfection medium after 10 min transfection. The cells will then each contain about 60,000 MBs. Gene expression was detected at different time points using fluorescence microscopy. Nestin and NeuN mRNA were expressed in approximately 35% of the LUHMES cells grown in growth medium, and in 80–90% of cells after differentiation. MAP2 and tyrosine hydroxylase mRNAs were expressed 2 and 3 days post induction of differentiation, respectively. Oct 4 was not detected with MB in these cells and signal was not increased over time suggesting that MB are generally stable inside the cells. The gene expression changes measured using MBs were confirmed using qRT-PCR. These results suggest that MBs are simple to use sensors inside living cell, and particularly useful for studying dynamic gene expression in heterogeneous cell populations. PMID:24431988

Ilieva, Mirolyuba; Della Vedova, Paolo; Hansen, Ole; Dufva, Martin

2013-01-01

272

Molecular Screening of Blast Resistance Genes in Rice using SSR Markers  

PubMed Central

Rice Blast is the most devastating disease causing major yield losses in every year worldwide. It had been proved that using resistant rice varieties would be the most effective way to control this disease. Molecular screening and genetic diversities of major rice blast resistance genes were determined in 192 rice germplasm accessions using simple sequence repeat (SSR) markers. The genetic frequencies of the 10 major rice blast resistance genes varied from 19.79% to 54.69%. Seven accessions IC337593, IC346002, IC346004, IC346813, IC356117, IC356422 and IC383441 had maximum eight blast resistance gene, while FR13B, Hourakani, Kala Rata 1–24, Lemont, Brown Gora, IR87756-20-2-2-3, IC282418, IC356419, PKSLGR-1 and PKSLGR-39 had seven blast resistance genes. Twenty accessions possessed six genes, 36 accessions had five genes, 41 accessions had four genes, 38 accessions had three genes, 26 accessions had two genes, 13 accessions had single R gene and only one accession IC438644 does not possess any one blast resistant gene. Out of 192 accessions only 17 accessions harboured 7 to 8 blast resistance genes. PMID:25774106

Singh, A. K.; Singh, P. K.; Arya, Madhuri; Singh, N. K.; Singh, U. S.

2015-01-01

273

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

PubMed Central

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

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

2009-01-01

274

A test of the maximum heterozygosity hypothesis using molecular markers in tetraploid potatoes.  

PubMed

It has been theorized that in cross-pollinated polyploid species hybrid vigor is maximized by the frequent occurrence of more than two alleles per chromosomal locus. In polyploid crops this condition of maximum heterozygosity has been reported to be associated with increased yield and optimum field performance. We report herein the first direct test of the maximum heterozygosity hypothesis. Molecular markers were used to examine the association between maximum heterozygosity and several components of yield in three different populations of tetraploid potatoes. The results indicate that the value of maximum heterozygosity is not universal but dependent on the genetic background of the material under evaluation. In a cross between adapted breeding lines, homozygosity was negatively correlated with tuber yield, and maximum heterozygosity was positively correlated with the proportion of tuber yield in the large-size fraction. In contrast, in crosses between adapted and unadapted parents, maximum heterozygosity had no detectable effect on any character. Quantitative trait locus (QTL) analysis of the three populations reveals that, regardless of the genetic background, additive genetic effects are more strongly correlated with the components of yield than are any measures of heterozygosity and that some common QTLs may be influencing yield in all three populations. PMID:24193596

Bonierbale, M W; Plaisted, R L; Tanksley, S D

1993-05-01

275

Molecular Screening of Blast Resistance Genes in Rice using SSR Markers.  

PubMed

Rice Blast is the most devastating disease causing major yield losses in every year worldwide. It had been proved that using resistant rice varieties would be the most effective way to control this disease. Molecular screening and genetic diversities of major rice blast resistance genes were determined in 192 rice germplasm accessions using simple sequence repeat (SSR) markers. The genetic frequencies of the 10 major rice blast resistance genes varied from 19.79% to 54.69%. Seven accessions IC337593, IC346002, IC346004, IC346813, IC356117, IC356422 and IC383441 had maximum eight blast resistance gene, while FR13B, Hourakani, Kala Rata 1-24, Lemont, Brown Gora, IR87756-20-2-2-3, IC282418, IC356419, PKSLGR-1 and PKSLGR-39 had seven blast resistance genes. Twenty accessions possessed six genes, 36 accessions had five genes, 41 accessions had four genes, 38 accessions had three genes, 26 accessions had two genes, 13 accessions had single R gene and only one accession IC438644 does not possess any one blast resistant gene. Out of 192 accessions only 17 accessions harboured 7 to 8 blast resistance genes. PMID:25774106

Singh, A K; Singh, P K; Arya, Madhuri; Singh, N K; Singh, U S

2015-03-01

276

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

PubMed Central

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

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

2010-01-01

277

Correlation analysis of ultrasonic characteristics, pathological type, and molecular markers of thyroid nodules.  

PubMed

The present study was conducted to analyze the correlation between ultrasonic characteristics, pathological type, and molecular markers of thyroid-tumor-related genes as well as to evaluate the diagnosis and prognosis of thyroid nodules. The acoustic characteristics of 130 thyroid specimens were detected. Pathological sectioning and immunohistochemical detection were performed to determine the correlation between tumor gene expression and ultrasonic characteristics. Ultrasonic testing revealed that malignant nodules were normally accompanied by lymph nodes. Expression of the human telomerase reverse transcriptase, Ki67, vascular endothelial growth factor, Ret, and P53 genes exhibited statistically significant differences in malignant, benign, and normal tissues. The performance of thyroid malignant nodules showed different degrees of correlation with the expression of the human telomerase reverse transcriptase, Ki67, VEGF, Ret, and P53 genes. Color Doppler ultrasound is highly sensitive for thyroid nodules and is therefore effective for identifying thyroid nodules and early diagnosis of thyroid cancer. Color Doppler ultrasound can identify benign or malignant thyroid nodules based on 5 characteristic indicators. Tumor pathology and gene expression are associated with the sonographic features of thyroid cancer. Therefore, determining the pathological basis of ultrasonography would facilitate prognostic assessments of thyroid cancer. PMID:25729930

Su, J J; Hui, L Z; Xi, C J; Su, G Q

2015-01-01

278

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

PubMed Central

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

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

2014-01-01

279

Tumor Immunology  

E-print Network

Every cell in a multicellular organism has the potential to die by apoptosis, but tumour cells often have faulty apoptotic pathways. These defects not only increase tumour mass, but also render the tumour resistant to therapy. So, what are the molecular mechanisms of tumour resistance to apoptosis and how can we use this knowledge to resensitize tumour cells to cancer therapy?

280

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. PMID:22805587

2012-01-01

281

A high-affinity folate binding protein in human amniotic fluid. Radioligand binding characteristics, immunological properties and molecular size  

Microsoft Academic Search

The presence of a folate binding protein of high-affinity type (affinity constant 5 · 109M-1, maximum folate binding 3 nM) in human amniotic fluid was demonstrated in equilibrium dialysis experiments (37°C, pH 7.4) with the radioligand3H-folate. Dissociation of3H-folate from the binding protein was slow at pH 7.4 but rapid at pH 3.5. By use of rabbit antibodies against low molecular

Jan Holm; Steen Ingemann Hansen; Mimi Høier-Madsen

1990-01-01

282

Role of molecular mimicry of hepatitis C virus protein with platelet GPIIIa in hepatitis C–related immunologic thrombocytopenia  

PubMed Central

Patients with HIV-1 immune-related thrombocytopenia (HIV-1–ITP) have a unique Ab against platelet GPIIIa49-66 capable of inducing oxidative platelet fragmentation in the absence of complement. HIV-1–seropositive drug abusers are more prone to develop immune thrombocytopenia than non–drug abusers and have a higher coinfection with hepatitis C virus (HCV) than non–drug abusers (90% vs 30%). Molecular mimicry was sought by screening a phage peptide library with anti–GPIIIa49-66 antibody as bait for peptides sharing homology sequences with HCV. Several phage peptide clones had 70% homology with HCV protein. Sera from dually infected thrombocytopenic patients with HCV and HIV-ITP reacted strongly with 4 nonconserved peptides from HCV core envelope 1. Reactivity correlated inversely with platelet count (r2 = 0.7, P < .01). Ab raised against peptide PHC09 in GPIIIa?/? mice induced thrombocytopenia in wild-type mice. Affinity-purified IgG against PHC09 induced oxidative platelet fragmentation in vitro. Drug abusers dually infected with HCV and HIV-1 had a greater incidence and severity of thrombocytopenia as well as titer of anti–GPIIIa49-66/PHC09 Ab. NZB/W F1 mice injected with recombinant core envelope 1 developed Ab versus PHC09 and significantly decreased their platelet count (P < .001). Thus, HCV core envelope 1 can induce thrombocytopenia by molecular mimicry with GPIIIa49-66. PMID:19023115

Zhang, Wei; Nardi, Michael A.; Borkowsky, William

2009-01-01

283

Review of the molecular profile and modern prognostic markers for gastric lymphoma: How do they affect clinical practice?  

PubMed Central

Primary gastric lymphoma is a rare cancer of the stomach with an indeterminate prognosis. Recently, a series of molecular prognostic markers has been introduced to better describe this clinical entity. This review describes the clinical importance of several oncogenes, apoptotic genes and chromosomal mutations in the initiation and progress of primary non-Hodgkin gastric lymphoma and their effect on patient survival. We also outline the prognostic clinical importance of certain cellular adhesion molecules, such as ICAM and PECAM-1, in patients with gastric lymphoma, and we analyze the correlation of these molecules with apoptosis, angiogenesis, tumour growth and metastatic potential. We also focus on the host–immune response and the impact of Helicobacter pylori infection on gastric lymphoma development and progression. Finally, we explore the therapeutic methods currently available for gastric lymphoma, comparing the traditional invasive approach with more recent conservative options, and we stress the importance of the application of novel molecular markers in clinical practice. PMID:22564515

Alevizos, Leonidas; Gomatos, Ilias P.; Smparounis, Spyridon; Konstadoulakis, Manousos M.; Zografos, Georgios

2012-01-01

284

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

PubMed Central

Positional cloning in maize (Zea mays) requires development of markers in the region of interest. We found that primers designed to amplify annotated insertion–deletion polymorphisms of seven base pairs or greater between B73 and Mo17 produce polymorphic markers at a 97% frequency with 49% of the products showing co-dominant fragment length polymorphisms. When the same polymorphisms are used to develop markers for B73 and W22 or Mo17 and W22 mapping populations, 22% and 31% of markers are co-dominant, respectively. There are 38,223 Indel polymorphisms that can be converted to markers providing high-density coverage throughout the maize genome. This strategy significantly increases the efficiency of marker development for fine-mapping in maize. PMID:24747759

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

2014-01-01

285

Efficient molecular marker design using the MaizeGDB Mo17 SNPs and Indels track.  

PubMed

Positional cloning in maize (Zea mays) requires development of markers in the region of interest. We found that primers designed to amplify annotated insertion-deletion polymorphisms of seven base pairs or greater between B73 and Mo17 produce polymorphic markers at a 97% frequency with 49% of the products showing co-dominant fragment length polymorphisms. When the same polymorphisms are used to develop markers for B73 and W22 or Mo17 and W22 mapping populations, 22% and 31% of markers are co-dominant, respectively. There are 38,223 Indel polymorphisms that can be converted to markers providing high-density coverage throughout the maize genome. This strategy significantly increases the efficiency of marker development for fine-mapping in maize. PMID:24747759

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

2014-06-01

286

Development of a sex-specific molecular marker for Japanese hop Humulus Japonicus Siebold & Zucc  

Microsoft Academic Search

Japanese hop (Humulus japonicus Siebold & Zucc.) is a dioecious plant and a suitable model for studying the XX\\/XY1Y2 system of sex chromosomes. To develop a sex-specific marker, 12 RAPD and 36 ISSR markers were analyzed on the basis of pools\\u000a of male and female plants identified after flowering. We were the first to identify ISSR marker K-16, which manifested

O. S. Aleksandrov; M. G. Divashuk; G. I. Karlov

2011-01-01

287

Inheritance and development of molecular markers linked to angular leaf spot resistance genes in the common bean accession G10909  

Microsoft Academic Search

Angular leaf spot (ALS) is one of the major diseases of the common bean (Phaseolus vulgaris L.). Different sources of resistance have been identified but few have been characterized. Studies were conducted to elucidate\\u000a the inheritance of ALS resistance in the bean accession G10909 and to identify molecular markers linked to these genes. Evaluation\\u000a of parental genotypes, F1, F2 and

George S. MahukuMaria; María Antonia Henríquez; Carmenza Montoya; Carlos Jara; Henry Teran; Stephen Beebe

2011-01-01

288

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

Microsoft Academic Search

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

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

2009-01-01

289

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

Microsoft Academic Search

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

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

2013-01-01

290

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

Microsoft Academic Search

A fire blight resistance QTL explaining 34.3%-46.6% of the phenotypic variation was recently identified on linkage group 7 of apple cultivar 'Fiesta' (F7). However, markers flanking this QTL were AFLP and RAPD markers un- suitable for marker-assisted selection (MAS). Two RAPD markers bracketing the QTL have been transformed into SCAR (sequence-characterized amplified region) markers, and an SSR marker specific for

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

2007-01-01

291

Predicting Quantitative Traits With Regression Models for Dense Molecular Markers and Pedigree  

PubMed Central

The availability of genomewide dense markers brings opportunities and challenges to breeding programs. An important question concerns the ways in which dense markers and pedigrees, together with phenotypic records, should be used to arrive at predictions of genetic values for complex traits. If a large number of markers are included in a regression model, marker-specific shrinkage of regression coefficients may be needed. For this reason, the Bayesian least absolute shrinkage and selection operator (LASSO) (BL) appears to be an interesting approach for fitting marker effects in a regression model. This article adapts the BL to arrive at a regression model where markers, pedigrees, and covariates other than markers are considered jointly. Connections between BL and other marker-based regression models are discussed, and the sensitivity of BL with respect to the choice of prior distributions assigned to key parameters is evaluated using simulation. The proposed model was fitted to two data sets from wheat and mouse populations, and evaluated using cross-validation methods. Results indicate that inclusion of markers in the regression further improved the predictive ability of models. An R program that implements the proposed model is freely available. PMID:19293140

de los Campos, Gustavo; Naya, Hugo; Gianola, Daniel; Crossa, José; Legarra, Andrés; Manfredi, Eduardo; Weigel, Kent; Cotes, José Miguel

2009-01-01

292

Virtual Immunology: Software for Teaching Basic Immunology  

ERIC Educational Resources Information Center

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

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

2013-01-01

293

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

294

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

PubMed Central

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

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

2014-01-01

295

Sex determination in 58 bird species and evaluation of CHD gene as a universal molecular marker in bird sexing.  

PubMed

The aim of this research was to test the CHD gene (Chromo Helicase DNA-binding gene) as a universal molecular marker for sexing birds of relatively distant species. The CHD gene corresponds to the aim because of its high degree of conservation and different lengths in Z and W chromosomes due to different intron sizes. DNA was isolated from feathers and the amplification of the CHD gene was performed with the following sets of polymerase chain reaction (PCR) primers: 2550F/2718R and P2/P8. Sex determination was attempted in 284 samples of 58 bird species. It was successful in 50 bird species; in 16 of those (Alopochen aegyptiacus, Ara severus, Aratinga acuticaudata, Bucorvus leadbeateri, Cereopsis novaehollandiae, Columba arquatrix, Corvus corax, C. frugilegus, Cyanoliseus patagonus, Guttera plumifera, Lamprotornis superbus, Milvus milvus, Neophron percnopterus, Ocyphaps lophotes, Podiceps cristatus, and Poicephalus senegalus), it was carried out for the first time using molecular markers and PCR. It is reasonable to assume that extensive research is necessary to define the CHD gene as a universal molecular marker for successful sex determination in all bird species (with exception of ratites). The results of this study may largely contribute to the aim. PMID:22553188

Vucicevic, Milos; Stevanov-Pavlovic, Marija; Stevanovic, Jevrosima; Bosnjak, Jasna; Gajic, Bojan; Aleksic, Nevenka; Stanimirovic, Zoran

2013-01-01

296

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

PubMed

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

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

2009-12-01

297

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

PubMed Central

Echinacea, native to the Canadian prairies and the prairie states of the United States, has a long tradition as a folk medicine for the Native Americans. Currently, Echinacea are among the top 10 selling herbal medicines in the U.S. and Europe, due to increasing popularity for the treatment of common cold and ability to stimulate the immune system. However, the genetic relationship within the species of this genus is unclear, making the authentication of the species used for the medicinal industry more difficult. We report the construction of a novel Subtracted Diversity Array (SDA) for Echinacea species and demonstrate the potential of this array for isolating highly polymorphic sequences. In order to selectively isolate Echinacea-specific sequences, a Suppression Subtractive Hybridization (SSH) was performed between a pool of twenty-four Echinacea genotypes and a pool of other angiosperms and non-angiosperms. A total of 283 subtracted genomic DNA (gDNA) fragments were amplified and arrayed. Twenty-seven Echinacea genotypes including four that were not used in the array construction could be successfully discriminated. Interestingly, unknown samples of E. paradoxa and E. purpurea could be unambiguously identified from the cluster analysis. Furthermore, this Echinacea-specific SDA was also able to isolate highly polymorphic retrotransposon sequences. Five out of the eleven most discriminatory features matched to known retrotransposons. This is the first time retrotransposon sequences have been used to fingerprint Echinacea, highlighting the potential of retrotransposons as based molecular markers useful for fingerprinting and studying diversity patterns in Echinacea. PMID:23940565

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

2013-01-01

298

Molecular markers of trichloroethylene-induced toxicity in human kidney cells  

SciTech Connect

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

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

2005-08-07

299

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. PMID:22238660

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

2012-01-01

300

Croce named 2012 Distinguished University Professor Carlo Croce, chair, Department of Molecular Virology, Immunology, and Medical Genetics; John W. Wolfe Chair in Human  

E-print Network

Virology, Immunology, and Medical Genetics; John W. Wolfe Chair in Human Cancer Genetics; and director Foundation CAREER Award, an Eli Lilly Young Investigator Award in Analytical Chemistry, and a New

301

MOLECULAR PHYLOGENY OF CUCUMIS SPECIES AS REVEALED BY CCSSR MARKER LENGTH AND SEQUENCE VARIATION  

Technology Transfer Automated Retrieval System (TEKTRAN)

The genus Cucumis has been partitioned into two subgenera Cucumis (x = 7) and Melo (x = 12). Although the genetic relationships among species within this two subgenera have been well studied using nuclear genetic markers, recent development of chloroplast markers consensus chloroplast simple sequen...

302

The First Sex-Specific Molecular Marker Discovered in the Moss Pseudocalliergon trifarium  

Microsoft Academic Search

Most dioecious plants do not exhibit discernible sexual dimorphism before sexual maturity. Therefore, it is impossible to address any sex-related questions during the prereproductive phase unless a genetic sex marker is available for gender determination. The aim of the present study was to develop a genetic sex marker for the moss Pseudocalliergon trifarium to allow gender and sex ratio determination

HELENA KORPELAINEN; I RENE BISANG; L ARS HEDENAS; JOHANNA KOLEHMAINEN

2008-01-01

303

Harnessing the annotated EST information in molecular marker development for crop improvement  

Technology Transfer Automated Retrieval System (TEKTRAN)

Marker-assisted selection has become an integral component of many crop breeding programs in both the private and public sectors throughout the world. Various markers, such as RFLP, RAPD, AFLP and SSR are being used by the crop breeding community. The advent of high throughput sequencing technology ...

304

A Molecular Marker-Based Linkage Map of Phaseolus vulgaris L  

Microsoft Academic Search

A seed and flower color marker (P), nine seed protein, nine isozyme and 224 restriction fragment length polymorphism marker loci were used to construct a linkage map of the common bean, Phaseolus vulgaris L. (n = 11). The mapping population consisted of a backcross progeny between the Mesoamerican breeding line 'XR-235-1-1' and the Andean cultivar 'Calima'; the former was used

C. Eduardo Vallejos; Ney S. Sakiyama; Christine D. Chase

1992-01-01

305

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 PMID:2912898

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

1989-01-01

306

Development of user-friendly functional molecular markers for VvDXS gene conferring muscat flavor in grapevine.  

PubMed

High fruit and wine quality combined with good climatic adaptation and disease resistance are essential objectives of grape breeding. While several molecular markers are available for pyramiding resistance to fungal pathogens, molecular tools for predicting fruit composition are still scarce. Muscat flavor, caused by the accumulation of monoterpenoids in the berry, is an important target trait for breeding, sought after in both table grapes and wine. Four missense mutations in the VvDXS gene in grape germplasm have been shown to be tightly linked to muscat flavor. Here we present highly reproducible and breeder-friendly functional markers for each of the targeted polymorphisms developed by using either the multiplexed minisequencing SNaPshot™ method, the high-resolution melting (HRM) assay or the cleaved amplified polymorphic sequence system. A total of 242 grapevine accessions were analyzed to optimize these different genotyping methods and to provide allele-specific markers for accurate selection of muscat flavor at early stages of grape breeding programs. The HRM and the minisequencing SNaPshot multiplex assays allow for high-throughput automated screening and are suitable for large-scale breeding programs and germplasm characterization. PMID:24482604

Emanuelli, F; Sordo, M; Lorenzi, S; Battilana, J; Grando, M S

2014-01-01

307

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

PubMed Central

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

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

2014-01-01

308

Age-related degeneration of articular cartilage in the pathogenesis of osteoarthritis: molecular markers of senescent chondrocytes.  

PubMed

Aging is a natural process by which every single living organism approaches its twilight of existence in a natural way. However, aging is also linked to the pathogenesis of a number of complex diseases. This is the case for osteoarthritis (OA), where age is considered to be a major risk factor of this important and increasingly common joint disorder. Half of the world's population, aged 65 and older, suffers from OA. Although the relationship between the development of OA and aging has not yet been completely understood, it is thought that age-related changes correlate with other risk factors. The most prominent hypothesis linking aging and OA is that chondrocytes undergo premature aging due to several factors, such as excessive mechanical load or oxidative stress, which induce the so called "stress-induced senescent state", which is ultimately responsible for the onset of OA. This review focuses on molecular markers and mechanisms implicated in chondrocyte aging and the pathogenesis of OA. We discuss the most important age-related morphological and biological changes that affect articular cartilage and chondrocytes. We also identify the main senescence markers that may be used to recognize molecular alterations in the extracellular matrix of cartilage as related to senescence. Since the aging process is strongly associated with the onset of osteoarthritis, we believe that strategies aimed at preventing chondrocyte senescence, as well as the identification of new increasingly sensitive senescent markers, could have a positive impact on the development of new therapies for this severe disease. PMID:25010513

Musumeci, Giuseppe; Szychlinska, Marta Anna; Mobasheri, Ali

2015-01-01

309

[RAPD and SCAR molecular markers linked to the sexuality of cycads (Cycas tanqingii D. Y. Wang)].  

PubMed

The random amplified polymorphic DNA (RAPD) technique was used to amplify DNA fragment, aiming at finding markers linked to the sex trait in Cycas tanqingii D. Y. Wang. A total number of 160 random primers were screened in the RAPD-PCR and more than 2500 RAPD fragments were generated from the male or the female plants. One fragment of about 500 bp was amplified steadily and repeatedly by the S0465 (CCCCGGTAAC) primer only from female plants but not male plants. The RAPD marker was then converted into female-linked dominant SCAR (Sequence Characterized Amplified Regions) marker named STQC-S465-483. The development of this sex-linked SCAR marker provides a possibility of identifying the sex of Cycas tanqingii before sexual maturation, which is very important to in situ or ex situ conservation. PMID:18257243

Jing, Jian-Zhou; Jin, Hong; Li, Dong-Liang; Chen, Xiao-Ke; Zhang, Yong

2007-11-01

310

Integrated analysis of pediatric glioblastoma reveals a subset of biologically favorable tumors with associated molecular prognostic markers.  

PubMed

Pediatric glioblastoma (pedGBM) is amongst the most common malignant brain tumors of childhood and carries a dismal prognosis. In contrast to adult GBM, few molecular prognostic markers for the pediatric counterpart have been established. We, therefore, investigated the prognostic significance of genomic and epigenetic alterations through molecular analysis of 202 pedGBM (1-18 years) with comprehensive clinical annotation. Routinely prepared formalin-fixed paraffin-embedded tumor samples were assessed for genome-wide DNA methylation profiles, with known candidate genes screened for alterations via direct sequencing or FISH. Unexpectedly, a subset of histologically diagnosed GBM (n = 40, 20 %) displayed methylation profiles similar to those of either low-grade gliomas or pleomorphic xanthoastrocytomas (PXA). These tumors showed a markedly better prognosis, with molecularly PXA-like tumors frequently harboring BRAF V600E mutations and 9p21 (CDKN2A) homozygous deletion. The remaining 162 tumors with pedGBM molecular signatures comprised four subgroups: H3.3 G34-mutant (15 %), H3.3/H3.1 K27-mutant (43 %), IDH1-mutant (6 %), and H3/IDH wild-type (wt) GBM (36 %). These subgroups were associated with specific cytogenetic aberrations, MGMT methylation patterns and clinical outcomes. Analysis of follow-up data identified a set of biomarkers feasible for use in risk stratification: pedGBM with any oncogene amplification and/or K27M mutation (n = 124) represents a particularly unfavorable group, with 3-year overall survival (OS) of 5 %, whereas tumors without these markers (n = 38) define a more favorable group (3-year OS ~70 %).Combined with the lower grade-like lesions, almost 40 % of pedGBM cases had distinct molecular features associated with a more favorable outcome. This refined prognostication method for pedGBM using a molecular risk algorithm may allow for improved therapeutic choices and better planning of clinical trial stratification for this otherwise devastating disease. PMID:25752754

Korshunov, Andrey; Ryzhova, Marina; Hovestadt, Volker; Bender, Sebastian; Sturm, Dominik; Capper, David; Meyer, Jochen; Schrimpf, Daniel; Kool, Marcel; Northcott, Paul A; Zheludkova, Olga; Milde, Till; Witt, Olaf; Kulozik, Andreas E; Reifenberger, Guido; Jabado, Nada; Perry, Arie; Lichter, Peter; von Deimling, Andreas; Pfister, Stefan M; Jones, David T W

2015-05-01

311

Application of ISSR markers to analyze molecular relationships in Iranian jasmine (Jasminum spp.) accessions.  

PubMed

There are many species of jasmines in different regions of Iran in natural or cultivated form, and there is no information about their genetic status. Therefore, inter-simple sequence repeat (ISSR) analysis was used to evaluate genetic variations of the 53 accessions representing eight species of Jasminum collected from different regions of Iran. A total of 21 ISSR primers were used which generated 981 bands of different sizes. Mean percentage of polymorphic bands was 90.64 %. Maximum resolving power, polymorphic information content average, and marker index values were 21.55, 0.35, and 14.42 for primers of 3, 4, and 3 respectively. The unweighted pair group method with arithmetic mean dendrogram based on Jaccard's coefficients indicated that 53 accessions were divided into two major clusters. The first major cluster was divided into two subclusters; the subcluster A included Jasminum grandiflorum L., J. officinale L., and J. azoricum L. and the subcluster B consisted of three forms of J. sambac L. (single, semi-double, and double flowers). The second major cluster was divided into two subclusters; the first subcluster (C) included J. humile L., J. primulinum Hemsl., J. nudiflorum Lindl. and the second subcluster (D) consisted of J. fruticans L. At the species level, the highest percentage of polymorphism (34.05 %), numbers of effective alleles (1.16), Shannon index (0.151), and Nei's genetic diversity (0.098) were observed in J. officinale. The lowest values of percentage polymorphism (0.011), number of effective alleles (1.009), Shannon index (0.007), and Nei's genetic diversity (0.005) were obtained for J. nudiflorum. Based on pairwise population matrix of Nei's unbiased genetic identity, the highest identity (0.85) was found between J.officinale and J. azoricum and the lowest identity (0.69) was between J. grandiflorum and J. perimulinum. Based on analysis of molecular variance, the amount of genetic variations among the eight populations was 83 %. This study demonstrated that the ISSR is an useful tool in jasmine genomic diversity studies and to detect their relationships. PMID:25189463

Ghasemi Ghehsareh, Masood; Salehi, Hassan; Khosh-Khui, Morteza; Niazi, Ali

2015-01-01

312

Chromosomal origin of small ring marker chromosomes in man: characterization by molecular genetics.  

PubMed Central

Ten cases of small ring chromosomes which did not stain with distamycinA/DAPI and did not possess satellite regions associated with nucleolus-organizing regions are described. In situ hybridization with a battery of biotinylated pericentric repeat probes specific either for individual chromosomes or for groups of chromosomes allowed the identification of the chromosomal origin of these marker chromosomes. There was one example of a marker derived from each of chromosomes 1, 3, 6, 14, 16, 18, 20, 13 or 21, and the X, and there were two examples of markers derived from chromosome 12. One case possessed two markers, one derived from chromosome 6, and one derived from the X. The mechanism of generation of ring marker chromosomes is discussed. Five of seven cases who could be phenotypically assessed were abnormal. Three of these--the first with a ring chromosome derived from chromosome 1; the second with two markers, one derived from chromosome 6 and the other from the X chromosome; and the third with a ring chromosome derived from chromosome 20--each possessed distinctive facies. Additional cases with identified rings may allow the delineation of new chromosomal syndromes. Images Figure 1 p776-a Figure 2 p778-a p779-a p780-a p781-a PMID:2014800

Callen, D F; Eyre, H J; Ringenbergs, M L; Freemantle, C J; Woodroffe, P; Haan, E A

1991-01-01

313

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

NASA Astrophysics Data System (ADS)

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

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

2011-01-01

314

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

PubMed Central

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

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

2007-01-01

315

Towards the Development of a Molecular Map in Switchgrass: I. Microsatellite Marker Development  

SciTech Connect

The long-term goal of the switchgrass breeding program is to improve regionally adapted varieties and increase biomass yield and feedstock quality. Although, to some extent, biomass yields are dependent on environmental constraints, increased yield can be achieved through the development of genotypes with improved seasonal adaptation, tolerance to unfavorable environmental conditions, and improved resistance to pest and disease. To date, improvement in switchgrass has relied on recurrent breeding strategies based on phenotypic or genotypic selection. Yield improvements have been modest by this method. If we expect to make significant increase in yields, we need tools that will allow us to map complex traits and uncover the genes that influence them. A genetic linkage map could be a powerful tool for accelerating switchgrass development through marker-assisted selection, breeding and recombination. This type of mapping requires the development of markers that can be associated with phenotypic traits in a population of known pedigree. The most commonly used markers for mapping include restriction fragment length polymorphisms (RFLP) and simple sequence repeats (SSR). At ORNL, we have been concentrating on the development of SSR markers, while our colleagues at the University of Georgia are developing RFLP markers in order to select parents to produce a mapping population and from there to create a framework map from {approx}100 F1 progeny.

Gunter, L.E.

2001-08-23

316

Sources of Bias in Specimens for Research About Molecular Markers for Cancer  

PubMed Central

Claims about the diagnostic or prognostic accuracy of markers often prove disappointing when “discrimination” found between cancers versus normals is due to bias, a systematic difference between compared groups. This article describes a framework to help simplify and organize current problems in marker research by focusing on the role of specimens as a source of bias in observational research and using that focus to address problems and improve reliability. The central idea is that the “fundamental comparison” in research about markers (ie, the comparison done to assess whether a marker discriminates) involves two distinct processes that are “connected” by specimens. If subject selection (first process) creates baseline inequality between groups being compared, then laboratory analysis of specimens (second process) may erroneously find positive results. Although both processes are important, subject selection more fundamentally influences the quality of marker research, because it can hardwire bias into all comparisons in a way that cannot be corrected by any refinement in laboratory analysis. An appreciation of the separateness of these two processes—and placing investigators with appropriate expertise in charge of each—may increase the reliability of research about cancer biomarkers. PMID:20038718

Ransohoff, David F.; Gourlay, Margaret L.

2010-01-01

317

Modelling Immunological Memory  

E-print Network

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

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

2010-01-01

318

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

PubMed

The objective was to characterize virulence markers and ?-lactam resistance in Klebsiella pneumoniae isolates from renal transplant patients and to evaluate their genetic relatedness. Two main genetic lineages were detected: 1 carried bla(CTX-M-15) not associated to IncFIIA plasmid replicon, which was found on the other lineage not expressing CTX-M-type enzyme. PAI III(536) and PAI II(CFT073) were detected for the first time in K. pneumoniae in 1 clone, while the siderophore kfu was carried by the other, with only PAI IV(536). The molecular data indicate colonization before admission and fuel the discussion on implementation of antibiotherapy before surgery. PMID:24746826

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

2014-07-01

319

Overexpression of hMTH1 mRNA: a molecular marker of oxidative stress in lung cancer cells  

Microsoft Academic Search

Human MutT homologue (hMTH1) mRNA was overexpressed in SV-40-transformed non-tumorigenic human bronchial epithelial cells (BEAS-2B cells) and in 11 out of 12 human lung cancer cell lines relative to normal human bronchial epithelial cells. Expression levels of hMTH1 mRNA were inversely proportional to cellular levels of 8-oxo-deoxyguanosine. Together, these results suggest that hMTH1 gene expression may represent a molecular marker

Christopher H Kennedy; Rafael Cueto; Steven A Belinsky; John F Lechner; William A Pryor

1998-01-01

320

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

PubMed Central

Background As a result of the widespread resistance to chloroquine and sulphadoxine-pyrimethamine, artemisinin-based combination therapy (ACT) (including artemether-lumefantrine and artesunate-amodiaquine) has been recommended as a first-line anti-malarial regimen in Senegal since 2006. Intermittent preventive treatments with anti-malarial drugs based on sulphadoxine-pyrimethamine are also given to children or pregnant women once per month during the transmission season. Since 2006, there have been very few reports on the susceptibility of Plasmodium falciparum to anti-malarial drugs. To estimate the prevalence of resistance to several anti-malarial drugs since the introduction of the widespread use of ACT, the presence of molecular markers associated with resistance to chloroquine and sulphadoxine-pyrimethamine was assessed in local isolates at the military hospital of Dakar. Methods The prevalence of genetic polymorphisms in genes associated with anti-malarial drug resistance, i.e., Pfcrt, Pfdhfr, Pfdhps and Pfmdr1, and the copy number of Pfmdr1 were evaluated for a panel of 174 isolates collected from patients recruited at the military hospital of Dakar from 14 October 2009 to 19 January 2010. Results The Pfcrt 76T mutation was identified in 37.2% of the samples. The Pfmdr1 86Y and 184F mutations were found in 16.6% and 67.6% of the tested samples, respectively. Twenty-eight of the 29 isolates with the 86Y mutation were also mutated at codon 184. Only one isolate (0.6%) had two copies of Pfmdr1. The Pfdhfr 108N/T, 51I and 59R mutations were identified in 82.4%, 83.5% and 74.1% of the samples, respectively. The double mutant (108N and 51I) was detected in 83.5% of the isolates, and the triple mutant (108N, 51I and 59R) was detected in 75.3%. The Pfdhps 437G, 436F/A and 613S mutations were found in 40.2%, 35.1% and 1.8% of the samples, respectively. There was no double mutant (437G and 540E) or no quintuple mutant (Pfdhfr 108N, 51I and 59R and Pfdhps 437G and 540E). The prevalence of the quadruple mutant (Pfdhfr 108N, 51I and 59R and Pfdhps 437G) was 36.5%. Conclusions Since 2004, the prevalence of chloroquine resistance had decreased. The prevalence of isolates with high-level pyrimethamine resistance is 83.5%. The prevalence of isolates resistant to sulphadoxine is 40.2%. However, no quintuple mutant (Pfdhfr 108N, 51I and 59R and Pfdhps 437G and 540E), which is associated with a high level of sulphadoxine-pyrimethamine resistance, has been identified to date. The resistance to amodiaquine remains moderate. PMID:22694921

2012-01-01

321

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

322

Conservation phylogenetics of helodermatid lizards using multiple molecular markers and a supertree approach  

Microsoft Academic Search

We analyzed both mitochondrial (mt-) and nuclear (n) DNAs in a conservation phylogenetic framework to examine deep and shallow histories of the Beaded Lizard (Heloderma horridum) and Gila Monster (H. suspectum) throughout their geographic ranges in North and Central America. Both mtDNA and intron markers clearly partitioned each species. One intron and mtDNA further subdivided H. horridum into its four

Michael E. Douglas; Marlis R. Douglas; Gordon W. Schuett; Daniel D. Beck; Brian K. Sullivan

2010-01-01

323

Development of nuclear gene-derived molecular markers linked to legume genetic maps  

Microsoft Academic Search

The systematic identification of the orthologous features of related organisms greatly facilitates comparative genomics, including research on genome evolution and comparative genetic mapping. In this study, we selected 274 unique gene sequences for the development of PCR-based genetic markers across fifteen legume genomes, representing six crop or model legume species from the phaseoloid and inverted repeat loss clades (IRLC). DNA

Hong-Kyu Choi; Melissa A. Luckow; Jeff Doyle; Douglas R. Cook

2006-01-01

324

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

325

Molecular markers to determine ecological fate of Bacillus thuringiensis subsp. kurstaki  

Technology Transfer Automated Retrieval System (TEKTRAN)

Bacillus thuringiensis (“Bt”) is a ubiquitous soil bacterium with entomopathogenic properties. One strain, Bt subsp. kurstaki (“Btk”), is highly toxic to lepidopteran larvae and used in many commercial products for biological pest control. We designed a set of DNA markers that successfully identifi...

326

A molecular marker-based linkage map of Phaseolus vulgaris L.  

PubMed

A seed and flower color marker (P), nine seed protein, nine isozyme and 224 restriction fragment length polymorphism marker loci were used to construct a linkage map of the common bean, Phaseolus vulgaris L. (n = 11). The mapping population consisted of a backcross progeny between the Mesoamerican breeding line 'XR-235-1-1' and the Andean cultivar 'Calima'; the former was used as the recurrent parent. A bean PstI genomic library enriched for single copy sequences (95%) was the source of DNA probes. Sixty percent of the probes tested detected polymorphisms between the parental genotypes with at least one of the four restriction enzymes used here (DraI, EcoRI, EcoRV and HindIII). The computer software Mapmaker was used to determine the linkage relationships and linear order of segregating markers. These markers assorted into 11 linkage groups covering 960 cM of the bean genome. Partial linkage data were used to estimate the total length of the genome at 1200 cM. This estimate and that for the physical size of the genome yield an average ratio of 530 kb/cM. The relatively small size of the genome makes this crop species a good candidate for the isolation of genes via chromosome walking techniques. PMID:1352759

Vallejos, C E; Sakiyama, N S; Chase, C D

1992-07-01

327

Molecular markers in circulating tumour cells from metastatic colorectal cancer patients  

PubMed Central

Abstract 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

2010-01-01

328

Identification of molecular markers associated with low chill/heat tolerance in raspberry  

Technology Transfer Automated Retrieval System (TEKTRAN)

New genetic markers were developed which are linked to cold and heat tolerant raspberries. Raspberry is a cool season crop, and as such, cannot tolerate the high temperatures of the South during the normal growing season. Expanding the commercial growth range of raspberry production to the southern...

329

Molecular markers associated with resistance to Aspergillus flavus in maize: QTL and discriminant analyses  

Technology Transfer Automated Retrieval System (TEKTRAN)

Aflatoxin contamination of maize (Zea mays L.) grain caused by Aspergillus flavus is a serious health hazard to animals and humans. Resistance to infection by A. flavus is poorly understood. The objectives of this investigation were to identify potential candidate markers associated with resistance ...

330

Molecular genetic characterization of lasquerella new industrial crop using DArTseq markers  

Technology Transfer Automated Retrieval System (TEKTRAN)

DArTseq, a new SNP-based marker platform, was developed and used to analyze the genetic diversity of the US germplasm collection of lesquerella. Lesquerella is a new oilseed crop in the Brassica family found native in the American Southwest. The potential of the species as a domestic source of indu...

331

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

PubMed Central

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

2013-01-01

332

IMMUNOLOGICAL COMPUTATION: THEORY AND APPLICATIONS  

E-print Network

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

Dasgupta, Dipankar

333

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

334

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

335

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

336

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

337

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...

338

Distinct immunologic effects of different intravenous iron preparations on monocytes  

PubMed Central

Background Iron deficiency contributes to anaemia in patients with chronic kidney disease. I.v. iron is therefore widely used for anaemia treatment, although it may induce oxidative stress and activate monocytes. Different i.v. iron preparations are available, but interestingly their substance-specific immunologic effects are poorly studied. Methods We analysed the effect of iron sucrose, ferric carboxymaltose, iron isomaltoside 1000, low-molecular-weight iron dextran and ferumoxytol on classical, intermediate and nonclassical monocyte biology. We therefore stimulated in vitro mature monocytes and haematopoietic CD34+ stem cells during their differentiation into monocytes with different concentrations (0.133, 0.266, 0.533 mg/mL) of i.v. iron preparations. Alterations of monocyte subset distribution, expression of surface markers (CD86, CCR5, CX3CR1), as well as production of pro-inflammatory cytokines (TNF-?, IL-1?) and reactive oxygen species were measured using flow cytometry. Additionally, we analysed phagocytosis and antigen presentation capacity. Results We found specific immunologic effects after stimulation with iron sucrose which were not induced by the other iron preparations. Iron sucrose activated monocyte subsets leading to significantly increased CD86 expression. Simultaneously CD16 and CX3CR1 expression and monocytic phagocytosis capacity were decreased. Additionally, differentiation of monocytes from haematopoietic CD34+ stem cells was almost completely abolished after stimulation with iron sucrose. Conclusions Our findings demonstrate that specific immunologic effects of distinct i.v. iron preparations exist. The clinical relevance of these findings requires further investigation. PMID:24523357

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

2014-01-01

339

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

Microsoft Academic Search

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

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

2006-01-01

340

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

341

Molecular identification of five Indian sciaenids (pisces: perciformes, sciaenidae) using RAPD markers  

Microsoft Academic Search

The randomly amplified polymorphic DNA (RAPD) markers were used to detect interspecific genetic variability and genetic relatedness\\u000a among five Indian sciaenids namely Otolithes cuvieri, Johnieops sina, Johnieops macrorhynus, Johnieops vogleri and Protonibea diacanthus for the first time. Eight RAPD primers (OPA01, OPA06, OPA07, OPA18, OPP12, OPP14, OPP16 and OPP11) generated 40 species specific\\u000a diagnostic bands. The highest genetic divergence was

Wazir S. Lakra; M. Goswami; V. Mohindra; K. K. Lal; P. Punia

2007-01-01

342

The utility of fast evolving molecular markers for studying speciation in the Antarctic benthos  

Microsoft Academic Search

The Southern Ocean is surprisingly rich in species that coexist in one of the most extreme environments on Earth yet the processes\\u000a leading to speciation in this ecosystem are not well understood. To remedy this, tools that measure the genetic connectedness\\u000a within a species are needed. Although useful for phylogenetic purposes, the readily available mitochondrial markers (e.g.\\u000a 16S, COI) suffer

Christoph Held; Florian Leese

2007-01-01

343

Citrus phylogeny and genetic origin of important species as investigated by molecular markers  

Microsoft Academic Search

Citrus phylogeny was investigated using RAPD, SCAR and cpDNA markers. The genotypes analyzed included 36 accessions belonging\\u000a to Citrus together with 1 accession from each of the related genera Poncirus, Fortunella, Microcitrus and Eremocitrus. Phylogenetic analysis with 262 RAPDs and 14 SCARs indicated that Fortunella is phylogenetically close to Citrus while the other three related genera are distant from Citrus

E. Nicolosi; Z. N. Deng; A. Gentile; S. La Malfa; G. Continella; E. Tribulato

2000-01-01

344

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

PubMed

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

Gaur, Rashmi; Bhatia, Sabhyata; Gupta, Meetu

2014-07-01

345

Influence of different colloids on molecular markers of haemostasis and platelet function in patients undergoing major abdominal surgery.  

PubMed

Synthetic colloids have been reported to cause haemorrhagic complications. The effects of perioperative volume replacement with 4% gelatin (n = 20), 6% low-molecular weight (LMW) hydroxyethyl starch (HES) (Mw: 70,000 dalton; HES 70/0.5; n = 20) and 6% medium-molecular weight (MMW) HES (Mw: 200,000 dalton; HES 200/0.5; n = 20) on haemostasis were assessed in patients undergoing major abdominal surgery. Volume was administered to keep central venous pressure (CVP) between 10 and 14 mm Hg. Conventional global coagulation tests, molecular markers of coagulation, and platelet function (using a platelet function analyser (PFA-100) with ADP as inductor) were monitored prior to surgery (T0), at the end of surgery (T1), 4 h after the end of surgery (T2), and on the morning of the first postoperative day (T3). Significantly more gelatin (2900 (SD 320) ml) than HES 200 (2150 (312) ml) was given during the study period. Bleeding and the use of allogeneic blood-blood products were similar in all groups. Markers of thrombin generation (F1 + 2), of thrombin neutralization (TAT III complex), and of fibrin formation and its degradation (D-dimer) increased significantly during and after surgery without showing significant group differences. Factor VIII and von Willebrand factor (vWF) also increased in all groups beyond the normal range, showing the significantly highest increase in the gelatin-treated group (VIII: from 173 (36) to 266 (33) U dl-1; vWF: from 164(33) to 238 (31) U dl-1). Platelet function remained within the normal range and without group differences throughout the study period. We can conclude that all three solutions can be used safely in patients undergoing major abdominal surgery with regard to the haemostatic process. PMID:11103184

Hüttner, I; Boldt, J; Haisch, G; Suttner, S; Kumle, B; Schulz, H

2000-09-01

346

The diversity of immunological synapses.  

PubMed

Immunological synapses (ISs) are specialised signalling domains characterised by complex molecular clustering and segregation at the contact site between cells of the immune system. T lymphocytes form different ISs depending on their state of activation and on the antigen-presenting cells with which they interact. The structural features of the various ISs are better established than the functions they carry out. Recent advances point to the importance of taking into account diversity in both the structures and the functions of IS. PMID:12787748

Trautmann, Alain; Valitutti, Salvatore

2003-06-01

347

A multi-molecular marker assessment of organic pollution in shore sediments from the Río de la Plata Estuary, SW Atlantic.  

PubMed

Organic pollution was evaluated in surface sediments along the middle portion of the Río de la Plata Estuary, SW Atlantic. A multi-molecular marker approach was performed to identify major sources of organic compounds using diagnostic indices. The relative contribution of different sources of hydrocarbons was quantified by source apportionment employing Principal Component Analysis/Multiple Linear Regression (PCA/MLR) as chemometric technique. All molecular markers indicated high chronic organic pollution in the stations of Montevideo Bay. Main sources of aliphatic and polycyclic aromatic hydrocarbons were petroleum inputs and combustion, due to oil transport and refinement, harbour activities and vehicular emissions. Major sources of linear alkylbenzenes and steroids were industrial and domestic sewage. Although, significant anthropogenic inputs, a natural footprint of terrestrial higher plants contribution was recognized. Multi-molecular marker and comprehensive assessments can improve the establishment of more precise regulation actions to reduce pollution levels. PMID:25060626

Venturini, Natalia; Bícego, Márcia C; Taniguchi, Satie; Sasaki, Silvio T; García-Rodríguez, Felipe; Brugnoli, Ernesto; Muniz, Pablo

2015-02-28

348

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

349

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...

350

Immunological synapse: center of attention again.  

PubMed

The functional role of molecular clustering in the center of the immunological synapse is controversial. In this issue of Immunity, Cemerski et al. (2008) report that the synapse center can serve as a major site of sustained signal transduction. PMID:18799146

Valitutti, Salvatore

2008-09-19

351

Immunology, Microbiology & Immunology, and Institute for Immunity, Transplantation & Infection  

E-print Network

at Barrier Sites: Roles of Commensals and Nutrients Microbiology and Immunology sponsored seminars in black Immunology sponsored seminars in red All are welcome to join us for refreshments before the Immunology Seminars at 3:45pm For questions, please contact Nicki Barnes, Immunology at nbarnes@stanford.edu or Sara

Ford, James

352

The bioenergetic signature of lung adenocarcinomas is a molecular marker of cancer diagnosis and prognosis.  

PubMed

The aim of this study was to investigate the mitochondrial bioenergetic signature of lung adenocarcinomas as a prognostic marker of cancer progression. For this purpose, a series of 90 lung adenocarcinomas and 10 uninvolved lung samples were examined for quantitative differences in protein expression using two-dimensional polyacrylamide gel electrophoresis. The beta subunit of the mitochondrial H(+)-ATP synthase (beta-F1-ATPase) and heat shock protein 60 (Hsp 60), and the glycolytic glyceraldehyde-3-phosphate dehydrogenase (GAPDH), used to define the bioenergetic cellular (BEC) index, were identified using mass spectrometry and specific antibodies. Correlations of the expression level of the protein markers and of the BEC index were established with the clinicopathological information of the tumors and the follow-up data of the patients. The expression of beta-F1-ATPase is significantly reduced in lung adenocarcinomas in the absence of significant changes in the expression of Hsp 60 and of a major GAPDH isoform. Cross-validation analysis using the beta-F1-ATPase/Hsp 60 ratio and GAPDH expression as predictor variables revealed a classification sensitivity of 97.3%. The beta-F1-ATPase/Hsp 60 ratio is significantly higher in well differentiated and bronchioloalveolar tumors than in moderate or poorly differentiated and in bronchial-derived tumors. The BEC index of T1 tumors was significantly higher than that of T2 tumors. Likewise, stage IA tumors had a higher BEC index than stage IB tumors. Kaplan-Meier survival analysis using the BEC index as predictor of survival revealed that within tumors of the same size or stage I or with no lymph node metastasis (N0) the patients bearing 'low' BEC index tumors had a significant worse prognosis. We conclude that the bioenergetic signature of lung adenocarcinomas is altered, further providing a relevant marker for the diagnosis and classification of lung adenocarcinomas, and for the prognosis of lung cancer patients. PMID:14963017

Cuezva, José M; Chen, Guoan; Alonso, Andrés M; Isidoro, Antonio; Misek, David E; Hanash, Samir M; Beer, David G

2004-07-01

353

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

PubMed

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

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

2010-07-01

354

Activation loop phosphorylation of a protein kinase is a molecular marker of organelle size that dynamically reports flagellar length  

PubMed Central

Specification of organelle size is crucial for cell function, yet we know little about the molecular mechanisms that report and regulate organelle growth and steady-state dimensions. The biflagellated green alga Chlamydomonas requires continuous-length feedback to integrate the multiple events that support flagellar assembly and disassembly and at the same time maintain the sensory and motility functions of the organelle. Although several length mutants have been characterized, the requisite molecular reporter of length has not been identified. Previously, we showed that depletion of Chlamydomonas aurora-like protein kinase CALK inhibited flagellar disassembly and that a gel-shift–associated phosphorylation of CALK marked half-length flagella during flagellar assembly. Here, we show that phosphorylation of CALK on T193, a consensus phosphorylation site on the activation loop required for kinase activity, is distinct from the gel-shift–associated phosphorylation and is triggered when flagellar shortening is induced, thereby implicating CALK protein kinase activity in the shortening arm of length control. Moreover, CALK phosphorylation on T193 is dynamically related to flagellar length. It is reduced in cells with short flagella, elevated in the long flagella mutant, lf4, and dynamically tracks length during both flagellar assembly and flagellar disassembly in WT, but not in lf4. Thus, phosphorylation of CALK in its activation loop is implicated in the disassembly arm of a length feedback mechanism and is a continuous and dynamic molecular marker of flagellar length during both assembly and disassembly. PMID:23836633

Cao, Muqing; Meng, Dan; Wang, Liang; Bei, Shuqing; Snell, William J.; Pan, Junmin

2013-01-01

355

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. PMID:23211669

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

2012-01-01

356

Molecular mapping of restriction-site associated DNA markers in allotetraploid upland cotton.  

PubMed

Upland cotton (Gossypium hirsutum L., 2n = 52, AADD) is an allotetraploid, therefore the discovery of single nucleotide polymorphism (SNP) markers is difficult. The recent emergence of genome complexity reduction technologies based on the next-generation sequencing (NGS) platform has greatly expedited SNP discovery in crops with highly repetitive and complex genomes. Here we applied restriction-site associated DNA (RAD) sequencing technology for de novo SNP discovery in allotetraploid cotton. We identified 21,109 SNPs between the two parents and used these for genotyping of 161 recombinant inbred lines (RILs). Finally, a high dense linkage map comprising 4,153 loci over 3500-cM was developed based on the previous result. Using this map quantitative trait locus (QTLs) conferring fiber strength and Verticillium Wilt (VW) resistance were mapped to a more accurate region in comparison to the 1576-cM interval determined using the simple sequence repeat (SSR) genetic map. This suggests that the newly constructed map has more power and resolution than the previous SSR map. It will pave the way for the rapid identification of the marker-assisted selection in cotton breeding and cloning of QTL of interest traits. PMID:25894395

Wang, Yangkun; Ning, Zhiyuan; Hu, Yan; Chen, Jiedan; Zhao, Rui; Chen, Hong; Ai, Nijiang; Guo, Wangzhen; Zhang, Tianzhen

2015-01-01

357

Multivariate analysis of molecular markers in peripheral blood associated with recurrence and metastasis of hepatocellular carcinoma.  

PubMed

Invasion, metastasis, and recurrence are the most common causes of death in patients with hepatocellular carcinoma (HCC) and are therefore critical factors for both therapy and prognosis. Current methods for diagnosis of HCC rely mainly on serological markers such as alpha-fetoprotein and liver enzymes, together with physical assessment and imaging techniques. The availability of more accurate serum markers may facilitate screening and early diagnosis, which will improve prognosis. This retrospective cohort analysis included 50 consecutive patients with cirrhosis and single or multifocal HCC and 40 control subjects with no liver disease or risk factors for viral hepatitis. Expression of epidermal growth factor-like domain 7 (EGFL7), osteopontin (OPN), and prostaglandin E2 (PGE2) were detected using an enzyme-linked immunosorbent assay. The mean serum levels of EGFL7, OPN, and PGE2 in the HCC group were 132.11 pg/mL, 11.77 ng/mL, and 179.37 pg/mL, respectively, which were all significantly higher than the levels in the control group (23.03 pg/mL, 2.31 ng/mL, and 47.36 pg/mL, respectively; P < 0.001). Serum levels of EGFL7, OPN, and PGE2 levels may thus be useful for screening and surveillance of HCC among high-risk populations, and have the potential to improve prognosis of these patients. PMID:25730089

Liu, X J; Wang, B; Jiang, W G; Li, Y J; Liu, J B; Zhang, M

2015-01-01

358

A molecular marker associated with low-temperature induction of dormancy in red osier dogwood (Cornus sericea).  

PubMed

Dormancy induction in temperate deciduous plants is thought to be regulated by short photoperiods, but low temperature has been shown to eliminate the short photoperiod requirement in northern ecotypes. An F2 population (191 plants) red osier dogwood (Cornus sericea L.) derived from a polycross of an F1 population produced from reciprocal crosses of the parental clonal ecotypes, Northwest Territories (NWT, 62 degrees N) and Utah (42 degrees N), was examined to identify molecular markers of temperature-induced endodormancy. Dormancy induction curves were generated for each individual in the F2 population and a standard point prior to vegetative maturity (i-VM) was inferred from the change in slope of the dormancy acquisition curve. Under Saskatoon, Saskatchewan field conditions (52 degrees N), the NWT ecotype entered i-VM on average 5-6 weeks before the Utah ecotype. Two sub-populations of the F2 population were distinguishable based on VM acquisition on exposure to low temperature but not to short photoperiods. A sequence characterized amplified region (SCAR) marker was developed that correctly (> 92%) identified individual plants within the F2 subpopulation that were responsive to low-temperature induction of VM. Timing of bud break was strongly associated with the timing of VM in the geographical ecotypes but not in the F2 population, indicating that these are separate traits under genetic control. PMID:17241980

Svendsen, Erl; Wilen, Ron; Stevenson, Robert; Liu, Rensong; Tanino, Karen K

2007-03-01

359

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

PubMed

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

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

2009-07-01

360

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

NASA Astrophysics Data System (ADS)

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

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

2014-09-01

361

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

PubMed

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

Wongsawad, Pheravut; Peerapornpisal, Yuwadee

2014-11-01

362

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

PubMed Central

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

Wongsawad, Pheravut; Peerapornpisal, Yuwadee

2014-01-01

363

Next-Generation Sequencing: A powerful tool for the discovery of molecular markers in breast ductal carcinoma in situ  

PubMed Central

Mammographic screening leads to frequent biopsies and concomitant overdiagnosis of breast cancer, particularly ductal carcinoma in situ (DCIS). Some DCIS lesions rapidly progress to invasive carcinoma whereas others remain indolent. Because we cannot yet predict which lesions will not progress, all DCIS is regarded as malignant, and many women are overtreated. Thus, there is a pressing need for a panel of molecular markers in addition to the current clinical and pathologic factors to provide prognostic information. Genomic technologies such as microarrays have made major contributions to defining sub-types of breast cancer. Next-generation sequencing (NGS) modalities offer unprecedented depth of expression analysis through revealing transcriptional boundaries, mutations, rare transcripts and alternative splice variants. NGS approaches are just beginning to be applied to DCIS. Here, we review the applications and challenges of NGS in discovering novel potential therapeutic targets and candidate biomarkers in the premalignant progression of breast cancer. PMID:23477556

Kaur, Hitchintan; Mao, Shihong; Shah, Seema; Gorski, David H.; Krawetz, Stephen A.; Sloane, Bonnie F.; Mattingly, Raymond R.

2013-01-01

364

Developing genome-wide microsatellite markers of bamboo and their applications on molecular marker assisted taxonomy for accessions in the genus Phyllostachys  

PubMed Central

Morphology-based taxonomy via exiguously reproductive organ has severely limitation on bamboo taxonomy, mainly owing to infrequent and unpredictable flowering events of bamboo. Here, we present the first genome-wide analysis and application of microsatellites based on the genome of moso bamboo (Phyllostachys edulis) to assist bamboo taxonomy. Of identified 127,593 microsatellite repeat-motifs, the primers of 1,451 microsatellites were designed and 1,098 markers were physically mapped on the genome of moso bamboo. A total of 917 markers were successfully validated in 9 accessions with ~39.8% polymorphic potential. Retrieved from validated microsatellite markers, 23 markers were selected for polymorphic analysis among 78 accessions and 64 alleles were detected with an average of 2.78 alleles per primers. The cluster result indicated the majority of the accessions were consistent with their current taxonomic classification, confirming the suitability and effectiveness of the developed microsatellite markers. The variations of microsatellite marker in different species were confirmed by sequencing and in silico comparative genome mapping were investigated. Lastly, a bamboo microsatellites database (http://www.bamboogdb.org/ssr) was implemented to browse and search large information of bamboo microsatellites. Consequently, our results of microsatellite marker development are valuable for assisting bamboo taxonomy and investigating genomic studies in bamboo and related grass species. PMID:25620112

Zhao, Hansheng; Yang, Li; Peng, Zhenhua; Sun, Huayu; Yue, Xianghua; Lou, Yongfeng; Dong, Lili; Wang, Lili; Gao, Zhimin

2015-01-01

365

DEGREE PROGRAMME BSc (Hons) Immunology  

E-print Network

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

Levi, Ran

366

Stanford Immunology Graduate Program Handbook  

E-print Network

participate in seminars, journal clubs, and the annual Stanford Immunology Scientific Conference at Asilomar1 Stanford Immunology Graduate Program Handbook 2013-2014 #12;PhD Program in Immunology 2013-2014 PhD Handbook 2 The PhD Program in Immunology is one of thirteen Stanford Biosciences programs

Puglisi, Joseph

367

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

PubMed

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

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

2011-01-01

368

Identification and cloning of molecular markers for UV-B tolerant gene in wild sugarcane (Saccharum spontaneum L.).  

PubMed

Previously we have selected wild sugarcane (Saccharum spontaneum L.) sterile lines that are tolerant or susceptible to UV-B radiation based on response index (RI) in a field screening test. The RI was established according to plant height, tiller number, leaf index, total biomass and brix under enhanced ultraviolet-B (UV-B, 280-310 nm) radiation. In this experiment, molecular markers linked to the UV-B tolerant and susceptible genes were identified and cloned. RAPD (Randomly amplified polymorphic DNAs) assay using 100 arbitrary primers followed by clustering analysis separated the tolerant and susceptible lines into two groups at the genetic distance of 0.380. The UV-B tolerant and susceptible gene pools were constructed and compared using the Bulked Segregate Analysis (BSA) approach. Of the 100 arbitrary RAPD primers, primer OPR16 produced polymorphic DNA banding patterns from both gene pools. The OPR16-1200 bp DNA fragment was only amplified from the tolerant lines and the OPR16-800 bp from the susceptible ones. These two PCR fragments were cloned onto T-vector. DNA sequence alignment analysis determined that 42% homology existed between the reverse and forward sequences of the OPR16-1200 bp clone, and 36% homology between the forward sequences of the OPR16-800 bp and OPR16-1200 bp clones. The two DNA clones were determined to be linked to the UV-B tolerant and susceptible genes, and they can be used to develop molecular markers for the associated traits. PMID:21925894

Li, Yuan; He, Yongmei; Zu, Yanqun; Zhan, Fangdong

2011-11-01

369

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

PubMed Central

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

2012-01-01

370

Assessment of the canine intestinal microflora using molecular methods and serum markers  

E-print Network

. The aim of this study was to describe the composition and dynamics of the canine intestinal microflora using molecular methods based on identification of the 16S ribosomal DNA (16S rDNA) and to evaluate the clinical use of a 13C-glycocholic acid blood test...

Suchodolski, Jan S.

2007-04-25

371

Anthrax molecular epidemiology and forensics: using the appropriate marker for different evolutionary scales  

Microsoft Academic Search

Precise identification of Bacillus anthracis isolates has aided forensic and epidemiological analyses of natural anthrax cases, bioterrorism acts and industrial scale accidents by state-sponsored bioweapons programs. Because there is little molecular variation among B. anthracis isolates, identifying and using rare variation is crucial for precise strain identification. We think that mutation is the primary diversifying force in a clonal, recently

Paul Keim; Matthew N. Van Ert; Talima Pearson; Amy J. Vogler; Lynn Y. Huynh; David M. Wagner

2004-01-01

372

Molecular variation of Sporisorium scitamineum in mainland China revealed by RAPD and SRAP markers  

Technology Transfer Automated Retrieval System (TEKTRAN)

Sugarcane smut caused by the fungus Sporisorium scitamineum is found worldwide in sugarcane producing countries and can cause serious loss in stalk yield and sugar quality. In order to reveal the molecular evolution of S. scitamineum, twenty-three S. scitamineum isolates collected from the six prima...

373

Subdivisions of the adult zebrafish pallium based on molecular marker analysis  

PubMed Central

Background: The telencephalon shows a remarkable structural diversity among vertebrates. In particular, the everted telencephalon of ray-finned fishes has a markedly different morphology compared to the evaginated telencephalon of all other vertebrates. This difference in development has hampered the comparison between different areas of the pallium of ray-finned fishes and the pallial nuclei of all other vertebrates. Various models of homology between pallial subdivisions in ray-finned fishes and the pallial nuclei in tetrapods have been proposed based on connectional, neurochemical, gene expression and functional data. However, no consensus has been reached so far. In recent years, the analysis of conserved developmental marker genes has assisted the identification of homologies for different parts of the telencephalon among several tetrapod species. Results: We have investigated the gene expression pattern of conserved marker genes in the adult zebrafish ( Danio rerio) pallium to identify pallial subdivisions and their homology to pallial nuclei in tetrapods. Combinatorial expression analysis of ascl1a, eomesa, emx1, emx2, emx3, and Prox1 identifies four main divisions in the adult zebrafish pallium. Within these subdivisions, we propose that Dm is homologous to the pallial amygdala in tetrapods and that the dorsal subdivision of Dl is homologous to part of the hippocampal formation in mouse. We have complemented this analysis be examining the gene expression of emx1, emx2 and emx3 in the zebrafish larval brain. Conclusions: Based on our gene expression data, we propose a new model of subdivisions in the adult zebrafish pallium and their putative homologies to pallial nuclei in tetrapods. Pallial nuclei control sensory, motor, and cognitive functions, like memory, learning and emotion. The identification of pallial subdivisions in the adult zebrafish and their homologies to pallial nuclei in tetrapods will contribute to the use of the zebrafish system as a model for neurobiological research and human neurodegenerative diseases. PMID:25713698

Ganz, Julia; Kroehne, Volker; Freudenreich, Dorian; Machate, Anja; Geffarth, Michaela; Braasch, Ingo; Kaslin, Jan; Brand, Michael

2014-01-01

374

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

PubMed

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

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

2009-12-01

375

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

PubMed Central

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

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

2014-01-01

376

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

PubMed

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

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

2014-11-01

377

Optimization of the choice of molecular markers for varietal identification in Vitis vinifera L  

Microsoft Academic Search

The aim of this study was to develop a cultivar identification tool based on molecular analysis and a statistical approach.\\u000a From the PIC parameter we defined the D parameter, which evaluates the efficiency of a primer for the purpose of identification\\u000a of varieties; i.e. the probability that two randomly chosen individuals have different patterns. D can be used to compare

C. Tessier; J. David; P. This; J. M. Boursiquot; A. Charrier

1999-01-01

378

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

Microsoft Academic Search

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

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

2002-01-01

379

Molecular Profiling for Genetic Variability in Capsicum Species Based on ISSR and RAPD Markers  

Microsoft Academic Search

The taxonomic identity of Capsicum species is found to be difficult as it displays variations at morpho-chemical characters. Twenty-two accessions of six Capsicum species, namely, C. annuum, C. baccatum, C. chinense, C. eximium, C. frutescens, and C. luteum were investigated for phenotypic diversity based on flower color and for genetic differences by molecular makers. The genetic\\u000a cluster analyses of 27

Sanjog T. Thul; Mahendra P. Darokar; Ajit K. Shasany; Suman P. S. Khanuja

380

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

Microsoft Academic Search

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

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

2011-01-01

381

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

Microsoft Academic Search

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

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

2009-01-01

382

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

PubMed

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

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

2014-12-01

383

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

PubMed

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

Huse, Jason T; Aldape, Kenneth D

2014-11-15

384

A centennial record of anthropogenic impacts and extreme weather events in southwestern Taiwan: Evidence from sedimentary molecular markers in coastal margin  

SciTech Connect

A 100-year history of human and natural disturbances in southwestern Taiwan was reconstructed using a suite of molecular markers in four dated sediment cores from the upper slope region off the Gaoping River mouth. Trends in polycyclic aromatic hydrocarbons (PAHs) tracked Taiwan's industrialization/urbanization starting in the 1970s, and the enactment of environmental regulatory policies thereafter.

Kuo, Li-Jung; Lee, Chon-Lin; Louchouarn, Patrick; Huh, Chih-An; Liu, James T.; Chen, Jian-Cheng; Lee, Kun-Je

2014-09-15

385

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...

386

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

387

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

PubMed Central

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

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

2012-01-01

388

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

PubMed Central

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

2013-01-01

389

Identification of the IFITM family as a new molecular marker in human colorectal tumors.  

PubMed

We analyzed the expression profiles of intestinal adenomas from a new murine familial adenomatous polyposis model (Apc(delta14/+)) using suppression subtractive hybridization to identify novel diagnostic markers of colorectal carcinogenesis. We identified 18 candidate genes having increased expression levels in the adenoma. Subsequent Northern blotting, real-time reverse transcription-PCR, and in situ hybridization analysis confirmed their induction in beta-catenin-activated epithelial cells of murine adenomas. We showed that most of the genes also have altered expression levels in human colonic adenomas and carcinomas. We focused on the IFITM genes that encode IFN-inducible transmembrane proteins. Serial analyses of gene expression levels revealed high levels of expression in early and late intestinal neoplasm in both mice and humans. Using a conditional mouse model of Apc inactivation and a human colon carcinoma cell line, we showed that IFITM gene expression is rapidly induced after activation of the beta-catenin signaling. Using a large-scale analysis of human tumors, we showed that IFITM gene expression is significantly up-regulated specifically in colorectal tumors and thus may be a useful diagnostic tool in these tumors. PMID:16488993

Andreu, Pauline; Colnot, Sabine; Godard, Cécile; Laurent-Puig, Pierre; Lamarque, Dominique; Kahn, Axel; Perret, Christine; Romagnolo, Béatrice

2006-02-15

390

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

391

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

PubMed Central

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

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

2014-01-01

392

Molecular Characterization of Selected Local and Exotic Cattle Using RAPD Marker  

PubMed Central

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

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

2012-01-01

393

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

PubMed

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

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

2014-08-10

394

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

PubMed

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

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

2014-10-01

395

Isolation and characterization of novel microsatellite markers for molecular genetic diversity in Siganus fuscescens.  

PubMed

The rabbitfish Siganus fuscescens is an economically valuable species that is widely distributed throughout the estuaries, intertidal, and offshore coasts of the Indo-Pacific and eastern Mediterranean. Ten novel microsatellite loci from the genome of S. fuscescens were developed using the fast isolation protocol with amplified fragment length polymorphism of sequences containing repeats. Polymorphisms in these 10 microsatellite markers were determined from 32 wild individuals. The number of alleles per locus and the polymorphism information content ranged from 2 to 5 and from 0.059 to 0.668, respectively. The observed and expected heterozygosities varied from 0.063 to 0.781 and from 0.062 to 0.731, respectively. Although 1 locus (LZY-X7, P < 0.005) showed significant deviation from the Hardy-Weinberg equilibrium, no deviations were detected in the other 9 loci. These microsatellite loci may be useful for further population genetic studies, conservation studies, population structure assessment, and linkage map construction of S. fuscescens. PMID:25729939

Ning, Y F; Li, Z B; Li, Q H; Dai, G; Shangguan, J B; Yuan, Y; Huang, Y S

2015-01-01

396

Genetic identification of bucktooth parrotfish Sparisoma radians (Valenciennes, 1840) (Labridae, Scarinae) by chromosomal and molecular markers  

PubMed Central

Parrotfishes (Labridae, Scarinae) comprise a large marine fish group of difficult identification, particularly during juvenile phase when the typical morphology and coloration of adults are absent. Therefore, the goal of this study was to test cytogenetic markers and DNA barcoding in the identification of bucktooth parrtotfish Sparisoma radians from the northeastern coast of Brazil. Sequencing of cytochrome c oxidase subunit I (COI) confirmed all studied samples as S. radians, and all showed high similarity (99–100%) with Caribbean populations. The karyotype of this species was divergent from most marine Perciformes, being composed of 2n = 46 chromosomes. These consisted of a large number of metacentric and submetacentric pairs with small amounts of heterochromatin and GC-rich single nucleolar organizer regions (NORs) not syntenic to 5S rDNA clusters. These are the first data about DNA barcoding in parrotfish from the Brazilian province and the first refined chromosomal analysis in Scarinae, providing useful data to a reliable genetic identification of S. radians. PMID:25505839

Paim, Fabilene Gomes; Brandão, José Henrique Souza Galdino; Sampaio, Iracilda; de Mello Affonso, Paulo Roberto Antunes; Diniz, Débora

2014-01-01

397

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

PubMed

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

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

2003-01-01

398

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

399

Molecular Characterization of Selected Local and Exotic Cattle Using RAPD Marker.  

PubMed

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

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

2012-06-01

400

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

PubMed

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

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

2012-12-01

401

Rational approaches to the design of therapeutics targeting molecular markers: the case of chronic myelogenous leukemia.  

PubMed

Progress in understanding the molecular basis of signal transmission and transduction has contributed substantially to clarifying the mechanisms of leukemogenesis and of leukemia progression and has led to the identification of a number of specific molecular targets for treatment. Chronic myeloid leukemia (CML) has provided one of the best models, as the identification of a leukemia-specific hybrid tyrosine kinase (BCR-ABL, p210, p190) has led to the identification and the successful therapeutic application of a powerful tyrosine kinase inhibitor, imatinib. The BCR-ABL fusion gene is the result of a reciprocal translocation between the long arms of chromosomes 9 and 22, t(9;22)(q34;q11), which characterizes more than 95% of the cases of CML. The resulting chimeric proteins (P210 and P190), which retain a constitutively activated tyrosine kinase activity, have a causative role in the genesis of the leukemia process. In agreement with this observation, BCR-ABL tyrosine kinase inhibitors have recently emerged as powerful new therapeutic tools, obtaining extraordinary results in early chronic-phase CML as well as in more advanced phases of the disease. Although these results represent a remarkable breakthrough, there are still numerous issues, such as the emergence of resistance, that remain unsolved and that will need further investigation. In spite of its low incidence, CML remains a paradigmatic model for understanding the pathogenesis and therapeutic options of human leukemias. PMID:15650267

Saglio, Giuseppe; Morotti, Alessandro; Mattioli, Giovanna; Messa, Emanuela; Giugliano, Emilia; Volpe, Gisella; Rege-Cambrin, Giovanna; Cilloni, Daniela

2004-12-01

402

Molecular study of Trypanosoma caninum isolates based on different genetic markers.  

PubMed

Trypanosoma caninum is a parasite recently described in dogs, whose life cycle is rather unknown. Here, we performed a genetic study with T. caninum samples obtained in different Brazilian regions. The study was based on PCR assays target to small and large subunit ribosomal DNA (rDNA) (18S rDNA and 24S? rDNA), cytochrome B (Cyt b), and internal transcribed spacer 1 rDNA (ITS1 rDNA) following by the sequence analysis. Additionally, we used primers for the variable regions of kinetoplast DNA (kDNA) minicircles and endonucleases restriction in the ITS1 rDNA amplification product. T. caninum samples displayed the same patterns. Tree construction confirmed the close relationship between T. caninum samples, regardless of the molecular target used and endonuclease restriction digestion revealed that all samples have the same restriction profile. Therefore, T. caninum seems to be a genetically homogeneous specie. In the kDNA assay, T. caninum possessed a different molecular size profile with respect to others trypanosomes, 330 and 350 bp. This study provides nucleotide sequences from different regions of the genome of T. caninum that certainly facilitate future studies. PMID:25566771

Barros, Juliana H S; Toma, Helena K; de Fatima Madeira, Maria

2015-02-01

403

Cotton Marker Database  

Technology Transfer Automated Retrieval System (TEKTRAN)

To address the lack of available molecular markers for cotton, Cotton Incorporated has spearheaded an initiative to create the Cotton Microsatellite Database (CMD), and several groups are actively involved in projects to generate, screen and map cotton molecular markers. CMD is a centralized databas...

404

Conservation phylogenetics of helodermatid lizards using multiple molecular markers and a supertree approach.  

PubMed

We analyzed both mitochondrial (mt-) and nuclear (n) DNAs in a conservation phylogenetic framework to examine deep and shallow histories of the Beaded Lizard (Heloderma horridum) and Gila Monster (H. suspectum) throughout their geographic ranges in North and Central America. Both mtDNA and intron markers clearly partitioned each species. One intron and mtDNA further subdivided H. horridum into its four recognized subspecies (H. n. alvarezi, charlesbogerti,exasperatum, and horridum). However, the two subspecies of H. suspectum (H. s. suspectum and H. s. cinctum) were undefined. A supertree approach sustained these relationships. Overall, the Helodermatidae is reaffirmed as an ancient and conserved group. Its most recent common ancestor (MRCA) was Lower Eocene [35.4 million years ago (mya)], with a approximately 25 my period of stasis before the MRCA of H. horridum diversified in Lower Miocene. Another approximately 5 my passed before H. h. exasperatum and H. h. horridum diverged, followed by approximately 1.5 my before H. h. alvarezi and H. h. charlesbogerti separated. Heloderma suspectum reflects an even longer period of stasis (approximately 30 my) before diversifying from its MRCA. Both H. suspectum (México) and H. h. alvarezi also revealed evidence of historic range expansion following a recent bottleneck. Our conservation phylogenetic approach emphasizes the origin and diversification of this group, yields information on the manner by which past environmental variance may have impacted its populations and, in turn, allows us to disentangle historic from contemporary impacts that might threaten its long-term persistence. The value of helodermatid conservation resides in natural services and medicinal products, particularly venom constituents, and these are only now being realized. PMID:20006722

Douglas, Michael E; Douglas, Marlis R; Schuett, Gordon W; Beck, Daniel D; Sullivan, Brian K

2010-04-01

405

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

PubMed Central

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

2012-01-01

406

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

PubMed Central

Background This study aimed to analyze the efficiency of three new microsatellite multiplex panels, which were designed to evaluate a total of 16 loci of the rice genome, based on single PCR reactions of each panel. A sample of 548 accessions of traditional upland rice landraces collected in Brazil in the last 25 years was genotyped, a database of allelic frequencies was established, estimates of genetic parameters were performed and analysis of genetic structure of the collection was developed. Results The three panels yielded a combined matching probability of 6.4 × 10-21, polymorphism information content (PIC) of 0.637, and a combined power of exclusion greater than 99.99%. A few samples presented a genetic background of indica rice. The 16 SSR loci produced a total of 229 alleles. Gene diversity values averaged 0.667, and PIC values averaged 0.637. Genetic structure analysis of the collection using a Bayesian approach detected three possible major clusters, with an overall FST value of 0.177. Important inputs on the knowledge about upland rice germplasm differentiations which happened in Brazil in the last few centuries were also achieved and are discussed. Conclusion The three multiplex panels described here represent a powerful tool for rice genetic analysis, offering a rapid and efficient option for rice germplasm characterization. The data gathered demonstrates the feasibility of genotyping extensive germplasm collections using panels of multiplexed microsatellite markers. It contributes to the advancement of research on large scale characterization and management of germplasm banks, as well as identification, protection and assessments of genetic relationship of rice germplasm. PMID:17517133

Pessoa-Filho, Marco; Beló, André; Alcochete, António AN; Rangel, Paulo HN; Ferreira, Márcio E

2007-01-01

407

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

PubMed Central

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

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

2014-01-01

408

Cell-free DNA and RNA in plasma as a new molecular marker for prostate and breast cancer.  

PubMed

In this study, we examined several molecular markers in prostate and breast cancer patients and in normal individuals. The markers tested were: variations in the quantity of plasma DNA, glutathione-S-transferase P1 gene (GSTP1), Ras association domain family 1A (RASSF1A), and ataxia telangiectasia mutated (ATM) methylation status in plasma, carcinoembryonic antigen (CEA) and prostate-specific membrane antigen (PSMA) mRNA in peripheral blood mononuclear cells (PBMC) and plasma samples from prostate cancer patients. DNA quantification in plasma was performed using real-time PCR (RT-PCR). We assessed the methylation status of GSTP1 in plasma DNA using methylation-specific PCR (MSP) assay, while the methylation status of RASSF1A and ATM genes was examined by the MethyLight technology. RT-PCR analysis was used for the detection of mRNA, PSMA, and CEA. In 58.3% of newly diagnosed prostate cancer patients and 26.7% of prostate cancer patients under therapy, plasma DNA levels were increased. Additionally, 48.5% of breast cancer patients showed plasma DNA levels above the cutoff limit. GSTP1 Promotor hypermethylation was detectable in 75% of plasma samples obtained from patients with newly diagnosed prostate cancer and in 36.8% of patients under therapy, whereas 26% and 14% of the breast cancer patients tested were positive for RASSF1A and ATM methylation, respectively. The combination of DNA load and promotor methylation status identified 88% of prostate cancer patients and 54% of breast cancer patients. This study shows that free-circulating DNA can be detected in cancer patients compared with disease-free individuals, and suggests a new, noninvasive approach for early detection of cancer. PMID:17108217

Papadopoulou, Eirini; Davilas, Elias; Sotiriou, Vasilios; Georgakopoulos, Eleftherios; Georgakopoulou, Stavroula; Koliopanos, Alexander; Aggelakis, Filipos; Dardoufas, Konstantinos; Agnanti, Niki J; Karydas, Irini; Nasioulas, Georgios

2006-09-01

409

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

NASA Astrophysics Data System (ADS)

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

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

2013-12-01

410

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

NASA Astrophysics Data System (ADS)

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

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

2013-11-01

411

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

PubMed

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

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

2014-01-01

412

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

PubMed Central

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

2014-01-01

413

Molecular markers to assess short-term disease local recurrence in nasopharyngeal carcinoma  

PubMed Central

An important challenge in nasopharyngeal carcinoma (NPC) research is to develop effective predictors of tumor recurrence following treatment to determine whether immediate adjuvant therapy is necessary. We retrospectively analyzed archived specimens collected from 45 patients with paired samples of primary NPC (pNPC) and recurrent NPC (rNPC). Clinical samples were collected from the Cancer Center Databases of the First People’s Hospital of Foshan and Shantou Central Hospital (affiliates of Sun Yat-Sen University) between 2001 and 2012. Expression levels of phosphor-Stat3 (p-Stat3), signalosome complex subunit 5 (Jab1/Csn5), Akt1, C/EBP homologous protein (CHOP), Ki-67, and apoptosis were determined by immunohistochemistry in pNPC and rNPC samples from the same patients. Differences in these markers between the short-term interval to recurrence (ITR) group (ITR <18 months) and long-term ITR group (ITR ?18 months) were further analyzed. In Cox’s regression analysis, the ITR was significantly associated as an independent-negative prognostic factor for overall survival (hazard ratio, 0.211; 95% confidence interval, 0.053–0.841; P=0.027). p-Stat3 was increased in the short-term ITR group (ITR <18 months) and tended to be lower in the long-term ITR group (ITR ?18 months). In the short-term ITR group, nuclear Akt expression was significantly increased in paired rNPC (P=0.028). In the long-term ITR group, the expression of nuclear Jab1/Csn5 (P=0.047) and assessment of apoptosis measured with TdT-mediated dUTP nick end-labeling (TUNEL) (P=0.003) was significantly increased in paired rNPC. The results suggest that differences between short- and long-term ITR may predict outcome in rNPC. Furthermore, the overexpression of Jab1/Csn5 and Akt may contribute to the carcinogenesis of rNPC, and Akt seems to promote the progression of short-term ITR. Intra-individual changes of Jab1/Csn5, Akt, and TUNEL may help to identify short-term ITR. PMID:25607111

XU, TAO; SU, BOJIN; WANG, CHUNHUA; WANG, SUMEI; HUANG, HECHENG; PAN, YUNBAO; WANG, DONGHUI; WEI, WEIHONG; CLARET, FRANÇOIS X.; YANG, HUILING

2015-01-01

414

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. PMID:20398375

2010-01-01

415

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

416

FROM RAPDS TO SNPS: THE DEVELOPMENT OF MORE EFFECTIVE AND EFFICIENT MOLECULAR MARKERS IN CUCUMBER (CUCUMIS SATIVUS L.)  

Technology Transfer Automated Retrieval System (TEKTRAN)

The genetic base of cucumber is narrow (3-8%), and thus, the recovery of new markers from screening experiments is typically low. The majority of markers on current genetic linkage maps are RAPDs, which are inefficient for genotyping numerous individuals during marker-assisted selection (MAS). The...

417

Construction of a genetic linkage map using MFLP and identification of molecular markers linked to domestication genes in narrow-leafed lupin (Lupinus angustifolius L.).  

PubMed

A mapping population of F(8)derived recombinant inbred lines (RILs) was established from a cross between a domesticated breeding line 83A:476 and a wild type P27255 in narrow-leaf lupin (Lupinus angustifolius L.). The parents together with the 89 RILs were subjected to DNA fingerprinting using microsatellite-anchored fragment length polymorphism (MFLP) to rapidly generate DNA markers to construct a linkage map. Five hundred and twenty two unique markers of which 21% were co-dominant, were generated and mapped. Phenotypic data for the domestication traits: mollis (soft seeds), leucospermus (white flower and seed colour); Lentus (reduced pod-shattering), iucundis (low alkaloid), Ku (early flowering) and moustache pattern on seed coats; were included. Three to 7 molecular markers were identified within 5 cM of each of these domestication genes. The anthracnose resistance gene Lanr1 was also mapped. Linkage groups were constructed using MapManager version QTXb20, resulting in 21 linkage groups consisting of 7 or more markers. The total map length was 1543 cM, with an average distance of 3.4 cM between adjacent markers. This is the first published map for a lupin species. The map can be exploited for marker assisted selection for genetic improvement in lupin breeding programs. PMID:16010297

Boersma, Jeffrey G; Pallotta, Margaret; Li, Chengdao; Buirchell, Bevan J; Sivasithamparam, Krishnapillai; Yang, Huaan

2005-01-01

418

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

PubMed Central

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

2011-01-01

419

Molecular marker based taxonomy and phylogeny of Guinea yam (Dioscorea rotundata - D. cayenensis).  

PubMed

Four different molecular techniques were used to assess relationships among 21 accessions of Guinea yam (Dioscorea rotundata and Dioscorea cayenensis) and 21 accessions belonging to seven putative progenitor species. Random amplified polymorphic DNA (RAPD) and microsatellite-primed PCR (MP-PCR) analysis yielded 246 informative characters that were transformed into a matrix of pairwise distances and analyzed by neighbor joining or split decomposition. Both methods gave congruent results. Well-separated groups were formed that corresponded to their species designation. Dioscorea rotundata and D. cayenensis accessions were clearly separated from each other, supporting the concept that both are distinct species. Two morphological intermediates grouped together with D. rotundata. All investigated species fell into two main clusters, one comprising D. rotundata, D. cayenensis, Dioscorea abyssinica, Dioscorea liebrechtsiana, and Dioscorea praehensilis, the other comprising Dioscorea smilacifolia, Dioscorea minutiflora, Dioscorea burkilliana, and Dioscorea togoensis. The same grouping was also obtained by comparative sequence analysis of chloroplast DNA, which supports earlier studies of nuclear rDNA variation and chloroplast restriction fragment length polymorphisms. We also analyzed the same set of Dioscorea samples with the recently developed random amplified microsatellite polymorphism (RAMPO) technique. A series of diagnostic RAMPO bands was identified that clearly distinguished between D. rotundata and D. cayenensis. Some of these bands could also be traced back to the putative progenitors of both species. The evolutionary origin of Guinea yam is discussed in light of the present results. PMID:18464876

Ramser, J; Weising, K; Terauchi, R; Kahl, G; Lopez-Peralta, C; Terhalle, W

1997-12-01

420

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

PubMed Central

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

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

2014-01-01