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Sample records for additional molecular markers

  1. Ribotyping as an additional molecular marker for studying Neisseria meningitidis serogroup B epidemic strains.

    PubMed Central

    Tondella, M L; Sacchi, C T; Neves, B C

    1994-01-01

    The molecular method of ribotyping was used as an additional epidemiological marker to study the epidemic strains of Neisseria meningitidis serogroup B, referred to as the ET-5 complex, responsible for the epidemic which occurred in greater São Paulo, Brazil. Ribotyping analysis of these strains showed only a single rRNA gene restriction pattern (Rb1), obtained with ClaI restriction enzyme. This method, as well as multilocus enzyme electrophoresis, provided useful information about the clonal characteristics of the N. meningitidis serogroup B strains isolated during this epidemic. The N. meningitidis serogroup B isolates obtained from epidemics which occurred in Norway, Chile, and Cuba also demonstrated the same pattern (Rb1). Ribotyping was a procedure which could be applied to a large number of isolates and was felt to be appropriate for routine use in laboratories, especially because of the convenience of using nonradioactive probes. Images PMID:7852566

  2. An improved UPLC method for the detection of undeclared horse meat addition by using myoglobin as molecular marker.

    PubMed

    Di Giuseppe, Antonella M A; Giarretta, Nicola; Lippert, Martina; Severino, Valeria; Di Maro, Antimo

    2015-02-15

    In 2013, following the scandal of the presence of undeclared horse meat in various processed beef products across the Europe, several researches have been undertaken for the safety of consumer health. In this framework, an improved UPLC separation method has been developed to detect the presence of horse myoglobin in raw meat samples. The separation of both horse and beef myoglobins was achieved in only seven minutes. The methodology was improved by preparing mixtures with different composition percentages of horse and beef meat. By using myoglobin as marker, low amounts (0.50mg/0.50g, w/w; ∼0.1%) of horse meat can be detected and quantified in minced raw meat samples with high reproducibility and sensitivity, thus offering a valid alternative to conventional PCR techniques.

  3. Modulation of Molecular Markers by CLA

    DTIC Science & Technology

    1999-10-01

    AD __ _ _ _ _ _ Award Number: DAMD17-94-J-4274 TITLE: Modulation of Molecular Markers by CLA PRINCIPAL INVESTIGATOR: Henry Thompson, Ph.D...DATES COVERED October 1999 Final (14 Sep 94 - 13 Sep 99) 4. TITLE AND SUBTITLE 5. FUNDING NUMBERS Modulation of Molecular Markers by CLA DAMD1 7-94-J...for the prevention of human breast cancer. 14. SUBJECT TERMS 15. NUMBER OF PAGES Breast Cancer, Molecular Markers 10 9 16. PRICE CODE 17. SECURITY

  4. Molecular markers for colorectal cancer screening

    PubMed Central

    Dickinson, Brandon T.; Kisiel, John; Ahlquist, David A.; Grady, William M.

    2016-01-01

    Colorectal cancer (CRC), although a significant cause of morbidity and mortality worldwide, has seen a declining incidence and mortality in countries with programmatic screening. Fecal occult blood testing (FOBT) and endoscopic approaches are the predominant screening methods currently. The discovery of the adenoma→carcinoma sequence and a greater understanding of the genetic and epigenetic changes that drive the formation of CRC have contributed to innovative research to identify molecular markers for highly accurate, non-invasive screening tests for CRC. DNA, proteins, messenger RNA, and micro-RNA have all been evaluated. The observation of tumor cell exfoliation into the mucocellular layer of the colonic epithelium and proven stability of DNA in a harsh stool environment make stool DNA a particularly promising marker. The development of a clinically useful stool DNA test has required numerous technical advances, including optimization in DNA stabilization, the development of assays with high analytical sensitivity, and the identification of specific and broadly informative molecular markers. A multi-target stool DNA (MT-sDNA) test, which combines both mutant and methylated DNA markers and a fecal immunochemical test (FIT), recently performed favorably in a large cross-sectional validation study and has been approved by the US Food and Drug Administration (FDA) for the screening of asymptomatic, average risk individuals. The ultimate way in which molecular marker screening assays will be used in clinical practice will require additional studies to determine optimal screening intervals, factors affecting compliance, management of false positive results, and the use of these assays in high-risk populations, as well as other considerations. PMID:25994221

  5. Molecular markers for colorectal cancer screening.

    PubMed

    Dickinson, Brandon T; Kisiel, John; Ahlquist, David A; Grady, William M

    2015-09-01

    Colorectal cancer (CRC), although a significant cause of morbidity and mortality worldwide, has seen a declining incidence and mortality in countries with programmatic screening. Faecal occult blood testing and endoscopic approaches are the predominant screening methods currently. The discovery of the adenoma-carcinoma sequence and a greater understanding of the genetic and epigenetic changes that drive the formation of CRC have contributed to innovative research to identify molecular markers for highly accurate, non-invasive screening tests for CRC. DNA, proteins, messenger RNA and micro-RNA have all been evaluated. The observation of tumour cell exfoliation into the mucocellular layer of the colonic epithelium and proven stability of DNA in a harsh stool environment make stool DNA a particularly promising marker. The development of a clinically useful stool DNA test has required numerous technical advances, including optimisation in DNA stabilisation, the development of assays with high analytical sensitivity, and the identification of specific and broadly informative molecular markers. A multitarget stool DNA test, which combines mutant and methylated DNA markers and a faecal immunochemical test, recently performed favourably in a large cross-sectional validation study and has been approved by the US Food and Drug Administration for the screening of asymptomatic, average-risk individuals. The ultimate way in which molecular marker screening assays will be used in clinical practice will require additional studies to determine optimal screening intervals, factors affecting compliance, management of false-positive results, and the use of these assays in high-risk populations, as well as other considerations.

  6. (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...

  7. 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...

  8. Glioblastoma: pathology, molecular mechanisms and markers.

    PubMed

    Aldape, Kenneth; Zadeh, Gelareh; Mansouri, Sheila; Reifenberger, Guido; von Deimling, Andreas

    2015-06-01

    Recent advances in genomic technology have led to a better understanding of key molecular alterations that underlie glioblastoma (GBM). The current WHO-based classification of GBM is mainly based on histologic features of the tumor, which frequently do not reflect the molecular differences that describe the diversity in the biology of these lesions. The current WHO definition of GBM relies on the presence of high-grade astrocytic neoplasm with the presence of either microvascular proliferation and/or tumor necrosis. High-throughput analyses have identified molecular subtypes and have led to progress in more accurate classification of GBM. These findings, in turn, would result in development of more effective patient stratification, targeted therapeutics, and prediction of patient outcome. While consensus has not been reached on the precise nature and means to sub-classify GBM, it is clear that IDH-mutant GBMs are clearly distinct from GBMs without IDH1/2 mutation with respect to molecular and clinical features, including prognosis. In addition, recent findings in pediatric GBMs regarding mutations in the histone H3F3A gene suggest that these tumors may represent a 3rd major category of GBM, separate from adult primary (IDH1/2 wt), and secondary (IDH1/2 mut) GBMs. In this review, we describe major clinically relevant genetic and epigenetic abnormalities in GBM-such as mutations in IDH1/2, EGFR, PDGFRA, and NF1 genes-altered methylation of MGMT gene promoter, and mutations in hTERT promoter. These markers may be incorporated into a more refined classification system and applied in more accurate clinical decision-making process. In addition, we focus on current understanding of the biologic heterogeneity and classification of GBM and highlight some of the molecular signatures and alterations that characterize GBMs as histologically defined. We raise the question whether IDH-wild type high grade astrocytomas without microvascular proliferation or necrosis might best be

  9. Generation and release of molecular markers for Poa Arachnifera Torr

    Technology Transfer Automated Retrieval System (TEKTRAN)

    DNA based molecular markers can be utilized in a wide array of plant genetic studies, marker-trait associations, seed purity evaluations and cultivar protection. However, for the genus Poa, the use of molecular markers is limited by the current lack of informative DNA based markers. This report r...

  10. Molecular markers in oral lichen planus: A systematic review

    PubMed Central

    Sagari, Shitalkumar; Sanadhya, Sudhanshu; Doddamani, Mallikarjun; Rajput, Rajan

    2016-01-01

    Oral lichen planus (OLP) is a chronic inflammatory mucosal disease that is usually detected in 0.5–2.2% of the human population. Among these, only 0.5–2.9% of the lesions progress to carcinoma. However, there are no prognostic markers available presently to recognize the increased risk in malignant transformation of the lesions. Selected markers for cell proliferation, adhesion, apoptosis and lymphocytic infiltration were analyzed by immunohistochemistry in addition to static cytometry for DNA content. The concept linking OLP and oral squamous cell carcinoma states that chronic inflammation results in crucial DNA damage, which further progresses to development of carcinoma. Even though in the past decade, enormous information has been accumulated on malignant potential of OLP, its transformation still remains unclear. Hence, the purpose of this article was to review cellular and molecular markers to understand the pathogenesis of OLP and its progression toward malignancy. PMID:27194873

  11. Molecular Marker Systems for Oenothera Genetics

    PubMed Central

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

    2008-01-01

    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

  12. Novel Molecular Markers for Breast Cancer

    PubMed Central

    Inoue, Kazushi; Fry, Elizabeth A.

    2016-01-01

    The use of molecular biomarkers assures that breast cancer (BC) patients receive optimal treatment. Established biomarkers, such as estrogen receptor, progesterone receptor, HER2, and Ki67, have been playing significant roles in the subcategorization of BC to predict the prognosis and decide the specific therapy to each patient. Antihormonal therapy using 4-hydroxytamoxifen or aromatase inhibitors have been employed in patients whose tumor cells express hormone receptors, while monoclonal antibody to HER2 has been administered to HER2-positive BCs. Although new therapeutic agents have been developed in the past few decades, many patients still die of the disease due to relapse; thus, novel molecular markers that predict therapeutic failure and those that can be targets for specific therapy are expected. We have chosen four of such molecules by reviewing recent publications, which are cyclin E, B-Myb, Twist, and DMP1β. The oncogenicity of these molecules has been demonstrated in vivo and/or in vitro through studies using transgenic mice or siRNAs, and their expressions have been shown to be associated with shortened overall or disease-free survival of BC patients. The former three molecules have been shown to accelerate epithelial–mesenchymal transition that is often associated with cancer stem cell-ness and metastasis; all these four can be novel therapeutic targets as well. Thus, large prospective studies employing immunohistochemistry will be needed to establish the predictive values of these molecules in patients with BC. PMID:26997872

  13. Molecular markers: a potential resource for ginger genetic diversity studies.

    PubMed

    Ismail, Nor Asiah; Rafii, M Y; Mahmud, T M M; Hanafi, M M; Miah, Gous

    2016-12-01

    Ginger is an economically important and valuable plant around the world. Ginger is used as a food, spice, condiment, medicine and ornament. There is available information on biochemical aspects of ginger, but few studies have been reported on its molecular aspects. The main objective of this review is to accumulate the available molecular marker information and its application in diverse ginger studies. This review article was prepared by combing material from published articles and our own research. Molecular markers allow the identification and characterization of plant genotypes through direct access to hereditary material. In crop species, molecular markers are applied in different aspects and are useful in breeding programs. In ginger, molecular markers are commonly used to identify genetic variation and classify the relatedness among varieties, accessions, and species. Consequently, it provides important input in determining resourceful management strategies for ginger improvement programs. Alternatively, a molecular marker could function as a harmonizing tool for documenting species. This review highlights the application of molecular markers (isozyme, RAPD, AFLP, SSR, ISSR and others such as RFLP, SCAR, NBS and SNP) in genetic diversity studies of ginger species. Some insights on the advantages of the markers are discussed. The detection of genetic variation among promising cultivars of ginger has significance for ginger improvement programs. This update of recent literature will help researchers and students select the appropriate molecular markers for ginger-related research.

  14. Theory of atomic additivity in molecular hyperpolizabilities

    NASA Technical Reports Server (NTRS)

    Baird, James K.

    1987-01-01

    Hyperpolarizability is a function of frequency. This is called dispersion. Because of the Kramers-Kronig relations, researchers expect that a material that is dispersing light is also absorbing it. Where there is both dispersion and absorption, the molecular polarizabilities are complex functions of the frequency. This led researchers to consider atomic additivity in both the real and imaginary parts of the ordinary and hyperpolarizabilities. This effort is desirable not only from a theoretical point of view, but also because of the existence of a large body of complex refractive index data, which may be used to test the additivity principle with the complex valued ordinary dipole polarizability.

  15. c-GAMMA:Comparative Genome Analysis of Molecular Markers

    NASA Astrophysics Data System (ADS)

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

    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.

  16. Molecular markers and strategies to control aflatoxin in peanut

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Methods of isolation of molecular markers and software developed in ARS for finding the most informative markers will be presented. Also, two different approaches being used at the NPRL to reduce aflatoxin in peanut will be discussed. One is the development of phytoalexin-detoxification enzyme inh...

  17. Molecular marker systems in insects: current trends and future avenues.

    PubMed

    Behura, Susanta K

    2006-10-01

    Insects comprise the largest species composition in the entire animal kingdom and possess a vast undiscovered genetic diversity and gene pool that can be better explored using molecular marker techniques. Current trends of application of DNA marker techniques in diverse domains of insect ecological studies show that mitochondrial DNA (mtDNA), microsatellites, random amplified polymorphic DNA (RAPD), expressed sequence tags (EST) and amplified fragment length polymorphism (AFLP) markers have contributed significantly for progresses towards understanding genetic basis of insect diversity and for mapping medically and agriculturally important genes and quantitative trait loci in insect pests. Apart from these popular marker systems, other novel approaches including transposon display, sequence-specific amplification polymorphism (S-SAP), repeat-associated polymerase chain reaction (PCR) markers have been identified as alternate marker systems in insect studies. Besides, whole genome microarray and single nucleotide polymorphism (SNP) assays are becoming more popular to screen genome-wide polymorphisms in fast and cost effective manner. However, use of such methodologies has not gained widespread popularity in entomological studies. The current study highlights the recent trends of applications of molecular markers in insect studies and explores the technological advancements in molecular marker tools and modern high throughput genotyping methodologies that may be applied in entomological researches for better understanding of insect ecology at molecular level.

  18. Molecular markers of serine protease evolution

    PubMed Central

    Krem, Maxwell M.; Di Cera, Enrico

    2001-01-01

    The evolutionary history of serine proteases can be accounted for by highly conserved amino acids that form crucial structural and chemical elements of the catalytic apparatus. These residues display non- random dichotomies in either amino acid choice or serine codon usage and serve as discrete markers for tracking changes in the active site environment and supporting structures. These markers categorize serine proteases of the chymotrypsin-like, subtilisin-like and α/β-hydrolase fold clans according to phylogenetic lineages, and indicate the relative ages and order of appearance of those lineages. A common theme among these three unrelated clans of serine proteases is the development or maintenance of a catalytic tetrad, the fourth member of which is a Ser or Cys whose side chain helps stabilize other residues of the standard catalytic triad. A genetic mechanism for mutation of conserved markers, domain duplication followed by gene splitting, is suggested by analysis of evolutionary markers from newly sequenced genes with multiple protease domains. PMID:11406580

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

    PubMed

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

    2014-09-01

    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.

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

    PubMed Central

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

    2014-01-01

    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

  1. SNP Markers as Additional Information to Resolve Complex Kinship Cases

    PubMed Central

    Pontes, M. Lurdes; Fondevila, Manuel; Laréu, Maria Victoria; Medeiros, Rui

    2015-01-01

    Summary Background DNA profiling with sets of highly polymorphic autosomal short tandem repeat (STR) markers has been applied in various aspects of human identification in forensic casework for nearly 20 years. However, in some cases of complex kinship investigation, the information provided by the conventionally used STR markers is not enough, often resulting in low likelihood ratio (LR) calculations. In these cases, it becomes necessary to increment the number of loci under analysis to reach adequate LRs. Recently, it has been proposed that single nucleotide polymorphisms (SNPs) could be used as a supportive tool to STR typing, eventually even replacing the methods/markers now employed. Methods In this work, we describe the results obtained in 7 revised complex paternity cases when applying a battery of STRs, as well as 52 human identification SNPs (SNPforID 52plex identification panel) using a SNaPshot methodology followed by capillary electrophoresis. Results Our results show that the analysis of SNPs, as complement to STR typing in forensic casework applications, would at least increase by a factor of 4 total PI values and correspondent Essen-Möller's W value. Conclusions We demonstrated that SNP genotyping could be a key complement to STR information in challenging casework of disputed paternity, such as close relative individualization or complex pedigrees subject to endogamous relations. PMID:26733770

  2. Biological (molecular and cellular) markers of toxicity

    SciTech Connect

    McCarthy, J.F.

    1990-04-01

    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.

  3. Ecological proteomics: finding molecular markers that matter.

    PubMed

    Dalziel, Anne C; Schulte, Patricia M

    2012-07-01

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

  4. Biological (molecular and cellular) markers of toxicity

    SciTech Connect

    Shugart, L.R.

    1990-10-01

    The overall objective of this study is to evaluate the use of the small aquarium fish, Japanese Medaka (Oryzias latipes), as a predictor of potential genotoxicity following exposure to carcinogens. This will be accomplished by quantitatively investigating the early molecular events associated with genotoxicity of various tissues of Medaka subsequent to exposure of the organism to several known carcinogens, such as diethylnitrosamine (DEN) and benzo(a)pyrene (BaP). Because of the often long latent period between initial contact with certain chemical and physical agents in our environment and subsequent expression of deleterious health or ecological impact, the development of sensitive methods for detecting and estimating early exposure is needed so that necessary interventions can ensue. A promising biological endpoint for detecting early exposure to damaging chemicals is the interaction of these compounds with cellular macromolecules such as Deoxyribonucleic acids (DNA). This biological endpoint assumes significance because it can be one of the critical early events leading eventually to adverse effects (neoplasia) in the exposed organism.

  5. Confirmation of hybrid origin in Arisaema (Araceae) using molecular markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A population of hybrids between Arisaema triphyllum subsp. stewardsonii and A. dracontium was investigated using molecular markers to document the hybrid origin. Total genomic DNA was extracted from A. triphyllum, A. dracontium, and the hybrids, and subjected to sequence analysis of various regions...

  6. Acceleration of peanut breeding programs by molecular marker assisted selection

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  7. Molecular markers linked to the apple scab resistance gene Vbj derived from Malus baccata jackii.

    PubMed

    Gygax, M; Gianfranceschi, L; Liebhard, R; Kellerhals, M; Gessler, C; Patocchi, A

    2004-11-01

    Breeding for scab-resistant apple cultivars by pyramiding several resistance genes in the same genetic background is a promising way to control apple scab caused by the fungus Venturia inaequalis. To achieve this goal, DNA markers linked to the genes of interest are required in order to select seedlings with the desired resistance allele combinations. For several apple scab resistance genes, molecular markers are already available; but until now, none existed for the apple scab resistance gene Vbj originating from the crab apple Malus baccata jackii. Using bulk segregant analysis, three RAPD markers linked to Vbj were first identified. These markers were transformed into more reliable sequence-characterised amplified region (SCAR) markers that proved to be co-dominant. In addition, three SSR markers and one SCAR were identified by comparing homologous linkage groups of existing genetic maps. Discarding plants showing genotype-phenotype incongruence (GPI plants) plants, a linkage map was calculated. Vbj mapped between the markers CH05e03 (SSR) and T6-SCAR, at 0.6 cM from CH05e03 and at 3.9 cM from T6-SCAR. Without the removal of the GPI plants, Vbj was placed 15 cM away from the closest markers. Problems and pitfalls due to GPI plants and the consequences for mapping the resistance gene accurately are discussed. Finally, the usefulness of co-dominant markers for pedigree analysis is also demonstrated.

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

    PubMed

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

    2013-10-17

    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.

  9. Molecular Markers for Breast Cancer: Prediction on Tumor Behavior

    PubMed Central

    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

    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

  10. Development of molecular markers tightly linked to Pvr4 gene in pepper using next-generation sequencing.

    PubMed

    Devran, Zübeyir; Kahveci, Erdem; Özkaynak, Ercan; Studholme, David J; Tör, Mahmut

    It is imperative to identify highly polymorphic and tightly linked markers of a known trait for molecular marker-assisted selection. Potyvirus resistance 4 (Pvr4) locus in pepper confers resistance to three pathotypes of potato virus Y and to pepper mottle virus. We describe the use of next-generation sequencing technology to generate molecular markers tightly linked to Pvr4. Initially, comparative genomics was carried out, and a syntenic region of tomato on chromosome ten was used to generate PCR-based markers and map Pvr4. Subsequently, the genomic sequence of pepper was used, and more than 5000 single-nucleotide variants (SNVs) were identified within the interval. In addition, we identified nucleotide binding site-leucine-rich repeat-type disease resistance genes within the interval. Several of these SNVs were converted to molecular markers desirable for large-scale molecular breeding programmes.

  11. De Novo Transcriptome Assembly of Pummelo and Molecular Marker Development

    PubMed Central

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

    2015-01-01

    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

  12. Data resolution: a jackknife procedure for determining the consistency of molecular marker datasets.

    PubMed

    van Hintum, Th J L

    2007-08-01

    The results of genetic diversity studies using molecular markers not only depend on the biology of the studied objects but also on the quality of the marker data. Poor data quality may hamper the correct answering of biological questions. A new statistic is proposed to estimate the quality of a marker data set with regard to its ability to describe the structure of the biological material under study. This statistic is called data resolution (DR). It is calculated by splitting a marker data set at random into two sets each with half the number of markers. In each set, similarities between all pairs of objects are calculated. Subsequently, the similarities obtained for the two sets are correlated. This process is repeated a large number of times. The average of the correlation coefficients obtained in this way is the DR of the dataset. In the present paper, the DR statistic is applied to four studies involving amplified fragment length polymorphism as well as micro-satellite markers. In addition, some properties and possible applications of DR are discussed, including the prediction of the added value of scoring additional markers, and the determination of which similarity measure is, apart from genetical considerations, most appropriate for analyzing the data.

  13. Estimating ancestry and heterozygosity of hybrids using molecular markers

    PubMed Central

    2012-01-01

    Background Hybridization, genetic mixture of distinct populations, gives rise to myriad recombinant genotypes. Characterizing the genomic composition of hybrids is critical for studies of hybrid zone dynamics, inheritance of traits, and consequences of hybridization for evolution and conservation. Hybrid genomes are often summarized either by an estimate of the proportion of alleles coming from each ancestral population or classification into discrete categories like F1, F2, backcross, or merely “hybrid” vs. “pure”. In most cases, it is not realistic to classify individuals into the restricted set of classes produced in the first two generations of admixture. However, the continuous ancestry index misses an important dimension of the genotype. Joint consideration of ancestry together with interclass heterozygosity (proportion of loci with alleles from both ancestral populations) captures all of the information in the discrete classification without the unrealistic assumption that only two generations of admixture have transpired. Methods I describe a maximum likelihood method for joint estimation of ancestry and interclass heterozygosity. I present two worked examples illustrating the value of the approach for describing variation among hybrid populations and evaluating the validity of the assumption underlying discrete classification. Results Naively classifying natural hybrids into the standard six line cross categories can be misleading, and false classification can be a serious problem for datasets with few molecular markers. My analysis underscores previous work showing that many (50 or more) ancestry informative markers are needed to avoid erroneous classification. Conclusion Although classification of hybrids might often be misleading, valuable inferences can be obtained by focusing directly on distributions of ancestry and heterozygosity. Estimating and visualizing the joint distribution of ancestry and interclass heterozygosity is an effective way

  14. The Promise of Novel Molecular Markers in Bladder Cancer

    PubMed Central

    Miremami, Jahan; Kyprianou, Natasha

    2014-01-01

    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

  15. Determinant molecular markers for peri-gastrulating bovine embryo development.

    PubMed

    Hue, Isabelle

    2016-01-01

    Peri-gastrulation defines the time frame between blastocyst formation and implantation that also corresponds in cattle to elongation, pregnancy recognition and uterine secretion. Optimally, this developmental window prepares the conceptus for implantation, placenta formation and fetal development. However, this is a highly sensitive period, as evidenced by the incidence of embryo loss or early post-implantation mortality after AI, embryo transfer or somatic cell nuclear transfer. Elongation markers have often been used within this time frame to assess developmental defects or delays, originating either from the embryo, the uterus or the dam. Comparatively, gastrulation markers have not received great attention, although elongation and gastrulation are linked by reciprocal interactions at the molecular and cellular levels. To make this clearer, this peri-gastrulating period is described herein with a focus on its main developmental landmarks, and the resilience of the landmarks in the face of biotechnologies is questioned.

  16. Molecular Markers of Lung Cancer in MAYAK Workers

    SciTech Connect

    Steven A. Belinsky, PhD

    2007-02-15

    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

  17. [Molecular markers: an important tool in the diagnosis, treatment and epidemiology of invasive aspergillosis].

    PubMed

    Frías-de León, María Guadalupe; Acosta-Altamirano, Gustavo; Duarte-Escalante, Esperanza; Martínez-Hernández, José Enrique; Martínez-Rivera, María de Los Ángeles; Reyes-Montes, María Del Rocío

    2014-01-01

    Increase in the incidence of invasive aspergillosis has represented a difficult problem for management of patients with this infection due to its high rate of mortality, limited knowledge concerning its diagnosis, and therapeutic practice. The difficulty in management of patients with aspergillosis initiates with detection of the fungus in the specimens of immunosuppressed patients infected with Aspergillus fumigatus; in addition, difficulty exists in terms of the development of resistance to antifungals as a consequence of their indiscriminate use in prophylactic and therapeutic practice and to ignorance concerning the epidemiological data of aspergillosis. With the aim of resolving these problems, molecular markers is employed at present with specific and accurate results. However, in Mexico, the use of molecular markers has not yet been implemented in the routine of intrahospital laboratories; despite the fact that these molecular markers has been widely referred in the literature, it is necessary for it to validated and standardized to ensure that the results obtained in any laboratory would be reliable and comparable. In the present review, we present an update on the usefulness of molecular markers in accurate identification of A. fumigatus, detection of resistance to antifugal triazoles, and epidemiological studies for establishing the necessary measures for prevention and control of aspergillosis.

  18. A single molecular marker to distinguish between species of Dioscorea.

    PubMed

    Techen, Natascha; Parveen, Iffat; Khan, Ikhlas A

    2017-03-01

    Yams are species of the genus Dioscorea (family Dioscoreaceae), which consists of approximately 630 species. The majority of the world production of yams occurs in Africa with 58.8 million t annually, but they are also produced in the Americas and Asia. The saponins in yams have been reported to possess various properties to improve health. The tuber and aerial parts of various species often share morphological similarities, which can cause problems in the proper identification of sample material. For example, the rootstocks and aerial parts of Dioscorea villosa L. share similarities with Dioscorea polystachia Turcz. Dioscorea bulbifera L. may be mistaken for Dioscorea alata L. owing to similar morphologies. Various molecular analyses have been published to help with the identification of species and varieties within the genus Dioscorea. The multi-loci or single-locus analysis has resulted in varying success, some with only a limited discrimination rate. In the present study, a single nuclear genomic region, biparentally inherited, was analyzed for its usefulness as a molecular marker for species identification and discrimination between D. bulbifera, D. villosa, D. nipponica, D. alata, D. caucasica, and D. deltoidea samples. The results of this study show that the LFY genomic region can be useful as a molecular marker to distinguish between samples.

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

    PubMed

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

    2014-01-01

    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.

  20. A molecular marker of artemisinin-resistant Plasmodium falciparum malaria

    PubMed Central

    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

    2016-01-01

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

  1. A molecular marker of artemisinin-resistant Plasmodium falciparum malaria.

    PubMed

    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

    2014-01-02

    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.

  2. A molecular marker of artemisinin-resistant Plasmodium falciparum malaria

    NASA Astrophysics Data System (ADS)

    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

    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.

  3. Intelligent DNA-based molecular diagnostics using linked genetic markers

    SciTech Connect

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

    1994-12-31

    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.

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

    PubMed

    Navajas, M; Fenton, B

    2000-01-01

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

  5. Molecular markers of cell adhesion in ameloblastomas. An update

    PubMed Central

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

    2014-01-01

    Ameloblastoma is the most common odontogenic tumor of epithelial origin, and though it is of a benign nature, it frequently infiltrates the bone, has a high rate of recurrence and could potentially become malignant. Cellular adhesion potentially plays an important role in the manifestation of these characteristics and in the tumor biology of ameloblastomas. Losses of cell-cell and extracellular matrix adhesion and cohesion are among the first events that occur in the invasion and growth of tumors of epithelial origin. The present review includes a description of the molecules that are involved in cell adhesion as reported for various types of ameloblastomas and discusses the possible roles of these molecules in the biological behaviors of this odontogenic tumor. Knowledge of the complex mechanisms in which these molecules play a role is critical for the research and discovery of future therapeutic targets. Key words:Ameloblastoma, cellular adhesion, molecular markers, cell-cell adhesion, extracellular matrix-cell adhesion. PMID:23986011

  6. [Matrix metalloproteases as molecular markers in gastric cancer].

    PubMed

    de la Peña, Sol; Sampieri, Clara L; León-Córdoba, Kenneth

    2010-02-06

    Gastric cancer is the second leading cause of cancer-associated mortality in the world. Prognosis in patients with gastric cancer is difficult to establish because it is commonly diagnosed when gastric wall invasion and metastasis have occurred. Currently, some members of the extracellular matrix metalloproteinases have been identified, whose expression in gastric tumor tissue is significantly elevated compared to healthy gastric tissue. Matrix metalloproteinases are 24 zinc-dependent endopeptidases that catalyze the proteolysis of the extracellular matrix. This degradation allows the cancer cells invade the surrounding stroma and trigger metastasis. Upregulation of certain matrix metalloproteinases in gastric cancer has been associated with a poor prognosis and elevated invasive capacity. This review compiles evidence about the genetic expression of matrix metalloproteinases in gastric cancer and their role in tumour invasion and metastasis, emphasizing their potential as molecular markers of prognosis.

  7. Genetic diversity assessment of summer squash landraces using molecular markers.

    PubMed

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

    2013-07-01

    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.

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

    PubMed

    Put, Stéphanie; Westhovens, René; Lahoutte, Tony; Matthys, Patrick

    2014-04-15

    Early diagnosis and effective monitoring of rheumatoid arthritis (RA) are important for a positive outcome. Instant treatment often results in faster reduction of inflammation and, as a consequence, less structural damage. Anatomical imaging techniques have been in use for a long time, facilitating diagnosis and monitoring of RA. However, mere imaging of anatomical structures provides little information on the processes preceding changes in synovial tissue, cartilage, and bone. Molecular imaging might facilitate more effective diagnosis and monitoring in addition to providing new information on the disease pathogenesis. A limiting factor in the development of new molecular imaging techniques is the availability of suitable probes. Here, we review which cells and molecules can be targeted in the RA joint and discuss the advances that have been made in imaging of arthritis with a focus on such molecular targets as folate receptor, F4/80, macrophage mannose receptor, E-selectin, intercellular adhesion molecule-1, phosphatidylserine, and matrix metalloproteinases. In addition, we discuss a new tool that is being introduced in the field, namely the use of nanobodies as tracers. Finally, we describe additional molecules displaying specific features in joint inflammation and propose these as potential new molecular imaging targets, more specifically receptor activator of nuclear factor κB and its ligand, chemokine receptors, vascular cell adhesion molecule-1, αVβ₃ integrin, P2X7 receptor, suppression of tumorigenicity 2, dendritic cell-specific transmembrane protein, and osteoclast-stimulatory transmembrane protein.

  9. Molecular Imaging Markers to Track Huntington’s Disease Pathology

    PubMed Central

    Wilson, Heather; De Micco, Rosa; Niccolini, Flavia; Politis, Marios

    2017-01-01

    Huntington’s disease (HD) is a progressive, monogenic dominant neurodegenerative disorder caused by repeat expansion mutation in the huntingtin gene. The accumulation of mutant huntingtin protein, forming intranuclear inclusions, subsequently leads to degeneration of medium spiny neurons in the striatum and cortical areas. Genetic testing can identify HD gene carriers before individuals develop overt cognitive, psychiatric, and chorea symptoms. Thus, HD gene carriers can be studied in premanifest stages to understand and track the evolution of HD pathology. While advances have been made, the precise pathophysiological mechanisms underlying HD are unclear. Magnetic resonance imaging (MRI) and positron emission tomography (PET) have been employed to understand HD pathology in presymptomatic and symptomatic disease stages. PET imaging uses radioactive tracers to detect specific changes, at a molecular level, which could be used as markers of HD progression and to monitor response to therapeutic treatments for HD gene expansion carriers (HDGECs). This review focuses on available PET techniques, employed in cross-sectional and longitudinal human studies, as biomarkers for HD, and highlights future potential PET targets. PET studies have assessed changes in postsynaptic dopaminergic receptors, brain metabolism, microglial activation, and recently phosphodiesterase 10A (PDE10A) as markers to track HD progression. Alterations in PDE10A expression are the earliest biochemical change identified in HD gene carriers up to 43 years before predicted symptomatic onset. Thus, PDE10A expression could be a promising marker to track HD progression from early premanifest disease stages. Other PET targets which have been less well investigated as biomarkers include cannabinoid, adenosine, and GABA receptors. Future longitudinal studies are required to fully validate these PET biomarkers for use to track disease progression from far-onset premanifest to manifest HD stages. PET

  10. Molecular Imaging Markers to Track Huntington's Disease Pathology.

    PubMed

    Wilson, Heather; De Micco, Rosa; Niccolini, Flavia; Politis, Marios

    2017-01-01

    Huntington's disease (HD) is a progressive, monogenic dominant neurodegenerative disorder caused by repeat expansion mutation in the huntingtin gene. The accumulation of mutant huntingtin protein, forming intranuclear inclusions, subsequently leads to degeneration of medium spiny neurons in the striatum and cortical areas. Genetic testing can identify HD gene carriers before individuals develop overt cognitive, psychiatric, and chorea symptoms. Thus, HD gene carriers can be studied in premanifest stages to understand and track the evolution of HD pathology. While advances have been made, the precise pathophysiological mechanisms underlying HD are unclear. Magnetic resonance imaging (MRI) and positron emission tomography (PET) have been employed to understand HD pathology in presymptomatic and symptomatic disease stages. PET imaging uses radioactive tracers to detect specific changes, at a molecular level, which could be used as markers of HD progression and to monitor response to therapeutic treatments for HD gene expansion carriers (HDGECs). This review focuses on available PET techniques, employed in cross-sectional and longitudinal human studies, as biomarkers for HD, and highlights future potential PET targets. PET studies have assessed changes in postsynaptic dopaminergic receptors, brain metabolism, microglial activation, and recently phosphodiesterase 10A (PDE10A) as markers to track HD progression. Alterations in PDE10A expression are the earliest biochemical change identified in HD gene carriers up to 43 years before predicted symptomatic onset. Thus, PDE10A expression could be a promising marker to track HD progression from early premanifest disease stages. Other PET targets which have been less well investigated as biomarkers include cannabinoid, adenosine, and GABA receptors. Future longitudinal studies are required to fully validate these PET biomarkers for use to track disease progression from far-onset premanifest to manifest HD stages. PET imaging

  11. Identification of sex-specific molecular markers using restriction site-associated DNA sequencing.

    PubMed

    Gamble, Tony; Zarkower, David

    2014-09-01

    A major barrier to evolutionary studies of sex determination and sex chromosomes has been a lack of information on the types of sex-determining mechanisms that occur among different species. This is particularly problematic in groups where most species lack visually heteromorphic sex chromosomes, such as fish, amphibians and reptiles, because cytogenetic analyses will fail to identify the sex chromosomes in these species. We describe the use of restriction site-associated DNA (RAD) sequencing, or RAD-seq, to identify sex-specific molecular markers and subsequently determine whether a species has male or female heterogamety. To test the accuracy of this technique, we examined the lizard Anolis carolinensis. We performed RAD-seq on seven male and ten female A. carolinensis and found one male-specific molecular marker. Anolis carolinensis has previously been shown to possess male heterogamety and the recently published A. carolinensis genome facilitated the characterization of the sex-specific RAD-seq marker. We validated the male specificity of the new marker using PCR on additional individuals and also found that it is conserved in some other Anolis species. We discuss the utility of using RAD-seq to identify sex-determining mechanisms in other species with cryptic or homomorphic sex chromosomes and the implications for the evolution of male heterogamety in Anolis.

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

    PubMed

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

    2012-02-01

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

  13. Molecular markers that can be utilized in diet and dietary supplement research.

    PubMed

    Moyad, Mark A; Wojno, Kirk J

    2011-08-01

    Prostate and other cancers have a multitude of potential markers that can be used in laboratory and clinical studies of diet and dietary supplement interventions. More overt clinical markers include imaging tests, biopsy samples, prostate-specific antigen kinetics, and urinary testing. Many molecular markers are currently available, including antiapoptotic and apoptotic proteins, cell adhesion molecules, cell cycle compounds, growth factors, angiogenic markers, and proliferative and inflammatory signals. Protein kinases and transcription factors should also be considered for diversity. Testing of numerous molecular markers has become critical in gaining preliminary insight into the potential impact of a novel diet and supplemental agents.

  14. Identification of molecular markers to study the Garcinia spp. diversity.

    PubMed

    Parthasarathy, Utpala; Nandakishore, O P; Rosana, O B; Babu, K Nirmal; Kumar, R Senthil; Parthasarathy, V A

    2016-06-01

    The genus Garcinia shows a considerable variation in its morphological characters such as leaf, flower and fruit with taxonomic ambiguity. It is a potential under-exploited multipurpose crop that gained considerable attention for the presence of (-) hydroxycitric acid, an anti-obesity compound, in its fruit rind and leaves. Here, we evaluated the genetic relationship through molecular markers among the selected 9 species commonly available in the Western Ghats and the Northeastern Himalayan foot hills of India. The nucleotide sequence data obtained from two prominent monomorphic bands generated in ISSR profiling of the species was utilized for the study. The selected bands were found to be of ITS region (700 bp) and partial region of KNOX-1 gene (600 bp). The evolutionary cluster was formed using MEGA5 software. The study indicated 2 major clusters, influenced by floral morphology of the species and availability of (-) hydroxycitric acid in their fruit rinds. In the subclusters, one species from the Western Ghats were paired with another from Northeastern Himalayas with relatively similar morphological traits.

  15. Rat hippocampal GABAergic molecular markers are differentially affected by ageing.

    PubMed

    Vela, José; Gutierrez, Antonia; Vitorica, Javier; Ruano, Diego

    2003-04-01

    We previously reported that the pharmacological properties of the hippocampal GABAA receptor and the expression of several subunits are modified during normal ageing. However, correlation between these post-synaptic modifications and pre-synaptic deficits were not determined. To address this issue, we have analysed the mRNA levels of several GABAergic molecular markers in young and old rat hippocampus, including glutamic acid decarboxylase enzymes, parvalbumin, calretinin, somatostatin, neuropeptide Y and vasoactive intestinal peptide (VIP). There was a differential age-related decrease in these interneuronal mRNAs that was inversely correlated with up-regulation of the alpha1 GABA receptor subunit. Somatostatin and neuropeptide Y mRNAs were most frequently affected (75% of the animals), then calretinin and VIP mRNAs (50% of the animals), and parvalbumin mRNA (25% of the animals) in the aged hippocampus. This selective vulnerability was well correlated at the protein/cellular level as analysed by immunocytochemistry. Somatostatin interneurones, which mostly innervate principal cell distal dendrites, were more vulnerable than calretinin interneurones, which target other interneurones. Parvalbumin interneurones, which mostly innervate perisomatic domains of principal cells, were preserved. This age-dependent differential reduction of specific hippocampal inteneuronal subpopulations might produce functional alterations in the GABAergic tone which might be compensated, at the post-synaptic level, by up-regulation of the expression of the alpha1 GABAA receptor subunit.

  16. Genetic characterization of fig tree mutants with molecular markers.

    PubMed

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

    2012-08-06

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

  17. Molecular beacon imaging of tumor marker gene expression in pancreatic cancer cells.

    PubMed

    Yang, Lily; Cao, Zehong; Lin, Yiming; Wood, William C; Staley, Charles A

    2005-05-01

    We have developed a fluorescence imaging-based approach to detect expression of tumor marker genes in pancreatic cancer cells using molecular beacons (MBs). MBs are short hairpin oligonucleotide probes that bind to specific oligonucleotide sequences and produce fluorescent signals. MBs targeting transcripts of two tumor marker genes, mutant K-ras and survivin, were synthesized and their specificity in detection of the expression of those genes in pancreatic cancer cells was examined. We found that K-ras MBs differentially bind to mutant K-ras mRNAs, resulting in strong fluorescent signals in pancreatic cancer cells with specific mutant K-ras genes but not in normal cells or cancer cells expressing either wild type or a different mutation of the K-ras gene. Additionally, MBs targeting survivin mRNA produced a bright fluorescent signal specifically in pancreatic cancer cells. We also demonstrated that MBs labeled with different fluorophores could detect survivin and mutant K-ras mRNAs simultaneously in single cancer cells. Furthermore, we showed that survivin and K-ras MBs have a high specificity in identifying cancer cells on frozen sections of pancreatic cancer tissues. In conclusion, molecular beacon-based imaging of expression of tumor marker genes has potential for the development of novel approaches for the detection of pancreatic cancer cells.

  18. Molecular markers for genetics and plant breeding: the MFLP marker system and its application in narrow-leafed lupin (Lupinus angustifolius).

    PubMed

    Shahidul, Islam; Yang, Huaan; Yan, Guijun

    2013-01-01

    Since the development of molecular markers to tag genes of agronomic traits of interests, molecular markers have played an increasingly significant role in breeding programs. Molecular markers have been implemented for large-scale marker-assisted selection in the breeding program of many important crops including lupin. So far, more than a dozen molecular markers for disease resistance genes and for other agronomic traits of interest have been developed in lupin. The DNA fingerprinting method, "MFLP" has played a pivotal role in the success of lupin breeding program in Australia. Here, we describe the MFLP technique used in lupin breeding which could be easily transferable to other crop species.

  19. The molecular marker of kdr against fenpropathrin in Tetranychus cinnabarinus.

    PubMed

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

    2013-12-01

    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.

  20. Determination of specific molecular markers of biomass burning in lake sediments

    NASA Astrophysics Data System (ADS)

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

    2014-05-01

    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

  1. Molecular markers associated with cold-hardiness in Camellia

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Sequence-characterized amplified region (SCAR) markers from expressed sequence tag-polymerase chain reaction (EST-PCR) and random amplified polymorphic DNA (RAPD) markers were developed with the goal to separate cold hardy camellias from non-cold hardy ones. A total of 28 cold hardy and non-cold h...

  2. New Strategies in Personalized Medicine for Solid Tumors: Molecular Markers and Clinical Trial Designs

    PubMed Central

    Jürgensmeier, Juliane M.; Eder, Joseph P.; Herbst, Roy S.

    2017-01-01

    The delineation of signaling pathways to understand tumor biology combined with the rapid development of technologies that allow broad molecular profiling and data analysis, has led to a new era of personalized medicine in oncology. Many academic institutions now routinely profile patients and discuss them in personalized medicine tumor boards before making treatment recommendations. Clinical trials initiated by pharmaceutical companies often require specific markers for enrollment or at least explore multiple options for future markers. In addition to the still small number of targeted agents that are approved for the therapy of patients with histological and molecularly defined tumors, there is a broad range of novel targeted agents in development that are undergoing clinical studies with companion profiling to determine the best responding patient population. While the present focus of profiling are genetic analyses, additional testing of RNA, protein and immune parameters are being developed and incorporated in clinical research and are likely to contribute significantly to future patient selection and treatment approaches. As the advances in tumor biology and human genetics have identified promising tumor targets, the ongoing clinical evaluation of novel agents will now need to show if the promise can be translated into benefit for patients. PMID:25183480

  3. Molecular Aluminum Additive for Burn Enhancement of Hydrocarbon Fuels.

    PubMed

    Guerieri, Philip M; DeCarlo, Samantha; Eichhorn, Bryan; Connell, Terrence; Yetter, Richard A; Tang, Xin; Hicks, Zachary; Bowen, Kit H; Zachariah, Michael R

    2015-11-12

    Additives to hydrocarbon fuels are commonly explored to change the combustion dynamics, chemical distribution, and/or product integrity. Here we employ a novel aluminum-based molecular additive, Al(I) tetrameric cluster [AlBrNEt3]4 (Et = C2H5), to a hydrocarbon fuel and evaluate the resultant single-droplet combustion properties. This Al4 cluster offers a soluble alternative to nanoscale particulate additives that have recently been explored and may mitigate the observed problems of particle aggregation. Results show the [AlBrNEt3]4 additive to increase the burn rate constant of a toluene-diethyl ether fuel mixture by ∼20% in a room temperature oxygen environment with only 39 mM of active aluminum additive (0.16 wt % limited by additive solubility). In comparison, a roughly similar addition of nano-aluminum particulate shows no discernible difference in burn properties of the hydrocarbon fuel. High speed video shows the [AlBrNEt3]4 to induce microexplosive gas release events during the last ∼30% of the droplet combustion time. We attribute this to HBr gas release based on results of temperature-programmed reaction (TPR) experiments of the [AlBrNEt3]4 dosed with O2 and D2O. A possible mechanism of burn rate enhancement is presented that is consistent with microexplosion observations and TPR results.

  4. Indel Group in Genomes (IGG) Molecular Genetic Markers1[OPEN

    PubMed Central

    Burkart-Waco, Diana; Kuppu, Sundaram; Britt, Anne; Chetelat, Roger

    2016-01-01

    Genetic markers are essential when developing or working with genetically variable populations. Indel Group in Genomes (IGG) markers are primer pairs that amplify single-locus sequences that differ in size for two or more alleles. They are attractive for their ease of use for rapid genotyping and their codominant nature. Here, we describe a heuristic algorithm that uses a k-mer-based approach to search two or more genome sequences to locate polymorphic regions suitable for designing candidate IGG marker primers. As input to the IGG pipeline software, the user provides genome sequences and the desired amplicon sizes and size differences. Primer sequences flanking polymorphic insertions/deletions are produced as output. IGG marker files for three sets of genomes, Solanum lycopersicum/Solanum pennellii, Arabidopsis (Arabidopsis thaliana) Columbia-0/Landsberg erecta-0 accessions, and S. lycopersicum/S. pennellii/Solanum tuberosum (three-way polymorphic) are included. PMID:27436831

  5. A molecular marker based linkage map of Vitis.

    PubMed

    Lodhi, M A; Daly, M J; Ye, G N; Weeden, N F; Reisch, B I

    1995-08-01

    Genetic linkage maps of Vitis (2n = 38) have been constructed from a single interspecific hybrid grape population (60 seedlings) of 'Cayuga White' X 'Aurore'. The maps were primarily based on 422 RAPD markers but also included 16 RFLP and isozyme markers. These maps had an average distance of 6.1 cM between markers and were developed using a double-pseudotestcross strategy. The 'Cayuga White' map had 214 markers covering 1196 cM and that of 'Aurore' spanned over 1477 cM with 225 markers. The 'Cayuga White' map consisted of 20 linkage groups, whereas 22 linkage groups comprised the 'Aurore' map. The number of groups reduced to 19, as in some instances two or more groups from one parent showed homology with a single group from the other parent on the basis of markers heterozygous in both parents. Each linkage group ranged in size from 14 to 135 cM in 'Aurore' and from 14 to 124 cM in 'Cayuga White'. These maps provide enough coverage of the genome to allow quantitative trait locus analysis and map-based gene cloning.

  6. 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...

  7. Molecular markers and mapping of root-knot nematode resistance in cotton.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Host-plant resistance is economic and highly effective for root-knot nematode (RKN) Meloidogyne incognita control in cotton Gossypium hirsutum. Recently, nematode R gene mapping in cotton has revealed relationships between resistance sources and linked molecular markers. Markers are important for th...

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

    EPA Science Inventory

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

  9. Labeling and analysis of chicken taste buds using molecular markers in oral epithelial sheets

    PubMed Central

    Rajapaksha, Prasangi; Wang, Zhonghou; Venkatesan, Nandakumar; Tehrani, Kayvan F.; Payne, Jason; Swetenburg, Raymond L.; Kawabata, Fuminori; Tabata, Shoji; Mortensen, Luke J.; Stice, Steven L.; Beckstead, Robert; Liu, Hong-Xiang

    2016-01-01

    In chickens, the sensory organs for taste are the taste buds in the oral cavity, of which there are ~240–360 in total number as estimated by scanning electron microscopy (SEM). There is not an easy way to visualize all taste buds in chickens. Here, we report a highly efficient method for labeling chicken taste buds in oral epithelial sheets using the molecular markers Vimentin and α-Gustducin. Immediate tissue fixation following incubation with sub-epithelially injected proteases enabled us to peel off whole epithelial sheets, leaving the shape and integrity of the tissue intact. In the peeled epithelial sheets, taste buds labeled with antibodies against Vimentin and α-Gustducin were easily identified and counted under a light microscope and many more taste buds, patterned in rosette-like clusters, were found than previously reported with SEM. Broiler-type, female-line males have more taste buds than other groups and continue to increase the number of taste buds over stages after hatch. In addition to ovoid-shaped taste buds, big tube-shaped taste buds were observed in the chicken using 2-photon microscopy. Our protocol for labeling taste buds with molecular markers will factilitate future mechanistic studies on the development of chicken taste buds in association with their feeding behaviors. PMID:27853250

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

    PubMed Central

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

    2015-01-01

    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. PMID:25821599

  11. Markers

    ERIC Educational Resources Information Center

    Healthy Schools Network, Inc., 2011

    2011-01-01

    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…

  12. 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...

  13. Molecular marker-based prediction of hybrid performance in maize using unbalanced data from multiple experiments with factorial crosses.

    PubMed

    Schrag, Tobias A; Möhring, Jens; Maurer, Hans Peter; Dhillon, Baldev S; Melchinger, Albrecht E; Piepho, Hans-Peter; Sørensen, Anker P; Frisch, Matthias

    2009-02-01

    In hybrid breeding, the prediction of hybrid performance (HP) is extremely important as it is difficult to evaluate inbred lines in numerous cross combinations. Recent developments such as doubled haploid production and molecular marker technologies have enhanced the prospects of marker-based HP prediction to accelerate the breeding process. Our objectives were to (1) predict HP using a combined analysis of hybrids and parental lines from a breeding program, (2) evaluate the use of molecular markers in addition to phenotypic and pedigree data, (3) evaluate the combination of line per se data with marker-based estimates, (4) study the effect of the number of tested parents, and (5) assess the advantage of haplotype blocks. An unbalanced dataset of 400 hybrids from 9 factorial crosses tested in different experiments and data of 79 inbred parents were subjected to combined analyses with a mixed linear model. Marker data of the inbreds were obtained with 20 AFLP primer-enzyme combinations. Cross-validation was used to assess the performance prediction of hybrids of which no or only one parental line was testcross evaluated. For HP prediction, the highest proportion of explained variance (R (2)), 46% for grain yield (GY) and 70% for grain dry matter content (GDMC), was obtained from line per se best linear unbiased prediction (BLUP) estimates plus marker effects associated with mid-parent heterosis (TEAM-LM). Our study demonstrated that HP was efficiently predicted using molecular markers even for GY when testcross data of both parents are not available. This can help in improving greatly the efficiency of commercial hybrid breeding programs.

  14. Developing biochemical and molecular markers for cyanobacterial inoculants.

    PubMed

    Prasanna, R; Madhan, K; Singh, R N; Chauhan, A K; Nain, L

    2010-09-01

    Markers for evaluating the establishment of cyanobacteria based on their sensitivity or resistance to antibiotics, saccharide utilization patterns and PCR generated fingerprints were developed. Four selected strains (isolates from rhizosphere soils of diverse agro-ecosystems) have shown potential as diazotrophs and exhibited plant growth promoting abilities. Different responses were obtained on screening against 40 antibiotics, which aided in developing selectable antibiotic markers for each strain. Biochemical profiles generated using standardized chromogenic identification system (including saccharide utilization tests) revealed that 53 % of the saccharides tested were not utilized by any strain, while some strains exhibited unique ability for utilization of saccharides such as melibiose, cellobiose, maltose and glucosamine. PCR based amplification profiles developed using a number of primers based on repeat sequences revealed the utility of 3 primers in providing unique fingerprints for the strains.

  15. De novo Transcriptome Analysis and Molecular Marker Development of Two Hemarthria Species

    PubMed Central

    Huang, Xiu; Yan, Hai-Dong; Zhang, Xin-Quan; Zhang, Jian; Frazier, Taylor P.; Huang, De-Jun; Lu, Lu; Huang, Lin-Kai; Liu, Wei; Peng, Yan; Ma, Xiao; Yan, Yan-Hong

    2016-01-01

    Hemarthria R. Br. is an important genus of perennial forage grasses that is widely used in subtropical and tropical regions. Hemarthria grasses have made remarkable contributions to the development of animal husbandry and agro-ecosystem maintenance; however, there is currently a lack of comprehensive genomic data available for these species. In this study, we used Illumina high-throughput deep sequencing to characterize of two agriculturally important Hemarthria materials, H. compressa “Yaan” and H. altissima “1110.” Sequencing runs that used each of four normalized RNA samples from the leaves or roots of the two materials yielded more than 24 million high-quality reads. After de novo assembly, 137,142 and 77,150 unigenes were obtained for “Yaan” and “1110,” respectively. In addition, a total of 86,731 “Yaan” and 48,645 “1110” unigenes were successfully annotated. After consolidating the unigenes for both materials, 42,646 high-quality SNPs were identified in 10,880 unigenes and 10,888 SSRs were identified in 8330 unigenes. To validate the identified markers, high quality PCR primers were designed for both SNPs and SSRs. We randomly tested 16 of the SNP primers and 54 of the SSR primers and found that the majority of these primers successfully amplified the desired PCR product. In addition, high cross-species transferability (61.11–87.04%) of SSR markers was achieved for four other Poaceae species. The amount of RNA sequencing data that was generated for these two Hemarthria species greatly increases the amount of genomic information available for Hemarthria and the SSR and SNP markers identified in this study will facilitate further advancements in genetic and molecular studies of the Hemarthria genus. PMID:27148320

  16. A Combination of Molecular Markers and Clinical Features Improve the Classification of Pancreatic Cysts

    PubMed Central

    Springer, Simeon; Wang, Yuxuan; Molin, Marco Dal; Masica, David L.; Jiao, Yuchen; Kinde, Isaac; Blackford, Amanda; Raman, Siva P.; Wolfgang, Christopher L.; Tomita, Tyler; Niknafs, Noushin; Douville, Christopher; Ptak, Janine; Dobbyn, Lisa; Allen, Peter J.; Klimstra, David S.; Schattner, Mark A.; Schmidt, C. Max; Yip-Schneider, Michele; Cummings, Oscar W.; Brand, Randall E.; Zeh, Herbert J.; Singhi, Aatur D.; Scarpa, Aldo; Salvia, Roberto; Malleo, Giuseppe; Zamboni, Giuseppe; Falconi, Massimo; Jang, Jin-Young; Kim, Sun-Whe; Kwon, Wooil; Hong, Seung-Mo; Song, Ki-Byung; Kim, Song Cheol; Swan, Niall; Murphy, Jean; Geoghegan, Justin; Brugge, William; Fernandez-Del Castillo, Carlos; Mino-Kenudson, Mari; Schulick, Richard; Edil, Barish H.; Adsay, Volkan; Paulino, Jorge; van Hooft, Jeanin; Yachida, Shinichi; Nara, Satoshi; Hiraoka, Nobuyoshi; Yamao, Kenji; Hijioka, Susuma; van der Merwe, Schalk; Goggins, Michael; Canto, Marcia Irene; Ahuja, Nita; Hirose, Kenzo; Makary, Martin; Weiss, Matthew J.; Cameron, John; Pittman, Meredith; Eshleman, James R.; Diaz, Luis A.; Papadopoulos, Nickolas; Kinzler, Kenneth W.; Karchin, Rachel; Hruban, Ralph H.; Vogelstein, Bert; Lennon, Anne Marie

    2016-01-01

    Background & Aims The management of pancreatic cysts poses challenges to both patients and their physicians. We investigated whether a combination of molecular markers and clinical information could improve the classification of pancreatic cysts and management of patients. Methods We performed a multi-center, retrospective study of 130 patients with resected pancreatic cystic neoplasms (12 serous cystadenomas, 10 solid-pseudopapillary neoplasms, 12 mucinous cystic neoplasms, and 96 intraductal papillary mucinous neoplasms). Cyst fluid was analyzed to identify subtle mutations in genes known to be mutated in pancreatic cysts (BRAF, CDKN2A, CTNNB1, GNAS, KRAS, NRAS, PIK3CA, RNF43, SMAD4, TP53 and VHL); to identify loss of heterozygozity at CDKN2A, RNF43, SMAD4, TP53, and VHL tumor suppressor loci; and to identify aneuploidy. The analyses were performed using specialized technologies for implementing and interpreting massively parallel sequencing data acquisition. An algorithm was used to select markers that could classify cyst type and grade. The accuracy of the molecular markers were compared with that of clinical markers, and a combination of molecular and clinical markers. Results We identified molecular markers and clinical features that classified cyst type with 90%–100% sensitivity and 92%–98% specificity. The molecular marker panel correctly identified 67 of the 74 patients who did not require surgery, and could therefore reduce the number of unnecessary operations by 91%. Conclusions We identified a panel of molecular markers and clinical features that show promise for the accurate classification of cystic neoplasms of the pancreas and identification of cysts that require surgery. PMID:26253305

  17. 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 ...

  18. Molecular markers of dental pulp tissue during orthodontic tooth movement: a pilot study.

    PubMed

    Abdul Wahab, Rohaya Megat; Zainal Ariffin, Shahrul Hisham; Yeen, Wong Woan; Ahmad, Nurul Atikah; Senafi, Sahidan

    2012-01-01

    Three specific orthodontic tooth movement genes, that is, FCRL1, HSPG2, and LAMB2 were detected at upper first premolar (with appliance) dental pulp tissue by using GeneFishing technique as compared to lower first premolar (without appliance). These three differentially expressed genes have the potential as molecular markers during orthodontic tooth movement by looking at molecular changes of pulp tissue.

  19. The addition of whole soy flour to cafeteria diet reduces metabolic risk markers in wistar rats

    PubMed Central

    2013-01-01

    Background Soybean is termed a functional food because it contains bioactive compounds. However, its effects are not well known under unbalanced diet conditions. This work is aimed at evaluating the effect of adding whole soy flour to a cafeteria diet on intestinal histomorphometry, metabolic risk and toxicity markers in rats. Methods In this study, 30 male adult Wistar rats were used, distributed among three groups (n = 10): AIN-93 M diet, cafeteria diet (CAF) and cafeteria diet with soy flour (CAFS), for 56 days. The following parameters were measured: food intake; weight gain; serum concentrations of triglycerides, total cholesterol, HDL-c, glycated hemoglobin (HbA1c), aspartate (AST) and alanine (ALT) aminotransferases and Thiobarbituric Acid Reactive Substances (TBARS); humidity and lipid fecal content; weight and fat of the liver. The villous height, the crypt depth and the thickness of the duodenal and ileal circular and longitudinal muscle layers of the animals were also measured. Results There was a significant reduction in the food intake in the CAF group. The CAFS showed lower serum concentrations of triglycerides and serum TBARS and a lower percentage of hepatic fat, with a corresponding increase in thickness of the intestinal muscle layers. In the CAF group, an increase in the HbA1c, ALT, lipid excretion, liver TBARS and crypt depth, was observed associated with lower HDL-c and villous height. The addition of soy did not promote any change in these parameters. Conclusions The inclusion of whole soy flour in a high-fat diet may be helpful in reducing some markers of metabolic risk; however, more studies are required to clarify its effects on unbalanced diets. PMID:24119309

  20. RNA polymerase beta subunit (rpoB) gene and the 16S-23S rRNA intergenic transcribed spacer region (ITS) as complementary molecular markers in addition to the 16S rRNA gene for phylogenetic analysis and identification of the species of the family Mycoplasmataceae.

    PubMed

    Volokhov, Dmitriy V; Simonyan, Vahan; Davidson, Maureen K; Chizhikov, Vladimir E

    2012-01-01

    Conventional classification of the species in the family Mycoplasmataceae is mainly based on phenotypic criteria, which are complicated, can be difficult to measure, and have the potential to be hampered by phenotypic deviations among the isolates. The number of biochemical reactions suitable for phenotypic characterization of the Mycoplasmataceae is also very limited and therefore the strategy for the final identification of the Mycoplasmataceae species is based on comparative serological results. However, serological testing of the Mycoplasmataceae species requires a performance panel of hyperimmune sera which contains anti-serum to each known species of the family, a high level of technical expertise, and can only be properly performed by mycoplasma-reference laboratories. In addition, the existence of uncultivated and fastidious Mycoplasmataceae species/isolates in clinical materials significantly complicates, or even makes impossible, the application of conventional bacteriological tests. The analysis of available genetic markers is an additional approach for the primary identification and phylogenetic classification of cultivable species and uncultivable or fastidious organisms in standard microbiological laboratories. The partial nucleotide sequences of the RNA polymerase β-subunit gene (rpoB) and the 16S-23S rRNA intergenic transcribed spacer (ITS) were determined for all known type strains and the available non-type strains of the Mycoplasmataceae species. In addition to the available 16S rRNA gene data, the ITS and rpoB sequences were used to infer phylogenetic relationships among these species and to enable identification of the Mycoplasmataceae isolates to the species level. The comparison of the ITS and rpoB phylogenetic trees with the 16S rRNA reference phylogenetic tree revealed a similar clustering patterns for the Mycoplasmataceae species, with minor discrepancies for a few species that demonstrated higher divergence of their ITS and rpoB in

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

    PubMed Central

    Kirk, Heather; Freeland, Joanna R.

    2011-01-01

    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

  2. Usefulness of molecular markers in the diagnosis of occupational and recreational histoplasmosis outbreaks.

    PubMed

    Frías-De-León, María Guadalupe; Ramírez-Bárcenas, José Antonio; Rodríguez-Arellanes, Gabriela; Velasco-Castrejón, Oscar; Taylor, Maria Lucia; Reyes-Montes, María Del Rocío

    2017-03-01

    Histoplasmosis is considered the most important systemic mycosis in Mexico, and its diagnosis requires fast and reliable methodologies. The present study evaluated the usefulness of PCR using Hcp100 and 1281-1283(220) molecular markers in detecting Histoplasma capsulatum in occupational and recreational outbreaks. Seven clinical serum samples of infected individuals from three different histoplasmosis outbreaks were processed by enzyme-linked immunosorbent assay (ELISA) to titre anti-H. capsulatum antibodies and to extract DNA. Fourteen environmental samples were also processed for H. capsulatum isolation and DNA extraction. Both clinical and environmental DNA samples were analysed by PCR with Hcp100 and 1281-1283(220) markers. Antibodies to H. capsulatum were detected by ELISA in all serum samples using specific antigens, and in six of these samples, the PCR products of both molecular markers were amplified. Four environmental samples amplified one of the two markers, but only one sample amplified both markers and an isolate of H. capsulatum was cultured from this sample. All PCR products were sequenced, and the sequences for each marker were analysed using the Basic Local Alignment Search Tool (BLASTn), which revealed 95-98 and 98-100 % similarities with the reference sequences deposited in the GenBank for Hcp100 and 1281-1283(220), respectively. Both molecular markers proved to be useful in studying histoplasmosis outbreaks because they are matched for pathogen detection in either clinical or environmental samples.

  3. Phylogeny of African cichlid fishes as revealed by molecular markers.

    PubMed

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

    1998-06-01

    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.

  4. Segmental distribution of some common molecular markers for colorectal cancer (CRC): influencing factors and potential implications.

    PubMed

    Papagiorgis, Petros Christakis

    2016-05-01

    Proximal and distal colorectal cancers (CRCs) are regarded as distinct disease entities, evolving through different genetic pathways and showing multiple clinicopathological and molecular differences. Segmental distribution of some common markers (e.g., KRAS, EGFR, Ki-67, Bcl-2, COX-2) is clinically important, potentially affecting their prognostic or predictive value. However, this distribution is influenced by a variety of factors such as the anatomical overlap of tumorigenic molecular events, associations of some markers with other clinicopathological features (stage and/or grade), and wide methodological variability in markers' assessment. All these factors represent principal influences followed by intratumoral heterogeneity and geographic variation in the frequency of detection of particular markers, whereas the role of other potential influences (e.g., pre-adjuvant treatment, interaction between markers) remains rather unclear. Better understanding and elucidation of the various influences may provide a more accurate picture of the segmental distribution of molecular markers in CRC, potentially allowing the application of a novel patient stratification for treatment, based on particular molecular profiles in combination with tumor location.

  5. A Rapid Molecular Test for Determining Yersinia pestis Susceptibility to Ciprofloxacin by the Quantification of Differentially Expressed Marker Genes

    PubMed Central

    Steinberger-Levy, Ida; Shifman, Ohad; Zvi, Anat; Ariel, Naomi; Beth-Din, Adi; Israeli, Ofir; Gur, David; Aftalion, Moshe; Maoz, Sharon; Ber, Raphael

    2016-01-01

    Standard antimicrobial susceptibility tests used to determine bacterial susceptibility to antibiotics are growth dependent and time consuming. The long incubation time required for standard tests may render susceptibility results irrelevant, particularly for patients infected with lethal bacteria that are slow growing on agar but progress rapidly in vivo, such as Yersinia pestis. Here, we present an alternative approach for the rapid determination of antimicrobial susceptibility, based on the quantification of the changes in the expression levels of specific marker genes following exposure to growth-inhibiting concentrations of the antibiotic, using Y. pestis and ciprofloxacin as a model. The marker genes were identified by transcriptomic DNA microarray analysis of the virulent Y. pestis Kimberley53 strain after exposure to specific concentrations of ciprofloxacin for various time periods. We identified several marker genes that were induced following exposure to growth-inhibitory concentrations of ciprofloxacin, and we confirmed the marker expression profiles at additional ciprofloxacin concentrations using quantitative RT-PCR. Eleven candidate marker transcripts were identified, of which four mRNA markers were selected for a rapid quantitative RT-PCR susceptibility test that correctly determined the Minimal Inhibitory Concentration (MIC) values and the categories of susceptibility of several Y. pestis strains and isolates harboring various ciprofloxacin MIC values. The novel molecular susceptibility test requires just 2 h of antibiotic exposure in a 7-h overall test time, in contrast to the 24 h of antibiotic exposure required for a standard microdilution test. PMID:27242774

  6. Molecular and cellular markers of toxicity in the Japanese Medaka @

    SciTech Connect

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

    1990-01-01

    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.

  7. Molecular characterization and chromosome-specific TRAP-marker development for Langdon durum D-genome disomic substitution lines.

    PubMed

    Li, J; Klindworth, D L; Shireen, F; Cai, X; Hu, J; Xu, S S

    2006-12-01

    The aneuploid stocks of durum wheat (Triticum turgidum L. subsp. durum (Desf.) Husnot) and common wheat (T. aestivum L.) have been developed mainly in 'Langdon' (LDN) and 'Chinese Spring' (CS) cultivars, respectively. The LDN-CS D-genome chromosome disomic substitution (LDN-DS) lines, where a pair of CS D-genome chromosomes substitute for a corresponding homoeologous A- or B-genome chromosome pair of LDN, have been widely used to determine the chromosomal locations of genes in tetraploid wheat. The LDN-DS lines were originally developed by crossing CS nulli-tetrasomics with LDN, followed by 6 backcrosses with LDN. They have subsequently been improved with 5 additional backcrosses with LDN. The objectives of this study were to characterize a set of the 14 most recent LDN-DS lines and to develop chromosome-specific markers, using the newly developed TRAP (target region amplification polymorphism)-marker technique. A total of 307 polymorphic DNA fragments were amplified from LDN and CS, and 302 of them were assigned to individual chromosomes. Most of the markers (95.5%) were present on a single chromosome as chromosome-specific markers, but 4.5% of the markers mapped to 2 or more chromosomes. The number of markers per chromosome varied, from a low of 10 (chromosomes 1A and 6D) to a high of 24 (chromosome 3A). There was an average of 16.6, 16.6, and 15.9 markers per chromosome assigned to the A-, B-, and D-genome chromosomes, respectively, suggesting that TRAP markers were detected at a nearly equal frequency on the 3 genomes. A comparison of the source of the expressed sequence tags (ESTs), used to derive the fixed primers, with the chromosomal location of markers revealed that 15.5% of the TRAP markers were located on the same chromosomes as the ESTs used to generate the fixed primers. A fixed primer designed from an EST mapped on a chromosome or a homoeologous group amplified at least 1 fragment specific to that chromosome or group, suggesting that the fixed primers

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

    PubMed

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

    2011-05-01

    A transcript map has been constructed by the development and integration of genic molecular markers (GMMs) including single nucleotide polymorphism (SNP), genic microsatellite or simple sequence repeat (SSR) and intron spanning region (ISR)-based markers, on an inter-specific mapping population of chickpea, the third food legume crop of the world and the first food legume crop of India. For SNP discovery through allele re-sequencing, primer pairs were designed for 688 genes/expressed sequence tags (ESTs) of chickpea and 657 genes/ESTs of closely related species of chickpea. High-quality sequence data obtained for 220 candidate genic regions on 2-20 genotypes representing 9 Cicer species provided 1,893 SNPs with an average frequency of 1/35.83 bp and 0.34 PIC (polymorphism information content) value. On an average 2.9 haplotypes were present in 220 candidate genic regions with an average haplotype diversity of 0.6326. SNP2CAPS analysis of 220 sequence alignments, as mentioned above, provided a total of 192 CAPS candidates. Experimental analysis of these 192 CAPS candidates together with 87 CAPS candidates identified earlier through in silico mining of ESTs provided scorable amplification in 173 (62.01%) cases of which predicted assays were validated in 143 (82.66%) cases (CGMM). Alignments of chickpea unigenes with Medicago truncatula genome were used to develop 121 intron spanning region (CISR) markers of which 87 yielded scorable products. In addition, optimization of 77 EST-derived SSR (ICCeM) markers provided 51 scorable markers. Screening of easily assayable 281 markers including 143 CGMMs, 87 CISRs and 51 ICCeMs on 5 parental genotypes of three mapping populations identified 104 polymorphic markers including 90 markers on the inter-specific mapping population. Sixty-two of these GMMs together with 218 earlier published markers (including 64 GMM loci) and 20 other unpublished markers could be integrated into this genetic map. A genetic map developed here

  9. Molecular predictive markers in tumors of the gastrointestinal tract

    PubMed Central

    Papadopoulou, Eirini; Metaxa-Mariatou, Vasiliki; Tsaousis, Georgios; Tsoulos, Nikolaos; Tsirigoti, Angeliki; Efstathiadou, Chrisoula; Apessos, Angela; Agiannitopoulos, Konstantinos; Pepe, Georgia; Bourkoula, Eugenia; Nasioulas, George

    2016-01-01

    Gastrointestinal malignancies are among the leading causes of cancer-related deaths worldwide. Like all human malignancies they are characterized by accumulation of mutations which lead to inactivation of tumor suppressor genes or activation of oncogenes. Advances in Molecular Biology techniques have allowed for more accurate analysis of tumors’ genetic profiling using new breakthrough technologies such as next generation sequencing (NGS), leading to the development of targeted therapeutical approaches based upon biomarker-selection. During the last 10 years tremendous advances in the development of targeted therapies for patients with advanced cancer have been made, thus various targeted agents, associated with predictive biomarkers, have been developed or are in development for the treatment of patients with gastrointestinal cancer patients. This review summarizes the advances in the field of molecular biomarkers in tumors of the gastrointestinal tract, with focus on the available NGS platforms that enable comprehensive tumor molecular profile analysis. PMID:27895815

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

    PubMed

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

    2006-01-01

    "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.

  11. Transport of sewage molecular markers through saturated soil column and effect of easily biodegradable primary substrate on their removal.

    PubMed

    Foolad, Mahsa; Ong, Say Leong; Hu, Jiangyong

    2015-11-01

    Pharmaceutical and personal care products (PPCPs) and artificial sweeteners (ASs) are emerging organic contaminants (EOCs) in the aquatic environment. The presence of PPCPs and ASs in water bodies has an ecologic potential risk and health concern. Therefore, it is needed to detect the pollution sources by understanding the transport behavior of sewage molecular markers in a subsurface area. The aim of this study was to evaluate transport of nine selected molecular markers through saturated soil column experiments. The selected sewage molecular markers in this study were six PPCPs including acetaminophen (ACT), carbamazepine (CBZ), caffeine (CF), crotamiton (CTMT), diethyltoluamide (DEET), salicylic acid (SA) and three ASs including acesulfame (ACF), cyclamate (CYC), and saccharine (SAC). Results confirmed that ACF, CBZ, CTMT, CYC and SAC were suitable to be used as sewage molecular markers since they were almost stable against sorption and biodegradation process during soil column experiments. In contrast, transport of ACT, CF and DEET were limited by both sorption and biodegradation processes and 100% removal efficiency was achieved in the biotic column. Moreover, in this study the effect of different acetate concentration (0-100mg/L) as an easily biodegradable primary substrate on a removal of PPCPs and ASs was also studied. Results showed a negative correlation (r(2)>0.75) between the removal of some selected sewage chemical markers including ACF, CF, ACT, CYC, SAC and acetate concentration. CTMT also decreased with the addition of acetate, but increasing acetate concentration did not affect on its removal. CBZ and DEET removal were not dependent on the presence of acetate.

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

    PubMed

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

    2014-05-01

    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.

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

    PubMed Central

    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

    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-γ– 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

  14. Molecular trophic markers in marine food webs and their potential use for coral ecology.

    PubMed

    Leal, Miguel Costa; Ferrier-Pagès, Christine

    2016-10-01

    Notable advances in ecological genomics have been driven by high-throughput sequencing technology and taxonomically broad sequence repositories that allow us to accurately assess species interactions with great taxonomic resolution. The use of DNA as a marker for ingested food is particularly relevant to address predator-prey interactions and disentangle complex marine food webs. DNA-based methods benefit from reductionist molecular approaches to address ecosystem scale processes, such as community structure and energy flow across trophic levels, among others. Here we review how molecular trophic markers have been used to better understand trophic interactions in the marine environment and their advantages and limitations. We focus on animal groups where research has been focused, such as marine mammals, seabirds, fishes, pelagic invertebrates and benthic invertebrates, and use case studies to illustrate how DNA-based methods unraveled food-web interactions. The potential of molecular trophic markers for disentangling the complex trophic ecology of corals is also discussed.

  15. Molecular Markers of Secondary Organic Aerosol in Mumbai, India.

    PubMed

    Fu, Pingqing; Aggarwal, Shankar G; Chen, Jing; Li, Jie; Sun, Yele; Wang, Zifa; Chen, Huansheng; Liao, Hong; Ding, Aijun; Umarji, G S; Patil, R S; Chen, Qi; Kawamura, Kimitaka

    2016-05-03

    Biogenic secondary organic aerosols (SOA) are generally considered to be more abundant in summer than in winter. Here, polar organic marker compounds in urban background aerosols from Mumbai were measured using gas chromatography-mass spectrometry. Surprisingly, we found that concentrations of biogenic SOA tracers at Mumbai were several times lower in summer (8-14 June 2006; wet season; n = 14) than in winter (13-18 February 2007; dry season; n = 10). Although samples from less than 10% of the season are extrapolated to the full season, such seasonality may be explained by the predominance of the southwest summer monsoon, which brings clean marine air masses to Mumbai. While heavy rains are an important contributor to aerosol removal during the monsoon season, meteorological data (relative humidity and T) suggest no heavy rains occurred during our sampling period. However, in winter, high levels of SOA and their day/night differences suggest significant contributions of continental aerosols through long-range transport together with local sources. The winter/summer pattern of SOA loadings was further supported by results from chemical transport models (NAQPMS and GEOS-Chem). Furthermore, our study suggests that monoterpene- and sesquiterpene-derived secondary organic carbon (SOC) were more significant than those of isoprene- and toluene-SOC at Mumbai.

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

    PubMed

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

    2011-01-01

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

  17. Molecular Markers Involved in Tumorigenesis of Thyroid Carcinoma: Focus on Aggressive Histotypes.

    PubMed

    Penna, Gustavo C; Vaisman, Fernanda; Vaisman, Mario; Sobrinho-Simões, Manuel; Soares, Paula

    2017-02-24

    Thyroid cancer derived from follicular cells (TCDFC) comprises well-differentiated (papillary and follicular) carcinoma, poorly differentiated carcinoma, and anaplastic carcinoma. Papillary thyroid carcinoma is the most common endocrine cancer, and its incidence is steadily increasing. Lethality and aggressiveness of TCDFC is inversely correlated with differentiation degree. In this review, an emphasis has been put on molecular markers involved in tumorigenesis of thyroid carcinoma with a focus on aggressive histotypes and the role of such biomarkers in predicting thyroid cancer outcome. Genetic rearrangements in TCDFC (RET/PTC, PAX8/PPARG) and mutations in RAS, BRAF, TERT promoter (TERTp), TP53, PIK3CA, and AKT1 are discussed. The majority of the studies to date indicate that TERTp mutations can serve as a marker of more aggressive disease in all the subtypes of thyroid carcinoma, being the best current marker of poor prognosis, due to its independent association with distant metastases and increased disease-specific mortality. Some studies suggested that a more accurate prediction of thyroid cancer outcome may be possible through a more extensive genetic analysis. The same is true concerning the identification of other mutations that are only relatively frequent in advanced tumors (e.g., TP53, PIK3CA, or AKT1). A better understanding of the prognostic role of TERTp mutation (together with additional ones like BRAF, RAS, PIK3CA, AKT1, or TP53) and the clarification of their putative role in fine-needle aspiration biopsies are likely to allow, in the future, an early refinement of the stratification risk in patients with well-differentiated carcinomas. It is worth noting that, as with any categorical staging system, the risk evaluation within each category (low, intermediate, and high) varies depending on the specific clinicopathologic features of individual patients and the specific biological behavior of the tumor. Finally, besides the diagnostic and

  18. Highly isotopically depleted isoprenoids: Molecular markers for ancient methane venting

    SciTech Connect

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

    1999-12-01

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

  19. Biomedical wellness monitoring system based upon molecular markers

    NASA Astrophysics Data System (ADS)

    Ingram, Whitney

    2012-06-01

    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.

  20. Molecular Analysis of Genetic Markers for Non-Hodgkin Lymphomas.

    PubMed

    Sholl, Lynette M; Longtine, Janina; Kuo, Frank C

    2017-04-06

    Molecular analysis complements the clinical and histopathologic tools used to diagnose and subclassify hematologic malignancies. The presence of clonal antigen-receptor gene rearrangements can help to confirm the diagnosis of a B or T cell lymphoma and can serve as a fingerprint of that neoplasm to be used in identifying concurrent disease at disparate sites or recurrence at future time points. Certain lymphoid malignancies harbor a characteristic chromosomal translocation, a finding that may have significant implications for an individual's prognosis or response to therapy. The polymerase chain reaction (PCR) is typically used to detect antigen-receptor gene rearrangements as well as specific translocations that can be supplemented by fluorescence in situ hybridization (FISH) and karyotype analysis. © 2017 by John Wiley & Sons, Inc.

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

    SciTech Connect

    Shugart, L.R.

    1991-04-01

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

  2. Molecular Markers of Dental Pulp Tissue during Orthodontic Tooth Movement: A Pilot Study

    PubMed Central

    Abdul Wahab, Rohaya Megat; Zainal Ariffin, Shahrul Hisham; Yeen, Wong Woan; Ahmad, Nurul Atikah; Senafi, Sahidan

    2012-01-01

    Three specific orthodontic tooth movement genes, that is, FCRL1, HSPG2, and LAMB2 were detected at upper first premolar (with appliance) dental pulp tissue by using GeneFishing technique as compared to lower first premolar (without appliance). These three differentially expressed genes have the potential as molecular markers during orthodontic tooth movement by looking at molecular changes of pulp tissue. PMID:22629122

  3. Molecular identity of ramie germplasms using simple sequence repeat markers.

    PubMed

    Luan, M B; Chen, B F; Zou, Z Z; Zhu, J J; Wang, X F; Xu, Y; Sun, Z M; Chen, J H

    2015-03-27

    DNA identity is highly effective and efficient for distinguishing crop varieties regardless of their phenotypic similarities. To establish DNA identity in ramie, 21 simple sequence repeat primers were amplified in 108 accessions of domestic and exotic ramie germplasms. Sixty polymorphic bands were obtained, with an average of 2.9 bands per locus and 2-8 band types per primer locus (average of 5.19 band types). The Simpson's diversity index of the 21 simple sequence repeat loci ranged from 0.158 to 0.808 with an average of 0.612. There was large difference in the specific index in the germplasm tested, from 44.082 to 218.163, with an average of 83.620. Based on allele band type, 8 primer pairs were selected for DNA fingerprinting of the 108 genotypes. The combination of the 8 primer pairs were found to be very effective for distinguishing these genotypes, indicating that they can be used in the molecular DNA identity of ramie.

  4. Urinary enzymes and low molecular weight proteins as markers of tubular dysfunction.

    PubMed

    Jung, K

    1994-11-01

    Reference intervals of different tubular markers, that is, low molecular weight proteins and urinary enzymes, show divergent data and wide ranges. The problems in establishing reference intervals for the tubular markers are caused by the necessarily different analytical methods. Also, the general rules of determining reference limits as well as the numerous physiological variables influencing tubular function are often not sufficiently taken into consideration. Compared to blood components, urinary tubular markers show a wide variability of values. This is due to the fact that the excretion of enzymes and proteins into urine represents an excretion into an open system. The influences of variables like age, sex, physical exercise, different urine flow rates, and biorhythms are immediately reflected by changed excretion rates of tubular markers. The problems occurring when the second morning urine sample is being used as a "standardized" collection method and the basis to characterize tubular function by analyte/creatinine ratios are discussed in this paper.

  5. 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...

  6. 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...

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

    ERIC Educational Resources Information Center

    Helms, T. C.; Doetkott, C.

    2007-01-01

    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…

  8. A novel molecular marker for the study of Neotropical cichlid phylogeny.

    PubMed

    Fabrin, T M C; Gasques, L S; Prioli, S M A P; Prioli, A J

    2015-12-22

    The use of molecular markers has contributed to phylogeny and to the reconstruction of species' evolutionary history. Each region of the genome has different evolution rates, which may or may not identify phylogenetic signal at different levels. Therefore, it is important to assess new molecular markers that can be used for phylogenetic reconstruction. Regions that may be associated with species characteristics and are subject to selective pressure, such as opsin genes, which encode proteins related to the visual system and are widely expressed by Cichlidae family members, are interesting. Our aim was to identify a new nuclear molecular marker that could establish the phylogeny of Neotropical cichlids and is potentially correlated with the visual system. We used Bayesian inference and maximum likelihood analysis to support the use of the nuclear opsin LWS gene in the phylogeny of eight Neotropical cichlid species. Their use concatenated to the mitochondrial gene COI was also tested. The LWS gene fragment comprised the exon 2-4 region, including the introns. The LWS gene provided good support for both analyses up to the genus level, distinguishing the studied species, and when concatenated to the COI gene, there was a good support up to the species level. Another benefit of utilizing this region, is that some polymorphisms are associated with changes in spectral properties of the LWS opsin protein, which constitutes the visual pigment that absorbs red light. Thus, utilization of this gene as a molecular marker to study the phylogeny of Neotropical cichlids is promising.

  9. Improving a Lecture-Size Molecular Model Set by Repurposing Used Whiteboard Markers

    ERIC Educational Resources Information Center

    Dragojlovic, Veljko

    2015-01-01

    Preparation of an inexpensive model set from whiteboard markers and either HGS molecular model set or atoms made of wood is described. The model set is relatively easy to prepare and is sufficiently large to be suitable as an instructor set for use in lectures.

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

    EPA Science Inventory

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

  11. QUANTITATION, DETECTION AND MEASUREMENT PRECISION OF ORGANIC MOLECULAR MARKERS IN URBAN PARTICULATE MATTER FROM PHILADELPHIA, PA

    EPA Science Inventory

    This work focuses on analysis of organic molecular markers in airborne particulate matter (PM) by Gas Chromatography/Ion Trap Mass Spectrometry (GC/IT MS). The particulate samples used in the method development were collected as PM10 in metropolitan Philadelphia during...

  12. Transposable elements and two other molecular markers as typing tools for the genus Paracoccidioides.

    PubMed

    Alves, Fernanda Lourenço; Ribeiro, Mariceli Araújo; Hahn, Rosane Christine; de Melo Teixeira, Marcus; de Camargo, Zoilo Pires; Cisalpino, Patrícia Silva; Marini, Marjorie Mendes

    2015-02-01

    Studies comparing Paracoccidioides brasiliensis and Paracoccidioides lutzii have shown that these fungi have significant genomic differences that may have implications in the clinical manifestation, diagnosis, and treatment of paracoccidioidomycosis caused by them. Thus, molecular typing methods are required that can distinguish between various species of Paracoccidioides. The aim of this study was to explore the potential use as molecular markers of the transposable elements Trem A-H recently identified and characterized in the genus Paracoccidioides as a means of differentiating the species. We take advantage of the abundance and distribution of these transposons in the Paracoccidioides genomes to develop a simple and highly reproducible polymerase chain reaction (PCR)-based technique. Furthermore we compare the performance of this test with two other molecular markers already in use to identify these fungi.

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

    PubMed

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

    2001-05-01

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

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

    PubMed Central

    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

    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

  15. Molecular marker development and genetic diversity exploration by RNA-seq in Platycodon grandiflorum.

    PubMed

    Kim, Hyun Jung; Jung, Jungsu; Kim, Myung-Shin; Lee, Je Min; Choi, Doil; Yeam, Inhwa

    2015-10-01

    Platycodon grandiflorum, generally known as the bellflower or balloon flower, is the only species in the genus Platycodon of the family Campanulaceae. Platycodon plants have been traditionally used as a medicinal crop in East Asia for their antiphlogistic, antitussive, and expectorant properties. Despite these practical uses, marker-assisted selection and molecular breeding in platycodons have lagged due to the lack of genetic information on this genus. In this study, we performed RNA-seq analysis of three platycodon accessions to develop molecular markers and explore genetic diversity. First, genic simple sequence repeats (SSRs) were retrieved and compared; dinucleotide motifs were the most abundant repeats (39%-40%) followed by trinucleotide (25%-31%), tetranucleotide (1.5%-1.9%), and pentanucleotide (0.3%-1.0%) repeats. The result of in silico SSR analysis, three SSR markers were detected and showed possibility to distinguish three platycodon accessions. After several filtering procedures, 180 single nucleotide polymorphisms (SNPs) were used to design 40 cleaved amplified polymorphic sequence (CAPS) markers. Twelve of these PCR-based markers were validated as highly polymorphic and utilized to investigate genetic diversity in 21 platycodon accessions collected from various regions of South Korea. Collectively, the 12 markers yielded 35 alleles, with an average of 3 alleles per locus. Polymorphism information content (PIC) values ranged from 0.087 to 0.693, averaging 0.373 per locus. Since platycodon genetics have not been actively studied, the sequence information and the DNA markers generated from our research have the potential to contribute to further genetic improvements, genomic studies, and gene discovery in this genus.

  16. Efficiency of the use of pedigree and molecular marker information in conservation programs.

    PubMed

    Fernández, Jesús; Villanueva, Beatriz; Pong-Wong, Ricardo; Toro, Miguel Angel

    2005-07-01

    The value of molecular markers and pedigree records, separately or in combination, to assist in the management of conserved populations has been tested. The general strategy for managing the population was to optimize contributions of parents to the next generation for minimizing the global weighted coancestry. Strategies differed in the type of information used to compute global coancestries, the number and type of evaluated individuals, and the system of mating. Genealogical information proved to be very useful (at least for 10 generations of management) to arrange individuals' contributions via the minimization of global coancestry. In fact, the level of expected heterozygosity after 10 generations yielded by this strategy was 88-100% of the maximum possible improvement obtained if the genotype for all loci was known. Marker information was of very limited value if used alone. The amount and degree of polymorphism of markers to be used to compute molecular coancestry had to be high to mimic the performance of the strategy relying on pedigree, especially in the short term (for example, >10 markers per chromosome with 10 alleles each were needed if only the parents' genotype was available). When both sources of information are combined to calculate the coancestry conditional on markers, clear increases in effective population size (Ne) were found, but observed diversity levels (either gene or allelic diversity) in the early generations were quite similar to the ones obtained with pedigree alone. The advantage of including molecular information is greater when information is available on a greater number of individuals (offspring and parents vs. parents only). However, for realistic situations (i.e., large genomes) the benefits of using information on offspring are small. The same conclusions were reached when comparing the use of the different types of information (genealogical or/and molecular) to perform minimum coancestry matings.

  17. [The application of DNA molecular markers in conservation of the rare and endangered medicinal plants].

    PubMed

    Yan, Zhi-Feng; Zhang, Ben-Gang; Zhang, Zhao; Xia, Tian-Rui

    2005-12-01

    In this paper, the advance in DNA molecular markers techniques in recent years was reviewed. The application of DNA markers in conservation of the rare and endangered medicinal plants was explicated, of which included identification of germ-plasm resource, determination of the habitats unite which should be protected in situ, sampling strategies of ex-situ conservation, evaluation of the conservation effects of the rare and endangered medicinal plants, as well as elucidation of their endangered mechanism etc. The information could help drawing up conservation strategies and conservation measures for references.

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

    USGS Publications Warehouse

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

    1997-01-01

    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.

  19. Candidate genes and molecular markers associated with heat tolerance in colonial Bentgrass.

    PubMed

    Jespersen, David; Belanger, Faith C; Huang, Bingru

    2017-01-01

    Elevated temperature is a major abiotic stress limiting the growth of cool-season grasses during the summer months. The objectives of this study were to determine the genetic variation in the expression patterns of selected genes involved in several major metabolic pathways regulating heat tolerance for two genotypes contrasting in heat tolerance to confirm their status as potential candidate genes, and to identify PCR-based markers associated with candidate genes related to heat tolerance in a colonial (Agrostis capillaris L.) x creeping bentgrass (Agrostis stolonifera L.) hybrid backcross population. Plants were subjected to heat stress in controlled-environmental growth chambers for phenotypic evaluation and determination of genetic variation in candidate gene expression. Molecular markers were developed for genes involved in protein degradation (cysteine protease), antioxidant defense (catalase and glutathione-S-transferase), energy metabolism (glyceraldehyde-3-phosphate dehydrogenase), cell expansion (expansin), and stress protection (heat shock proteins HSP26, HSP70, and HSP101). Kruskal-Wallis analysis, a commonly used non-parametric test used to compare population individuals with or without the gene marker, found the physiological traits of chlorophyll content, electrolyte leakage, normalized difference vegetative index, and turf quality were associated with all candidate gene markers with the exception of HSP101. Differential gene expression was frequently found for the tested candidate genes. The development of candidate gene markers for important heat tolerance genes may allow for the development of new cultivars with increased abiotic stress tolerance using marker-assisted selection.

  20. Candidate genes and molecular markers associated with heat tolerance in colonial Bentgrass

    PubMed Central

    Jespersen, David; Belanger, Faith C.; Huang, Bingru

    2017-01-01

    Elevated temperature is a major abiotic stress limiting the growth of cool-season grasses during the summer months. The objectives of this study were to determine the genetic variation in the expression patterns of selected genes involved in several major metabolic pathways regulating heat tolerance for two genotypes contrasting in heat tolerance to confirm their status as potential candidate genes, and to identify PCR-based markers associated with candidate genes related to heat tolerance in a colonial (Agrostis capillaris L.) x creeping bentgrass (Agrostis stolonifera L.) hybrid backcross population. Plants were subjected to heat stress in controlled-environmental growth chambers for phenotypic evaluation and determination of genetic variation in candidate gene expression. Molecular markers were developed for genes involved in protein degradation (cysteine protease), antioxidant defense (catalase and glutathione-S-transferase), energy metabolism (glyceraldehyde-3-phosphate dehydrogenase), cell expansion (expansin), and stress protection (heat shock proteins HSP26, HSP70, and HSP101). Kruskal-Wallis analysis, a commonly used non-parametric test used to compare population individuals with or without the gene marker, found the physiological traits of chlorophyll content, electrolyte leakage, normalized difference vegetative index, and turf quality were associated with all candidate gene markers with the exception of HSP101. Differential gene expression was frequently found for the tested candidate genes. The development of candidate gene markers for important heat tolerance genes may allow for the development of new cultivars with increased abiotic stress tolerance using marker-assisted selection. PMID:28187136

  1. Identification of molecular markers associated with mite resistance in coconut (Cocos nucifera L.).

    PubMed

    Shalini, K V; Manjunatha, S; Lebrun, P; Berger, A; Baudouin, L; Pirany, N; Ranganath, R M; Prasad, D Theertha

    2007-01-01

    Coconut mite (Aceria guerreronis 'Keifer') has become a major threat to Indian coconut (Coçcos nucifera L.) cultivators and the processing industry. Chemical and biological control measures have proved to be costly, ineffective, and ecologically undesirable. Planting mite-resistant coconut cultivars is the most effective method of preventing yield loss and should form a major component of any integrated pest management stratagem. Coconut genotypes, and mite-resistant and -susceptible accessions were collected from different parts of South India. Thirty-two simple sequence repeat (SSR) and 7 RAPD primers were used for molecular analyses. In single-marker analysis, 9 SSR and 4 RAPD markers associated with mite resistance were identified. In stepwise multiple regression analysis of SSRs, a combination of 6 markers showed 100% association with mite infestation. Stepwise multiple regression analysis for RAPD data revealed that a combination of 3 markers accounted for 83.86% of mite resistance in the selected materials. Combined stepwise multiple regression analysis of RAPD and SSR data showed that a combination of 5 markers explained 100% of the association with mite resistance in coconut. Markers associated with mite resistance are important in coconut breeding programs and will facilitate the selection of mite-resistant plants at an early stage as well as mother plants for breeding programs.

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

    PubMed Central

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

    2014-01-01

    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

  3. Identification of molecular markers linked to the mildew resistance gene Pl-d in apple.

    PubMed

    James, C M; Clarke, J B; Evans, K M

    2004-12-01

    Powdery mildew poses a serious problem for apple growers, and resistance to the disease is a major objective in breeding programmes for cultivar improvement. As selective pressure allows pathogens to overcome previously reliable resistances, there is a need for the introduction of novel resistance genes into new breeding lines. This investigation is concerned with the identification of the first set of molecular markers linked to the gene for mildew resistance, Pl-d, from the accession 'D12'. As no prior information on the map position or markers for Pl-d were available, a bulked-segregant approach was used to test 49 microsatellite primers, 176 amplified fragment length polymorphism (AFLP) primers and 80 random amplified polymorphic DNA (RAPD) primers in a progeny segregating for Pl-d resistance, 'Fiesta' (susceptible) x A871-14 ('Worcester Pearmain' x 'D12'). The segregations of the markers identified in the resistant and susceptible bulks were scored in the progeny, then the recombination fractions between Pl-d and the most tightly linked markers were calculated and a map prepared. Three AFLP, one RAPD and two microsatellite markers were identified. One AFLP was developed into a sequence-characterised amplified region marker, while the microsatellites CH03C02 and CH01D03 were flanking markers, 7 and 11 recombination units, respectively, from Pl-d. Two more distant microsatellites on the same linkage group, CH01D09 and CH01G12, confirmed the orientation of the markers on the linkage group. These microsatellites place Pl-d on the bottom of linkage group 12 in published apple maps, a region where a number of other disease resistance genes have been identified.

  4. Discovery of molecular markers to discriminate corneal endothelial cells in the human body.

    PubMed

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

    2015-01-01

    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.

  5. A SCAR MOLECULAR MARKER SPECIFICALLY RELATED TO THE FEMALE GAMETOPHYTES OF SACCHARINA (LAMINARIA) JAPONICA (PHAEOPHYTA)(1).

    PubMed

    Liu, Y-S; Li, L-H; Wu, W-K; Zhou, Z-G

    2009-08-01

    PCR amplification was employed to identify female or male gametophyte associated markers in Saccharina japonica (Aresch.) C. E. Lane, C. Mayes et G. W. Saunders (=Laminaria japonica Aresch.). One pair of the primers, P5, was screened from five pairs designed based on a specific sequence (GenBank accession no. AB069714) of Marchantia polymorpha Y chromosome, resulting in a differential band ∼500 bp in size between female and male gametophytes of Rongfu strain of S. japonica. According to the SCAR (sequence-characterized amplified regions) strategies, one pair of primers, P51, was designed on the basis of the sequence of this band that was only present in female gametophytes. A SCAR marker, designated FRML-494 (494-bp Female-Related Marker of S. japonica, GenBank accession no. EU931619), was developed successfully by PCR amplification using the designed P51 primer pair. The SCAR marker was verified to be present only in female gametophytes of another variety 901 of this kelp that was a hybrid between S. japonica as paternal and S. longissima (Miyabe) C. E. Lane, C. Mayes, Druehl et G. W. Saunders (=Laminaria longissima Miyabe) as maternal, suggesting that the FRML-494 marker was specifically related to female gametophytes of the genus. This marker is the first molecular tool reported for sex identification in kelps. This study was beneficial for identifying gametophyte gender during vegetative growth and for judging whether the monogenetic sporophytes came from exclusive male or female gametophytes, as well as for further research on sex determination at the molecular level in kelps.

  6. Molecular marker development from transcript sequences and germplasm evaluation for cultivated peanut (Arachis hypogaea L.).

    PubMed

    Peng, Ze; Gallo, Maria; Tillman, Barry L; Rowland, Diane; Wang, Jianping

    2016-02-01

    Molecular markers are important tools for genotyping in genetic studies and molecular breeding. The SSR and SNP are two commonly used marker systems developed from genomic or transcript sequences. The objectives of this study were to: (1) assemble and annotate the publicly available ESTs in Arachis and the in-house short reads, (2) develop and validate SSR and SNP markers, and (3) investigate the genetic diversity and population structure of the peanut breeding lines and the U.S. peanut mini core collection using developed SSR markers. An NCBI EST dataset with 252,951 sequences and an in-house 454 RNAseq dataset with 288,701 sequences were assembled separately after trimming. Transcript sequence comparison and phylogenetic analysis suggested that peanut is closer to cowpea and scarlet bean than to soybean, common bean and Medicago. From these two datasets, 6455 novel SSRs and 11,902 SNPs were identified. Of the discovered SSRs, 380 representing various SSR types were selected for PCR validation. The amplification rate was 89.2 %. Twenty-two (6.5 %) SSRs were polymorphic between at least one pair of four genotypes. Sanger sequencing of PCR products targeting 110 SNPs revealed 13 true SNPs between tetraploid genotypes and 193 homoeologous SNPs within genotypes. Eight out of the 22 polymorphic SSR markers were selected to evaluate the genetic diversity of Florida peanut breeding lines and the U.S. peanut mini core collection. This marker set demonstrated high discrimination power by displaying an average polymorphism information content value of 0.783, a combined probability of identity of 10(-11), and a combined power of exclusion of 0.99991. The structure analysis revealed four sub-populations among the peanut accessions and lines evaluated. The results of this study enriched the peanut genomic resources, provided over 6000 novel SSR markers and the credentials for true peanut SNP marker development, and demonstrated the power of newly developed SSR markers in

  7. Plasmodium falciparum kelch 13: a potential molecular marker for tackling artemisinin-resistant malaria parasites.

    PubMed

    Mita, Toshihiro; Tachibana, Shin-Ichiro; Hashimoto, Muneaki; Hirai, Makoto

    2016-01-01

    Although artemisinin combination therapies have been deployed as a first-line treatment for uncomplicated malaria in almost all endemic countries, artemisinin-resistant parasites have emerged and have gradually spread across the Greater Mekong subregions. There is growing concern that the resistant parasites may migrate to or emerge indigenously in sub-Saharan Africa, which might provoke a global increase in malaria-associated morbidity and mortality. Therefore, development of molecular markers that enable identification of artemisinin resistance with high sensitivity is urgently required to combat this issue. In 2014, a potential artemisinin-resistance responsible gene, Plasmodium falciparum kelch13, was discovered. Here, we review the genetic features of P. falciparum kelch13 and discuss its related resistant mechanisms and potential as a molecular marker.

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

    PubMed

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

    2013-10-15

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

  9. The Membrane Marker mCLING Reveals the Molecular Composition of Trafficking Organelles.

    PubMed

    Revelo, Natalia H; Rizzoli, Silvio O

    2016-01-04

    mCLING is a fixable endocytosis marker that can be combined with immunolabeling techniques to study the molecular composition of trafficking organelles. mCLING can be used both in cultured cells and in tissue if critical sample preparation steps, such as fixation, are correctly performed. This unit describes protocols for the application of mCLING and for the subsequent sample processing. We include immunostaining protocols and embedding procedures for confocal and high-resolution microscopy.

  10. Molecular Identification of Sex in Phoenix dactylifera Using Inter Simple Sequence Repeat Markers

    PubMed Central

    Al-Ameri, Abdulhafed A.; Al-Qurainy, Fahad; Gaafar, Abdel-Rhman Z.; Khan, Salim; Nadeem, M.

    2016-01-01

    Early sex identification of Date Palm (Phoenix dactylifera L.) at seedling stage is an economically desirable objective, which will significantly increase the profits of seed based cultivation. The utilization of molecular markers at this stage for early and rapid identification of sex is important due to the lack of morphological markers. In this study, a total of two hundred Inter Simple Sequence Repeat (ISSR) primers were screened among male and female Date palm plants to identify putative sex-specific marker, out of which only two primers (IS_A02 and IS_A71) were found to be associated with sex. The primer IS_A02 produced a unique band of size 390 bp and was found clearly in all female plants, while it was absent in all male plants. Contrary to this, the primer IS_A71 produced a unique band of size 380 bp and was clearly found in all male plants, whereas it was absent in all the female plants. Subsequently, these specific fragments were excised, purified, and sequenced for the development of sequence specific markers further in future for the implementation on dioecious Date Palm for sex determination. These markers are efficient, highly reliable, and reproducible for sex identification at the early stage of seedling. PMID:27419132

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

    PubMed

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

    2014-11-01

    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.

  12. Molecular markers reveal only two mud crab species of genus Scylla (Brachyura: Portunidae) in Indian coastal waters.

    PubMed

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

    2014-08-01

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

  13. [Use of genes of carbon metabolism enzymes as molecular markers of Chlorobi Phylum representatives].

    PubMed

    Turova, T P; Kovaleva, O L; Gorlenko, V M; Ivanovskiĭ, R N

    2014-01-01

    This work examined the feasibility of using certain genes of carbon metabolism enzymes as molecular markers adequate for studying phylogeny and ecology of green sulfur bacteria (GSB) of the Chlorobi phylum. Primers designed to amplify the genes of ATP citrate lyase (aclB) and citrate synthase (gltA) revealed the respective genes in the genomes of all of the newly studied GSB strains. The phylogenetic trees constructed based on nucleotide sequences of these genes and amino acid sequences of the conceptually translated proteins were on the whole congruent with the 16S rRNA gene tree, with the single exception of GltA of Chloroherpeton thalassium, which formed a separate branch beyond the cluster comprised by other representatives of the Chlorobi phylum. Thus, the aclB genes but not gltA genes proved to be suitable for the design of primers specific to all Chlorobi representatives. Therefore, it was the aclB gene that was further used asa molecular marker to detect GSB in enrichment cultures and environmental samples. AclB phylotypes of GSB were revealed in all of the samples studied, with the exception of environmental samples from soda lakes. The identification of the revealed phylotypes was in agreement with the identification based on the FMO protein gene (fmo), is a well-known Chlorobi-specific molecular marker.

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

    NASA Astrophysics Data System (ADS)

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

    2010-05-01

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

  15. Evaluation of Pakistan wheat germplasms for stripe rust resistance using molecular markers.

    PubMed

    Sobia, Tabassum; Muhammad, Ashraf; Chen, XianMing

    2010-09-01

    Wheat production in Pakistan is seriously constrained due to rust diseases and stripe rust (yellow) caused by Puccinia striiformis f. sp. tritici, which could limit yields. Thus development and cultivation of genetically diverse and resistant varieties is the most sustainable solution to overcome these diseases. The first objective of the present study was to evaluate 100 Pakistan wheat cultivars that have been grown over the past 60 years. These cultivars were inoculated at the seedling stage with two virulent stripe rust isolates from the United States and two from Pakistan. None of the wheat cultivars were resistant to all tested stripe rust isolates, and 16% of cultivars were susceptible to the four isolates at the seedling stage. The data indicated that none of the Pakistan wheat cultivars contained either Yr5 or Yr15 genes that were considered to be effective against most P. striiformis f. sp. tritici isolates from around the world. Several Pakistan wheat cultivars may have gene Yr10, which is effective against isolate PST-127 but ineffective against PST-116. It is also possible that these cultivars may have other previously unidentified genes or gene combinations. The second objective was to evaluate the 100 Pakistan wheat cultivars for stripe rust resistance during natural epidemics in Pakistan and Washington State, USA. It was found that a higher frequency of resistance was present under field conditions compared with greenhouse conditions. Thirty genotypes (30% of germplasms) were found to have a potentially high temperature adult plant (HTAP) resistance. The third objective was to determine the genetic diversity in Pakistan wheat germplasms using molecular markers. This study was based on DNA fingerprinting using resistance gene analog polymorphism (RGAP) marker analysis. The highest polymorphism detected with RGAP primer pairs was 40%, 50% and 57% with a mean polymorphism of 36%. A total of 22 RGAP markers were obtained in this study. RGAP, simple

  16. A Reductionist Approach to Extract Robust Molecular Markers from Microarray Data Series -Isolating Markers to Track Osseointegration.

    PubMed

    Barik, Anwesha; Banerjee, Satarupa; Dhara, Santanu; Chakravorty, Nishant

    2017-03-10

    Complexities in the full genome expression studies hinder the extraction of tracker genes to analyze the course of biological events. In this study, we demonstrate the applications of supervised machine learning methods to reduce the irrelevance in microarray data series and thereby extract robust molecular markers to track biological processes. The methodology has been illustrated by analyzing whole genome expression studies on bone-implant integration (ossointegration). Being a biological process, osseointegration is known to leave a trail of genetic footprint during the course. In spite of existence of enormous amount of raw data in public repositories, researchers still do not have access to a panel of genes that can definitively track osseointegrtion. The results from our study revealed panels comprising of matrix metalloproteinases and collagen genes were able to track osseointegration on implant surfaces (MMP9 and COL1A2 on micro-textured; MMP12 and COL6A3 on superimposed nano-textured surfaces) 100% classification accuracy, specificity and sensitivity. Further, our analysis showed the importance of the progression of the duration in establishment of the mechanical connection at bone-implant surface. The findings from this study are expected to be useful to researchers investigating osseointegration of novel implant materials especially at the early stage. The methodology demonstrated can be easily adapted by scientists in different fields to analyze large databases for other biological processes.

  17. Transcriptome Analysis and Development of SSR Molecular Markers in Glycyrrhiza uralensis Fisch.

    PubMed

    Liu, Yaling; Zhang, Pengfei; Song, Meiling; Hou, Junling; Qing, Mei; Wang, Wenquan; Liu, Chunsheng

    2015-01-01

    Licorice is an important traditional Chinese medicine with clinical and industrial applications. Genetic resources of licorice are insufficient for analysis of molecular biology and genetic functions; as such, transcriptome sequencing must be conducted for functional characterization and development of molecular markers. In this study, transcriptome sequencing on the Illumina HiSeq 2500 sequencing platform generated a total of 5.41 Gb clean data. De novo assembly yielded a total of 46,641 unigenes. Comparison analysis using BLAST showed that the annotations of 29,614 unigenes were conserved. Further study revealed 773 genes related to biosynthesis of secondary metabolites of licorice, 40 genes involved in biosynthesis of the terpenoid backbone, and 16 genes associated with biosynthesis of glycyrrhizic acid. Analysis of unigenes larger than 1 Kb with a length of 11,702 nt presented 7,032 simple sequence repeats (SSR). Sixty-four of 69 randomly designed and synthesized SSR pairs were successfully amplified, 33 pairs of primers were polymorphism in in Glycyrrhiza uralensis Fisch., Glycyrrhiza inflata Bat., Glycyrrhiza glabra L. and Glycyrrhiza pallidiflora Maxim. This study not only presents the molecular biology data of licorice but also provides a basis for genetic diversity research and molecular marker-assisted breeding of licorice.

  18. A bayesian mixed regression based prediction of quantitative traits from molecular marker and gene expression data.

    PubMed

    Bhattacharjee, Madhuchhanda; Sillanpää, Mikko J

    2011-01-01

    Both molecular marker and gene expression data were considered alone as well as jointly to serve as additive predictors for two pathogen-activity-phenotypes in real recombinant inbred lines of soybean. For unobserved phenotype prediction, we used a bayesian hierarchical regression modeling, where the number of possible predictors in the model was controlled by different selection strategies tested. Our initial findings were submitted for DREAM5 (the 5th Dialogue on Reverse Engineering Assessment and Methods challenge) and were judged to be the best in sub-challenge B3 wherein both functional genomic and genetic data were used to predict the phenotypes. In this work we further improve upon this previous work by considering various predictor selection strategies and cross-validation was used to measure accuracy of in-data and out-data predictions. The results from various model choices indicate that for this data use of both data types (namely functional genomic and genetic) simultaneously improves out-data prediction accuracy. Adequate goodness-of-fit can be easily achieved with more complex models for both phenotypes, since the number of potential predictors is large and the sample size is not small. We also further studied gene-set enrichment (for continuous phenotype) in the biological process in question and chromosomal enrichment of the gene set. The methodological contribution of this paper is in exploration of variable selection techniques to alleviate the problem of over-fitting. Different strategies based on the nature of covariates were explored and all methods were implemented under the bayesian hierarchical modeling framework with indicator-based covariate selection. All the models based in careful variable selection procedure were found to produce significant results based on permutation test.

  19. Molecular characterization of Brazilian equid herpesvirus type 1 strains based on neuropathogenicity markers

    PubMed Central

    Mori, Enio; Lara, Maria do Carmo C.S.H.; Cunha, Elenice M.S.; Villalobos, Eliana M.C.; Mori, Claudia M.C.; Soares, Rodrigo M.; Brandão, Paulo E.; Fernandes, Wilson R.; Richtzenhain, Leonardo J.

    2015-01-01

    Partial nucleotide sequences of ORF72 (glycoprotein D, gD), ORF64 (infected cell protein 4, ICP4) and ORF30 (DNA polymerase) genes were compared with corresponding sequences of EHV-1 reference strains to characterize the molecular variability of Brazilian strains. Virus isolation assays were applied to 74 samples including visceral tissue, total blood, cerebrospinal fluid (CSF) and nasal swabs of specimens from a total of 64 animals. Only one CSF sample (Iso07/05 strain) was positive by virus isolation in cell culture. EHV-1 Iso07/05 neurologic strain and two abortion visceral tissues samples (Iso11/06 and Iso33/06) were PCR-positive for ORF33 (glycoprotein B, gB) gene of EHV-1. A sequence analysis of the ORF72, ORF64 and ORF30 genes from three EHV-1 archival strains (A3/97, A4/72, A9/92) and three clinical samples (Iso07/05, Iso11/06 and Iso33/06) suggested that among Brazilian EHV-1 strains, the amplified region of the gD gene sequence is highly conserved. Additionally, the analysis of ICP4 gene showed high nucleotide and amino acid identities when compared with genotype P strains, suggesting that the EHV-1 Brazilian strains belonged to the same group. All the EHV-1 Brazilian strains were classified as non-neuropathogenic variants (N752) based on the ORF30 analysis. These findings indicate a high conservation of the gD-, ICP4- and ORF30-encoding sequences. Different pathotypes of the EHV-1 strain might share identical genes with no specific markers, and tissue tropism is not completely dependent on the gD envelope, immediate-early ICP4 and DNA polymerase proteins. PMID:26273275

  20. The proteome signature of the inflammatory breast cancer plasma membrane identifies novel molecular markers of disease

    PubMed Central

    Suárez-Arroyo, Ivette J; Feliz-Mosquea, Yismeilin R; Pérez-Laspiur, Juliana; Arju, Rezina; Giashuddin, Shah; Maldonado-Martínez, Gerónimo; Cubano, Luis A; Schneider, Robert J; Martínez-Montemayor, Michelle M

    2016-01-01

    Inflammatory Breast Cancer (IBC) is the most lethal form of breast cancer with a 35% 5-year survival rate. The accurate and early diagnosis of IBC and the development of targeted therapy against this deadly disease remain a great medical challenge. Plasma membrane proteins (PMPs) such as E-cadherin and EGFR, play an important role in the progression of IBC. Because the critical role of PMPs in the oncogenic processes they are the perfect candidates as molecular markers and targets for cancer therapies. In the present study, Stable Isotope Labeling with Amino Acids in Cell Culture (SILAC) followed by mass spectrometry analysis was used to compare the relative expression levels of membrane proteins (MP) between non-cancerous mammary epithelial and IBC cells, MCF-10A and SUM-149, respectively. Six of the identified PMPs were validated by immunoblotting using the membrane fractions of non-IBC and IBC cell lines, compared with MCF-10A cells. Immunohistochemical analysis using IBC, invasive ductal carcinoma or normal mammary tissue samples was carried out to complete the validation method in nine of the PMPs. We identified and quantified 278 MPs, 76% of which classified as PMPs with 1.3-fold or higher change. We identified for the first time the overexpression of the novel plasminogen receptor, PLGRKT in IBC and of the carrier protein, SCAMP3. Furthermore, we describe the positive relationship between L1CAM expression and metastasis in IBC patients and the role of SCAMP3 as a tumor-related protein. Overall, the membrane proteomic signature of IBC reflects a global change in cellular organization and suggests additional strategies for cancer progression. Together, this study provides insight into the specialized IBC plasma membrane proteome with the potential to identify a number of novel therapeutic targets for IBC. PMID:27648361

  1. Assessment of genetic relationship in Persea spp by traditional molecular markers.

    PubMed

    Reyes-Alemán, J C; Valadez-Moctezuma, E; Barrientos-Priego, A F

    2016-04-04

    Currently, the reclassification of the genus Persea is under discussion with molecular techniques for DNA analysis representing an alternative for inter- and intra-specific differentiation. In the present study, the traditional random-amplified polymorphic DNA (RAPD) and the inter simple sequence repeat (ISSR) markers were used to determine the genomic relationship of different species and hybrids representative of the subgenera Eriodaphne and Persea in a population conserved in a germplasm bank. The data were analyzed statistically using multivariate methods. In the RAPD analysis, a total of 190 polymorphic bands were produced, with an average of 23.7 bands per primer, the percentage contribution of each primer was from 7.66 to 19.63; the polymorphic information content (PIC) ranged from 0.23 to 0.45, with an average of 0.35. In the ISSR analysis, a total of 111 polymorphic bands were considered, with an average of 18.5 bands per primer, the percentage contribution of each was from 11.83 to 19.57; the PIC ranged from 0.35 to 0.48, with an average of 0.42. The phenograms obtained in each technique showed the relationship among the accessions through the clusters formed. In general, both the techniques grouped representatives of the Persea americana races (P. americana var. drymifolia, P. americana var. guatemalensis, and P. americana var. americana). However, it was not possible to separate the species of Persea used as reference into independent clades. In addition, they tended to separate the representatives of subgenera Eriodaphne and Persea.

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

    PubMed Central

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

    2012-01-01

    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

  3. Identification of a molecular marker for genotyping human lymphatic filarial nematode parasite Wuchereria bancrofti.

    PubMed

    Patra, K P; Ramu, Thangadurai; Hoti, S L; Pragasam, G Siva; Das, P K

    2007-05-01

    In India, Mass Drug Administration is on going towards elimination of lymphatic filariasis in many areas, which might lead to intense selection pressure on the parasite populations and their genetic restructuring. This calls for molecular finger printing of Wuchereria bancrofti parasite populations at national level and monitoring genetic changes in the future. For this purpose a reliable, less expensive, rapid, and reproducible molecular tool is necessary, which is not available for W. bancrofti at this time. We identified robust molecular markers based on the comparison of random amplified polymorphic DNA (RAPD) and amplified fragment length polymorphism (AFLP) profiles and the genetic data generated from parasite populations collected from areas in Northern (Varanasi, Uttar Pradesh state), Southern (Kozhikode, Kerala State) and Central regions (Jagdalpur, Chattisgarh state) of India, where lymphatic filariasis is endemic for many decades. RAPD profiles for these parasite populations were generated using three different primers and the dendrograms constructed using the profiles were all different. In order to identify appropriate RAPD primer(s), we compared the results of RAPD with the fingerprint profile and genetic data obtained by the more reliable AFLP technique, using the parasite populations from the same areas. RAPD marker (OP8) primer produced phylogenetic data almost similar to that of AFLP analysis. The marker was able to reveal variations between the parasite populations collected from Varanasi, Kozhikode, and Jagdalpur. Most importantly, RAPD primer OP8 produced reproducible results, when tested in three different trials. In view of the limited availability of W. bancrofti parasite DNA, along with a lower cost and ease of performance, RAPD appears to be more suitable compared to AFLP at the present juncture, since complete genome information of this parasite is still not available. Thus, RAPD primer OP8 can be a very useful molecular maker for DNA

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

    PubMed

    Potokina, E K; Aleksandrova, T G

    2008-11-01

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

  5. Recent trends and perspectives of molecular markers against fungal diseases in wheat

    PubMed Central

    Goutam, Umesh; Kukreja, Sarvjeet; Yadav, Rakesh; Salaria, Neha; Thakur, Kajal; Goyal, Aakash K.

    2015-01-01

    Wheat accounts for 19% of the total production of major cereal crops in the world. In view of ever increasing population and demand for global food production, there is an imperative need of 40–60% increase in wheat production to meet the requirement of developing world in coming 40 years. However, both biotic and abiotic stresses are major hurdles for attaining the goal. Among the most important diseases in wheat, fungal diseases pose serious threat for widening the gap between actual and attainable yield. Fungal disease management, mainly, depends on the pathogen detection, genetic and pathological variability in population, development of resistant cultivars and deployment of effective resistant genes in different epidemiological regions. Wheat protection and breeding of resistant cultivars using conventional methods are time-consuming, intricate and slow processes. Molecular markers offer an excellent alternative in development of improved disease resistant cultivars that would lead to increase in crop yield. They are employed for tagging the important disease resistance genes and provide valuable assistance in increasing selection efficiency for valuable traits via marker assisted selection (MAS). Plant breeding strategies with known molecular markers for resistance and functional genomics enable a breeder for developing resistant cultivars of wheat against different fungal diseases. PMID:26379639

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

    PubMed

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

    2014-11-24

    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.

  7. Prediction of Genetic Values of Quantitative Traits in Plant Breeding Using Pedigree and Molecular Markers

    PubMed Central

    Crossa, José; Campos, Gustavo de los; Pérez, Paulino; Gianola, Daniel; Burgueño, Juan; Araus, José Luis; Makumbi, Dan; Singh, Ravi P.; Dreisigacker, Susanne; Yan, Jianbing; Arief, Vivi; Banziger, Marianne; Braun, Hans-Joachim

    2010-01-01

    The availability of dense molecular markers has made possible the use of genomic selection (GS) for plant breeding. However, the evaluation of models for GS in real plant populations is very limited. This article evaluates the performance of parametric and semiparametric models for GS using wheat (Triticum aestivum L.) and maize (Zea mays) data in which different traits were measured in several environmental conditions. The findings, based on extensive cross-validations, indicate that models including marker information had higher predictive ability than pedigree-based models. In the wheat data set, and relative to a pedigree model, gains in predictive ability due to inclusion of markers ranged from 7.7 to 35.7%. Correlation between observed and predictive values in the maize data set achieved values up to 0.79. Estimates of marker effects were different across environmental conditions, indicating that genotype × environment interaction is an important component of genetic variability. These results indicate that GS in plant breeding can be an effective strategy for selecting among lines whose phenotypes have yet to be observed. PMID:20813882

  8. 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...

  9. THCVA-A - a new additional marker for illegal cannabis consumption.

    PubMed

    Radünz, Lars; Westphal, Folker; Maser, Edmund; Rochholz, Gertrud

    2012-02-10

    The aim of the present investigations was to find markers for differentiating between the consumption of illegal cannabis products and legal medication containing fully synthetic Δ9-tetrahydrocannabinol (Δ9-THC), e.g., Marinol capsules. Δ9-Tetrahydrocannabinolic acid A (Δ9-THCA-A) and Δ9-tetrahydrocannabivarinic acid A (Δ9-THCVA-A) were taken into consideration for analysis, because these substances are the precursors of Δ9-THC and Δ9-tetrahydrocannabivarin (Δ9-THCV) in plant material of Cannabis sativa and are not contained in medical THC formulations. Whereas Δ9-THCA-A is an already well investigated substance, there is little analytical data on Δ9-THCVA-A. The reason for the presented investigations was a case in which a man was tested positive for Δ9-THC during a routine traffic control claiming that the positive serum sample resulted from the intake of a THC medication (Marinol) and not from consuming illegal cannabis products. Sample preparation consisted of a protein precipitation with acetonitrile. Analysis was carried out on a Thermo Fisher LCQ Deca ion trap LC-MS-MS-system using electron spray ionization (ESI) in negative mode. MS(2)- and MS(3)-full scan spectra were recorded for Δ9-THCA-A and Δ9-THCVA-A starting from [M-H](-). Reference spectra were obtained by measuring a Δ9-THCA-A reference solution and an ethanolic cannabis extract for Δ9-THCVA-A as there is no reference material for this cannabinoid available on the market yet. Main transitions for Δ9-THCA-A were m/z 357→313 and 339 in the MS(2)-spectrum and m/z 313→245 and 191 in the MS(3)-spectrum. Fragmentation pattern of Δ9-THCVA-A was identical with a difference of 28 amu less for the precursor ion as well as the fragments due to a shorter alkyl side chain in the molecule (MS(2): m/z 329→285 and 311; MS(3): m/z 285→217 and 163). The two plant cannabinoids Δ9-THCA-A and Δ9-THCVA-A could be detected in the serum sample by LC-MS-MS which proved the intake of illegal

  10. Comparative mitochondrial genomics toward exploring molecular markers in the medicinal fungus Cordyceps militaris

    PubMed Central

    Zhang, Shu; Hao, Ai-Jing; Zhao, Yu-Xiang; Zhang, Xiao-Yu; Zhang, Yong-Jie

    2017-01-01

    Cordyceps militaris is a fungus used for developing health food, but knowledge about its intraspecific differentiation is limited due to lack of efficient markers. Herein, we assembled the mitochondrial genomes of eight C. militaris strains and performed a comparative mitochondrial genomic analysis together with three previously reported mitochondrial genomes of the fungus. Sizes of the 11 mitochondrial genomes varied from 26.5 to 33.9 kb mainly due to variable intron contents (from two to eight introns per strain). Nucleotide variability varied according to different regions with non-coding regions showing higher variation frequency than coding regions. Recombination events were identified between some locus pairs but seemed not to contribute greatly to genetic variations of the fungus. Based on nucleotide diversity fluctuations across the alignment of all mitochondrial genomes, molecular markers with the potential to be used for future typing studies were determined. PMID:28071691

  11. Comparative mitochondrial genomics toward exploring molecular markers in the medicinal fungus Cordyceps militaris.

    PubMed

    Zhang, Shu; Hao, Ai-Jing; Zhao, Yu-Xiang; Zhang, Xiao-Yu; Zhang, Yong-Jie

    2017-01-10

    Cordyceps militaris is a fungus used for developing health food, but knowledge about its intraspecific differentiation is limited due to lack of efficient markers. Herein, we assembled the mitochondrial genomes of eight C. militaris strains and performed a comparative mitochondrial genomic analysis together with three previously reported mitochondrial genomes of the fungus. Sizes of the 11 mitochondrial genomes varied from 26.5 to 33.9 kb mainly due to variable intron contents (from two to eight introns per strain). Nucleotide variability varied according to different regions with non-coding regions showing higher variation frequency than coding regions. Recombination events were identified between some locus pairs but seemed not to contribute greatly to genetic variations of the fungus. Based on nucleotide diversity fluctuations across the alignment of all mitochondrial genomes, molecular markers with the potential to be used for future typing studies were determined.

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

    PubMed

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

    2010-12-01

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

  13. Multidrug resistance as a dominant molecular marker in transformation of wine yeast.

    PubMed

    Kozovska, Z; Maraz, A; Magyar, I; Subik, J

    2001-12-14

    Pure wine yeast cultures are increasingly used in winemaking to perform controlled fermentations and produce wine of reproducible quality. For the genetic manipulation of natural wine yeast strains dominant selective markers are obviously useful. Here we demonstrate the successful use of the mutated PDR3 gene as a dominant molecular marker for the selection of transformants of prototrophic wine yeast Saccharomyces cerevisiae. The selected transformants displayed a multidrug resistance phenotype that was resistant to strobilurin derivatives and azoles used to control pathogenic fungi in agriculture and medicine, respectively. Random amplification of DNA sequences and electrophoretic karyotyping of the host and transformed strains after microvinification experiments resulted in the same gel electrophoresis patterns. The chemical and sensory analysis of experimental wines proved that the used transformants preserved all their useful winemaking properties indicating that the pdr3-9 allele does not deteriorate the technological properties of the transformed wine yeast strain.

  14. Novel molecular markers for the detection of methanogens and phylogenetic analyses of methanogenic communities

    PubMed Central

    Dziewit, Lukasz; Pyzik, Adam; Romaniuk, Krzysztof; Sobczak, Adam; Szczesny, Pawel; Lipinski, Leszek; Bartosik, Dariusz; Drewniak, Lukasz

    2015-01-01

    Methanogenic Archaea produce approximately one billion tons of methane annually, but their biology remains largely unknown. This is partially due to the large phylogenetic and phenotypic diversity of this group of organisms, which inhabit various anoxic environments including peatlands, freshwater sediments, landfills, anaerobic digesters and the intestinal tracts of ruminants. Research is also hampered by the inability to cultivate methanogenic Archaea. Therefore, biodiversity studies have relied on the use of 16S rRNA and mcrA [encoding the α subunit of the methyl coenzyme M (methyl-CoM) reductase] genes as molecular markers for the detection and phylogenetic analysis of methanogens. Here, we describe four novel molecular markers that should prove useful in the detailed analysis of methanogenic consortia, with a special focus on methylotrophic methanogens. We have developed and validated sets of degenerate PCR primers for the amplification of genes encoding key enzymes involved in methanogenesis: mcrB and mcrG (encoding β and γ subunits of the methyl-CoM reductase, involved in the conversion of methyl-CoM to methane), mtaB (encoding methanol-5-hydroxybenzimidazolylcobamide Co-methyltransferase, catalyzing the conversion of methanol to methyl-CoM) and mtbA (encoding methylated [methylamine-specific corrinoid protein]:coenzyme M methyltransferase, involved in the conversion of mono-, di- and trimethylamine into methyl-CoM). The sensitivity of these primers was verified by high-throughput sequencing of PCR products amplified from DNA isolated from microorganisms present in anaerobic digesters. The selectivity of the markers was analyzed using phylogenetic methods. Our results indicate that the selected markers and the PCR primer sets can be used as specific tools for in-depth diversity analyses of methanogenic consortia. PMID:26217325

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

    PubMed

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

    2008-09-01

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

  16. Additives

    NASA Technical Reports Server (NTRS)

    Smalheer, C. V.

    1973-01-01

    The chemistry of lubricant additives is discussed to show what the additives are chemically and what functions they perform in the lubrication of various kinds of equipment. Current theories regarding the mode of action of lubricant additives are presented. The additive groups discussed include the following: (1) detergents and dispersants, (2) corrosion inhibitors, (3) antioxidants, (4) viscosity index improvers, (5) pour point depressants, and (6) antifouling agents.

  17. Cerebrospinal fluid tau levels are a marker for molecular subtype in sporadic Creutzfeldt-Jakob disease.

    PubMed

    Karch, André; Hermann, Peter; Ponto, Claudia; Schmitz, Matthias; Arora, Amandeep; Zafar, Saima; Llorens, Franc; Müller-Heine, Annika; Zerr, Inga

    2015-05-01

    The molecular subtype of sporadic Creutzfeldt-Jakob disease (sCJD) is an important prognostic marker for patient survival. However, subtype determination is not possible during lifetime. Because the rate of disease progression is associated with the molecular subtype, this study aimed at investigating if total tau, a marker of neuronal death, allows premortem diagnosis of molecular subtype when codon 129 genotype is known. Two hundred ninety-six sCJD patients were tested for their cerebrospinal fluid total tau level at the time of diagnosis and were investigated for their sCJD subtype postmortem. There was a significant association between tau levels and the prion protein type in patients with codon 129 MM (p < 0.001), MV (p = 0.004), and VV (p = 0.001) genotype. Receiver operating characteristic analyses showed values of area under the curve of 0.76-0.80 for the different genotypes indicating a good diagnostic validity of the test. Total tau can be used as a diagnostic test for the assessment of prion protein type when codon 129 genotype is known. It provides valuable information for physicians and next of kin about the further course of disease.

  18. Extracellular Molecular Markers and Soma Size of Inhibitory Neurons: Evidence for Four Subtypes of GABAergic Cells in the Inferior Colliculus

    PubMed Central

    Beebe, Nichole L.; Young, Jesse W.; Mellott, Jeffrey G.

    2016-01-01

    Inhibition plays an important role in shaping responses to stimuli throughout the CNS, including in the inferior colliculus (IC), a major hub in both ascending and descending auditory pathways. Subdividing GABAergic cells has furthered the understanding of inhibition in many brain areas, most notably in the cerebral cortex. Here, we seek the same understanding of subcortical inhibitory cell types by combining staining for two types of extracellular markers—perineuronal nets (PNs) and perisomatic rings of terminals expressing vesicular glutamate transporter 2 (VGLUT2) —to subdivide IC GABAergic cells in adult guinea pigs. We found four distinct groups of GABAergic cells in the IC: (1) those with both a PN and a VGLUT2 ring; (2) those with only a PN; (3) those with only a VGLUT2 ring; and (4) those with neither marker. In addition, these four GABAergic subtypes differ in their soma size and distribution among IC subdivisions. Functionally, the presence or absence of VGLUT2 rings indicates differences in inputs, whereas the presence or absence of PNs indicates different potential for plasticity and temporal processing. We conclude that these markers distinguish four GABAergic subtypes that almost certainly serve different roles in the processing of auditory stimuli within the IC. SIGNIFICANCE STATEMENT GABAergic inhibition plays a critical role throughout the brain. Identification of subclasses of GABAergic cells (up to 15 in the cerebral cortex) has furthered the understanding of GABAergic roles in circuit modulation. Inhibition is also prominent in the inferior colliculus, a subcortical hub in auditory pathways. Here, we use two extracellular markers to identify four distinct groups of GABAergic cells. Perineuronal nets and perisomatic rings of glutamatergic boutons are present in many subcortical areas and often are associated with inhibitory cells, but they have rarely been used to identify inhibitory subtypes. Our results further the understanding of

  19. Molecular Markers Predict Distant Metastases After Adjuvant Chemoradiation for Rectal Cancer

    SciTech Connect

    Kim, Jun Won; Kim, Yong Bae; Choi, Jun Jeong; Koom, Woong Sub; Kim, Hoguen; Kim, Nam-Kyu; Ahn, Joong Bae; Lee, Ikjae; Cho, Jae Ho; Keum, Ki Chang

    2012-12-01

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

  20. Oral keratinocyte stem/progenitor cells: specific markers, molecular signaling pathways and potential uses.

    PubMed

    Calenic, Bogdan; Greabu, Maria; Caruntu, Constantin; Tanase, Cristiana; Battino, Maurizio

    2015-10-01

    Oral keratinocyte stem cells reside in the basal layers of the oral epithelium, representing a minor population of cells with a great potential to self-renew and proliferate over the course of their lifetime. As a result of the potential uses of oral keratinocyte stem cells in regenerative medicine and the key roles they play in tissue homeostasis, inflammatory conditions, wound healing and tumor initiation and progression, intense scientific efforts are currently being undertaken to identify, separate and reprogram these cells. Although currently there is no specific marker that can characterize and isolate oral keratinocyte stem cells, several suggestions have been made. Thus, different stem/progenitor-cell subpopulations have been categorized based on combinations of positive and/or negative membrane-surface markers, which include integrins, clusters of differentiation and cytokeratins. Important advances have also been made in understanding the molecular pathways that govern processes such as self-renewal, differentiation, proliferation, wound healing and programmed cell death. A thorough understanding of stem-cell biology and the molecular players that govern cellular fate is paramount in the quest for using stem-cell-derived therapies in the treatment of various oral pathologies. The current review focuses on recent advances in understanding the molecular signaling pathways coordinating the behavior of these cells and in identifying suitable markers used for their isolation and characterization. Special emphasis will also be placed on the roles played by oral keratinocyte stem and progenitor cells in normal and diseased oral tissues and on their potential uses in the fields of general medicine and dentistry.

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

    PubMed

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

    2015-07-01

    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.

  2. Isolation of female-specific AFLP markers and molecular identification of genetic sex in half-smooth tongue sole (Cynoglossus semilaevis).

    PubMed

    Chen, Song-Lin; Li, Jing; Deng, Si-Ping; Tian, Yong-Sheng; Wang, Qing-Yin; Zhuang, Zhi-Meng; Sha, Zhen-Xia; Xu, Jian-Yong

    2007-01-01

    The sex-specific molecular marker is a useful gene resource for studying sex- determining mechanisms and controlling fish sex. Artificially produced male and female half-smooth tongue sole (Cynoglossus semilaevis) were used to screen sex-specific amplified fragment length polymorphism (AFLPs) molecular markers. The phenotypic sex of 28 tongue soles was determined by histological sectioning of gonads. The AFLP analysis of 15 females and 13 males via 64 primer combinations produced a total of 4681 scorable bands, of which 42.11% and 43.39% of bands were polymorphic in females and males, respectively. Seven female-specific AFLP markers were identified and designated as CseF382, CseF575, CseF783, CseF464, CseF136, CseF618, and CseF305, respectively. One female-specific AFLP marker (CseF382) was amplified, recovered from the gels, cloned, and sequenced (accession no. DQ487760). This female-specific AFLP marker was converted into a single-locus polymerase-chain reaction (PCR) marker of a sequence-characterized amplified region (SCAR). A simple PCR method of using the specific primers was developed for identifying genetic sex of half-smooth tongue sole. PCR products demonstrated that the initial 15 females produced the female-specific band of about 350 bp, but the initial 13 male individuals failed to produce the band. We also investigated the applicability of the PCR primers in other tongue sole individuals. The same female-specific fragment of about 350 bp was found in the additional 59 female individuals, but not in the additional 58 male individuals. This AFLP-based molecular sexing technique may have great application potential in elucidation of sex determination mechanisms and sex control in half-smooth tongue sole.

  3. Appraisal of progenitor markers in the context of molecular classification of breast cancers.

    PubMed

    Haviv, Izhak

    2011-01-25

    Clinical management of breast cancer relies on case stratification, which increasingly employs molecular markers. The motivation behind delineating breast epithelial differentiation is to better target cancer cases through innate sensitivities bequeathed to the cancer from its normal progenitor state. A combination of histopathological and molecular classification of breast cancer cases suggests a role for progenitors in particular breast cancer cases. Although a remarkable fraction of the real tissue repertoire is maintained within a population of independent cell line cultures, some steps that are closer to the terminal differentiation state and that form a majority of primary human breast tissues are missing in the cell line cultures. This raises concerns about current breast cancer models.

  4. Population structure and genotypic variation of Crataegus pontica inferred by molecular markers.

    PubMed

    Rahmani, Mohammad-Shafie; Shabanian, Naghi; Khadivi-Khub, Abdollah; Woeste, Keith E; Badakhshan, Hedieh; Alikhani, Leila

    2015-11-01

    Information about the natural patterns of genetic variability and their evolutionary bases are of fundamental practical importance for sustainable forest management and conservation. In the present study, the genetic diversity of 164 individuals from fourteen natural populations of Crataegus pontica K.Koch was assessed for the first time using three genome-based molecular techniques; inter-retrotransposon amplified polymorphism (IRAP); inter-simple sequence repeats (ISSR) and start codon targeted (SCoT) polymorphism. IRAP, ISSR and SCoT analyses yielded 126, 254 and 199 scorable amplified bands, respectively, of which 90.48, 93.37 and 83.78% were polymorphic. ISSR revealed efficiency over IRAP and SCoT due to high effective multiplex ratio, marker index and resolving power. The dendrograms based on the markers used and combined data divided individuals into three major clusters. The correlation between the coefficient matrices for the IRAP, ISSR and SCoT data was significant. A higher level of genetic variation was observed within populations than among populations based on the markers used. The lower divergence levels depicted among the studied populations could be seen as evidence of gene flow. The promotion of gene exchange will be very beneficial to conserve and utilize the enormous genetic variability.

  5. Detection of Variation in Long-Term Micropropagated Mature Pistachio via DNA-Based Molecular Markers.

    PubMed

    Akdemir, Hülya; Suzerer, Veysel; Tilkat, Engin; Onay, Ahmet; Çiftçi, Yelda Ozden

    2016-12-01

    Determination of genetic stability of in vitro-grown plantlets is needed for safe and large-scale production of mature trees. In this study, genetic variation of long-term micropropagated mature pistachio developed through direct shoot bud regeneration using apical buds (protocol A) and in vitro-derived leaves (protocol B) was assessed via DNA-based molecular markers. Randomly amplified polymorphic DNA (RAPD), inter-simple sequence repeat (ISSR), and amplified fragment length polymorphism (AFLP) were employed, and the obtained PIC values from RAPD (0.226), ISSR (0.220), and AFLP (0.241) showed that micropropagation of pistachio for different periods of time resulted in "reasonable polymorphism" among donor plant and its 18 clones. Mantel's test showed a consistence polymorphism level between marker systems based on similarity matrices. In conclusion, this is the first study on occurrence of genetic variability in long-term micropropagated mature pistachio plantlets. The obtained results clearly indicated that different marker approaches used in this study are reliable for assessing tissue culture-induced variations in long-term cultured pistachio plantlets.

  6. Evolutionary redefinition of immunoglobulin light chain isotypes in tetrapods using molecular markers.

    PubMed

    Das, Sabyasachi; Nikolaidis, Nikolas; Klein, Jan; Nei, Masatoshi

    2008-10-28

    The phylogenetic relationships of Ig light chain (IGL) genes are difficult to resolve, because these genes are short and evolve relatively fast. Here, we classify the IGL sequences from 12 tetrapod species into three distinct groups (kappa, lambda, and sigma isotypes) using conserved amino acid residues, recombination signal sequences, and genomic organization of IGL genes as cladistic markers. From the distribution of the markers we conclude that the earliest extant tetrapods, the amphibians, possess three IGL isotypes: kappa, lambda, and sigma. Of these, two (kappa and lambda) are also found in reptiles and some mammals. The lambda isotype is found in all tetrapods tested to date, whereas the kappa isotype seems to have been lost at least in some birds and in the microbat. Conservation of the cladistic molecular markers suggests that they are associated with functional specialization of the three IGL isotypes. The genomic maps of IGL loci reveal multiple gene rearrangements that occurred in the evolution of tetrapod species. These rearrangements have resulted in interspecific variation of the genomic lengths of the IGL loci and the number and order of IGL constituent genes, but the overall organization of the IGL loci has not changed.

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

    PubMed

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

    2014-07-02

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

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

    NASA Astrophysics Data System (ADS)

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

    2011-01-01

    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 α-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 α-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 α-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.

  9. Expression of Molecular Markers in Primary Sites and Metastatic Lymph Nodes of Lung Cancer Patients

    PubMed Central

    Li, Jie; Zhang, Wen; Guo, Nannan; Yu, Jiangqi; Zhao, Yingnan; Li, Shaojun

    2017-01-01

    Background Recently, there is an increasing interest in developing specific treatments while managing lung cancer cases. We tested the expressions of six molecular markers in the primary tumor and the metastatic lymph nodes of lung cancer patients at a single institution in China. Material/Methods A total of 48 patients with lung cancer who were admitted to the Department of Cardiothoracic Surgery, the First Affiliated Hospital of General Hospital of the Chinese People’s Liberation Army, from September 2010 to February 2011 were retrospectively reviewed. Results One of the six biomarkers’ expressions, excision repair cross-complementation group 1 (ERCC-1), was found to be significantly different in primary tumors and metastatic sites in different cancer subtypes. Conclusions The onset and pathogenesis of small-cell lung carcinoma (SCLC) and non-small-cell lung carcinoma (NSCLC) are not completely understood, and the predictions of prognosis are not very reliable. The use of molecular markers to guide treatment of these cancers is currently in its initial stages. PMID:28130961

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

    PubMed

    Ismail, Roba M

    2013-01-01

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

  11. Screening white spot syndrome virus (WSSV)-resistant molecular markers from Fenneropenaeus chinensis

    NASA Astrophysics Data System (ADS)

    Wu, Yingying; Meng, Xianhong; Kong, Jie; Luan, Sheng; Luo, Kun; Wang, Qingyin; Zheng, Yongyun

    2017-02-01

    White spot syndrome virus (WSSV)-resistant molecular markers were screened from the selectively bred new variety `Huanghai No. 2' of Fenneropenaeus chinensis using unlabeled-probe high-resolution melting (HRM) technique. After the artificial infection with WSSV, the first 96 dead shrimps and the last 96 surviving shrimps were collected, representing WSSV-susceptible and -resistant populations, respectively. The genotypes at well-developed 39 single nucleotide polymorphisms (SNPs) loci were obtained. As revealed in the Chi-square test, 3 SNPs, genotype A/A of contig C364-89AT, genotype A/A of C2635-527CA and genotype C/T of contig C12355-592CT, were positively correlated with disease-resistance traits. Other 2 SNPs, genotype G/G of contig C283-145AG and genotype C/C of contig C12355-592CT, were negatively correlated. Moreover, analysis with BlastX program for disease-resistant SNPs indicated that 3 contigs, Contig283, Contig364 and Contig12355, matched to the functional genes of effector caspase of Penaeus monodon, peptide transporter family 1-like protein, and 40S ribosomal protein S2 of Perca flavescens with high sequence similarity. The results will be helpful to provide theoretical and technical supports for molecular marker-assisted selective breeding of F. chinensis.

  12. Expression of Molecular Differentiation Markers Does Not Correlate with Histological Differentiation Grade in Intrahepatic Cholangiocarcinoma

    PubMed Central

    Demarez, Céline; Hubert, Catherine; Sempoux, Christine; Lemaigre, Frédéric P.

    2016-01-01

    The differentiation status of tumor cells, defined by histomorphological criteria, is a prognostic factor for survival of patients affected with intrahepatic cholangiocarcinoma (ICC). To strengthen the value of morphological differentiation criteria, we wished to correlate histopathological differentiation grade with expression of molecular biliary differentiation markers and of microRNAs previously shown to be dysregulated in ICC. We analysed a series of tumors that were histologically classified as well, moderately or poorly differentiated, and investigated the expression of cytokeratin 7, 19 and 903 (CK7, CK19, CK903), SRY-related HMG box transcription factors 4 and 9 (SOX4, SOX9), osteopontin (OPN), Hepatocyte Nuclear Factor-1 beta (HNF1β), Yes-associated protein (YAP), Epithelial cell adhesion molecule (EPCAM), Mucin 1 (MUC1) and N-cadherin (NCAD) by qRT-PCR and immunostaining, and of miR-31, miR-135b, miR-132, miR-200c, miR-221 and miR-222. Unexpectedly, except for subcellular location of SOX9 and OPN, no correlation was found between the expression levels of these molecular markers and histopathological differentiation grade. Therefore, our data point toward necessary caution when investigating the evolution and prognosis of ICC on the basis of cell differentiation criteria. PMID:27280413

  13. Expression of Neuroendocrine Markers in Different Molecular Subtypes of Breast Carcinoma

    PubMed Central

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

    2014-01-01

    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

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

    PubMed Central

    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

    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

  15. Assessment of genetic diversity among faba bean genotypes using agro-morphological and molecular markers

    PubMed Central

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

    2015-01-01

    Forty faba bean (Vicia faba L.) genotypes were evaluated for their agro-morphological performance and molecular diversity under Central Region of Saudi Arabia conditions during 2010–11 and 2011–12 seasons. Field performance results showed that faba genotypes exhibited a significant amount of variation for their agro-morphological studied parameters. Giza40 recorded the tallest genotype (139.5 cm), highest number of seeds per plants (100.8), and the highest seed yield per plant (70.8 g). The best performing genotypes were Giza40, FLIP03-014FB, Gazira1 and Goff1. Genetic variability among genotypes was determined using Sequence Related Amplified Polymorphism (SRAP) and Amplified Fragment Length Polymorphism (AFLP) markers. A total of 183 amplified fragments (alleles) and 1758 polymorphic fragments (bands) in SRAP and 202 alleles and 716 bands in AFLP were obtained using six SRAP and four AFLP primer combinations respectively. Polymorphism information content (PIC) values for AFLP and SRAP markers were higher than 0.8, indicating the existence of a considerable amount of genetic diversity among faba tested genotypes. The UPGMA based clustering of faba genotypes was largely based on origin and/or genetic background. Result of cluster analysis based on SRAP showed weak and not significant correlation while, it was highly significant based on AFLP analysis with agro-morphological characters (r = 0.01, p > 0.54 and r = 0.26, p < 0.004 respectively). Combined SRAP and AFLP markers proved to be significantly useful for genetic diversity assessment at molecular level. They exhibited high discrimination power, and were able to distinguish the faba bean genotypes with high efficiency and accuracy levels. PMID:25972757

  16. At3g08030 transcript: a molecular marker of seed ageing

    PubMed Central

    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

    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

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

    PubMed Central

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

    2016-01-01

    The success of drought tolerance breeding programs can be enhanced through molecular assortment of germplasm. This study was designed to characterize molecular diversity within and between Lens species with different adaptations to drought stress conditions using SSR markers. Drought stress was applied at seedling stage to study the effects on morpho-physiological traits under controlled condition, where tolerant cultivars and wilds showed 12.8–27.6% and 9.5–23.2% reduction in seed yield per plant respectively. When juxtaposed to field conditions, the tolerant cultivars (PDL-1 and PDL-2) and wild (ILWL-314 and ILWL-436) accessions showed 10.5–26.5% and 7.5%–15.6% reduction in seed yield per plant, respectively under rain-fed conditions. The reductions in seed yield in the two tolerant cultivars and wilds under severe drought condition were 48–49% and 30.5–45.3% respectively. A set of 258 alleles were identified among 278 genotypes using 35 SSR markers. Genetic diversity and polymorphism information contents varied between 0.321–0.854 and 0.299–0.836, with mean value of 0.682 and 0.643, respectively. All the genotypes were clustered into 11 groups based on SSR markers. Tolerant genotypes were grouped in cluster 6 while sensitive ones were mainly grouped into cluster 7. Wild accessions were separated from cultivars on the basis of both population structure and cluster analysis. Cluster analysis has further grouped the wild accessions on the basis of species and sub-species into 5 clusters. Physiological and morphological characters under drought stress were significantly (P = 0.05) different among microsatellite clusters. These findings suggest that drought adaptation is variable among wild and cultivated genotypes. Also, genotypes from contrasting clusters can be selected for hybridization which could help in evolution of better segregants for improving drought tolerance in lentil. PMID:26808306

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

    PubMed

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

    2016-01-01

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

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

    PubMed

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

    2009-06-17

    Supported by the Office of International Affairs, National Cancer Institute (NCI), the "US-Japan Workshop on Immunological Biomarkers in Oncology" was held in March 2009. The workshop was related to a task force launched by the International Society for the Biological Therapy of Cancer (iSBTc) and the United States Food and Drug Administration (FDA) to identify strategies for biomarker discovery and validation in the field of biotherapy. The effort will culminate on October 28th 2009 in the "iSBTc-FDA-NCI Workshop on Prognostic and Predictive Immunologic Biomarkers in Cancer", which will be held in Washington DC in association with the Annual Meeting. The purposes of the US-Japan workshop were a) to discuss novel approaches to enhance the discovery of predictive and/or prognostic markers in cancer immunotherapy; b) to define the state of the science in biomarker discovery and validation. The participation of Japanese and US scientists provided the opportunity to identify shared or discordant themes across the distinct immune genetic background and the diverse prevalence of disease between the two Nations. Converging concepts were identified: enhanced knowledge of interferon-related pathways was found to be central to the understanding of immune-mediated tissue-specific destruction (TSD) of which tumor rejection is a representative facet. Although the expression of interferon-stimulated genes (ISGs) likely mediates the inflammatory process leading to tumor rejection, it is insufficient by itself and the associated mechanisms need to be identified. It is likely that adaptive immune responses play a broader role in tumor rejection than those strictly related to their antigen-specificity; likely, their primary role is to trigger an acute and tissue-specific inflammatory response at the tumor site that leads to rejection upon recruitment of additional innate and adaptive immune mechanisms. Other candidate systemic and/or tissue-specific biomarkers were recognized that

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

    PubMed Central

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

    2009-01-01

    Supported by the Office of International Affairs, National Cancer Institute (NCI), the "US-Japan Workshop on Immunological Biomarkers in Oncology" was held in March 2009. The workshop was related to a task force launched by the International Society for the Biological Therapy of Cancer (iSBTc) and the United States Food and Drug Administration (FDA) to identify strategies for biomarker discovery and validation in the field of biotherapy. The effort will culminate on October 28th 2009 in the "iSBTc-FDA-NCI Workshop on Prognostic and Predictive Immunologic Biomarkers in Cancer", which will be held in Washington DC in association with the Annual Meeting. The purposes of the US-Japan workshop were a) to discuss novel approaches to enhance the discovery of predictive and/or prognostic markers in cancer immunotherapy; b) to define the state of the science in biomarker discovery and validation. The participation of Japanese and US scientists provided the opportunity to identify shared or discordant themes across the distinct immune genetic background and the diverse prevalence of disease between the two Nations. Converging concepts were identified: enhanced knowledge of interferon-related pathways was found to be central to the understanding of immune-mediated tissue-specific destruction (TSD) of which tumor rejection is a representative facet. Although the expression of interferon-stimulated genes (ISGs) likely mediates the inflammatory process leading to tumor rejection, it is insufficient by itself and the associated mechanisms need to be identified. It is likely that adaptive immune responses play a broader role in tumor rejection than those strictly related to their antigen-specificity; likely, their primary role is to trigger an acute and tissue-specific inflammatory response at the tumor site that leads to rejection upon recruitment of additional innate and adaptive immune mechanisms. Other candidate systemic and/or tissue-specific biomarkers were recognized that

  1. Molecular Genetic Markers of Intra- and Interspecific Divergence within Starfish and Sea Urchins (Echinodermata).

    PubMed

    Petrov, N B; Vladychenskaya, I P; Drozdov, A L; Kedrova, O S

    2016-09-01

    A fragment of the mitochondrial COI gene from isolates of several echinoderm species was sequenced. The isolates were from three species of starfish from the Asteriidae family (Asterias amurensis and Aphelasterias japonica collected in the Sea of Japan and Asterias rubens collected in the White Sea) and from the sea urchin Echinocardium cordatum (family Loveniidae) collected in the Sea of Japan. Additionally, regions including internal transcribed spacers and 5.8S rRNA (ITS1 - 5.8S rDNA - ITS2) were sequenced for the three studied starfish species. Phylogenetic analysis of the obtained COI sequences together with earlier determined homologous COI sequences from Ast. forbesii, Ast. rubens, and Echinocardium laevigaster from the North Atlantic and E. cordatum from the Yellow and North Seas (GenBank) placed them into strictly conspecific clusters with high bootstrap support (99% in all cases). Only two exceptions - Ast. rubens DQ077915 sequence placed with the Ast. forbesii cluster and Aph. japonica DQ992560 sequence placed with the Ast. amurensis cluster - were likely results of species misidentification. The intraspecific polymorphism for the COI gene within the Asteriidae family varied within a range of 0.2-0.9% as estimated from the genetic distances. The corresponding intrageneric and intergeneric values were 10.4-12.1 and 21.8-29.8%, respectively. The interspecific divergence for the COI gene in the sea urchin of Echinocardium genus (family Loveniidae) was significantly higher (17.1-17.7%) than in the starfish, while intergeneric divergence (14.6-25.7%) was similar to that in asteroids. The interspecific genetic distances for the nuclear transcribed sequences (ITS1 - 5.8S rDNA - ITS2) within the Asteriidae family were lower (3.1-4.5%), and the intergeneric distances were significantly higher (32.8-35.0%), compared to the corresponding distances for the COI gene. These results suggest that the investigated molecular-genetic markers could be used for segregation

  2. Combustion inputs into a terrestrial archive over 265 years as evidenced by BPCA molecular markers

    NASA Astrophysics Data System (ADS)

    Hanke, Ulrich M.; Eglinton, Timothy I.; Wiedemeier, Daniel B.; Schmidt, Michael W. I.

    2015-04-01

    Pyrogenic organic matter (PyOM) such as char and soot is produced during the incomplete combustion of biomass and fossil fuel. It is composed of condensed aromatic structures and can resist degradation processes, maybe over long periods of time. Land-use changes, industrial activity and its transport by wind and water affect the fluxes of PyOM from the source to its sedimentary archive. Investigating environmental PyOM with the molecular marker benzene polycarboxylic acid (BPCA) method provides various information about quantity, quality (BPCA distribution pattern) and about its isotopic composition (13C and 14C). Assessing PyOM quality can indicate whether it is mostly combustion condensate (soot) or combustion residue (charcoal) and potentially allow source apportionment. Our study area is the Pettaquamscutt River catchment area (35 km2), Rhode Island, U.S.A. It is located down-wind of industrial areas recording deposition of long-distance atmospheric transport as well as local catchment inputs, both from natural and anthropogenic sources. We investigated 50 samples of a sediment record over a time span of 265 years (1733-1998 AD). Previous investigations provided information on the age of deposition, the content of polycyclic aromatic hydrocarbons (PAH) as well as of the radiocarbon contents of total organic carbon (TOC) and PAH (Lima, 2004). We used the BPCA molecular marker method to quantify and characterize PyOM in the same record. First results show that quantity and quality of PyOM change over 265 years. Our investigation aims at understanding how different sources of PyOM are reflected in terrestrial archives by comparing the results of BPCA with radiocarbon-dated TOC and PAH records. Among other aspects, the PAH record reflects the Great Depression and the 1970s oil embargo in North America. We interpret the BPCA distribution patterns regarding the simultaneous shift of dominant fuels including wood, coal, petroleum and gas. Future work will include

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

    PubMed Central

    2011-01-01

    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

  4. Detection and source identification of faecal pollution in non-sewered catchment by means of host-specific molecular markers.

    PubMed

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

    2008-01-01

    Multiple host-specific molecular markers were used to detect the sources of faecal pollution in a mixed land use non-sewered catchment in Southeast Queensland, Australia. These markers included human-specific Bacteroides (HF183 and HF134), cattle-specific Bacteroides (CF128), dog-specific Bacteroides (BacCan) and human-specific enterococci surface protein (esp) markers. The sensitivity and specificity of these markers were determined by testing 197 faecal samples from 13 host groups. The overall sensitivity and specificity of these markers was high (sensitivity>/=85% and specificity>/=93%) indicating their suitability for detecting the sources of faecal pollution. Of the 16 samples collected from the study area, 14 (87%) were positive for at least one of the molecular marker tested. Amongst all the markers, cattle-specific CF128 was more prevalent than others, followed by human-specific HF183 which was consistently detected in samples collected from sites within close proximity to urban development. Significant correlations were found between E. coli and enterococci concentrations with the positive/negative results of human-specific Bacteroides HF183 (p<0.001, p<0.0001) and HF134 (p<0.001, p<0.004) markers. No correlations were found between faecal indicators (E. coli or enterococci) with the CF128 or BacCan markers. A significant correlation was also found between enterococci concentrations and the presence/absence of the esp marker (p<0.02). Based on the results, it appears that the host-specific markers such as HF183 and esp are a sensitive measure of sources of human faecal pollution in surface waters in Southeast Queensland, Australia.

  5. Isolation of Ty1-copia retrotransposon in myrtle genome and development of S-SAP molecular marker.

    PubMed

    Woodrow, Pasqualina; Pontecorvo, Giovanni; Ciarmiello, Loredana F

    2012-04-01

    Long terminal repeat (LTR)-retrotransposons are mobile genetic elements that are ubiquitous in plants and constitute a major portion of their nuclear genomes. LTR- retrotransposons possess unique properties that make them appropriate for investigating relationships between populations, varieties and closely related species. Myrtus communis L. is an evergreen shrub growing spontaneously throughout the Mediterranean area. Accessions show significant variations for agriculturally important traits, so the development of specific molecular markers for conservation and characterization of myrtle germplasm is desirable to conserve biodiversity. In this study, we isolated the first retrotransposon Ty1-copia-like element (Tmc1) in Myrtus communis L. genome and used this as a molecular marker. We successfully employed the S-SAP marker system to specifically characterize four myrtle accessions belonging to different areas in the province of Caserta (Italy). The high level of polymorphism detected in isolated LTRs, make Tmc1 a good molecular marker for this species. Our findings confirm that retrotransposon-based molecular markers are particularly valuable tools for plant molecular characterization studies.

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

    PubMed Central

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

    2014-01-01

    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

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

    PubMed

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

    2009-02-01

    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.

  8. A slippery molecular assembly allows water as a self-erasable security marker

    PubMed Central

    Thirumalai, Rajasekaran; Mukhopadhyay, Rahul Dev; Praveen, Vakayil K.; Ajayaghosh, Ayyappanpillai

    2015-01-01

    Protection of currency and valuable documents from counterfeit continues to be a challenge. While there are many embedded security features available for document safety, they are not immune to forgery. Fluorescence is a sensitive property, which responds to external stimuli such as solvent polarity, temperature or mechanical stress, however practical use in security applications is hampered due to several reasons. Therefore, a simple and specific stimuli responsive security feature that is difficult to duplicate is of great demand. Herein we report the design of a fluorescent molecular assembly on which water behaves as a self-erasable security marker for checking the authenticity of documents at point of care. The underlying principle involves the disciplined self-assembly of a tailor-made fluorescent molecule, which initially form a weak blue fluorescence (λem = 425 nm, Φf = 0.13) and changes to cyan emission (λem = 488 nm,Φf = 0.18) in contact with water due to a reversible molecular slipping motion. This simple chemical tool, based on the principles of molecular self-assembly and fluorescence modulation, allows creation of security labels and optically masked barcodes for multiple documents authentication. PMID:25940779

  9. A slippery molecular assembly allows water as a self-erasable security marker.

    PubMed

    Thirumalai, Rajasekaran; Mukhopadhyay, Rahul Dev; Praveen, Vakayil K; Ajayaghosh, Ayyappanpillai

    2015-05-05

    Protection of currency and valuable documents from counterfeit continues to be a challenge. While there are many embedded security features available for document safety, they are not immune to forgery. Fluorescence is a sensitive property, which responds to external stimuli such as solvent polarity, temperature or mechanical stress, however practical use in security applications is hampered due to several reasons. Therefore, a simple and specific stimuli responsive security feature that is difficult to duplicate is of great demand. Herein we report the design of a fluorescent molecular assembly on which water behaves as a self-erasable security marker for checking the authenticity of documents at point of care. The underlying principle involves the disciplined self-assembly of a tailor-made fluorescent molecule, which initially form a weak blue fluorescence (λem = 425 nm, Φf = 0.13) and changes to cyan emission (λem = 488 nm,Φf = 0.18) in contact with water due to a reversible molecular slipping motion. This simple chemical tool, based on the principles of molecular self-assembly and fluorescence modulation, allows creation of security labels and optically masked barcodes for multiple documents authentication.

  10. Root trait diversity, molecular marker diversity, and trait-marker associations in a core collection of Lupinus angustifolius

    PubMed Central

    Chen, Yinglong; Shan, Fucheng; Nelson, Matthew N; Siddique, Kadambot HM; Rengel, Zed

    2016-01-01

    Narrow-leafed lupin (Lupinus angustifolius L.) is the predominant grain legume crop in southern Australia, contributing half of the total grain legume production of Australia. Its yield in Australia is hampered by a range of subsoil constraints. The adaptation of lupin genotypes to subsoil constraints may be improved by selecting for optimal root traits from new and exotic germplasm sources. We assessed root trait diversity and genetic diversity of a core collection of narrow-leafed lupin (111 accessions) using 191 Diversity Arrays Technology (DArT) markers. The genetic relationship among accessions was determined using the admixture model in STRUCTURE. Thirty-eight root-associated traits were characterized, with 21 having coefficient of variation values >0.5. Principal coordinate analysis and cluster analysis of the DArT markers revealed broad diversity among the accessions. An ad hoc statistics calculation resulted in 10 distinct populations with significant differences among and within them (P < 0.001). The mixed linear model test in TASSEL showed a significant association between all root traits and some DArT markers, with the numbers of markers associated with an individual trait ranging from 2 to 13. The percentage of phenotypic variation explained by any one marker ranged from 6.4 to 21.8%, with 15 associations explaining >10% of phenotypic variation. The genetic variation values ranged from 0 to 7994, with 23 associations having values >240. Root traits such as deeper roots and lateral root proliferation at depth would be useful for this species for improved adaptation to drier soil conditions. This study offers opportunities for discovering useful root traits that can be used to increase the yield of Australian cultivars across variable environmental conditions. PMID:27049020

  11. Analysis of molecular markers as predictive factors of lymph node involvement in breast carcinoma.

    PubMed

    Paula, Luciana Marques; De Moraes, Luis Henrique Ferreira; Do Canto, Abaeté Leite; Dos Santos, Laurita; Martin, Airton Abrahão; Rogatto, Silvia Regina; De Azevedo Canevari, Renata

    2017-01-01

    Nodal status is the most significant independent prognostic factor in breast cancer. Identification of molecular markers would allow stratification of patients who require surgical assessment of lymph nodes from the large numbers of patients for whom this surgical procedure is unnecessary, thus leading to a more accurate prognosis. However, up to now, the reported studies are preliminary and controversial, and although hundreds of markers have been assessed, few of them have been used in clinical practice for treatment or prognosis in breast cancer. The purpose of the present study was to determine whether protein phosphatase Mg2+/Mn2+ dependent 1D, β-1,3-N-acetylglucosaminyltransferase, neural precursor cell expressed, developmentally down-regulated 9, prohibitin, phosphoinositide-3-kinase regulatory subunit 5 (PIK3R5), phosphatidylinositol-5-phosphate 4-kinase type IIα, TRF1-interacting ankyrin-related ADP-ribose polymerase 2, BCL2 associated agonist of cell death, G2 and S-phase expressed 1 and PAX interacting protein 1 genes, described as prognostic markers in breast cancer in a previous microarray study, are also predictors of lymph node involvement in breast carcinoma Reverse transcription-quantitative polymerase chain reaction analysis was performed on primary breast tumor tissues from women with negative lymph node involvement (n=27) compared with primary tumor tissues from women with positive lymph node involvement (n=23), and was also performed on primary tumors and paired lymph node metastases (n=11). For all genes analyzed, only the PIK3R5 gene exhibited differential expression in samples of primary tumors with positive lymph node involvement compared with primary tumors with negative lymph node involvement (P=0.0347). These results demonstrate that the PIK3R5 gene may be considered predictive of lymph node involvement in breast carcinoma. Although the other genes evaluated in the present study have been previously characterized to be involved with

  12. Molecular markers as a method to evaluate the movement of Hypothenemus hampei (Ferrari)

    PubMed Central

    Gil, Zulma Nancy; Benavides, Pablo; Souza, Og De; Acevedo, Flor Edith; Lima, Eraldo

    2015-01-01

    The objective of this research was to develop a methodology to describe the movement of the coffee berry borer Hypothenemus hampei (Coleoptera: Curculionidae) in the field through: (i) the evaluation of allele variation of a microsatellite marker on polymorphic Colombian H. hampei populations; (ii) the invention of a device for releasing H. hampei adults; (iii) the standardization of a release-recapture technique for H. hampei populations; (iv) the estimation of the flight distance of the insect; and (v) the calculation of a mathematical expression that describes the movement of H. hampei in space over time. The results indicated that: (i) the microsatellite molecular marker HHK.1.6 was exclusively present in a population from Guapotá-Santander, was dominant and allows the evaluation of H. hampei movement for several generations; (ii) a device that released 88.8% of H. hampei adults in 2 s was designed; (iii) this device was used as H. hampei populations containing HHK.1.6 marker release strategy, and coffee seeds as recapture strategy; (iv) it was estimated that H. hampei adults flew as far as 65 m, however, 90% were recovered in a radius of <40 m. Finally, (v) the mathematical expression that described the movement of H. hampei in space over time was Y^=αβXi, being Y^ the average number of borer beetles recaptured per tree, and x the distance in meters. This method will allow to determine the movement of H. hampei from different environmental and ecological scenarios. PMID:26078300

  13. Molecular markers as a method to evaluate the movement of Hypothenemus hampei (Ferrari).

    PubMed

    Gil, Zulma Nancy; Benavides, Pablo; De Souza, Og; Acevedo, Flor Edith; Lima, Eraldo

    2015-01-01

    The objective of this research was to develop a methodology to describe the movement of the coffee berry borer Hypothenemus hampei (Coleoptera: Curculionidae) in the field through: (i) the evaluation of allele variation of a microsatellite marker on polymorphic Colombian H. hampei populations; (ii) the invention of a device for releasing H. hampei adults; (iii) the standardization of a release-recapture technique for H. hampei populations; (iv) the estimation of the flight distance of the insect; and (v) the calculation of a mathematical expression that describes the movement of H. hampei in space over time. The results indicated that: (i) the microsatellite molecular marker HHK.1.6 was exclusively present in a population from Guapotá-Santander, was dominant and allows the evaluation of H. hampei movement for several generations; (ii) a device that released 88.8% of H. hampei adults in 2 s was designed; (iii) this device was used as H. hampei populations containing HHK.1.6 marker release strategy, and coffee seeds as recapture strategy; (iv) it was estimated that H. hampei adults flew as far as 65 m, however, 90% were recovered in a radius of <40 m. Finally, (v) the mathematical expression that described the movement of H. hampei in space over time was [Formula: see text], being [Formula: see text] the average number of borer beetles recaptured per tree, and x the distance in meters. This method will allow to determine the movement of H. hampei from different environmental and ecological scenarios.

  14. Analysis of molecular markers as predictive factors of lymph node involvement in breast carcinoma

    PubMed Central

    Paula, Luciana Marques; De Moraes, Luis Henrique Ferreira; Do Canto, Abaeté Leite; Dos Santos, Laurita; Martin, Airton Abrahão; Rogatto, Silvia Regina; De Azevedo Canevari, Renata

    2017-01-01

    Nodal status is the most significant independent prognostic factor in breast cancer. Identification of molecular markers would allow stratification of patients who require surgical assessment of lymph nodes from the large numbers of patients for whom this surgical procedure is unnecessary, thus leading to a more accurate prognosis. However, up to now, the reported studies are preliminary and controversial, and although hundreds of markers have been assessed, few of them have been used in clinical practice for treatment or prognosis in breast cancer. The purpose of the present study was to determine whether protein phosphatase Mg2+/Mn2+ dependent 1D, β-1,3-N-acetylglucosaminyltransferase, neural precursor cell expressed, developmentally down-regulated 9, prohibitin, phosphoinositide-3-kinase regulatory subunit 5 (PIK3R5), phosphatidylinositol-5-phosphate 4-kinase type IIα, TRF1-interacting ankyrin-related ADP-ribose polymerase 2, BCL2 associated agonist of cell death, G2 and S-phase expressed 1 and PAX interacting protein 1 genes, described as prognostic markers in breast cancer in a previous microarray study, are also predictors of lymph node involvement in breast carcinoma Reverse transcription-quantitative polymerase chain reaction analysis was performed on primary breast tumor tissues from women with negative lymph node involvement (n=27) compared with primary tumor tissues from women with positive lymph node involvement (n=23), and was also performed on primary tumors and paired lymph node metastases (n=11). For all genes analyzed, only the PIK3R5 gene exhibited differential expression in samples of primary tumors with positive lymph node involvement compared with primary tumors with negative lymph node involvement (P=0.0347). These results demonstrate that the PIK3R5 gene may be considered predictive of lymph node involvement in breast carcinoma. Although the other genes evaluated in the present study have been previously characterized to be involved with

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

    PubMed

    Fauré, S; Noyer, J L; Horry, J P; Bakry, F; Lanaud, C; Gońzalez de León, D

    1993-12-01

    A partial molecular linkage map of the Musa acuminata diploid genome is presented. This map is based on 58 RFLP, four isozyme and 28 RAPD markers segregating in an F2 population of 92 individuals. A total of 90 loci was detected, 77 of which were placed on 15 linkage groups while 13 segregated independently. Segregation distortions were shown by 36% of all loci, mostly favoring the male parent. Chromosome structural rearrangements were believed to be one of the main causes of these distortions. The use of genetic linkage data to further the genetic and evolutionary knowledge of the genus Musa, as well as to help improve the design of breeding strategies, is discussed.

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

    SciTech Connect

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

    1991-12-15

    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.

  17. 2007 EORTC-NCI-ASCO annual meeting: molecular markers in cancer.

    PubMed

    Lukan, C

    2008-01-01

    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.

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

    PubMed

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

    2011-09-01

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

  19. Molecular Characterization of Cyclamen Species Collected from Different Parts of Turkey by RAPD and SRAP Markers.

    PubMed

    Simsek, Ozhan; Curuk, Pembe; Aslan, Fatma; Bayramoglu, Melda; Izgu, Tolga; da Silva, Jaime A Teixeira; Kacar, Yildiz Aka; Mendi, Yesim Yalcin

    2017-02-01

    The genus Cyclamen (family Myrsinaceae) contains about 20 species, most of which occur in the Mediterranean region. Turkey has critically important Cyclamen genetic resources. Molecular characterization of plant materials collected from different regions of Turkey in which Cyclamen species grow naturally, namely Adana, Antalya, Aydın, Muğla, İzmir, Denizli, Kahramanmaraş, Osmaniye, Eskişehir, Trabzon, and Rize provinces, was performed using RAPD and SRAP markers. DNA was successfully amplified by 30 RAPD primers and 14 SRAP primer pairs. Among the 470 bands generated by the RAPD primers, 467 were polymorphic. The number of bands detected by a single primer set ranged from 11 to 22 (average of 15.6). The percentage polymorphism was 99.3 % based on the RAPD data. In the SRAP analysis, a total of 216 bands were generated, showing 100 % polymorphism. The number of bands detected by a single primer set ranged from 9 to 22 (average of 15.4). All data were scored and UPGMA dendrograms were constructed with similar results in both marker systems, i.e., different species from nine provinces of Turkey were separated from each other in the dendrograms with the same species being clustered together.

  20. Identifying molecular markers for the sensitive detection of residual atypical teratoid rhabdoid tumor cells.

    PubMed

    Vu-Han, Tu-Lan; Frühwald, Michael C; Hasselblatt, Martin; Kerl, Kornelius; Nagel, Inga; Obser, Tobias; Oyen, Florian; Siebert, Reiner; Schneppenheim, Reinhard

    2014-09-01

    Atypical teratoid rhabdoid tumor (AT/RT), a rare and highly malignant tumor entity of the central nervous system that presents in early childhood, has a poor prognosis. AT/RTs are characterized by biallelic inactivating mutations of the gene SMARCB1 in 98% of patients; these mutations may serve as molecular markers for residual tumor cell detection in liquid biopsies. We developed a marker-specific method to detect residual AT/RT cells. Seven of 150 patient samples were selected, each with a histological and genetically ascertained diagnosis of AT/RT. Tumor tissue was either formalin fixed or fresh frozen. DNA was extracted from the patients' peripheral blood leukocytes (PBL) and cerebrospinal fluid (CSF). Multiplex ligation-dependent probe amplification, DNA sequencing, and fluorescence in situ hybridization were used to characterize the tumors' mutations. Residual tumor cell detection used mutation-specific primers and real-time PCR. The detection limit for the residual tumor cell search was 1-18%, depending on the quality of the template provided. The residual tumor cell search in PBL and CSF was negative for all seven patients. The SMARCB1 region of chromosome 22 is prone to DNA double-strand breaks. The individual breakpoints and breakpoint-specific PCR offer the option to detect minimal residual tumor cells in CSF or blood. Even if we did not detect minimal residual tumor cells in the investigated material, proof of principle for this method was confirmed.

  1. Hypothermic machine preservation reduces molecular markers of ischemia/reperfusion injury in human liver transplantation.

    PubMed

    Henry, S D; Nachber, E; Tulipan, J; Stone, J; Bae, C; Reznik, L; Kato, T; Samstein, B; Emond, J C; Guarrera, J V

    2012-09-01

    Hypothermic machine perfusion (HMP) is in its infancy in clinical liver transplantation. Potential benefits include diminished preservation injury (PI) and improved graft function. Molecular data to date has been limited to extrapolation of animal studies. We analyzed liver tissue and serum collected during our Phase 1 trial of liver HMP. Grafts preserved with HMP were compared to static cold stored (SCS) transplant controls. Reverse transcription polymerase chain reaction (RT-PCR), immunohistochemistry and transmission electron microscopy (TEM) were performed on liver biopsies. Expression of inflammatory cytokines, adhesion molecules and chemokines, oxidation markers, apoptosis and acute phase proteins and the levels of CD68 positive macrophages in tissue sections were evaluated. RT-PCR of reperfusion biopsy samples in the SCS group showed high expression of inflammatory cytokines, adhesion molecules and chemokines, oxidative markers and acute phase proteins. This upregulation was significantly attenuated in livers that were preserved by HMP. Immunofluorescence showed larger numbers of CD68 positive macrophages in the SCS group when compared to the HMP group. TEM samples also revealed ultrastructural damage in the SCS group that was not seen in the HMP group. HMP significantly reduced proinflammatory cytokine expression, relieving the downstream activation of adhesion molecules and migration of leukocytes, including neutrophils and macrophages when compared to SCS controls.

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

    PubMed

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

    2012-03-15

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

  3. Comparison of the utility of barley retrotransposon families for genetic analysis by molecular marker techniques.

    PubMed

    Leigh, F; Kalendar, R; Lea, V; Lee, D; Donini, P; Schulman, A H

    2003-07-01

    The Sequence-Specific Amplification Polymorphism (S-SAP) method, and the related molecular marker techniques IRAP (inter-retrotransposon amplified polymorphism) and REMAP (retrotransposon-microsatellite amplified polymorphism), are based on retrotransposon activity, and are increasingly widely used. However, there have been no systematic analyses of the parameters of these methods or of the utility of different retrotransposon families in producing polymorphic, scorable fingerprints. We have generated S-SAP, IRAP, and REMAP data for three barley (Hordeum vulgare L.) varieties using primers based on sequences from six retrotransposon families (BARE-1, BAGY-1, BAGY-2, Sabrina, Nikita and Sukkula). The effect of the number of selective bases on the S-SAP profiles has been examined and the profiles obtained with eight MseI+3 selective primers compared for all the elements. Polymorphisms detected in the insertion pattern of all the families show that each can be used for S-SAP. The uniqueness of each transposition event and differences in the historic activity of each family suggest that the use of multiple retrotransposon families for genetic analysis will find applications in mapping, fingerprinting, and marker-assisted selection and evolutionary studies, not only in barley and other Hordeum species and related taxa, but also more generally.

  4. Three Molecular Markers Show No Evidence of Population Genetic Structure in the Gouldian Finch (Erythrura gouldiae)

    PubMed Central

    West, Andrea J.; Cardilini, Adam P. A.; Clark, Jennalee A.; Maute, Kimberley L.; Legge, Sarah; Brazill-Boast, James; Griffith, Simon C.; Rollins, Lee A.

    2016-01-01

    Assessment of genetic diversity and connectivity between regions can inform conservation managers about risk of inbreeding, potential for adaptation and where population boundaries lie. The Gouldian finch (Erythrura gouldiae) is a threatened species in northern Australia, occupying the savannah woodlands of the biogeographically complex monsoon tropics. We present the most comprehensive population genetic analysis of diversity and structure the Gouldian finch using 16 microsatellite markers, mitochondrial control region and 3,389 SNPs from genotyping-by-sequencing. Mitochondrial diversity is compared across three related, co-distributed finches with different conservation threat-statuses. There was no evidence of genetic differentiation across the western part of the range in any of the molecular markers, and haplotype diversity but not richness was lower than a common co-distributed species. Individuals within the panmictic population in the west may be highly dispersive within this wide area, and we urge caution when interpreting anecdotal observations of changes to the distribution and/or flock sizes of Gouldian finch populations as evidence of overall changes to the population size of this species. PMID:27936082

  5. Direct determination of the chromosomal location of bunching onion and bulb onion markers using bunching onion-shallot monosomic additions and allotriploid-bunching onion single alien deletions.

    PubMed

    Tsukazaki, Hikaru; Yamashita, Ken-ichiro; Yaguchi, Shigenori; Yamashita, Koichiro; Hagihara, Takuya; Shigyo, Masayoshi; Kojima, Akio; Wako, Tadayuki

    2011-02-01

    To determine the chromosomal location of bunching onion (Allium fistulosum L.) simple sequence repeats (SSRs) and bulb onion (A. cepa L.) expressed sequence tags (ESTs), we used a complete set of bunching onion-shallot monosomic addition lines and allotriploid bunching onion single alien deletion lines as testers. Of a total of 2,159 markers (1,198 bunching onion SSRs, 324 bulb onion EST-SSRs and 637 bulb onion EST-derived non-SSRs), chromosomal locations were identified for 406 markers in A. fistulosum and/or A. cepa. Most of the bunching onion SSRs with identified chromosomal locations showed polymorphism in bunching onion (89.5%) as well as bulb onion lines (66.1%). Using these markers, we constructed a bunching onion linkage map (1,261 cM), which consisted of 16 linkage groups with 228 markers, 106 of which were newly located. All linkage groups of this map were assigned to the eight basal Allium chromosomes. In this study, we assigned 513 markers to the eight chromosomes of A. fistulosum and A. cepa. Together with 254 markers previously located on a separate bunching onion map, we have identified chromosomal locations for 766 markers in total. These chromosome-specific markers will be useful for the intensive mapping of desirable genes or QTLs for agricultural traits, and to obtain DNA markers linked to these.

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

    PubMed

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

    2004-09-01

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

  7. Molecular Markers in Patients with Chronic Wounds to Guide Surgical Debridement

    PubMed Central

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

    2007-01-01

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

  8. A better surgical resectability of WHO grade II gliomas is independent of favorable molecular markers.

    PubMed

    Cordier, Dominik; Gozé, Catherine; Schädelin, Sabine; Rigau, Valérie; Mariani, Luigi; Duffau, Hugues

    2015-01-01

    A higher extent of resection (EOR) in WHO grade II gliomas (GIIG) is correlated with longer survival. However, the molecular markers also feature prognostic relevance. Here, we examined whether maximal EOR was related to the genetic profile. We retrospectively investigated the predictive value of 1p19q, IDH1, 53 expression and Ki67 index for the EOR in 200 consecutive GIIGs (2007-2013). Data were modeled in a linear model. The analysis was performed with two statistical methods (arcsin-sqrt and Beta-regression model with logit link). There was no deletion 1p19q in 118 cases, codeletion 1p19q (57 cases), single deletion 1p (4 cases) or19q (16 cases). 155 patients had a mutation of IDH1. p53 was graded in 4 degrees (0:92 cases, 1:52 cases, 2:31 cases, 3:8 cases). Mean Ki67 index was 5.2 % (range 1-20 %). Mean preoperative tumor volume was 60.8 cm(3) (range 3.3-250 cm(3)) and mean EOR was 0.917 (range 0.574-1). The statistical analysis was significant for a lower EOR in patients with codeletion 1p19q (OR 0.738, p = 0.0463) and with a single deletion 19q (OR 0.641, p = 0.0168). There was no significant correlation between IDH1 or p53 and the EOR. Higher Ki67 was marginally associated with higher EOR (p = 0.0603). The study demonstrates in a large cohort of GIIG that a higher EOR is not attributable to favorable genetic markers. This original result supports maximal surgical resection as an important therapeutic factor per se to optimize prognosis, independently of the molecular pattern.

  9. The use of genetic markers in the molecular epidemiology of histoplasmosis: a systematic review.

    PubMed

    Damasceno, L S; Leitão, T M J S; Taylor, M L; Muniz, M M; Zancopé-Oliveira, R M

    2016-01-01

    Histoplasmosis is a systemic mycosis caused by Histoplasma capsulatum, a dimorphic fungal pathogen that can infect both humans and animals. This disease has worldwide distribution and affects mainly immunocompromised individuals. In the environment, H. capsulatum grows as mold but undergoes a morphologic transition to the yeast morphotype under special conditions. Molecular techniques are important tools to conduct epidemiologic investigations for fungal detection, identification of infection sources, and determination of different fungal genotypes associated to a particular disease symptom. In this study, we performed a systematic review in the PubMed database to improve the understanding about the molecular epidemiology of histoplasmosis. This search was restricted to English and Spanish articles. We included a combination of specific keywords: molecular typing [OR] genetic diversity [OR] polymorphism [AND] H. capsulatum; molecular epidemiology [AND] histoplasmosis; and molecular epidemiology [AND] Histoplasma. In addition, we used the specific terms: histoplasmosis [AND] outbreaks. Non-English or non-Spanish articles, dead links, and duplicate results were excluded from the review. The results reached show that the main methods used for molecular typing of H. capsulatum were: restriction fragment length polymorphism, random amplified polymorphic DNA, microsatellites polymorphism, sequencing of internal transcribed spacers region, and multilocus sequence typing. Different genetic profiles were identified among H. capsulatum isolates, which can be grouped according to their source, geographical origin, and clinical manifestations.

  10. Addition of four-hundred fifty-five microsatellite marker loci to the high density Gossypium hirsutum TM-1 x G. barbadense 3-79 genetic map

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A high density genetic linkage map plays important roles in understanding genome structure of tetraploid cotton, dissecting economically important traits, identifying molecular markers associated with a trait, and cloning a gene of interest through map-based cloning strategy. Four hundred fifty f...

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

    PubMed

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

    2006-01-01

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

  12. MicroRNA-155 is a potential molecular marker of natural killer/T-cell lymphoma

    PubMed Central

    Huang, Ruixia; Li, Lifeng; Wang, Xinhua; Li, Ling; Fu, Xiaorui; Sun, Zhenchang; Li, Zhaoming; Chen, Qingjiang; Zhang, Mingzhi

    2016-01-01

    Natural killer/T-cell lymphoma (NKTCL) is characterized by its highly aggressive nature and rapid progression. MicroRNAs (miRNAs) play key roles in the development of NKTCL. We utilized next-generation Solexa high-throughput sequencing to compare miRNA expression in the SNK-6 and YTS NKTCL cell lines with expression in normal NK cells. We found that 195 miRNAs were upregulated in the SNK-6 cells and 286 miRNAs were upregulated in the YTS cells. Based on those results, we selected six miRNAs, including miRNA-155, and confirmed their expression using real-time polymerase chain reaction. Expression of miRNA-155 was higher in SNK-6 and YKS cells than in normal NK cells. We next determined the levels of miRNA-155 in the serum of healthy individuals and NKTCL patients, and correlated its expression with clinical parameters and inflammatory factors detected using enzyme-linked immunoabsorbent assays. Levels of miRNA-155 were higher in NKTCL patients’ serum than in serum from healthy individuals. miRNA-155 expression was higher in patients with stable or progressive disease (SD+PD) than in those with partial or complete remission (PR+CR). While further studies are needed to clarify the underlying molecular mechanisms, it appears miRNA-155 may be a molecular marker of NKTCL. PMID:27462776

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

    PubMed

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

    2007-01-01

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

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

    PubMed

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

    2012-09-27

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

  15. Molecular cytogenetic identification of a wheat-rye 1R addition line with multiple spikelets and resistance to powdery mildew.

    PubMed

    Yang, Wujuan; Wang, Changyou; Chen, Chunhuan; Wang, Yajuan; Zhang, Hong; Liu, Xinlun; Ji, Wanquan

    2016-04-01

    Alien addition lines are important for transferring useful genes from alien species into common wheat. Rye is an important and valuable gene resource for improving wheat disease resistance, yield, and environment adaptation. A new wheat-rye addition line, N9436B, was developed from the progeny of the cross of common wheat (Triticum aestivum L., 2n = 6x = 42, AABBDD) cultivar Shaanmai 611 and rye (Secale cereal L., 2n = 2x = 14, RR) accession Austrian rye. We characterized this new line by cytology, genomic in situ hybridization (GISH), fluorescence in situ hybridization (FISH), molecular markers, and disease resistance screening. N9436B was stable in morphology and cytology, with a chromosome composition of 2n = 42 + 2t = 22II. GISH investigations showed that this line contained two rye chromosomes. GISH, FISH, and molecular maker identification suggested that the introduced R chromosome and the missing wheat chromosome arms were 1R chromosome and 2DL chromosome arm, respectively. N9436B exhibited 30-37 spikelets per spike and a high level of resistance to powdery mildew (Blumeria graminis f. sp. tritici, Bgt) isolate E09 at the seedling stage. N9436B was cytologically stable, had the trait of multiple spikelets, and was resistant to powdery mildew; this line should thus be useful in wheat improvement.

  16. Searching for non-genetic molecular and imaging PTSD risk and resilience markers: Systematic review of literature and design of the German Armed Forces PTSD biomarker study.

    PubMed

    Schmidt, Ulrike; Willmund, Gerd-Dieter; Holsboer, Florian; Wotjak, Carsten T; Gallinat, Jürgen; Kowalski, Jens T; Zimmermann, Peter

    2015-01-01

    Biomarkers allowing the identification of individuals with an above average vulnerability or resilience for posttraumatic stress disorder (PTSD) would especially serve populations at high risk for trauma exposure like firefighters, police officers and combat soldiers. Aiming to identify the most promising putative PTSD vulnerability markers, we conducted the first systematic review on potential imaging and non-genetic molecular markers for PTSD risk and resilience. Following the PRISMA guidelines, we systematically screened the PubMed database for prospective longitudinal clinical studies and twin studies reporting on pre-trauma and post-trauma PTSD risk and resilience biomarkers. Using 25 different combinations of search terms, we retrieved 8151 articles of which we finally included and evaluated 9 imaging and 27 molecular studies. In addition, we briefly illustrate the design of the ongoing prospective German Armed Forces (Bundeswehr) PTSD biomarker study (Bw-BioPTSD) which not only aims to validate these previous findings but also to identify novel and clinically applicable molecular, psychological and imaging risk, resilience and disease markers for deployment-related psychopathology in a cohort of German soldiers who served in Afghanistan.

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

    PubMed Central

    2008-01-01

    Background Natural selection and genetic drift are major forces responsible for temporal genetic changes in populations. Furthermore, these evolutionary forces may interact with each other. Here we study the impact of an ongoing adaptive process at the molecular genetic level by analyzing the temporal genetic changes throughout 40 generations of adaptation to a common laboratory environment. Specifically, genetic variability, population differentiation and demographic structure were compared in two replicated groups of Drosophila subobscura populations recently sampled from different wild sources. Results We found evidence for a decline in genetic variability through time, along with an increase in genetic differentiation between all populations studied. The observed decline in genetic variability was higher during the first 14 generations of laboratory adaptation. The two groups of replicated populations showed overall similarity in variability patterns. Our results also revealed changing demographic structure of the populations during laboratory evolution, with lower effective population sizes in the early phase of the adaptive process. One of the ten microsatellites analyzed showed a clearly distinct temporal pattern of allele frequency change, suggesting the occurrence of positive selection affecting the region around that particular locus. Conclusion Genetic drift was responsible for most of the divergence and loss of variability between and within replicates, with most changes occurring during the first generations of laboratory adaptation. We also found evidence suggesting a selective sweep, despite the low number of molecular markers analyzed. Overall, there was a similarity of evolutionary dynamics at the molecular level in our laboratory populations, despite distinct genetic backgrounds and some differences in phenotypic evolution. PMID:18302790

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

    PubMed Central

    2012-01-01

    Background Small supernumerary marker chromosomes (sSMC) are detected in 0.043% of general population and can be characterized for their chromosomal origin, genetic content and shape by molecular cytogenetic approaches. Even though recently progress was achieved towards genotype-phenotype-correlations of sSMC, nothing is known on the influence that an additional derivative extra chromosome has on the nuclear architecture. Results Here we present the first three-dimensional interphase fluorescence in situ hybridization (FISH) studies for the nuclear architecture of sSMC. It could be shown that sSMC derived from chromosomes 15, 16 or 18 preferentially colocalized with one of their corresponding sister chromosomes. This was true in B- and T-lymphocytes as well as in skin fibroblasts. Additionally, a case with a complex sSMC with a karyotype 47,XY,+der(18)t(8;18)(8p23.2 ~ 23.1;18q11.1) was studied. Here the sSMC co-localized with one homologous chromosome 8 instead of 18. Conclusion Overall, there is a kind of "attraction" between an sSMC and one of its homologous sister chromosomes. This seems to be transmitted by the euchromatic part of the sSMC rather than its heterochromatic one. PMID:22413994

  19. Molecular characterization of cultivated bromeliad accessions with Inter-Simple Sequence Repeat (ISSR) Markers.

    PubMed

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

    2012-01-01

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

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

    PubMed Central

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

    2012-01-01

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

  1. GERD—Barrett—Adenocarcinoma: Do We Have Suitable Prognostic and Predictive Molecular Markers?

    PubMed Central

    Illig, Romana; Klieser, Eckhard; Kiesslich, Tobias; Neureiter, Daniel

    2013-01-01

    Due to unfavorable lifestyle habits (unhealthy diet and tobacco abuse) the incidence of gastroesophageal reflux disease (GERD) in western countries is increasing. The GERD-Barrett-Adenocarcinoma sequence currently lacks well-defined diagnostic, progressive, predictive, and prognostic biomarkers (i) providing an appropriate screening method identifying the presence of the disease, (ii) estimating the risk of evolving cancer, that is, the progression from Barrett's esophagus (BE) to esophageal adenocarcinoma (EAC), (iii) predicting the response to therapy, and (iv) indicating an overall survival—prognosis for EAC patients. Based on histomorphological findings, detailed screening and therapeutic guidelines have been elaborated, although epidemiological studies could not support the postulated increasing progression rates of GERD to BE and EAC. Additionally, proposed predictive and prognostic markers are rather heterogeneous by nature, lack substantial proofs, and currently do not allow stratification of GERD patients for progression, outcome, and therapeutic effectiveness in clinical practice. The aim of this paper is to discuss the current knowledge regarding the GERD-BE-EAC sequence mainly focusing on the disputable and ambiguous status of proposed biomarkers to identify promising and reliable markers in order to provide more detailed insights into pathophysiological mechanisms and thus to improve prognostic and predictive therapeutic approaches. PMID:23573078

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

    PubMed Central

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

    2012-01-01

    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

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

    PubMed Central

    Thomas, Stuart C

    2005-01-01

    Molecular marker data collected from natural populations allows information on genetic relationships to be established without referencing an exact pedigree. Numerous methods have been developed to exploit the marker data. These fall into two main categories: method of moment estimators and likelihood estimators. Method of moment estimators are essentially unbiased, but utilise weighting schemes that are only optimal if the analysed pair is unrelated. Thus, they differ in their efficiency at estimating parameters for different relationship categories. Likelihood estimators show smaller mean squared errors but are much more biased. Both types of estimator have been used in variance component analysis to estimate heritability. All marker-based heritability estimators require that adequate levels of the true relationship be present in the population of interest and that adequate amounts of informative marker data are available. I review the different approaches to relationship estimation, with particular attention to optimizing the use of this relationship information in subsequent variance component estimation. PMID:16048788

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

    PubMed

    Öz, M H; Vurgun, H; Bakir, M; Büyük, İ; Yüksel, C; Ünlü, H M; Çukadar, K; Karadoğan, B; Köse, Ö; Ergül, A

    2013-11-07

    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.

  5. Molecular Assay for Detection of Genetic Markers Associated with Decreased Susceptibility to Cephalosporins in Neisseria gonorrhoeae

    PubMed Central

    Peterson, S. W.; Martin, I.; Demczuk, W.; Bharat, A.; Hoang, L.; Wylie, J.; Allen, V.; Lefebvre, B.; Tyrrell, G.; Horsman, G.; Haldane, D.; Garceau, R.; Wong, T.

    2015-01-01

    The incidence of antimicrobial-resistant Neisseria gonorrhoeae continues to rise in Canada; however, antimicrobial resistance data are lacking for approximately 70% of gonorrhea infections that are diagnosed directly from clinical specimens by nucleic acid amplification tests (NAATs). We developed a molecular assay for surveillance use to detect mutations in genes associated with decreased susceptibility to cephalosporins that can be applied to both culture isolates and clinical samples. Real-time PCR assays were developed to detect single nucleotide polymorphisms (SNPs) in ponA, mtrR, penA, porB, and one N. gonorrhoeae-specific marker (porA). We tested the real-time PCR assay with 252 gonococcal isolates, 50 nongonococcal isolates, 24 N. gonorrhoeae-negative NAAT specimens, and 34 N. gonorrhoeae-positive NAAT specimens. Twenty-four of the N. gonorrhoeae-positive NAAT specimens had matched culture isolates. Assay results were confirmed by comparison with whole-genome sequencing data. For 252 N. gonorrhoeae strains, the agreement between the DNA sequence and real-time PCR was 100% for porA, ponA, and penA, 99.6% for mtrR, and 95.2% for porB. The presence of ≥2 SNPs correlated with decreased susceptibility to ceftriaxone (sensitivities of >98%) and cefixime (sensitivities of >96%). Of 24 NAAT specimens with matched cultures, the agreement between the DNA sequence and real-time PCR was 100% for porB, 95.8% for ponA and mtrR, and 91.7% for penA. We demonstrated the utility of a real-time PCR assay for sensitive detection of known markers for the decreased susceptibility to cephalosporins in N. gonorrhoeae. Preliminary results with clinical NAAT specimens were also promising, as they correlated well with bacterial culture results. PMID:25878350

  6. Evaluation of molecular markers in canine mammary tumors: correlation with histological grading.

    PubMed

    Vinothini, G; Balachandran, C; Nagini, S

    2009-01-01

    The objective of this study was to evaluate molecular markers involved in mammary tumorigenesis in a canine model that mimics many essential elements of human breast cancer. Thirty mammary gland tumors and control tissues obtained from female dogs were included in the study. We analyzed changes in the expression of markers of hormone and receptor status (estradiol, estrogen receptor; ER and HER-2/neu), hormone metabolism (CYP1A1 and CYP1B1), cell proliferation and survival [proliferating cell nuclear antigen (PCNA), glutathione S-transferase-P (GST-P), nuclear factor-kappaB (NF-kappaB-p50, NF-kappaB-p65), phosphorylated-inhibitor of kappaB-alpha (p-IkappaB-alpha) and IkappaB], apoptosis (Bcl-2, Bax, caspases, Apaf-1, cytochrome-C, and PARP), invasion [matrix metalloproteinases-2 and -9 (MMP-2, MMP-9), tissue inhibitor of matrix metalloproteinase-2 (TIMP-2), and reversion-inducing cysteine-rich protein with Kazal motifs (RECK)], angiogenesis [vascular endothelial growth factor (VEGF)], and epigenetics [DNA methyltransferase (Dnmt-1), histone deacetylase (HDAC-1)] by immunohistochemical localization and Western blot analysis and correlated these with histological grade. The present study provides evidence that increased expression of ER, HER-2/neu, estradiol, and its metabolizing enzymes, as well as proteins involved in cell proliferation, apoptosis evasion, invasion, and angiogenesis may confer a selective growth advantage to canine mammary tumors. To our knowledge this is the first report on the hallmark capabilities of canine mammary tumors, which lends credence to the view that the dog is a valuable model for human breast cancer studies.

  7. 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...

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

    NASA Astrophysics Data System (ADS)

    Weitkamp, Emily A.

    Particulate matter (PM) is solid particles and liquid droplets of complex composition suspended in the atmosphere. In 1997, the National Ambient Air Quality Standards (NAAQS) for PM was modified to include new standards for fine particulate (particles smaller than 2.5mum, PM2.5) because of their association with adverse health effects, mortality and visibility reduction. Fine PM may also have large impacts on the global climate. Chemically, fine particulate is a complex mixture of organic and inorganic material, from both natural and anthropogenic sources. A large fraction of PM2.5 is organic. The first objective was to investigate heterogeneous oxidation of condensed-phase molecular markers for two major organic source categories, meat-cooking emissions and motor vehicle exhaust. Effective reaction rate constants of key molecular markers were measured over a range of atmospherically relevant experimental conditions, including a range of concentrations and relative humidities, and with SOA condensed on the particles. Aerosolized meat grease was reacted with ozone to investigate the oxidation of molecular markers for meat-cooking emissions. Aerosolized motor oil, which is chemically similar to vehicle exhaust aerosol and contains the molecular markers used in source apportionment, was reacted with the hydroxyl radical (OH) to investigate oxidation of motor vehicle molecular markers. All molecular markers of interest - oleic acid, palmitoleic acid, and cholesterol for meat-cooking emissions, and hopanes and steranes for vehicle exhaust - reacted at rates that are significant for time scales on the order of days assuming typical summertime oxidant concentrations. Experimental conditions influenced the reaction rate constants. For both systems, experiments conducted at high relative humidity (RH) had smaller reaction rate constants than those at low RH. SOA coating slowed the reaction rate constants for meat-cooking markers, but had no effect on the oxidation of

  9. Critical Evaluation of Molecular Monitoring in Malaria Drug Efficacy Trials and Pitfalls of Length-Polymorphic Markers

    PubMed Central

    Messerli, Camilla; Hofmann, Natalie E.

    2016-01-01

    ABSTRACT Estimation of drug efficacy in antimalarial drug trials requires parasite genotyping to distinguish new infections from treatment failures. When using length-polymorphic molecular markers, preferential amplification of short fragments can compromise detection of coinfections, potentially leading to misclassification of treatment outcome. We quantified minority clone detectability and competition among msp1, msp2, and glurp amplicons using mixtures of Plasmodium falciparum strains and investigated the impact of template competition on genotyping outcomes in 44 paired field samples. Substantial amplification bias was detected for all three markers, with shorter fragments outperforming larger fragments. The strongest template competition was observed for the marker glurp. Detection of glurp fragments in multiclonal infections was severely compromised. Eight of 44 sample pairs were identified as new infections by all three markers. Ten pairs were defined as new infections based on one marker alone, seven of which were defined by the questionable marker glurp. The impact of size-dependent template competition on genotyping outcomes therefore calls for necessary amendments to the current WHO recommendations for PCR correction of malaria drug trial endpoints. Accuracy of genotyping outcomes could be improved by separate amplification reactions per allelic family and basing results on markers msp1 and msp2 first, with glurp only used to resolve discordant results. PMID:27821442

  10. Seedling Resistance to Stem Rust and Molecular Marker Analysis of Resistance Genes in Wheat Cultivars of Yunnan, China

    PubMed Central

    Li, Tian Ya; Cao, Yuan Yin; Wu, Xian Xin; Xu, Xiao Feng; Wang, Wan Lin

    2016-01-01

    Stem rust is one of the most potentially harmful wheat diseases, but has been effectively controlled in China since 1970s. However, the interest in breeding wheat with durable resistance to stem rust has been renewed with the emergence of Ug99 (TTKSK) virulent to the widely used resistance gene Sr31, and by which the wheat stem rust was controlled for 40 years in wheat production area worldwide. Yunnan Province, located on the Southwest border of China, is one of the main wheat growing regions, playing a pivotal role in the wheat stem rust epidemic in China. This study investigated the levels of resistance in key wheat cultivars (lines) of Yunnan Province. In addition, the existence of Sr25, Sr26, Sr28, Sr31, Sr32, and Sr38 genes in 119 wheat cultivars was assessed using specific DNA markers. The results indicated that 77 (64.7%) tested wheat varieties showed different levels of resistance to all the tested races of Puccinia graminis f. sp. tritici. Using molecular markers, we identified the resistance gene Sr31 in 43 samples; Sr38 in 10 samples; Sr28 in 12 samples, and one sample which was resistant against Ug99 (avirulent to Sr32). No Sr25 or Sr26 (effective against Ug99) was identified in any cultivars tested. Furthermore, 5 out of 119 cultivars tested carried both Sr31 and Sr38 and eight contained both Sr31 and Sr28. The results enable the development of appropriate strategies to breed varieties resistant to stem rust. PMID:27792757

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

    PubMed Central

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

    2017-01-01

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

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

    PubMed Central

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

    2010-01-01

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

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

    PubMed

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

    2013-12-01

    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.

  14. Mitochondrial DNA damage: molecular marker of vulnerable nigral neurons in Parkinson's disease.

    PubMed

    Sanders, Laurie H; McCoy, Jennifer; Hu, Xiaoping; Mastroberardino, Pier G; Dickinson, Bryan C; Chang, Christopher J; Chu, Charleen T; Van Houten, Bennett; Greenamyre, J T

    2014-10-01

    DNA damage can cause (and result from) oxidative stress and mitochondrial impairment, both of which are implicated in the pathogenesis of Parkinson's disease (PD). We therefore examined the role of mitochondrial DNA (mtDNA) damage in human postmortem brain tissue and in in vivo and in vitro models of PD, using a newly adapted histochemical assay for abasic sites and a quantitative polymerase chain reaction (QPCR)-based assay. We identified the molecular identity of mtDNA damage to be apurinic/apyrimidinic (abasic) sites in substantia nigra dopamine neurons, but not in cortical neurons from postmortem PD specimens. To model the systemic mitochondrial impairment of PD, rats were exposed to the pesticide rotenone. After rotenone treatment that does not cause neurodegeneration, abasic sites were visualized in nigral neurons, but not in cortex. Using a QPCR-based assay, a single rotenone dose induced mtDNA damage in midbrain neurons, but not in cortical neurons; similar results were obtained in vitro in cultured neurons. Importantly, these results indicate that mtDNA damage is detectable prior to any signs of degeneration - and is produced selectively in midbrain neurons under conditions of mitochondrial impairment. The selective vulnerability of midbrain neurons to mtDNA damage was not due to differential effects of rotenone on complex I since rotenone suppressed respiration equally in midbrain and cortical neurons. However, in response to complex I inhibition, midbrain neurons produced more mitochondrial H2O2 than cortical neurons. We report selective mtDNA damage as a molecular marker of vulnerable nigral neurons in PD and suggest that this may result from intrinsic differences in how these neurons respond to complex I defects. Further, the persistence of abasic sites suggests an ineffective base excision repair response in PD.

  15. Detection of stanozolol O- and N-sulfate metabolites and their evaluation as additional markers in doping control.

    PubMed

    Balcells, Georgina; Matabosch, Xavier; Ventura, Rosa

    2016-10-07

    Stanozolol (STAN) is one of the most frequently detected anabolic androgenic steroids in sports drug testing. STAN misuse is commonly detected by monitoring metabolites excreted conjugated with glucuronic acid after enzymatic hydrolysis or using direct detection by liquid chromatography-tandem mass spectrometry (LC-MS/MS). It is well known that some of the previously described metabolites are the result of the formation of sulfate conjugates in C17, which are converted to their 17-epimers in urine. Therefore, sulfation is an important phase II metabolic pathway of STAN that has not been comprehensively studied. The aim of this work was to evaluate the sulfate fraction of STAN metabolism by LC-MS/MS to establish potential long-term metabolites valuable for doping control purposes. STAN was administered to six healthy male volunteers involving oral or intramuscular administration and urine samples were collected up to 31 days after administration. Sulfation of the phase I metabolites commercially available as standards was performed in order to obtain MS data useful to develop analytical strategies (neutral loss scan, precursor ion scan and selected reaction monitoring acquisitions modes) to detect potential sulfate metabolites. Eleven sulfate metabolites (M-I to M-XI) were detected and characterized by LC-MS/MS. This paper provides valuable data on the ionization and fragmentation of O-sulfates and N-sulfates. For STAN, results showed that sulfates do not improve the retrospectivity of the detection compared to the previously described long-term metabolite (epistanozolol-N-glucuronide). However, sulfate metabolites could be additional markers for the detection of STAN misuse.

  16. Population Structure, Genetic Diversity and Molecular Marker-Trait Association Analysis for High Temperature Stress Tolerance in Rice

    PubMed Central

    Barik, Saumya Ranjan; Sahoo, Ambika; Mohapatra, Sudipti; Nayak, Deepak Kumar; Mahender, Anumalla; Meher, Jitandriya; Anandan, Annamalai

    2016-01-01

    Rice exhibits enormous genetic diversity, population structure and molecular marker-traits associated with abiotic stress tolerance to high temperature stress. A set of breeding lines and landraces representing 240 germplasm lines were studied. Based on spikelet fertility percent under high temperature, tolerant genotypes were broadly classified into four classes. Genetic diversity indicated a moderate level of genetic base of the population for the trait studied. Wright’s F statistic estimates showed a deviation of Hardy-Weinberg expectation in the population. The analysis of molecular variance revealed 25 percent variation between population, 61 percent among individuals and 14 percent within individuals in the set. The STRUCTURE analysis categorized the entire population into three sub-populations and suggested that most of the landraces in each sub-population had a common primary ancestor with few admix individuals. The composition of materials in the panel showed the presence of many QTLs representing the entire genome for the expression of tolerance. The strongly associated marker RM547 tagged with spikelet fertility under stress and the markers like RM228, RM205, RM247, RM242, INDEL3 and RM314 indirectly controlling the high temperature stress tolerance were detected through both mixed linear model and general linear model TASSEL analysis. These markers can be deployed as a resource for marker-assisted breeding program of high temperature stress tolerance. PMID:27494320

  17. Population Structure, Genetic Diversity and Molecular Marker-Trait Association Analysis for High Temperature Stress Tolerance in Rice.

    PubMed

    Pradhan, Sharat Kumar; Barik, Saumya Ranjan; Sahoo, Ambika; Mohapatra, Sudipti; Nayak, Deepak Kumar; Mahender, Anumalla; Meher, Jitandriya; Anandan, Annamalai; Pandit, Elssa

    2016-01-01

    Rice exhibits enormous genetic diversity, population structure and molecular marker-traits associated with abiotic stress tolerance to high temperature stress. A set of breeding lines and landraces representing 240 germplasm lines were studied. Based on spikelet fertility percent under high temperature, tolerant genotypes were broadly classified into four classes. Genetic diversity indicated a moderate level of genetic base of the population for the trait studied. Wright's F statistic estimates showed a deviation of Hardy-Weinberg expectation in the population. The analysis of molecular variance revealed 25 percent variation between population, 61 percent among individuals and 14 percent within individuals in the set. The STRUCTURE analysis categorized the entire population into three sub-populations and suggested that most of the landraces in each sub-population had a common primary ancestor with few admix individuals. The composition of materials in the panel showed the presence of many QTLs representing the entire genome for the expression of tolerance. The strongly associated marker RM547 tagged with spikelet fertility under stress and the markers like RM228, RM205, RM247, RM242, INDEL3 and RM314 indirectly controlling the high temperature stress tolerance were detected through both mixed linear model and general linear model TASSEL analysis. These markers can be deployed as a resource for marker-assisted breeding program of high temperature stress tolerance.

  18. Comparison of algorithms to infer genetic population structure from unlinked molecular markers.

    PubMed

    Peña-Malavera, Andrea; Bruno, Cecilia; Fernandez, Elmer; Balzarini, Monica

    2014-08-01

    Identifying population genetic structure (PGS) is crucial for breeding and conservation. Several clustering algorithms are available to identify the underlying PGS to be used with genetic data of maize genotypes. In this work, six methods to identify PGS from unlinked molecular marker data were compared using simulated and experimental data consisting of multilocus-biallelic genotypes. Datasets were delineated under different biological scenarios characterized by three levels of genetic divergence among populations (low, medium, and high FST) and two numbers of sub-populations (K=3 and K=5). The relative performance of hierarchical and non-hierarchical clustering, as well as model-based clustering (STRUCTURE) and clustering from neural networks (SOM-RP-Q). We use the clustering error rate of genotypes into discrete sub-populations as comparison criterion. In scenarios with great level of divergence among genotype groups all methods performed well. With moderate level of genetic divergence (FST=0.2), the algorithms SOM-RP-Q and STRUCTURE performed better than hierarchical and non-hierarchical clustering. In all simulated scenarios with low genetic divergence and in the experimental SNP maize panel (largely unlinked), SOM-RP-Q achieved the lowest clustering error rate. The SOM algorithm used here is more effective than other evaluated methods for sparse unlinked genetic data.

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

    PubMed

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

    2011-01-11

    Several interspecific Passiflora hybrids are produced in the northern hemisphere for the ornamental plant market. In Brazil, production of passion flower hybrids is limited to the introgression of genes into the main cultivated species, yellow passion fruit, to be used as rootstocks. Confirmation of hybridization in the initial developmental stage is important for breeding perennial and sub-perennial plants, such as passion flowers, reducing time and costs in plant stock maintenance. In order to obtain F₁ hybrids with ornamental potential, four species of Passiflora (P. alata, P. gardneri, P. gibertii, and P. watsoniana) from the Active Germplasm Bank at UESC were hybridized. Flower buds, in pre-anthesis, of the genitors were previously protected, and the female buds were emasculated. To confirm hybridization, the genomic DNA of the genitor species and the supposed hybrids was extracted and RAPD primers were used to obtain molecular markers and select passion flower interspecific hybrids. Eight primers were used to confirm hybrids derived from P. gardneri with P. alata, P. watsoniana with P. alata, P. watsoniana with P. gardneri, and P. gardneri with P. gibertii; 75, 50, 45, and 46% of the informative bands, respectively, confirmed the hybrid nature of these plants. The RAPD technique was effective in the early identification of hybrids; this will be useful for development of hybrid Passiflora progeny.

  20. Relationships among pest flour beetles of the genus Tribolium (Tenebrionidae) inferred from multiple molecular markers

    PubMed Central

    Angelini, David R.; Jockusch, Elizabeth L.

    2008-01-01

    Model species often provide initial hypotheses and tools for studies of development, genetics, and molecular evolution in closely related species. Flour beetles of the genus Tribolium MacLeay (1825) are one group with potential for such comparative studies. Tribolium castaneum (Herbst 1797) is an increasingly useful developmental genetic system. The convenience with which congeneric and other species of tenebrionid flour beetles can be reared in the laboratory makes this group attractive for comparative studies on a small phylogenetic scale. Here we present the results of phylogenetic analyses of relationships among the major pest species of Tribolium based on two mitochondrial and three nuclear markers (cytochrome oxidase 1, 16S ribosomal DNA, wingless, 28S ribosomal DNA, histone H3). The utility of partitioning the dataset in a manner informed by biological structure and function is demonstrated by comparing various partitioning strategies. In parsimony and partitioned Bayesian analyses of the combined dataset, the castaneum and confusum species groups are supported as monophyletic and as each other’s closest relatives. However, a sister group relationship between this clade and Tribolium brevicornis (Leconte 1859) is not supported. Therefore, we suggest transferring brevicornis group species to the genus Aphanotus Leconte (1862). The inferred phylogeny provides an evolutionary framework for comparative studies using flour beetles. PMID:18024090

  1. Genetic diversity analysis of Croton antisyphiliticus Mart. using AFLP molecular markers.

    PubMed

    Oliveira, T G; Pereira, A M S; Coppede, J S; França, S C; Ming, L C; Bertoni, B W

    2016-02-19

    Croton antisyphiliticus Mart. is a medicinal plant native to Cerrado vegetation in Brazil, and it is popularly used to treat urogenital tract infections. The objective of the present study was to assess the genetic variability of natural C. antisyphiliticus populations using AFLP molecular markers. Accessions were collected in the states of Minas Gerais, São Paulo, and Goiás. The genotyping of individuals was performed using a LI-COR® DNA Analyzer 4300. The variability within populations was found to be greater than the variability between them. The F(ST) value was 0.3830, which indicated that the populations were highly structured. A higher percentage of polymorphic loci (92.16%) and greater genetic diversity were found in the population accessions from Pratinha-MG. Gene flow was considered restricted (N(m) = 1.18), and there was no correlation between genetic and geographic distances. The populations of C. antisyphiliticus exhibited an island-model structure, which demonstrates the vulnerability of the species.

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

    PubMed

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

    2015-03-01

    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.

  3. Combining Cadherin Expression with Molecular Markers Discriminates Invasiveness in Growth Hormone and Prolactin Pituitary Adenomas.

    PubMed

    Chauvet, N; Romanò, N; Meunier, A-C; Galibert, E; Fontanaud, P; Mathieu, M-N; Osterstock, G; Osterstock, P; Baccino, E; Rigau, V; Loiseau, H; Bouillot-Eimer, S; Barlier, A; Mollard, P; Coutry, N

    2016-02-01

    Although growth hormone (GH)- and prolactin (PRL)-secreting pituitary adenomas are considered benign, in many patients, tumour growth and/or invasion constitute a particular challenge. In other tumours, progression relies in part on dysfunction of intercellular adhesion mediated by the large family of cadherins. In the present study, we have explored the contribution of cadherins in GH and PRL adenoma pathogenesis, and evaluated whether this class of adherence molecules was related to tumour invasiveness. We have first established, by quantitative polymerase chain reaction and immunohistochemistry, the expression profile of classical cadherins in the normal human pituitary gland. We show that the cadherin repertoire is restricted and cell-type specific. Somatotrophs and lactotrophs express mainly E-cadherin and cadherin 18, whereas N-cadherin is present in the other endocrine cell types. This repertoire undergoes major differential modification in GH and PRL tumours: E-cadherin is significantly reduced in invasive GH adenomas, and this loss is associated with a cytoplasmic relocalisation of cadherin 18 and catenins. In invasive prolactinomas, E-cadherin distribution is altered and is accompanied by a mislocalisation of cadherin 18, β-catenin and p120 catenin. Strikingly, de novo expression of N-cadherin is present in a subset of adenomas and cells exhibit a mesenchymal phenotype exclusively in invasive tumours. Binary tree analysis, performed by combining the cadherin repertoire with the expression of a subset of known molecular markers, shows that cadherin/catenin complexes play a significant role in discrimination of tumour invasion.

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

    PubMed

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

    2003-07-01

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

  5. Plasma DNA integrity index as a potential molecular diagnostic marker for breast cancer.

    PubMed

    Kamel, Azza M; Teama, Salwa; Fawzy, Amal; El Deftar, Mervat

    2016-06-01

    Plasma DNA integrity index is increased in various malignancies including breast cancer, the most common cancer in women worldwide; early detection is crucial for successful treatment. Current screening methods fail to detect many cases of breast cancer at an early stage. In this study, we evaluated the level of plasma DNA integrity index in 260 females (95 with breast cancer, 95 with benign breast lesions, and 70 healthy controls) to verify its potential value in discriminating malignant from benign breast lesions. The criteria of the American Joint Committee on Cancer were used for staging of breast cancer patients. DNA integrity index was measured by real-time PCR. DNA integrity index was significantly higher in breast cancer than in benign breast patients and healthy subjects (P = <0.001). DNA integrity index is correlated with TNM stage. Given 100 % specificity, the highest sensitivity achieved in detecting cancer group was 85.3 % at 0.55 DNA integrity index cutoff. In conclusion, the plasma DNA integrity index may be a promising molecular diagnostic marker of malignancy in breast lesions.

  6. Matrix metalloproteinases and their tissue inhibitors in gastric cancer as molecular markers.

    PubMed

    Sampieri, Clara L; León-Córdoba, Kenneth; Remes-Troche, Jos Maria

    2013-01-01

    Gastric cancer is a complex disease that involves a range of biological individuals and tumors with histopathological features. The pathogenesis of this disease is multi-factorial and includes the interaction of genetic predisposition with environmental factors. Gastric cancer is normally diagnosed in advanced stages where there are few alternatives to offer and the prognosis is difficult to establish. Metastasis is the leading cause of cancer deaths. Identification of key genes and signaling pathways involved in metastasis and recurrence could predict these events and thereby identify therapeutic targets. In this context, the extracellular matrix metalloproteinases (MMPs) and their inhibitors (TIMPs) represent a potential prognostic tool, because both genetic families regulate growth, angiogenesis, invasion, immune response, epithelial mesenchymal transition and cellular survival. Proteolytic parameters based on MMP/TIMP expression could be useful in the identification of patients with a high probability of developing distant metastases or peritoneal dissemination for each degree of histological malignancy. It is also probable that these parameters can allow improvement in the extent of surgery and dictate the most suitable therapy. We reviewed papers focused on human gastric epithelial cancer as a model and focus on the potential use of MMPs and TIMPs as molecular markers; also we include literature regarding gastric cancer risk factors, classification systems and MMP/TIMP regulation.

  7. [Relationship Between Molecular Marker of Western Main Pig H-FABP Gene and IMF Content.].

    PubMed

    Pang, Wei-Jun; Sun, Shi-Duo; Li, Ying; Chen, Guo-Dong; Yang, Gong-She

    2005-05-01

    By using 265 pigs from eight breeds including Duroc,Landrace,Large White,Neijiang,Rongchang,Hanjiang Black,Hanzhong White,Bamei and wild ones, the genetic variations of 5'-upstream region from and the second intron in porcine H-FABP gene were checked by PCR-RFLP molecular marker with HinfI, Hae III and MspI,and effect of H-FABP gene on IMF content was then analyzed by least square analysis.The results showed as follows:(1) 8 pig breeds and wild pig had polymorphism at Hinf I-RFLP site. In above detected breeds,large white,Bamei pig, Hanjiang Black,Hanzhong White pig breeds and wild pig presented low polymorphism while other breeds have mediate polymorphism;(2)Among the tested breeds only 4 Chinese local pig breeds had no polymorphism at the Hae III-RFLP and Msp I-RFLP sites,but Duroc,Landrace,Largewhite, Hanzhong White pig breeds and wild pig had polymorphism. Wild pig at the Hae III-RFLP , Landrace,Largewhite and wild pig at the Hae III-RFLP and Msp I-RFLP sites were low polymorphism,others were mediate polymorphism;(3) H-FABP gene increased IMF content significantly(p0.05). Genetic effect of H-FABP gene on IMF content were HH>Hh>hh,DD.

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

    PubMed Central

    Bennett, Michael; Mashimo, Hiroshi

    2014-01-01

    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

  9. Pink berry grape (Vitis vinifera L.) characterization: Reflectance spectroscopy, HPLC and molecular markers.

    PubMed

    Rustioni, Laura; De Lorenzis, Gabriella; Hârţa, Monica; Failla, Osvaldo

    2016-01-01

    Color has a fundamental role for the qualitative evaluation and cultivar characterization of fruits. In grape, a normally functional pigment biosynthesis leads to the accumulation of a high quantity of anthocyanins. In this work, 28 Vitis vinifera L. cultivars accumulating low anthocyanins in berries were studied to characterize the biosynthetic dysfunctions in both a phenotypic and genotypic point of view. Reflectance spectroscopy, HPLC profiles and molecular markers related to VvMybA1 and VvMybA2 genes allowed a detailed description of the pigment-related characteristics of these cultivars. Data were consistent concerning the heterozygosity of the non-functional allele in both investigated genes, resulting in a low colored phenotype as described by reflectance. However, the variability in berry colour among our samples was not fully explained by MybA locus, probably due to specific interferences among the biosynthetic pathways, as suggested by the anthocyanin profile variations detected among our samples. The results presented in this work confirmed the importance of the genetic background: grapes accumulating high levels of cyanidin-3-O-glucosides (di-substituted anthocyanin) are generally originated by white cultivar retro-mutations and they seem to preserve the anomalies in the flavonoid hydroxylases enzymes which negatively affect the synthesis of tri-substituted anthocyanins.

  10. A comparison of molecular markers to detect Lutzomyia longipalpis naturally infected with Leishmania (Leishmania) infantum

    PubMed Central

    Freitas-Lidani, Kárita Cláudia; de Messias-Reason, Iara J; Ishikawa, Edna Aoba Y

    2014-01-01

    The aim of the present study was to detect natural infection by Leishmania (Leishmania) infantum in Lutzomyia longipalpis captured in Barcarena, state of Pará, Brazil, through the use of three primer sets. With this approach, it is unnecessary to previously dissect the sandfly specimens. DNA of 280 Lu. longipalpis female specimens were extracted from the whole insects. PCR primers for kinetoplast minicircle DNA (kDNA), the mini-exon gene and the small subunit ribosomal RNA (SSU-rRNA) gene of Leishmania were used, generating fragments of 400 bp, 780 bp and 603 bp, respectively. Infection by the parasite was found with the kDNA primer in 8.6% of the cases, with the mini-exon gene primer in 7.1% of the cases and with the SSU-rRNA gene primer in 5.3% of the cases. These data show the importance of polymerase chain reaction as a tool for investigating the molecular epidemiology of visceral leishmaniasis by estimating the risk of disease transmission in endemic areas, with the kDNA primer representing the most reliable marker for the parasite. PMID:25004147

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

    NASA Astrophysics Data System (ADS)

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

    2015-01-01

    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.

  12. Identification of novel molecular prognostic markers for paediatric T-cell acute lymphoblastic leukaemia.

    PubMed

    Gottardo, Nicholas G; Hoffmann, Katrin; Beesley, Alex H; Freitas, Joseph R; Firth, Martin J; Perera, Kanchana U; de Klerk, Nicolas H; Baker, David L; Kees, Ursula R

    2007-05-01

    In the last four decades the survival of patients with newly diagnosed childhood T-cell acute lymphoblastic leukaemia (T-ALL) has improved dramatically. In sharp contrast, relapsed T-ALL continues to confer a dismal prognosis. We sought to determine if gene expression profiling could uncover a signature of outcome for children with T-ALL. Using 12 patient specimens obtained before therapy started, we examined the gene expression profile by oligonucleotide microarrays. We identified three genes, CFLAR, NOTCH2 and BTG3, whose expression at the time of diagnosis accurately distinguished the patients according to disease outcome. These genes are involved in the regulation of apoptosis and cellular proliferation. The prognostic value of the three predictive genes was assessed in an independent cohort of 25 paediatric T-ALL patients using quantitative real-time reverse transcription polymerase chain reaction. Patients assigned to the adverse outcome group had a significantly higher cumulative incidence of relapse compared with patients assigned to the favourable outcome group (46% vs. 8%, P = 0.029). Five-year overall survival was also significantly worse in the patients assigned to the adverse outcome group (P = 0.0039). The independent influence of the 3-gene predictor was confirmed by multivariate analysis. Our study provides proof of principle that genome-wide expression profiling can detect novel molecular prognostic markers in paediatric T-ALL.

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

    PubMed Central

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

    2010-01-01

    Staphylococcus (S.) aureus and Pseudomonas (Ps.) aeruginosa are two of the most frequently opportunistic pathogens isolated in nosocomial infections, responsible for severe infections in immunocompromised hosts. The frequent emergence of antibiotic-resistant S. aureus and Ps. aeruginosa strains has determined the development of new strategies in order to elucidate the different mechanisms used by these bacteria at different stages of the infectious process, providing the scientists with new procedures for preventing, or at least improving, the control of S. aureus and Ps. aeruginosa infections. The purpose of this study was to characterize the molecular markers of virulence in S. aureus and Ps. aeruginosa strains isolated from different clinical specimens. We used multiplex and uniplex PCR assays to detect the genes encoding different cell-wall associated and extracellular virulence factors, in order to evaluate potential associations between the presence of putative virulence genes and the outcome of infections caused by these bacteria. Our results demonstrate that all the studied S. aureus and Ps. aeruginosa strains synthesize the majority of the investigated virulence determinants, probably responsible for different types of infections. PMID:21614207

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

    PubMed Central

    Diaz-Cano, Salvador J.

    2012-01-01

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

  15. Acute molecular markers of rodent hepatic carcinogenesis identified by transcription profiling.

    PubMed

    Kramer, Jeffrey A; Curtiss, Sandra W; Kolaja, Kyle L; Alden, Carl L; Blomme, Eric A G; Curtiss, William C; Davila, Julio C; Jackson, Carmen J; Bunch, Roderick T

    2004-04-01

    Currently, the only way to identify nongenotoxic hepatocarcinogens is through long-term repeat dose studies such as the 2 year rodent carcinogenicity assay. Such assays are both time consuming and expensive and require large amounts of active pharmaceutical or chemical ingredients. Thus, the results of the 2 year assay are not known until very late in the discovery and development process for new pharmaceutical entities. Although in many cases nongenotoxic carcinogenicity in rodents is considered to be irrelevant for humans, a positive finding in a 2 year carcinogenicity assay may increase the number of studies to demonstrate the lack of relevance to humans, delay final submission and subsequent registration of a product, and may result in a "black box" carcinogenicity warning on the label. To develop early identifiers of carcinogenicity, we applied transcription profiling using several prototype rodent genotoxic and nongenotoxic carcinogens, as well as two noncarcinogenic hepatotoxicants, in a 5 day repeat dose in vivo toxicology study. Fluorescent-labeled probes generated from liver mRNA prepared from male Sprague-Dawley rats treated with one of three dose levels of bemitradine, clofibrate, doxylamine, methapyrilene, phenobarbital, tamoxifen, 2-acetylaminofluorene, 4-acetylaminofluorene, or isoniazid were hybridized against rat cDNA microarrays. Correlation of the resulting data with an estimated carcinogenic potential of each compound and dose level identified several candidate molecular markers of rodent nongenotoxic carcinogenicity, including transforming growth factor-beta stimulated clone 22 and NAD(P)H cytochrome P450 oxidoreductase.

  16. Phosphorylated S6K1 (Thr389) is a molecular adipose tissue marker of altered glucose tolerance.

    PubMed

    Moreno-Navarrete, José María; Ortega, Francisco; Sánchez-Garrido, Miguel Ángel; Sabater, Mònica; Ricart, Wifredo; Zorzano, Antonio; Tena-Sempere, Manuel; Fernández-Real, José Manuel

    2013-01-01

    Molecular tissue markers of altered glucose metabolism will be useful as potential targets for antidiabetic drugs. S6K1 is a downstream signal of insulin action. We aimed to evaluate (pThr389)S6K1 and total S6K1 levels in human and rat fat depots as candidate markers of altered glucose metabolism. (pThr389)S6K1 and total S6K1 levels were measured using enzyme linked immune sorbent assay (ELISA) in 49 adipose tissue samples from subjects with morbid obesity and in 18 peri-renal white adipose tissue samples from rats. The effects of high glucose and rosiglitazone have been explored in human preadipocytes. (pThr389)S6K1/(total)S6K1 in subcutaneous adipose tissue was significantly increased subjects with Type 2 diabetes (0.78 ± 0.26 vs. 0.55 ± 0.14, P=.02) and associated with fasting glucose (r=0.46, P=.04) and glycated hemoglobin (r=0.63, P=.02) in SAT. Similar associations with fasting glucose (r=0.43, P=.03) and IRS1 (r=-0.41, P=.04) gene expression were found in visceral adipose tissue. In addition, rat experiments confirmed the higher (pThr389)S6K1/totalS6K1 levels in adipose tissue in association with obesity-associated metabolic disturbances. (pThr389)S6K1/totalS6K1 was validated using western blot in rat adipose tissue. Both ELISA and western blot data significantly correlated (r=0.85, P=.005). In human preadipocytes, high glucose medium led to increased (pThr389)S6K1/total S6K1 levels in comparison with normal glucose medium, which was significantly decreased under rosiglitazone administration. In conclusion, in human and rat adipose tissue, phosphorylated S6K1 is a marker for increased glucose levels.

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

    PubMed

    Patzak, Josef; Vrba, Lukás; Matousek, Jaroslav

    2007-01-01

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

  18. Validation of molecular markers associated with boron tolerance, powdery mildew resistance and salinity tolerance in field peas

    PubMed Central

    Javid, Muhammad; Rosewarne, Garry M.; Sudheesh, Shimna; Kant, Pragya; Leonforte, Antonio; Lombardi, Maria; Kennedy, Peter R.; Cogan, Noel O. I.; Slater, Anthony T.; Kaur, Sukhjiwan

    2015-01-01

    Field pea (Pisum sativum L.) is an important grain legume consumed both as human food and animal feed. However, productivity in low rainfall regions can be significantly reduced by inferior soils containing high levels of boron and/or salinity. Furthermore, powdery mildew (PM) (Erysiphe pisi) disease also causes significant yield loss in warmer regions. Breeding for tolerance to these abiotic and biotic stresses are major aims for pea breeding programs and the application of molecular markers for these traits could greatly assist in developing improved germplasm at a faster rate. The current study reports the evaluation of a near diagnostic marker, PsMlo, associated with PM resistance and boron (B) tolerance as well as linked markers associated with salinity tolerance across a diverse set of pea germplasm. The PsMlo1 marker predicted the PM and B phenotypic responses with high levels of accuracy (>80%) across a wide range of field pea genotypes, hence offers the potential to be widely adapted in pea breeding programs. In contrast, linked markers for salinity tolerance were population specific; therefore, application of these markers would be suitable to relevant crosses within the program. Our results also suggest that there are possible new sources of salt tolerance present in field pea germplasm that could be further exploited. PMID:26579164

  19. Genetic diversity in Tunisian populations of faba bean (Vicia faba L.) based on morphological traits and molecular markers.

    PubMed

    Backouchi, I Z; Aouida, M; Khemiri, N; Jebara, M

    2015-07-13

    Genetic diversity within Vicia faba L. is key to the genetic improvement of this important species. In this study, morphological traits and RAPD molecular markers were used to assess the levels of polymorphism across 12 Tunisian populations, three major and nine minor from different locations. Analysis of morphological traits indicated that the three major populations showed significant differences and the nine minor populations exhibited considerable variation for most traits. The grain yield of the Alia population could be increased by inoculation. Of the seven primers tested, it was clear that the Cs12 primer would be recommend for genetic diversity analysis of V. faba.Within population genetic diversity exhibited 94% of total diversity. Intra-population genetic diversity (HS) was 0.16, which was clearly higher than between population genetic diversity (DST = 0.06) UPG-MA showed a high level of genetic variation between major and minor populations of V. faba L. Particularly the minor populations showed a high level of diversity and was divided into two subclusters. Ltaifia was separated from the other populations. In addition to a high grain yield, these populations showed the lowest Nei and Shannon indices (H = 0.08 and I = 0.13) justifying their homogeneity. For these reasons, these cultivars can be considered a selected population. However, the Takelsa population showed the highest Nei and Shannon indices (H = 0.13 and I = 0.21), indicating that this population was the most heterogeneous, which is interesting for breeding programs.

  20. A simple and effective set of PCR-based molecular markers for the monitoring of the Saccharomyces cerevisiae cell population during bioethanol fermentation.

    PubMed

    Carvalho-Netto, Osmar V; Carazzolle, Marcelo F; Rodrigues, Aline; Bragança, Welbe O; Costa, Gustavo G L; Argueso, Juan Lucas; Pereira, Gonçalo A G

    2013-12-01

    One of the defining features of the fermentation process used in the production of bioethanol from sugarcane feedstock is the dynamic nature of the yeast population. Minisatellite molecular markers are particularly useful for monitoring yeast communities because they produce polymorphic PCR products that typically display wide size variations. We compared the coding sequences derived from the genome of the sugarcane bioethanol strain JAY270/PE-2 to those of the reference Saccharomyces cerevisiae laboratory strain S288c, and searched for genes containing insertion or deletion polymorphisms larger than 24 bp. We then designed oligonucleotide primers flanking nine of these sites, and used them to amplify differentially sized PCR products. We analyzed the banding patterns in the most widely adopted sugarcane bioethanol strains and in several indigenous yeast contaminants, and found that our marker set had very good discriminatory power. Subsequently, these markers were used to successfully monitor the yeast cell populations in six sugarcane bioethanol distilleries. Additionally, we showed that most of the markers described here are also polymorphic among strains unrelated to bioethanol production, suggesting that they may be applied universally in S. cerevisiae. Because the relatively large polymorphisms are detectable in conventional agarose gels, our method is well suited to modestly equipped on-site laboratories at bioethanol distilleries, therefore providing both cost and time savings.

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

    NASA Astrophysics Data System (ADS)

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

    2011-02-01

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

  2. Use of microsatellite markers in molecular analysis of segregating populations of papaya (Carica papaya L.) derived from backcrossing.

    PubMed

    Pinto, F O; Pereira, M G; Luz, L N; Cardozo, D L; Ramos, H C C; Macedo, C M P

    2013-07-08

    Brazil is the world leader in papaya production. However, only a small number of cultivars are registered for commercial planting, mainly owing to delays in obtaining cultivars and the high costs of the field phase of breeding programs. These costs can be reduced when molecular tools are combined with conventional breeding methods. In the present study, we conducted a molecular analysis of a self-fertilized population of a first backcrossing generation of BC1S1 papaya plants via microsatellite markers both to monitor the level of homozygosity and the gene/allele transfer that confers the Golden trait (fruit color) and to assess the parental genomic proportion in the genotypes studied. Based on the analysis of 20 polymorphic microsatellite loci, 19 genotypes with the Golden trait belonging to BC1S1 were evaluated in addition to the parental genotypes. Genetic distance was estimated through weighted index. The genotypes were then grouped using the hierarchical nearest neighbor method, and the analysis of principal coordinates was used to measure the proportion of parental genomes in the segregating genotypes. The mean value of the inbreeding coefficient was 0.36. The analysis of the principal coordinates revealed that on average, 64% of the recurrent parent genome was present in the population. Together, the analyses allowed the selection of 3 individuals for the next backcross cycle (33BC1S1-18, 34BC1S1-16, and 37BC1S1-10). These individuals had a higher proportion of the recurrent parent and were grouped close to the recurrent parent in the cluster analysis.

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

    PubMed

    Huse, Jason T; Aldape, Kenneth D

    2014-11-15

    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.

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

    PubMed Central

    Zhang, Shouan; Gao, Muqiang; Zaitlin, David

    2012-01-01

    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

  5. Molecular and Contextual Markers of Hepatitis C Virus and Drug Abuse

    PubMed Central

    Shapshak, Paul; Somboonwit, Charurut; Drumright, Lydia N.; Frost, Simon D.W.; Commins, Deborah; Tellinghuisen, Timothy L.; Scott, William K.; Duncan, Robert; McCoy, Clyde; Page, J. Bryan; Giunta, Brian; Fernandez, Francisco; Singer, Elyse; Levine, Andrew; Minagar, Alireza; Oluwadara, Oluwadayo; Kotila, Taiwo; Chiappelli, Francesco; Sinnott, John T.

    2015-01-01

    The spread of hepatitis C virus (HCV) infection involves a complex interplay of social risks, and molecular factors of both virus and host. Injection drug abuse is the most powerful risk factor for HCV infection, followed by sexual transmission and additional non-injection drug abuse factors such as co-infection with other viruses and barriers to treatment. It is clearly important to understand the wider context in which the factors related to HCV infection occur. This understanding is required for a comprehensive approach leading to the successful prevention, diagnosis, and treatment of HCV. An additional consideration is that current treatments and advanced molecular methods are generally unavailable to socially disadvantaged patients. Thus, the recognition of behavioral/social, viral, and host factors as components of an integrated approach to HCV is important to help this vulnerable group. Equally important, this approach is key to the development of personalized patient treatment – a significant goal in global healthcare. In this review, we discuss recent findings concerning the impact of drug abuse, epidemiology, social behavior, virology, immunopathology, and genetics on HCV infection and the course of disease. PMID:19650670

  6. Molecular serum and urine marker repertoire supporting clinical research on joint diseases.

    PubMed

    Qvist, Per; Bay-Jensen, Anne-Christine; Christiansen, Claus; Sondergaard, Bodil Cecilie; Karsdal, Morten A

    2011-12-01

    The need for improved analytical techniques in the study of slow, degenerative diseases such as rheumatoid arthritis and osteoarthritis has driven major efforts aimed at identifying biochemical markers of pathological processes in both diseases. A series of novel biochemical markers has surfaced and their careful validation has become a critical requirement for further use in clinical research. This report aims at providing a critical review of biochemical markers applied in clinical research of joint diseases, in particular those markers reflecting the turnover of cartilage tissue.

  7. Properties and Microstructural Characteristic of Kaolin Geopolymer Ceramics with Addition of Ultra High Molecular Weight Polyethylene

    NASA Astrophysics Data System (ADS)

    Ahmad, Romisuhani; Bakri Abdullah, Mohd Mustafa Al; Hussin, Kamarudin; Sandu, Andrei Victor; Binhussain, Mohammed; Ain Jaya, Nur

    2016-06-01

    In this paper, the mechanical properties and microstructure of kaolin geopolymer ceramics with addition of Ultra High Molecular Weight Polyethylene were studied. Inorganic polymers based on alumina and silica polysialate units were synthesized at room temperature from kaolin and sodium silicate in a highly alkaline medium, followed by curing and drying at 80 °C. Alkaline activator was formed by mixing the 12 M NaOH solution with sodium silicate at a ratio of 0.24. Addition of Ultra High Molecular Weight Polyethylene to the kaolin geopolymer are fabricated with Ultra High Molecular Weight Polyethylene content of 2, 4, 6 and 8 (wt. %) by using powder metallurgy method. The samples were heated at 1200 °C and the strength and morphological were tested. It was found that the flexural strength for the kaolin geopolymer ceramics with addition of UHMWPE were improved and generally increased with the increasing of UHMWPE loading. The result revealed that the optimum flexural strength was obtained at UHMWPE loading of 4 wt. % (92.1 MPa) and the flexural strength started to decrease. Microstructural analysis showed the samples appeared to have more number of pores and connected of pores increased with the increasing of UHMWPE content.

  8. Construction of an SSR and RAD-Marker Based Molecular Linkage Map of Vigna vexillata (L.) A. Rich

    PubMed Central

    Chankaew, Sompong; Kaga, Akito; Naito, Ken; Ehara, Hiroshi; Tomooka, Norihiko

    2015-01-01

    Vigna vexillata (L.) A. Rich. (tuber cowpea) is an underutilized crop for consuming its tuber and mature seeds. Wild form of V. vexillata is a pan-tropical perennial herbaceous plant which has been used by local people as a food. Wild V. vexillata has also been considered as useful gene(s) source for V. unguiculata (cowpea), since it was reported to have various resistance gene(s) for insects and diseases of cowpea. To exploit the potential of V. vexillata, an SSR-based linkage map of V. vexillata was developed. A total of 874 SSR markers successfully amplified single DNA fragment in V. vexillata among 1,336 SSR markers developed from Vigna angularis (azuki bean), V. unguiculata and Phaseolus vulgaris (common bean). An F2 population of 300 plants derived from a cross between salt resistant (V1) and susceptible (V5) accessions was used for mapping. A genetic linkage map was constructed using 82 polymorphic SSR markers loci, which could be assigned to 11 linkage groups spanning 511.5 cM in length with a mean distance of 7.2 cM between adjacent markers. To develop higher density molecular linkage map and to confirm SSR markers position in a linkage map, RAD markers were developed and a combined SSR and RAD markers linkage map of V. vexillata was constructed. A total of 559 (84 SSR and 475 RAD) markers loci could be assigned to 11 linkage groups spanning 973.9 cM in length with a mean distance of 1.8 cM between adjacent markers. Linkage and genetic position of all SSR markers in an SSR linkage map were confirmed. When an SSR genetic linkage map of V. vexillata was compared with those of V. radiata and V. unguiculata, it was suggested that the structure of V. vexillata chromosome was considerably differentiated. This map is the first SSR and RAD marker-based V. vexillata linkage map which can be used for the mapping of useful traits. PMID:26398819

  9. Population genetic structure of rare and endangered plants using molecular markers

    USGS Publications Warehouse

    Raji, Jennifer; Atkinson, Carter T.

    2013-01-01

    This study was initiated to assess the levels of genetic diversity and differentiation in the remaining populations of Phyllostegia stachyoides and Melicope zahlbruckneri in Hawai`i Volcanoes National Park and determine the extent of gene flow to identify genetically distinct individuals or groups for conservation purposes. Thirty-six Amplified Fragment Length Polymorphic (AFLP) primer combinations generated a total of 3,242 polymorphic deoxyribonucleic acid (DNA) fragments in the P. stachyoides population with a percentage of polymorphic bands (PPB) ranging from 39.3 to 65.7% and 2,780 for the M. zahlbruckneri population with a PPB of 18.8 to 64.6%. Population differentiation (Fst) of AFLP loci between subpopulations of P. stachyoides was low (0.043) across populations. Analysis of molecular variance of P. stachyoides showed that 4% of the observed genetic differentiation occurred between populations in different kīpuka and 96% when individuals were pooled from all kīpuka. Moderate genetic diversity was detected within the M. zahlbruckneri population. Bayesian and multivariate analyses both classified the P. stachyoides and M. zahlbruckneri populations into genetic groups with considerable sub-structuring detected in the P. stachyoides population. The proportion of genetic differentiation among populations explained by geographical distance was estimated by Mantel tests. No spatial correlation was found between genetic and geographic distances in both populations. Finally, a moderate but significant gene flow that could be attributed to insect or bird-mediated dispersal of pollen across the different kīpuka was observed. The results of this study highlight the utility of a multi-allelic DNA-based marker in screening a large number of polymorphic loci in small and closely related endangered populations and revealed the presence of genetically unique groups of individuals in both M. zahlbruckneri and P. stachyoides populations. Based on these findings

  10. Molecular markers of trichloroethylene-induced toxicity in human kidney cells

    SciTech Connect

    Lash, Lawrence H. . E-mail: l.h.lash@wayne.edu; Putt, David A.; Hueni, Sarah E.; Horwitz, Beth P.

    2005-08-07

    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.

  11. Ki-67 as a prognostic marker according to breast cancer molecular subtype

    PubMed Central

    Soliman, Nahed A.; Yussif, Shaimaa M.

    2016-01-01

    Objective: Ki-67 plays an important function in cell division, but its exact role is still unknown. Moreover, few works regarding its overall function were published. The present study evaluated the clinical significance of Ki-67 index as a prognostic marker and predictor of recurrence in different molecular subtypes of breast cancer. The relationship of Ki-67 index with different clinicopathological factors was also analyzed. Methods: Ki-67 index was measured in 107 cases of primary breast cancer from 2010-2012. These patients were evaluated for estrogen receptor, progesterone receptor, and HER2. Ki-67 was divided according to percentage levels: < 15% and > 15%. Follow-up ranged from 32 months up to 6 years. Results: Approximately 44, 23, 15, and 25 cases were grouped as luminal A, luminal B, HER2 subtype, and triple-negative (TN), respectively. No luminal A patients showed Ki-67 level higher than 15%, and their recurrence was 20%. In luminal B group, Ki-67 level higher than 15% was observed in 69% of patients, and recurrence was 39%. In HER2 subtype, Ki-67 was higher than 15% in 34% of cases, and recurrence was 40%. In triple-negative cases, Ki-67 was higher than 15% in 60% of cases, and recurrence was detected in 32% of patients. Patients with Ki-67 less than 15% displayed better overall survival than those with Ki-67 higher than 15% (P = 0.01). Patients with Ki-67 higher than 15% exhibited higher incidence of metastasis and recurrence than those with Ki-67 less than 15% (P = 0.000). Conclusions: Ki-67 may be considered as a valuable biomarker in breast cancer patients. PMID:28154782

  12. Cytogenetic and molecular identification of three Triticum aestivum-Leymus racemosus translocation addition lines.

    PubMed

    Wang, Le; Yuan, Jianhua; Bie, Tongde; Zhou, Bo; Chen, Peidu

    2009-06-01

    Chromosome 2C from Aegilops cylindrica has the ability to induce chromosome breakage in common wheat (Tritivum aestivum). In the BC(1)F(3) generation of the T. aestivum cv. Chinese Spring and a hybrid between T. aestivum-Leymus racemosus Lr.7 addition line and T. aestivum-Ae. cylindrica 2C addition line, three disomic translocation addition lines (2n = 44) were selected by mitotic chromosome C-banding and genomic in situ hybridization. We further characterized these T. aestivum-L. racemosus translocation addition lines, NAU636, NAU637 and NAU638, by chromosome C-banding, in situ hybridization using the A- and D-genome-specific bacterial artificial chromosome (BAC) clones 676D4 and 9M13; plasmids pAs1 and pSc119.2, and 45S rDNA; as well as genomic DNA of L. racemosus as probes, in combination with double ditelosomic test cross and SSR marker analysis. The translocation chromosomes were designated as T3AS-Lr7S, T6BS-Lr7S, and T5DS-Lr7L. The translocation line T3AS-Lr7S was highly resistant to Fusarium head blight and will be useful germplasm for resistance breeding.

  13. [Detection of an NA gene molecular marker in H7N9 subtype avian influenza viruses by pyrosequencing].

    PubMed

    Zhao, Yong-Gang; Liu, Hua-Lei; Wang, Jing-Jing; Zheng, Dong-Xia; Zhao, Yun-Ling; Ge, Sheng-Qiang; Wang, Zhi-Liang

    2014-07-01

    This study aimed to establish a method for the detection and identification of H7N9 avian influenza viruses based on the NA gene by pyrosequencing. According to the published NA gene sequences of the avian influenza A (H7N9) virus, a 15-nt deletion was found in the NA gene of H7N9 avian influenza viruses. The 15-nt deletion of the NA gene was targeted as the molecular marker for the rapid detection and identification of H7N9 avian influenza viruses by pyrosequencing. Three H7N9 avian influenza virus isolates underwent pyrosequencing using the same assay, and were proven to have the same 15-nt deletion. Pyrosequencing technology based on the NA gene molecular marker can be used to identify H7N9 avian influenza viruses.

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

    PubMed

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

    2015-05-25

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

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

    PubMed Central

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

    2008-01-01

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

  16. Ricebase: a breeding and genetics platform for rice, integrating individual molecular markers, pedigrees and whole-genome-based data

    PubMed Central

    Edwards, J. D.; Baldo, A. M.; Mueller, L. A.

    2016-01-01

    Ricebase (http://ricebase.org) is an integrative genomic database for rice (Oryza sativa) with an emphasis on combining datasets in a way that maintains the key links between past and current genetic studies. Ricebase includes DNA sequence data, gene annotations, nucleotide variation data and molecular marker fragment size data. Rice research has benefited from early adoption and extensive use of simple sequence repeat (SSR) markers; however, the majority of rice SSR markers were developed prior to the latest rice pseudomolecule assembly. Interpretation of new research using SNPs in the context of literature citing SSRs requires a common coordinate system. A new pipeline, using a stepwise relaxation of stringency, was used to map SSR primers onto the latest rice pseudomolecule assembly. The SSR markers and experimentally assayed amplicon sizes are presented in a relational database with a web-based front end, and are available as a track loaded in a genome browser with links connecting the browser and database. The combined capabilities of Ricebase link genetic markers, genome context, allele states across rice germplasm and potentially user curated phenotypic interpretations as a community resource for genetic discovery and breeding in rice. PMID:27515824

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

    PubMed

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

    2014-01-01

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

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

    PubMed

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

    2013-02-01

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

  19. Metal-proteinase ADAM12, kinesin 14 and checkpoint suppressor 1 as new molecular markers of laryngeal carcinoma.

    PubMed

    Markowski, Jarosław; Tyszkiewicz, Tomasz; Jarzab, Michał; Oczko-Wojciechowska, Małgorzata; Gierek, Tatiana; Witkowska, Małgorzata; Paluch, Jarosław; Kowalska, Małgorzata; Wygoda, Zbigniew; Lange, Dariusz; Jarzab, Barbara

    2009-10-01

    The assessment of gene expression profile in laryngeal cancer allows implementation of molecular biology methods in diagnostics, as well as in prognosticating the course of disease, thus allowing taking most optimal decisions as regards the method of treatment, scope of surgical procedure, or the necessity of adding complementary radiotherapy. The aim of the project was to analyze the gene expression profile in laryngeal cancer using oligonucleotide microarrays, having in mind searching new molecular markers for that carcinoma. The study comprised a group of 43 patients (38 males and 5 females) suffering from squamous cell laryngeal carcinoma, diagnosed and surgically treated in the years 2005-2007 in the ENT Department of the Silesian Medical University in Katowice, Poland. RNA was isolated from frozen tissue fragments, with the use of columns RNeasy Midi and Mini Kit (Qiagen). For the examination of gene expression profile, oligonucleotide microarrays of high density were used, provided by Affymetrix (U 133 2.0 PLUS) containing over 54,000 probes for over 47,000 transcripts. Four genes previously not examined in that respect in laryngeal carcinoma, occurred to be good markers of the neoplasm. They are: metal-proteinase ADAM12, cyclin-dependent kinase 2-CDK2, kinesin 14-KIF14, suppressor 1 of checkpoint-CHES1. The analysis of gene expression profile allows, in laryngeal carcinoma, to point out to new genes, which in future may become molecular markers of the carcinoma.

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

    PubMed

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

    2013-01-01

    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.

  1. Direct Analysis of Low-Volatile Molecular Marker Extract from Airborne Particulate Matter Using Sensitivity Correction Method

    PubMed Central

    Irei, Satoshi

    2016-01-01

    Molecular marker analysis of environmental samples often requires time consuming preseparation steps. Here, analysis of low-volatile nonpolar molecular markers (5-6 ring polycyclic aromatic hydrocarbons or PAHs, hopanoids, and n-alkanes) without the preseparation procedure is presented. Analysis of artificial sample extracts was directly conducted by gas chromatography-mass spectrometry (GC-MS). After every sample injection, a standard mixture was also analyzed to make a correction on the variation of instrumental sensitivity caused by the unfavorable matrix contained in the extract. The method was further validated for the PAHs using the NIST standard reference materials (SRMs) and then applied to airborne particulate matter samples. Tests with the SRMs showed that overall our methodology was validated with the uncertainty of ~30%. The measurement results of airborne particulate matter (PM) filter samples showed a strong correlation between the PAHs, implying the contributions from the same emission source. Analysis of size-segregated PM filter samples showed that their size distributions were found to be in the PM smaller than 0.4 μm aerodynamic diameter. The observations were consistent with our expectation of their possible sources. Thus, the method was found to be useful for molecular marker studies. PMID:27127511

  2. Spin-probe ESR and molecular modeling studies on calcium carbonate dispersions in overbased detergent additives.

    PubMed

    Montanari, Luciano; Frigerio, Francesco

    2010-08-15

    Oil-soluble calcium carbonate colloids are used as detergent additives in lubricating oils. They are colloidal dispersions of calcium carbonate particles stabilized by different surfactants; in this study alkyl-aryl-sulfonates and sulfurized alkyl-phenates, widely used in the synthesis of these additives, are considered. The physical properties of surfactant layers surrounding the surfaces of calcium carbonate particles were analyzed by using some nitroxide spin-probes (stable free radicals) and observing the corresponding ESR spectra. The spin-probe molecules contain polar groups which tend to tether them to the carbonate particle polar surface. They can reach these surfaces only if the surfactant layers are not very compact, hence the relative amounts of spin-probe molecules accessing carbonate surfaces are an index of the compactness of surfactant core. ESR signals of spin-probe molecules dissolved in oil or "locked" near the carbonate surfaces are different because of the different molecular mobility. Through deconvolution of the ESR spectra, the fraction of spin-probes penetrating surfactant shells have been calculated, and differences were observed according to the surfactant molecular structures. Moreover, by using specially labeled spin-probes based on stearic acids, functionalized at different separations from the carboxylic acid group, it was possible to interrogate the molecular physical behavior of surfactant shells at different distances from carbonate surfaces. Molecular modeling was applied to generate some three-dimensional micellar models of the colloidal stabilizations of the stabilized carbonate particles with different molecular structures of the surfactant. The diffusion of spin-probe molecules into the surfactant shells were studied by applying a starting force to push the molecules towards the carbonate surfaces and then observing the ensuing behavior. The simulations are in accordance with the ESR data and show that the geometrical

  3. [Escherichia coli, other Enterobacteriaceae and additional indicators as markers of microbiologic quality of food: advantages and limitations].

    PubMed

    Mossel, D A; Struijk, C B

    1995-03-01

    The 93/43 European Union directive assigns to the food and catering industries the main responsibility for an integrated safety and quality assurance strategy in the food chain. Relying on hazard analysis, followed by design and adoption of control of all critical points and practices ("HACCP"). Hiatus-free compliance with such HACCP-based Codes of Good Practices is to be assessed by monitoring, recording results on process performance charts and gauging such data against experimentally established, attainable and maintainable references ranges ("standards"). Marker microorganisms are a major analytical tool for validating compliance in the sense of the EU directive. They should be expertly chosen amongst microbes usually present in food so that their, whose presence in quantities exceeding predetermined levels point to a lack of microbiological integrity of a food product. This may encompass (i) the potential presence of taxonomically, physiologically and ecologically related pathogens, markers are called index organisms; or else (ii) a lack of process integrity; in this case, markers are termed indicator organisms. The classical index organism was E. coli, introduced in the 1980's to monitor drinking water supplies. It is still used as an appropriate marker to assess the bacteriological safety of raw foods. In the 1920's the coli-aerogenes ("coliform") group was adopted as an indicator to validate the adequate processing, i.e. pasteurization of dairy products. Since the 1950's the entire Enterobacteriaceae taxon is preferred for the latter purpose because it is better defined in determinative sense and includes more organisms of significance. In some food and water supplies, processed for safety, more vigorous or more resistant organisms than the Gram-negative rods are reliable supplementary markers. These include Enterococcus spp., spores of the Clostridium genus, and bacteriophages of E. coli and Bacteroides fragilis mimicking the fate of enteric viruses under

  4. Identification of molecular markers associated with Verticillium wilt resistance in alfalfa (Medicago sativa L.) using high-resolution melting.

    PubMed

    Zhang, Tiejun; Yu, Long-Xi; McCord, Per; Miller, David; Bhamidimarri, Suresh; Johnson, David; Monteros, Maria J; Ho, Julie; Reisen, Peter; Samac, Deborah A

    2014-01-01

    Verticillium wilt, caused by the soilborne fungus, Verticillium alfalfae, is one of the most serious diseases of alfalfa (Medicago sativa L.) worldwide. To identify loci associated with resistance to Verticillium wilt, a bulk segregant analysis was conducted in susceptible or resistant pools constructed from 13 synthetic alfalfa populations, followed by association mapping in two F1 populations consisted of 352 individuals. Simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers were used for genotyping. Phenotyping was done by manual inoculation of the pathogen to replicated cloned plants of each individual and disease severity was scored using a standard scale. Marker-trait association was analyzed by TASSEL. Seventeen SNP markers significantly associated with Verticillium wilt resistance were identified and they were located on chromosomes 1, 2, 4, 7 and 8. SNP markers identified on chromosomes 2, 4 and 7 co-locate with regions of Verticillium wilt resistance loci reported in M. truncatula. Additional markers identified on chromosomes 1 and 8 located the regions where no Verticillium resistance locus has been reported. This study highlights the value of SNP genotyping by high resolution melting to identify the disease resistance loci in tetraploid alfalfa. With further validation, the markers identified in this study could be used for improving resistance to Verticillium wilt in alfalfa breeding programs.

  5. Targeted next-generation sequencing for the detection of ciprofloxacin resistance markers using molecular inversion probes

    PubMed Central

    Stefan, Christopher P.; Koehler, Jeffrey W.; Minogue, Timothy D.

    2016-01-01

    Antibiotic resistance (AR) is an epidemic of increasing magnitude requiring rapid identification and profiling for appropriate and timely therapeutic measures and containment strategies. In this context, ciprofloxacin is part of the first-line of countermeasures against numerous high consequence bacteria. Significant resistance can occur via single nucleotide polymorphisms (SNP) and deletions within ciprofloxacin targeted genes. Ideally, use of ciprofloxacin would be prefaced with AR determination to avoid overuse or misuse of the antibiotic. Here, we describe the development and evaluation of a panel of 44 single-stranded molecular inversion probes (MIPs) coupled to next-generation sequencing (NGS) for the detection of genetic variants known to confer ciprofloxacin resistance in Bacillus anthracis, Yersinia pestis, and Francisella tularensis. Sequencing results demonstrate MIPs capture and amplify targeted regions of interest at significant levels of coverage. Depending on the genetic variant, limits of detection (LOD) for high-throughput pooled sequencing ranged from approximately 300–1800 input genome copies. LODs increased 10-fold in the presence of contaminating human genome DNA. In addition, we show that MIPs can be used as an enrichment step with high resolution melt (HRM) real-time PCR which is a sensitive assay with a rapid time-to-answer. Overall, this technology is a multiplexable upfront enrichment applicable with multiple downstream molecular assays for the detection of targeted genetic regions. PMID:27174456

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

    PubMed

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

    2015-02-01

    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 24Sα 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.

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

    PubMed

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

    2012-12-01

    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 .

  8. [Liquid Biopsy: Detection of Molecular Markers for Treatment Decisions in Lung Cancer].

    PubMed

    Brückl, W M; Wirtz, R M; Bertsch, T; Ficker, J H; Jung, A

    2017-02-14

    Personalized, individualized, targeted therapy has successfully found entrance in the palliative treatment of lung cancer as they enable a personalized and individualized strategy going ahead with biomarker testing. Due to the crescending amount of predictive molecular and immunhistochemical analyses at different time points during therapy the need for more and actual tumor tissue increases; however these samples cannot always be obtained without major discomfort for the patients. Therefore, analyses from blood, the so called "liquid biopsy", is an alternative or additional method. Activating mutations in the EGFR gene and the inhibitory mutation T790 M can already be detected from blood during clinical routine. This review presents the status of liquid biopsy for diagnosis, prognosis and as predictive parameter during the course of therapy in lung cancer and gives an outlook on future developments.

  9. Detergent-dispersant additives based on high-molecular-weight alkylphenols

    SciTech Connect

    Kulieva, K.N.; Namazova, I.I.; Ismailova, N.D.; Dorokhina, I.V.

    1988-09-01

    This article describes the synthesis and investigation of Mannich bases produced for alkylphenols, obtained in turn from ethylene oligomers. These oligomers are the still bottoms from distillation products of high-temperature oligomerization of ethylene in the presence of triethylaluminum. Two narrow cuts obtained from the distillation of oligomer fraction were used to study the influence of ethylene oligomer molecular weight on the properties of the additives. The additives were blended in DS-11 oil to evaluate their detergency-dispersancy and other properties. Comparison blends were made with succinimide additives based on the same ethylene oligomers. The Mannich bases give improvements in the oxidation resistance, anticorrosion properties, and detergency-dispersancy of the DS-11 diesel oil.

  10. Uncovering molecular details of urea crystal growth in the presence of additives.

    PubMed

    Salvalaglio, Matteo; Vetter, Thomas; Giberti, Federico; Mazzotti, Marco; Parrinello, Michele

    2012-10-17

    Controlling the shape of crystals is of great practical relevance in fields like pharmacology and fine chemistry. Here we examine the paradigmatic case of urea which is known to crystallize from water with a needle-like morphology. To prevent this undesired effect, inhibitors that selectively favor or discourage the growth of specific crystal faces can be used. In urea the most relevant faces are the {001} and the {110} which are known to grow fast and slow, respectively. The relevant growth speed difference between these two crystal faces is responsible for the needle-like structure of crystals grown in water solution. To prevent this effect, additives are used to slow down the growth of one face relative to another, thus controlling the shape of the crystal. We study the growth of fast {001} and slow {110} faces in water solution and the effect of shape controlling inhibitors like biuret. Extensive sampling through molecular dynamics simulations provides a microscopic picture of the growth mechanism and of the role of the additives. We find a continuous growth mechanism on the {001} face, while the slow growing {110} face evolves through a birth and spread process, in which the rate-determining step is the formation on the surface of a two-dimensional crystalline nucleus. On the {001} face, growth inhibitors like biuret compete with urea for the adsorption on surface lattice sites; on the {110} face instead additives cannot interact specifically with surface sites and play a marginal sterical hindrance of the crystal growth. The free energies of adsorption of additives and urea are evaluated with advanced simulation methods (well-tempered metadynamics) allowing a microscopic understanding of the selective effect of additives. Based on this case study, general principles for the understanding of the anisotropic growth of molecular crystals from solutions are laid out. Our work is a step toward a rational development of novel shape-affecting additives.

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

    PubMed

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

    2007-11-01

    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.

  12. Size distribution of particle-phase molecular markers during a severe winter pollution episode.

    PubMed

    Kleeman, Michael J; Riddle, Sarah G; Jakober, Chris A

    2008-09-01

    Airborne particulate matter was collected using filter samplers and cascade impactors in six size fractions below 1.8 microm during a severe winter air pollution event at three sites in the Central Valley of California. The smallest size fraction analyzed was 0.056 < Dp <0.1 microm particle diameter, which accounts for the majority of the mass in the ultrafine (PM0.1) size range. Separate samples were collected during the daytime (10 a.m. to 6 p.m. PST) and nighttime (8 p.m. to 8 a.m. PST) to characterize diurnal patterns. Each sample was extracted with organic solvents and analyzed using gas chromatography mass spectrometry for molecular markers that can be used for size-resolved source apportionment calculations. Colocated impactor and filter measurements were highly correlated (R8 > 0.8) for retene, benzo[ghi]flouranthene, chrysene, benzo[b]fluoranthene, benzo[k]fluoranthene, benzo[e]pyrene, benzo[a]pyrene, perylene, indeno[1,2,3-cd]pyrene, benzo[ghi]perylene, coronene, MW302 polycyclic aromatic hydrocarbon (PAHs), 17beta(H)-21alpha(H)-30-norhopane, 17alpha(H)-21beta(H)-hopane, alphabetabeta-20R-C29-ethylcholestane, levoglucosan, and cholesterol. Of these compounds, levoglucosan was present in the highest concentration (60-2080 ng m(-3)) followed by cholesterol (6-35 ng m(-3)), PAHs (2-38 ng m(-3)), and hopanes and steranes (0-2 ng m(-3)). Nighttime concentrations were higher than daytime concentrations in all cases. Organic compound size distributions were generally similar to the total carbon size distributions during the nighttime but showed greater variability during the daytime. This may reflect the dominance of fresh emission in the stagnant surface layer during the evening hours and the presence of aged organic aerosol at the surface during the daytime when the atmosphere is better mixed. All of the measured organic compound particle size distributions had a single mode that peaked somewhere between 0.18 and 0.56 microm, but the width of each distribution

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

    PubMed

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

    2015-01-01

    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

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

    PubMed

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

    2013-03-01

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

  15. Molecular studies in olive (Olea europaea L.): overview on DNA markers applications and recent advances in genome analysis.

    PubMed

    Bracci, T; Busconi, M; Fogher, C; Sebastiani, L

    2011-04-01

    Olive (Olea europaea L.) is one of the oldest agricultural tree crops worldwide and is an important source of oil with beneficial properties for human health. This emblematic tree crop of the Mediterranean Basin, which has conserved a very wide germplasm estimated in more than 1,200 cultivars, is a diploid species (2n = 2x = 46) that is present in two forms, namely wild (Olea europaea subsp. europaea var. sylvestris) and cultivated (Olea europaea subsp. europaea var. europaea). In spite of its economic and nutritional importance, there are few data about the genetic of olive if compared with other fruit crops. Available molecular data are especially related to the application of molecular markers to the analysis of genetic variability in Olea europaea complex and to develop efficient molecular tools for the olive oil origin traceability. With regard to genomic research, in the last years efforts are made for the identification of expressed sequence tag, with particular interest in those sequences expressed during fruit development and in pollen allergens. Very recently the sequencing of chloroplast genome provided new information on the olive nucleotide sequence, opening the olive genomic era. In this article, we provide an overview of the most relevant results in olive molecular studies. A particular attention was given to DNA markers and their application that constitute the most part of published researches. The first important results in genome analysis were reported.

  16. Polydimethylsiloxane as a Macromolecular Additive for Enhanced Performance of Molecular Bulk Heterojunction Organic Solar Cells

    SciTech Connect

    Graham, Kenneth R.; Mei, Jianguo; Stalder, Romain; Shim, Jae Won; Cheun, Hyeunseok; Steffy, Fred; So, Franky; Kippelen, Bernard; Reynolds, John R.

    2011-03-15

    The effect of the macromolecular additive, polydimethylsiloxane (PDMS), on the performance of solution processed molecular bulk heterojunction solar cells is investigated, and the addition of PDMS is shown to improve device power conversion efficiency by ~70% and significantly reduce cell-to-cell variation, from a power conversion efficiency of 1.25 ± 0.37% with no PDMS to 2.16 ± 0.09% upon the addition of 0.1 mg/mL PDMS to the casting solution. The cells are based on a thiophene and isoindigo containing oligomer as the electron donor and [6,6]-phenyl-C61 butyric acid methyl ester (PC61BM) as the electron acceptor. PDMS is shown to have a strong influence on film morphology, with a significant decrease in film roughness and feature size observed. The morphology change leads to improved performance parameters, most notably an increase in the short circuit current density from 4.3 to 6.8 mA/cm2 upon addition of 0.1 mg/mL PDMS. The use of PDMS is of particular interest, as this additive appears frequently as a lubricant in plastic syringes commonly used in device fabrication; therefore, PDMS may unintentionally be incorporated into device active layers.

  17. Molecular diversity and population structure of the forage grass Hemarthria compressa (Poaceae) in south China based on SRAP markers.

    PubMed

    Huang, L-K; Zhang, X-Q; Xie, W-G; Zhang, J; Cheng, L; Yan, H D

    2012-08-16

    Hemarthria compressa is one of the most important and widely utilized forage crops in south China, owing to its high forage yield and capability of adaptation to hot and humid conditions. We examined the population structure and genetic variation within and among 12 populations of H. compressa in south China using sequence-related amplified polymorphism (SRAP) markers. High genetic diversity was found in these samples [percentage polymorphic bands (PPB) = 82.21%, Shannon's diversity index (I) = 0.352]. However, there was relatively low level of genetic diversity at the population level (PPB = 29.17%, I = 0.155). A high degree of genetic differentiation among populations was detected based on other measures and molecular markers (Nei's genetic diversity analysis: G(ST) = 54.19%; AMOVA analysis: F(ST) = 53.35%). The SRAP markers were found to be more efficient than ISSR markers for evaluating population diversity. Based on these findings, we propose changes in sampling strategies for appraising and utilizing the genetic resources of this species.

  18. Molecular scale evidence of new particle formation via sequential addition of HIO3

    PubMed Central

    Sipilä, Mikko; Sarnela, Nina; Jokinen, Tuija; Henschel, Henning; Junninen, Heikki; Kontkanen, Jenni; Richters, Stefanie; Kangasluoma, Juha; Franchin, Alessandro; Peräkylä, Otso; Rissanen, Matti P.; Ehn, Mikael; Vehkamäki, Hanna; Kurten, Theo; Berndt, Torsten; Petäjä, Tuukka; Worsnop, Douglas; Ceburnis, Darius; Kerminen, Veli-Matti; Kulmala, Markku; O’Dowd, Colin

    2016-01-01

    Homogeneous nucleation and subsequent cluster growth leads to the formation of new aerosol particles in the atmosphere1. Nucleation of sulphuric acid and organic vapours is thought to be responsible for new particle formation over continents1,2 while iodine oxide vapours have been implicated in particle formation over coastal regions3–7. Molecular clustering pathways involved in atmospheric particle formation have been elucidated in controlled laboratory studies of chemically simple systems2,8–10. But no direct molecular-level observations of nucleation in atmospheric field conditions involving either sulphuric acid, organic or iodine oxide vapours have been reported to date11. Here we report field data from Mace Head, Ireland and supporting data from northern Greenland and Queen Maud Land, Antarctica that allow for the identification of the molecular steps involved in new particle formation in an iodine-rich, coastal atmospheric environment. We find that the formation and initial growth process is almost exclusively driven by iodine oxoacids and iodine oxide vapours with average resulting cluster O:I ratios of 2.4. Based on the high O:I ratio, together with observed high concentrations of iodic acid, HIO3, we suggest that cluster formation primarily proceeds by sequential addition of iodic acid HIO3, followed by intra-cluster restructuring to I2O5 and recycling of water in the atmosphere or upon drying. Overall, our study provides ambient atmospheric molecular-level observations of nucleation, supporting the previously suggested role of iodine containing species in new particle formation3–7, 12–18, and identifies the key nucleating compound. PMID:27580030

  19. Ionic imbalance, in addition to molecular crowding, abates cytoskeletal dynamics and vesicle motility during hypertonic stress.

    PubMed

    Nunes, Paula; Roth, Isabelle; Meda, Paolo; Féraille, Eric; Brown, Dennis; Hasler, Udo

    2015-06-16

    Cell volume homeostasis is vital for the maintenance of optimal protein density and cellular function. Numerous mammalian cell types are routinely exposed to acute hypertonic challenge and shrink. Molecular crowding modifies biochemical reaction rates and decreases macromolecule diffusion. Cell volume is restored rapidly by ion influx but at the expense of elevated intracellular sodium and chloride levels that persist long after challenge. Although recent studies have highlighted the role of molecular crowding on the effects of hypertonicity, the effects of ionic imbalance on cellular trafficking dynamics in living cells are largely unexplored. By tracking distinct fluorescently labeled endosome/vesicle populations by live-cell imaging, we show that vesicle motility is reduced dramatically in a variety of cell types at the onset of hypertonic challenge. Live-cell imaging of actin and tubulin revealed similar arrested microfilament motility upon challenge. Vesicle motility recovered long after cell volume, a process that required functional regulatory volume increase and was accelerated by a return of extracellular osmolality to isosmotic levels. This delay suggests that, although volume-induced molecular crowding contributes to trafficking defects, it alone cannot explain the observed effects. Using fluorescent indicators and FRET-based probes, we found that intracellular ATP abundance and mitochondrial potential were reduced by hypertonicity and recovered after longer periods of time. Similar to the effects of osmotic challenge, isovolumetric elevation of intracellular chloride concentration by ionophores transiently decreased ATP production by mitochondria and abated microfilament and vesicle motility. These data illustrate how perturbed ionic balance, in addition to molecular crowding, affects membrane trafficking.

  20. Molecular-scale evidence of aerosol particle formation via sequential addition of HIO3

    NASA Astrophysics Data System (ADS)

    Sipilä, Mikko; Sarnela, Nina; Jokinen, Tuija; Henschel, Henning; Junninen, Heikki; Kontkanen, Jenni; Richters, Stefanie; Kangasluoma, Juha; Franchin, Alessandro; Peräkylä, Otso; Rissanen, Matti P.; Ehn, Mikael; Vehkamäki, Hanna; Kurten, Theo; Berndt, Torsten; Petäjä, Tuukka; Worsnop, Douglas; Ceburnis, Darius; Kerminen, Veli-Matti; Kulmala, Markku; O'Dowd, Colin

    2016-09-01

    Homogeneous nucleation and subsequent cluster growth leads to the formation of new aerosol particles in the atmosphere. The nucleation of sulfuric acid and organic vapours is thought to be responsible for the formation of new particles over continents, whereas iodine oxide vapours have been implicated in particle formation over coastal regions. The molecular clustering pathways that are involved in atmospheric particle formation have been elucidated in controlled laboratory studies of chemically simple systems, but direct molecular-level observations of nucleation in atmospheric field conditions that involve sulfuric acid, organic or iodine oxide vapours have yet to be reported. Here we present field data from Mace Head, Ireland, and supporting data from northern Greenland and Queen Maud Land, Antarctica, that enable us to identify the molecular steps involved in new particle formation in an iodine-rich, coastal atmospheric environment. We find that the formation and initial growth process is almost exclusively driven by iodine oxoacids and iodine oxide vapours, with average oxygen-to-iodine ratios of 2.4 found in the clusters. On the basis of this high ratio, together with the high concentrations of iodic acid (HIO3) observed, we suggest that cluster formation primarily proceeds by sequential addition of HIO3, followed by intracluster restructuring to I2O5 and recycling of water either in the atmosphere or on dehydration. Our study provides ambient atmospheric molecular-level observations of nucleation, supporting the previously suggested role of iodine-containing species in the formation of new aerosol particles, and identifies the key nucleating compound.

  1. Molecular-scale evidence of aerosol particle formation via sequential addition of HIO3.

    PubMed

    Sipilä, Mikko; Sarnela, Nina; Jokinen, Tuija; Henschel, Henning; Junninen, Heikki; Kontkanen, Jenni; Richters, Stefanie; Kangasluoma, Juha; Franchin, Alessandro; Peräkylä, Otso; Rissanen, Matti P; Ehn, Mikael; Vehkamäki, Hanna; Kurten, Theo; Berndt, Torsten; Petäjä, Tuukka; Worsnop, Douglas; Ceburnis, Darius; Kerminen, Veli-Matti; Kulmala, Markku; O'Dowd, Colin

    2016-09-22

    Homogeneous nucleation and subsequent cluster growth leads to the formation of new aerosol particles in the atmosphere. The nucleation of sulfuric acid and organic vapours is thought to be responsible for the formation of new particles over continents, whereas iodine oxide vapours have been implicated in particle formation over coastal regions. The molecular clustering pathways that are involved in atmospheric particle formation have been elucidated in controlled laboratory studies of chemically simple systems, but direct molecular-level observations of nucleation in atmospheric field conditions that involve sulfuric acid, organic or iodine oxide vapours have yet to be reported. Here we present field data from Mace Head, Ireland, and supporting data from northern Greenland and Queen Maud Land, Antarctica, that enable us to identify the molecular steps involved in new particle formation in an iodine-rich, coastal atmospheric environment. We find that the formation and initial growth process is almost exclusively driven by iodine oxoacids and iodine oxide vapours, with average oxygen-to-iodine ratios of 2.4 found in the clusters. On the basis of this high ratio, together with the high concentrations of iodic acid (HIO3) observed, we suggest that cluster formation primarily proceeds by sequential addition of HIO3, followed by intracluster restructuring to I2O5 and recycling of water either in the atmosphere or on dehydration. Our study provides ambient atmospheric molecular-level observations of nucleation, supporting the previously suggested role of iodine-containing species in the formation of new aerosol particles, and identifies the key nucleating compound.

  2. Towards the design of new and improved drilling fluid additives using molecular dynamics simulations.

    PubMed

    Anderson, Richard L; Greenwel, H Christopher; Suter, James L; Jarvis, Rebecca M; Coveney, Peter V

    2010-03-01

    During exploration for oil and gas, a technical drilling fluid is used to lubricate the drill bit, maintain hydrostatic pressure, transmit sensor readings, remove rock cuttings and inhibit swelling of unstable clay based reactive shale formations. Increasing environmental awareness and resulting legislation has led to the search for new, improved biodegradable drilling fluid components. In the case of additives for clay swelling inhibition, an understanding of how existing effective additives interact with clays must be gained to allow the design of improved molecules. Owing to the disordered nature and nanoscopic dimension of the interlayer pores of clay minerals, computer simulations have become an increasingly useful tool for studying clay-swelling inhibitor interactions. In this work we briefly review the history of the development of technical drilling fluids, the environmental impact of drilling fluids and the use of computer simulations to study the interactions between clay minerals and swelling inhibitors. We report on results from some recent large-scale molecular dynamics simulation studies on low molecular weight water-soluble macromolecular inhibitor molecules. The structure and interactions of poly(propylene oxide)-diamine, poly(ethylene glycol) and poly(ethylene oxide)-diacrylate inhibitor molecules with montmorillonite clay are studied.

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A number of molecular marker linkage maps have been developed for melon (Cucumis melo L.) over the last two decades. However, these maps were constructed using different marker sets, thus, making comparative analysis among maps difficult. In order to solve this problem, a consensus genetic map in ...

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

    SciTech Connect

    Gunter, L.E.

    2001-08-23

    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.

  5. Genomic-Enabled Prediction Based on Molecular Markers and Pedigree Using the Bayesian Linear Regression Package in R

    PubMed Central

    Pérez, Paulino; de los Campos, Gustavo; Crossa, José; Gianola, Daniel

    2010-01-01

    The availability of dense molecular markers has made possible the use of genomic selection in plant and animal breeding. However, models for genomic selection pose several computational and statistical challenges and require specialized computer programs, not always available to the end user and not implemented in standard statistical software yet. The R-package BLR (Bayesian Linear Regression) implements several statistical procedures (e.g., Bayesian Ridge Regression, Bayesian LASSO) in a unifi ed framework that allows including marker genotypes and pedigree data jointly. This article describes the classes of models implemented in the BLR package and illustrates their use through examples. Some challenges faced when applying genomic-enabled selection, such as model choice, evaluation of predictive ability through cross-validation, and choice of hyper-parameters, are also addressed. PMID:21566722

  6. Gene Classification and Mining of Molecular Markers Useful in Red Clover (Trifolium pratense) Breeding

    PubMed Central

    Ištvánek, Jan; Dluhošová, Jana; Dluhoš, Petr; Pátková, Lenka; Nedělník, Jan; Řepková, Jana

    2017-01-01

    Red clover (Trifolium pratense) is an important forage plant worldwide. This study was directed to broadening current knowledge of red clover's coding regions and enhancing its utilization in practice by specific reanalysis of previously published assembly. A total of 42,996 genes were characterized using Illumina paired-end sequencing after manual revision of Blast2GO annotation. Genes were classified into metabolic and biosynthetic pathways in response to biological processes, with 7,517 genes being assigned to specific pathways. Moreover, 17,727 enzymatic nodes in all pathways were described. We identified 6,749 potential microsatellite loci in red clover coding sequences, and we characterized 4,005 potential simple sequence repeat (SSR) markers as generating polymerase chain reaction products preferentially within 100–350 bp. Marker density of 1 SSR marker per 12.39 kbp was achieved. Aligning reads against predicted coding sequences resulted in the identification of 343,027 single nucleotide polymorphism (SNP) markers, providing marker density of one SNP marker per 144.6 bp. Altogether, 95 SSRs in coding sequences were analyzed for 50 red clover varieties and a collection of 22 highly polymorphic SSRs with pooled polymorphism information content >0.9 was generated, thus obtaining primer pairs for application to diversity studies in T. pratense. A set of 8,623 genome-wide distributed SNPs was developed and used for polymorphism evaluation in individual plants. The polymorphic information content ranged from 0 to 0.375. Temperature switch PCR was successfully used in single-marker SNP genotyping for targeted coding sequences and for heterozygosity or homozygosity confirmation in validated five loci. Predicted large sets of SSRs and SNPs throughout the genome are key to rapidly implementing genome-based breeding approaches, for identifying genes underlying key traits, and for genome-wide association studies. Detailed knowledge of genetic relationships among

  7. Molecular characterization and marker based chemotaxonomic studies of Podophyllum hexandrum Royle.

    PubMed

    Sultan, Phalisteen; Shawl, A S; Rehman, Suriya; Ahmed, S Fayaz; Ramteke, P W

    2010-06-01

    Detailed chemical studies and RAPD analysis were done in different populations of Podophyllum hexandrum collected from high altitude regions of North Western Himalayas. Random amplified polymorphic DNA (RAPD) analysis revealed a high degree of genetic diversity among the 12 collected accessions, attributed to their geographical and climatic conditions. HPLC analysis also revealed variation in the concentration of two major marker compounds which lead to the identification of a chemotype. The study demonstrated that RAPD and chemical markers are very useful tools to compare the genetic relationship and pattern of variation among such prioritized and endangered medicinal plants.

  8. Comparison of RAPD, ISSR, and AFLP Molecular Markers to Reveal and Classify Orchardgrass (Dactylis glomerata L.) Germplasm Variations

    PubMed Central

    Costa, Rita; Pereira, Graça; Garrido, Inmaculada; Tavares-de-Sousa, Manuel María; Espinosa, Francisco

    2016-01-01

    Three different DNA-based techniques, Random Amplified Polymorphic DNA (RAPD), Inter Simple Sequence Repeat (ISSR) and Amplified Fragment Length Polymorphism (AFLP) markers, were used for fingerprinting Dactylis glomerata genotypes and for detecting genetic variation between the three different subspecies. In this study, RAPD assays produced 97 bands, of which 40 were polymorphic (41.2%). The ISSR primers amplified 91 bands, and 54 showed polymorphism (59.3%). Finally, the AFLP showed 100 bands, of which 92 were polymorphic (92%). The fragments were scored as present (1) or absent (0), and those readings were entered in a computer file as a binary matrix (one for each marker). Three cluster analyses were performed to express–in the form of dendrograms–the relationships among the genotypes and the genetic variability detected. All DNA-based techniques used were able to amplify all of the genotypes. There were highly significant correlation coefficients between cophenetic matrices based on the genetic distance for the RAPD, ISSR, AFLP, and combined RAPD-ISSR-AFLP data (0.68, 0.78, 0.70, and 0.70, respectively). Two hypotheses were formulated to explain these results; both of them are in agreement with the results obtained using these three types of molecular markers. We conclude that when we study genotypes close related, the analysis of variability could require more than one DNA-based technique; in fact, the genetic variation present in different sources could interfere or combine with the more or less polymorphic ability, as our results showed for RAPD, ISSR and AFLP markers. Our results indicate that AFLP seemed to be the best-suited molecular assay for fingerprinting and assessing genetic relationship among genotypes of Dactylis glomerata. PMID:27070939

  9. Evaluation of white spot syndrome virus variable DNA loci as molecular markers of virus spread at intermediate spatiotemporal scales.

    PubMed

    Dieu, Bui Thi Minh; Marks, Hendrik; Zwart, Mark P; Vlak, Just M

    2010-05-01

    Variable genomic loci have been employed in a number of molecular epidemiology studies of white spot syndrome virus (WSSV), but it is unknown which loci are suitable molecular markers for determining WSSV spread on different spatiotemporal scales. Although previous work suggests that multiple introductions of WSSV occurred in central Vietnam, it is largely uncertain how WSSV was introduced and subsequently spread. Here, we evaluate five variable WSSV DNA loci as markers of virus spread on an intermediate (i.e. regional) scale, and develop a detailed and statistically supported model for the spread of WSSV. The genotypes of 17 WSSV isolates from along the coast of Vietnam--nine of which were newly characterized in this study--were analysed to obtain sufficient samples on an intermediate scale and to allow statistical analysis. Only the ORF23/24 variable region is an appropriate marker on this scale, as geographically proximate isolates show similar deletion sizes. The ORF14/15 variable region and variable-number tandem repeat (VNTR) loci are not useful as markers on this scale. ORF14/15 may be suitable for studying larger spatiotemporal scales, whereas VNTR loci are probably suitable for smaller scales. For ORF23/24, there is a clear pattern in the spatial distribution of WSSV: the smallest genomic deletions are found in central Vietnam, and larger deletions are found in the south and the north. WSSV genomic deletions tend to increase over time with virus spread in cultured shrimp, and our data are therefore congruent with the hypothesis that WSSV was introduced in central Vietnam and then radiated out.

  10. Comparison of RAPD, ISSR, and AFLP Molecular Markers to Reveal and Classify Orchardgrass (Dactylis glomerata L.) Germplasm Variations.

    PubMed

    Costa, Rita; Pereira, Graça; Garrido, Inmaculada; Tavares-de-Sousa, Manuel María; Espinosa, Francisco

    2016-01-01

    Three different DNA-based techniques, Random Amplified Polymorphic DNA (RAPD), Inter Simple Sequence Repeat (ISSR) and Amplified Fragment Length Polymorphism (AFLP) markers, were used for fingerprinting Dactylis glomerata genotypes and for detecting genetic variation between the three different subspecies. In this study, RAPD assays produced 97 bands, of which 40 were polymorphic (41.2%). The ISSR primers amplified 91 bands, and 54 showed polymorphism (59.3%). Finally, the AFLP showed 100 bands, of which 92 were polymorphic (92%). The fragments were scored as present (1) or absent (0), and those readings were entered in a computer file as a binary matrix (one for each marker). Three cluster analyses were performed to express--in the form of dendrograms--the relationships among the genotypes and the genetic variability detected. All DNA-based techniques used were able to amplify all of the genotypes. There were highly significant correlation coefficients between cophenetic matrices based on the genetic distance for the RAPD, ISSR, AFLP, and combined RAPD-ISSR-AFLP data (0.68, 0.78, 0.70, and 0.70, respectively). Two hypotheses were formulated to explain these results; both of them are in agreement with the results obtained using these three types of molecular markers. We conclude that when we study genotypes close related, the analysis of variability could require more than one DNA-based technique; in fact, the genetic variation present in different sources could interfere or combine with the more or less polymorphic ability, as our results showed for RAPD, ISSR and AFLP markers. Our results indicate that AFLP seemed to be the best-suited molecular assay for fingerprinting and assessing genetic relationship among genotypes of Dactylis glomerata.

  11. Molecular diagnostic assays for cervical neoplasia: emerging markers for the detection of high-grade cervical disease.

    PubMed

    Malinowski, Douglas P

    2005-04-01

    The accurate detection and diagnosis of cervical carcinoma and its malignant precursors (collectively referred to as high-grade cervical disease) represents one of the current challenges in clinical medicine and cytopathology. The advent of molecular diagnostics and the use of whole-genome profiling using DNA microarrays promises to yield improved understanding of the disease process with the subsequent development of more accurate diagnostic procedures based upon these discoveries. Recent reports describing a variety of experimental approaches have identified a series of candidate genes that are overexpressed in cervical carcinoma. In this article, representative examples of these markers and the resulting translational research will be reviewed within the context of improved cervical disease detection. An emerging class of markers, the minichromosome maintenance protein family of DNA licensing factors (MCM-2, MCM-6, MCM-7), shows promise for the specific detection of high-grade cervical disease using simple antibody-based immunochemistry formats. These proteins are overexpressed in cervical disease as a result of infection by oncogenic strains of human papillomavirus (HPV) and subsequent uncontrolled activation of gene transcription and aberrant S-phase induction, mediated through the E2F transcription factor pathway. This behavior appears to be a hallmark of high-grade cervical disease and provides the link between oncogenic HPV infections and the molecular behavior of cervical neoplasia (CN). The use of these molecular descriptors of CN in simple immunochemistry formats compatible with conventional cytology preparations is anticipated to improve the screening and detection of cervical disease within the healthcare system.

  12. Small renal masses: The molecular markers associated with outcome of patients with kidney tumors 7 cm or less

    NASA Astrophysics Data System (ADS)

    Spirina, L. V.; Usynin, Y. A.; Kondakova, I. V.; Yurmazov, Z. A.; Slonimskaya, E. M.; Pikalova, L. V.

    2016-08-01

    The investigation of molecular mechanisms of tumor cell behavior in small renal masses is required to achieve the better cancer survival. The aim of the study is to find molecular markers associated with outcome of patients with kidney tumors 7 cm or less. A homogenous group of 20 patients T1N0M0-1 (mean age 57.6 ± 2.2 years) with kidney cancer was selected for the present analysis. The content of transcription and growth factors was determined by ELISA. The levels of AKT-mTOR signaling pathway components were measured by Western blotting analysis. The molecular markers associated with unfavorable outcome of patients with kidney tumors 7 cm or less were high levels of NF-kB p50, NF-kB p65, HIF-1, HIF-2, VEGF and CAIX. AKT activation with PTEN loss also correlated with the unfavorable outcome of kidney cancer patients with tumor size 7 cm or less. It is observed that the biological features of kidney cancer could predict the outcome of patients.

  13. Serum levels of GFAP and EGFR in primary and recurrent high-grade gliomas: correlation to tumor volume, molecular markers, and progression-free survival.

    PubMed

    Kiviniemi, Aida; Gardberg, Maria; Frantzén, Janek; Parkkola, Riitta; Vuorinen, Ville; Pesola, Marko; Minn, Heikki

    2015-09-01

    Our aim was to study the association of two potential serum biomarkers glial fibrillary acidic protein (GFAP) and epidermal growth factor receptor (EGFR) with prognostic markers such as IDH1 mutation, tumor burden, and survival in patients with high-grade gliomas (HGG). Additionally, our objective was to evaluate the potential of serum EGFR as a surrogate marker for EGFR status in the tumor. Pre-operative serum samples were prospectively collected from patients with primary (n = 17) or recurrent (n = 10) HGG. Serum GFAP and EGFR levels were determined by ELISA and studied for correlation with molecular markers including EGFR amplification, tumor volume in contrast-enhanced T1-weighted MRI, and progression-free survival (PFS). Pre-operative serum GFAP level of ≥0.014 ng/ml was 86 % sensitive and 85 % specific for the diagnosis of glioblastoma. High GFAP was related to the lack of IDH1 mutation (P = 0.016), high Ki67 proliferation index (P < 0.001), and poor PFS (HR 5.9, CI 1.2-29.9, P = 0.032). Serum GFAP correlated with enhancing tumor volume in primary (r = 0.64 P = 0.005), but also in recurrent HGGs (r = 0.76 P = 0.011). In contrast, serum EGFR levels did not differ between HGG patients and 13 healthy controls, and were not related to EGFR status in the tumor. We conclude that high serum GFAP associates with IDH1 mutation-negative HGG, and poor PFS. Correlation with tumor burden in recurrent HGG implicates the potential of serum GFAP for detection of tumor recurrence. Our results suggest that circulating EGFR is not derived from glioma cells and cannot be used as a marker for EGFR status in the tumor.

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

    PubMed Central

    2013-01-01

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

  15. A Molecular Marker-Based Linkage Map of Phaseolus Vulgaris L

    PubMed Central

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

    1992-01-01

    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 betwen 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

  16. Molecular characterization of the marker chromosome associated with cat eye syndrome

    SciTech Connect

    Mears, A.J.; McDermid, H.E. ); Duncan, A.M.V. ); Budarf, M.L.; Emanuel, B.S.; Sellinger, B. ); Siegel-Bartelt, J. ); Greenberg, C.R. )

    1994-07-01

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

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

    PubMed

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

    1992-07-01

    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.

  18. Molecular characterization of the marker chromosome associated with cat eye syndrome.

    PubMed

    Mears, A J; Duncan, A M; Budarf, M L; Emanuel, B S; Sellinger, B; Siegel-Bartelt, J; Greenberg, C R; McDermid, H E

    1994-07-01

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

  19. 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...

  20. Molecular characterization of peach [Prunus persica (L.) Batsch] germplasm in the United States using microsatellite markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Peach [Prunus persica (L.) Batsch] is an important medicinal fruit with immense health benefits and antioxidant activity. In this study, microsatellite markers were used as DNA fingerprinting tools for the identification and characterization of peach germplasm in the United States. Eleven microsatel...

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

    EPA Science Inventory

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

  2. Molecular characterization of the marker chromosome associated with cat eye syndrome.

    PubMed Central

    Mears, A. J.; Duncan, A. M.; Budarf, M. L.; Emanuel, B. S.; Sellinger, B.; Siegel-Bartelt, J.; Greenberg, C. R.; McDermid, H. E.

    1994-01-01

    Cat eye syndrome (CES) is associated with a supernumerary bisatellited marker chromosome which is derived from duplicated regions of 22pter-22q11.2. In this study we have used dosage and RFLP analyses on 10 CES patients with marker chromosomes, by using probes to five loci mapped to 22q11.2. The sequences recognized by the probes D22S9, D22S43, and D22S57 are in four copies in all patients, but the sequences at the more distal loci, D22S36 and D22S75, are duplicated only in some individuals. D22S36 is present in three copies in some individuals, and D22S75 is present in two copies in the majority of cases. Only three individuals have a duplication of the most distal locus examined (D22S75), and these individuals have the largest marker chromosomes identified in this study. From the dosage analysis it was found that the marker chromosomes are variable in size and can be asymmetric in nature. There is no obvious correlation between the severity of the phenotype and the size of the duplication. The distal boundary of the CES critical region (D22S36) is proximal to that of DiGeorge syndrome, a contiguous-gene-deletion syndrome of 22q11.2. Images Figure 1 Figure 2 Figure 3 PMID:7912885

  3. Molecular Markers of Diabetic Retinopathy: Potential Screening Tool of the Future?

    PubMed Central

    Pusparajah, Priyia; Lee, Learn-Han; Abdul Kadir, Khalid

    2016-01-01

    Diabetic retinopathy (DR) is among the leading causes of new onset blindness in adults. Effective treatment may delay the onset and progression of this disease provided it is diagnosed early. At present retinopathy can only be diagnosed via formal examination of the eye by a trained specialist, which limits the population that can be effectively screened. An easily accessible, reliable screening biomarker of diabetic retinopathy would be of tremendous benefit in detecting the population in need of further assessment and treatment. This review highlights specific biomarkers that show promise as screening markers to detect early diabetic retinopathy or even to detect patients at increased risk of DR at the time of diagnosis of diabetes. The pathobiology of DR is complex and multifactorial giving rise to a wide array of potential biomarkers. This review provides an overview of these pathways and looks at older markers such as advanced glycation end products (AGEs), inflammatory markers, vascular endothelial growth factor (VEGF) as well as other newer proteins with a role in the pathogenesis of DR including neuroprotective factors such as brain derived neurotrophic factor (BDNF) and Pigment Epithelium Derived Factor (PEDF); SA100A12, pentraxin 3, brain natriuretic peptide, apelin 3, and chemerin as well as various metabolites such as lipoprotein A, folate, and homocysteine. We also consider the possible role of proteins identified through proteomics work whose levels are altered in the sera of patients with DR as screening markers though their role in pathophysiology remains to be characterized. The role of microRNA as a promising new screening marker is also discussed. PMID:27313539

  4. Molecular Markers of Diabetic Retinopathy: Potential Screening Tool of the Future?

    PubMed

    Pusparajah, Priyia; Lee, Learn-Han; Abdul Kadir, Khalid

    2016-01-01

    Diabetic retinopathy (DR) is among the leading causes of new onset blindness in adults. Effective treatment may delay the onset and progression of this disease provided it is diagnosed early. At present retinopathy can only be diagnosed via formal examination of the eye by a trained specialist, which limits the population that can be effectively screened. An easily accessible, reliable screening biomarker of diabetic retinopathy would be of tremendous benefit in detecting the population in need of further assessment and treatment. This review highlights specific biomarkers that show promise as screening markers to detect early diabetic retinopathy or even to detect patients at increased risk of DR at the time of diagnosis of diabetes. The pathobiology of DR is complex and multifactorial giving rise to a wide array of potential biomarkers. This review provides an overview of these pathways and looks at older markers such as advanced glycation end products (AGEs), inflammatory markers, vascular endothelial growth factor (VEGF) as well as other newer proteins with a role in the pathogenesis of DR including neuroprotective factors such as brain derived neurotrophic factor (BDNF) and Pigment Epithelium Derived Factor (PEDF); SA100A12, pentraxin 3, brain natriuretic peptide, apelin 3, and chemerin as well as various metabolites such as lipoprotein A, folate, and homocysteine. We also consider the possible role of proteins identified through proteomics work whose levels are altered in the sera of patients with DR as screening markers though their role in pathophysiology remains to be characterized. The role of microRNA as a promising new screening marker is also discussed.

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

    PubMed

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

    2011-08-30

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

  6. Molecular Imprinting of Silica Nanoparticle Surfaces via Reversible Addition-Fragmentation Polymerization for Optical Biosensing Applications

    NASA Astrophysics Data System (ADS)

    Oluz, Zehra; Nayab, Sana; Kursun, Talya Tugana; Caykara, Tuncer; Yameen, Basit; Duran, Hatice

    Azo initiator modified surface of silica nanoparticles were coated via reversible addition-fragmentation polymerization (RAFT) of methacrylic acid and ethylene glycol dimethacrylate using 2-phenylprop 2-yl dithobenzoate as chain transfer agent. Using L-phenylalanine anilide as template during polymerization led molecularly imprinted nanoparticles. RAFT polymerization offers an efficient control of grafting process, while molecularly imprinted polymers shows enhanced capacity as sensor. L-phenylalanine anilide imprinted silica particles were characterized by X-Ray photoelectron spectroscopy (XPS), atomic force microscopy (AFM). Performances of the particles were followed by surface plasmon resonance spectroscopy (SPR) after coating the final product on gold deposited glass substrate against four different analogous of analyte molecules: D-henylalanine anilide, L-tyrosine, L-tryptophan and L-phenylalanine. Characterizations indicated that silica particles coated with polymer layer do contain binding sites for L-phenylalanine anilide, and are highly selective for the molecule of interest. This project was supported by TUBITAK (Project No:112M804).

  7. Power conversion efficiency enhancement in OPV devices using spin 1/2 molecular additives

    NASA Astrophysics Data System (ADS)

    Basel, Tek; Vardeny, Valy; Yu, Luping

    2014-03-01

    We investigated the power conversion efficiency of bulk heterojunction OPV cells based on the low bandgap polymer PTB7, blend with C61-PCBM. We also employed the technique of photo-induced absorption, PA; electrical and magneto-PA (MPA) techniques to understand the details of the photocurrent generation process in this blend. We found that spin 1/2 molecular additives, such as Galvinoxyl (Gxl) radicals dramatically enhance the cell efficiency; we obtained 20% increase in photocurrent upon Gxl doping with 2% weight. We explain our finding by the ability of the spin 1/2 radicals to interfere with the known major loss mechanism in the cell due to recombination of charge transfer exciton at the D-A interface via triplet excitons in the polymer donors. Supported by National Science Foundation-Material Science & Engineering Center (NSF-MRSEC), University of Utah.

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

    PubMed

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

    2012-01-01

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

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

    PubMed Central

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

    2012-01-01

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

  10. Solid phase extraction cleanup for non-polar and moderately polar molecular markers of PM 2.5 sources

    NASA Astrophysics Data System (ADS)

    Turlington, John M.; McDow, Stephen R.

    2010-06-01

    A solid phase extraction cleanup step substantially improved analytical efficiency and data quality for measurements of non-polar and moderately polar organic molecular marker concentrations in airborne particulate matter. Rapid gas chromatography column deterioration was evident after very few samples in the absence of a cleanup step, resulting in the need for frequent recalibration. High molecular weight polycyclic aromatic hydrocarbons, were among the species most strongly impacted by the deterioration, exhibiting deviations as high as 30-40% from expected calibration verification standard values after only a few injections. Column deterioration and calibration verification failure were eliminated by introducing a solid phase extraction step prior to analysis and a total of 58 samples were analyzed with no unacceptable deviation of calibration verification standards from target values

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

    PubMed

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

    2008-10-01

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

  12. Reconstruction of molecular phylogeny of closely related Amorphophallus species of India using plastid DNA marker and fingerprinting approaches.

    PubMed

    Gholave, Avinash R; Pawar, Kiran D; Yadav, Shrirang R; Bapat, Vishwas A; Jadhav, Jyoti P

    2017-01-01

    Plastid DNA markers sequencing and DNA fingerprinting approaches were used and compared for resolving molecular phylogeny of closely related, previously unexplored Amorphophallus species of India. The utility of individual plastid markers namely rbcL, matK, trnH-psbA, trnLC-trnLD, their combined dataset and two fingerprinting techniques viz. RAPD and ISSR were tested for their efficacy to resolves Amorphophallus species into three sections specific clades namely Rhaphiophallus, Conophallus and Amorphophallus. In the present study, sequences of these four plastid DNA regions as well as RAPD and ISSR profiles of 16 Amorphophallus species together with six varieties of two species were generated and analyzed. Maximum likelihood and Bayesian Inference based construction of phylogenetic trees indicated that among the four plastid DNA regions tested individually and their combined dataset, rbcL was found best suited for resolving closely related Amorphophallus species into section specific clades. When analyzed individually, rbcL exhibited better discrimination ability than matK, trnH-psbA, trnLC-trnLD and combination of all four tested plastid markers. Among two fingerprinting techniques used, the resolution of Amorphophallus species using RAPD was better than ISSR and combination of RAPD +ISSR and in congruence with resolution based on rbcL.

  13. Molecular markers for tolerance of European ash (Fraxinus excelsior) to dieback disease identified using Associative Transcriptomics

    PubMed Central

    Harper, Andrea L.; McKinney, Lea Vig; Nielsen, Lene Rostgaard; Havlickova, Lenka; Li, Yi; Trick, Martin; Fraser, Fiona; Wang, Lihong; Fellgett, Alison; Sollars, Elizabeth S. A.; Janacek, Sophie H.; Downie, J. Allan; Buggs, Richard. J. A.; Kjær, Erik Dahl; Bancroft, Ian

    2016-01-01

    Tree disease epidemics are a global problem, impacting food security, biodiversity and national economies. The potential for conservation and breeding in trees is hampered by complex genomes and long lifecycles, with most species lacking genomic resources. The European Ash tree Fraxinus excelsior is being devastated by the fungal pathogen Hymenoscyphus fraxineus, which causes ash dieback disease. Taking this system as an example and utilizing Associative Transcriptomics for the first time in a plant pathology study, we discovered gene sequence and gene expression variants across a genetic diversity panel scored for disease symptoms and identified markers strongly associated with canopy damage in infected trees. Using these markers we predicted phenotypes in a test panel of unrelated trees, successfully identifying individuals with a low level of susceptibility to the disease. Co-expression analysis suggested that pre-priming of defence responses may underlie reduced susceptibility to ash dieback. PMID:26757823

  14. Assessment of genetic diversity in indigenous turmeric (Curcuma longa) germplasm from India using molecular markers.

    PubMed

    Verma, Sushma; Singh, Shweta; Sharma, Suresh; Tewari, S K; Roy, R K; Goel, A K; Rana, T S

    2015-04-01

    Curcuma longa L., commonly known as turmeric, is one of the economically and medicinally important plant species. It is predominantly cultivated in the tropical and sub tropical countries. India is the largest producer, and exporter of turmeric in the world, followed by China, Indonesia, Bangladesh and Thailand. In the present study, Directed Amplification of Minisatellite DNA (DAMD) and Inter Simple Sequence Repeats (ISSR), methods were used to estimate the genetic variability in indigenous turmeric germplasm. Cumulative data analysis for DAMD (15) and ISSR (13) markers resulted into 478 fragments, out of which 392 fragments were polymorphic, revealing 82 % polymorphism across the turmeric genotypes. Wide range of pairwise genetic distances (0.03-0.59) across the genotypes revealed that these genotypes are genetically quite diverse. The UPGMA dendrogram generated using cumulative data showed significant relationships amongst the genotypes. All 29 genotypes studied grouped into two clusters irrespective of their geographical affiliations with 100 % bootstrap value except few genotypes, suggesting considerable diversity amongst the genotypes. These results suggested that the current collection of turmeric genotypes preserve the vast majority of natural variations. The results further demonstrate the efficiency and reliability of DAMD and ISSR markers in determining the genetic diversity and relationships among the indigenous turmeric germplasm. DAMD and ISSR profiling have identified diverse turmeric genotypes, which could be further utilized in various genetic improvement programmes including conventional as well as marker assisted breeding towards development of new and desirable turmeric genotypes.

  15. Supernumerary marker chromosomes derived from chromosome 6: cytogenetic, molecular cytogenetic, and array CGH characterization.

    PubMed

    Huang, Bing; Pearle, Phyllis; Rauen, Katherine A; Cotter, Philip D

    2012-07-01

    Supernumerary marker chromosomes (SMC) are relatively common in prenatal diagnosis. As the clinical outcomes vary greatly, a better understanding of the karyotype-phenotype correlation for different SMCs will be important for genetic counseling. We present two cases of prenatally detected de novo, small SMCs. The markers were present in 80% of amniocyte colonies in Case 1 and 38% of the colonies in Case 2. The SMCs were determined to be derived from chromosome 6 during postnatal confirmation studies. Although the sizes and the chromosomal origin of the SMCs in these two cases appeared to be similar, the clinical outcomes varied. The clinical manifestations observed in Case 1 included small for gestational age, feeding difficulty at birth, hydronephrosis, deviated septum and dysmorphic features, while the phenotype is apparently normal in Case 2. Array comparative genomic hybridization (CGH) was performed and showed increase in dosage for approximately 26 Mb of genetic material from the proximal short and long arms of chromosome 6 in Case 1. Results of array CGH were uninformative in Case 2, either due to mosaicism or lack of detectable euchromatin. The difference in the clinical presentation in these two patients may have resulted from the difference in the actual gene contents of the marker chromosomes and/or the differential distribution of the mosaicism.

  16. Diagnostic potential in prostate cancer of a panel of urinary molecular tumor markers.

    PubMed

    Talesa, Vincenzo N; Antognelli, Cinzia; Del Buono, Chiara; Stracci, Fabrizio; Serva, Maria R; Cottini, Emanuele; Mearini, Ettore

    2009-01-01

    Prostate cancer (PCa) is a heterogeneous, multifactorial and multifocal disease. Therefore, the search for a combination of assays using a panel of tumor markers is fundamental for a more precise and reliable diagnosis. In the present study we investigated the diagnostic value of five different genes, associated with PCa carcinogenesis, encoding for prostate-specific membrane antigen (PSMA), serine protease Hepsin, PCa antigen 3 (PCA3), UDP-N-acetyl-alpha-D-galatosamine transferase (GalNAC-T3) and prostate-specific antigen (PSA). Forty-four patients, with previously untreated, histologically verified PCa and forty-six patients with benign prostatic hyperplasia (BPH) were enrolled in this study. Absolute concentration of the transcript levels of each gene was calculated by quantitative Real-Time PCR analysis in urine sediments of men suffering from PCa or BPH after prostatic massage. The diagnostic value of a concomitant examination of these markers was evaluated by logistic regression analysis. We demonstrated that the diagnostic potential of the combined urinary PSA and PSMA level was significantly better than that of each singularly considered marker, including total serum PSA, the present gold standard test for PCa diagnosis.

  17. Tailoring the morphology of high molecular weight PLLA scaffolds through bioglass addition.

    PubMed

    Barroca, N; Daniel-da-Silva, A L; Vilarinho, P M; Fernandes, M H V

    2010-09-01

    Thermally induced phase separation (TIPS) has proven to be a suitable method for the preparation of porous structures for tissue engineering applications, and particular attention has been paid to increasing the pore size without the use of possible toxic surfactants. Within this context, an alternative method to control the porosity of polymeric scaffolds via the combination with a bioglass is proposed in this work. The addition of a bioactive glass from the 3CaO x P2O5-MgO-SiO2 system enables the porous structure of high molecular weight poly(l-lactic) acid (PLLA) scaffolds prepared by TIPS to be tailored. Bioglass acts as a nucleating catalyst agent of the PLLA matrix, promoting its crystallization, and the glass solubility controls the pore size. A significant increase in the pore size is observed as the bioglass content increases and scaffolds with large pore size (approximately 150 microm) can be prepared. In addition, the bioactive character of the scaffolds is proved by in vitro tests in synthetic plasma. The importance of this approach resides on the combination of the ability to tailor the porosity of polymeric scaffolds via the tunable solubility of bioglasses, without the use of toxic surfactants, leading to a composite structure with suitable properties for bone tissue engineering applications.

  18. Early Detection of Ovarian Cancer by Molecular Targeted Ultrasound Imaging Together with Serum Markers of Tumor-Associated Nuclear Change and Angiogenesis

    DTIC Science & Technology

    2013-10-01

    ultrasound molecular imaging agents enhances signal intensity and detection of OVCA’ was examined in specific aim 1 described in Year-1 report...improved the detection of OVCA at early stage. This improvement in OVCA detectability was due to the enhanced ultrasound imaging signal intensity ...Molecular Targeted Ultrasound Imaging Together with Serum Markers of Tumor-Associated Nuclear Change and Angiogenesis PRINCIPAL

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

    PubMed

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

    2007-06-01

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

  20. RNA-Seq SSRs of Moth Orchid and Screening for Molecular Markers across Genus Phalaenopsis (Orchidaceae)

    PubMed Central

    Lin, Yu-Shium; Chang, Chia-Hung; Chiang, Yu-Chung; Chou, Chang-Hung

    2015-01-01

    Background The moth orchid (Phalaenopsis species) is an ornamental crop that is highly commercialized worldwide. Over 30,000 cultivars of moth orchids have been registered at the Royal Horticultural Society (RHS). These cultivars were obtained by artificial pollination of interspecific hybridization. Therefore, the identification of different cultivars is highly important in the worldwide market. Methods/Results We used Illumina sequencing technology to analyze an important species for breeding, Phalaenopsis aphrodite subsp. formosana and develop the expressed sequence tag (EST)-simple sequence repeat (SSR) markers. After de novo assembly, the obtained sequence covered 29.1 Mb, approximately 2.2% of the P. aphrodite subsp. formosana genome (1,300 Mb), and a total of 1,439 EST-SSR loci were detected. SSR occurs in the exon region, including the 5’ untranslated region (UTR), coding region (CDS), and 3’UTR, on average every 20.22 kb. The di- and tri-nucleotide motifs (51.49% and 35.23%, respectively) were the two most frequent motifs in the P. aphrodite subsp. formosana. To validate the developed EST-SSR loci and to evaluate the transferability to the genus Phalaenopsis, thirty tri-nucleotide motifs of the EST-SSR loci were randomly selected to design EST-SSR primers and to evaluate the polymorphism and transferability across 22 native Phalaenopsis species that are usually used as parents for moth orchid breeding. Of the 30 EST-SSR loci, ten polymorphic and transferable SSR loci across the 22 native taxa can be obtained. The validated EST-SSR markers were further proven to discriminate 12 closely related Phalaenopsis cultivars. The results show that it is not difficult to obtain universal SSR markers by transcriptome deep sequencing in Phalaenopsis species. Conclusions This study supported that transcriptome analysis based on deep sequencing is a powerful tool to develop SSR loci in non-model species. A large number of EST-SSR loci can be isolated, and about 33

  1. Molecular Markers in Low-Grade Glioma-Toward Tumor Reclassification.

    PubMed

    Olar, Adriana; Sulman, Erik P

    2015-07-01

    Low-grade diffuse gliomas are a heterogeneous group of primary glial brain tumors with highly variable survival. Currently, patients with low-grade diffuse gliomas are stratified into risk subgroups by subjective histopathologic criteria with significant interobserver variability. Several key molecular signatures have emerged as diagnostic, prognostic, and predictor biomarkers for tumor classification and patient risk stratification. In this review, we discuss the effect of the most critical molecular alterations described in diffuse (IDH1/2, 1p/19q codeletion, ATRX, TERT, CIC, and FUBP1) and circumscribed (BRAF-KIAA1549, BRAF(V600E), and C11orf95-RELA fusion) gliomas. These molecular features reflect tumor heterogeneity and have specific associations with patient outcome that determine appropriate patient management. This has led to an important, fundamental shift toward developing a molecular classification of World Health Organization grade II-III diffuse glioma.

  2. Molecular and immunocytochemical characterization of primary neuronal cultures from adult rat brain: Differential expression of neuronal and glial protein markers.

    PubMed

    Ray, Balmiki; Bailey, Jason A; Sarkar, Sumit; Lahiri, Debomoy K

    2009-11-15

    Neurobiological studies using primary neuronal cultures commonly employ fetal-derived neurons, but much less often adult brain-derived neurons. Our goal is to perform morphological and molecular characterization of primary neuronal cultures from adult rat brain, including the relative expression of neuronal and glial cell markers at different time points. We tested the hypothesis that long-term neuronal viability is compatible with glial proliferation in adult neuron culture. We examined neuron culture from adult rat brain, which was maintained at steady state up to 24 days, and characterized them on the basis of cellular, molecular and biochemical properties at different time points of the culture. We identified neuronal and glial cells by both immunocytochemical and western immunoblotting techniques using NSE and Tau as neuronal markers and GFAP as glial protein marker, which revealed the presence of predominantly neuronal cells in the initial phase of the culture and a rise in glial cells from day 12 onwards. Notably, neuronal cells were preserved in the culture along with the glial cells even at day 24. Transfection of the cultured cells with a GFP expression vector and plasmids containing a luciferase reporter gene under the control of two different gene promoters demonstrated DNA transfectability. Taken together, these results suggest a differential expression of neuronal and glial cells at different time points and long-term neuronal viability in the presence of glial proliferation. Such adult neurons serve as a suitable system for the application of neurodegeneration models and for drug target discovery in various brain disorders including Alzheimer's disease.

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

    PubMed Central

    2013-01-01

    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

  4. Integrated Development of Serum Molecular Markers for Early Diagnosis of Breast Cancer

    DTIC Science & Technology

    2006-09-01

    Molecular Makers for Early Diagnosis of Breast Cancer PRINCIPAL INVESTIGATOR: Anna Lokshin, Ph.D. CONTRACTING ORGANIZATION: University of...NUMBER Integrated Development of Serum Molecular Makers for Early Diagnosis of Breast Cancer 5b. GRANT NUMBER DAMD17-03-1-0696 5c. PROGRAM...Therefore, studies at this stage involve screening people and lead to diagnosis and treatment. The aims of this phase include assessment of (i) the

  5. Identification of Brucella melitensis Rev.1 vaccine-strain genetic markers: Towards understanding the molecular mechanism behind virulence attenuation.

    PubMed

    Issa, Mohammad Nouh; Ashhab, Yaqoub

    2016-09-22

    Brucella melitensis Rev.1 is an avirulent strain that is widely used as a live vaccine to control brucellosis in small ruminants. Although an assembled draft version of Rev.1 genome has been available since 2009, this genome has not been investigated to characterize this important vaccine. In the present work, we used the draft genome of Rev.1 to perform a thorough genomic comparison and sequence analysis to identify and characterize the panel of its unique genetic markers. The draft genome of Rev.1 was compared with genome sequences of 36 different Brucella melitensis strains from the Brucella project of the Broad Institute of MIT and Harvard. The comparative analyses revealed 32 genetic alterations (30 SNPs, 1 single-bp insertion and 1 single-bp deletion) that are exclusively present in the Rev.1 genome. In silico analyses showed that 9 out of the 17 non-synonymous mutations are deleterious. Three ABC transporters are among the disrupted genes that can be linked to virulence attenuation. Out of the 32 mutations, 11 Rev.1 specific markers were selected to test their potential to discriminate Rev.1 using a bi-directional allele-specific PCR assay. Six markers were able to distinguish between Rev.1 and a set of control strains. We succeeded in identifying a panel of 32 genome-specific markers of the B. melitensis Rev.1 vaccine strain. Extensive in silico analysis showed that a considerable number of these mutations could severely affect the function of the associated genes. In addition, some of the discovered markers were able to discriminate Rev.1 strain from a group of control strains using practical PCR tests that can be applied in resource-limited settings.

  6. Imaging and Molecular Markers for Patients with Lung Cancer: Approaches with Molecular Targets, Complementary/Innovative Treatment, and Therapeutic Modalities

    DTIC Science & Technology

    2011-02-01

    as an official Department of the Army position, policy or decision unless so designated by other documentation. REPORT DOCUMENTATION PAGE Form...aim was completed as reported in the previous annual report. Aim 3 To design tools for molecular imaging of lung tumors. Summary of Research...Findings This project involves a clinical trial that is designed to evaluate the biological activity of RAD001 in patients with early stage non

  7. IMPACT (Imaging and Molecular Markers for Patients with Lung Cancer: Approaches with Molecular Targets and Complementary, Innovative and Therapeutic Modalities)

    DTIC Science & Technology

    2009-03-01

    or in combination with each other or with chemo and /or radiotherapy • To explore applications of molecular imaging for targeted therapy and...kinase) with/without radiotherapy for stage III NSCLC to improve the therapeutic ratio (i.e., increase malignant cell cytotoxicity without increasing...radiation therapy); 2) compliance, which is defined to be completion of concurrent chemoradiation and erlotinib/ radiotherapy with no more than minor

  8. Identification of molecular markers associated with leptine in reciprocal backcross families of diploid potato.

    PubMed

    Medina, B.; Fogelman, E.; Chani, E.; Miller, R.; Levin, I.; Levy, D.; Veilleux, E.

    2002-11-01

    Solanum phureja clone 1-3 and S. chacoense clone 80-1 have a zero and high leptine content in their foliage, respectively. An F(1) hybrid (CP2) was intermediate for the trait, but self-incompatible. Two reciprocal backcross families, PBCp ( phu 1-3 x CP2) and PBCc (CP2 x phu 1-3), and a family of monoploids derived by anther culture of CP2, were characterized for leptine as the aglycon, acetylleptinidine (ALD), content in leaves by gas chromatography. ALD was present in 43 of 87 genotypes in the PBCp backcross, implying simple genetic control by a dominant gene. However, the ALD levels were low compared to CP2. In the PBCc backcross, only 7 of 42 genotypes expressed ALD at a level generally higher than in PBCp. This ratio was significantly different from the 1:1 segregation observed in the reciprocal backcross and suggests a cytoplasmic influence. ALD levels in the CP2 monoploids ranged from 0 to 8,968 &mgr;g.g(-1) of dry weight (dw) with 18 individuals expressing ALD and five with 0 ALD content. Ten high (mean ALD = 546 &mgr;g.g(-1) of dw) and ten low (mean ALD = 0) individual plants within PBCp and seven high (mean ALD = 3,037 &mgr;g.g(-1) of dw) and eight low (mean ALD = 0) individual plants within PBCc were used for bulk segregant analysis (BSA) using 214 RAPD (randomly amplified polymorphic DNA) primers. Three RAPD primers (OPQ-2, OPT-16 and OPT-20) amplified bands exclusively in bulks containing DNA mixes of high ALD producers in both PBCp and PBCc populations. These results suggest that these markers were associated in coupling to ALD content. ANOVAs for ALD content verified association between the markers and the trait. A CAPS (cleaved amplified polymorphic sequence) marker, GP82A, was also significantly associated with ALD production in both the monoploid and the PBCp populations. None of the RAPD markers was associated to ALD in the monoploids but one was associated in repulsion. The monoploid data indicate the likelihood of a recessive gene(s) that

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

    PubMed Central

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

    2012-01-01

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

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

    PubMed

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

    2012-01-01

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

  11. Toolbox Approaches Using Molecular Markers and 16S rRNA Gene Amplicon Data Sets for Identification of Fecal Pollution in Surface Water

    PubMed Central

    Staley, C.; Sadowsky, M. J.; Gyawali, P.; Sidhu, J. P. S.; Palmer, A.; Beale, D. J.; Toze, S.

    2015-01-01

    In this study, host-associated molecular markers and bacterial 16S rRNA gene community analysis using high-throughput sequencing were used to identify the sources of fecal pollution in environmental waters in Brisbane, Australia. A total of 92 fecal and composite wastewater samples were collected from different host groups (cat, cattle, dog, horse, human, and kangaroo), and 18 water samples were collected from six sites (BR1 to BR6) along the Brisbane River in Queensland, Australia. Bacterial communities in the fecal, wastewater, and river water samples were sequenced. Water samples were also tested for the presence of bird-associated (GFD), cattle-associated (CowM3), horse-associated, and human-associated (HF183) molecular markers, to provide multiple lines of evidence regarding the possible presence of fecal pollution associated with specific hosts. Among the 18 water samples tested, 83%, 33%, 17%, and 17% were real-time PCR positive for the GFD, HF183, CowM3, and horse markers, respectively. Among the potential sources of fecal pollution in water samples from the river, DNA sequencing tended to show relatively small contributions from wastewater treatment plants (up to 13% of sequence reads). Contributions from other animal sources were rarely detected and were very small (<3% of sequence reads). Source contributions determined via sequence analysis versus detection of molecular markers showed variable agreement. A lack of relationships among fecal indicator bacteria, host-associated molecular markers, and 16S rRNA gene community analysis data was also observed. Nonetheless, we show that bacterial community and host-associated molecular marker analyses can be combined to identify potential sources of fecal pollution in an urban river. This study is a proof of concept, and based on the results, we recommend using bacterial community analysis (where possible) along with PCR detection or quantification of host-associated molecular markers to provide information on

  12. Molecular genetic survey of European mistletoe (Viscum album) subspecies with allele-specific and dCAPS type markers specific for chloroplast and nuclear DNA sequences.

    PubMed

    Piotrowski, Arkadiusz; Ochocka, J Renata; Stefanowicz, Justyna; ŁUczkiewicz, Maria

    2003-10-01

    The qualitative and quantitative content of mistletoe metabolites, and bioactivity of extracts is related to the subspecies of Viscum album L. These were indicated to be genetically distinct and host specific. We aimed to check (i) whether the specificity is strict and (ii) how frequently hybridization occurs among the subspecies. We designed two sets of allele-specific and dCAPS molecular genetic markers that would facilitate identification of Viscum album L. subspecies and their hybrid derivatives on the basis of chloroplast trnH(GUG)- trnK(UUU) and nuclear rDNA ITS1&2 sequences. Out of 118 plants surveyed, 103 displayed characteristics that confirmed strict host specificity of the subspecies, in addition, the results were compliant between nuclear and chloroplast markers showing no indication of hybridization among subspecies. From 15 samples that showed deviations from this model 13 came from the Mediterranean Sea basin, and only two originated from Central and Western Europe. Abbreviations. dCAPS:derived Cleaved Amplified Polymorphic Sequence ITS1&2:Internal Transcribed Spacers 1&2 MAMA:Mismatch Amplification Mutation Assay

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

    PubMed Central

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

    2009-01-01

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

  14. ITS-RFLP fingerprinting and molecular marker for detection of Fusarium oxysporum f.sp. ciceris.

    PubMed

    Dubey, S C; Tripathi, A; Singh, S R

    2010-11-01

    Genetic diversity of 11 representative isolates of Fusarium oxysporum f.sp. ciceris causing chickpea wilt was determined through internal transcribed spacer (ITS) region of the ribosomal DNA-restriction fragment length polymorphism (ITS-RFLP). ITS1+5.8s+ITS2 regions of the isolates were amplified with a set of primers ITS1 and ITS4 and amplified products were digested with 4 restriction enzymes (AluI, MboI, RsaI, MseI). Six different kinds of ITS-RFLP patterns were obtained. The ITS region of these isolates was sequenced and deposited to NCBI GeneBank. The nucleotide sequence homology of ITS region grouped the isolates into 5 categories. Primers were designed with sequence information using Primer 3 software. F. oxysporum f.sp. ciceris specific markers (FOC F2 and FOC R2) based on ITS region were developed for the first time for detection of the pathogen. The markers produced an amplicon of 292 bp; they were validated against the isolates of the pathogen collected from different locations of India.

  15. Diagnostic/prognostic molecular cytogenetic follow-up applied in satellited marker cases

    SciTech Connect

    Papenhausen, P.R.; Anderson, S.

    1994-09-01

    Special caution needs to be exercised in offering a good prognosis in Prader-Willi probe negative 15-derived marker cases, since it is clear that phenotypic effects can still be associated with the apparent presence of proximal sequences. We have had two postnatal cases in this category, one which was inherited from an unaffected paternal (non-mosaic) carrier, possibly demonstrating imprinting effects. Familial studies are continuing in this case. Although the D22/S9 locus appears diagnostic of cateye syndrome (CES), the dual specificity of the 14/22 centromeric probe leaves the possibility of a poor prognosis 14 derivation when the CES probe is negative. Therefore, it is imperative that proximal long arm 13, 14, 21 and more proximal 15 FISH probes be implemented so that a phenotypically correlated database may indicate the proper FISH probes necessary for accurate prognosis. Bisatellited markers is which a bipartite centromeric probe signal was found were considered to be higher risk than those with the single signal in counseling.

  16. Molecular marker assisted gene stacking for biotic and abiotic stress resistance genes in an elite rice cultivar

    PubMed Central

    Das, Gitishree; Rao, G. J. N.

    2015-01-01

    Severe yield loss due to various biotic stresses like bacterial blight (BB), gall midge (insect) and Blast (disease) and abiotic stresses like submergence and salinity are a serious constraint to the rice productivity throughout the world. The most effective and reliable method of management of the stresses is the enhancement of host resistance, through an economical and environmentally friendly approach. Through the application of marker assisted selection (MAS) technique, the present study reports a successful pyramidization of genes/QTLs to confer resistance/tolerance to blast (Pi2, Pi9), gall Midge (Gm1, Gm4), submergence (Sub1), and salinity (Saltol) in a released rice variety CRMAS2621-7-1 as Improved Lalat which had already incorporated with three BB resistance genes xa5, xa13, and Xa21 to supplement the Xa4 gene present in Improved Lalat. The molecular analysis revealed clear polymorphism between the donor and recipient parents for all the markers that are tagged to the target traits. The conventional backcross breeding approach was followed till BC3F1 generation and starting from BC1F1 onwards, marker assisted selection was employed at each step to monitor the transfer of the target alleles with molecular markers. The different BC3F1s having the target genes/QTLs were inter crossed to generate hybrids with all 10 stress resistance/tolerance genes/QTLs into a single plant/line. Homozygous plants for resistance/tolerance genes in different combinations were recovered. The BC3F3 lines were characterized for their agronomic and quality traits and promising progeny lines were selected. The SSR based background selection was done. Most of the gene pyramid lines showed a high degree of similarity to the recurrent parent for both morphological, grain quality traits and in SSR based background selection. Out of all the gene pyramids tested, two lines had all the 10 resistance/tolerance genes and showed adequate levels of resistance/tolerance against the five target

  17. Targeted next generation sequencing for the detection of ciprofloxacin resistance markers using molecular inversion probes

    DTIC Science & Technology

    2016-07-06

    detection of genetic variants known to confer ciprofloxacin resistance in Bacillus anthracis, Yersinia pestis, and Francisella tularensis. Sequencing...results demonstrate MIPs capture and amplify targeted regions of interest at significant levels of coverage. Depending on the genetic variant...multiple downstream molecular assays for the detection of targeted genetic regions. TR-16-130 DISTRIBUTION STATEMENT A: Approved for public release

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

    PubMed Central

    2012-01-01

    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

  19. Development of Molecular Markers for Determining Continental Origin of Wood from White Oaks (Quercus L. sect. Quercus)

    PubMed Central

    Schroeder, Hilke; Cronn, Richard; Yanbaev, Yulai; Jennings, Tara; Mader, Malte; Degen, Bernd; Kersten, Birgit

    2016-01-01

    To detect and avoid illegal logging of valuable tree species, identification methods for the origin of timber are necessary. We used next-generation sequencing to identify chloroplast genome regions that differentiate the origin of white oaks from the three continents; Asia, Europe, and North America. By using the chloroplast genome of Asian Q. mongolica as a reference, we identified 861 variant sites (672 single nucleotide polymorphisms (SNPs); 189 insertion/deletion (indel) polymorphism) from representative species of three continents (Q. mongolica from Asia; Q. petraea and Q. robur from Europe; Q. alba from North America), and we identified additional chloroplast polymorphisms in pools of 20 individuals each from Q. mongolica (789 variant sites) and Q. robur (346 variant sites). Genome sequences were screened for indels to develop markers that identify continental origin of oak species, and that can be easily evaluated using a variety of detection methods. We identified five indels and one SNP that reliably identify continent-of-origin, based on evaluations of up to 1078 individuals representing 13 white oak species and three continents. Due to the size of length polymorphisms revealed, this marker set can be visualized using capillary electrophoresis or high resolution gel (acrylamide or agarose) electrophoresis. With these markers, we provide the wood trading market with an instrument to comply with the U.S. and European laws that require timber companies to avoid the trade of illegally harvested timber. PMID:27352242

  20. Development of Molecular Markers for Determining Continental Origin of Wood from White Oaks (Quercus L. sect. Quercus).

    PubMed

    Schroeder, Hilke; Cronn, Richard; Yanbaev, Yulai; Jennings, Tara; Mader, Malte; Degen, Bernd; Kersten, Birgit

    2016-01-01

    To detect and avoid illegal logging of valuable tree species, identification methods for the origin of timber are necessary. We used next-generation sequencing to identify chloroplast genome regions that differentiate the origin of white oaks from the three continents; Asia, Europe, and North America. By using the chloroplast genome of Asian Q. mongolica as a reference, we identified 861 variant sites (672 single nucleotide polymorphisms (SNPs); 189 insertion/deletion (indel) polymorphism) from representative species of three continents (Q. mongolica from Asia; Q. petraea and Q. robur from Europe; Q. alba from North America), and we identified additional chloroplast polymorphisms in pools of 20 individuals each from Q. mongolica (789 variant sites) and Q. robur (346 variant sites). Genome sequences were screened for indels to develop markers that identify continental origin of oak species, and that can be easily evaluated using a variety of detection methods. We identified five indels and one SNP that reliably identify continent-of-origin, based on evaluations of up to 1078 individuals representing 13 white oak species and three continents. Due to the size of length polymorphisms revealed, this marker set can be visualized using capillary electrophoresis or high resolution gel (acrylamide or agarose) electrophoresis. With these markers, we provide the wood trading market with an instrument to comply with the U.S. and European laws that require timber companies to avoid the trade of illegally harvested timber.

  1. Polar organic marker compounds in atmospheric aerosol in the Po Valley during the Supersito campaigns - Part 1: Low molecular weight carboxylic acids in cold seasons

    NASA Astrophysics Data System (ADS)

    Pietrogrande, Maria Chiara; Bacco, Dimitri; Visentin, Marco; Ferrari, Silvia; Poluzzi, Vanes

    2014-04-01

    In the framework of the “Supersito” project, three intensive experimental campaigns were conducted in the Po Valley (Northern Italy) in cold seasons, such as late autumn, pre-winter and deep-winter, over three years from 2011 to 2013. As a part of a study on polar marker compounds, including carboxylic acids, sugar derivatives and lignin phenols, the present study reports a detailed discussion on the atmospheric concentrations of 14 low molecular weight carboxylic acids, mainly dicarboxylic and oxo-hydroxy carboxylic acids, as relevant markers of primary and secondary organic aerosols. PM2.5 samples were collected in two monitoring sites, representing urban and rural background stations. The total quantities of carboxylic acids were 262, 167 and 249 ng m-3 at the urban site and 308, 115, 248 ng m-3 at the rural site in pre-winter, fall and deep-winter, respectively. These high concentrations can be explained by the large human emission sources in the urbanized region, combined with the stagnant atmospheric conditions during the cold seasons that accumulate the organic precursors and accelerate the secondary atmospheric reactions. The distribution profiles of the investigated markers suggest the dominant contributions of primary anthropogenic sources, such as traffic, domestic heating and biomass burning. These results are confirmed by comparison with additional emission tracers, such as anhydro-saccharides for biomass burning and fatty acids originated from different anthropogenic sources. In addition, some secondary constituents were detected in both sites, as produced by in situ photo-chemical reactions from both biogenic (e.g. pinonic acid) and anthropogenic precursors (e.g. phthalic and adipic acids). The impact of different sources from human activities was elucidated by investigating the week pattern of carboxylic and fatty acid concentrations. The weekly trends of analytes during the warmer campaign (fall 2012; mean temperature: 12 °C) may be related to

  2. Molecular cloning and characterisation of the RESA gene, a marker of genetic diversity of Plasmodium falciparum.

    PubMed

    Moyano, Eva M; González, Luis Miguel; Cuevas, Laureano; Perez-Pastrana, Esperanza; Santa-Maria, Ysmael; Benito, Agustín

    2010-07-01

    To identity immunodiagnostic antigen genes, a Plasmodium falciparum (Dd2 clone) expression library was screened using human immune sera. The ring-infected erythrocyte surface antigen (RESA) was isolated: this antigen of the resistant clone presents repeat tandem sequences like the 3D7 clone, albeit in different numbers. RESA has been studied as a marker of genetic diversity, with different sizes being observed in different isolates and clones of Plasmodium falciparum. The native protein was localised in cultures by western-blot and immuno-transmission electron microscopy. The antigenicity of RESA was evaluated by ELISA, using the carboxy-terminal repeat region as antigen. The assay's sensitivity and specificity were 78.2 and 94% respectively.

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

    PubMed

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

    2014-11-01

    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.

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

    PubMed

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

    2009-12-01

    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.

  5. Subdivisions of the adult zebrafish pallium based on molecular marker analysis

    PubMed Central

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

    2015-01-01

    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

  6. Development of SCAR Markers Based on Improved RAPD Amplification Fragments and Molecular Cloning for Authentication of Herbal Medicines Angelica sinensis, Angelica acutiloba and Levisticum officinale.

    PubMed

    Zhang, Chun; Mei, Zhiqiang; Cheng, Jingliang; He, Yin; Khan, Md Asaduzzaman; Luo, Peiyi; Imani, Saber; Fu, Junjiang

    2015-10-01

    Molecular cloning from DNA fragments of improved RAPD amplification of Angelica sinensis, Angelica acutiloba and Levisticum officinale, provided novel sequence-characterized amplified region (SCAR) markers A13, A23, A1-34 and A1-0 whose sequences were deposited in the GenBank database with the accession numbers KP641315, KP641316, KP641317 and KP641318, respectively. By optional PCR amplification, the SCAR markers A13 and A23 are Levisticum officinale-specific, whereas the SCAR marker A1-34 is Angelica acutiloba-specific, and the SCAR marker A1-0 is Angelica sinensis-specific. These diagnostic SCAR markers may be useful for genetic authentications, for ecological conservation of all three medicinal plants and as a helpful tool for the genetic authentication of adulterant samples.

  7. Simultaneous analysis of five molecular markers provides a well-supported phylogenetic hypothesis for the living bony-tongue fishes (Osteoglossomorpha: Teleostei).

    PubMed

    Lavoué, Sébastien; Sullivan, John P

    2004-10-01

    Fishes of the Superorder Osteoglossomorpha (the "bonytongues") constitute a morphologically heterogeneous group of basal teleosts, including highly derived subgroups such as African electric fishes, the African butterfly fish, and Old World knifefishes. Lack of consensus among hypotheses of osteoglossomorph relationships advanced during the past 30 years may be due in part to the difficulty of identifying shared derived characters among the morphologically differentiated extant families of this group. In this study, we present a novel phylogenetic hypothesis for this group, based on the analysis of more than 4000 characters from five molecular markers (the mitochondrial cytochrome b, 12S and 16S rRNA genes, and the nuclear genes RAG2 and MLL). Our taxonomic sampling includes one representative of each extant non-mormyrid osteoglossomorph genus, one representative for the monophyletic family Mormyridae, and four outgroup taxa within the basal Teleostei. Maximum parsimony analysis of combined and equally weighted characters from the five molecular markers and Bayesian analysis provide a single, well-supported, hypothesis of osteoglossomorph interrelationships and show the group to be monophyletic. The tree topology is the following: (Hiodon alosoides, (Pantodon buchholzi, (((Osteoglossum bicirrhosum, Scleropages sp.), (Arapaima gigas, Heterotis niloticus)), ((Gymnarchus niloticus, Ivindomyrus opdenboschi), ((Notopterus notopterus, Chitala ornata), (Xenomystus nigri, Papyrocranus afer)))))). We compare our results with previously published phylogenetic hypotheses based on morpho-anatomical data. Additionally, we explore the consequences of the long terminal branch length for the taxon Pantodon buchholzi in our phylogenetic reconstruction and we use the obtained phylogenetic tree to reconstruct the evolutionary history of electroreception in the Notopteroidei.

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

    PubMed

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

    2011-06-01

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

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

    PubMed Central

    2014-01-01

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

  10. The 50- and 58-kdalton keratin classes as molecular markers for stratified squamous epithelia: cell culture studies

    PubMed Central

    1983-01-01

    The keratins are a highly heterogeneous group of proteins that form intermediate filaments in a wide variety of epithelial cells. These proteins can be divided into at least seven major classes according to their molecular weight and their immunological reactivity with monoclonal antibodies. Tissue-distribution studies have revealed a correlation between the expression of specific keratin classes and different morphological features of in vivo epithelial differentiation (simple vs. stratified; keratinized vs. nonkeratinized). Specifically, a 50,000- and a 58,000-dalton keratin class were found in all stratified epithelia but not in simple epithelia, and a 56,500- and a 65-67,000-dalton keratin class were found only in keratinized epidermis. To determine whether these keratin classes can serve as markers for identifying epithelial cells in culture, we analyzed cytoskeletal proteins from various cultured human cells by the immunoblot technique using AE1 and AE3 monoclonal antikeratin antibodies. The 56,500- and 65-67,000-dalton keratins were not expressed in any cultured epithelial cells examined so far, reflecting the fact that none of them underwent morphological keratinization. The 50,000- and 58,000-dalton keratin classes were detected in all cultured cells that originated from stratified squamous epithelia, but not in cells that originated from simple epithelia. Furthermore, human epidermal cells growing as a monolayer in low calcium medium continued to express the 50,000- and 58,000-dalton keratin classes. These findings suggest that the 50,000- and 58,000-dalton keratin classes may be regarded as "permanent" markers for stratified squamous epithelial cells (keratinocytes), and that the expression of these keratin markers does not depend on the process of cellular stratification. The selective expression of the 50,000- and 58,000-dalton keratin classes, which are synthesized in large quantities on a per cell basis, may explain the high keratin content of

  11. Sensitivity and bias of molecular marker-based aerosol source apportionment models to small conltibutions of coal combustion soot.

    PubMed

    Rutter, Andrew P; Snyder, David C; Schauer, James J; DeMinter, Jeff; Shelton, Brandon

    2009-10-15

    Carbonaceous atmospheric particulate matter (PM25) collected in the midwestern United States revealed that soot emissions from incomplete coal combustion were important sources of several organic molecular markers used in source apportionment studies. Despite not constituting a major source of organic carbon in the PM25, coal soot was an important source of polyaromatic hydrocarbons, hopanes, and elemental carbon. These marker compounds are becoming widely used for source apportionment of atmospheric organic PM, meaning that significant emissions of these marker compounds from unaccounted sources such as coal soot could bias apportionment results. This concept was demonstrated using measurements of atmospheric PM collected on a 1-in-6 day schedule at three monitoring sites in Ohio: Mingo Junction (near Steubenville), Cincinnati, and Cleveland. Impacts of coal sootwere measured to be significant at Mingo Junction and small at Cleveland and Cincinnati. As a result, biases in apportionment results were substantial at Mingo Junction and insignificant at Cleveland and Cincinnati. Misapportionments of organic carbon mass at Mingo Junction were significant when coal soot was detected in the particulate samples as identified bythe presence of picene, but when coal soot was not included in the model: gasoline engines (+8% to +58% of OC), smoking engines (0% to -17% of OC), biomass combustion (+1% to +11% of OC), diesel engines (-1% to -2% of OC), natural gas combustion (0% to -2% of OC), and unapportioned OC (0% to -47% of OC). These results suggest that the role of coal soot in source apportionment studies needs to be better examined in many parts of the United States and other parts of the world.

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

    PubMed

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

    2003-07-01

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

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

    PubMed Central

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

    2015-01-01

    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

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

    PubMed

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

    2015-01-26

    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.

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

    PubMed

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

    2015-02-28

    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.

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

    DTIC Science & Technology

    2014-12-01

    that this line of investigation should be extended to deeper DNA sequencing on a clinically relevant number of cases in order to establish prognostic...molecular biomarkers for PCa. 15. SUBJECT TERMS Prostate cancer, prognosis, diagnosis, CNV, genomics, DNA sequence, biopsy 16. SECURITY...begun our work on Objective 2. 2. KEYWORDS Prostate; cancer; biopsy; DNA copy number; DNA sequencing; biomarkers; lineage; single-cell DNA

  17. Genetic variation assessment of acid lime accessions collected from south of Iran using SSR and ISSR molecular markers.

    PubMed

    Sharafi, Ata Allah; Abkenar, Asad Asadi; Sharafi, Ali; Masaeli, Mohammad

    2016-01-01

    Iran has a long history of acid lime cultivation and propagation. In this study, genetic variation in 28 acid lime accessions from five regions of south of Iran, and their relatedness with other 19 citrus cultivars were analyzed using Simple Sequence Repeat (SSR) and Inter-Simple Sequence Repeat (ISSR) molecular markers. Nine primers for SSR and nine ISSR primers were used for allele scoring. In total, 49 SSR and 131 ISSR polymorphic alleles were detected. Cluster analysis of SSR and ISSR data showed that most of the acid lime accessions (19 genotypes) have hybrid origin and genetically distance with nucellar of Mexican lime (9 genotypes). As nucellar of Mexican lime are susceptible to phytoplasma, these acid lime genotypes can be used to evaluate their tolerance against biotic constricts like lime "witches' broom disease".

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

    NASA Astrophysics Data System (ADS)

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

    2014-09-01

    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.

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

    PubMed

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

    2011-05-01

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

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

    PubMed

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

    2005-12-01

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

  1. Development of molecular markers linked to disease resistance genes in common bean based on whole genome sequence.

    PubMed

    Meziadi, Chouaïb; Richard, Manon M S; Derquennes, Amandine; Thareau, Vincent; Blanchet, Sophie; Gratias, Ariane; Pflieger, Stéphanie; Geffroy, Valérie

    2016-01-01

    Common bean (Phaseolus vulgaris) is the most important grain legume for direct human consumption in the world, particularly in developing countries where it constitutes the main source of protein. Unfortunately, common bean yield stability is constrained by a number of pests and diseases. As use of resistant genotypes is the most economic and ecologically safe means for controlling plant diseases, efforts have been made to genetically characterize resistance genes (R genes) in common bean. Despite its agronomic importance, genomic resources available in common bean were limited until the recent sequencing of common bean genome (Andean genotype G19833). Besides allowing the annotation of Nucleotide Binding-Leucine Rich Repeat (NB-LRR) encoding gene family, which is the prevalent class of disease R genes in plants, access to the whole genome sequence of common bean can be of great help for intense selection to increase the overall efficiency of crop improvement programs using marker-assisted selection (MAS). This review presents the state of the art of common bean NB-LRR gene clusters, their peculiar location in subtelomeres and correlation with genetically characterized monogenic R genes, as well as how the availability of the whole genome sequence can boost the development of molecular markers for MAS.

  2. Transient In Vivo Resistance Mechanisms of Burkholderia pseudomallei to Ceftazidime and Molecular Markers for Monitoring Treatment Response

    PubMed Central

    Cummings, Jason E.; Slayden, Richard A.

    2017-01-01

    Much is known about the mode of action of drugs and resistance mechanisms under laboratory growth conditions, but research on the bacterial transcriptional response to drug pressure in vivo or efficacious mode of action and transient resistance mechanisms of clinically employed drugs is limited. Accordingly, to assess active alternative metabolism and transient resistance mechanisms, and identify molecular markers of treatment response, the in vivo transcriptional response of Burkholderia pseudomallei 1026b to treatment with ceftazidime in infected lungs was compared to the in vitro bacterial response in the presence of drug. There were 1,688 transcriptionally active bacterial genes identified that were unique to in vivo treated conditions. Of the in vivo transcriptionally active bacterial genes, 591 (9.4% coding capacity) genes were differentially expressed by ceftazidime treatment. In contrast, only 186 genes (2.7% coding capacity) were differentially responsive to ceftazidime treatment under in vitro culturing conditions. Within the genes identified were alternative PBP proteins that may compensate for target inactivation and transient resistance mechanisms, such as β-lactamses that may influence the potency of ceftazidime. This disparate observation is consistent with the thought that the host environment significantly alters the bacterial metabolic response to drug exposure compared to the response observed under in vitro growth. Notably, this study revealed 184 bacterial genes and ORFs that were unique to in vivo ceftazidime treatment and thus provide candidate molecular markers for treatment response. This is the first report of the unique transcriptional response of B. pseudomallei from host tissues in an animal model of infection and elucidates the in vivo metabolic vulnerabilities, which is important in terms of defining the efficacious mode of action and transient resistance mechanisms of a frontline meliodosis chemotherapeutic, and biomarkers for

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

    PubMed

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

    2011-11-03

    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.

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

    PubMed

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

    2012-07-19

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

  5. Dynamics of Virus Distribution in a Defined Swine Production Network Using Enteric Viruses as Molecular Markers.

    PubMed

    Lachapelle, Virginie; Letellier, Ann; Fravalo, Philippe; Brassard, Julie; L'Homme, Yvan

    2017-02-15

    Modern swine production systems represent complex and dynamic networks involving numerous stakeholders. For instance, livestock transporters carry live animals between fattening sites, abattoirs, and other premises on a daily basis. This interconnected system may increase the risk of microbial spread within and between networks, although little information is available in that regard. In the present study, a swine network composed of 10 finishing farms, one abattoir, and three types of stakeholders (veterinarians, livestock transporters, and nutritional technicians) in Quebec, Canada, was selected to investigate specific vectors and reservoirs of enteric viruses. Environmental samples were collected from the premises over a 12-month period. Samples were screened using targeted reverse transcription-PCR and sequencing of two selected viral markers, group A rotaviruses (RVA) and porcine astroviruses (PoAstV), both prevalent and genetically heterogeneous swine enteric viruses. The results revealed frequent contamination of farm sites (21.4 to 100%), livestock transporter vehicles (30.6 to 68.8%) and, most importantly, the abattoir yard (46.7 to 94.1%), depending on the sample types. Although high levels of strain diversity for both viruses were found, identical PoAstV and RVA strains were detected in specific samples from farms, the abattoir yard, and the livestock transporter vehicle, suggesting interconnections between these premises and transporters. Overall, the results from this study underscore the potential role of abattoirs and livestock transport as a reservoir and transmission route for enteric viruses within and between animal production networks, respectively.

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

    SciTech Connect

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

    1991-12-01

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

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

    PubMed Central

    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

    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

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

    PubMed

    Haider, N; Nabulsi, I

    2012-02-01

    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.

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

    PubMed

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

    2014-10-01

    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.

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

    PubMed

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

    2014-10-01

    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.

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

    PubMed Central

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

    2014-01-01

    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

  12. Acrocomia emensis (Arecaceae) genetic structure and diversity using SSR molecular markers.

    PubMed

    Neiva, D S; Melo Júnior, A F; Oliveira, D A; Royo, V A; Brandão, M M; Menezes, E V

    2016-03-24

    Acrocomia emensis, popularly known as the creeping tucum, belongs to the family Arecaceae, and is an oilseed specie of the Brazilian Savannah. The expansion of agricultural activity has rapidly destroyed its natural habitat, leading to a decrease in its population size. Genetic studies can be used to investigate the genetic variability, and may assist with the charting future conservation strategies. In this study the genetic diversity and structure of 150 individuals sampled in three locations in Minas Gerais were analysed, based on the transferability of six microsatellite markers, previously developed for A. aculeata. The results indicate that the populations studied have low levels of genetic variability (Ho = 0.148) and high, positive and significant inbreeding coefficient, indicating an excess of homozygotes. The average heterozygosity within the population (Hs = 0.700) accounted for 95.03% of the total genetic diversity, indicating that there is greater variability within population than between them, consistent with low genetic differentiation between population (GST = 0.046). Bayesian analysis identified three distinct groups; however, populations shared large numbers of alleles, which can be explained by the reduced distance between populations. These results reveal the need to implement genetic conservation programs for the maintenance of this species and to prioritize population from Bonito and Brasília, which showed the lowest values of genetic diversity.

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

    NASA Astrophysics Data System (ADS)

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

    2008-01-01

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

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

    PubMed

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

    2014-05-01

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

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

    PubMed

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

    2014-01-01

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

  16. Stretching human mesenchymal stromal cells on stiffness-customized collagen type I generates a smooth muscle marker profile without growth factor addition

    NASA Astrophysics Data System (ADS)

    Rothdiener, Miriam; Hegemann, Miriam; Uynuk-Ool, Tatiana; Walters, Brandan; Papugy, Piruntha; Nguyen, Phong; Claus, Valentin; Seeger, Tanja; Stoeckle, Ulrich; Boehme, Karen A.; Aicher, Wilhelm K.; Stegemann, Jan P.; Hart, Melanie L.; Kurz, Bodo; Klein, Gerd; Rolauffs, Bernd

    2016-10-01

    Using matrix elasticity and cyclic stretch have been investigated for inducing mesenchymal stromal cell (MSC) differentiation towards the smooth muscle cell (SMC) lineage but not in combination. We hypothesized that combining lineage-specific stiffness with cyclic stretch would result in a significantly increased expression of SMC markers, compared to non-stretched controls. First, we generated dense collagen type I sheets by mechanically compressing collagen hydrogels. Atomic force microscopy revealed a nanoscale stiffness range known to support myogenic differentiation. Further characterization revealed viscoelasticity and stable biomechanical properties under cyclic stretch with >99% viable adherent human MSC. MSCs on collagen sheets demonstrated a significantly increased mRNA but not protein expression of SMC markers, compared to on culture flasks. However, cyclic stretch of MSCs on collagen sheets significantly increased both mRNA and protein expression of α-smooth muscle actin, transgelin, and calponin versus plastic and non-stretched sheets. Thus, lineage-specific stiffness and cyclic stretch can be applied together for inducing MSC differentiation towards SMCs without the addition of recombinant growth factors or other soluble factors. This represents a novel stimulation method for modulating the phenotype of MSCs towards SMCs that could easily be incorporated into currently available methodologies to obtain a more targeted control of MSC phenotype.

  17. Stretching human mesenchymal stromal cells on stiffness-customized collagen type I generates a smooth muscle marker profile without growth factor addition

    PubMed Central

    Rothdiener, Miriam; Hegemann, Miriam; Uynuk-Ool, Tatiana; Walters, Brandan; Papugy, Piruntha; Nguyen, Phong; Claus, Valentin; Seeger, Tanja; Stoeckle, Ulrich; Boehme, Karen A.; Aicher, Wilhelm K.; Stegemann, Jan P.; Hart, Melanie L.; Kurz, Bodo; Klein, Gerd; Rolauffs, Bernd

    2016-01-01

    Using matrix elasticity and cyclic stretch have been investigated for inducing mesenchymal stromal cell (MSC) differentiation towards the smooth muscle cell (SMC) lineage but not in combination. We hypothesized that combining lineage-specific stiffness with cyclic stretch would result in a significantly increased expression of SMC markers, compared to non-stretched controls. First, we generated dense collagen type I sheets by mechanically compressing collagen hydrogels. Atomic force microscopy revealed a nanoscale stiffness range known to support myogenic differentiation. Further characterization revealed viscoelasticity and stable biomechanical properties under cyclic stretch with >99% viable adherent human MSC. MSCs on collagen sheets demonstrated a significantly increased mRNA but not protein expression of SMC markers, compared to on culture flasks. However, cyclic stretch of MSCs on collagen sheets significantly increased both mRNA and protein expression of α-smooth muscle actin, transgelin, and calponin versus plastic and non-stretched sheets. Thus, lineage-specific stiffness and cyclic stretch can be applied together for inducing MSC differentiation towards SMCs without the addition of recombinant growth factors or other soluble factors. This represents a novel stimulation method for modulating the phenotype of MSCs towards SMCs that could easily be incorporated into currently available methodologies to obtain a more targeted control of MSC phenotype. PMID:27775041

  18. Identification of molecular markers to follow up the bioremediation of sites contaminated with chlorinated compounds.

    PubMed

    Marzorati, Massimo; Balloi, Annalisa; De Ferra, Francesca; Daffonchio, Daniele

    2010-01-01

    The use of microorganisms to clean up xenobiotics from polluted ecosystems (soil and water) represents an ecosustainable and powerful alternative to traditional remediation processes. Recent developments in molecular-biology-based techniques have led to rapid and sensitive strategies for monitoring and identifying bacteria and catabolic genes involved in the degradation of xenobiotics. This chapter provides a description of recently developed molecular-biology-based techniques, such as PCR with degenerate primers set, real-time quantitative PCR (qPCR), reverse transcription PCR (RT-PCR), southern blot hybridization, and long-range PCR, used to give a picture of the catabolically relevant microorganisms and of the functional genes present in a polluted system. By using a case study of a groundwater aquifer contaminated with 1,2-dichloroethane (1,2-DCA), we describe the identification of microorganisms potentially involved in the 1,2-DCA dehalorespiration (Dehalobacter sp. and Desulfitobacterium sp.) and a complete new gene cluster encoding for a 1,2-DCA reductive dehalogenase. The application of these techniques to bioremediation can improve our understanding of the inner mechanisms to evaluate the feasibility of a given treatment and provide us with a method to follow up bacteria and catabolic genes involved in the degradation of contaminants during the activities in situ.

  19. The importance of molecular markers for diagnosis and selection of targeted treatments in patients with cancer.

    PubMed

    Tobin, N P; Foukakis, T; De Petris, L; Bergh, J

    2015-12-01

    The past 30 years have seen the introduction of a number of cancer therapies with the aim of restricting the growth and spread of primary and metastatic tumours. A shared commonality among these therapies is their targeting of various aspects of the cancer hallmarks, that is traits that are essential to successful tumour propagation and dissemination. The evolution of molecular-scale technology has been central to the identification of new cancer targets, and it is not a coincidence that improved therapies have emerged at the same time as gene expression arrays and DNA sequencing have enhanced our understanding of cancer genetics. Modern tumour pathology is now viewed at the molecular level ranging from IHC biomarkers, to gene signature classifiers and gene mutations, all of which provide crucial information about which patients will respond to targeted therapy regimens. In this review, we briefly discuss the general types of targeted therapies used in a clinical setting and provide a short background on immunohistochemical, gene expression and DNA sequencing technologies, before focusing on three tumour types: breast, lung and colorectal cancers. For each of these cancer types, we provide a background to the disease along with an overview of the current standard therapies and then focus on the relevant targeted therapies and the pathways they inhibit. Finally, we highlight several strategies that are pivotal to the successful development of targeted anti-cancer drugs.

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

    PubMed

    Breitbach, Sarah; Tug, Suzan; Simon, Perikles

    2012-07-01

    The phenomenon of circulating cell-free DNA (cfDNA) concentrations is of importance for many biomedical disciplines including the field of exercise physiology. Increases of cfDNA due to exercise are described to be a potential hallmark for the overtraining syndrome and might be related to, or trigger adaptations of, immune function induced by strenuous exercise. At the same time, exercise provides a practicable model for studying the phenomenon of cfDNA that is described to be of pathophysiological relevance for different topics in clinical medicine like autoimmune diseases and cancer. In this review, we are summarizing the current knowledge of exercise-based acute and chronic alterations in cfDNA levels and their physiological significance. The effects of acute exercise on cfDNA concentrations have been investigated in resistance exercises and in continuous, stepwise and interval endurance exercises of different durations. cfDNA concentrations peaked immediately after acute exercise and showed a rapid return to baseline levels. Typical markers of skeletal muscle damage (creatine kinase, uric acid, C-reactive protein) show delayed kinetics compared with the cfDNA peak response. Exercise parameters such as intensity, duration or average energy expenditure do not explain the extent of increasing cfDNA concentrations after strenuous exercise. This could be due to complex processes inside the human organism during and after physical activity. Therefore, we hypothesize composite effects of different physiological stress parameters that come along with exercise to be responsible for increasing cfDNA concentrations. We suggest that due to acute stress, cfDNA levels increase rapidly by a spontaneous active or passive release mechanism that is not yet known. As a result of the rapid and parallel increase of cfDNA and lactate in an incremental treadmill test leading to exhaustion within 15-20 minutes, it is unlikely that cfDNA is released into the plasma by typical necrosis

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

    PubMed Central

    2012-01-01

    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

  2. Metabolomic approach for identifying and visualizing molecular tissue markers in tadpoles of Xenopus tropicalis by mass spectrometry imaging

    PubMed Central

    Kashiwagi, Akihiko; Kashiwagi, Keiko; Mori, Tsukasa

    2016-01-01

    ABSTRACT In developmental and cell biology it is crucial to evaluate the dynamic profiles of metabolites. An emerging frog model system using Xenopus tropicalis, whose genome sequence and inbred strains are available, is now ready for metabolomics investigation in amphibians. In this study we applied matrix-assisted laser desorption/ionization (MALDI)-mass spectrometry imaging (MSI) analysis to identify and visualize metabolomic molecular markers in tadpoles of Xenopus tropicalis. We detected tissue-specific peaks and visualized their distribution in tissues, and distinguished 19 tissues and their specific peaks. We identified, for the first time, some of their molecular localizations via tandem mass spectrometric analysis: hydrocortisone in artery, L-DOPA in rhombencephalon, taurine in eye, corticosterone in gill, heme in heart, inosine monophosphate and carnosine in muscle, dopamine in nerves, and phosphatidylethanolamine (16:0/20:4) in pharynx. This is the first MALDI-MSI study of X. tropicalis tadpoles, as in small tadpoles it is hard to distinguish and dissect the various organs. Furthermore, until now there has been no data about the metabolomic profile of each organ. Our results suggest that MALDI-MSI is potentially a powerful tool for examining the dynamics of metabolomics in metamorphosis as well as conformational changes due to metabolic changes. PMID:27422901

  3. Molecular characterization and population structure of the macaw palm, Acrocomia aculeata (Arecaceae), ex situ germplasm collection using microsatellites markers.

    PubMed

    Lanes, Éder C M; Motoike, Sérgio Y; Kuki, Kacilda N; Nick, Carlos; Freitas, Renata D

    2015-01-01

    The Acrocomia aculeata is one of the most promising plants for sustainable production of renewable energy. In order to understand patterns of the distribution of the allelic diversity of A. aculeata ex situ germplasm collection, the present study investigated the hypothesis that the genetic variability of the accessions may match their geographical origin. A genotypic analysis of 77 A. aculeata accessions was conducted with 6 simple sequence repeat markers. A high degree of molecular diversity among the accessions was found, with an average of 9 alleles per locus and a polymorphic information content with a mean of 0.76. A total of 4 clusters was identified by the Bayesian analysis of population structure. The highest subpopulation diversity was identified in Pop1, mainly formed by accessions from State of Mato Grosso do Sul. The populations Pop2A, Pop2B, and Pop2C, all from the State of Minas Gerais, showed high genetic variability as determined by a higher F st, and a wide genetic variance, which were identified within and among the population by analysis of molecular variance. Based on our results and on Vavilov's theory on crop origins, one possible diversity center for A. aculeata is proposed to be in a region in southeast Brazil.

  4. Population structure of Aggarwals of north India as revealed by molecular markers.

    PubMed

    Gupta, Vipin; Khadgawat, Rajesh; Ng, Hon Keung Tony; Kumar, Satish; Rao, Vadlamudi Raghavendra; Sachdeva, Mohinder Pal

    2010-12-01

    Using molecular genetic data on Aggarwals (Vaish/Vysya), an endogamous population group of north India, we provide evidence of its homogeneous unstratified population structure. We found the mean average heterozygosity value of 0.33 for 14 single nucleotide polymorphisms belonging to four genes (TCF7L2-, HHEX-, KCNJ11-, and ADIPOQ-) in the Aggarwal population (sample of 184 individuals) and tried to evaluate the genomic efficiency of endogamy in this population with the help of clan-based stratified analysis. We concluded that the sociocultural identity of the endogamous population groups could act as a robust proxy maker for inferring their homogeneity and population structure in India, which is ideal also for population selection for future genome-wide association studies in the country.

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

    PubMed Central

    Baxter, Alan G.; Jordan, Margaret A.

    2012-01-01

    By the year 2000, a draft of the human genome sequence was completed. Millions of single-nucleotide polymorphisms (SNPs) had been deposited into public databases, and high throughput technologies were under development for SNP genotyping. At that time, it was predicted that large case control association studies would provide far better resolution and power than genome-wide linkage studies. Type 1 diabetes was one of the first phenotypes to be examined by genome-wide association studies (GWAS), and to date over 50 genomic regions have been associated with the disease. In general, the great majority of these loci individually contribute a relatively small degree of risk, and most loci lie outside of coding sequences. The identification of molecular mechanisms from these genomic data therefore remains a significant challenge. Here, we summarize genetic candidate, linkage, and association studies of type 1 diabetes and discuss a potential strategy to identify mechanisms of disease from genomic data. PMID:23804261

  6. Implementation of molecular marker technologies in the apple rootstock breeding program in Geneva - challenges and successes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The Geneva® Apple Rootstock Breeding program was initiated in the early 1970’s with the overarching goal of developing disease resistant, productive and precocious apple rootstocks. Near the turn of the century the program was joined with USDA ARS resources and in addition to focusing on releasing ...

  7. Sequestration of organic nitrogen in a paddy soil chronosequence as assessed by amino sugars molecular markers

    NASA Astrophysics Data System (ADS)

    Roth, Philipp; Lehndorff, E.; Cao, Z.; Amelung, W.

    2010-05-01

    Available nitrogen is a limiting factor in paddy rice systems due to ammonia volatilization, denitrification and stabilization in organic complexes. Soil organic nitrogen (SON) might therefore constitute a critical component of the nitrogen cycle in rice systems. The objective of this study was to elucidate the role of microorganisms for the sequestration of paddy N in organic forms. For this purpose we analyzed amino sugars as markers for the residues of bacteria and fungi in a chronosequence of soils that were used for paddy rice production for a period of 0 to 2000 years in the Hangzhou bay area in Southeast China. Within the soil profile, amino sugar concentrations were generally highest in the puddled Ap horizon and decreased with increasing depth along with organic carbon concentrations regardless of the time of rice cultivation. Nevertheless, a sharp increase of total amino sugar concentration from 0.1 g kg-1 to 0.3 g kg-1 was observed in the Ah horizon when comparing tidal wetland to salt marsh that had been impoldered 30 years ago, indicating an increasing importance of microbial residues in SON stabilization following the conversion of the semiaquatic marsh to a terrestrial system. With increased time of paddy rice cropping, amino sugar concentrations continued to increase up to a maximum of 2.1 g kg-1 after 300 years of paddy cultivation but declined again to 1 g kg-1 in soils with 700-2000 years history of cultivation despite increasing organic matter accumulation. Changes in the composition of the amino sugars were also most pronounced at initial stages of paddy rice management. The proportions of glucosamine (abundant in fungal chitin) decreased during the first 50 years of cultivation relative to mainly galactosamine (abundant in bacterial gums) and muramic acid (abundant in bacterial peptidoglycan), that remained at constantly low levels. At later stages of paddy rice cultivation, the ratios of glucosamine to galactosamine and to muramic acid re

  8. Development and significance of SCAR marker QG12-5 for Canarium album (Lour.) Raeusch by molecular cloning from improved RAPD amplification.

    PubMed

    Cheng, J L; Yin, Z C; Mei, Z Q; Wei, C L; Chen, H C; Wu, X S; Fu, J J

    2016-08-26

    Sequence-characterized amplified region (SCAR) is a valuable molecular marker for the genetic identification of any species. This marker is mainly derived from molecular cloning of random amplified polymorphic DNA (RAPD). We have previously reported the use of an improved RAPD technique for the genetic characterization of different samples of Canarium album (Lour.) Raeusch (C. album). In this study, DNA fragments were amplified using improved RAPD amplified from different samples of C. album. The amplified DNA fragment was excised, purified from an agarose gel and cloned into a pGM-T vector; subsequently, a positive clone, called QG12-5 was identified by PCR amplification and enzymatic digestion and sequenced by Sanger di-deoxy sequencing method. This clone was revealed consisting of 510 nucleotides of C. album. The SCAR marker QG12-5 was developed using specifically designed PCR primers and optimized PCR conditions. This SCAR marker expressed seven continuous "TATG" [(TATG)n] tandem repeats, which was found to characterize C. album. Subsequently, this novel SCAR marker was deposited in GenBank with accession No. KT359568. Therefore, we successfully developed a C. album-specific SCAR marker for the identification and authentication of different C. album species in this study.

  9. Genetic analysis of molecular markers for propamocarb residue in Cucumis sativus using quantitative trait locus mapping.

    PubMed

    Xin, M; Wang, L; Ma, B H; Qin, Z W; Zhou, X Y

    2016-11-03

    The use of pesticides to protect plants against harmful organisms, such as pathogenic microorganisms, is one of the most effective ways to improve agricultural production. However, the continuous use of pesticides might present a risk to human health, animals, and the environment. In this study, two cucumber (Cucumis sativus) varieties containing different levels of pesticide residues, D9320 and D0351, were selected to establish an F2 population. A genetic model and genetic linkage map were constructed. The results showed that the heredity of pesticide residues was dominated by an additive effect and was significantly influenced by non-additive factors in cucumber. QCp1 was detected as a quantitative trait locus (QTL) that might be involved in regulating the levels of pesticide residue in cucumber. Moreover, the cucumber genetic map was compared with the LG6 map, and the results indicated that this QTL was closely related to the level of pesticide residue in cucumber.

  10. Genetic diversity of Capsicum chinensis (Solanaceae) accessions based on molecular markers and morphological and agronomic traits.

    PubMed

    Finger, F L; Lannes, S D; Schuelter, A R; Doege, J; Comerlato, A P; Gonçalves, L S A; Ferreira, F R A; Clovis, L R; Scapim, C A

    2010-09-21

    We estimated the genetic diversity of 49 accessions of the hot pepper species Capsicum chinensis through analyses of 12 physicochemical traits of the fruit, eight multi-categorical variables, and with 32 RAPD primers. Data from the physicochemical traits were submitted to analysis of variance to estimate the genetic parameters, and their means were clustered by the Scott-Knott test. The matrices from the individual and combined distance were estimated by multivariate analyses before applying Tocher's optimization method. All physicochemical traits were examined for genetic variability by analysis of variance. The responses of these traits showed more contribution from genetic than from environmental factors, except the percentage of dry biomass, content of soluble solids and vitamin C level. Total capsaicin had the greatest genetic divergence. Nine clusters were formed from the quantitative data based on the generalized distance of Mahalanobis, using Tocher's method; four were formed from the multi-categorical data using the Cole-Rodgers coefficient, and eight were formed from the molecular data using the Nei and Li coefficient. The accessions were distributed into 14 groups using Tocher's method, and no significant correlation between pungency and origin was detected. Uni- and multivariate analyses permitted the identification of marked genetic diversity and fruit attributes capable of being improved through breeding programs.

  11. Molecular evolution of a widely-adopted taxonomic marker (COI) across the animal tree of life

    PubMed Central

    Pentinsaari, Mikko; Salmela, Heli; Mutanen, Marko; Roslin, Tomas

    2016-01-01

    DNA barcodes are widely used for identification and discovery of species. While such use draws on information at the DNA level, the current amassment of ca. 4.7 million COI barcodes also offers a unique resource for exploring functional constraints on DNA evolution. Here, we explore amino acid variation in a crosscut of the entire animal kingdom. Patterns of DNA variation were linked to functional constraints at the level of the amino acid sequence in functionally important parts of the enzyme. Six amino acid sites show variation with possible effects on enzyme function. Overall, patterns of amino acid variation suggest convergent or parallel evolution at the protein level connected to the transition into a parasitic life style. Denser sampling of two diverse insect taxa revealed that the beetles (Coleoptera) show more amino acid variation than the butterflies and moths (Lepidoptera), indicating fundamental difference in patterns of molecular evolution in COI. Several amino acid sites were found to be under notably strong purifying selection in Lepidoptera as compared to Coleoptera. Overall, these findings demonstrate the utility of the global DNA barcode library to extend far beyond identification and taxonomy, and will hopefully be followed by a multitude of work. PMID:27734964

  12. Optimized measurements of separations and angles between intra-molecular fluorescent markers

    PubMed Central

    Mortensen, Kim I.; Sung, Jongmin; Flyvbjerg, Henrik; Spudich, James A.

    2015-01-01

    We demonstrate a novel, yet simple tool for the study of structure and function of biomolecules by extending two-colour co-localization microscopy to fluorescent molecules with fixed orientations and in intra-molecular proximity. From each colour-separated microscope image in a time-lapse movie and using only simple means, we simultaneously determine both the relative (x,y)-separation of the fluorophores and their individual orientations in space with accuracy and precision. The positions and orientations of two domains of the same molecule are thus time-resolved. Using short double-stranded DNA molecules internally labelled with two fixed fluorophores, we demonstrate the accuracy and precision of our method using the known structure of double-stranded DNA as a benchmark, resolve 10-base-pair differences in fluorophore separations, and determine the unique 3D orientation of each DNA molecule, thereby establishing short, double-labelled DNA molecules as probes of 3D orientation of anything to which one can attach them firmly. PMID:26509412

  13. Association of Bax Expression and Bcl2/Bax Ratio with Clinical and Molecular Prognostic Markers in Chronic Lymphocytic Leukemia

    PubMed Central

    Vucicevic, Ksenija; Jakovljevic, Vladimir; Colovic, Natasa; Tosic, Natasa; Kostic, Tatjana; Glumac, Irena; Pavlovic, Sonja; Colovic, Milica

    2016-01-01

    Summary Background In chronic lymphocytic leukemia (CLL), in vivo apoptotic resistance of malignant B lymphocytes results, in part, from the intrinsic defects of their apoptotic machinery. These include genetic alterations and aberrant expression of many apoptosis regulators, among which the Bcl2 family members play a central role. Aim The aim of this study was to investigate the association of pro-apoptotic Bax gene expression and Bcl2/Bax ratio with the clinical features of CLL patients as well as with molecular prognostic markers, namely the mutational status of rearranged immunoglobulin heavy variable (IGHV) genes and lipoprotein lipase (LPL) gene expression. Methods We analyzed the expression of Bax mRNA and Bcl2/Bax mRNA ratio in the peripheral blood mononuclear cells of 58 unselected CLL patients and 10 healthy controls by the quantitative reverse-transcriptase polymerase chain reaction. Results We detected significant Bax gene overexpression in CLL samples compared to non-leukemic samples (p=0.003), as well as an elevated Bcl2/Bax ratio (p=<0.001). Regarding the association with prognostic markers, the Bcl2/Bax ratio showed a negative correlation to lymphocyte doubling time (r=-0.307; p=0.0451), while high-level Bax expression was associated with LPL-positive status (p=0.035). Both the expression of Bax and Bcl2/Bax ratio were higher in patients with unmutated vs. mutated IGHV rearrangements, but this difference did not reach statistical significance. Conclusions Our results suggest that dysregulated expression of Bcl2 and Bax, which leads to a high Bcl2/Bax ratio in leukemic cells, contributes to the pathogenesis and clinical course of CLL. PMID:28356875

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

    SciTech Connect

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

    2014-09-15

    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.

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

    NASA Astrophysics Data System (ADS)

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

    2013-12-01

    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 δ13C 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

  16. Identification of Molecular Markers of Delayed Graft Function Based on the Regulation of Biological Ageing

    PubMed Central

    McGuinness, Dagmara; Leierer, Johannes; Shapter, Olivier; Mohammed, Suhaib; Gingell-Littlejohn, Marc; Kingsmore, David B.; Little, Ann-Margaret; Kerschbaum, Julia; Schneeberger, Stefan; Maglione, Manuel; Nadalin, Silvio; Wagner, Sylvia; Königsrainer, Alfred; Aitken, Emma; Whalen, Henry; Clancy, Marc; McConnachie, Alex; Koppelstaetter, Christian; Stevenson, Karen S.; Shiels, Paul G.

    2016-01-01

    Introduction Delayed graft function is a prevalent clinical problem in renal transplantation for which there is no objective system to predict occurrence in advance. It can result in a significant increase in the necessity for hospitalisation post-transplant and is a significant risk factor for other post-transplant complications. Methodology The importance of microRNAs (miRNAs), a specific subclass of small RNA, have been clearly demonstrated to influence many pathways in health and disease. To investigate the influence of miRNAs on renal allograft performance post-transplant, the expression of a panel of miRNAs in pre-transplant renal biopsies was measured using qPCR. Expression was then related to clinical parameters and outcomes in two independent renal transplant cohorts. Results Here we demonstrate, in two independent cohorts of pre-implantation human renal allograft biopsies, that a novel pre-transplant renal performance scoring system (GRPSS), can determine the occurrence of DGF with a high sensitivity (>90%) and specificity (>60%) for donor allografts pre-transplant, using just three senescence associated microRNAs combined with donor age and type of organ donation. Conclusion These results demonstrate a relationship between pre-transplant microRNA expression levels, cellular biological ageing pathways and clinical outcomes for renal transplantation. They provide for a simple, rapid quantitative molecular pre-transplant assay to determine post-transplant allograft function and scope for future intervention. Furthermore, these results demonstrate the involvement of senescence pathways in ischaemic injury during the organ transplantation process and an indication of accelerated bio-ageing as a consequence of both warm and cold ischaemia. PMID:26734715

  17. Molecular Markers as Prognostic Factors in DCIS and Small Invasive Breast Cancers.

    PubMed

    Sänger, N; Engels, K; Graf, A; Ruckhäberle, E; Effenberger, K E; Fehm, T; Holtrich, U; Becker, S; Karn, T

    2014-11-01

    Ductal carcinoma in situ (DCIS) accounts for up to half of screen-detected breast cancers and thus constitutes a major public health problem. Despite effective current treatment many patients with DCIS are either over- or undertreated because of the paucity of precise models to predict recurrence or progression. The combination of clinical and molecular factors as already applied for invasive disease may help to build such models also for DCIS. We compared 53 DCIS (36.6 %) and 92 (63.4 %) invasive breast cancer cases and found no significant differences in age, receptor status of ER, PR, and HER2, and the use of radiotherapy. Interestingly, the proportion of disseminated tumor cells (DTC) did also not significantly differ between DCIS and invasive cases (p = 0.57). A negative PR status was associated with the detection of DTCs (p = 0.026). We then compared relationships of clinical parameters and biomarkers with patients' prognosis in 43 DCIS and 40 small invasive tumors ≤ 5 mm (T1a). ER negativity was associated with shorter relapse free survival in the complete cohort (p = 0.004) and showed a trend in both subgroups (p = 0.053 for DCIS and p = 0.046 for T1a, respectively). In conclusion, we found markedly similar properties of both DCIS and small invasive breast cancers with respect to the distribution of several parameters as well as to the prognostic value of biomarkers. DCIS with a luminal phenotype seem to be characterized by a favourable prognosis.

  18. Molecular signature of salivary gland tumors: potential use as diagnostic and prognostic marker.

    PubMed

    Fonseca, Felipe Paiva; Sena Filho, Marcondes; Altemani, Albina; Speight, Paul M; Vargas, Pablo Agustin

    2016-02-01

    Salivary gland tumors are a highly heterogeneous group of lesions with diverse microscopic appearances and variable clinical behavior. The use of clinical and histological parameters to predict patient prognosis and survival rates has been of limited utility, and the search for new biomarkers that could not only aid in a better understanding of their pathogenesis but also be reliable auxiliaries for prognostic determination and useful diagnostic tools has been performed in the last decades with very exciting results. Hence, gene rearrangements such as CRTC1-MAML2 in mucoepidermoid carcinomas have shown excellent specificity, and more than that, it has been strongly correlated with low-grade tumors and consequently with an increased survival rate and better prognosis of patients affected by neoplasms carrying this translocation. Moreover, MYB-NFIB and EWSR1-ATF1 gene fusions were shown to be specifically found in cases of adenoid cystic carcinomas and hyalinizing clear cell carcinomas, respectively, in the context of salivary gland tumors, becoming reliable diagnostic tools for these entities and potential therapeutic targets for future therapeutic protocols. Finally, the identification of ETV6-NTRK3 in cases previously diagnosed as uncommon acinic cell carcinomas, cystadenocarcinomas, and adenocarcinomas not otherwise specified led to the characterization of a completely new and now widely accepted entity, including, therefore, mammary analogue secretory carcinoma in the list of well-recognized salivary gland carcinomas. Thus, further molecular investigations of salivary gland tumors are warranted, and the recognition of other genetic abnormalities can lead to the acknowledgment of new entities and the acquirement of reliable biomarkers.

  19. Molecular markers of apoptosis in cancer patients exposed to ionizing radiation: the post-Chornobyl view.

    PubMed

    Philchenkov, A A; Balcer-Kubiczek, E K

    2016-12-01

    During the past three decades, the deleterious consequences of Chornobyl accident including carcinogenic effects in the people who were accidentally exposed to radiation have been intensively studied. In particular, recent studies provided increased knowledge of the molecular pathogenesis of thyroid tumors in children exposed to Chornobyl fallout. The risk of several forms of leukemia including myelodysplastic syndromes is elevated in Chornobyl liquidators. Furthermore, the upward trends of increases in a variety of other tumors including breast cancer, cancers of central nervous system and renal cancer have been reported in the persons exposed to Chornobyl fallout. There is growing evidence that insufficient apoptosis allows irradiated cells to survive and thereby contributes to carcinogenesis. The purpose of the present survey is to summarize the recent findings related to apoptotic biomarkers among cancer patients from the different populations affected by the Chornobyl catastrophe. Among the particularly radiosensitive cancer sites, we focused on thyroid cancer and leukemia. Several genes and/or proteins controlling apoptosis directly or indirectly have been incorporated into the analysis. The data reviewed here provide a mechanistic link between the apoptosis alterations and development of radiation-related cancer in the 30-year post-Chornobyl period. We suggest that the type of mutations arising from misrepair of DNA double strand breaks (gene fusion and amplification) is the initial signature event in radiation-induced thyroid cancer. Much work has to be done over the next years to elucidate central questions related to the nature of human radiation carcinogenesis. This article is part of a Special Issue entitled "The Chornobyl Nuclear Accident: Thirty Years After".

  20. Molecular differentiation of Central European blowfly species (Diptera, Calliphoridae) using mitochondrial and nuclear genetic markers.

    PubMed

    GilArriortua, Maite; Saloña Bordas, Marta I; Köhnemann, Stephan; Pfeiffer, Heidi; de Pancorbo, Marian M

    2014-09-01

    A challenging step in medical, veterinary and forensic entomology casework is the rapid and accurate identification of insects to estimate the period of insect activity (PIA), which usually approximates the post-mortem interval (PMI). The morphological identification of insect evidence is hampered by species similarities, especially at the early larval stages. However, DNA-based species identification is more accurate and reliable. In this study, we improved the suitability and efficacy of the standard mitochondrial cytochrome c oxidase subunit I (COI) barcode region of 658 bp combined with an additional region of 616 bp of the same gene. We also tested the usefulness of other mitochondrial and nuclear loci, such as the non-coding region included in mitochondrial Cyt-b-tRNA(ser)-ND1 (495-496 bp) and the second internal transcribed spacer (ITS2) region of nuclear ribosomal DNA (rDNA) (310-337 bp). We classified a total of 54 specimens from five blowfly species belonging to three Calliphoridae genera commonly found in Central Europe: Phormia (P. regina), Calliphora (C. vicina) and Lucilia (L. sericata, L. ampullacea and L. caesar). Additionally included were the Cyt-b (307 bp) sequences for P. regina species and GenBank recorded information about the studied loci for select species. The results revealed the robustness of COI (616 bp) and ITS2 (310-337 bp) as diagnostic tools to be added to the widely established COI barcode (658 bp). Their higher discriminatory power allows for more precise and reliable identifications, even within more complex genera (Lucilia). This work also contributes new nucleotide sequences that are useful for accurate species diagnosis and new sequence data of Calliphoridae interspecific variability in the European Westphalia region (Germany).

  1. CAPS markers using mitochondrial consensus primers for molecular identification of Panax species and Korean ginseng cultivars (Panax ginseng C. A. Meyer).

    PubMed

    Lee, Jei-Wan; Bang, Kyong-Hwan; Kim, Young-Chang; Seo, A-Yeon; Jo, Ick-Hyun; Lee, Jeong-Hoon; Kim, Ok-Tae; Hyun, Dong-Yun; Cha, Seon-Woo; Cho, Joon-Hyeong

    2012-01-01

    Cleaved amplified polymorphic sequence (CAPS) marker system using mitochondrial consensus primers was applied for molecular identification of Korean ginseng cultivars (Panax ginseng). Initially, a total of 34 primers were tested to six Korean ginseng cultivars and two foreign Panax species, P. quinquefolius and P. notoginseng. In the polymerase chain reaction (PCR) amplification results, four primers (mt7, mt11, mt13, and mt18) generated co-dominant polymorphic banding patterns discriminating the Korean ginseng cultivars from P. quinquefolius and P. notoginseng. In the CAPS analysis results, the majority of the cleaved PCR products also yielded additional latent polymorphisms between the Korean ginseng cultivars and two foreign Panax species. Specific latent CAPS polymorphisms for cultivar Gopoong and Chunpoong were detected from internal region amplified with mt9 primer by treating HinfI and Tsp509I endonucleases, respectively. Sequencing analysis revealed that the length of amplified region of Korean ginseng cultivars was 2,179 bp, and those of P. quinquefolius and P. notoginseng were 2,178 and 2,185 bp, respectively. Blast search revealed that the amplified region was a mitochondrial cytochrome oxidase subunit 2 (cox2) gene intron II region. Nineteen single nucleotide polymorphisms (SNP) including each specific SNP for Gopoong and Chunpoong, and three insertion and deletion (InDel) polymorphisms were detected by sequence alignment. The CAPS markers developed in this study, which are specific to Gopoong and Chunpoong, and between the Korean ginseng cultivars and two foreign Panax species, will serve as a practical and reliable tool for their identification, purity maintenance, and selection of candidate lines and cultivars.

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  3. Design rules for rational control of polymer glass formation behavior and mechanical properties with small molecular additives

    NASA Astrophysics Data System (ADS)

    Mangalara, Jayachandra Hari; Simmons, David

    Small molecule additives have long been employed to tune polymers' glass formation, mechanical and transport properties. For example, plasticizers are commonly employed to suppress polymer Tg and soften the glassy state, while antiplasticizers, which stiffen the glassy state of a polymer while suppressing its Tg, are employed to enhance protein and tissue preservation in sugar glasses. Recent literature indicates that additives can have a wide range of possible effects, but all of these have not been clearly understood and well appreciated. Here we employ molecular dynamics simulations to establish design rules for the selection of small molecule additives with size, molecular stiffness, and interaction energy chosen to achieve targeted effects on polymer properties. We furthermore find that a given additive's effect on a polymer's Tg can be predicted from its Debye-Waller factor via a function previously found to describe nanoconfinement effects on the glass transition. These results emphasize the potential for a new generation of targeted molecular additives to contribute to more targeted rational design of polymers. We acknowledge the Keck Foundation and the Ohio Supercomputing Center for financial and computational support of this effort, respectively.

  4. Multi-spectroscopic and molecular modeling studies of bovine serum albumin interaction with sodium acetate food additive.

    PubMed

    Mohammadzadeh-Aghdash, Hossein; Ezzati Nazhad Dolatabadi, Jafar; Dehghan, Parvin; Panahi-Azar, Vahid; Barzegar, Abolfazl

    2017-08-01

    Sodium acetate (SA) has been used as a highly effective protectant in food industry and the possible effect of this additive on the binding to albumin should be taken into consideration. Therefore, for the first time, the mechanism of SA interaction with bovine serum albumin (BSA) has been investigated by multi-spectroscopic and molecular modeling methods under physiological conditions. Stern-Volmer fluorescence quenching analysis showed an increase in the fluorescence intensity of BSA upon increasing the amounts of SA. The high affinity of SA to BSA was demonstrated by a binding constant value (1.09×10(3) at 310°K). The thermodynamic parameters indicated that hydrophobic binding plays a main role in the binding of SA to Albumin. Furthermore, the results of UV-vis spectra confirmed the interaction of this additive to BSA. In addition, molecular modeling study demonstrated that A binding sites of BSA play the main role in the interaction with acetate.

  5. Monitoring molecular dynamics of bacterial cellulose composites reinforced with graphene oxide by carboxymethyl cellulose addition.

    PubMed

    Sanchis, M J; Carsí, M; Gómez, C M; Culebras, M; Gonzales, K N; Torres, F G

    2017-02-10

    Broadband Dielectric Relaxation Spectroscopy was performed to study the molecular dynamics of dried Bacterial Cellulose/Carboxymethyl Cellulose-Graphene Oxide (BC/CMC-GO) composites as a function of the concentration of CMC in the culture media. At low temperature the dielectric spectra are dominated by a dipolar process labelled as a β-relaxation, whereas electrode polarization and the contribution of dc-conductivity dominate the spectra at high temperatures and low frequency. The CMC concentration affects the morphological structure of cellulose and subsequently alters its physical properties. X-ray diffractometry measurements show that increasing the concentration of CMC promotes a decrease of the Iα/Iβ ratio. This structural change in BC, that involves a variation in inter- and intramolecular interactions (hydrogen-bonding interactions), affects steeply their molecular dynamics. So, an increase of CMC concentration produces a significantly decrease of the β-relaxation strength and an increase of the dc-conductivity.

  6. Fungal diversity in rock beneath a crustose lichen as revealed by molecular markers.

    PubMed

    Bjelland, Torbjørg; Ekman, Stefan

    2005-05-01

    Lichen-forming fungi have been assumed to be more or less restricted to the surface of the substrate on which they grow, Conclusive identification of hyphae or an assessment of the fungal diversity inside lichen-covered rock has not been possible using methods based on direct observation. We circumvented this problem by using a DNA sequencing approach. Cores were drilled from a Devonian arcosic sandstone rock harboring the crustose lichen Ophioparma ventosa (L.) Norman on the surface. The cores were cut vertically, and DNA was extracted from the pulverized rock slices. A series of polymerase chain reactions using fungal-specific primers as well as Ophioparma ventosa specific primers were employed to amplify the internal transcribed spacer region of the nuclear ribosomal DNA. The results show that hyphae of O. ventosa penetrate approximately 10-12 mm into the rock. Consequently, the hyphal layer formed by the lichen fungus inside the rock could be 7-12 times as thick as the symbiotic thallus at the surface of the rock. In addition, eight non-lichenized fungal taxa and five that could not be identified to species were encountered. One fungal species in the order Helotiales occurs in six of the eight cores. The significance of these results to the colonization and weathering of rock by lichenized fungi is discussed.

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

    PubMed Central

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

    2014-01-01

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

  8. Molecular Markers of Radiation Induced Attenuation in Intrahepatic Plasmodium falciparum Parasites

    PubMed Central

    Oakley, Miranda S.; Verma, Nitin; Zheng, Hong; Anantharaman, Vivek; Takeda, Kazuyo; Gao, Yamei; Myers, Timothy G.; Pham, Phuong Thao; Mahajan, Babita; Kumar, Nirbhay; Sangweme, Davison; Tripathi, Abhai K.; Mlambo, Godfree; Aravind, L.; Kumar, Sanjai

    2016-01-01

    Experimental immunization with radiation attenuated sporozoites (RAS) and genetically attenuated sporozoites has proved to be a promising approach for malaria vaccine development. However, parasite biomarkers of growth attenuation and enhanced immune protection in response to radiation remain poorly understood. Here, we report on the effect of an attenuating dose of γ-irradiation (15 krad) on the Plasmodium falciparum sporozoite (PfSPZ) ultrastructure by electron microscopy, growth rate of liver stage P. falciparum in liver cell cultures, and genome-wide transcriptional profile of liver stage parasites by microarray. We find that γ-irradiation treated PfSPZ retained a normal cellular structure except that they were vacuous with a partially disrupted plasma membrane and inner membrane complex. A similar infection rate was observed by γ-irradiation-treated and untreated PfSPZ in human HCO-4 liver cells (0.47% versus 0.49%, respectively) on day 3 post-infection. In the microarray studies, cumulatively, 180 liver stage parasite genes were significantly transcriptionally altered on day 3 and/or 6 post-infection. Among the transcriptionally altered biomarkers, we identified a signature of seven candidate parasite genes that associated with functionally diverse pathways that may regulate radiation induced cell cycle arrest of the parasite within the hepatocyte. A repertoire of 14 genes associated with protein translation is transcriptionally overexpressed within the parasite by radiation. Additionally, 37 genes encode proteins expressed on the cell surface or exported into the host cell, 4 encode membrane associated transporters, and 10 encode proteins related to misfolding and stress-related protein processing. These results have significantly increased the repertoire of novel targets for 1) biomarkers of safety to define proper attenuation, 2) generating genetically attenuated parasite vaccine candidates, and 3) subunit candidate vaccines against liver stage malaria

  9. Novel molecular markers differentiate Oncorhynchus mykiss (rainbow trout and steelhead) and the O. clarki (cutthroat trout) subspecies

    USGS Publications Warehouse

    Ostberg, C.O.; Rodriguez, R.J.

    2002-01-01

    A suite of 26 PCR-based markers was developed that differentiates rainbow (Oncorhynchus mykiss) and coastal cutthroat trout (O. clarki clarki). The markers also differentiated rainbow from other cutthroat trout subspecies (O. clarki), and several of the markers differentiated between cutthroat trout subspecies. This system has numerous positive attributes, including: nonlethal sampling, high species-specificity and products that are easily identified and scored using agarose gel electrophoresis. The methodology described for developing the markers can be applied to virtually any system in which numerous markers are desired for identifying or differentiating species or subspecies.

  10. Anti-RAINBOW dye-specific antibodies as universal tools for the visualization of prestained protein molecular weight markers in Western blot analysis

    PubMed Central

    Schüchner, Stefan; Andorfer, Peter; Mudrak, Ingrid; Ogris, Egon

    2016-01-01

    Western blotting is one of the most widely used techniques in molecular biology and biochemistry. Prestained proteins are used as molecular weight standards in protein electrophoresis. In the chemiluminescent Western blot analysis, however, these colored protein markers are invisible leaving researchers with the unsatisfying situation that the signal for the protein of interest and the signal for the markers are not captured simultaneously and have to be merged in an error-prone step. To allow the simultaneous detection of marker proteins we generated monoclonal antibodies specific for the protein dyes. To elicit a dye rather than protein specific immune response we immunized mice sequentially with dye-carrier protein complexes, in which a new carrier protein was used for each subsequent immunization. Moreover, by sequentially immunizing with dye-carrier protein complexes, in which different but structurally related dyes were used, we could also generate an antibody, termed anti-RAINBOW, that cross-reacted even with structurally related dyes not used in the immunizations. Our novel antibodies represent convenient tools for the simultaneous Western blot detection of commercially available prestained marker proteins in combination with the detection of any specific protein of interest. These antibodies will render obsolete the anachronistic tradition of manually charting marker bands on film. PMID:27531616

  11. Evaluation of distribution and sources of sewage molecular marker (LABs) in selected rivers and estuaries of Peninsular Malaysia.

    PubMed

    Magam, Sami M; Zakaria, Mohamad Pauzi; Halimoon, Normala; Aris, Ahmad Zaharin; Kannan, Narayanan; Masood, Najat; Mustafa, Shuhaimi; Alkhadher, Sadeq; Keshavarzifard, Mehrzad; Vaezzadeh, Vahab; Sani, Muhamad S A; Latif, Mohd Talib

    2016-03-01

    This is the first extensive report on linear alkylbenzenes (LABs) as sewage molecular markers in surface sediments collected from the Perlis, Kedah, Merbok, Prai, and Perak Rivers and Estuaries in the west of Peninsular Malaysia. Sediment samples were extracted, fractionated, and analyzed using gas chromatography mass spectrometry (GC-MS). The concentrations of total LABs ranged from 68 to 154 (Perlis River), 103 to 314 (Kedah River), 242 to 1062 (Merbok River), 1985 to 2910 (Prai River), and 217 to 329 ng g(-1) (Perak River) dry weight (dw). The highest levels of LABs were found at PI3 (Prai Estuary) due to the rapid industrialization and population growth in this region, while the lowest concentrations of LABs were found at PS1 (upstream of Perlis River). The LABs ratio of internal to external isomers (I/E) in this study ranged from 0.56 at KH1 (upstream of Kedah River) to 1.35 at MK3 (Merbok Estuary) indicating that the rivers receive raw sewage and primary treatment effluents in the study area. In general, the results of this paper highlighted the necessity of continuation of water treatment system improvement in Malaysia.

  12. Wood burning pollution in southern Chile: PM2.5 source apportionment using CMB and molecular markers.

    PubMed

    Villalobos, Ana M; Barraza, Francisco; Jorquera, Héctor; Schauer, James J

    2017-03-16

    Temuco is a mid-size city representative of severe wood smoke pollution in southern Chile; i.e., ambient 24-h PM2.5 concentrations have exceeded 150 μg/m(3) in the winter season and the top concentration reached 372 μg/m(3) in 2010. Annual mean concentrations have decreased but are still above 30 μg/m(3). For the very first time, a molecular marker source apportionment of ambient organic carbon (OC) and PM2.5 was conducted in Temuco. Primary resolved sources for PM2.5 were wood smoke (37.5%), coal combustion (4.4%), diesel vehicles (3.3%), dust (2.2%) and vegetative detritus (0.7%). Secondary inorganic PM2.5 (sulfates, nitrates and ammonium) contributed 4.8% and unresolved organic aerosols (generated from volatile emissions from incomplete wood combustion), including secondary organic aerosols, contributed 47.1%. Adding the contributions of unresolved organic aerosols to those from primary wood smoke implies that wood burning is responsible for 84.6% of the ambient PM2.5 in Temuco. This predominance of wood smoke is ultimately due to widespread poverty and a lack of efficient household heating methods. The government has been implementing emission abatement policies but achieving compliance with ambient air quality standards for PM2.5 in southern Chile remains a challenge.

  13. [Evaluation of Molecular Genetic Diversity of Wild Apple Malus sieversii Populations from Zailiysky Alatau by Microsatellite Markers].

    PubMed

    Omasheva, M E; Chekalin, S V; Galiakparov, N N

    2015-07-01

    The territory of Kazakhstan is part of the distribution range of Malus sieversii, which is one of the ancestors of cultivated apple tree varieties. The collected samples of Sievers apple leaves from five populations growing in the Zailiysky Alatau region served as a source not only for the creation of a bank of genomic DNA but also for determination ofthe wild apple genetic polymorphism. The seven microsatellite markers used in this study revealed 86 alleles with different frequencies, as well as the characteristic pools of rare alleles for each of the populations. Molecular genetic analysis showed a high level of genetic diversity (H(o) = 0.704; PIC = 0.752; I = 1.617). Moreover, interpopulation variability accounted only for 7.5% of total variability, confirming the genetic closeness of the populations examined. Based on phylogenetic analysis, it was demonstrated that the Bel'bulak and Almaty Reserve populations were closest to each other, while the most distant were the Ketmen and Great Almaty gorge populations, which suggests the dependence of genetic distance on the geographical.

  14. Mathematically combined half-cell reduction potentials of low-molecular-weight thiols as markers of seed ageing.

    PubMed

    Birtić, Simona; Colville, Louise; Pritchard, Hugh W; Pearce, Stephen R; Kranner, Ilse

    2011-09-01

    The half-cell reduction potential of the glutathione disulphide (GSSG)/glutathione (GSH) redox couple appears to correlate with cell viability and has been proposed to be a marker of seed viability and ageing. This study investigated the relationship between seed viability and the individual half-cell reduction potentials (E(i)s) of four low-molecular-weight (LMW) thiols in Lathyrus pratensis seeds subjected to artificial ageing: GSH, cysteine (Cys), cysteinyl-glycine (Cys-Gly) and γ-glutamyl-cysteine (γ-Glu-Cys). The standard redox potential of γ-Glu-Cys was previously unknown and was experimentally determined. The E(i)s were mathematically combined to define a LMW thiol-disulphide based redox environment (E(thiol-disulphide)). Loss of seed viability correlated with a shift in E(thiol-disulphide) towards more positive values, with a LD(50) value of -0.90 ± 0.093 mV M (mean ± SD). The mathematical definition of E(thiol-disulphide) is envisaged as a step towards the definition of the overall cellular redox environment, which will need to include all known redox-couples.

  15. FADB: a food additive molecular database for in silico screening in food toxicology.

    PubMed

    Ginex, Tiziana; Spyrakis, Francesca; Cozzini, Pietro

    2014-01-01

    A crucial limit to in silico preliminary toxicological evaluations in the "food safety" area is the lack of a specific, efficient and available free dataset of 3D small molecules. In this direction, we present the first version of FADB (Food Additives Data Base), a suitable and freely available food additives dataset. FADB is the 3D version of the EAFUS (Everything Added to Food in the United States) list, a sum of WHO, FAO food additive databases and could be a useful starting material in preliminary stages of toxicological assessments. Molecules in FADB are represented through several chemical and 1D identifies, physical properties and 3D (SD and Mol2 file) file formats. FADB also contains important information about functional uses of chemicals as food additives. The aim of the work is to put together substances potentially relevant to food into a "computational" library for virtual screening and docking studies with interesting scenarios for toxicology.

  16. Application of subtracted gDNA microarray-assisted Bulked Segregant Analysis for rapid discovery of molecular markers associated with day-neutrality in strawberry (Fragaria x ananassa)

    PubMed Central

    Gor, Mian Chee; Mantri, Nitin; Pang, Edwin

    2016-01-01

    A Fragaria Discovery Panel (FDP; strawberry-specific SDA) containing 287 features was constructed by subtracting the pooled gDNA of nine non-angiosperm species from the pooled gDNA of five strawberry genotypes. This FDP was used for Bulk Segregant Analysis (BSA) to enable identification of molecular markers associated with day-neutrality. Analysis of hybridisation patterns of a short day (SD) DNA bulk and three day-neutral (DN) DNA bulks varying in flowering strength allowed identification of a novel feature, FaP2E11, closely linked to CYTOKININ OXIDASE 1 (CKX1) gene possibly involved in promoting flowering under non-inductive condition. The signal intensities of FaP2E11 feature obtained from the strong DN bulk (DN1) is three fold higher than the short day bulk (SD), indicating that the putative marker may linked to a CKX1 variant allele with lower enzyme activity. We propose a model for flowering regulation based on the hypothesis that flowering strength may be regulated by the copy number of FaP2E11-linked CKX1 alleles. This study demonstrates the feasibility of the SDA-based BSA approach for the identification of molecular markers associated with day-neutrality in strawberry. This innovative strategy is an efficient and cost-effective approach for molecular marker discovery. PMID:27586242

  17. Effect of low molecular weight additives on immobilization strength, activity, and conformation of protein immobilized on PVC and UHMWPE.

    PubMed

    Kondyurin, Alexey; Nosworthy, Neil J; Bilek, Marcela M M

    2011-05-17

    Horseradish peroxidase (HRP) was immobilized onto both plasticized and unplasticized polyvinylchloride (PVC) and ultrahigh molecular weight polyethylene (UHMWPE). Plasma immersion ion implantation (PIII) in a nitrogen plasma with 20 kV bias was used to facilitate covalent immobilization and to improve the wettability of the surfaces. The surfaces and immobilized protein were studied using attenuated total reflection infrared (ATR-IR) spectroscopy and water contact angle measurements. Protein elution on exposure to repeated sodium dodecyl sulfate (SDS) washing was used to assess the strength of HRP immobilization. The presence of low molecular weight components (plasticizer, additives in solvent, unreacted monomers, adsorbed molecules on surface) was found to have a major influence on the strength of immobilization and the conformation of the protein on the samples not exposed to the PIII treatment. A phenomenological model considering interactions between the low molecular weight components, the protein molecule, and the surface is developed to explain these observations.

  18. [Genetic diversity revealed by ISSR molecular marker in common wheat, spelt, compactum and progeny of recurrent selection].

    PubMed

    Du, Jin-Kun; Yao, Ying-Yin; Ni, Zhong-Fu; Peng, Hui-Ru; Sun, Qi-Xin

    2002-05-01

    It is important to estimate the genetic diversity between the parents for improving the heterosis of hybrid wheat. In this study, ISSR(inter-simple sequence repeat) marker was used to measure the genetic diversity within and among common wheat (Triticum aestivum L.), spelt (Triticum spelta L.), compactum (Triticum compactum Host.) and progeny of foreign wheat-based recurrent selection, and the possibility of establishing the new heterotic group was also assessed. Forty seven genotypes were used for ISSR analysis, which included 14 common wheat, 10 spelt wheat, 11 compactum and 12 progeny of recurrent selection. Eleven of 33 ISSR primers that can produce distinguishable bands were selected for PCR amplification. A total of 238 bands were amplified, among which 207 (87%) bands were polymorphic. The polymorphic bands amplified by each primer ranged from 11 to 38, with an averaged of 18.8. The percentage of polymorphic band (80.3%) in common wheat was higher than that in progeny of recurrent selection (78.7%), spelt (75.0%) and compactum (74.9%). The 238 polymorphic products were used to calculate Nei's similarity index (GS) and the genetic distance (GD). It was found that the mean genetic distance between different wheat types (0.3115-0.3442) was obviously higher than that within common wheat (0.2743), spelt (0.2351), compactum (0.2622). In addition, progeny of recurrent selection also showed much higher genetic distance with other three wheat types (0.3217, 0.3256, 0.3198). The cluster analysis was performed based on the genetic distance (GD) matrix by using UPGMA method. Common wheat, spelt, compactum and progeny of recurrent selection were classified into four different groups. In this study, ISSR marker was firstly used to assess genetic diversity among common wheat, spelt, compactum and progeny of recurrent selection, and can differentiate the wheat cultivars (lines) that selected from the same cross combination. It was concluded that spelt, compactum and progeny

  19. BCL2 in breast cancer: a favourable prognostic marker across molecular subtypes and independent of adjuvant therapy received

    PubMed Central

    Dawson, S-J; Makretsov, N; Blows, F M; Driver, K E; Provenzano, E; Le Quesne, J; Baglietto, L; Severi, G; Giles, G G; McLean, C A; Callagy, G; Green, A R; Ellis, I; Gelmon, K; Turashvili, G; Leung, S; Aparicio, S; Huntsman, D; Caldas, C; Pharoah, P

    2010-01-01

    Background: Breast cancer is heterogeneous and the existing prognostic classifiers are limited in accuracy, leading to unnecessary treatment of numerous women. B-cell lymphoma 2 (BCL2), an antiapoptotic protein, has been proposed as a prognostic marker, but this effect is considered to relate to oestrogen receptor (ER) status. This study aimed to test the clinical validity of BCL2 as an independent prognostic marker. Methods: Five studies of 11 212 women with early-stage breast cancer were analysed. Individual patient data included tumour size, grade, lymph node status, endocrine therapy, chemotherapy and mortality. BCL2, ER, progesterone receptor (PR) and human epidermal growth factor receptor 2 (HER2) levels were determined in all tumours. A Cox model incorporating the time-dependent effects of each variable was used to explore the prognostic significance of BCL2. Results: In univariate analysis, ER, PR and BCL2 positivity was associated with improved survival and HER2 positivity with inferior survival. For ER and PR this effect was time dependent, whereas for BCL2 and HER2 the effect persisted over time. In multivariate analysis, BCL2 positivity retained independent prognostic significance (hazard ratio (HR) 0.76, 95% confidence interval (CI) 0.66–0.88, P<0.001). BCL2 was a powerful prognostic marker in ER− (HR 0.63, 95% CI 0.54–0.74, P<0.001) and ER+ disease (HR 0.56, 95% CI 0.48–0.65, P<0.001), and in HER2− (HR 0.55, 95% CI 0.49–0.61, P<0.001) and HER2+ disease (HR 0.70, 95% CI 0.57–0.85, P<0.001), irrespective of the type of adjuvant therapy received. Addition of BCL2 to the Adjuvant! Online prognostic model, for a subset of cases with a 10-year follow-up, improved the survival prediction (P=0.0039). Conclusions: BCL2 is an independent indicator of favourable prognosis for all types of early-stage breast cancer. This study establishes the rationale for introduction of BCL2 immunohistochemistry to improve prognostic stratification. Further work

  20. Molecular epidemiology of malaria in Cameroon. XXX. sequence analysis of Plasmodium falciparum ATPase 6, dihydrofolate reductase, and dihydropteroate synthase resistance markers in clinical isolates from children treated with an artesunate-sulfadoxine-pyrimethamine combination.

    PubMed

    Menemedengue, Virginie; Sahnouni, Khalifa; Basco, Leonardo; Tahar, Rachida

    2011-07-01

    Plasmodium falciparum dihydrofolate reductase (dhfr) and dihydropteroate synthase (dhps) genes are reliable molecular markers for antifolate resistance. The P. falciparum ATPase 6 (pfatp6) gene has been proposed to be a potential marker for artemisinin resistance. In our previous clinical study, we showed that artesunate-sulfadoxine-pyrimethamine is highly effective against uncomplicated malaria in Yaoundé, Cameroon. In the present study, dhfr, dhps, and pfatp6 mutations in P. falciparum isolates obtained from children treated with artesunate-sulfadoxine-pyrimethamine were determined. All 61 isolates had wild-type Pfatp6 263, 623, and 769 alleles, and 11 (18%) had a single E431K substitution. Three additional mutations, E643Q, E432K, and E641Q, were detected. The results did not indicate any warning signal of serious concern (i.e., no parasites were seen with quintuple dhfr-dhps, DHFR Ile164Leu, or pfatp6 mutations), as confirmed by the high clinical efficacy of artesunate-sulfadoxine-pyrimethamine. Further studies are required to identify a molecular marker that reliably predicts artemisinin resistance.

  1. The development of genetic and molecular markers to register and commercialize Penicillium rubens (formerly Penicillium oxalicum) strain 212 as a biocontrol agent.

    PubMed

    Villarino, Maria; De Cal, Antonieta; Melgarejo, Paloma; Larena, Inmaculada; Espeso, Eduardo A

    2016-01-01

    Penicillium oxalicum strain 212 (PO212) is an effective biocontrol agent (BCA) against a large number of economically important fungal plant pathogens. For successful registration as a BCA in Europe, PO212 must be accurately identified. In this report, we describe the use of classical genetic and molecular markers to characterize and identify PO212 in order to understand its ecological role in the environment or host. We successfully generated pyrimidine (pyr-) auxotrophic mutants. In addition we also designed specific oligonucleotides for the pyrF gene at their untranslated regions for rapid and reliable identification and classification of strains of P. oxalicum and P. rubens, formerly P. chrysogenum. Using these DNA-based technologies, we found that PO212 is a strain of P. rubens, and is not a strain of P. oxalicum. This work presents PO212 as the unique P. rubens strain to be described as a BCA and the information contained here serves for its registration and commercialization in Europe.

  2. Effect of Walking Exercise on Changes in Cardiorespiratory Fitness, Metabolic Syndrome Markers, and High-molecular-weight Adiponectin in Obese Middle-aged Women.

    PubMed

    Kim, Dae-Young; Seo, Byoung-Do; Kim, Dong-Je

    2014-11-01

    [Purpose] The purpose of this study was to assess the effect of a 24-week exercise intervention on cardiorespiratory fitness, metabolic syndrome markers, and high-molecular-weight (HMW) adiponectin among obese middle-aged women. [Subjects] The subjects were 14 obese middle-aged women. [Methods] The exercise program involved walking at 50-60% of the maximum oxygen consumption, 3 times a week, for 24 weeks. Body composition analysis, blood pressure measurements, and blood analysis were performed before the exercise program and at weeks 6, 12, 18, and 24. [Results] The results showed that after 24 weeks in the exercise program, the obesity indices and metabolic risk factors, namely, weight, body fat, body mass index, waist circumference, systolic blood pressure, diastolic blood pressure, and triglycerides decreased significantly, whereas HDLC, a metabolic improvement factor, increased significantly. Additionally, VO2max increased significantly, together with the level of total and HMW adiponectins. Correlation analysis of the changes in measured variables (∆ score) during resulting from the 24-week exercise program showed that body fat had a significant negative correlation and VO2max had a significant positive correlation with HMW adiponectin. [Conclusion] Among obese middle-aged women, regular exercise increases cardiorespiratory fitness and HMW adiponectin expression and therefore can be effective in the prevention and treatment of obesity and metabolic syndrome.

  3. Molecular tagging and validation of microsatellite markers linked to the low germination stimulant gene (lgs) for Striga resistance in sorghum [Sorghum bicolor (L.) Moench].

    PubMed

    Satish, Kanuganti; Gutema, Zenbaba; Grenier, Cécile; Rich, Patrick J; Ejeta, Gebisa

    2012-04-01

    Striga is a devastating parasitic weed in Africa and parts of Asia. Low Striga germination stimulant activity, a well-known resistance mechanism in sorghum, is controlled by a single recessive gene (lgs). Molecular markers linked to the lgs gene can accelerate development of Striga-resistant cultivars. Using a high density linkage map constructed with 367 markers (DArT and SSRs) and an in vitro assay for germination stimulant activity towards Striga asiatica in 354 recombinant inbred lines derived from SRN39 (low stimulant) × Shanqui Red (high stimulant), we precisely tagged and mapped the lgs gene on SBI-05 between two tightly linked microsatellite markers SB3344 and SB3352 at a distance of 0.5 and 1.5 cM, respectively. The fine-mapped lgs region was delimited to a 5.8 cM interval with the closest three markers SB3344, SB3346 and SB3343 positioned at 0.5, 0.7 and 0.9 cM, respectively. We validated tightly linked markers in a set of 23 diverse sorghum accessions, most of which were known to be Striga resistant, by genotyping and phenotyping for germination stimulant activity towards both S. asiatica and S. hermonthica. The markers co-segregated with Striga germination stimulant activity in 21 of the 23 tested lines. The lgs locus similarly affected germination stimulant activity for both Striga species. The identified markers would be useful in marker-assisted selection for introgressing this trait into susceptible sorghum cultivars. Examination of the sorghum genome sequence and comparative analysis with the rice genome suggests some candidate genes in the fine-mapped region (400 kb) that may affect strigolactone biosynthesis or exudation. This work should form a foundation for map-based cloning of the lgs gene and aid in elucidation of an exact mechanism for resistance based on low Striga germination stimulant activity.

  4. Molecular analysis of an additional case of hybrid sterility in rice (Oryza sativa L.).

    PubMed

    Zhao, Z G; Zhu, S S; Zhang, Y H; Bian, X F; Wang, Y; Jiang, L; Liu, X; Chen, L M; Liu, S J; Zhang, W W; Ikehashi, H; Wan, J M

    2011-03-01

    Hybrid sterility hinders the exploitation of the heterosis displayed by japonica × indica rice hybrids. The variation in pollen semi-sterility observed among hybrids between the japonica recipient cultivar and each of two sets of chromosome segment substitution lines involving introgression from an indica cultivar was due to a factor on chromosome 5 known to harbor the gene S24. S24 was fine mapped to a 42 kb segment by analyzing a large F(2) population bred from the cross S24-NIL × Asominori, while the semi-sterility shown by the F(1) hybrid was ascribable to mitotic failure at the early bicellular pollen stage. Interestingly, two other pollen sterility genes (f5-Du and Sb) map to the same region (Li et al. in Chin Sci Bull 51:675-680, 2006; Wang et al. in Theor Appl Genet 112:382-387, 2006), allowing a search for candidate genes in the 6.4 kb overlap between the three genes. By sequencing the overlapped fragment in wild rice, indica cultivars and japonica cultivars, a protein ankyrin-3 encoded by the ORF2 was identified as the molecular base for S24. A cultivar Dular was found to have a hybrid-sterility-neutral allele, S24-n, in which an insertion of 30 bp was confirmed. Thus, it was possible to add one more case of molecular bases for the hybrid sterility. No gamete abortion is caused on heterozygous maternal genotype with an impaired sequence from the hybrid-sterility-neutral genotype. This result will be useful in understanding of wide compatibility in rice breeding.

  5. Molecular aspects of aromatic C additions to soils: Implications of biochar quality for ecosystem functionality

    EPA Science Inventory

    Solid residues of incomplete combustion (biochar or char) are continuously being added to soils due to natural vegetation fires in many ecosystems. However, new strategies for carbon sequestration in soils are likely to include the active addition of biochar to soils. Since bioc...

  6. Characterization of high molecular weight glutenin subunits in Thinopyrum intermedium, Th. bessarabicum, Lophopyrum elongatum, Aegilops markgrafii, and their addition lines in wheat

    Technology Transfer Automated Retrieval System (TEKTRAN)

    High molecular weight (HMW) glutenin subunits (GSs) play an important role in determining dough viscoelastic properties and end-use quality in cultivated wheat, and they are also excellent protein markers for genotype identification. The HMW-GSs in wheat species (Triticum ssp.) and Aegilops tauschii...

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

    PubMed

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

    2014-01-01

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

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed

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

    2013-03-01

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

  10. Functional molecular markers (EST-SSR) in the full-sib reciprocal recurrent selection program of maize (Zea mays L.).

    PubMed

    Galvão, K S C; Ramos, H C C; Santos, P H A D; Entringer, G C; Vettorazzi, J C F; Pereira, M G

    2015-07-03

    This study aimed to improve grain yield in the full-sib reciprocal recurrent selection program of maize from the North Fluminense State University. In the current phase of the program, the goal is to maintain, or even increase, the genetic variability within and among populations, in order to increase heterosis of the 13th cycle of reciprocal recurrent selection. Microsatellite expressed sequence tags (EST-SSRs) were used as a tool to assist the maximization step of genetic variability, targeting the functional genome. Eighty S1 progenies of the 13th recur-rent selection cycle, 40 from each population (CIMMYT and Piranão), were analyzed using 20 EST-SSR loci. Genetic diversity, observed heterozygosity, information content of polymorphism, and inbreeding co-efficient were estim